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A global in-situ data set for validation of ocean-colour products from the ESA Ocean Colour Climate Change Initiative (OC-CCI) is presented. This version of the compilation, starting in 1997, now extends to 2021, which is important for the validation of the most recent satellite optical sensors such as Sentinel 3B OLCI and NOAA-20 VIIRS. The data set comprises in-situ observations of the following variables: spectral remote-sensing reflectance, concentration of chlorophyll-a, spectral inherent optical properties, spectral diffuse attenuation coefficient and total suspended matter. Data were obtained from multi-project archives acquired via open internet services, or from individual projects, acquired directly from data providers. Methodologies were implemented for homogenisation, quality control and merging of all data. Minimal changes were made on the original data, other than conversion to a standard format, elimination of some points after quality control and averaging of observations that were close in time and space. The result is a merged table available in text format. Overall, the size of the data set grew with 151,673 rows, with each row representing a unique station in space and time (cf 136,250 rows in previous version; Valente et al., 2019). Observations of remote-sensing reflectance increased to 68,641 (cf 59,781 in previous version; Valente et al., 2019). There was also a near tenfold increase in chlorophyll data since 2016. Metadata of each in situ measurement (original source, cruise or experiment, principal investigator) are included in the final table. By making the metadata available, provenance is better documented, and it is also possible to analyse each set of data separately. The compiled data are available at https://doi.pangaea.de/10.1594/PANGAEA.941318 (Valente et al., 2022)., SI

Bulachite specimens from Cap Garonne, France, comprise two intimately mixed hydrated aluminium arsenate minerals with the same Al:As ratio of 2:1 and with different water contents. The crystal structures of both minerals have been solved using data from low-dose electron diffraction tomography combined with synchrotron powder X-ray diffraction. One of the minerals has the same powder X-ray diffraction pattern (PXRD) as for published bulachite. It has orthorhombic symmetry, space group Pnma with unit-cell parameters a = 15.3994(3), b = 17.6598(3), c = 7.8083(1) Å and Z = 4, with the formula [Al6(AsO4)3(OH)9(H2O)4]⋅2H2O. The second mineral is a higher hydrate with composition [Al6(AsO4)3(OH)9(H2O)4]⋅8H2O. It has the same Pnma space group and unit-cell parameters a = 19.855(4), b = 17.6933(11) and c = 7.7799(5) Å i.e. almost the same b and c parameters but a much larger a parameter. The structures are based on polyhedral layers, parallel to (100), of composition [Al6(AsO4)3(OH)9(H2O)4] and with H-bonded H2O between the layers. The layers contain [001] spiral chains of edge-shared octahedra, decorated with corner connected AsO4 tetrahedra that are the same as in the mineral liskeardite. The spiral chains are joined together by octahedral edge-sharing to form layers parallel to (100). Synchrotron PXRD patterns collected at different temperatures during heating of the specimen show that the higher-hydrate mineral starts transforming to bulachite when heated to 50°C, and the transformation is complete between 75 and 100°C.

There is a wealth of materials that are beam sensitive and only exist in nanometric crystals, because the growth of bigger crystals is either impossible or so complicated that it is not reasonable to spend enough time and resources to grow big crystals before knowing their potential for research or applications. This difficulty is encountered in minerals, zeolites, metal-organic frameworks or molecular crystals, including pharmaceuticals and biological crystals. In order to study these crystals a structure determination method for beam sensitive crystals of nanometric size is needed. The nanometric size makes them destined for electron diffraction, since electrons interact much more strongly with matter than X-rays or neutrons. In addition, for the same amount of beam damage, electron diffraction yields more information than X-rays. The recently developed low-dose electron diffraction tomography (LD-EDT) not only combines the advantages inherent in electron diffraction, but is also optimized for minimizing the electron dose used for the data collection. The data quality is high, allowing not only the solution of complex unknown structures, but also their refinement taking into account the dynamical diffraction effects. Here we present several examples of crystals solved and refined by this method. The range of the crystals presented includes two synthetic oxides, Sr5CuGe9O24 and (Na2/3Mn1/3)3Ge5O12, a natural mineral (bulachite), and a metal organic framework (Mn-formiate). The dynamical refinement can be successfully performed on data sets that needed less than 0.1 e−/Å2 for the entire data set.

