Comparison of post-COVID-19 symptoms in patients infected with the SARS-CoV-2 variants delta and omicron-results of the Cross-Sectoral Platform of the German National Pandemic Cohort Network (NAPKON-SUEP).

PURPOSE: The influence of new SARS-CoV-2 variants on the post-COVID-19 condition (PCC) remains unanswered. Therefore, we examined the prevalence and predictors of PCC-related symptoms in patients infected with the SARS-CoV-2 variants delta or omicron. METHODS: We compared prevalences and risk factors of acute and PCC-related symptoms three months after primary infection (3MFU) between delta- and omicron-infected patients from the Cross-Sectoral Platform of the German National Pandemic Cohort Network. Health-related quality of life (HrQoL) was determined by the EQ-5D-5L index score and trend groups were calculated to describe changes of HrQoL between different time points. RESULTS: We considered 758 patients for our analysis (delta: n = 341; omicron: n = 417). Compared with omicron patients, delta patients had a similar prevalence of PCC at the 3MFU (p = 0.354), whereby fatigue occurred most frequently (n = 256, 34%). HrQoL was comparable between the groups with the lowest EQ-5D-5L index score (0.75, 95% CI 0.73-0.78) at disease onset. While most patients (69%, n = 348) never showed a declined HrQoL, it deteriorated substantially in 37 patients (7%) from the acute phase to the 3MFU of which 27 were infected with omicron. CONCLUSION: With quality-controlled data from a multicenter cohort, we showed that PCC is an equally common challenge for patients infected with the SARS-CoV-2 variants delta and omicron at least for the German population. Developing the EQ-5D-5L index score trend groups showed that over two thirds of patients did not experience any restrictions in their HrQoL due to or after the SARS-CoV-2 infection at the 3MFU. CLINICAL TRAIL REGISTRATION: The cohort is registered at ClinicalTrials.gov since February 24, 2021 (Identifier: NCT04768998).

Tensorial Properties via the Neuroevolution Potential Framework: Fast Simulation of Infrared and Raman Spectra.

Infrared and Raman spectroscopy are widely used for the characterization of gases, liquids, and solids, as the spectra contain a wealth of information concerning, in particular, the dynamics of these systems. Atomic scale simulations can be used to predict such spectra but are often severely limited due to high computational cost or the need for strong approximations that limit the application range and reliability. Here, we introduce a machine learning (ML) accelerated approach that addresses these shortcomings and provides a significant performance boost in terms of data and computational efficiency compared with earlier ML schemes. To this end, we generalize the neuroevolution potential approach to enable the prediction of rank one and two tensors to obtain the tensorial neuroevolution potential (TNEP) scheme. We apply the resulting framework to construct models for the dipole moment, polarizability, and susceptibility of molecules, liquids, and solids and show that our approach compares favorably with several ML models from the literature with respect to accuracy and computational efficiency. Finally, we demonstrate the application of the TNEP approach to the prediction of infrared and Raman spectra of liquid water, a molecule (PTAF-), and a prototypical perovskite with strong anharmonicity (BaZrO3). The TNEP approach is implemented in the free and open source software package gpumd, which makes this methodology readily available to the scientific community.

GPAW: An open Python package for electronic structure calculations.

We review the GPAW open-source Python package for electronic structure calculations. GPAW is based on the projector-augmented wave method and can solve the self-consistent density functional theory (DFT) equations using three different wave-function representations, namely real-space grids, plane waves, and numerical atomic orbitals. The three representations are complementary and mutually independent and can be connected by transformations via the real-space grid. This multi-basis feature renders GPAW highly versatile and unique among similar codes. By virtue of its modular structure, the GPAW code constitutes an ideal platform for the implementation of new features and methodologies. Moreover, it is well integrated with the Atomic Simulation Environment (ASE), providing a flexible and dynamic user interface. In addition to ground-state DFT calculations, GPAW supports many-body GW band structures, optical excitations from the Bethe-Salpeter Equation, variational calculations of excited states in molecules and solids via direct optimization, and real-time propagation of the Kohn-Sham equations within time-dependent DFT. A range of more advanced methods to describe magnetic excitations and non-collinear magnetism in solids are also now available. In addition, GPAW can calculate non-linear optical tensors of solids, charged crystal point defects, and much more. Recently, support for graphics processing unit (GPU) acceleration has been achieved with minor modifications to the GPAW code thanks to the CuPy library. We end the review with an outlook, describing some future plans for GPAW.

