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In the field of computational science and engineering, workflows often entail the application of various software, for instance, for simulation or pre- and postprocessing. Typically, these components have to be combined in arbitrarily complex workflows to address a specific research question. In order for peer researchers to understand, reproduce and (re)use the findings of a scientific publication, several challenges have to be addressed. For instance, the employed workflow has to be automated and information on all used software must be available for a reproduction of the results. Moreover, the results must be traceable and the workflow documented and readable to allow for external verification and greater trust. In this paper, existing workflow management systems (WfMSs) are discussed regarding their suitability for describing, reproducing and reusing scientific workflows. To this end, a set of general requirements for WfMSs were deduced from user stories that we deem relevant in the domain of computational science and engineering. On the basis of an exemplary workflow implementation, publicly hosted at GitHub (https://github.com/BAMresearch/NFDI4IngScientificWorkflowRequirements), a selection of different WfMSs is compared with respect to these requirements, to support fellow scientists in identifying the WfMSs that best suit their requirements.

Carbon dioxide removal from the atmosphere and storage over long times scales in terrestrial and marine reservoirs is urgently needed to limit global warming and for sustainable management of the global carbon cycle. Ocean alkalinity enhancement by the artificial addition of carbonate minerals to the seafloor has been proposed as a method to sequester atmospheric CO2 and store it in the ocean as dissolved bicarbonate. Here, a reaction-transport model is used to scrutinize the efficacy of calcite addition and dissolution at a well-studied site in the southwestern Baltic Sea – a brackish coastal water body in northern Europe. We find that most calcite is simply buried without dissolution under moderate addition rates. Applying the model to other sites in the Baltic Sea suggests that dissolution rates and efficiencies are higher in areas with low salinity and undersaturated bottom waters. A simple box model predicts a tentative net CO2 uptake rate from the atmosphere of 3.2 megatonnes of carbon dioxide per year for the wider Baltic Sea after continually adding calcite to muddy sediments for 10 years. More robust estimates now require validation by field studies.

Carbon dioxide removal from the atmosphere and storage over long times scales in terrestrial and marine reservoirs is urgently needed to limit global warming and for sustainable management of the global carbon cycle. Ocean alkalinity enhancement by the artificial addition of carbonate minerals to the seafloor has been proposed as a method to sequester atmospheric CO2 and store it in the ocean as dissolved bicarbonate. Here, a reaction-transport model is used to scrutinize the efficacy of calcite addition and dissolution at a well-studied site in the southwestern Baltic Sea – a brackish coastal water body in northern Europe. We find that most calcite is simply buried without dissolution under moderate addition rates. Applying the model to other sites in the Baltic Sea suggests that dissolution rates and efficiencies are higher in areas with low salinity and undersaturated bottom waters. A simple box model predicts a tentative net CO2 uptake rate from the atmosphere of 3.2 megatonnes of carbon dioxide per year for the wider Baltic Sea after continually adding calcite to muddy sediments for 10 years. More robust estimates now require validation by field studies.

Carbon dioxide removal from the atmosphere and storage over long times scales in terrestrial and marine reservoirs is urgently needed to limit global warming and for sustainable management of the global carbon cycle. Ocean alkalinity enhancement by the artificial addition of carbonate minerals to the seafloor has been proposed as a method to sequester atmospheric CO2 and store it in the ocean as dissolved bicarbonate. Here, a reaction-transport model is used to scrutinize the efficacy of calcite addition and dissolution at a well-studied site in the southwestern Baltic Sea – a brackish coastal water body in northern Europe. We find that most calcite is simply buried without dissolution under moderate addition rates. Applying the model to other sites in the Baltic Sea suggests that dissolution rates and efficiencies are higher in areas with low salinity and undersaturated bottom waters. A simple box model predicts a tentative net CO2 uptake rate from the atmosphere of 3.2 megatonnes of carbon dioxide per year for the wider Baltic Sea after continually adding calcite to muddy sediments for 10 years. More robust estimates now require validation by field studies.

Desmosomes are dynamic complex protein structures involved in cellular adhesion. Disruption of these structures by loss-of-function variants in desmosomal genes leads to a variety of skin- and heart-related phenotypes. In this study, we report TUFT1 as a desmosome-associated protein, implicated in epidermal integrity. In two siblings with mild skin fragility, woolly hair, and mild palmoplantar keratoderma but without a cardiac phenotype, we identified a homozygous splice-site variant in the TUFT1 gene, leading to aberrant mRNA splicing and loss of TUFT1 protein. Patients’ skin and keratinocytes showed acantholysis, perinuclear retraction of intermediate filaments, and reduced mechanical stress resistance. Immunolabeling and transfection studies showed that TUFT1 is positioned within the desmosome and that its location is dependent on the presence of the desmoplakin carboxy-terminal tail. A Tuft1-knockout mouse model mimicked the patients’ phenotypes. Altogether, this study reveals TUFT1 as a desmosome-associated protein, whose absence causes skin fragility, woolly hair, and palmoplantar keratoderma.

In the field of computational science and engineering, workflows often entail the application of various software, for instance, for simulation or pre- and postprocessing. Typically, these components have to be combined in arbitrarily complex workflows to address a specific research question. In order for peer researchers to understand, reproduce and (re)use the findings of a scientific publication, several challenges have to be addressed. For instance, the employed workflow has to be automated and information on all used software must be available for a reproduction of the results. Moreover, the results must be traceable and the workflow documented and readable to allow for external verification and greater trust. In this paper, existing workflow management systems (WfMSs) are discussed regarding their suitability for describing, reproducing and reusing scientific workflows. To this end, a set of general requirements for WfMSs were deduced from user stories that we deem relevant in the domain of computational science and engineering. On the basis of an exemplary workflow implementation, publicly hosted at GitHub (https://github.com/BAMresearch/NFDI4IngScientificWorkflowRequirements), a selection of different WfMSs is compared with respect to these requirements, to support fellow scientists in identifying the WfMSs that best suit their requirements.

