Search

Abstract The use of monoclonal antibodies for the control of drug resistant nosocomial bacteria may alleviate a reliance on broad spectrum antimicrobials for treatment of infection. We identify monoclonal antibodies that may prevent infection caused by carbapenem resistant Acinetobacter baumannii. We use human immune repertoire mice (Kymouse platform mice) as a surrogate for human B cell interrogation to establish an unbiased strategy to probe the antibody-accessible target landscape of clinically relevant A. baumannii. After immunisation of the Kymouse platform mice with A. baumannii derived outer membrane vesicles (OMV) we identify 297 antibodies and analyse 26 of these for functional potential. These antibodies target lipooligosaccharide (OCL1), the Oxa-23 protein, and the KL49 capsular polysaccharide. We identify a single monoclonal antibody (mAb1416) recognising KL49 capsular polysaccharide to demonstrate prophylactic in vivo protection against a carbapenem resistant A. baumannii lineage associated with neonatal sepsis mortality in Asia. Our end-to-end approach identifies functional monoclonal antibodies with prophylactic potential against major lineages of drug resistant bacteria accounting for phylogenetic diversity and clinical relevance without existing knowledge of a specific target antigen. Such an approach might be scaled for a additional clinically important bacterial pathogens in the post-antimicrobial era.

Abstract Environmental variability can significantly impact individual survival and reproduction. Meanwhile, high population densities can lead to resource scarcity and increased exposure to parasites and pathogens. Studies with insects can offer valuable insights into eco-immunology, allowing us to explore the connections between these variables. Here we use the moth Anticarsia gemmatalis to examine how increases in population density and immunological challenge during the larval stage shape its investment in immune defence and reproduction. Larvae reared at a high population density exhibited greater lytic activity against bacteria compared to those reared at low density, whilst bacterial challenge (i.e. bacteria-immersed needles) also increased lytic activity. There was no interaction between the variables population density and bacterial challenge, indicating that these are independent. Surprisingly, neither increase in lytic activity carried through to activity in prepupal haemolymph. Rearing of larvae at a high density delayed pupation and decreased pupal weight. The immunological stimulus did not significantly influence pupal development. Lower population density as a larva resulted in greater adult weight, but did not significantly influence lytic activity in the eggs or the number of eggs laid. Negative correlations were found between lytic activity in the eggs and the number of eggs, as well as between adult weight and the number of eggs. Overall, this study demonstrates that high population density and immune challenge trigger increased lytic activity in caterpillars, but this effect is transient, not persisting into later stages. The trade-offs observed, such as delayed pupation and reduced prepupal weights under high density, suggest a balancing act between immune investment and developmental aspects. The findings hint at a short-term adaptive response rather than a sustained strategy. The implications of delayed pupation and smaller adult moths could influence the moth's life history strategy, impacting its role in the ecosystem. Further research tracking larval immune investment and subsequent reproductive success will unveil the evolutionary dynamics of this relationship in changing environments.

Abstract Patients undergoing allogenic hematopoietic stem cell transplantation (allo-HSCT) are highly susceptible to infections. The consequent use of masks on wards for allo-HSCT has been controversial in the past decades and was not common before the COVID-19 pandemic. We retrospectively compared incidence and outcomes of viral respiratory infections during allo-HSCT on our specialized ward between 01/2018 and 09/2020 to the era of FFP2 masking between 10/2020 and 10/2022 covering similar seasons of the year. Each group consisted of 150 matched patients. The usage of FFP2 masks reduced the incidence of viral respiratory infections from 22.1 to 2.1% (p

Abstract The vaginal microbiome of trans men and menopausal women is suspected to be similar due to a lack of estrogen leading to the absence of lactobacilli. However, data are scarce. We performed an analysis of the vaginal microbiome of trans men (n = 25) in comparison to that of menopausal (n = 25) and premenopausal women (n = 25). The vaginal microbiome of trans men and menopausal women showed a higher alpha diversity than that of premenopausal women. Various beta diversity indices (e.g., Bray‒Curtis (Un-)Weigthed Unifrac), showed significant differences in community composition between trans men and premenopausal (p