Reimagining Medication Adherence: A Novel Holistic Model for Hypertension Therapy.

Purpose: Patients' adherence to the prescribed therapy is influenced by several personal and social factors. However, existing studies have mostly focused on individual aspects. We took a holistic approach to develop a higher-level impact factor model. Patients and Methods: In this independent, non-interventional, cross-sectional and anonymous study design the pharmacist recruited patients who entered the pharmacy and handed in a prescription for a blood pressure medication. The patients received a paper questionnaire with a stamped return envelope to volunteer participation. A total of 476 patients in Germany who reported having at least high normal blood pressure according to the Global Hypertension Practice Guidelines were surveyed. In this study, each patient received an average of 2.49 antihypertensive prescriptions and 7.9% of all patients received a fixed-dose combination. Partial least squares structural equation modeling was performed for model analytics since it enables robust analysis of complex relationships. Results: Emotional attitude, behavioral control, and therapy satisfaction directly explained 65% of therapy adherence. The predictive power of the out-of-sample model for the Q2-statistic was significant. The patient's overall therapy satisfaction determined medication adherence. The medication scheme's complexity also influenced the adherence levels. Therapy satisfaction was significantly shaped by the complexity of the medication scheme, behavioral control, and emotional attitude. The results demonstrated the superior performance of fixed-dose combinations against combinations of mono-agents according to the adherence level. Additionally, patient-physician and patient-pharmacist relationships influenced behavioral control of medication therapy execution. According to the A14-scale to measure the level of adherence, 49.6% of patients were classified as adherent and the remainder as non-adherent. Conclusion: The results enable healthcare stakeholders to target attractive variables for intervention to achieve maximum effectiveness. Moreover, the proven predictive power of the model framework enables clinicians to make predictions about the adherence levels of their hypertensive patients.

Machine Learning for Polaritonic Chemistry: Accessing Chemical Kinetics.

Altering chemical reactivity and material structure in confined optical environments is on the rise, and yet, a conclusive understanding of the microscopic mechanisms remains elusive. This originates mostly from the fact that accurately predicting vibrational and reactive dynamics for soluted ensembles of realistic molecules is no small endeavor, and adding (collective) strong light-matter interaction does not simplify matters. Here, we establish a framework based on a combination of machine learning (ML) models, trained using density-functional theory calculations and molecular dynamics to accelerate such simulations. We then apply this approach to evaluate strong coupling, changes in reaction rate constant, and their influence on enthalpy and entropy for the deprotection reaction of 1-phenyl-2-trimethylsilylacetylene, which has been studied previously both experimentally and using ab initio simulations. While we find qualitative agreement with critical experimental observations, especially with regard to the changes in kinetics, we also find differences in comparison with previous theoretical predictions. The features for which the ML-accelerated and ab initio simulations agree show the experimentally estimated kinetic behavior. Conflicting features indicate that a contribution of dynamic electronic polarization to the reaction process is more relevant than currently believed. Our work demonstrates the practical use of ML for polaritonic chemistry, discusses limitations of common approximations, and paves the way for a more holistic description of polaritonic chemistry.

Over 100 years of vitamin E: An overview from synthesis and formulation to application in animal nutrition.

The groundbreaking discovery of vitamin E by Evans and Bishop in 1922 was an important milestone in vitamin research, inspiring further investigation into its crucial role in both human and animal nutrition. Supplementing vitamin E has been proved to enhance multiple key physiological systems such as the reproductive, circulatory, nervous and muscular systems. As the main antioxidant in the blood and on a cellular level, vitamin E maintains the integrity of both cellular and vascular membranes and thus modulates the immune system. This overview showcases important and innovative routes for synthesizing vitamin E on a commercial scale, provides cutting-edge insights into formulation concepts for successful product form development and emphasizes the importance and future of vitamin E in healthy and sustainable animal nutrition.

