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Abstract Atmospheric new particle formation (NPF) is a naturally occurring phenomenon, during which high concentrations of sub-10 nm particles are created through gas to particle conversion. The NPF is observed in multiple environments around the world. Although it has observable influence onto annual total and ultrafine particle number concentrations (PNC and UFP, respectively), only limited epidemiological studies have investigated whether these particles are associated with adverse health effects. One plausible reason for this limitation may be related to the absence of NPF identifiers available in UFP and PNC data sets. Until recently, the regional NPF events were usually identified manually from particle number size distribution contour plots. Identification of NPF across multi-annual and multiple station data sets remained a tedious task. In this work, we introduce a regional NPF identifier, created using an automated, machine learning based algorithm. The regional NPF event tag was created for 65 measurement sites globally, covering the period from 1996 to 2023. The discussed data set can be used in future studies related to regional NPF.

Abstract Current guidelines recommend reflex testing for hepatitis D virus (HDV) coinfection in hepatitis B surface antigen (HBsAg)-positive patients over risk-factor based screening. We aimed to evaluate the feasibility and diagnostic yield of reflex anti-HDV testing at a Central European tertiary care center. We retrospectively included 560 consecutive patients who had a recorded (first) positive HBsAg test result at the Vienna General Hospital between 2018 and 2022. While reflex anti-HDV testing had been implemented in our hepatitis outpatient clinic (n = 153, ‘reflex testing cohort’), HDV screening needed to be manually ordered in the remaining patients (n = 407, ‘standard testing cohort’). Overall, 98.0% and 65.1% of patients in the reflex and standard testing cohort were screened for anti-HDV, respectively, and the overall seroprevalence of anti-HDV among screened patients was 6.7% (n = 28, reflex testing cohort: 9.3%, standard testing cohort: 5.3%). Risk factors for HDV were present in 49.1% of all included and in 89.3% of anti-HDV positive patients, respectively. Anti-HDV positive patients showed higher ALT (54 [33–83] vs. 29 [19–49] U/L; p = 0.005) and a higher proportion of low-to-undetectable HBV-DNA (61.5% vs. 33.2%; p

Abstract The current limitations in utilizing metal-organic frameworks for (photo)electrochemical applications stem from their diminished electrochemical stability. In our study, we illustrate a method to bolster the activity and stability of (photo)electrocatalytically active metal-organic frameworks through ligand engineering. We synthesize four distinct mixed-ligand versions of zeolitic imidazolate framework-67, and conduct a comprehensive investigation into the structural evolution and self-reconstruction during electrocatalytic oxygen evolution reactions. In contrast to the conventional single-ligand ZIF, where the framework undergoes a complete transformation into CoOOH via a stepwise oxidation, the ligand-engineered zeolitic imidazolate frameworks manage to preserve the fundamental framework structure by in-situ forming a protective cobalt (oxy)hydroxide layer on the surface. This surface reconstruction facilitates both conductivity and catalytic activity by one order of magnitude and considerably enhances the (photo)electrochemical stability. This work highlights the vital role of ligand engineering for designing advanced and stable metal-organic frameworks for photo- and electrocatalysis.

Abstract Deep single-cell multi-omic profiling offers a promising approach to understand and overcome drug resistance in relapsed or refractory (rr) acute myeloid leukemia (AML). Here, we combine single-cell ex vivo drug profiling (pharmacoscopy) with single-cell and bulk DNA, RNA, and protein analyses, alongside clinical data from 21 rrAML patients. Unsupervised data integration reveals reduced ex vivo response to the Bcl-2 inhibitor venetoclax (VEN) in patients treated with both a hypomethylating agent (HMA) and VEN, compared to those pre-exposed to chemotherapy or HMA alone. Integrative analysis identifies both known and unreported mechanisms of innate and treatment-related VEN resistance and suggests alternative treatments, like targeting increased proliferation with the PLK inhibitor volasertib. Additionally, high CD36 expression in VEN-resistant blasts associates with sensitivity to CD36-targeted antibody treatment ex vivo. This study demonstrates how single-cell multi-omic profiling can uncover drug resistance mechanisms and treatment vulnerabilities, providing a valuable resource for future AML research.

Abstract Pharmaceutical formulations are increasingly based on drug nanoparticles or carrier nanoparticles encapsulating drugs or mRNA molecules. Sizes and monodispersity of the nanoparticles regulate bioavailability, pharmacokinetics and pharmacology. Microfluidic mixers promise unique conditions for their continuous preparation. A novel microfluidic antisolvent precipitation device was realized by two-photon-polymerization with a mixing channel in which the organic phase formed a sheet with a homogeneous thickness of down to 7 μm completely wrapped in the aqueous phase. Homogeneous diffusion through the sheet accelerates mixing. Optical access was implemented to allow in-situ dynamic light scattering. By centering the thin sheet in the microchannel cross-section, two important requirements are met. On the one hand, the organic phase never reaches the channel walls, avoiding fouling and unstable flow conditions. On the other hand, in the sheet positioned at the maximum of the parabolic flow profile the nanoparticle velocities are homogenized which enables flow-compensated Dynamic Light Scattering (flowDLS). These unique features allowed in-situ particle size determination for the first time. Monitoring of lipid nanoparticle precipitation was demonstrated for different rates of solvent and antisolvent flows. This breakthrough innovation will not only enable feedback control of nanoparticle production but also will provide new insights into the dynamics of nanoparticle precipitation.

Abstract Mycobacterial HelD is a transcription factor that recycles stalled RNAP by dissociating it from nucleic acids and, if present, from the antibiotic rifampicin. The rescued RNAP, however, must disengage from HelD to participate in subsequent rounds of transcription. The mechanism of release is unknown. We show that HelD from Mycobacterium smegmatis forms a complex with RNAP associated with the primary sigma factor σA and transcription factor RbpA but not CarD. We solve several structures of RNAP-σA-RbpA-HelD without and with promoter DNA. These snapshots capture HelD during transcription initiation, describing mechanistic aspects of HelD release from RNAP and its protective effect against rifampicin. Biochemical evidence supports these findings, defines the role of ATP binding and hydrolysis by HelD in the process, and confirms the rifampicin-protective effect of HelD. Collectively, these results show that when HelD is present during transcription initiation, the process is protected from rifampicin until the last possible moment.