Alveolar macrophages (AMs) play a critical role during Mycobacterium tuberculosis (Mtb) infection as the first cells in the lung to encounter bacteria. We previously showed that AMs initially respond to Mtb in vivo by mounting a cell-protective, rather than pro-inflammatory response. However, the plasticity of the initial AM response was unknown. Here, we characterize how previous exposure to Mycobacterium, either through subcutaneous vaccination with Mycobacterium bovis (scBCG) or through a contained Mtb infection (coMtb) that mimics aspects of concomitant immunity, impacts the initial response by AMs. We find that both scBCG and coMtb accelerate early innate cell activation and recruitment and generate a stronger pro-inflammatory response to Mtb in vivo by AMs. Within the lung environment, AMs from scBCG vaccinated mice mount a robust interferon-associated response, while AMs from coMtb mice produce a broader inflammatory response that is not dominated by Interferon Stimulated Genes. Using scRNAseq, we identify changes to the frequency and phenotype of airway-resident macrophages following Mycobacterium exposure, with enrichment for both interferon-associated and pro-inflammatory populations of AMs. In contrast, minimal changes were found for airway-resident T cells and dendritic cells after exposures. Ex vivo stimulation of AMs with Pam3Cys, LPS and Mtb reveal that scBCG and coMtb exposures generate stronger interferon-associated responses to LPS and Mtb that are cell-intrinsic changes. However, AM profiles that were unique to each exposure modality following Mtb infection in vivo are dependent on the lung environment and do not emerge following ex vivo stimulation. Overall, our studies reveal significant and durable remodeling of AMs following exposure to Mycobacterium, with evidence for both AM-intrinsic changes and contributions from the altered lung microenvironments. Comparisons between the scBCG and coMtb models highlight the plasticity of AMs in the airway

Despite their high relative abundance in our Universe, neutrinos are the least understood fundamental particles of nature. They also provide a unique system to study quantum coherence and the wavelike nature of particles in fundamental systems due to their extremely weak interaction probabilities. In fact, the quantum properties of neutrinos emitted in experimentally relevant sources are virtually unknown and the spatial extent of the neutrino wavepacket is only loosely constrained by reactor neutrino oscillation data with a spread of 13 orders of magnitude. Here, we present the first direct limits of this quantity through a new experimental concept to extract the energy width, $\sigma_{\textrm{N},E}$, of the recoil daughter nucleus emitted in the nuclear electron capture (EC) decay of $^7$Be. The final state in the EC decay process contains a recoiling $^7$Li nucleus and an electron neutrino ($\nu_e$) which are entangled at their creation. The $^7$Li energy spectrum is measured to high precision by directly embedding $^7$Be radioisotopes into a high resolution superconducting tunnel junction that is operated as a cryogenic sensor. The lower limit on the spatial uncertainty of the recoil daughter was found to be $\sigma_{\textrm{N}, x} \geq 6.2$\,pm, which implies the final-state system is localized at a scale more than a thousand times larger than the nucleus itself. From this measurement, the first direct lower limits on the spatial extent of the neutrino wavepacket were extracted using two different theoretical methods. These results have wide-reaching implications in several areas including the nature of spatial localization at sub-atomic scales, interpretation of neutrino physics data, and the potential reach of future large-scale experiments., Comment: 20 pages, 3 figures, v3 corrects and updates one of the wavepacket width calculations

Bullous pemphigoid (BP) is characterized by deposition of immunoglobulins and complement along the epidermal basement membrane (BM). In humans, there is a lack of functional studies targeting the complement system (CS). This study investigates activation of all complement pathways in BP skin biopsies. Moreover, pharmacological inhibition at different levels of the CS was investigated using anti-complement compounds in a complement fixation BP assay. In this retrospective study, 21 frozen biopsies from BP patients were stained by direct immunofluorescence for C1q, MBL, ficolin-2, C4d, properdin, C3c and C5b-9. Sera from 10 patients were analysed in a complement fixation assay in the presence of C1 inhibitor, anti-factor B monoclonal antibody (mAb), anti-C3 mAb and anti-C5 mAb and compared with dexamethasone. The two readouts were the quantity of complement deposited along the BM and the release of sC5b-9 in the supernatant. Our results show classical and alternative complement pathway activation in BP skin biopsies, but could not demonstrate significant lectin pathway activation. In contrast to dexamethasone, complement deposition along the BM could be selectively inhibited by anti-C1 and anti- factor B. More downstream, selective intervention at the level of C3 and C5 could effectively reduce complement deposition along the BM and the release of sC5b-9 in the supernatant. This study shows that selective intervention in either the classical, alternative or terminal pathway prevented deposition of complement along the BM in an in vitro BP model. The results of our study greatly encourage the clinical development of complement inhibitors for the treatment of BP.

Item does not contain fulltext, Birt-Hogg-Dubé syndrome (BHD) is an autosomal dominant disorder characterized by fibrofolliculomas, pulmonary cysts, pneumothoraces and renal cell carcinomas. Here, we reveal a novel hereditary disorder in a family with skin and mucosal lesions, extensive lipomatosis and renal cell carcinomas. The proband was initially diagnosed with BHD based on the presence of fibrofolliculomas, but no pathogenic germline variant was detected in FLCN, the gene associated with BHD. By whole exome sequencing we identified a heterozygous missense variant (p.(Cys677Tyr)) in a zinc-finger encoding domain of the PRDM10 gene which co-segregated with the phenotype in the family. We show that PRDM10Cys677Tyr loses affinity for a regulatory binding motif in the FLCN promoter, abrogating cellular FLCN mRNA and protein levels. Overexpressing inducible PRDM10Cys677Tyr in renal epithelial cells altered the transcription of multiple genes, showing overlap but also differences with the effects of knocking out FLCN. We propose that PRDM10 controls an extensive gene program and acts as a critical regulator of FLCN gene transcription in human cells. The germline variant PRDM10Cys677Tyr curtails cellular folliculin expression and underlies a distinguishable syndrome characterized by extensive lipomatosis, fibrofolliculomas and renal cell carcinomas.