Collective Strong Coupling Modifies Aggregation and Solvation.

Intermolecular (Coulombic) interactions are pivotal for aggregation, solvation, and crystallization. We demonstrate that the collective strong coupling of several molecules to a single optical mode results in notable changes in the molecular excitations around a single perturbed molecule, thus representing an impurity in an otherwise ordered system. A competition between short-range coulombic and long-range photonic correlations inverts the local transition density in a polaritonic state, suggesting notable changes in the polarizability of the solvation shell. Our results provide an alternative perspective on recent work in polaritonic chemistry and pave the way for the rigorous treatment of cooperative effects in aggregation, solvation, and crystallization.

Systematic discovery of protein interaction interfaces using AlphaFold and experimental validation.

Structural resolution of protein interactions enables mechanistic and functional studies as well as interpretation of disease variants. However, structural data is still missing for most protein interactions because we lack computational and experimental tools at scale. This is particularly true for interactions mediated by short linear motifs occurring in disordered regions of proteins. We find that AlphaFold-Multimer predicts with high sensitivity but limited specificity structures of domain-motif interactions when using small protein fragments as input. Sensitivity decreased substantially when using long protein fragments or full length proteins. We delineated a protein fragmentation strategy particularly suited for the prediction of domain-motif interfaces and applied it to interactions between human proteins associated with neurodevelopmental disorders. This enabled the prediction of highly confident and likely disease-related novel interfaces, which we further experimentally corroborated for FBXO23-STX1B, STX1B-VAMP2, ESRRG-PSMC5, PEX3-PEX19, PEX3-PEX16, and SNRPB-GIGYF1 providing novel molecular insights for diverse biological processes. Our work highlights exciting perspectives, but also reveals clear limitations and the need for future developments to maximize the power of Alphafold-Multimer for interface predictions.

Estimates of protection levels against SARS-CoV-2 infection and severe COVID-19 in Germany before the 2022/2023 winter season: the IMMUNEBRIDGE project.

PURPOSE: Despite the need to generate valid and reliable estimates of protection levels against SARS-CoV-2 infection and severe course of COVID-19 for the German population in summer 2022, there was a lack of systematically collected population-based data allowing for the assessment of the protection level in real time. METHODS: In the IMMUNEBRIDGE project, we harmonised data and biosamples for nine population-/hospital-based studies (total number of participants n = 33,637) to provide estimates for protection levels against SARS-CoV-2 infection and severe COVID-19 between June and November 2022. Based on evidence synthesis, we formed a combined endpoint of protection levels based on the number of self-reported infections/vaccinations in combination with nucleocapsid/spike antibody responses ("confirmed exposures"). Four confirmed exposures represented the highest protection level, and no exposure represented the lowest. RESULTS: Most participants were seropositive against the spike antigen; 37% of the participants ≥ 79 years had less than four confirmed exposures (highest level of protection) and 5% less than three. In the subgroup of participants with comorbidities, 46-56% had less than four confirmed exposures. We found major heterogeneity across federal states, with 4-28% of participants having less than three confirmed exposures. CONCLUSION: Using serological analyses, literature synthesis and infection dynamics during the survey period, we observed moderate to high levels of protection against severe COVID-19, whereas the protection against SARS-CoV-2 infection was low across all age groups. We found relevant protection gaps in the oldest age group and amongst individuals with comorbidities, indicating a need for additional protective measures in these groups.

Increased circulating fibronectin, depletion of natural IgM and heightened EBV, HSV-1 reactivation in ME/CFS and long COVID.