Abstract To what extent and how post-transcriptional dysregulation affects aging proteome remains unclear. Here, we provide proteomic data of whole-tissue lysates (WTL) and low-solubility protein-enriched fractions (LSF) of major tissues collected from mice of 6, 15, 24, and 30 months of age. Low-solubility proteins are preferentially affected by age and the analysis of LSF doubles the number of proteins identified to be differentially expressed with age. Simultaneous analysis of proteome and transcriptome using the same tissue homogenates reveals the features of age-related post-transcriptional dysregulation. Post-transcriptional dysregulation becomes evident especially after 24 months of age and age-related post-transcriptional dysregulation leads to accumulation of core matrisome proteins and reduction of mitochondrial membrane proteins in multiple tissues. Based on our in-depth proteomic data and sample-matched transcriptome data of adult, middle-aged, old, and geriatric mice, we construct the Mouse aging proteomic atlas ( https://aging-proteomics.info/ ), which provides a thorough and integrative view of age-related gene expression changes.

Abstract A precise quantification of mitral regurgitation (MR) severity is essential for treatment and outcome of patients with MR. 3D echocardiography facilitates estimation of MR but selection of patients with necessity of invasive treatment remains challenging. We investigate effective regurgitation orifice area (EROA) quantification by 3D compared to 2D echocardiography in patients with MR and highlight the improved discrimination of MR severity. We consecutively enrolled fifty patients with primary or secondary and at least moderate MR undergoing 2D and 3D colour Doppler echocardiography prior to transcatheter edge-to-edge repair (TEER). Improved accuracy of MR grading using 3D vena contracta area (VCA) as an estimate of EROA was compared to 2D proximal isovelocity surface area (PISA) quantification method and a multiparameter reference standard. Quantification of EROA remarkably varies between 2D and 3D echocardiography and the discrimination between moderate and severe MR was significantly (p = 0.001) different using 2D PISA or 3D VCA, respectively. 3D VCA correlated significantly (r = 0.501, p

Abstract Butyl octyl magnesium solutions are important raw materials in various chemical processes but suffer from their high reactivity with even traces of water, protic solvents or oxygen and an increased viscosity in hydrocarbon solution due to the formation of polymeric structures. N 1,N 2-diphenylacenaphthylene-1,2-diimines (BIANs) have already been identified as potential candidates to reduce the viscosity of alkyl magnesium solutions and this study provides a systematic insight into the dependence of this ability on the position and structures of substituents on the BIAN. Besides the various BIANs, ZnCl2 complexes and hydrogenated derivatives were characterized and tested for their ability to reduce the viscosity. HPLC-high resolution mass spectrometry, MALDI-ToF mass spectrometry, but most important FTIR and NMR experiments under inert conditions have been used to shine light on the interaction of the different BIAN derivatives with alkyl magnesium solutions. Hydrogenated BIANs, especially those with bulky alkyl groups in the ortho position(s) have been identified as the most promising candidates. An additional benefit of the hydrogenated species is that in contrast to BIANs and BIAN-Zn complexes they do not undergo permanent chemical modification and can be reused after extraction.

Abstract Rheumatoid arthritis (RA) is a complex immune-mediated inflammatory disorder in which patients suffer from inflammatory-erosive arthritis. Recent advances on histopathology heterogeneity of RA synovial tissue revealed three distinct phenotypes based on cellular composition (pauci-immune, diffuse and lymphoid), suggesting that distinct etiologies warrant specific targeted therapy which motivates a need for cost effective phenotyping tools in preclinical and clinical settings. To this end, we developed an automated multi-scale computational pathotyping (AMSCP) pipeline for both human and mouse synovial tissue with two distinct components that can be leveraged together or independently: (1) segmentation of different tissue types to characterize tissue-level changes, and (2) cell type classification within each tissue compartment that assesses change across disease states. Here, we demonstrate the efficacy, efficiency, and robustness of the AMSCP pipeline as well as the ability to discover novel phenotypes. Taken together, we find AMSCP to be a valuable cost-effective method for both pre-clinical and clinical research.

Abstract The incidence of spondylodiscitis has witnessed a significant increase in recent decades. Surgical intervention becomes necessary in case of bone destruction to remove infected tissue and restore spinal stability, often involving the implantation of a cage. Despite appropriate treatment, relapses occur in up to 20 percent of cases, resulting in substantial economic and social burdens. The formation of biofilm has been identified as a major contributor to relapse development. Currently, there is no consensus among German-speaking spinal surgeons or in the existing literature regarding the preferred choice of material to minimize relapse rates. Thus, the objective of this study is to investigate whether certain materials used in spinal implants exhibit varying degrees of susceptibility to bacterial attachment, thereby providing valuable insights for improving treatment outcomes.Eight cages of each PEEK, titanium-coated PEEK (Ti-PEEK), titanium (Ti), polyetherketoneketone (PEKK), tantalum (Ta) and antibiotic-loaded bone cement were incubated with 20% human plasma for 24 h. Subsequently, four implants were incubated with S. aureus for 24 h or 48 h each. The biofilm was then removed by sonication and the attained solution plated for Colony Forming Units (CFU) counting. Scanning electron microscopy was used to confirm bacterial attachment. The CFUs have been compared directly and in relation to the cages surface area. The surface area of the implants was PEEK 557 mm2, Ti-PEEK 472 mm2, Ti 985 mm2, PEKK 594 mm2, Ta 706 mm2, bone cement 123 mm2. The mean CFU count per implant and per mm2 surface area after 24 h and after 48 h was calculated. Bone cement was found to have significantly more CFUs per mm2 surface area than the other materials tested. When comparing the CFU count per implant, bone cement was statistically significantly more prone to biofilm formation than PEEK after 48 h. There was no statistical significance between the other materials when comparing both CFU count per mm2 surface area and CFU count per implant. The electron microscopic analysis showed the attachment of the bacteria, as well as production of extracellular polymeric substances (EPS) as a sign for beginning biofilm formation. Antibiotic-loaded bone cement has shown statistically significantly more bacterial attachment than the other examined materials. No difference was found between the other materials regarding bacterial attachment after 24 h and 48 h. Proposed hypotheses for further studies include testing whether differences become apparent after longer incubation or with different pathogens involved in the pathogenesis of pyogenic spondylodiscitis.