Item does not contain fulltext, Birt-Hogg-Dubé syndrome (BHD) is an autosomal dominant disorder characterized by fibrofolliculomas, pulmonary cysts, pneumothoraces and renal cell carcinomas. Here, we reveal a novel hereditary disorder in a family with skin and mucosal lesions, extensive lipomatosis and renal cell carcinomas. The proband was initially diagnosed with BHD based on the presence of fibrofolliculomas, but no pathogenic germline variant was detected in FLCN, the gene associated with BHD. By whole exome sequencing we identified a heterozygous missense variant (p.(Cys677Tyr)) in a zinc-finger encoding domain of the PRDM10 gene which co-segregated with the phenotype in the family. We show that PRDM10Cys677Tyr loses affinity for a regulatory binding motif in the FLCN promoter, abrogating cellular FLCN mRNA and protein levels. Overexpressing inducible PRDM10Cys677Tyr in renal epithelial cells altered the transcription of multiple genes, showing overlap but also differences with the effects of knocking out FLCN. We propose that PRDM10 controls an extensive gene program and acts as a critical regulator of FLCN gene transcription in human cells. The germline variant PRDM10Cys677Tyr curtails cellular folliculin expression and underlies a distinguishable syndrome characterized by extensive lipomatosis, fibrofolliculomas and renal cell carcinomas.

Maximizing the production of heterologous biomolecules is a complex problem that can be addressed with a systems-level understanding of cellular metabolism and regulation. Specifically, growth-coupling approaches can increase product titers and yields and also enhance production rates. However, implementing these methods for non-canonical carbon streams is challenging due to gaps in metabolic models. Over four design-build-test-learn cycles, we rewire Pseudomonas putida KT2440 for growth-coupled production of indigoidine from para-coumarate. We explore 4,114 potential growth-coupling solutions and refine one design through laboratory evolution and ensemble data-driven methods. The final growth-coupled strain produces 7.3 g/L indigoidine at 77% maximum theoretical yield in para-coumarate minimal medium. The iterative use of growth-coupling designs and functional genomics with experimental validation was highly effective and agnostic to specific hosts, carbon streams, and final products and thus generalizable across many systems.

Cellular Ca2+ signaling is highly organized in time and space. Locally restricted and short-lived regions of Ca2+ increase, called Ca2+ microdomains, constitute building blocks that are differentially arranged to create cellular Ca2+ signatures controlling physiological responses. Here, we focus on Ca2+ microdomains occurring in restricted cytosolic spaces between the plasma membrane and the endoplasmic reticulum, called endoplasmic reticulum-plasma membrane junctions. In T cells, these microdomains have been finely characterized. Enough quantitative data are thus available to develop detailed computational models of junctional Ca2+ dynamics. Simulations are able to predict the characteristics of Ca2+ increases at the level of single channels and in junctions of different spatial configurations, in response to various signaling molecules. Thanks to the synergy between experimental observations and computational modeling, a unified description of the molecular mechanisms that create Ca2+ microdomains in the first seconds of T cell stimulation is emerging., SCOPUS: re.j, info:eu-repo/semantics/published

During an immune response, T cells migrate from blood vessel walls into inflamed tissues by migrating across the endothelium and through extracellular matrix (ECM). Integrins facilitate T cell binding to endothelial cells and ECM proteins. Here, we report that Ca2+ microdomains observed in the absence of T cell receptor (TCR)/CD3 stimulation are initial signaling events triggered by adhesion to ECM proteins that increase the sensitivity of primary murine T cells to activation. Adhesion to the ECM proteins collagen IV and laminin-1 increased the number of Ca2+ microdomains in a manner dependent on the kinase FAK, phospholipase C (PLC), and all three inositol 1,4,5-trisphosphate receptor (IP3R) subtypes and promoted the nuclear translocation of the transcription factor NFAT-1. Mathematical modeling predicted that the formation of adhesion-dependent Ca2+ microdomains required the concerted activity of two to six IP3Rs and ORAI1 channels to achieve the increase in the Ca2+ concentration in the ER-plasma membrane junction that was observed experimentally and that required SOCE. Further, adhesion-dependent Ca2+ microdomains were important for the magnitude of the TCR-induced activation of T cells on collagen IV as assessed by the global Ca2+ response and NFAT-1 nuclear translocation. Thus, adhesion to collagen IV and laminin-1 sensitizes T cells through a mechanism involving the formation of Ca2+ microdomains, and blocking this low-level sensitization decreases T cell activation upon TCR engagement., SCOPUS: ar.j, info:eu-repo/semantics/published

Knowledge of earthquake source faults is crucial for the calculation of robust Coulomb stress models. However, source faults are often poorly constrained, especially for pre-instrumental events, and these historical earthquakes are commonly studied with little or no consideration of other nearby events. We introduce an approach using Coulomb Stress Transfer (CST) modeling to investigate historical earthquake sequences and constrain possible source faults. Using historical and instrumental records from the Büyük Menderes Graben, western Türkiye, we create an ensemble of earthquake sequences featuring multiple rupture scenarios for individual earthquakes, and model both coseismic and interseismic CST. We filter and evaluate the models based on criteria to gain knowledge on historical earthquakes and their source faults and assess the current stress state and related seismic hazard of the investigated fault network. For our study area, the results provide further constraints on the source faults of several historical earthquakes, including the destructive MW 7.0 earthquake in 1899. The approach presented herein is applicable to other tectonically active areas where the causative faults of historical earthquakes are poorly constrained from existing data sets (e.g., paleoseismology, damage records), providing a new tool to help decipher historical earthquake sequences and improve modeling studies.

