SwePub - search: WFRF:(Ludwig Michael)

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1.	Menkveld, Albert J., et al. (author) Nonstandard Errors 2024 In: JOURNAL OF FINANCE. - : Wiley-Blackwell. - 0022-1082 .- 1540-6261. ; 79:3, s. 2339-2390 Journal article (peer-reviewed)abstract In statistics, samples are drawn from a population in a data-generating process (DGP). Standard errors measure the uncertainty in estimates of population parameters. In science, evidence is generated to test hypotheses in an evidence-generating process (EGP). We claim that EGP variation across researchers adds uncertainty-nonstandard errors (NSEs). We study NSEs by letting 164 teams test the same hypotheses on the same data. NSEs turn out to be sizable, but smaller for more reproducible or higher rated research. Adding peer-review stages reduces NSEs. We further find that this type of uncertainty is underestimated by participants.
2.	Hess, Timo, et al. (author) Dissecting the genetic heterogeneity of gastric cancer 2023 In: EBioMedicine. - : Elsevier. - 2352-3964. ; 92 Journal article (peer-reviewed)abstract Background: Gastric cancer (GC) is clinically heterogenous according to location (cardia/non-cardia) and histopathology (diffuse/intestinal). We aimed to characterize the genetic risk architecture of GC according to its subtypes. Another aim was to examine whether cardia GC and oesophageal adenocarcinoma (OAC) and its precursor lesion Barrett's oesophagus (BO), which are all located at the gastro-oesophageal junction (GOJ), share polygenic risk architecture.Methods: We did a meta-analysis of ten European genome-wide association studies (GWAS) of GC and its subtypes. All patients had a histopathologically confirmed diagnosis of gastric adenocarcinoma. For the identification of risk genes among GWAS loci we did a transcriptome-wide association study (TWAS) and expression quantitative trait locus (eQTL) study from gastric corpus and antrum mucosa. To test whether cardia GC and OAC/BO share genetic aetiology we also used a European GWAS sample with OAC/BO.Findings: Our GWAS consisting of 5816 patients and 10,999 controls highlights the genetic heterogeneity of GC according to its subtypes. We newly identified two and replicated five GC risk loci, all of them with subtype-specific association. The gastric transcriptome data consisting of 361 corpus and 342 antrum mucosa samples revealed that an upregulated expression of MUC1, ANKRD50, PTGER4, and PSCA are plausible GC-pathomechanisms at four GWAS loci. At another risk locus, we found that the blood-group 0 exerts protective effects for non-cardia and diffuse GC, while blood-group A increases risk for both GC subtypes. Furthermore, our GWAS on cardia GC and OAC/BO (10,279 patients, 16,527 controls) showed that both cancer entities share genetic aetiology at the polygenic level and identified two new risk loci on the single-marker level.Interpretation: Our findings show that the pathophysiology of GC is genetically heterogenous according to location and histopathology. Moreover, our findings point to common molecular mechanisms underlying cardia GC and OAC/BO.
3.	Demichev, Vadim, et al. (author) A time-resolved proteomic and prognostic map of COVID-19 2021 In: Cell Systems. - : Elsevier BV. - 2405-4712 .- 2405-4720. ; 12:8, s. 780-794.e7 Journal article (peer-reviewed)abstract COVID-19 is highly variable in its clinical presentation, ranging from asymptomatic infection to severe organ damage and death. We characterized the time-dependent progression of the disease in 139 COVID-19 inpatients by measuring 86 accredited diagnostic parameters, such as blood cell counts and enzyme activities, as well as untargeted plasma proteomes at 687 sampling points. We report an initial spike in a systemic inflammatory response, which is gradually alleviated and followed by a protein signature indicative of tissue repair, metabolic reconstitution, and immunomodulation. We identify prognostic marker signatures for devising risk-adapted treatment strategies and use machine learning to classify therapeutic needs. We show that the machine learning models based on the proteome are transferable to an independent cohort. Our study presents a map linking routinely used clinical diagnostic parameters to plasma proteomes and their dynamics in an infectious disease.
4.	Niemi, MEK, et al. (author) 2021 swepub:Mat__t
5.	Kanai, M, et al. (author) 2023 swepub:Mat__t
6.	Ludwig, Sebastian, et al. (author) Transcatheter Mitral Valve Replacement versus Medical Therapy for Secondary Mitral Regurgitation: A Propensity Score-Matched Comparison. 2023 In: Circulation. Cardiovascular interventions. - 1941-7632. ; 16:6 Journal article (peer-reviewed)abstract Background: Transcatheter mitral valve replacement (TMVR) is an emerging therapeutic alternative for patients with secondary mitral regurgitation (MR). Outcomes of TMVR versus guideline-directed medical therapy (GDMT) have not been investigated for this population. This study aimed to compare clinical outcomes of patients with secondary MR undergoing TMVR versus GDMT alone. Methods: The CHOICE-MI registry included patients with MR undergoing TMVR using dedicated devices. Patients with MR etiologies other than secondary MR were excluded. Patients treated with GDMT alone were derived from the control arm of the COAPT trial. We compared outcomes between the TMVR and GDMT groups, using propensity score (PS)-matching to adjust for baseline differences. Results: After PS-matching, 97 patient pairs undergoing TMVR (72.9±8.7 years, 60.8% male, transapical access 91.8%) versus GDMT (73.1±11.0 years, 59.8% male) were compared. At 1 and 2 years, residual MR was ≤1+ in all patients of the TMVR group compared to 6.9% and 7.7%, respectively, in those receiving GDMT alone (both p<0.001). The 2-year rate of HF hospitalization was significantly lower in the TMVR group (32.8% vs. 54.4%, HR 0.59, 95% CI 0.35-0.99; p=0.04). Among survivors, a higher proportion of patients were in NYHA functional class I or II in the TMVR group at 1 year (78.2% vs. 59.7%, p=0.03) and at 2 years (77.8% vs. 53.2%, p=0.09). Two-year mortality was similar in the two groups (TMVR vs. GDMT, 36.8% vs. 40.8%, HR 1.01, 95% CI 0.62-1.64; p=0.98). Conclusions: In this observational comparison, over 2-year follow-up, TMVR using mostly transapical devices in patients with secondary MR was associated with significant reduction of MR, symptomatic improvement, less frequent hospitalizations for HF and similar mortality compared with GDMT.