Abstract The sympathetic nervous system controls bodily functions including vascular tone, cardiac rhythm, and the “fight-or-flight response”. Sympathetic chain ganglia develop in parallel with preganglionic motor nerves extending from the neural tube, raising the question of whether axon targeting contributes to sympathetic chain formation. Using nerve-selective genetic ablations and lineage tracing in mouse, we reveal that motor nerve-associated Schwann cell precursors (SCPs) contribute sympathetic neurons and satellite glia after the initial seeding of sympathetic ganglia by neural crest. Motor nerve ablation causes mispositioning of SCP-derived sympathoblasts as well as sympathetic chain hypoplasia and fragmentation. Sympathetic neurons in motor-ablated embryos project precociously and abnormally towards dorsal root ganglia, eventually resulting in fusion of sympathetic and sensory ganglia. Cell interaction analysis identifies semaphorins as potential motor nerve-derived signaling molecules regulating sympathoblast positioning and outgrowth. Overall, central innervation functions both as infrastructure and regulatory niche to ensure the integrity of peripheral ganglia morphogenesis.

Abstract Converging evidence indicates that extra-embryonic yolk sac is the source of both macrophages and endothelial cells in adult mouse tissues. Prevailing views are that these embryonically derived cells are maintained after birth by proliferative self-renewal in their differentiated states. Here we identify clonogenic endothelial-macrophage (EndoMac) progenitor cells in the adventitia of embryonic and postnatal mouse aorta, that are independent of Flt3-mediated bone marrow hematopoiesis and derive from an early embryonic CX3CR1+ and CSF1R+ source. These bipotent progenitors are proliferative and vasculogenic, contributing to adventitial neovascularization and formation of perfused blood vessels after transfer into ischemic tissue. We establish a regulatory role for angiotensin II, which enhances their clonogenic and differentiation properties and rapidly stimulates their proliferative expansion in vivo. Our findings demonstrate that embryonically derived EndoMac progenitors participate in local vasculogenic responses in the aortic wall by contributing to the expansion of endothelial cells and macrophages postnatally.

Abstract Ge–Sb–Se–Te chalcogenides, namely Se-substituted Ge–Sb–Te, have been developed as an alternative optical phase change material (PCM) with a high figure-of-merit. A need for the integration of such new PCMs onto a variety of photonic platforms has necessitated the development of fabrication processes compatible with diverse material compositions as well as substrates of varying material types, shapes, and sizes. This study explores the application of chemical solution deposition as a method capable of creating conformally coated layers and delves into the resulting modifications in the structural and optical properties of Ge–Sb–Se–Te PCMs. Specifically, we detail the solution-based deposition of Ge–Sb–Se–Te layers and present a comparative analysis with those deposited via thermal evaporation. We also discuss our ongoing endeavor to improve available choice of processing-material combinations and how to realize solution-derived high figure-of-merit optical PCM layers, which will enable a new era for the development of reconfigurable photonic devices.

Abstract Amber captures a snapshot of life and death from millions of years in the past. Here, the fate of three fossil Darwin wasps in Baltic amber is virtually dissected with the help of micro-CT scanning, to better understand the taphonomic processes that affected their preservation. The states of the fossils range from nearly perfect preservation, including remains of internal organs, to empty casts that were strongly affected by decomposition. We describe the three specimens as new taxa, Osparvis aurorae gen. et sp. nov., Grana harveydenti gen. et sp. nov. and Xorides? romeo sp. nov. Based on the taphonomic and morphological interpretations, we conclude that two specimens were trapped alive, and the third ended up in resin post-mortem. The morphology and classification of the specimens provide clues regarding their ecology, and we discuss their likely hosts and parasitation modes. Taken together, our three wasp fossils showcase how an integrative analysis of amber taphonomy, taxonomic association and morphology can shed light onto past biodiversity and offer valuable insights for interpreting their evolutionary history.

Abstract Metabolic dysfunction-associated steatotic liver disease (MASLD) and related steatohepatitis (MASH) are common among obese patients and may improve after metabolic/bariatric surgery (MBS). 93 Patients undergoing MBS in 2021–2022 were prospectively enrolled. Liver stiffness measurement (LSM; via vibration-controlled transient elastography [VCTE], point [pSWE] and 2D [2DSWE] shear wave elastography) and non-invasive steatosis assessment (via controlled attenuation parameter [CAP]) were performed before (baseline [BL]) and three months (M3) after surgery. 93 patients (median age 40.9 years, 68.8% female, median BL-BMI: 46.0 kg/m2) were included. BL-liver biopsy showed MASLD in 82.8% and MASH in 34.4% of patients. At M3 the median relative total weight loss (%TWL) was 20.1% and the median BMI was 36.1 kg/m2. LSM assessed by VCTE and 2DSWE, as well as median CAP all decreased significantly from BL to M3 both in the overall cohort and among patients with MASH. There was a decrease from BL to M3 in median levels of ALT (34.0 U/L to 31 U/L; p = 0.025), gamma glutamyl transferase (BL: 30.0 to 21.0 U/L; p

Abstract Pyrocumulonimbus (pyroCb) firestorm systems have been shown to inject significant amounts of black carbon (BC) to the stratosphere with a residence time of several months. Injected BC warms the local stratospheric air, consequently perturbing transport and hence spatial distributions of ozone and water vapor. A distinguishing feature of BC-containing particles residing within pyroCb smoke is their thick surface coatings made of condensed organic matter. When coated with non-refractory materials, BC’s absorption is enhanced, yet the absorption enhancement factor (E abs ) for pyroCb BC is not well constrained. Here, we perform particle-scale measurements of BC mass, morphology, and coating thickness from inside a pyroCb cloud and quantify E abs using an established particle-resolved BC optics model. We find that the population-averaged E abs for BC asymptotes to 2.0 with increasing coating thickness. This value denotes the upper limit of E abs for thickly coated BC in the atmosphere. Our results provide observationally constrained parameterizations of BC absorption for improved radiative transfer calculations of pyroCb events.