In the six years I have been walking around in this faculty, I have gained theoretical knowledge, but foremost gained practical handholds to design strategically. For this last stretch, I have defined a project brief with personal attachment, one that presents a complex problem that I wanted to find a solution for. In collaboration with the Nationaal Archief, I have enriched the current visitor journey of the ‘Centraal Archief Bijzondere Rechtspleging’ (CABR) - an archive containing files of the more than 300.000 people who were accused of collaborating with the German occupiers, of joining the German’s armed forces, of treason or of membership of the NSB after the Second World War. Specific chapters of Dutch national history have remained a sensitive topic. It has taken 150 years for our parliament and monarchy to apologize and ask for forgiveness for their role in the colonial past. It took the monarchy 75 years and two generations to speak about its role in the Second World War. To apologize, one needs to acknowledge something went wrong. To acknowledge, one needs to know about what has happened and process this. As I am a firm believer in that we can learn and grow from our diverse cultures and historical backgrounds, I wanted to contribute to the perceived significance of history. To be able to acknowledge a part of one’s past, one needs to gain knowledge of what has happened, interpret, and process this. I have been driven to apply strategic design thinking and its principles into this historical context, to show and understand the added value. The knowledge and experience I gained throughout my studies, enabled me to structurally analyze and enrich the visitor journey and create interventions that aim to support people in the exploration of their familial history. To support them to understand their ancestor’s role within the historical context, to give them support to process this information, and to g, Strategic Product Design

In this article, a methodology for fine scale modeling of large scale linear elastic structures is proposed, which combines the variational multiscale method, domain decomposition and model order reduction. The influence of the fine scale on the coarse scale is modeled by the use of an additive split of the displacement field, addressing applications without a clear scale separation. Local reduced spaces are constructed by solving an oversampling problem with random boundary conditions. Herein, we inform the boundary conditions by a global reduced problem and compare our approach using physically meaningful correlated samples with existing approaches using uncorrelated samples. The local spaces are designed such that the local contribution of each subdomain can be coupled in a conforming way, which also preserves the sparsity pattern of standard finite element assembly procedures. Several numerical experiments show the accuracy and efficiency of the method, as well as its potential to reduce the size of the local spaces and the number of training samples compared to the uncorrelated sampling.

Aims: Despite recommendations in international clinical guidelines, lifestyle-related treatment modalities (LRTMs) are currently underutilised in the conservative treatment of patients with hip and/or knee osteoarthritis. This study aimed to identify implementation strategies in order to address barriers to implementing LRTMs from the perspective of healthcare professionals (HCPs). Methods: The Consolidated Framework for Implementation Research (CFIR)-Expert Recommendations for Implementing Change (ERIC) Implementation Strategy Matching Tool was applied. First, previously identified influencing factors among primary and secondary HCPs were mapped onto the corresponding CFIR constructs/subconstructs by two researchers. Second, the CFIR-based barriers relevant for all HCPs were entered into the tool. Third, the CFIR-based barriers specific to one or more subgroups of HCPs served as additional input for the tool. Finally, a selection of ERIC implementation strategies was made based on the tool's output. Results: Fourteen implementation strategies were selected. The strategy most endorsed by the tool was ‘build a coalition’. Eight of the selected strategies belonged to the ERIC cluster ‘develop stakeholder interrelationships’. Other strategies were part of the clusters ‘use evaluative and iterative strategies’ (n = 3), ‘utilise financial strategies’ (n = 2), and ‘engage consumers’ (n = 1). Conclusions: The findings emphasise the importance of an interdisciplinary approach when addressing the implementation of LRTMs in osteoarthritis care. The final selection of implementation strategies forms the basis for a tailored implementation plan. Future work should focus on further operationalising the implementation strategies and evaluating the effectiveness of the resulting implementation plan.

Bullous pemphigoid (BP) is characterized by deposition of immunoglobulins and complement along the epidermal basement membrane (BM). In humans, there is a lack of functional studies targeting the complement system (CS). This study investigates activation of all complement pathways in BP skin biopsies. Moreover, pharmacological inhibition at different levels of the CS was investigated using anti-complement compounds in a complement fixation BP assay. In this retrospective study, 21 frozen biopsies from BP patients were stained by direct immunofluorescence for C1q, MBL, ficolin-2, C4d, properdin, C3c and C5b-9. Sera from 10 patients were analysed in a complement fixation assay in the presence of C1 inhibitor, anti-factor B monoclonal antibody (mAb), anti-C3 mAb and anti-C5 mAb and compared with dexamethasone. The two readouts were the quantity of complement deposited along the BM and the release of sC5b-9 in the supernatant. Our results show classical and alternative complement pathway activation in BP skin biopsies, but could not demonstrate significant lectin pathway activation. In contrast to dexamethasone, complement deposition along the BM could be selectively inhibited by anti-C1 and anti- factor B. More downstream, selective intervention at the level of C3 and C5 could effectively reduce complement deposition along the BM and the release of sC5b-9 in the supernatant. This study shows that selective intervention in either the classical, alternative or terminal pathway prevented deposition of complement along the BM in an in vitro BP model. The results of our study greatly encourage the clinical development of complement inhibitors for the treatment of BP.