7.	Muus, Christoph, et al. (author) Single-cell meta-analysis of SARS-CoV-2 entry genes across tissues and demographics 2021 In: Nature Medicine. - : Springer Science and Business Media LLC. - 1078-8956 .- 1546-170X. ; 27:3, s. 546-559 Journal article (peer-reviewed)abstract Angiotensin-converting enzyme 2 (ACE2) and accessory proteases (TMPRSS2 and CTSL) are needed for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) cellular entry, and their expression may shed light on viral tropism and impact across the body. We assessed the cell-type-specific expression of ACE2, TMPRSS2 and CTSL across 107 single-cell RNA-sequencing studies from different tissues. ACE2, TMPRSS2 and CTSL are coexpressed in specific subsets of respiratory epithelial cells in the nasal passages, airways and alveoli, and in cells from other organs associated with coronavirus disease 2019 (COVID-19) transmission or pathology. We performed a meta-analysis of 31 lung single-cell RNA-sequencing studies with 1,320,896 cells from 377 nasal, airway and lung parenchyma samples from 228 individuals. This revealed cell-type-specific associations of age, sex and smoking with expression levels of ACE2, TMPRSS2 and CTSL. Expression of entry factors increased with age and in males, including in airway secretory cells and alveolar type 2 cells. Expression programs shared by ACE2(+)TMPRSS2(+) cells in nasal, lung and gut tissues included genes that may mediate viral entry, key immune functions and epithelial-macrophage cross-talk, such as genes involved in the interleukin-6, interleukin-1, tumor necrosis factor and complement pathways. Cell-type-specific expression patterns may contribute to the pathogenesis of COVID-19, and our work highlights putative molecular pathways for therapeutic intervention. An integrated analysis of over 100 single-cell and single-nucleus transcriptomics studies illustrates severe acute respiratory syndrome coronavirus 2 viral entry gene coexpression patterns across different human tissues, and shows association of age, smoking status and sex with viral entry gene expression in respiratory cell populations.
8.	Rieke, Johanna Magdalena, et al. (author) SLC20A1Is Involved in Urinary Tract and Urorectal Development 2020 In: Frontiers in Cell and Developmental Biology. - : FRONTIERS MEDIA SA. - 2296-634X. ; 8 Journal article (peer-reviewed)abstract Previous studies in developingXenopusand zebrafish reported that the phosphate transporterslc20a1ais expressed in pronephric kidneys. The recent identification ofSLC20A1as a monoallelic candidate gene for cloacal exstrophy further suggests its involvement in the urinary tract and urorectal development. However, little is known of the functional role ofSLC20A1in urinary tract development. Here, we investigated this using morpholino oligonucleotide knockdown of the zebrafish orthologslc20a1a. This caused kidney cysts and malformations of the cloaca. Moreover, in morphants we demonstrated dysfunctional voiding and hindgut opening defects mimicking imperforate anus in human cloacal exstrophy. Furthermore, we performed immunohistochemistry of an unaffected 6-week-old human embryo and detectedSLC20A1in the urinary tract and the abdominal midline, structures implicated in the pathogenesis of cloacal exstrophy. Additionally, we resequencedSLC20A1in 690 individuals with bladder exstrophy-epispadias complex (BEEC) including 84 individuals with cloacal exstrophy. We identified two additional monoallelicde novovariants. One was identified in a case-parent trio with classic bladder exstrophy, and one additional novelde novovariant was detected in an affected mother who transmitted this variant to her affected son. To study the potential cellular impact ofSLC20A1variants, we expressed them in HEK293 cells. Here, phosphate transport was not compromised, suggesting that it is not a disease mechanism. However, there was a tendency for lower levels of cleaved caspase-3, perhaps implicating apoptosis pathways in the disease. Our results suggestSLC20A1is involved in urinary tract and urorectal development and implicateSLC20A1as a disease-gene for BEEC.
9.	Schwarz, Tanja, et al. (author) Opioid agonist treatment in transition : A cross-country comparison between Austria, Germany and Switzerland 2024 In: Drug And Alcohol Dependence. - 0376-8716 .- 1879-0046. ; 254 Journal article (peer-reviewed)abstract Background and Aims: OAT is a well developed and successful treatment strategy for opioid dependent patients in Europe. It has significantly contributed to the fight against the HIV and HCV pandemics, leading to an increased life expectancy in this population. Building on the OAT experiences in Austria, Germany, and Switzerland and their models of care, the objective of this study is to analyse experiences and changes in patient structures to identify necessary adaptations for the system of care.Methods: We analysed national register-based data from patients receiving OAT during the period spanning from 2010 to 2020 in Austria, Germany (cases), and Switzerland. We examined and compared OAT policies and practice at national levels through a review of literature and publicly available policy documents.Results: Across these three countries, the life expectancy of OAT patients increased substantially. The mean age increased from 33.0 in 2010 to 39.1 in 2020 in Austria, from 35.6 years to 41.5 years in Germany (cases), and from 39.6 to 47.1 in Switzerland, respectively. In all three countries, the percentage of patients/cases aged 60 years and older increased more than tenfold between 2010 and 2020.Conclusions: Integrated support models, reliable care structures, internationally comparable high treatment coverage, flexible prescribing practices, and a wide range of available OAT medications are successful strategies. The experiences in these countries indicate that it is possible to address the complex and chronic nature of opioid dependence and its concurrent mental and physical health challenges, resulting in an increasing life expectancy of OAT patients.