Abstract Climate change is exposing marine species to unsuitable temperatures while also creating new thermally suitable habitats of varying persistence. However, understanding how these different dynamics will unfold over time remains limited. We use yearly sea surface temperature projections to estimate temporal dynamics of thermal exposure (when temperature exceeds realised species’ thermal limits) and opportunity (when temperature at a previously unsuitable site becomes suitable) for 21,696 marine species globally until 2100. Thermal opportunities are projected to arise earlier and accumulate gradually, especially in temperate and polar regions. Thermal exposure increases later and occurs more abruptly, mainly in the tropics. Assemblages tend to show either high exposure or high opportunity, but seldom both. Strong emissions reductions reduce exposure around 100-fold whereas reductions in opportunities are halved. Globally, opportunities are projected to emerge faster than exposure until mid-century when exposure increases more rapidly under a high emissions scenario. Moreover, across emissions and dispersal scenarios, 76%-97% of opportunities are projected to persist until 2100. These results indicate thermal opportunities could be a major source of marine biodiversity change, especially in the near- and mid-term. Our work provides a framework for predicting where and when thermal changes will occur to guide monitoring efforts.

Aging is associated with a number of physiologic changes including perturbed circadian rhythms; however, mechanisms by which rhythms are altered remain unknown. To test the idea that circulating factors mediate age-dependent changes in peripheral rhythms, we compared the ability of human serum from young and old individuals to synchronize circadian rhythms in culture. We collected blood from apparently healthy young (age 25–30) and old (age 70–76) individuals at 14:00 and used the serum to synchronize cultured fibroblasts. We found that young and old sera are equally competent at initiating robust ~24 hr oscillations of a luciferase reporter driven by clock gene promoter. However, cyclic gene expression is affected, such that young and old sera promote cycling of different sets of genes. Genes that lose rhythmicity with old serum entrainment are associated with oxidative phosphorylation and Alzheimer’s Disease as identified by STRING and IPA analyses. Conversely, the expression of cycling genes associated with cholesterol biosynthesis increased in the cells entrained with old serum. Genes involved in the cell cycle and transcription/translation remain rhythmic in both conditions. We did not observe a global difference in the distribution of phase between groups, but found that peak expression of several clock-controlled genes (PER3, NR1D1, NR1D2, CRY1, CRY2, and TEF) lagged in the cells synchronized ex vivo with old serum. Taken together, these findings demonstrate that age-dependent blood-borne factors affect circadian rhythms in peripheral cells and have the potential to impact health and disease via maintaining or disrupting rhythms respectively.

Abstract Glioblastoma multiforme (GBM) encompasses brain malignancies marked by phenotypic and transcriptional heterogeneity thought to render these tumors aggressive, resistant to therapy, and inevitably recurrent. However, little is known about how the spatial organization of GBM genomes underlies this heterogeneity and its effects. Here, we compile a cohort of 28 patient-derived glioblastoma stem cell-like lines (GSCs) known to reflect the properties of their tumor-of-origin; six of these were primary-relapse tumor pairs from the same patient. We generate and analyze 5 kbp-resolution chromosome conformation capture (Hi-C) data from all GSCs to systematically map thousands of standalone and complex structural variants (SVs) and the multitude of neoloops arising as a result. By combining Hi-C, histone modification, and gene expression data with chromatin folding simulations, we explain how the pervasive, uneven, and idiosyncratic occurrence of neoloops sustains tumor-specific transcriptional programs via the formation of new enhancer-promoter contacts. We also show how even moderately recurrent neoloops can relate to patient-specific vulnerabilities. Together, our data provide a resource for dissecting GBM biology and heterogeneity, as well as for informing therapeutic approaches.

Abstract Over the last decades, cognitive neuroscience has identified a distributed set of brain regions that are critical for attention. Strong anatomical overlap with brain regions critical for oculomotor processes suggests a joint network for attention and eye movements. However, the role of this shared network in complex, naturalistic environments remains understudied. Here, we investigated eye movements in relation to (un)attended sentences of natural speech. Combining simultaneously recorded eye tracking and magnetoencephalographic data with temporal response functions, we show that gaze tracks attended speech, a phenomenon we termed ocular speech tracking. Ocular speech tracking even differentiates a target from a distractor in a multi-speaker context and is further related to intelligibility. Moreover, we provide evidence for its contribution to neural differences in speech processing, emphasizing the necessity to consider oculomotor activity in future research and in the interpretation of neural differences in auditory cognition.

Abstract Cluster analyzes of facial models of autistic patients aim to clarify whether it is possible to diagnose autism on the basis of facial features and further to stratify the autism spectrum disorder. We performed a cluster analysis of sets of 3D scans of ASD patients (116) and controls (157) using Euclidean and geodesic distances in order to recapitulate the published results on the Czech population. In the presented work, we show that the major factor determining the clustering structure and consequently also the correlation of resulting clusters with autism severity degree is body mass index corrected for age (BMIFA). After removing the BMIFA effect from the data in two independent ways, both the cluster structure and autism severity correlations disappeared. Despite the fact that the influence of body mass index (BMI) on facial dimensions was studied many times, this is the first time to our knowledge when BMI was incorporated into the faces clustering study and it thereby casts doubt on previous results. We also performed correlation analysis which showed that the only correction used in the existing clustering studies—dividing the facial distance by the average value within the face—is not eliminating correlation between facial distances and BMIFA within the facial cohort.

Abstract The composition of the microbial community in the intestine may influence the functions of distant organs such as the brain, lung, and skin. These microbes can promote disease or have beneficial functions, leading to the hypothesis that microbes in the gut explain the co-occurrence of intestinal and skin diseases. Here, we show that the reverse can occur, and that skin directly alters the gut microbiome. Disruption of the dermis by skin wounding or the digestion of dermal hyaluronan results in increased expression in the colon of the host defense genes Reg3 and Muc2, and skin wounding changes the composition and behavior of intestinal bacteria. Enhanced expression Reg3 and Muc2 is induced in vitro by exposure to hyaluronan released by these skin interventions. The change in the colon microbiome after skin wounding is functionally important as these bacteria penetrate the intestinal epithelium and enhance colitis from dextran sodium sulfate (DSS) as seen by the ability to rescue skin associated DSS colitis with oral antibiotics, in germ-free mice, and fecal microbiome transplantation to unwounded mice from mice with skin wounds. These observations provide direct evidence of a skin-gut axis by demonstrating that damage to the skin disrupts homeostasis in intestinal host defense and alters the gut microbiome.