A code is defined by the nature of the symbols, which are used to generate information-storing combinations (e.g. oligo- and polymers). Like nucleic acids and proteins, oligo- and polysac-charides are ubiquitous, and they are a biochemical platform for establishing molecular mes-sages. Of note, the letters of the sugar code system (third alphabet of life) excel in coding ca-pacity by making an unsurpassed versatility for isomer (code word) formation possible by var-iability in anomery and linkage position of the glycosidic bond, ring size and branching. The enzymatic machinery for glycan biosynthesis (writers) realizes this enormous potential for building a large vocabulary. It includes possibilities for dynamic editing/erasing as known from nucleic acids and proteins. Matching the glycome diversity, a large panel of sugar receptors (lectins) has developed based on more than a dozen folds. Lectins ‘read’ the glycan-encoded information. Hydrogen/coordination bonding and ionic pairing together with stacking and C-H/- interactions as well as modes of spatial glycan presentation underlie the selectivity and specificity of glycan-lectin recognition. Modular design of lectins together with glycan display and the nature of the cognate glycoconjugate account for the large number of post-binding events. They give an entry to the glycan vocabulary its functional, often context-dependent meaning(s), hereby building the dictionary of the sugar code

Proton nuclear magnetic resonance (NMR) N-acetyl signals (Glyc) from glycoproteins and supramolecular phospholipids composite peak (SPC) from phospholipid quaternary nitrogen methyls in subcompartments of lipoprotein particles) can give important systemic metabolic information, but their absolute quantification is compromised by overlap with interfering resonances from lipoprotein lipids themselves. We present a J-Edited DIffusional (JEDI) proton NMR spectroscopic approach to selectively augment signals from the inflammatory marker peaks Glyc and SPCs in blood serum NMR spectra, which enables direct integration of peaks associated with molecules found in specific compartments. We explore a range of pulse sequences that allow editing based on peak J-modulation, translational diffusion, and T2 relaxation time and validate them for untreated blood serum samples from SARS-CoV-2 infected patients (n = 116) as well as samples from healthy controls and pregnant women with physiological inflammation and hyperlipidemia (n = 631). The data show that JEDI is an improved approach to selectively investigate inflammatory signals in serum and may have widespread diagnostic applicability to disease states associated with systemic inflammation.

SARS-CoV-2 infection causes a significant reduction in lipoprotein-bound serum phospholipids give rise to supramolecular phospholipid composite (SPC) signals observed in diffusion and relaxation edited 1H NMR spectra. To characterize the chemical structural components and compartmental location of SPC and to understand further its possible diagnostic properties, we applied a Statistical HeterospectroscopY in n-dimensions (SHY-n) approach. This involved statistically linking a series of orthogonal measurements made on the same samples, using independent analytical techniques and instruments, to identify the major individual phospholipid components giving rise to the SPC signals. Thus, an integrated model for SARS-CoV-2 positive and control adults is presented that relates three identified diagnostic subregions of the SPC signal envelope (SPC1, SPC2, and SPC3) generated using diffusion and relaxation edited (DIRE) NMR spectroscopy to lipoprotein and lipid measurements obtained by in vitro diagnostic NMR spectroscopy and ultrahigh-performance liquid chromatography–tandem mass spectrometry (UHPLC–MS/MS). The SPC signals were then correlated sequentially with (a) total phospholipids in lipoprotein subfractions; (b) apolipoproteins B100, A1, and A2 in different lipoproteins and subcompartments; and (c) MS-measured total serum phosphatidylcholines present in the NMR detection range (i.e., PCs: 16.0,18.2; 18.0,18.1; 18.2,18.2; 16.0,18.1; 16.0,20.4; 18.0,18.2; 18.1,18.2), lysophosphatidylcholines (LPCs: 16.0 and 18.2), and sphingomyelin (SM 22.1). The SPC3/SPC2 ratio correlated strongly (r = 0.86) with the apolipoprotein B100/A1 ratio, a well-established marker of cardiovascular disease risk that is markedly elevated during acute SARS-CoV-2 infection. These data indicate the considerable potential of using a serum SPC measurement as a metric of cardiovascular risk based on a single NMR experiment. This is of specific interest in relation to understanding the potential for in

Proton nuclear magnetic resonance (NMR) N-acetyl signals (Glyc) from glycoproteins and supramolecular phospholipids composite peak (SPC) from phospholipid quaternary nitrogen methyls in subcompartments of lipoprotein particles) can give important systemic metabolic information, but their absolute quantification is compromised by overlap with interfering resonances from lipoprotein lipids themselves. We present a J-Edited DIffusional (JEDI) proton NMR spectroscopic approach to selectively augment signals from the inflammatory marker peaks Glyc and SPCs in blood serum NMR spectra, which enables direct integration of peaks associated with molecules found in specific compartments. We explore a range of pulse sequences that allow editing based on peak J-modulation, translational diffusion, and T2 relaxation time and validate them for untreated blood serum samples from SARS-CoV-2 infected patients (n = 116) as well as samples from healthy controls and pregnant women with physiological inflammation and hyperlipidemia (n = 631). The data show that JEDI is an improved approach to selectively investigate inflammatory signals in serum and may have widespread diagnostic applicability to disease states associated with systemic inflammation.