10.	Westbury, V, Michael, et al. (author) Hyena paleogenomes reveal a complex evolutionary history of cross-continental gene flow between spotted and cave hyena 2020 In: Science Advances. - : American Association for the Advancement of Science (AAAS). - 2375-2548. ; 6:11 Journal article (peer-reviewed)abstract The genus Crocuta (African spotted and Eurasian cave hyenas) includes several closely related extinct and extant lineages. The relationships among these lineages, however, are contentious. Through the generation of population-level paleogenomes from late Pleistocene Eurasian cave hyena and genomes from modern African spotted hyena, we reveal the cross-continental evolutionary relationships between these enigmatic hyena lineages. We find a deep divergence (similar to 2.5 Ma) between African and Eurasian Crocuta populations, suggesting that ancestral Crocuta left Africa around the same time as early Homo. Moreover, we find discordance between nuclear and mitochondrial phylogenies and evidence for bidirectional gene flow between African and Eurasian Crocuta after the lineages split, which may have complicated prior taxonomic classifications. Last, we find a number of introgressed loci that attained high frequencies within the recipient lineage, suggesting some level of adaptive advantage from admixture.
11.	Altmann, Patrick, et al. (author) Increased serum neurofilament light chain concentration indicates poor outcome in Guillain-Barré syndrome. 2020 In: Journal of neuroinflammation. - : Springer Science and Business Media LLC. - 1742-2094. ; 17:1 Journal article (peer-reviewed)abstract Guillain-Barré syndrome (GBS) is an autoimmune disease that results in demyelination and axonal damage. Five percent of patients die and 20% remain significantly disabled on recovery. Recovery is slow in most cases and eventual disability is difficult to predict, especially early in the disease. Blood or cerebrospinal fluid (CSF) biomarkers that could help identify patients at risk of poor outcome are required. We measured serum neurofilament light chain (sNfL) concentrations from blood taken upon admission and investigated a correlation between sNfL and clinical outcome.Baseline sNfL levels in 27 GBS patients were compared with a control group of 22 patients with diagnoses not suggestive of any axonal damage. Clinical outcome parameters for GBS patients included (i) the Hughes Functional Score (HFS) at admission, nadir, and discharge; (ii) the number of days hospitalised; and (iii) whether intensive care was necessary.The median sNfL concentration in our GBS sample on admission was 85.5pg/ml versus 9.1pg/ml in controls. A twofold increase in sNfL concentration at baseline was associated with an HFS increase of 0.6 at nadir and reduced the likelihood of discharge with favourable outcome by a factor of almost three. Higher sNfL levels upon admission correlated well with hospitalisation time (rs=0.69, p<0.0001), during which transfer to intensive care occurred more frequently at an odds ratio of 2.4. Patients with baseline sNfL levels below 85.5pg/ml had a 93% chance of being discharged with an unimpaired walking ability.sNfL levels measured at hospital admission correlated with clinical outcome in GBS patients. These results represent amounts of acute axonal damage and reflect mechanisms resulting in disability in GBS. Thus, sNfL may serve as a convenient blood-borne biomarker to personalise patient care by identifying those at higher risk of poor outcome.
12.	Berner, Logan T., et al. (author) The Arctic plant aboveground biomass synthesis dataset 2024 In: Scientific Data. - : Springer Nature. - 2052-4463. ; 11:1 Journal article (peer-reviewed)abstract Plant biomass is a fundamental ecosystem attribute that is sensitive to rapid climatic changes occurring in the Arctic. Nevertheless, measuring plant biomass in the Arctic is logistically challenging and resource intensive. Lack of accessible field data hinders efforts to understand the amount, composition, distribution, and changes in plant biomass in these northern ecosystems. Here, we present The Arctic plant aboveground biomass synthesis dataset, which includes field measurements of lichen, bryophyte, herb, shrub, and/or tree aboveground biomass (g m−2) on 2,327 sample plots from 636 field sites in seven countries. We created the synthesis dataset by assembling and harmonizing 32 individual datasets. Aboveground biomass was primarily quantified by harvesting sample plots during mid- to late-summer, though tree and often tall shrub biomass were quantified using surveys and allometric models. Each biomass measurement is associated with metadata including sample date, location, method, data source, and other information. This unique dataset can be leveraged to monitor, map, and model plant biomass across the rapidly warming Arctic.