Abstract Traumatic brain injury leads to a highly orchestrated immune- and glial cell response partially responsible for long-lasting disability and the development of secondary neurodegenerative diseases. A holistic understanding of the mechanisms controlling the responses of specific cell types and their crosstalk is required to develop an efficient strategy for better regeneration. Here, we combine spatial and single-cell transcriptomics to chart the transcriptomic signature of the injured male murine cerebral cortex, and identify specific states of different glial cells contributing to this signature. Interestingly, distinct glial cells share a large fraction of injury-regulated genes, including inflammatory programs downstream of the innate immune-associated pathways Cxcr3 and Tlr1/2. Systemic manipulation of these pathways decreases the reactivity state of glial cells associated with poor regeneration. The functional relevance of the discovered shared signature of glial cells highlights the importance of our resource enabling comprehensive analysis of early events after brain injury.

Abstract Intratumoral tertiary lymphoid structures (TLSs) have been associated with improved outcome in various cohorts of patients with cancer, reflecting their contribution to the development of tumor-targeting immunity. Here, we demonstrate that high-grade serous ovarian carcinoma (HGSOC) contains distinct immune aggregates with varying degrees of organization and maturation. Specifically, mature TLSs (mTLS) as forming only in 16% of HGSOCs with relatively elevated tumor mutational burden (TMB) are associated with an increased intratumoral density of CD8+ effector T (TEFF) cells and TIM3+PD1+, hence poorly immune checkpoint inhibitor (ICI)-sensitive, CD8+ T cells. Conversely, CD8+ T cells from immunologically hot tumors like non-small cell lung carcinoma (NSCLC) are enriched in ICI-responsive TCF1+ PD1+ T cells. Spatial B-cell profiling identifies patterns of in situ maturation and differentiation associated with mTLSs. Moreover, B-cell depletion promotes signs of a dysfunctional CD8+ T cell compartment among tumor-infiltrating lymphocytes from freshly isolated HGSOC and NSCLC biopsies. Taken together, our data demonstrate that – at odds with NSCLC – HGSOC is associated with a low density of follicular helper T cells and thus develops a limited number of mTLS that might be insufficient to preserve a ICI-sensitive TCF1+PD1+ CD8+ T cell phenotype. These findings point to key quantitative and qualitative differences between mTLSs in ICI-responsive vs ICI-irresponsive neoplasms that may guide the development of alternative immunotherapies for patients with HGSOC.

Abstract Advancements in congenital heart surgery have heightened the importance of durable biomaterials for adult survivors. Dystrophic calcification poses a significant risk to the long-term viability of prosthetic biomaterials in these procedures. Herein, we describe the natural history of calcification in the most frequently used vascular conduits, expanded polytetrafluoroethylene grafts. Through a retrospective clinical study and an ovine model, we compare the degree of calcification between tissue-engineered vascular grafts and polytetrafluoroethylene grafts. Results indicate superior durability in tissue-engineered vascular grafts, displaying reduced late-term calcification in both clinical studies (p

Summary: Both mental health and mental illness unfold in complex and unpredictable ways. Novel artificial intelligence approaches from the area of dynamical systems reconstruction can characterize such dynamics and help understand the underlying brain mechanisms, which can also be used as potential biomarkers. However, applying deep learning to model dynamical systems at the individual level must overcome numerous computational challenges to be reproducible and clinically useful. In this study, we performed an extensive analysis of these challenges using generative modeling of brain dynamics from fMRI data as an example and demonstrated their impact on classifying patients with schizophrenia and major depression. This study highlights the tendency of deep learning models to identify functionally unique solutions during parameter optimization, which severely impacts the reproducibility of downstream predictions. We hope this study guides the future development of individual-level generative models and similar machine learning approaches aimed at identifying reproducible biomarkers of mental illness.

Protein kinases act as central molecular switches in the control of cellular functions. Alterations in the regulation and function of protein kinases may provoke diseases including cancer. In this study we investigate the conformational states of such disease-associated kinases using the high sensitivity of the kinase conformation (KinCon) reporter system. We first track BRAF kinase activity conformational changes upon melanoma drug binding. Second, we also use the KinCon reporter technology to examine the impact of regulatory protein interactions on LKB1 kinase tumor suppressor functions. Third, we explore the conformational dynamics of RIP kinases in response to TNF pathway activation and small molecule interactions. Finally, we show that CDK4/6 interactions with regulatory proteins alter conformations which remain unaffected in the presence of clinically applied inhibitors. Apart from its predictive value, the KinCon technology helps to identify cellular factors that impact drug efficacies. The understanding of the structural dynamics of full-length protein kinases when interacting with small molecule inhibitors or regulatory proteins is crucial for designing more effective therapeutic strategies.

Abstract The intestinal microbiome plays an important role in mammalian health, disease, and immune function. In light of this function, recent studies have aimed to characterize the microbiomes of various bat species, which are noteworthy for their roles as reservoir hosts for several viruses known to be highly pathogenic in other mammals. Despite ongoing bat microbiome research, its role in immune function and disease, especially the effects of changes in the microbiome on host health, remains nebulous. Here, we describe a novel methodology to investigate the intestinal microbiome of captive Jamaican fruit bats (Artibeus jamaicensis). We observed a high degree of individual variation in addition to sex- and cohort-linked differences. The intestinal microbiome was correlated with intestinal metabolite composition, possibly contributing to differences in immune status. This work provides a basis for future infection and field studies to examine in detail the role of the intestinal microbiome in antiviral immunity.