Purpose The purpose of this study was to assess in which proportion of patients with degenerative knee disease aged 50+ in whom a knee arthroscopy is performed, no valid surgical indication is reported in medical records, and to explore possible explanatory factors. Methods A retrospective study was conducted using administrative data from January to December 2016 in 13 orthopedic centers in the Netherlands. Medical records were selected from a random sample of 538 patients aged 50+ with degenerative knee disease in whom arthroscopy was performed, and reviewed on reported indications for the performed knee arthroscopy. Valid surgical indications were predefined based on clinical national guidelines and expert opinion (e.g., truly locked knee). A knee arthroscopy without a reported valid indication was considered potentially low value care. Multivariate logistic regression analysis was performed to assess whether age, diagnosis (“Arthrosis” versus “Meniscal lesion”), and type of care trajectory (initial or follow-up) were associated with performing a potentially low value knee arthroscopy. Results Of 26,991 patients with degenerative knee disease, 2556 (9.5%) underwent an arthroscopy in one of the participating orthopedic centers. Of 538 patients in whom an arthroscopy was performed, 65.1% had a valid indication reported in the medical record and 34.9% without a reported valid indication. From the patients without a valid indication, a joint patient–provider decision or patient request was reported as the main reason. Neither age [OR 1.013 (95% CI 0.984–1.043)], diagnosis [OR 0.998 (95% CI 0.886–1.124)] or type of care trajectory [OR 0.989 (95% CI 0.948–1.032)] were significantly associated with performing a potentially low value knee arthroscopy. Conclusions In a random sample of knee arthroscopies performed in 13 orthopedic centers in 2016, 65% had valid indications reported in the medical records but 35% were performed wi

SARS-CoV-2 infection causes a significant reduction in lipoprotein-bound serum phospholipids give rise to supramolecular phospholipid composite (SPC) signals observed in diffusion and relaxation edited 1H NMR spectra. To characterize the chemical structural components and compartmental location of SPC and to understand further its possible diagnostic properties, we applied a Statistical HeterospectroscopY in n-dimensions (SHY-n) approach. This involved statistically linking a series of orthogonal measurements made on the same samples, using independent analytical techniques and instruments, to identify the major individual phospholipid components giving rise to the SPC signals. Thus, an integrated model for SARS-CoV-2 positive and control adults is presented that relates three identified diagnostic subregions of the SPC signal envelope (SPC1, SPC2, and SPC3) generated using diffusion and relaxation edited (DIRE) NMR spectroscopy to lipoprotein and lipid measurements obtained by in vitro diagnostic NMR spectroscopy and ultrahigh-performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS). The SPC signals were then correlated sequentially with (a) total phospholipids in lipoprotein subfractions; (b) apolipoproteins B100, A1, and A2 in different lipoproteins and subcompartments; and (c) MS-measured total serum phosphatidylcholines present in the NMR detection range (i.e., PCs: 16.0,18.2; 18.0,18.1; 18.2,18.2; 16.0,18.1; 16.0,20.4; 18.0,18.2; 18.1,18.2), lysophosphatidylcholines (LPCs: 16.0 and 18.2), and sphingomyelin (SM 22.1). The SPC3/SPC2 ratio correlated strongly (r = 0.86) with the apolipoprotein B100/A1 ratio, a well-established marker of cardiovascular disease risk that is markedly elevated during acute SARS-CoV-2 infection. These data indicate the considerable potential of using a serum SPC measurement as a metric of cardiovascular risk based on a single NMR experiment. This is of specific interest in relation to understanding the potential for in

SARS-CoV-2 infection causes a significant reduction in lipoprotein-bound serum phospholipids give rise to supramolecular phospholipid composite (SPC) signals observed in diffusion and relaxation edited 1H NMR spectra. To characterize the chemical structural components and compartmental location of SPC and to understand further its possible diagnostic properties, we applied a Statistical HeterospectroscopY in n-dimensions (SHY-n) approach. This involved statistically linking a series of orthogonal measurements made on the same samples, using independent analytical techniques and instruments, to identify the major individual phospholipid components giving rise to the SPC signals. Thus, an integrated model for SARS-CoV-2 positive and control adults is presented that relates three identified diagnostic subregions of the SPC signal envelope (SPC1, SPC2, and SPC3) generated using diffusion and relaxation edited (DIRE) NMR spectroscopy to lipoprotein and lipid measurements obtained by in vitro diagnostic NMR spectroscopy and ultrahigh-performance liquid chromatography–tandem mass spectrometry (UHPLC–MS/MS). The SPC signals were then correlated sequentially with (a) total phospholipids in lipoprotein subfractions; (b) apolipoproteins B100, A1, and A2 in different lipoproteins and subcompartments; and (c) MS-measured total serum phosphatidylcholines present in the NMR detection range (i.e., PCs: 16.0,18.2; 18.0,18.1; 18.2,18.2; 16.0,18.1; 16.0,20.4; 18.0,18.2; 18.1,18.2), lysophosphatidylcholines (LPCs: 16.0 and 18.2), and sphingomyelin (SM 22.1). The SPC3/SPC2 ratio correlated strongly (r = 0.86) with the apolipoprotein B100/A1 ratio, a well-established marker of cardiovascular disease risk that is markedly elevated during acute SARS-CoV-2 infection. These data indicate the considerable potential of using a serum SPC measurement as a metric of cardiovascular risk based on a single NMR experiment. This is of specific interest in relation to understanding the potential for in

Proton nuclear magnetic resonance (NMR) N-acetyl signals (Glyc) from glycoproteins and supramolecular phospholipids composite peak (SPC) from phospholipid quaternary nitrogen methyls in subcompartments of lipoprotein particles) can give important systemic metabolic information, but their absolute quantification is compromised by overlap with interfering resonances from lipoprotein lipids themselves. We present a J-Edited DIffusional (JEDI) proton NMR spectroscopic approach to selectively augment signals from the inflammatory marker peaks Glyc and SPCs in blood serum NMR spectra, which enables direct integration of peaks associated with molecules found in specific compartments. We explore a range of pulse sequences that allow editing based on peak J-modulation, translational diffusion, and T2 relaxation time and validate them for untreated blood serum samples from SARS-CoV-2 infected patients (n = 116) as well as samples from healthy controls and pregnant women with physiological inflammation and hyperlipidemia (n = 631). The data show that JEDI is an improved approach to selectively investigate inflammatory signals in serum and may have widespread diagnostic applicability to disease states associated with systemic inflammation.