BackgroundRecent studies in the area of transcriptomics performed on single-cell and population levels reveal noticeable variability in gene expression measurements provided by different RNA sequencing technologies. Due to increased noise and complexity of single-cell RNA-Seq (scRNA-Seq) data over the bulk experiment, there is a substantial number of variably-expressed genes and so-called dropouts, challenging the subsequent computational analysis and potentially leading to false positive discoveries. In order to investigate factors affecting technical variability between RNA sequencing experiments of different technologies, we performed a systematic assessment of single-cell and bulk RNA-Seq data, which have undergone the same pre-processing and sample preparation procedures.ResultsOur analysis indicates that variability between gene expression measurements as well as dropout events are not exclusively caused by biological variability, low expression levels, or random variation. Furthermore, we propose FAVSeq, a machine learning-assisted pipeline for detection of factors contributing to gene expression variability in matched RNA-Seq data provided by two technologies. Based on the analysis of the matched bulk and single-cell dataset, we found the 3’-UTR and transcript lengths as the most relevant effectors of the observed variation between RNA-Seq experiments, while the same factors together with cellular compartments were shown to be associated with dropouts.ConclusionsHere, we investigated the sources of variation in RNA-Seq profiles of matched single-cell and bulk experiments. In addition, we proposed the FAVSeq pipeline for analyzing multimodal RNA sequencing data, which allowed to identify factors affecting quantitative difference in gene expression measurements as well as the presence of dropouts. Hereby, the derived knowledge can be employed further in order to improve the interpretation of RNA-Seq data and identify genes that can be affected by assay-based deviations. Source code is available under the MIT license at https://github.com/slipnitskaya/FAVSeq.

Healthy adipose tissue remodeling depends on the balance between de novo adipogenesis from adipogenic progenitor cells and the hypertrophy of adipocytes. De novo adipogenesis has been shown to promote healthy adipose tissue expansion, which confers protection from obesity-associated insulin resistance. Here, we define the role and trajectory of different adipogenic precursor subpopulations and further delineate the mechanism and cellular trajectory of adipogenesis, using single-cell RNA-sequencing datasets of murine adipogenic precursors. We identify Rspo2 as a functional regulator of adipogenesis, which is secreted by a subset of CD142+ cells to inhibit maturation of early progenitors through the receptor Lgr4. Increased circulating RSPO2 in mice leads to adipose tissue hypertrophy and insulin resistance and increased RSPO2 levels in male obese individuals correlate with impaired glucose homeostasis. Taken together, these findings identify a complex cellular crosstalk that inhibits adipogenesis and impairs adipose tissue homeostasis., Nature Metabolism, 4 (1), ISSN:2522-5812