Abstract Laparoscopic hysterectomy is a commonly performed procedure. However, one high-risk complication is vaginal cuff dehiscence. Currently, there is no standardization regarding thread material or suturing technique for vaginal cuff closure. Therefore, this study aimed to compare extracorporeal and intracorporeal suturing techniques for vaginal cuff closure using a pelvic trainer model. Eighteen experts in laparoscopic surgery performed vaginal cuff closures with interrupted sutures using intracorporeal knotting, extracorporeal knotting and continuous, unidirectional barbed sutures. While using an artificial tissue suturing pad in a pelvic trainer, experts performed vaginal cuff closure using each technique according to block randomization. Task completion time, tension resistance, and the number of errors were recorded. After completing the exercises, participants answered a questionnaire concerning the suturing techniques and their performance. Experts completed suturing more quickly (p

Abstract Leptospirosis is a globally distributed zoonotic disease. The standard serological test, known as Microscopic Agglutination Test (MAT), requires the use of live Leptospira strains. To enhance its sensitivity and specificity, the usage of locally circulating strains is recommended. However, to date, no local strain is available from Austria. This study aimed to isolate circulating Leptospira strains from cattle in Austria to enhance the performances of the routine serological test for both humans and animals. We used a statistical approach combined with a comprehensive literature search to profile cattle with greater risk of leptospirosis infection and implemented a targeted sampling between November 2021 and October 2022. Urine and/or kidney tissue were sampled from 410 cattle considered at higher risk of infection. Samples were inoculated into EMJH-STAFF culture media within 2–6 h and a real-time PCR targeting the lipL32 gene was used to confirm the presence/absence of pathogenic Leptospira in each sample. Isolates were further characterised by core genome multilocus sequence typing (cgMLST). Nine out of 429 samples tested positive by PCR, from which three isolates were successfully cultured and identified as Leptospira borgpetersenii serogroup Sejroe serovar Hardjobovis, cgMLST cluster 40. This is the first report on the isolation and genotyping of local zoonotic Leptospira in Austria, which holds the potential for a significant improvement in diagnostic performance in the country. Although the local strain was identified as a cattle-adapted serovar, it possesses significant zoonotic implications. Furthermore, this study contributes to a better understanding of the epidemiology of leptospirosis in Europe.

Abstract The intracellular ATP-ribosyltransferases PARP1 and PARP2, contribute to DNA base excision repair (BER) and DNA demethylation and have been implicated in epigenetic programming in early mammalian development. Recently, proteomic analyses identified BER proteins to be covalently poly-ADP-ribosylated by PARPs. The role of this posttranslational modification in the BER process is unknown. Here, we show that PARP1 senses AP-sites and SSBs generated during TET-TDG mediated active DNA demethylation and covalently attaches PAR to each BER protein engaged. Covalent PARylation dissociates BER proteins from DNA, which accelerates the completion of the repair process. Consistently, inhibition of PARylation in mESC resulted both in reduced locus-specific TET-TDG-targeted DNA demethylation, and in reduced general repair of random DNA damage. Our findings establish a critical function of covalent protein PARylation in coordinating molecular processes associated with dynamic DNA methylation.

Abstract High-quality optical ring resonators can confine light in a small volume and store it for millions of roundtrips. They have enabled the dramatic size reduction from laboratory scale to chip level of optical filters, modulators, frequency converters, and frequency comb generators in the visible and the near-infrared. The mid-infrared spectral region (3−12 μm), as important as it is for molecular gas sensing and spectroscopy, lags behind in development of integrated photonic components. Here we demonstrate the integration of mid-infrared ring resonators and directional couplers, incorporating a quantum cascade active region in the waveguide core. It enables electrical control of the resonant frequency, its quality factor, the coupling regime and the coupling coefficient. We show that one device, depending on its operating point, can act as a tunable filter, a nonlinear frequency converter, or a frequency comb generator. These concepts extend to the integration of multiple active resonators and waveguides in arbitrary configurations, thus allowing the implementation of purpose-specific mid-infrared active photonic integrated circuits for spectroscopy, communication, and microwave generation.

Abstract Cerebral organoids recapitulate the structure and function of the developing human brain in vitro, offering a large potential for personalized therapeutic strategies. The enormous growth of this research area over the past decade with its capability for clinical translation makes a non-invasive, automated analysis pipeline of organoids highly desirable. This work presents a novel non-invasive approach to monitor and analyze cerebral organoids over time using high-field magnetic resonance imaging and state-of-the-art tools for automated image analysis. Three specific objectives are addressed, (I) organoid segmentation to investigate organoid development over time, (II) global cysticity classification and (III) local cyst segmentation for organoid quality assessment. We show that organoid growth can be monitored reliably over time and cystic and non-cystic organoids can be separated with high accuracy, with on par or better performance compared to state-of-the-art tools applied to brightfield imaging. Local cyst segmentation is feasible but could be further improved in the future. Overall, these results highlight the potential of the pipeline for clinical application to larger-scale comparative organoid analysis.

Abstract Anal cancer incidence is significantly higher in people living with HIV as HIV increases the oncogenic potential of human papillomavirus. The incidence of anal cancer in the United States has recently increased, with diagnosis and treatment hampered by high loss-to-follow-up rates. Novel methods for the automated, real-time diagnosis of AIN 2+ could enable "see and treat" strategies, reducing loss-to-follow-up rates. A previous retrospective study demonstrated that the accuracy of a high-resolution microendoscope (HRME) coupled with a deep learning model was comparable to expert clinical impression for diagnosis of AIN 2+ (sensitivity 0.92 [P = 0.68] and specificity 0.60 [P = 0.48]). However, motion artifacts and noise led to many images failing quality control (17%). Here, we present a high frame rate HRME (HF-HRME) with improved image quality, deployed in the clinic alongside a deep learning model and evaluated prospectively for detection of AIN 2+ in real-time. The HF-HRME reduced the fraction of images failing quality control to 4.6% by employing a high frame rate camera that enhances contrast and limits motion artifacts. The HF-HRME outperformed the previous HRME (P

Abstract The Mitochondrial Complex I Assembly (MCIA) complex is essential for the biogenesis of respiratory Complex I (CI), the first enzyme in the respiratory chain, which has been linked to Alzheimer’s disease (AD) pathogenesis. However, how MCIA facilitates CI assembly, and how it is linked with AD pathogenesis, is poorly understood. Here we report the structural basis of the complex formation between the MCIA subunits ECSIT and ACAD9. ECSIT binding induces a major conformational change in the FAD-binding loop of ACAD9, releasing the FAD cofactor and converting ACAD9 from a fatty acid β-oxidation (FAO) enzyme to a CI assembly factor. We provide evidence that ECSIT phosphorylation downregulates its association with ACAD9 and is reduced in neuronal cells upon exposure to amyloid-β (Aβ) oligomers. These findings advance our understanding of the MCIA complex assembly and suggest a possible role for ECSIT in the reprogramming of bioenergetic pathways linked to Aβ toxicity, a hallmark of AD.