Myalgic Encephalomyelitis/ Chronic Fatigue syndrome (ME/CFS) is a complex, debilitating, long-term illness without a diagnostic biomarker. ME/CFS patients share overlapping symptoms with long COVID patients, an observation which has strengthened the infectious origin hypothesis of ME/CFS. However, the exact sequence of events leading to disease development is largely unknown for both clinical conditions. Here we show antibody response to herpesvirus dUTPases, particularly to that of Epstein-Barr virus (EBV) and HSV-1, increased circulating fibronectin (FN1) levels in serum and depletion of natural IgM against fibronectin ((n)IgM-FN1) are common factors for both severe ME/CFS and long COVID. We provide evidence for herpesvirus dUTPases-mediated alterations in host cell cytoskeleton, mitochondrial dysfunction and OXPHOS. Our data show altered active immune complexes, immunoglobulin-mediated mitochondrial fragmentation as well as adaptive IgM production in ME/CFS patients. Our findings provide mechanistic insight into both ME/CFS and long COVID development. Finding of increased circulating FN1 and depletion of (n)IgM-FN1 as a biomarker for the severity of both ME/CFS and long COVID has an immediate implication in diagnostics and development of treatment modalities.

The Importance of Being FAIR and FAST - The Clinical Epidemiology and Study Platform of the German Network University Medicine (NUKLEUS).

The COVID-19 pandemic has urged the need to set up, conduct and analyze high-quality epidemiological studies within a very short time-scale to provide timely evidence on influential factors on the pandemic, e.g. COVID-19 severity and disease course. The comprehensive research infrastructure developed to run the German National Pandemic Cohort Network within the Network University Medicine is now maintained within a generic clinical epidemiology and study platform NUKLEUS. It is operated and subsequently extended to allow efficient joint planning, execution and evaluation of clinical and clinical-epidemiological studies. We aim to provide high-quality biomedical data and biospecimens and make its results widely available to the scientific community by implementing findability, accessibility, interoperability and reusability - i.e. following the FAIR guiding principles. Thus, NUKLEUS might serve as role model for FAIR and fast implementation of clinical epidemiological studies within the setting of University Medical Centers and beyond.

Don't be afraid of black holes: Vacuum sponge and vacuum stent treatment of leaks in the upper GI tract-a case series and mini-review.

The treatment of leaks in the upper gastrointestinal tract has been revolutionized by the advent of covered self-expanding metal stents (cSEMS), endoscopic vacuum therapy (EVT), and recently, vacuum stent therapy (VST). In this retrospective study, we report the experiences with EVT and VST at our institution. Patients and methods: Twenty-two patients (15 male, 7 female) with leaks in the esophagus, at the esophago-gastric junction or anastomotic leaks underwent EVT by placing a sponge connected to a negative pressure pump into or near the leak. VST was applied in three patients. Results: EVT led to closure of the leak in 18 of 22 Patients (82%). In 9 patients (41%), EVT was followed by application of a cSEMS. One patient (5%) died during the hospital stay due to an aorto-esophageal fistula near the leak, four others (18%) due to underlying disease. The stricture rate was 3/22 (14%). All three patients in whom VST was applied had closure of the leak and recovered. Reviewing the literature, we identified sixteen retrospective series of ten or more patients (n = 610) with an overall closure rate for EVT of 84%. In eight additional retrospective observations, a comparison between the efficacy of EVT and cSEMS therapy was performed that revealed a success rate of 89% and 69%, respectively (difference not significant, chi-square test). For VST, two small series show that closure is possible in the majority of patients. Conclusion: EVT and VST are valuable options in the treatment of leaks in the upper gastrointestinal tract.

Chiral Polaritonics: Analytical Solutions, Intuition, and Use.

Preferential selection of a given enantiomer over its chiral counterpart has become increasingly relevant in the advent of the next era of medical drug design. In parallel, cavity quantum electrodynamics has grown into a solid framework to control energy transfer and chemical reactivity, the latter requiring strong coupling. In this work, we derive an analytical solution to a system of many chiral emitters interacting with a chiral cavity similar to the widely used Tavis-Cummings and Hopfield models of quantum optics. We are able to estimate the discriminating strength of chiral polaritonics, discuss possible future development directions and exciting applications such as elucidating homochirality, and deliver much needed intuition to foster the newly flourishing field of chiral polaritonics.