The Eastern Boundary Current is an essential part of the water mass exchange between the subtropical and subpolar North Atlantic. Here, we study the offshore branch of the European Shelf Current (ESC) over the Goban Spur slope area off Ireland. Our analysis is based on current measurements obtained from a multiyear mooring effort, complemented by ship‐board observations along a hydrographic section, satellite‐derived estimates of absolute dynamic topography with geostrophic currents, and float trajectories. These data serve to quantify the offshore branch of the ESC on intraannual to interannual timescales. From the moored observations, we derive a mean poleward along‐slope volume flux of 3.7 ± 0.7 Sv for the period 2017–2019. Using a multilinear regression model and geostrophic surface velocities, we extend the time series to the period 1993–2019 and obtain a long‐term mean transport of 3.2 ± 0.4 Sv. Both time series show strong variability ranging from −7.5 to 15.7 Sv. The variability is linked to a dynamic eddy field, especially a stationary cyclonic circulation pattern near the mooring array, and meandering of current branches originating from the North Atlantic Current. We find no evidence of a consistent deep boundary current extending from the shelf break to the position of the offshore mooring (4,500 m depth), but confirm a persistent along‐slope flow at the shallower slope (1,500 m depth). Geostrophic surface velocities and float trajectories reveal that the offshore branch of the ESC does not follow a clear northward path from the eastern subtropical regions but rather indicate the intermittent character of the flow., Plain Language Summary: In this study, we describe the European Shelf Current (ESC) in the eastern North Atlantic. The study area is the deeper part of the Goban Spur area off Ireland. We use current measurements of instruments deployed in the water column from 2016 to 2019 combined with satellite observations of surface circulation and drifting float paths. We aim to quantify the contribution of the offshore branch to the ESC system. We calculate a poleward volume transport following the slope that is on average 3.7 ± 0.7 Sverdrup (Sv; 1 Sv = 1 million cubic meter per second) for the period 2017–2019. We use a mathematical relation between mooring data and satellite observations to extend the time series to the period 1993–2019 and obtain an average transport of 3.2 ± 0.4 Sv. There occur strong changes over time ranging from −5 to 15 Sv. These changes are caused by rotating vortices (eddies), especially a counter‐clockwise rotating circulation pattern near the moorings, and changing positions of currents branching from the North Atlantic Current. We find that the offshore branch of the ESC does not follow a clear northward path from the eastern subtropical regions of the North Atlantic. Instead, the flow is of rather unsteady character., Key Points: The analysis of multiplatform observational efforts is used to study the circulation at the North Atlantic Eastern Boundary. The volume transport of the offshore branch of the European Shelf Current is on average 3.2 ± 0.4 Sv for the period 1993–2019. Transport variability is in the range of −7.5–15.7 Sv and induced by eddies and meandering North Atlantic Current branches., Bundesministerium für Bildung und Forschung (BMBF) http://dx.doi.org/10.13039/501100002347, Deutsche Forschungsgemeinschaft (DFG) http://dx.doi.org/10.13039/501100001659

International audience; In the framework of expanding the range of copper-based compounds in the pyroxene family we have synthesized at high pressure and high temperature a powder containing a mixture of a new phase with stoichiometry Sr5CuGe9O24 with two identified impurity phases. Electron crystallography showed that the new phase crystallizes with a monoclinic structure with cell parameters a = 11.6 Å, b = 8.1 Å, c = 10.4 Å and β = 101° and space group P2/c. We applied the recently developed low-dose electron diffraction tomography method to solve the structure by direct methods. The obtained structure model contains all 9 independent cation positions and all 13 oxygen positions. A subsequent refinement against X-ray powder diffraction data ascertained the high quality of the structure solution, in particular the unusual structural arrangement that there are three different environments for Ge in this phase. Synopsis The high-pressure high-temperature phase Sr5CuGe9O24 was solved by low-dose electron diffraction tomography and refined against X-ray powder diffraction data. The Ge ions in this compound have three different coordination numbers.

Objective Sodium-glucose cotransporter 2 (SGLT2) inhibitors (SGLT2i), or gliflozins, are anti-diabetic drugs that lower glycemia by promoting glucosuria, but they also stimulate endogenous glucose and ketone body production. The likely causes of these metabolic responses are increased blood glucagon levels, and decreased blood insulin levels, but the mechanisms involved are hotly debated. This study verified whether or not SGLT2i affect glucagon and insulin secretion by a direct action on islet cells in three species, using multiple approaches. Methods We tested the in vivo effects of two selective SGLT2i (dapagliflozin, empagliflozin) and a SGLT1/2i (sotagliflozin) on various biological parameters (glucosuria, glycemia, glucagonemia, insulinemia) in mice. mRNA expression of SGLT2 and other glucose transporters was assessed in rat, mouse, and human FACS-purified α- and β-cells, and by analysis of two human islet cell transcriptomic datasets. Immunodetection of SGLT2 in pancreatic tissues was performed with a validated antibody. The effects of dapagliflozin, empagliflozin, and sotagliflozin on glucagon and insulin secretion were assessed using isolated rat, mouse and human islets and the in situ perfused mouse pancreas. Finally, we tested the long-term effect of SGLT2i on glucagon gene expression. Results SGLT2 inhibition in mice increased the plasma glucagon/insulin ratio in the fasted state, an effect correlated with a decline in glycemia. Gene expression analyses and immunodetections showed no SGLT2 mRNA or protein expression in rodent and human islet cells, but moderate SGLT1 mRNA expression in human α-cells. However, functional experiments on rat, mouse, and human (29 donors) islets and the in situ perfused mouse pancreas did not identify any direct effect of dapagliflozin, empagliflozin or sotagliflozin on glucagon and insulin secretion. SGLT2i did not affect glucagon gene expression in rat and human islets. Conclusions The data indicate that the SGLT2i-induced increase of the plasma glucagon/insulin ratio in vivo does not result from a direct action of the gliflozins on islet cells., Highlights • Gliflozins (SGLT2 and SGLT1/2 inhibitors) increase plasma glucagon/insulin ratio. • SGLT2 is not expressed in rodent and human pancreatic α- and β-cells. • SGLT1 is however expressed in human α-cells. • SGLT2 and SGLT1/2 inhibitors do not directly affect glucagon and insulin secretion.