13.	Buchholz, Angela, et al. (author) Patient-Centered Placement Matching of Alcohol-Dependent Patients Based on a Standardized Intake Assessment : Primary Outcomes of an Exploratory Randomized Controlled Trial 2020 In: European Addiction Research. - : S. Karger AG. - 1022-6877 .- 1421-9891. ; 26:3, s. 109-121 Journal article (peer-reviewed)abstract Background: Placement matching guidelines are promising means to optimize patient-centered care and to match patients' treatment needs. Despite considerable research regarding placement matching approaches to optimize alcohol abuse treatment, findings are inconclusive. Objectives: To investigate whether the use of patient-centered placement matching (PCPM) guidelines is more effective in reducing heavy drinking and costs 6 months after discharge from an inpatient alcohol withdrawal treatment compared to usual referral to aftercare. Secondary aims were to investigate whether age, gender, trial site or level of care (LOC) are moderators of efficacy and whether patients who were actually referred to the recommended LOC had better treatment outcomes compared to patients who were treated under- or overmatched. Methods: Design. Exploratory randomized controlled trial with measurements during withdrawal treatment and 6 months after initial assessment. Setting. Four German psychiatric clinics offering a 7-21 day inpatient qualified withdrawal program for patients suffering from alcohol dependence. Participants. From 1,927 patients who had a primary diagnosis of alcohol dependence and did not have organized aftercare when entering withdrawal treatment, 299 were invited to participate. Of those, 250 were randomized to the intervention group (IG, n = 123) or the control group (CG, n = 127). Intervention. The PCPM were applied to patients of the IG by feeding back a recommendation to a LOC for aftercare that was calculated from the Measurements in the Addictions for Triage and Evaluation (MATE) and discussed with the staff of the treatment unit. Patients of the CG received a general feedback regarding their MATE interview on request. Measurements. The MATE, the Client Socio-Demographic and Service Receipt Inventory--European Version and the MATE-Outcomes were administered. Data were analyzed using generalized linear models. Results: In the intention-to-treat analysis, there were no significant differences between IG and CG regarding days of heavy drinking (incident risk ratio [IRR] 1.09; p = 0.640), direct (IRR 1.06; p = 0.779), indirect (IRR 0.77; p = 0.392) and total costs (IRR 0.89; p = 0.496). Furthermore, none of the investigated moderator variables affected statistically significant drinking or cost-related primary outcomes. Regardless of group allocation, patients who received matched aftercare reported significantly fewer days of heavy drinking than undermatched patients (IRR 2.09; p = 0.004). For patients who were overmatched, direct costs were significantly higher (IRR 1.79; p = 0.024), but with no additional effects on alcohol consumption compared to matched patients. Conclusions: While the use of PCPM failed to affect the actual referral to aftercare, our findings suggest that treating patients on the recommended LOC may have the potential to reduce days of heavy drinking compared to undertreatment and costs compared to overtreatment.
14.	Buchholz, Angela, et al. (author) Patient-centered placement matching of alcohol-dependent patients based on a standardized intake assessment : process evaluation within an exploratory randomized controlled trial 2022 In: BMC Psychiatry. - : Springer Science and Business Media LLC. - 1471-244X. ; 22:1 Journal article (peer-reviewed)abstract Background: In the implementation of placement matching guidelines, feasibility has been concerned in previous research. Objectives of this process evaluation were to investigate whether the patient-centered matching guidelines (PCPM) are consistently applied in referral decision-making from an inpatient qualified withdrawal program to a level of care in aftercare, which factors affect whether patients actually receive matched aftercare according to PCPM, and whether its use is feasible and accepted by clinic staff.Methods: The study was conducted as process evaluation within an exploratory randomized controlled trial in four German psychiatric clinics offering a 7-to-21 day qualified withdrawal program for patients suffering from alcohol dependence, and with measurements taken during detoxification treatment and six months after the initial assessment. PCPM were used with patients in the intervention group by feeding back to them a recommendation for a level of care in aftercare that had been calculated from Measurements in the Addictions for Triage and Evaluation (MATE) and discussed with the staff on the treatment unit. As measurements, The MATE, the Client Socio-Demographic and Service Receipt Inventory—European Version, a documentation form, the Control Preference Scale, and the Motivation for Treatment Scale were administered. A workshop for the staff at the participating trial sites was conducted after data collection was finished.Results: Among 250 patients participating in the study, 165 were interviewed at follow-up, and 125 had received aftercare. Although consistency in the application of PCPM was moderate to substantial within the qualified withdrawal program (Cohen’s kappa ≥ .41), it was fair from discharge to follow-up. In multifactorial multinomial regression, the number of foregoing substance abuse treatments predicted whether patients received more likely undermatched (Odds Ratio=1.27; p=.018) or overmatched (Odds Ratio=0.78; p=.054) treatment. While the implementation process during the study was evaluated critically by the staff, they stated a potential of quality assurance, more transparency and patient-centeredness in the use of PCPM.Conclusions: While the use of PCPM has the potential to enhance the quality of referral decision making within treatment, it may not be sufficient to determine referral decisions for aftercare.Trial Registration: German Clinical Trials Register DRKS00005035. Registered 03/06/2013.
15.	Butler-Laporte, G, et al. (author) Exome-wide association study to identify rare variants influencing COVID-19 outcomes: Results from the Host Genetics Initiative 2022 In: PLoS genetics. - : Public Library of Science (PLoS). - 1553-7404 .- 1553-7390. ; 18:11, s. e1010367- Journal article (peer-reviewed)abstract Host genetics is a key determinant of COVID-19 outcomes. Previously, the COVID-19 Host Genetics Initiative genome-wide association study used common variants to identify multiple loci associated with COVID-19 outcomes. However, variants with the largest impact on COVID-19 outcomes are expected to be rare in the population. Hence, studying rare variants may provide additional insights into disease susceptibility and pathogenesis, thereby informing therapeutics development. Here, we combined whole-exome and whole-genome sequencing from 21 cohorts across 12 countries and performed rare variant exome-wide burden analyses for COVID-19 outcomes. In an analysis of 5,085 severe disease cases and 571,737 controls, we observed that carrying a rare deleterious variant in the SARS-CoV-2 sensor toll-like receptor TLR7 (on chromosome X) was associated with a 5.3-fold increase in severe disease (95% CI: 2.75–10.05, p = 5.41x10-7). This association was consistent across sexes. These results further support TLR7 as a genetic determinant of severe disease and suggest that larger studies on rare variants influencing COVID-19 outcomes could provide additional insights.