Abstract Pluripotent mouse embryonic stem cells (ESCs) can differentiate to all germ layers and serve as an in vitro model of embryonic development. To better understand the differentiation paths traversed by ESCs committing to different lineages, we track individual differentiating ESCs by timelapse imaging followed by multiplexed high-dimensional Imaging Mass Cytometry (IMC) protein quantification. This links continuous live single-cell molecular NANOG and cellular dynamics quantification over 5-6 generations to protein expression of 37 different molecular regulators in the same single cells at the observation endpoints. Using this unique data set including kinship history and live lineage marker detection, we show that NANOG downregulation occurs generations prior to, but is not sufficient for neuroectoderm marker Sox1 upregulation. We identify a developmental cell type co-expressing both the canonical Sox1 neuroectoderm and FoxA2 endoderm markers in vitro and confirm the presence of such a population in the post-implantation embryo. RNASeq reveals cells co-expressing SOX1 and FOXA2 to have a unique cell state characterized by expression of both endoderm as well as neuroectoderm genes suggesting lineage potential towards both germ layers.

Abstract The ability to image tissues in three dimensions (3D) with label-free molecular contrast at the mesoscale would be a valuable capability in biology and biomedicine. Here, we introduce Raman spectral projection tomography (RSPT) for volumetric molecular imaging with optical sub-millimeter spatial resolution. We have developed a RSPT imaging instrument capable of providing 3D molecular contrast in transparent and semi-transparent samples. We also created a computational pipeline for multivariate reconstruction to extract label-free spatial molecular information from Raman projection data. Using these tools, we demonstrate imaging and visualization of phantoms of various complex shapes with label-free molecular contrast. Finally, we apply RSPT as a tool for imaging of molecular gradients and extracellular matrix heterogeneities in fixed and living tissue-engineered constructs and explanted native cartilage tissues. We show that there exists a favorable balance wherein employing Raman spectroscopy, with its advantages in live cell imaging and label-free molecular contrast, outweighs the reduction in imaging resolution and blurring caused by diffuse photon propagation. Thus, RSPT imaging opens new possibilities for label-free molecular monitoring of tissues.

Abstract Microbial carbon use efficiency (CUE) affects the fate and storage of carbon in terrestrial ecosystems, but its global importance remains uncertain. Accurately modeling and predicting CUE on a global scale is challenging due to inconsistencies in measurement techniques and the complex interactions of climatic, edaphic, and biological factors across scales. The link between microbial CUE and soil organic carbon relies on the stabilization of microbial necromass within soil aggregates or its association with minerals, necessitating an integration of microbial and stabilization processes in modeling approaches. In this perspective, we propose a comprehensive framework that integrates diverse data sources, ranging from genomic information to traditional soil carbon assessments, to refine carbon cycle models by incorporating variations in CUE, thereby enhancing our understanding of the microbial contribution to carbon cycling.

Abstract Alterations in nuclear structure and function are hallmarks of cancer cells. Little is known about these changes in Cancer-Associated Fibroblasts (CAFs), crucial components of the tumor microenvironment. Loss of the androgen receptor (AR) in human dermal fibroblasts (HDFs), which triggers early steps of CAF activation, leads to nuclear membrane changes and micronuclei formation, independent of cellular senescence. Similar changes occur in established CAFs and are reversed by restoring AR activity. AR associates with nuclear lamin A/C, and its loss causes lamin A/C nucleoplasmic redistribution. AR serves as a bridge between lamin A/C and the protein phosphatase PPP1. Loss of AR decreases lamin-PPP1 association and increases lamin A/C phosphorylation at Ser 301, a characteristic of CAFs. Phosphorylated lamin A/C at Ser 301 binds to the regulatory region of CAF effector genes of the myofibroblast subtype. Expression of a lamin A/C Ser301 phosphomimetic mutant alone can transform normal fibroblasts into tumor-promoting CAFs.