In the framework of expanding the range of copper-based compounds in the pyroxene family, we have synthesized at high pressure and high temperature a powder containing a mixture of a new phase with stoichiometry Sr

Reliable data are the basis for successful research and scientific publishing. Open data policies assure the availability of publicly financed field measurements to the public, thus to all interested scientists. However, the variety of data sources and the availability or lack of detailed metadata cause a huge effort for each scientist to decide if the data are usable for their own research topic or not. Data end-user communities have different requirements in metadata details and data handling during data processing. For data providing institutes or agencies, these needs are essential to know, if they want to reach a wide range of end-user communities.The Federal Maritime and Hydrographic Agency (BSH, Bundesamt für Seeschifffahrt und Hydrographie, Hamburg, Germany) is collecting a large variety of field data in physical and chemical oceanography, regionally focused on the North Sea, Baltic Sea, and North Atlantic. Data types vary from vertical profiles, time-series, underway measurements as well as real-time or delayed-mode from moored or ship-based instruments. Along other oceanographic data, the BSH provides all physical data via the German Oceanographic Data Center (DOD). It is crucial to aim for a maximum in reliability of the published data to enhance the usage especially in the scientific community.Here, we present our newly established data processing and quality control procedures using agile project management and workflow techniques, and outline their implementation into metadata and accompanied documentation. To enhance the transparency of data quality control, we will apply a detailed quality flag along with the common data quality flag. This detailed quality flag, established by Mayumi Wilms within the research project RAVE Offshore service (research at alpha ventus) enables data end-users to review the result of several individual quality control checks done during processing and thus to identify easily if the data are usable for their research.

Since 2016 a moored observatory is operated at the eastern extension of the “North Atlantic Changes (NOAC)” array at 47°/48°N. This observatory is installed across the shelf break at Goban Spur and consists of two deep-sea moorings that are separated by about 60 km. The aim of this ongoing monitoring program is to quantify the variability and trends in the properties and transport rates of water masses that are advected northwards along the North Atlantic Eastern Boundary and modify the adjacent regions, i.e. the Northwest European Shelf, North Sea, Nordic Seas and Arctic Ocean. Furthermore, the continuous long term time series are essential for a thorough understanding of the circulation system in the eastern North Atlantic and the underlying physical mechanisms that govern its variability.Here, we present results of the analysis of temperature, salinity and current velocity time series from 2016 to 2019. These provide a descriptive view of the complex current structure and variability of water masses on daily to intra- and inter-annual time scales.The most pronounced signal in the variability of temperature and salinity is caused by the presence of Mediterranean Outflow Water located at about 1000 m depth. During the observation period we find significant positive trends in temperature and salinity in the depth range of 500 to 1500 m. The velocity measurements of the onshore mooring show a northeastward directed mean flow following the topography with along-slope variations, while the flow at the offshore mooring position is more unstable with predominantly cross-slope variations. The combination of our observations with float and altimeter data indicates that the presence of eddies and the interaction with the topography seems to play a crucial role for setting the variability of the flow in this region.Finally, we present an approach to evaluate the volume fluxes at the eastern boundary that will add toward an integrated estimate of the strength of the Atlantic Meridional Overturning Circulation at 47°/48°N.

