Learning single-cell perturbation responses using neural optimal transport.

Understanding and predicting molecular responses in single cells upon chemical, genetic or mechanical perturbations is a core question in biology. Obtaining single-cell measurements typically requires the cells to be destroyed. This makes learning heterogeneous perturbation responses challenging as we only observe unpaired distributions of perturbed or non-perturbed cells. Here we leverage the theory of optimal transport and the recent advent of input convex neural architectures to present CellOT, a framework for learning the response of individual cells to a given perturbation by mapping these unpaired distributions. CellOT outperforms current methods at predicting single-cell drug responses, as profiled by scRNA-seq and a multiplexed protein-imaging technology. Further, we illustrate that CellOT generalizes well on unseen settings by (1) predicting the scRNA-seq responses of holdout patients with lupus exposed to interferon-ß and patients with glioblastoma to panobinostat; (2) inferring lipopolysaccharide responses across different species; and (3) modeling the hematopoietic developmental trajectories of different subpopulations.

Enriching productive mutational paths accelerates enzyme evolution.

Darwinian evolution has given rise to all the enzymes that enable life on Earth. Mimicking natural selection, scientists have learned to tailor these biocatalysts through recursive cycles of mutation, selection and amplification, often relying on screening large protein libraries to productively modulate the complex interplay between protein structure, dynamics and function. Here we show that by removing destabilizing mutations at the library design stage and taking advantage of recent advances in gene synthesis, we can accelerate the evolution of a computationally designed enzyme. In only five rounds of evolution, we generated a Kemp eliminase-an enzymatic model system for proton transfer from carbon-that accelerates the proton abstraction step >108-fold over the uncatalyzed reaction. Recombining the resulting variant with a previously evolved Kemp eliminase HG3.17, which exhibits similar activity but differs by 29 substitutions, allowed us to chart the topography of the designer enzyme's fitness landscape, highlighting that a given protein scaffold can accommodate several, equally viable solutions to a specific catalytic problem.

ChromaX: a fast and scalable breeding program simulator.

SUMMARY: ChromaX is a Python library that enables the simulation of genetic recombination, genomic estimated breeding value calculations, and selection processes. By utilizing GPU processing, it can perform these simulations up to two orders of magnitude faster than existing tools with standard hardware. This offers breeders and scientists new opportunities to simulate genetic gain and optimize breeding schemes. AVAILABILITY AND IMPLEMENTATION: The documentation is available at https://chromax.readthedocs.io. The code is available at https://github.com/kora-labs/chromax.

Reconciling the EU forest, biodiversity, and climate strategies.

Forests provide important ecosystem services (ESs), including climate change mitigation, local climate regulation, habitat for biodiversity, wood and non-wood products, energy, and recreation. Simultaneously, forests are increasingly affected by climate change and need to be adapted to future environmental conditions. Current legislation, including the European Union (EU) Biodiversity Strategy, EU Forest Strategy, and national laws, aims to protect forest landscapes, enhance ESs, adapt forests to climate change, and leverage forest products for climate change mitigation and the bioeconomy. However, reconciling all these competing demands poses a tremendous task for policymakers, forest managers, conservation agencies, and other stakeholders, especially given the uncertainty associated with future climate impacts. Here, we used process-based ecosystem modeling and robust multi-criteria optimization to develop forest management portfolios that provide multiple ESs across a wide range of climate scenarios. We included constraints to strictly protect 10% of Europe's land area and to provide stable harvest levels under every climate scenario. The optimization showed only limited options to improve ES provision within these constraints. Consequently, management portfolios suffered from low diversity, which contradicts the goal of multi-functionality and exposes regions to significant risk due to a lack of risk diversification. Additionally, certain regions, especially those in the north, would need to prioritize timber provision to compensate for reduced harvests elsewhere. This conflicts with EU LULUCF targets for increased forest carbon sinks in all member states and prevents an equal distribution of strictly protected areas, introducing a bias as to which forest ecosystems are more protected than others. Thus, coordinated strategies at the European level are imperative to address these challenges effectively. We suggest that the implementation of the EU Biodiversity Strategy, EU Forest Strategy, and targets for forest carbon sinks require complementary measures to alleviate the conflicting demands on forests.