BACKGROUND: Prior data has demonstrated increased mortality in hospitalized patients with acute heart failure (AHF) and troponin elevation. No data has specifically examined the prognostic significance of troponin elevation in patients with AHF discharged after emergency department (ED) management. OBJECTIVE: Evaluate the relationship between troponin elevation and outcomes in patients with AHF who are treated and released from the ED. METHODS: This was a secondary analysis of the Get with the Guidelines to Reduce Disparities in AHF Patients Discharged from the ED (GUIDED-HF) trial, a randomized, controlled trial of ED patients with AHF who were discharged. Patients with elevated conventional troponin not due to acute coronary syndrome (ACS) were included. Our primary outcome was a composite endpoint: time to 30-day cardiovascular death and/or heart failure-related events. RESULTS: Of the 491 subjects included in the GUIDED-HF trial, 418 had troponin measured during the ED evaluation and 66 (16%) had troponin values above the 99th percentile. Median age was 63 years (interquartile range, 54-70), 62% (n = 261) were male, 63% (n = 265) were Black, and 16% (n = 67) experienced our primary outcome. There were no differences in our primary outcome between those with and without troponin elevation (12/66, 18.1% vs 55/352, 15.6%; P = 0.60). This effect was maintained regardless of assignment to usual care or the intervention arm. In multivariable regression analysis, there was no association between our primary outcome and elevated troponin (hazard ratio, 1.00; 95% confidence interval, 0.49-2.01, P = 0.994). CONCLUSION: If confirmed in a larger cohort, these findings may facilitate safe ED discharge for a group of patients with AHF without ACS when an elevated troponin is the primary reason for admission.

ObjectivesThe objective is to explore academic emergency medicine physicians' exposure to and needs regarding faculty development.MethodsWe conducted a prospective qualitative study of Society for Academic Emergency Medicine members in 2018 using focus groups selected by convenience and snowball sampling. One facilitator ensured representative engagement and responses were transcribed in real-time by an assistant after obtaining verbal consent. Results were analyzed using a grounded theory approach with a constructivist perspective. Thematic analysis was refined using the constant comparative method.ResultsSixteen physicians participated in the focus groups, representing a diverse group of perspectives. Six themes emerged about unmet needs in faculty development: knowledge and skills, relationships, specific programs or resources, and professional benefits.ConclusionsMembers of a national academic society identified three areas of focus important to developing academicians in emergency medicine: content for faculty developers, relationship-building among members, and support from the organization as a "professional home." Academic societies can use this to guide future programming.

Anthropogenic activities are modifying the oceanic environment rapidly and are causing ocean warming and deoxygenation, affecting biodiversity, productivity, and biogeochemical cycling. In coastal sediments, anaerobic organic matter degradation essentially fuels the production of hydrogen sulfide and methane. The release of these compounds from sediments is detrimental for the (local) environment and entails socio-economic consequences. Therefore, it is vital to understand which microbes catalyze the re-oxidation of these compounds under environmental dynamics, thereby mitigating their release to the water column. Here we use the seasonally dynamic Boknis Eck study site (SW Baltic Sea), where bottom waters annually fall hypoxic or anoxic after the summer months, to extrapolate how the microbial community and its activity reflects rising temperatures and deoxygenation. During October 2018, hallmarked by warmer bottom water and following a hypoxic event, modeled sulfide and methane production and consumption rates are higher than in March at lower temperatures and under fully oxic bottom water conditions. The microbial populations catalyzing sulfide and methane metabolisms are found in shallower sediment zones in October 2018 than in March 2019. DNA-and RNA profiling of sediments indicate a shift from primarily organotrophic to (autotrophic) sulfide oxidizing Bacteria, respectively. Previous studies using data collected over decades demonstrate rising temperatures, decreasing eutrophication, lower primary production and thus less fresh organic matter transported to the Boknis Eck sediments. Elevated temperatures are known to stimulate methanogenesis, anaerobic oxidation of methane, sulfate reduction and essentially microbial sulfide consumption, likely explaining the shift to a phylogenetically more diverse sulfide oxidizing community based on RNA.

Due to its unique ability to reduce carbon dioxide (CO2) into CO or formate at high versus low overpotentials, respectively, palladium is a promising catalyst for the electrochemical CO2-reduction reaction (CO2RR). Further improvements aim at increasing its activity and selectivity toward either of these value-added species, while reducing the amount of hydrogen produced as a side product. With this motivation, in this work, we synthesized a range of unsupported, bimetallic PdPt aerogels and pure Pt or Pd aerogels and extensively characterized them using various microscopic and spectroscopic techniques. These revealed that the aerogels’ porous web consists of homogenous alloys of Pt and Pd, with palladium and platinum being present on their surface for all compositions. The subsequent determination of these aeorgels’ CO2RR performance unveiled that the high activity of these Pt surface atoms toward hydrogen evolution causes all PdPt alloys to favor this reaction over CO2 reduction. In the case of the pure Pd aerogel, although, its unsupported nature leads to a suppression of H2 evolution and a concomitant increase in the selectivity toward CO when compared to a commercial, carbon-supported Pd-nanoparticle catalyst.