Abstract The North Temperate Lakes Long-Term Ecological Research (NTL-LTER) program has been extensively used to improve understanding of how aquatic ecosystems respond to environmental stressors, climate fluctuations, and human activities. Here, we report on the metagenomes of samples collected between 2000 and 2019 from Lake Mendota, a freshwater eutrophic lake within the NTL-LTER site. We utilized the distributed metagenome assembler MetaHipMer to coassemble over 10 terabases (Tbp) of data from 471 individual Illumina-sequenced metagenomes. A total of 95,523,664 contigs were assembled and binned to generate 1,894 non-redundant metagenome-assembled genomes (MAGs) with ≥50% completeness and ≤10% contamination. Phylogenomic analysis revealed that the MAGs were nearly exclusively bacterial, dominated by Pseudomonadota (Proteobacteria, N = 623) and Bacteroidota (N = 321). Nine eukaryotic MAGs were identified by eukCC with six assigned to the phylum Chlorophyta. Additionally, 6,350 high-quality viral sequences were identified by geNomad with the majority classified in the phylum Uroviricota. This expansive coassembled metagenomic dataset provides an unprecedented foundation to advance understanding of microbial communities in freshwater ecosystems and explore temporal ecosystem dynamics.

Abstract Normal respiratory rates (RR) for children under five in the tropics are well-documented, but data for older children are limited. This study tracked RR changes with age and examined associations with nutritional status and environmental factors. We monitored rural Gambian children aged 6 months to 14 years, recording RR during home visits twice weekly over two rainy seasons. Using a generalized additive model, we constructed RR reference curves, and a linear mixed-effect model identified factors influencing RR. A total of 830 children provided 67,512 RR measurements. Their median age was 6.07 years (interquartile range 4.21–8.55) and 400 (48.2%) were female. Age, stunting, ambient temperature, and time of RR measurement were independent predictors of respiratory rate. Strikingly, children showing signs of illness had greater variability in repeat RR measurements. We constructed a RR reference chart for children aged one to 13 years and proposed a cutoff of > 26 breaths/min for raised RR among children aged > 5 years bridging an important gap in this age group. Although the time of data collection, nutritional status, and ambient temperature were predictors of RR, their effect size is not clinically significant enough to warrant a change in the current WHO guidelines owing to the prevailing uncertainty in the measurement of RR. The finding that RRs between repeat measurements were more variable among children with signs of illness suggests that a single RR measurement may be inadequate to reliably assess the status of sick children—a population in which accurate diagnosis is essential to enable targeted interventions with lifesaving treatment.

Abstract Nitrogen (N) is an important nutrient element needed by cassava for optimum yield and it is a vital component of nucleotides (nucleic acids), enzymes, amino acids (proteins), chlorophyll molecules and hormones, among other essential compounds required for growth and development of cassava. Nitrogen stress is a major cassava production constraint, the study aimed to examine genotype by environment interaction (GEI) effects and fresh root yield stability of 203 diverse cassava clones to identify genotypes with stable performance under low and optimum nitrogen regimes across environments using AMMI and GGE biplot analysis. Experiments were conducted using an augmented block design with three replications for two years in three locations in Nigeria. There were significant differences (p

Abstract In a randomized, controlled study, whole-body electromyostimulation (WB-EMS) was investigated as a promising alternative treatment technique compared to conventional strength training for the management of knee osteoarthritis (OA). Seventy-two overweight participants with symptomatic knee OA were randomly assigned to WB-EMS (n = 36) or a usual care group (UCG, n = 36). For seven months, the WB-EMS group received three times per fortnight a WB-EMS training, while the UCG was prescribed six-times physiotherapeutic treatments. We observed significant effects for the primary outcome “pain”, as determined by the Knee injury and Osteoarthritis Outcome Score (KOOS), with more favourable changes in the WB-EMS group vs UCG (between-group difference 9.0 points, 95%CI 2.9–15.1, p = 0.004). Secondary outcomes, including the other KOOS subscales (symptoms, function in daily living, function in sports/recreational activities and quality of life), 7 day pain diary, hip/leg extensor strength and lower limb function (30s sit-to-stand test), were also statistically significant in favour of the WB-EMS group. Overall, WB-EMS was found to be effective in relieving knee pain symptoms and improving physical function in individuals with symptomatic knee OA compared to usual care treatment. WB-EMS could be used as an alternative therapy in the management of knee OA; particularly for patients that cannot be motivated for conventional training.