16.	Eckert, Sebastian, et al. (author) Electronic Structure Changes of an Aromatic Amine Photoacid along the Forster Cycle 2022 In: Angewandte Chemie International Edition. - : John Wiley & Sons. - 1433-7851 .- 1521-3773. ; 61:27 Journal article (peer-reviewed)abstract Photoacids show a strong increase in acidity in the first electronic excited state, enabling real-time studies of proton transfer in acid-base reactions, proton transport in energy storage devices and biomolecular sensor protein systems. Several explanations have been proposed for what determines photoacidity, ranging from variations in solvation free energy to changes in electronic structure occurring along the four stages of the Forster cycle. Here we use picosecond nitrogen K-edge spectroscopy to monitor the electronic structure changes of the proton donating group in a protonated aromatic amine photoacid in solution upon photoexcitation and subsequent proton transfer dynamics. Probing core-to-valence transitions locally at the amine functional group and with orbital specificity, we clearly reveal pronounced electronic structure, dipole moment and energetic changes on the conjugate photobase side. This result paves the way for a detailed electronic structural characterization of the photoacidity phenomenon.
17.	Ekimova, Maria, et al. (author) From Local Covalent Bonding to Extended Electric Field Interactions in Proton Hydration 2022 In: Angewandte Chemie International Edition. - : Wiley. - 1433-7851 .- 1521-3773. ; 61:46 Journal article (peer-reviewed)abstract Seemingly simple yet surprisingly difficult to probe, excess protons in water constitute complex quantum objects with strong interactions with the extended and dynamically changing hydrogen-bonding network of the liquid. Proton hydration plays pivotal roles in energy transport in hydrogen fuel cells and signal transduction in transmembrane proteins. While geometries and stoichiometry have been widely addressed in both experiment and theory, the electronic structure of these specific hydrated proton complexes has remained elusive. Here we show, layer by layer, how utilizing novel flatjet technology for accurate x-ray spectroscopic measurements and combining infrared spectral analysis and calculations, we find orbital-specific markers that distinguish two main electronic-structure effects: Local orbital interactions determine covalent bonding between the proton and neigbouring water molecules, while orbital-energy shifts measure the strength of the extended electric field of the proton. © 2022 The Authors. Angewandte Chemie International Edition published by Wiley-VCH GmbH.
18.	Fallerini, Chiara, et al. (author) Common, low-frequency, rare, and ultra-rare coding variants contribute to COVID-19 severity 2022 In: Human Genetics. - : Springer Nature. - 0340-6717 .- 1432-1203. ; 141:1, s. 147-173 Journal article (peer-reviewed)abstract The combined impact of common and rare exonic variants in COVID-19 host genetics is currently insufficiently understood. Here, common and rare variants from whole-exome sequencing data of about 4000 SARS-CoV-2-positive individuals were used to define an interpretable machine-learning model for predicting COVID-19 severity. First, variants were converted into separate sets of Boolean features, depending on the absence or the presence of variants in each gene. An ensemble of LASSO logistic regression models was used to identify the most informative Boolean features with respect to the genetic bases of severity. The Boolean features selected by these logistic models were combined into an Integrated PolyGenic Score that offers a synthetic and interpretable index for describing the contribution of host genetics in COVID-19 severity, as demonstrated through testing in several independent cohorts. Selected features belong to ultra-rare, rare, low-frequency, and common variants, including those in linkage disequilibrium with known GWAS loci. Noteworthily, around one quarter of the selected genes are sex-specific. Pathway analysis of the selected genes associated with COVID-19 severity reflected the multi-organ nature of the disease. The proposed model might provide useful information for developing diagnostics and therapeutics, while also being able to guide bedside disease management.
19.	Heidegren, Carl-Göran, et al. (author) Recognition in Philosophical Anthropology 2021 In: Handbuch Anerkennung. - Wiesbaden : Springer Fachmedien Wiesbaden. - 2524-373X .- 2524-3721. - 9783658195618 ; , s. 385-389 Book chapter (peer-reviewed)
20.	Hoffmann, Markus, et al. (author) Camostat mesylate inhibits SARS-CoV-2 activation by TMPRSS2-related proteases and its metabolite GBPA exerts antiviral activity 2021 In: EBioMedicine. - : Elsevier BV. - 2352-3964. ; 65 Journal article (peer-reviewed)abstract Background: Antivirals are needed to combat the COVID-19 pandemic, which is caused by SARS-CoV-2. The clinically-proven protease inhibitor Camostat mesylate inhibits SARS-CoV-2 infection by blocking the virus-activating host cell protease TMPRSS2. However, antiviral activity of Camostat mesylate metabolites and potential viral resistance have not been analyzed. Moreover, antiviral activity of Camostat mesylate in human lung tissue remains to be demonstrated. Methods: We used recombinant TMPRSS2, reporter particles bearing the spike protein of SARS-CoV-2 or authentic SARS-CoV-2 to assess inhibition of TMPRSS2 and viral entry, respectively, by Camostat mesylate and its metabolite GBPA. Findings: We show that several TMPRSS2-related proteases activate SARS-CoV-2 and that two, TMPRSS11D and TMPRSS13, are robustly expressed in the upper respiratory tract. However, entry mediated by these proteases was blocked by Camostat mesylate. The Camostat metabolite GBPA inhibited recombinant TMPRSS2 with reduced efficiency as compared to Camostat mesylate. In contrast, both inhibitors exhibited similar antiviral activity and this correlated with the rapid conversion of Camostat mesylate into GBPA in the presence of serum. Finally, Camostat mesylate and GBPA blocked SARS-CoV-2 spread in human lung tissue ex vivo and the related protease inhibitor Nafamostat mesylate exerted augmented antiviral activity. Interpretation: Our results suggest that SARS-CoV-2 can use TMPRSS2 and closely related proteases for spread in the upper respiratory tract and that spread in the human lung can be blocked by Camostat mesylate and its metabolite GBPA. Funding: NIH, Damon Runyon Foundation, ACS, NYCT, DFG, EU, Berlin Mathematics center MATH+, BMBF, Lower Saxony, Lundbeck Foundation, Novo Nordisk Foundation.