The DZHK research platform: maximisation of scientific value by enabling access to health data and biological samples collected in cardiovascular clinical studies.

The German Centre for Cardiovascular Research (DZHK) is one of the German Centres for Health Research and aims to conduct early and guideline-relevant studies to develop new therapies and diagnostics that impact the lives of people with cardiovascular disease. Therefore, DZHK members designed a collaboratively organised and integrated research platform connecting all sites and partners. The overarching objectives of the research platform are the standardisation of prospective data and biological sample collections among all studies and the development of a sustainable centrally standardised storage in compliance with general legal regulations and the FAIR principles. The main elements of the DZHK infrastructure are web-based and central units for data management, LIMS, IDMS, and transfer office, embedded in a framework consisting of the DZHK Use and Access Policy, and the Ethics and Data Protection Concept. This framework is characterised by a modular design allowing a high standardisation across all studies. For studies that require even tighter criteria additional quality levels are defined. In addition, the Public Open Data strategy is an important focus of DZHK. The DZHK operates as one legal entity holding all rights of data and biological sample usage, according to the DZHK Use and Access Policy. All DZHK studies collect a basic set of data and biosamples, accompanied by specific clinical and imaging data and biobanking. The DZHK infrastructure was constructed by scientists with the focus on the needs of scientists conducting clinical studies. Through this, the DZHK enables the interdisciplinary and multiple use of data and biological samples by scientists inside and outside the DZHK. So far, 27 DZHK studies recruited well over 11,200 participants suffering from major cardiovascular disorders such as myocardial infarction or heart failure. Currently, data and samples of five DZHK studies of the DZHK Heart Bank can be applied for.

Shining light on the microscopic resonant mechanism responsible for cavity-mediated chemical reactivity.

Strong light-matter interaction in cavity environments is emerging as a promising approach to control chemical reactions in a non-intrusive and efficient manner. The underlying mechanism that distinguishes between steering, accelerating, or decelerating a chemical reaction has, however, remained unclear, hampering progress in this frontier area of research. We leverage quantum-electrodynamical density-functional theory to unveil the microscopic mechanism behind the experimentally observed reduced reaction rate under cavity induced resonant vibrational strong light-matter coupling. We observe multiple resonances and obtain the thus far theoretically elusive but experimentally critical resonant feature for a single strongly coupled molecule undergoing the reaction. While we describe only a single mode and do not explicitly account for collective coupling or intermolecular interactions, the qualitative agreement with experimental measurements suggests that our conclusions can be largely abstracted towards the experimental realization. Specifically, we find that the cavity mode acts as mediator between different vibrational modes. In effect, vibrational energy localized in single bonds that are critical for the reaction is redistributed differently which ultimately inhibits the reaction.

Simulating Terahertz Field-Induced Ferroelectricity in Quantum Paraelectric SrTiO_{3}.

Recent experiments have demonstrated that light can induce a transition from the quantum paraelectric to the ferroelectric phase of SrTiO_{3}. Here, we investigate this terahertz field-induced ferroelectric phase transition by solving the time-dependent lattice Schrödinger equation based on first-principles calculations. We find that ferroelectricity originates from a light-induced mixing between ground and first excited lattice states in the quantum paraelectric phase. In agreement with the experimental findings, our study shows that the nonoscillatory second harmonic generation signal can be evidence of ferroelectricity in SrTiO_{3}. We reveal the microscopic details of this exotic phase transition and highlight that this phenomenon is a unique behavior of the quantum paraelectric phase.

The German National Pandemic Cohort Network (NAPKON): rationale, study design and baseline characteristics.