Abstract The emergence of the Middle Palaeolithic, and its variability over time and space are key questions in the field of prehistoric archaeology. Many sites have been documented in the south-eastern margins of the Massif central and the middle Rhône valley, a migration path that connects Northern Europe with the Mediterranean. Well-dated, long stratigraphic sequences are essential to understand Neanderthals dynamics and demise, and potential interactions with Homo sapiens in the area, such as the one displayed at the Maras rock shelter (“Abri du Maras”). The site is characterised by exceptional preservation of archaeological remains, including bones dated using radiocarbon (14C) and teeth using electron spin resonance combined with uranium series (ESR/U-series). Optically stimulated luminescence was used to date the sedimentary deposits. By combining the new ages with previous ones using Bayesian modelling, we are able to clarify the occupation time over a period spanning 200,000 years. Between ca. 250 and 40 ka, the site has been used as a long-term residence by Neanderthals, specifically during three interglacial periods: first during marine isotopic stage (MIS) 7, between 247 ± 34 and 223 ± 33 ka, and then recurrently during MIS 5 (between 127 ± 17 and 90 ± 9 ka) and MIS 3 (up to 39,280 cal BP).

Abstract Atherosclerosis is a chronic inflammatory condition of the arteries and represents the primary cause of various cardiovascular diseases. Despite ongoing progress, finding effective anti-inflammatory therapeutic strategies for atherosclerosis remains a challenge. Here, we assessed the potential of molecular magnetic resonance imaging (MRI) to visualize the effects of 01BSUR, an anti-interleukin-1β monoclonal antibody, for treating atherosclerosis in a murine model. Male apolipoprotein E-deficient mice were divided into a therapy group (01BSUR, 2 × 0.3 mg/kg subcutaneously, n = 10) and control group (no treatment, n = 10) and received a high-fat diet for eight weeks. The plaque burden was assessed using an elastin-targeted gadolinium-based contrast probe (0.2 mmol/kg intravenously) on a 3 T MRI scanner. T1-weighted imaging showed a significantly lower contrast-to-noise (CNR) ratio in the 01BSUR group (pre: 3.93042664; post: 8.4007067) compared to the control group (pre: 3.70679168; post: 13.2982156) following administration of the elastin-specific MRI probe (p

Abstract While multiple factors impact disease, artificial intelligence (AI) studies in medicine often use small, non-diverse patient cohorts due to data sharing and privacy issues. Federated learning (FL) has emerged as a solution, enabling training across hospitals without direct data sharing. Here, we present FL-PedBrain, an FL platform for pediatric posterior fossa brain tumors, and evaluate its performance on a diverse, realistic, multi-center cohort. Pediatric brain tumors were targeted due to the scarcity of such datasets, even in tertiary care hospitals. Our platform orchestrates federated training for joint tumor classification and segmentation across 19 international sites. FL-PedBrain exhibits less than a 1.5% decrease in classification and a 3% reduction in segmentation performance compared to centralized data training. FL boosts segmentation performance by 20 to 30% on three external, out-of-network sites. Finally, we explore the sources of data heterogeneity and examine FL robustness in real-world scenarios with data imbalances.

Abstract Collisions of the transcription and replication machineries on the same DNA strand can pose a significant threat to genomic stability. These collisions occur in part due to the formation of RNA-DNA hybrids termed R-loops, in which a newly transcribed RNA molecule hybridizes with the DNA template strand. This study investigated the role of RAD52, a known DNA repair factor, in preventing collisions by directing R-loop formation and resolution. We show that RAD52 deficiency increases R-loop accumulation, exacerbating collisions and resulting in elevated DNA damage. Furthermore, RAD52’s ability to interact with the transcription machinery, coupled with its capacity to facilitate R-loop dissolution, highlights its role in preventing collisions. Lastly, we provide evidence of an increased mutational burden from double-strand breaks at conserved R-loop sites in human tumor samples, which is increased in tumors with low RAD52 expression. In summary, this study underscores the importance of RAD52 in orchestrating the balance between replication and transcription processes to prevent collisions and maintain genome stability.