21.	Jury, Michael, 1984-, et al. (author) Bioorthogonally Cross‐Linked Hyaluronan–Laminin Hydrogels for 3D Neuronal Cell Culture and Biofabrication 2022 In: Advanced Healthcare Materials. - : Wiley. - 2192-2640 .- 2192-2659. ; 11:11 Journal article (peer-reviewed)abstract Laminins (LNs) are key components in the extracellular matrix of neuronal tissues in the developing brain and neural stem cell niches. LN-presenting hydrogels can provide a biologically relevant matrix for the 3D culture of neurons toward development of advanced tissue models and cell-based therapies for the treatment of neurological disorders. Biologically derived hydrogels are rich in fragmented LN and are poorly defined concerning composition, which hampers clinical translation. Engineered hydrogels require elaborate and often cytotoxic chemistries for cross-linking and LN conjugation and provide limited possibilities to tailor the properties of the materials. Here a modular hydrogel system for neural 3D cell cultures, based on hyaluronan and poly(ethylene glycol), that is cross-linked and functionalized with human recombinant LN-521 using bioorthogonal copper-free click chemistry, is shown. Encapsulated human neuroblastoma cells demonstrate high viability and grow into spheroids. Long-term neuroepithelial stem cells (lt-NES) cultured in the hydrogels can undergo spontaneous differentiation to neural fate and demonstrate significantly higher viability than cells cultured without LN. The hydrogels further support the structural integrity of 3D bioprinted structures and maintain high viability of bioprinted and syringe extruded lt-NES, which can facilitate biofabrication and development of cell-based therapies.
22.	Khalil, Michael, et al. (author) Neurofilaments as biomarkers in neurological disorders - towards clinical application. 2024 In: Nature Reviews Neurology. - 1759-4758 .- 1759-4766. ; 20:5, s. 269-287 Journal article (peer-reviewed)abstract Neurofilament proteins have been validated as specific body fluid biomarkers of neuro-axonal injury. The advent of highly sensitive analytical platforms that enable reliable quantification of neurofilaments in blood samples and simplify longitudinal follow-up has paved the way for the development of neurofilaments as a biomarker in clinical practice. Potential applications include assessment of disease activity, monitoring of treatment responses, and determining prognosis in many acute and chronic neurological disorders as well as their use as an outcome measure in trials of novel therapies. Progress has now moved the measurement of neurofilaments to the doorstep of routine clinical practice for the evaluation of individuals. In this Review, we first outline current knowledge on the structure and function of neurofilaments. We then discuss analytical and statistical approaches and challenges in determining neurofilament levels in different clinical contexts and assess the implications of neurofilament light chain (NfL) levels in normal ageing and the confounding factors that need to be considered when interpreting NfL measures. In addition, we summarize the current value and potential clinical applications of neurofilaments as a biomarker of neuro-axonal damage in a range of neurological disorders, including multiple sclerosis, Alzheimer disease, frontotemporal dementia, amyotrophic lateral sclerosis, stroke and cerebrovascular disease, traumatic brain injury, and Parkinson disease. We also consider the steps needed to complete the translation of neurofilaments from the laboratory to the management of neurological diseases in clinical practice.
23.	Kraus, Ludwig, et al. (author) Long waves of consumption or a unique social generation? Exploring recent declines in youth drinking 2020 In: Addiction Research and Theory. - : Informa UK Limited. - 1606-6359 .- 1476-7392. ; 28:3, s. 183-193 Journal article (peer-reviewed)abstract Background: There is growing evidence for recent declines in adolescent alcohol use in the Western world. While these changes have been subject to scientific debate, the reasons for this downward trend are not yet understood.Method: We consider broader theoretical framings that might be useful in understanding declines in youth drinking. In particular, we reflect on the historical observations of ‘long waves of alcohol consumption’, the ‘Total Consumption Model’, and the ‘Theory of Social Generations’. Based on this, we explore some of the main hypotheses that are presently discussed as possible explanations for changes in youth drinking.Results: We suggest there may have been a change in the social position of alcohol as a social reaction to the negative effects of alcohol, but also emphasize the importance of changes in technology, social norms, family relationships and gender identity, as well as trends in health, fitness, wellbeing and lifestyle behavior. As a result of the interplay of these factors, the ‘devaluation’ of alcohol and the use of it may have contributed to the decrease in youth drinking.Conclusions: For interrupting the recurrent cycle of the ‘long waves of alcohol consumption’, we need to take advantage of the present change in sentiment and “lock in” these changes by new control measures. The model of change presented here hinges on the assumption that the observed change in the position the present young generation takes on alcohol proceeds through the life course, eventually reducing alcohol use in the whole population.