The immune system is composed of two closely collaborative systems, an innate and an adaptive system. The innate immune system is a constitutive present system that can act rapidly to eradicate microbes. The primary cells of the innate immune system are macrophages, granulocytes, natural killer cells and dendritic cells. The adaptive system can be divided in a humoral and cellular response. The humoral response is characterized by activation of B-lymphocytes with subsequent maturation into plasma cells and production of antibodies, whereas a cellular immune response is characterized by transformation of T-lymphocytes into cytotoxic T-cells, capable of killing virally infected cells. Auto-reactive B- and T-lymphocytes can induce autoimmune diseases. Autoimmune blistering diseases are the result of type II hypersensitivity, e.g. autoantibodies are directed against cell or matrix components. In pemphigoid diseases antibodies are directed against hemidesmosomal components, whereas pemphigus is characterized by antibodies against desmosomal proteins.

Direct immunofluorescence plays an important role in the diagnosis of autoimmune blistering diseases. The purpose of direct immunofluorescence microscopy is to detect in vivo antibodies in patient's skin or mucosa. Direct immunofluorescence of pemphigus shows depositions of immunoglobulins and/or complement on the epithelial cell surface of keratinocytes, whereas pemphigoid shows linear deposition of immunoglobulins along the epidermal basement membrane zone. This linear deposition can be separated in an n-serrated pattern and a u-serrated pattern. An n-serrated pattern is seen in blistering diseases with binding above the lamina densa with antibodies against hemidesmosomal components, e.g. bullous pemphigoid, while a u-serrated pattern points to a sublamina densa binding diseases caused by autoantibodies against type VII collagen, e.g. epidermolysis bullosa acquisita. Finally, dermatitis herpetiformis shows a granular IgA deposition along the epidermal basement membrane zone.

The skin is an organ that is easy to access for microscopy. Sections of the skin may reveal the split level of the blister, the type and distribution of inflammatory cells, and the presence, class and distribution pattern of autoantibodies. A biopsy should be taken from a location with smallest change of sample error, and the specimen specially fixated and transported for the requested microscopic techniques. Taking biopsies is the area of expertise of the dermatologist, even taking conjunctiva biopsies for immunofluorescence (IF) is possible in cases of suspicion of an autoimmune blistering disease of the eye.

The purpose of indirect immunofluorescence microscopy is to detect circulating antibodies in patient's serum. For this purpose an adequate substrate is necessary to visualize these antibodies. Monkey esophagus is the most widely used substrate for detecting of circulating autoantibodies in patients with autoimmune blistering diseases. In all variants of pemphigus antibodies show an epithelial cell surface pattern, resulting from present autoantibodies against the desmosomal molecules desmoglein 1 and/or 3. This pattern is also called chicken wire or honeycomb pattern. In pemphigoid a linear deposition along the epithelial basement membrane can be observed, caused by autoantibodies against hemidesmosomes or their connecting proteins underneath. Human salt split skin is a valuable substrate in the diagnosis of subepidermal autoimmune blistering diseases. Important antigens in the roof of salt split skin are type XVII collagen (BP180) and BP230, whereas laminin 332, p200 and type IV collagen are situated in the floor of the blister. This implies that bullous pemphigoid, mucous membrane pemphigoid, pemphigoid gestationis, and lichen planus pemphigoides show staining of IgG on the epidermal side of the blister. On the other hand anti-laminin 332 pemphigoid, anti-p200 pemphigoid, epidermolysis bullosa acquisita, and bullous SLE show staining on the dermal side. Other less used, but valuable substrates in some instances, are rat bladder and knock-out skin.

Paraneoplastic pemphigus is a rare but severe potentially fatal autoimmune disease characterized by severe stomatitis and a variety of cutaneous manifestations in association with an underlying neoplasia. Pulmonary involvement may also occur. The pathogenesis involves the production of autoantibodies against desmogleins, plakins and the protease inhibitor alpha-2 macroglobuline like-1, but T-cell mediated autoimmunity is also thought to play a role. Diagnosis usually relies on the demonstration of a specific subset of circulating autoantibodies in patient serum, although in a small subset of patients these autoantibodies might be absent. Due to it's rarity, there are no guidelines for the treatment of PNP. The general approach includes a variety of immunosuppressive agents and treatment of the underlying neoplasia. Despite treatment, paraneoplastic pemphigus has high mortality rates, often due to sepsis, respiratory failure or progression of the underlying malignancy.

Background: Prior data has demonstrated increased mortality in hospitalized patients with acute heart failure (AHF) and troponin elevation. No data has specifically examined the prognostic significance of troponin elevation in patients with AHF discharged after emergency department (ED) management. Objective: Evaluate the relationship between troponin elevation and outcomes in patients with AHF who are treated and released from the ED. Methods: This was a secondary analysis of the Get with the Guidelines to Reduce Disparities in AHF Patients Discharged from the ED (GUIDED-HF) trial, a randomized, controlled trial of ED patients with AHF who were discharged. Patients with elevated conventional troponin not due to acute coronary syndrome (ACS) were included. Our primary outcome was a composite endpoint: time to 30-day cardiovascular death and/or heart failure-related events. Results: Of the 491 subjects included in the GUIDED-HF trial, 418 had troponin measured during the ED evaluation and 66 (16%) had troponin values above the 99th percentile. Median age was 63 years (interquartile range, 54-70), 62% (n = 261) were male, 63% (n = 265) were Black, and 16% (n = 67) experienced our primary outcome. There were no differences in our primary outcome between those with and without troponin elevation (12/66, 18.1% vs 55/352, 15.6%; P = 0.60). This effect was maintained regardless of assignment to usual care or the intervention arm. In multivariable regression analysis, there was no association between our primary outcome and elevated troponin (hazard ratio, 1.00; 95% confidence interval, 0.49-2.01, P = 0.994). Conclusion: If confirmed in a larger cohort, these findings may facilitate safe ED discharge for a group of patients with AHF without ACS when an elevated troponin is the primary reason for admission.