A Call for Gene Expression Analysis in Whole Blood of Patients With Rheumatoid Arthritis (RA) as a Biomarker for RA-Associated Interstitial Lung Disease.

OBJECTIVE: Rheumatoid arthritis (RA)-associated interstitial lung disease (ILD) is one of the most common and prognostic organ manifestations of RA. Therefore, to allow effective treatment, it is of crucial importance to diagnose RA-ILD at the earliest possible stage. So far, the gold standard of early detection has been high-resolution computed tomography (HRCT) of the lungs. This procedure involves considerable radiation exposure for the patient and is therefore unsuitable as a routine screening measure for ethical reasons. Here, we propose the analysis of characteristic gene expression patterns as a biomarker to aid in the early detection and initiation of appropriate, possibly antifibrotic, therapy. METHODS: To investigate unique molecular patterns of RA-ILD, whole blood samples were taken from 12 female patients with RA-ILD (n = 7) or RA (n = 5). The RNA was extracted, sequenced by RNA-Seq, and analyzed for characteristic differences in the gene expression patterns between patients with RA-ILD and those with RA without ILD. RESULTS: The differential gene expression analysis revealed 9 significantly upregulated genes in RA-ILD compared to RA without ILD: arginase 1 (ARG1), thymidylate synthetase (TYMS), sortilin 1 (SORT1), marker of proliferation Ki-67 (MKI67), olfactomedin 4 (OLFM4), baculoviral inhibitor of apoptosis repeat containing 5 (BIRC5), membrane spanning 4-domains A4A (MS4A4A), C-type lectin domain family 12 member A (CLEC12A), and the long intergenic nonprotein coding RNA (LINC02967). CONCLUSION: All gene products of these genes (except for LINC02967) are known from the literature to be involved in the pathogenesis of fibrosis. Further, for some, a contribution to the development of pulmonary fibrosis has even been demonstrated in experimental studies. Therefore, the results presented here provide an encouraging perspective for using specific gene expression patterns as biomarkers for the early detection and differential diagnosis of RA-ILD as a routine screening test.

3DReact: Geometric Deep Learning for Chemical Reactions.

Geometric deep learning models, which incorporate the relevant molecular symmetries within the neural network architecture, have considerably improved the accuracy and data efficiency of predictions of molecular properties. Building on this success, we introduce 3DReact, a geometric deep learning model to predict reaction properties from three-dimensional structures of reactants and products. We demonstrate that the invariant version of the model is sufficient for existing reaction data sets. We illustrate its competitive performance on the prediction of activation barriers on the GDB7-22-TS, Cyclo-23-TS, and Proparg-21-TS data sets in different atom-mapping regimes. We show that, compared to existing models for reaction property prediction, 3DReact offers a flexible framework that exploits atom-mapping information, if available, as well as geometries of reactants and products (in an invariant or equivariant fashion). Accordingly, it performs systematically well across different data sets, atom-mapping regimes, as well as both interpolation and extrapolation tasks.

Population pharmacokinetics of the dual endothelin receptor antagonist aprocitentan in subjects with or without essential or resistant hypertension.

Aprocitentan is a novel, potent, dual endothelin receptor antagonist that recently demonstrated efficacy in the treatment of difficult-to-treat (resistant) hypertension. The aim of this study was to develop a population pharmacokinetic (PK) model describing aprocitentan plasma concentration over time, to investigate relationships between subject-specific factors (covariates) and model parameters, and to quantify the influence of the identified covariates on the exposure to aprocitentan via model-based simulations, enabling judgment about the clinical relevance of the covariates.PK data from 902 subjects in ten Phase 1, one Phase 2, and one Phase 3 study were pooled to develop a joint population PK model. The concentration-time course of aprocitentan was described by a two-compartment model with absorption lag time, first-order absorption and elimination, and reduced relative bioavailability following very high doses of 300 and 600 mg.The population PK model described the observed data well. Volume and clearance parameters were associated with body weight. Renal function as reflected by estimated glomerular filtration rate (eGFR), hepatic impairment, and sex were identified as relevant covariates on clearance.The subject-specific characteristics of body weight, eGFR, hepatic impairment, and sex were shown to influence exposure parameters area under the concentration-time curve and maximum concentration in steady state to a limited extent, i.e., not more than 25% different from a reference subject, and therefore do not warrant dose adjustments.