24.	Mathey, Carina M, et al. (author) Molecular Genetic Screening in Patients With ACE Inhibitor/Angiotensin Receptor Blocker-Induced Angioedema to Explore the Role of Hereditary Angioedema Genes 2022 In: Frontiers in Genetics. - : Frontiers Media S.A.. - 1664-8021. ; 13 Journal article (peer-reviewed)abstract Angioedema is a relatively rare but potentially life-threatening adverse reaction to angiotensin-converting enzyme inhibitors (ACEi) and angiotensin receptor blockers (ARBs). As with hereditary forms of angioedema (HAE), this adverse reaction is mediated by bradykinin. Research suggests that ACEi/ARB-induced angioedema has a multifactorial etiology. In addition, recent case reports suggest that some ACEi/ARB-induced angioedema patients may carry pathogenic HAE variants. The aim of the present study was to investigate the possible association between ACEi/ARB-induced angioedema and HAE genes via systematic molecular genetic screening in a large cohort of ACEi/ARB-induced angioedema cases. Targeted re-sequencing of five HAE-associated genes (SERPING1, F12, PLG, ANGPT1, and KNG1) was performed in 212 ACEi/ARB-induced angioedema patients recruited in Germany/Austria, Sweden, and Denmark, and in 352 controls from a German cohort. Among patients, none of the identified variants represented a known pathogenic variant for HAE. Moreover, no significant association with ACEi/ARB-induced angioedema was found for any of the identified common [minor allele frequency (MAF) >5%] or rare (MAF < 5%) variants. However, several non-significant trends suggestive of possible protective effects were observed. The lowest p-value for an individual variant was found in PLG (rs4252129, p.R523W, p = 0.057, p.adjust > 0.999, Fisher's exact test). Variant p.R523W was found exclusively in controls and has previously been associated with decreased levels of plasminogen, a precursor of plasmin which is part of a pathway directly involved in bradykinin production. In addition, rare, potentially functional variants (MAF < 5%, Phred-scaled combined annotation dependent depletion score >10) showed a nominally significant enrichment in controls both: 1) across all five genes; and 2) in the F12 gene alone. However, these results did not withstand correction for multiple testing. In conclusion, our results suggest that HAE-associated mutations are, at best, a rare cause of ACEi/ARB-induced angioedema. Furthermore, we were unable to identify a significant association between ACEi/ARB-induced angioedema and other variants in the investigated genes. Further studies with larger sample sizes are warranted to draw more definite conclusions concerning variants with limited effect sizes, including protective variants.
25.	Matthiesen, Isabelle, et al. (author) Astrocyte 3D culture and bioprinting using peptide functionalized hyaluronan hydrogels 2023 In: Science and Technology of Advanced Materials. - : Informa UK Limited. - 1468-6996 .- 1878-5514. ; 24:1 Journal article (peer-reviewed)abstract Astrocytes play an important role in the central nervous system, contributing to the development of and maintenance of synapses, recycling of neurotransmitters, and the integrity and function of the blood-brain barrier. Astrocytes are also linked to the pathophysiology of various neurodegenerative diseases. Astrocyte function and organization are tightly regulated by interactions mediated by the extracellular matrix (ECM). Engineered hydrogels can mimic key aspects of the ECM and can allow for systematic studies of ECM-related factors that govern astrocyte behaviour. In this study, we explore the interactions between neuroblastoma (SH-SY5Y) and glioblastoma (U87) cell lines and human fetal primary astrocytes (FPA) with a modular hyaluronan-based hydrogel system. Morphological analysis reveals that FPA have a higher degree of interactions with the hyaluronan-based gels compared to the cell lines. This interaction is enhanced by conjugation of cell-adhesion peptides (cRGD and IKVAV) to the hyaluronan backbone. These effects are retained and pronounced in 3D bioprinted structures. Bioprinted FPA using cRGD functionalized hyaluronan show extensive and defined protrusions and multiple connections between neighboring cells. Possibilities to tailor and optimize astrocyte-compatible ECM-mimicking hydrogels that can be processed by means of additive biofabrication can facilitate the development of advanced tissue and disease models of the central nervous system.
26.	Messner, Christoph B., et al. (author) Ultra-High-Throughput Clinical Proteomics Reveals Classifiers of COVID-19 Infection 2020 In: Cell Systems. - : Elsevier BV. - 2405-4712 .- 2405-4720. ; 11:1, s. 11-24.E4 Journal article (peer-reviewed)abstract The COVID-19 pandemic is an unprecedented global challenge, and point-of-care diagnostic classifiers are urgently required. Here, we present a platform for ultra-high-throughput serum and plasma proteomics that builds on ISO13485 standardization to facilitate simple implementation in regulated clinical laboratories. Our low-cost workflow handles up to 180 samples per day, enables high precision quantification, and reduces batch effects for large-scale and longitudinal studies. We use our platform on samples collected from a cohort of early hospitalized cases of the SARS-CoV-2 pandemic and identify 27 potential biomarkers that are differentially expressed depending on the WHO severity grade of COVID-19. They include complement factors, the coagulation system, inflammation modulators, and pro-inflammatory factors upstream and downstream of interleukin 6. All protocols and software for implementing our approach are freely available. In total, this work supports the development of routine proteomic assays to aid clinical decision making and generate hypotheses about potential COVID-19 therapeutic targets.