The German government initiated the Network University Medicine (NUM) in early 2020 to improve national research activities on the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) pandemic. To this end, 36 German Academic Medical Centers started to collaborate on 13 projects, with the largest being the National Pandemic Cohort Network (NAPKON). The NAPKON's goal is creating the most comprehensive Coronavirus Disease 2019 (COVID-19) cohort in Germany. Within NAPKON, adult and pediatric patients are observed in three complementary cohort platforms (Cross-Sectoral, High-Resolution and Population-Based) from the initial infection until up to three years of follow-up. Study procedures comprise comprehensive clinical and imaging diagnostics, quality-of-life assessment, patient-reported outcomes and biosampling. The three cohort platforms build on four infrastructure core units (Interaction, Biosampling, Epidemiology, and Integration) and collaborations with NUM projects. Key components of the data capture, regulatory, and data privacy are based on the German Centre for Cardiovascular Research. By April 01, 2022, 34 university and 40 non-university hospitals have enrolled 5298 patients with local data quality reviews performed on 4727 (89%). 47% were female, the median age was 52 (IQR 36-62-) and 50 pediatric cases were included. 44% of patients were hospitalized, 15% admitted to an intensive care unit, and 12% of patients deceased while enrolled. 8845 visits with biosampling in 4349 patients were conducted by April 03, 2022. In this overview article, we summarize NAPKON's design, relevant milestones including first study population characteristics, and outline the potential of NAPKON for German and international research activities.Trial registration https://clinicaltrials.gov/ct2/show/NCT04768998 . https://clinicaltrials.gov/ct2/show/NCT04747366 . https://clinicaltrials.gov/ct2/show/NCT04679584.

Polaritonic Chemistry from First Principles via Embedding Radiation Reaction.

The coherent interaction of a large collection of molecules with a common photonic mode results in strong light-matter coupling, a feature that has proven highly beneficial for chemistry and has introduced the research topics polaritonic and QED chemistry. Here, we demonstrate an embedding approach to capture the collective nature while retaining the full ab initio representation of single molecules─an approach ideal for polaritonic chemistry. The accuracy of the embedding radiation-reaction ansatz is demonstrated for time-dependent density-functional theory. Then, by virtue of a simple proton-tunneling model, we illustrate that the influence of collective strong coupling on chemical reactions features a nontrivial dependence on the number of emitters and can alternate between strong catalyzing and an inhibiting effect. Bridging classical electrodynamics, quantum optical descriptions, and the ab initio description of realistic molecules, this work can serve as a guiding light for future developments and investigations in the quickly growing fields of QED chemistry and QED material design.

A perspective on ab initio modeling of polaritonic chemistry: The role of non-equilibrium effects and quantum collectivity.

This Perspective provides a brief introduction into the theoretical complexity of polaritonic chemistry, which emerges from the hybrid nature of strongly coupled light-matter states. To tackle this complexity, the importance of ab initio methods is highlighted. Based on those, novel ideas and research avenues are developed with respect to quantum collectivity, as well as for resonance phenomena immanent in reaction rates under vibrational strong coupling. Indeed, fundamental theoretical questions arise about the mesoscopic scale of quantum-collectively coupled molecules when considering the depolarization shift in the interpretation of experimental data. Furthermore, to rationalize recent findings based on quantum electrodynamical density-functional theory (QEDFT), a simple, but computationally efficient, Langevin framework is proposed based on well-established methods from molecular dynamics. It suggests the emergence of cavity-induced non-equilibrium nuclear dynamics, where thermal (stochastic) resonance phenomena could emerge in the absence of external periodic driving. Overall, we believe that the latest ab initio results indeed suggest a paradigmatic shift for ground-state chemical reactions under vibrational strong coupling from the collective quantum interpretation toward a more local, (semi)-classically and non-equilibrium dominated perspective. Finally, various extensions toward a refined description of cavity-modified chemistry are introduced in the context of QEDFT, and future directions of the field are sketched.

Shortcut to Self-Consistent Light-Matter Interaction and Realistic Spectra from First Principles.

We introduce a simple approach to how an electromagnetic environment can be efficiently embedded into state-of-the-art electronic structure methods, taking the form of radiation-reaction forces. We demonstrate that this self-consistently provides access to radiative emission, natural linewidth, Lamb shifts, strong coupling, electromagnetically induced transparency, Purcell-enhanced and superradiant emission. As an example, we illustrate its seamless integration into time-dependent density-functional theory with virtually no additional cost, presenting a convenient shortcut to light-matter interactions.