Training the next generation of pharmacometric modelers: a multisector perspective.

The current demand for pharmacometricians outmatches the supply provided by academic institutions and considerable investments are made to develop the competencies of these scientists on-the-job. Even with the observed increase in academic programs related to pharmacometrics, this need is unlikely to change in the foreseeable future, as the demand and scope of pharmacometrics applications keep expanding. Further, the field of pharmacometrics is changing. The field largely started when Lewis Sheiner and Stuart Beal published their seminal papers on population pharmacokinetics in the late 1970's and early 1980's and has continued to grow in impact and use since its inception. Physiological-based pharmacokinetics and systems pharmacology have grown rapidly in scope and impact in the last decade and machine learning is just on the horizon. While all these methodologies are categorized as pharmacometrics, no one person can be an expert in everything. So how do you train future pharmacometricians? Leading experts in academia, industry, contract research organizations, clinical medicine, and regulatory gave their opinions on how to best train future pharmacometricians. Their opinions were collected and synthesized to create some general recommendations.

Survey on the working, training, and research conditions of resident physicians in internistic and rheumatological continuing education-BEWUSST.

BACKGROUND: Data on the training and continuing education situation of residents in the field of internal medicine and rheumatology are not available for Germany. For this reason, the Commission for Education and Training of the German Society of Rheumatology (DGRh) initiated the BEWUSST survey on the working, training and research conditions of residents in rheumatology. METHODS: A total of 102 questions on the topics of working conditions in everyday professional life, continuing medical education and training, compatibility of career and family, compatibility of work and research, perspectives as a rheumatologist and practical activities were included in an online questionnaire. RESULTS: A total of 102 participants took part in the survey. Of the respondents 48.1% were satisfied with their professional situation, 40.2% of the participants were supervised by a specialist mentor and 54.9% were working as scientists during their work as a physician. A compatibility of family and career was possible for 34.7%. After completion of the residency 52.9% of the respondents aspired to a combined clinical and outpatient activity. CONCLUSION: Half of the trainee rheumatologists are satisfied with their professional activities, although mentoring of the assistants in training should be further improved. With respect to the desired combined clinical and outpatient activity, the existing options should be expanded or new professional fields of activity should be established, so that the specialty remains attractive for the upcoming generations.

[Current data on rheumatological care: annual report from the National database (NDB) of the regional collaborative arthritis centres in Germany]. / Aktuelle Zahlen zur rheumatologischen Versorgung ­ Jahresbericht aus der Kerndokumentation der regionalen kooperativen Rheumazentren.

In the National database (NDB) of the German regional collaborative arthritis centres, annual data on the rheumatological care of patients with inflammatory rheumatic diseases have been collected since 1993. This first annual report presents current cross-sectional data on medication and patient-reported outcomes gathered in 2022.

Eosinophilic fasciitis (Shulman syndrome)-recognition of the histological spectrum allows for new insights into possible pathomechanisms.

OBJECTIVES: EF is a rare disease characterized by fibrosis and inflammation of the fascia, scleroderma-like skin indurations and optional blood eosinophilia. We aimed to expand the knowledge about its aetiology and pathogenesis. METHODS: Biopsy specimens from 16 EF patients were assessed by histology, immunohistochemistry and quantitative reverse transcription PCR in comparison with anti-Mi-2+ DM patients and non-disease controls. RESULTS: Histologically, EF shows mild to severe inflammation at the muscle-fascia interface, with frequent involvement of the underlying muscle tissue, though varying in degree. CD206+ macrophages predominate and eosinophils are detected within the fascia in the majority of cases, however in quite small numbers, and seen infrequently within the muscle. Activators of the so-called Th2-M2 pathway like STAT6 and IL-4 are upregulated leading to high expression levels of CD206. Activators of the so-called Th1-M1 pathway like STAT1 and IFN-γ (IFNG) are also upregulated, though not translating into a significant upregulation of the effector molecule COX2. Interestingly, activators or chemoattractants of eosinophils show no significant upregulation in EF compared with DM. EF shows features of perifascicular pathology comparable to DM, with upregulation of MHC class I and II; however, this is not accompanied by perifascicular atrophy or any signs of a type I IFN response or hypoxia-mediated processes. CONCLUSIONS: Our findings highlight a specific immune phenotype of leucocyte infiltrates in EF along features of perifascicular pathology similar to DM, while there is no evidence of hypoxia-mediated or type I IFN-associated processes with perifascicular fibre atrophy, indicating different pathomechanisms of muscle involvement.