Abstract The inhibitor of κB (IκB) kinase (IKK) is a central regulator of NF-κB signaling. All IKK complexes contain hetero- or homodimers of the catalytic IKKβ and/or IKKα subunits. Here, we identify a YDDΦxΦ motif, which is conserved in substrates of canonical (IκBα, IκBβ) and alternative (p100) NF-κB pathways, and which mediates docking to catalytic IKK dimers. We demonstrate a quantitative correlation between docking affinity and IKK activity related to IκBα phosphorylation/degradation. Furthermore, we show that phosphorylation of the motif’s conserved tyrosine, an event previously reported to promote IκBα accumulation and inhibition of NF-κB gene expression, suppresses the docking interaction. Results from integrated structural analyzes indicate that the motif binds to a groove at the IKK dimer interface. Consistently, suppression of IKK dimerization also abolishes IκBα substrate binding. Finally, we show that an optimized bivalent motif peptide inhibits NF-κB signaling. This work unveils a function for IKKα/β dimerization in substrate motif recognition.

Abstract A long-held tenet in inositol-lipid signaling is that cleavage of membrane phosphoinositides by phospholipase Cβ (PLCβ) isozymes to increase cytosolic Ca2+ in living cells is exclusive to Gq- and Gi-sensitive G protein-coupled receptors (GPCRs). Here we extend this central tenet and show that Gs-GPCRs also partake in inositol-lipid signaling and thereby increase cytosolic Ca2+. By combining CRISPR/Cas9 genome editing to delete Gαs, the adenylyl cyclase isoforms 3 and 6, or the PLCβ1-4 isozymes, with pharmacological and genetic inhibition of Gq and G11, we pin down Gs-derived Gβγ as driver of a PLCβ2/3-mediated cytosolic Ca2+ release module. This module does not require but crosstalks with Gαs-dependent cAMP, demands Gαq to release PLCβ3 autoinhibition, but becomes Gq-independent with mutational disruption of the PLCβ3 autoinhibited state. Our findings uncover the key steps of a previously unappreciated mechanism utilized by mammalian cells to finetune their calcium signaling regulation through Gs-GPCRs.

Abstract The Permo-Triassic mass extinction was linked to catastrophic environmental changes and large igneous province (LIP) volcanism. In addition to the widespread marine losses, the Permo–Triassic event was the most severe terrestrial ecological crisis in Earth’s history and the only known mass extinction among insects, but the cause of extinction on land remains unclear. In this study, high-resolution Hg concentration records and multiple-archive S-isotope analyses of sediments from the Junggar Basin (China) provide evidence of repeated pulses of volcanic-S (acid rain) and increased Hg loading culminating in a crisis of terrestrial biota in the Junggar Basin coeval with the interval of LIP emplacement. Minor S-isotope analyses are, however, inconsistent with total ozone layer collapse. Our data suggest that LIP volcanism repeatedly stressed end-Permian terrestrial environments in the ~300 kyr preceding the marine extinction locally via S-driven acidification and deposition of Hg, and globally via pulsed addition of CO2.

Abstract The physical characterization of proteins in terms of their sizes, interactions, and assembly states is key to understanding their biological function and dysfunction. However, this has remained a difficult task because proteins are often highly polydisperse and present as multicomponent mixtures. Here, we address this challenge by introducing single-molecule microfluidic diffusional sizing (smMDS). This approach measures the hydrodynamic radius of single proteins and protein assemblies in microchannels using single-molecule fluorescence detection. smMDS allows for ultrasensitive sizing of proteins down to femtomolar concentrations and enables affinity profiling of protein interactions at the single-molecule level. We show that smMDS is effective in resolving the assembly states of protein oligomers and in characterizing the size of protein species within complex mixtures, including fibrillar protein aggregates and nanoscale condensate clusters. Overall, smMDS is a highly sensitive method for the analysis of proteins in solution, with wide-ranging applications in drug discovery, diagnostics, and nanobiotechnology.