27.	Pimienta, Pierre, et al. (author) Recommendation of RILEM TC 256-SPF on fire spalling assessment during standardised fire resistance tests : complementary guidance and requirements 2024 In: Materials and Structures/Materiaux et Constructions. - : Springer Science and Business Media B.V.. - 1359-5997 .- 1871-6873. ; 57:1 Journal article (peer-reviewed)abstract The recommendation is based on the co-authors’ work organized by the RILEM TC 256-SPF “Spalling of concrete due to fire: testing and modelling”. It aims to provide useful information, guidance and best practices in fire spalling assessment to laboratories that perform large-scale tests based on fire resistance test standards. It provides guidance on the spalling observation techniques during testing, as well as post-test spalling quantification/assessment methods. This document is intended to be used in conjunction with the fire resistance test standards, e.g. EN 1363-1 and ISO 834-1.
28.	Pimienta, Pierre, et al. (author) Recommendation of RILEM TC 256-SPF on the method of testing concrete spalling due to fire : material screening test 2023 In: Materials and Structures/Materiaux et Constructions. - : Springer Science and Business Media B.V.. - 1359-5997 .- 1871-6873. ; 56:9 Journal article (peer-reviewed)abstract The recommendation is based on the co-authors’ work organized by the RILEM TC 256-SPF “Spalling of concrete due to fire: testing and modelling”. The Committee has defined two types of screening tests for characterization of concrete propensity to fire spalling: Material screening tests and Product screening tests. Definitions of both types of tests are given in the paper. The following recommendations apply to Material screening tests. The material screening tests described in these recommendations are a set of minimum requirements to test concrete spalling propensity (for example, the minimal specimen size). This document covers the aspects of concrete characterization, specimen geometries, storage conditions, test methods and measured parameters.
29.	Pötzelsberger, Elisabeth, et al. (author) Biotic threats for 23 major non-native tree species in Europe 2021 In: Scientific Data. - : Nature Publishing Group. - 2052-4463. ; 8:1 Journal article (peer-reviewed)abstract For non-native tree species with an origin outside of Europe a detailed compilation of enemy species including the severity of their attack is lacking up to now. We collected information on native and non-native species attacking non-native trees, i.e. type, extent and time of first observation of damage for 23 important non-native trees in 27 European countries. Our database includes about 2300 synthesised attack records (synthesised per biotic threat, tree and country) from over 800 species. Insects (49%) and fungi (45%) are the main observed biotic threats, but also arachnids, bacteria including phytoplasmas, mammals, nematodes, plants and viruses have been recorded. This information will be valuable to identify patterns and drivers of attacks, and trees with a lower current health risk to be considered for planting. In addition, our database will provide a baseline to which future impacts on non-native tree species could be compared with and thus will allow to analyse temporal trends of impacts.
30.	Room, Robin, et al. (author) Supranational changes in drinking patterns : factors in explanatory models of substantial and parallel social change 2020 In: Addiction Research and Theory. - : Informa UK Limited. - 1606-6359 .- 1476-7392. ; 28:6, s. 467-473 Journal article (peer-reviewed)abstract Background: That there have been 'long waves' of consumption in parallel in different societies has previously been noted. Now there is a sustained drop in drinking among youth in most of Europe, Australia and North America. Can such changes be understood in a common frame? In terms of inexorable historical phenomena or forces, like Kondratieff waves? In terms of generational shifts, with a younger generation reacting against the habits of an older? Method: Such conceptual models for understanding the dynamics of social change are examined in terms of their potential contribution in explaining when and how substantial changes in levels of consumption occur roughly in concert in different societies, with particular reference to the decline in drinking and heavy drinking in current youth cohorts. Results and Conclusion: Timing tends to rule out economic change as a factor in the current widespread decline in youth drinking. The technological revolution of the electronic web and the smart phone seems a primary explanation, with the widespread change in social presentation and interaction - in habitus - between parents and children also involved. Directions for further research are suggested.
31.	Strauß, Theresa, et al. (author) Impact of Musashi-1 and Musashi-2 Double Knockdown on Notch Signaling and the Pathogenesis of Endometriosis. 2022 In: International journal of molecular sciences. - 1422-0067. ; 23:5 Journal article (peer-reviewed)abstract The stem cell marker and RNA-binding protein Musashi-1 is overexpressed in endometriosis. Musashi-1-siRNA knockdown in Ishikawa cells altered the expression of stem cell related genes, such as OCT-4. To investigate the role of both human Musashi homologues (MSI-1 and MSI-2) in the pathogenesis of endometriosis, immortalized endometriotic 12-Z cells and primary endometriotic stroma cells were treated with Musashi-1- and Musashi-2-siRNA. Subsequently, the impact on cell proliferation, cell apoptosis, cell necrosis, spheroid formation, stem cell phenotype and the Notch signaling pathway was studied in vitro. Using the ENDOMET Turku Endometriosis database, the gene expression of stem cell markers and Notch signaling pathway constituents were analyzed according to localization of the endometriosis lesions. The database analysis demonstrated that expression of Musashi and Notch pathway-related genes are dysregulated in patients with endometriosis. Musashi-1/2-double-knockdown increased apoptosis and necrosis and reduced stem cell gene expression, cell proliferation, and the formation of spheroids. Musashi silencing increased the expression of the anti-proliferation mediator p21. Our findings suggest the therapeutic potential of targeting the Musashi-Notch axis. We conclude that the Musashi genes have an impact on Notch signaling and the pathogenesis of endometriosis through the downregulation of proliferation, stemness characteristics and the upregulation of apoptosis, necrosis and of the cell cycle regulator p21.

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