[Two severe cases of disseminated cutaneous nontuberculous mycobacteriosis due to Mycobacterium haemophilum]. / Zwei schwere Fälle von disseminiert-kutanen, nichttuberkulösen Mykobakteriosen durch Mycobacterium haemophilum.

Mycobacterium haemophilum is a rare pathogen belonging to the group of slowly growing nontuberculous mycobacteria (NTM) that can cause infections, especially in immunocompromised patients. Detection by culturing is difficult because M. haemophilum only grows under special cultivation conditions. Therefore, it is believed that the pathogen is too rarely identified as a cause of disease overall. In addition to patients with severe immunodeficiency, e.g. due to acquired immunodeficiency syndrome (AIDS), chemotherapy or immunosuppression after transplantation, patients with underlying rheumatic diseases are increasingly described in the literature, who are at risk due to the immunosuppressive treatment regimen. Clinically, ulcerative skin alterations, lymphadenopathy and arthropathy are in the foreground. In immunosuppressed patients with unclear skin lesions, infections due to M. haemophilum should be considered and specific microbiological diagnostics should be initiated.

[Survey on the working, training, and research conditions of resident physicians in internistic and rheumatological continuing education-BEWUSST]. / Befragung zu den Arbeits-, Weiterbildungs- und Forschungsbedingungen von Assistenzärztinnen und -ärzten in der internistisch-rheumatologischen Weiterbildung ­ BEWUSST.

BACKGROUND: Data on the training and continuing education situation of residents in the field of internal medicine and rheumatology are not available for Germany. For this reason, the Commission for Education and Training of the German Society of Rheumatology (DGRh) initiated the BEWUSST survey on the working, training and research conditions of residents in rheumatology. METHODS: A total of 102 questions on the topics of working conditions in everyday professional life, continuing medical education and training, compatibility of career and family, compatibility of work and research, perspectives as a rheumatologist and practical activities were included in an online questionnaire. RESULTS: A total of 102 participants took part in the survey. Of the respondents 48.1% were satisfied with their professional situation, 40.2% of the participants were supervised by a specialist mentor and 54.9% were working as scientists during their work as a physician. A compatibility of family and career was possible for 34.7%. After completion of the residency 52.9% of the respondents aspired to a combined clinical and outpatient activity. CONCLUSION: Half of the trainee rheumatologists are satisfied with their professional activities, although mentoring of the assistants in training should be further improved. With respect to the desired combined clinical and outpatient activity, the existing options should be expanded or new professional fields of activity should be established, so that the specialty remains attractive for the upcoming generations.

[Rheumatology training positions in Germany]. / Rheumatologische Weiterbildungsstellen in Deutschland.

BACKGROUND: In the next few years many general practitioners and specialists will retire. As in other disciplines the question arises in rheumatology whether sufficient training positions are available to maintain or expand the supply of care according to demand. Therefore, the German Society of Rheumatology (DGRh) has assigned its committee for education and training to review the currently available training opportunities in Germany. The aim of this work is the quantitative survey of the training capacity to become a specialist in internal medicine and rheumatology. METHODS: Within the framework of this study, a survey was conducted via the homepages of the 17 state medical associations to determine the postgraduate medical officers, their place of work and the duration of their postgraduate training capabilities. Based on the data, a nationwide survey of training positions was conducted. RESULTS: Specialized rheumatology training is established at 229 training centers in Germany, whereby data from 187 training sites were available for analysis. The training locations are distributed as followed: 52.4% clinical sector and 47.6% outpatient sector. In total, 478.4 training positions are available in Germany (clinical sector: 391.4 and outpatient sector: 87) and 17.2% of the positions (clinical sector: 11.4% and outpatient sector: 43.1%) are not occupied. CONCLUSION: Based on this study, it can be shown that most of the continuing education positions are available in the clinical sector. In contrast, half of the training positions in the outpatient area are not filled. In order to improve the training situation, it is essential to integrate outpatient colleagues into the training program. This presupposes that further training is supported or financed by the healthcare system. In this context, optimal rheumatological care must be permanently guaranteed throughout Germany in order to provide sufficient care for the approximately 2 million patients with inflammatory rheumatic diseases.