Abstract Serological assays measuring antibodies against SARS-CoV-2 are key to describe the epidemiology, pathobiology or induction of immunity after infection or vaccination. Of those, multiplex assays targeting multiple antigens are especially helpful as closely related coronaviruses or other antigens can be analysed simultaneously from small sample volumes, hereby shedding light on patterns in the immune response that would otherwise remain undetected. We established a bead-based 17-plex assay detecting antibodies targeting antigens from all coronaviruses pathogenic for humans: SARS-CoV-2, SARS-CoV, MERS-CoV, HCoV strains 229E, OC43, HKU1, and NL63. The assay was validated against five commercial serological immunoassays, a commercial surrogate virus neutralisation test, and a virus neutralisation assay, all targeting SARS-CoV-2. It was found to be highly versatile as shown by antibody detection from both serum and dried blot spots and as shown in three case studies. First, we followed seroconversion for all four endemic HCoV strains and SARS-CoV-2 in an outbreak study in day-care centres for children. Second, we were able to link a more severe clinical course to a stronger IgG response with this 17-plex-assay, which was IgG1 and IgG3 dominated. Finally, our assay was able to discriminate recent from previous SARS-CoV-2 infections by calculating the IgG/IgM ratio on the N antigen targeting antibodies. In conclusion, due to the comprehensive method comparison, thorough validation, and the proven versatility, our multiplex assay is a valuable tool for studies on coronavirus serology.

A well-known technique to enhance the signal to noise ratio (SNR) of repetitive signals is to average them. The coherent parts of the signal add up constructively while the incoherent parts are averaged out. The prerequisite is that the signals are acquired under conditions of high repeatability, i.e., the signals must be sufficiently similar. In the present technical note, we describe an efficient method for maintaining signal similarity by ensuring spatial and temporal proximity of laser waveform signals obtained by a sensor operated from an airborne platform. The method makes use of a few auxiliary parameters such as laser pulse repetition rate, mirror rotation rate, platform altitude and flight speed. The method can be extended to be operated in real time.

Rice paddy soils have high organic carbon (OC) storage potential, but predicting OC stocks in these soils is difficult due to the complex OC stabilization mechanisms under fluctuating redox conditions. Especially in temperate climates, these mechanisms remain understudied and comparisons to OC stocks under natural vegetation are scarce. Semi-natural forests could have similar or higher OC inputs than rice paddies, but in the latter mineralization under anoxic conditions and interactions between OC and redox-sensitive minerals (in particular Fe oxyhydroxides, hereafter referred to as Fe oxides) could promote OC stabilization. Moreover, management-induced soil redox cycling in rice paddies can interact with pre-existing pedogenetic differences of soils having different degrees of evolution. To disentangle these drivers of soil OC stocks, we focused on a soil age gradient in Northern Italy with a long (30 + years) history of rice cultivation and remnant semi-natural forests. Irrespective of soil age, soils under semi-natural forest and paddy land-use showed comparable OC stocks. While, in topsoil, stocks of crystalline Fe and short-ranged Fe and Al oxides did not differ between land-uses, under paddy management more OC was found in the mineral-associated fraction. This hints to a stronger redox-driven OC stabilization in the paddy topsoil compared to semi-natural forest soils that might compensate for the presumed lower OC inputs under rice cropping. Despite the higher clay contents over the whole profile and more crystalline pedogenetic Fe stocks in the topsoil in older soils, OC stocks were higher in the younger soils, in particular in the 50–70 cm layer, where short-range ordered pedogenetic oxides were also more abundant. These patterns might be explained by differences in hydrological flows responsible for the translocation of Fe and dissolved OC to the subsoil, preferentially in the younger, coarse-textured soils. Taken together, these results indicate the importance of the complex interplay between redox-cycling affected by paddy-management and soil-age related hydrological properties.

Abstract Changes in upstream land-use have significantly transformed downstream coastal ecosystems around the globe. Restoration of coastal ecosystems often focuses on local-scale processes, thereby overlooking landscape-scale interactions that can ultimately determine restoration outcomes. Here we use an idealized bio-morphodynamic model, based on estuaries in New Zealand, to investigate the effects of both increased sediment inputs caused by upstream deforestation following European settlement and mangrove removal on estuarine morphology. Our results show that coastal mangrove removal initiatives, guided by knowledge on local-scale bio-morphodynamic feedbacks, cannot mitigate estuarine mud-infilling and restore antecedent sandy ecosystems. Unexpectedly, removal of mangroves enhances estuary-scale sediment trapping due to altered sedimentation patterns. Only reductions in upstream sediment supply can limit estuarine muddification. Our study demonstrates that bio-morphodynamic feedbacks can have contrasting effects at local and estuary scales. Consequently, human interventions like vegetation removal can lead to counterintuitive responses in estuarine landscape behavior that impede restoration efforts, highlighting that more holistic management approaches are needed.

Abstract Disease-causing mutations in genes encoding transcription factors (TFs) can affect TF interactions with their cognate DNA-binding motifs. Whether and how TF mutations impact upon the binding to TF composite elements (CE) and the interaction with other TFs is unclear. Here, we report a distinct mechanism of TF alteration in human lymphomas with perturbed B cell identity, in particular classic Hodgkin lymphoma. It is caused by a recurrent somatic missense mutation c.295 T > C (p.Cys99Arg; p.C99R) targeting the center of the DNA-binding domain of Interferon Regulatory Factor 4 (IRF4), a key TF in immune cells. IRF4-C99R fundamentally alters IRF4 DNA-binding, with loss-of-binding to canonical IRF motifs and neomorphic gain-of-binding to canonical and non-canonical IRF CEs. IRF4-C99R thoroughly modifies IRF4 function by blocking IRF4-dependent plasma cell induction, and up-regulates disease-specific genes in a non-canonical Activator Protein-1 (AP-1)-IRF-CE (AICE)-dependent manner. Our data explain how a single mutation causes a complex switch of TF specificity and gene regulation and open the perspective to specifically block the neomorphic DNA-binding activities of a mutant TF.