Synthetic riboswitches mediating ligand-dependent RNA cleavage or splicing-modulation represent elegant tools to control gene expression in various applications, including next-generation gene therapy. However, due to the limited understanding of context-dependent structure–function relationships, the identification of functional riboswitches requires large-scale-screening of aptamer-effector-domain designs, which is hampered by the lack of suitable cellular high-throughput methods. Here we describe a fast and broadly applicable method to functionally screen complex riboswitch libraries (~1.8 × 104 constructs) by cDNA-amplicon-sequencing in transiently transfected and stimulated human cells. The self-barcoding nature of each construct enables quantification of differential mRNA levels without additional pre-selection or cDNA-manipulation steps. We apply this method to engineer tetracycline- and guanine-responsive ON- and OFF-switches based on hammerhead, hepatitis-delta-virus and Twister ribozymes as well as U1-snRNP polyadenylation-dependent RNA devices. In summary, our method enables fast and efficient high-throughput riboswitch identification, thereby overcoming a major hurdle in the development cascade for therapeutically applicable gene switches., Riboswitches can mediate ligand-dependent RNA cleavage and splicing to control gene expression. Here the authors present a method to functionally screen large libraries and identify functional variants.

The focus of this study is on the magnetic properties of the very recently synthesized doubly ordered perovskite family NaLnCoWO6 (Ln = Y, La, Pr, Nd, Sm, Eu, Gd, Tb, Dy, Ho, Er, and Yb). Magnetic characterizations were performed by magnetic susceptibility vs. temperature, isothermal magnetization and heat capacity measurements. All these compounds have been determined as antiferromagnets with Neel temperatures from 4 K to 13.1 K. When the lanthanide is magnetic, additional transitions were observed below the Neel temperature which are attributed to the polarization of the magnetic Ln3+ sublattice by the ordered Co2+ one. Taking into account the magnetic ordering found in this study and the polar structure in the nine compounds NaLnCoWO6 (Ln = Y, Sm, Eu, Gd, Tb, Dy, Ho, Er, and Yb) reported before, these compounds can be classified as new Type I multiferroics.

Six surface drifters (drogued at about 1 m depth) deployed in the inner German Bight (North Sea) were tracked for between 14 and 54 days. Corresponding simulations were conducted offline based on surface currents from two independent models (BSHcmod and TRIM). Inclusion of a direct wind drag (0.6 % of 10 m wind) was needed for successful simulations based on BSHcmod currents archived for a 5 m depth surface layer. Adding 50 % of surface Stokes drift simulated with the third generation wave model WAM was tested as an alternative approach. Results resembled each other during most of the time. Successful simulations based on TRIM surface currents (1 m depth) suggest that both approaches were mainly needed to compensate insufficient vertical resolution of hydrodynamic currents. The study suggests that main sources of simulation errors were inaccurate Eulerian currents and lacking representation of sub-grid scale processes. Substantial model errors often occurred under low wind conditions. A lower limit of predictability (about 3–5 km per day) was estimated from two drifters that were initially spaced 20 km apart but converged quickly and diverged again after having stayed at a distance of 2 km and less for about 10 days. In most cases, errors in simulated 25 h drifter displacements were of similar order of magnitude.

Transcatheter aortic valve implantation (TAVI) is an alternative to surgical valve replacement for patients with aortic stenosis (AS). This study assessed the impact of changing from a self-expandable (SE) valve to a balloon-expandable (BE) valve on healthcare resource use and procedural costs in a population of inoperable AS patients.In this retrospective single center study, data for 195 patients who received either an SE or a BE valve between 2010-2014 were collected. Procedural and post-procedural healthcare resource use and cost parameters were determined for the two groups.The study showed that overall procedural time, including time required by medical personnel, was significantly shorter for TAVI using a BE compared with an SE valve. Post-surgery, patients in the BE valve group had significantly shorter hospital stays than the SE valve group, including significantly fewer days spent in the intensive care unit (ICU). Additionally, trends towards reduced 30-day mortality, incidence of new permanent pacemaker implantation, and incidence of blood transfusion were observed in the BE valve group compared with the SE valve group. Finally, total procedural costs were 24% higher in the SE compared with the BE valve group.The BE valve data were acquired in a single year, whereas the SE valve data were from a 5-year period. However, a year-by-year analysis of patient characteristics and study outcomes for the SE valve group showed few significant differences over this 5-year period.Overall, changing from an SE to a BE valve for TAVI in patients with severe AS reduced both healthcare resource use and procedure-related costs, while maintaining patient safety. For healthcare providers, this could increase efficiency and capacity within the healthcare system, with the added advantage of reducing costs.