[Consensus guideline on the interdisciplinary diagnosis of interstitial lung diseases]. / S1-Leitlinie Interdisziplinäre Diagnostik interstitieller Lungenerkrankungen im Erwachsenenalter.

The evaluation of a patient with interstitial lung disease (ILD) includes assessment of clinical, radiological, and often histopathological data. As there were no specific recommendations to guide the evaluation of patients under the suspicion of an ILD within the German practice landscape, this position statement from an interdisciplinary panel of ILD experts provides guidance related to the diagnostic modalities which should be used in the evaluation of ILD. This includes clinical assessment rheumatological evaluation, radiological examinations, histopathologic sampling and the need for a final discussion in a multidisciplinary team.

[Arthritis and pulmonary cavities]. / Arthritiden und Lungenkavernen.

This case report describes the very rare simultaneous occurrence of rheumatoid arthritis and granulomatosis with polyangiitis with the only organ manifestation of life-threatening bilateral pulmonary cavities. Due to the acuteness of the vasculitis, treatment was primarily with cyclophosphamide infusions and high-dose glucocorticoids, and in the further course with high-dose methotrexate. Routine thoracic imaging also seems to be useful when conventional basic rheumatologic treatment is newly initiated, as treatment-decisive changes are seen with a relevant frequency. The occurrence of both autoimmune diseases might be due to common genetic predispositions.

[Publicity campaign rheuma2025 of the Union for Rheumatology]. / Öffentlichkeitskampagne "rheuma2025" des Bündnisses für Rheumatologie.

The publicity campaign "rheuma2025", initiated by the Union for Rheumatology, aims at improvement of patient-centered care. For this the number of positions for trainees in rheumatology needs to increase to a level which matches the public needs. Students in medical school must have even more interest for the discipline and they must be recruited. Regulatory constraints in the approval by the authorities for opening a private rheumatology practice must become much more flexible. The possibilities for in-patient acute care of patients in specialized hospitals have to be strengthened. Finally, the public image of rheumatology per se must be sharpened. To achieve these goals a homepage for the campaign was created ( https://rheuma2025.de ), which provides a toolkit of items for the public, for physicians and students. Various media channels for rheuma2025 were established with specific contents for each target group.

Do patients with rheumatoid arthritis show a different course of COVID-19 compared to patients with spondyloarthritis?

OBJECTIVES: Rheumatoid arthritis (RA) and spondyloarthritis (SpA) are the most common inflammatory rheumatic diseases (IRD). The aim of this study was to elucidate differences in the outcome of SARS-CoV-2 infection in RA- and SpA-patients. METHODS: Data from the German COVID-19 registry for IRD patients from 30th March to 16th November 2020 were analysed. 208 RA and SpA patients were included in the study, matched for gender and age. RESULTS: 104 SpA patients (40% patients with ankylosing spondylitis, 54% with psoriatic arthritis and 6% with enteropathic arthritis) were compared to 104 RA patients. For both groups, median age was 56 years. TNF-i treatment was reported in 45% of the SpA and in 19% of RA patients (p=0.001). Glucocorticoids were used in 13% of the SpA and in 40% of the RA patients (p=0.001). In both groups, the majority of the patients (97% SpA, 95% RA) recovered from COVID-19. Hospitalisation was needed in 16% of the SpA and in 30% of the RA patients (p=0.05), and oxygen treatment in 10% and 18% respectively (p=ns). Three versus six (p=ns) fatal courses were reported in the SpA versus the RA group. CONCLUSIONS: The study revealed that the hospitalisation rate during COVID-19 infection, but not the mortality, was significantly higher in RA as compared to SpA patients. This could be explained either by different treatment strategies or by different susceptibilities of the two diseases.

Matsuda-Heck arylation of itaconates: a versatile approach to heterocycles from a renewable resource.

Itaconic acid esters and hemiesters undergo Pd-catalyzed coupling reactions with arene diazonium salts in high to excellent yields. The coupling products of ortho-nitro arene diazonium salts can be converted in one or two steps to benzazepine-2-ones.