Abstract Understanding the complex background of cancer requires genotype-phenotype information in single-cell resolution. Here, we perform long-read single-cell RNA sequencing (scRNA-seq) on clinical samples from three ovarian cancer patients presenting with omental metastasis and increase the PacBio sequencing depth to 12,000 reads per cell. Our approach captures 152,000 isoforms, of which over 52,000 were not previously reported. Isoform-level analysis accounting for non-coding isoforms reveals 20% overestimation of protein-coding gene expression on average. We also detect cell type-specific isoform and poly-adenylation site usage in tumor and mesothelial cells, and find that mesothelial cells transition into cancer-associated fibroblasts in the metastasis, partly through the TGF-β/miR-29/Collagen axis. Furthermore, we identify gene fusions, including an experimentally validated IGF2BP2::TESPA1 fusion, which is misclassified as high TESPA1 expression in matched short-read data, and call mutations confirmed by targeted NGS cancer gene panel results. With these findings, we envision long-read scRNA-seq to become increasingly relevant in oncology and personalized medicine.

Abstract Immunotherapies targeting cancer-specific neoantigens have revolutionized the treatment of cancer patients. Recent evidence suggests that epigenetic therapies synergize with immunotherapies, mediated by the de-repression of endogenous retroviral element (ERV)-encoded promoters, and the initiation of transcription. Here, we use deep RNA sequencing from cancer cell lines treated with DNA methyltransferase inhibitor (DNMTi) and/or Histone deacetylase inhibitor (HDACi), to assemble a de novo transcriptome and identify several thousand ERV-derived, treatment-induced novel polyadenylated transcripts (TINPATs). Using immunopeptidomics, we demonstrate the human leukocyte antigen (HLA) presentation of 45 spectra-validated treatment-induced neopeptides (t-neopeptides) arising from TINPATs. We illustrate the potential of the identified t-neopeptides to elicit a T-cell response to effectively target cancer cells. We further verify the presence of t-neopeptides in AML patient samples after in vivo treatment with the DNMT inhibitor Decitabine. Our findings highlight the potential of ERV-derived neoantigens in epigenetic and immune therapies.

Abstract Age at onset of epilepsy is an important predictor of deterioration in naming ability following epilepsy surgery. In 141 patients with left hemispheric epilepsy and language dominance who received epilepsy surgery at the Epilepsy Centre Erlangen, naming of objects (Boston naming test, BNT) was assessed preoperatively and 6 months postoperatively. Surgical lesions were plotted on postoperative MRI and normalized for statistical analysis using voxel-based lesion-symptom mapping (VBLSM). The correlation between lesion and presence of postoperative naming deterioration was examined varying the considered age range of epilepsy onsets. The VBLSM analysis showed that volumes of cortex areas in the left temporal lobe, which were associated with postoperative decline of naming, increased with each year of later epilepsy onset. In patients with later onset, an increasing left posterior temporobasal area was significantly associated with a postoperative deficit when included in the resection. For late epilepsy onset, the temporomesial expansion also included the left hippocampus. The results underline that early onset of epilepsy is a good prognostic factor for unchanged postoperative naming ability following epilepsy surgery. For later age of epilepsy onset, the extent of the area at risk of postoperative naming deficit at 6 months after surgery included an increasing left temporobasal area which finally also comprised the hippocampus.

Abstract Bats are described as the natural reservoir host for a wide range of viruses. Although an increasing number of bat-associated, potentially human pathogenic viruses were discovered in the past, the full picture of the bat viromes is not explored yet. In this study, the virome composition of Miniopterus phillipsi bats (formerly known as Miniopterus fuliginosus bats in Sri Lanka) inhabiting the Wavul Galge cave, Sri Lanka, was analyzed. To assess different possible excretion routes, oral swabs, feces and urine were collected and analyzed individually by using metagenomic NGS. The data obtained was further evaluated by using phylogenetic reconstructions, whereby a special focus was set on RNA viruses that are typically associated with bats. Two different alphacoronavirus strains were detected in feces and urine samples. Furthermore, a paramyxovirus was detected in urine samples. Sequences related to Picornaviridae, Iflaviridae, unclassified Riboviria and Astroviridae were identified in feces samples and further sequences related to Astroviridae in urine samples. No viruses were detected in oral swab samples. The comparative virome analysis in this study revealed a diversity in the virome composition between the collected sample types which also represent different potential shedding routes for the detected viruses. At the same time, several novel viruses represent first reports of these pathogens from bats in Sri Lanka. The detection of two different coronaviruses in the samples indicates the potential general persistence of this virus species in M. phillipsi bats. Based on phylogenetics, the identified viruses are closely related to bat-associated viruses with comparably low estimation of human pathogenic potential. In further studies, the seasonal variation of the virome will be analyzed to identify possible shedding patterns for particular viruses.

Abstract Successful development of novel therapies requires that clinical trials are conducted in patient cohorts with the highest benefit-to-risk ratio. Population-based biobanks with comprehensive health and genetic data from large numbers of individuals hold promise to facilitate identification of trial participants, particularly when interventions need to start while symptoms are still mild, such as for Alzheimer’s disease (AD). This study describes a process for clinical recall studies from FinnGen. We demonstrate the feasibility to systematically ascertain customized clinical data from FinnGen participants with ICD10 diagnosis of AD or mild cognitive disorder (MCD) in a single-center cross-sectional study testing blood-based biomarkers and cognitive functioning in-person, computer-based and remote. As a result, 19% (27/140) of a pre-specified FinnGen subcohort were successfully recalled and completed the study. Hospital records largely validated registry entries. For 8/12 MCD patients, other reasons than AD were identified as underlying diagnosis. Cognitive measures correlated across platforms, with highest consistencies for dementia screening (r = 0.818) and semantic fluency (r = 0.764), respectively, for in-person versus telephone-administered tests. Glial fibrillary acidic protein (GFAP) (p