Abstract Differences in brain size between the sexes are consistently reported. However, the consequences of this anatomical difference on sex differences in intrinsic brain function remain unclear. In the current study, we investigate whether sex differences in intrinsic cortical functional organization may be associated with differences in cortical morphometry, namely different measures of brain size, microstructure, and the geodesic distance of connectivity profiles. For this, we compute a low dimensional representation of functional cortical organization, the sensory-association axis, and identify widespread sex differences. Contrary to our expectations, sex differences in functional organization do not appear to be systematically associated with differences in total surface area, microstructural organization, or geodesic distance, despite these morphometric properties being per se associated with functional organization and differing between sexes. Instead, functional sex differences in the sensory-association axis are associated with differences in functional connectivity profiles and network topology. Collectively, our findings suggest that sex differences in functional cortical organization extend beyond sex differences in cortical morphometry.

Laser interferometry is a well-established and widely used technique for precise displacement measurements. In a non-contact atomic force microscope (NC-AFM), it facilitates the force measurement by recording the periodic displacement of an oscillating microcantilever. To understand signal generation in a NC-AFM-based Michelson-type interferometer, we evaluate the non-linear response of the interferometer to the harmonic displacement of the cantilever in the time domain. As the interferometer signal is limited in amplitude because of the spatial periodicity of the interferometer light field, an increasing cantilever oscillation amplitude creates an output signal with an increasingly complex temporal structure. By the fit of a model to the measured time-domain signal, all parameters governing the interferometric displacement signal can precisely be determined. It is demonstrated, that such an analysis specifically allows for the calibration of the cantilever oscillation amplitude with 2% accuracy.

Abstract The amount of dust deposited on tree leaves is a cost-effective indicator of air quality. Our aim was to explore the leaf surface deposition, and chlorophyll content of leaves along a road section that started at an intersection, and ended in a less disturbed suburban area in Debrecen, Hungary. We also assessed the impact of meteorological conditions on the amount of deposited dust. Leaf samples were collected in July, and September 2022 from Celtis occidentalis, a frequent species in green urban areas of Debrecen. We found a significant negative correlation between dust deposition, and the distance from the intersection in July. In September, dust deposition decreased considerably compared to July, due to rainfall before the second sampling. Surprisingly, we found a positive correlation between dust deposition and chlorophyll content in July. Our findings suggest that dust deposition on leaves serves as a reliable indicator of traffic intensity, because the excess dust caused by the proximity of vehicle traffic can be detected on the leaf surface. Although, rainfall can disrupt the patterns in dust deposition that have developed over an extended period through wash-off and resuspension. Hence, it is advisable to consider these effects while selecting the sampling time and evaluating the results.

Abstract Uveitis is characterised by breakdown of the blood-retinal barrier (BRB), allowing infiltration of immune cells that mediate intraocular inflammation, which can lead to irreversible damage of the neuroretina and the loss of sight. Treatment of uveitis relies heavily on corticosteroids and systemic immunosuppression due to limited understanding of disease pathogenesis. We performed single-cell RNA-sequencing of retinas, as well as bulk RNA-sequencing of retinal pigment epithelial (RPE) cells from mice with experimental autoimmune uveitis (EAU) versus healthy control. This revealed that the Th1/Th17-driven disease induced strong gene expression changes in response to inflammation in rods, cones, Müller glia and RPE. In particular, Müller glia and RPE cells were found to upregulate expression of chemokines, complement factors, leukocyte adhesion molecules and MHC class II, thus highlighting their contributions to immune cell recruitment and antigen presentation at the inner and outer BRB, respectively. Additionally, ligand-receptor interaction analysis with CellPhoneDB revealed key interactions between Müller glia and T cell / natural killer cell subsets via chemokines, galectin-9 to P4HB/TIM-3, PD-L1 to PD-1, and nectin-2/3 to TIGIT signalling axes. Our findings elucidate mechanisms contributing to breakdown of retinal immune privilege during uveitis and identify novel targets for therapeutic interventions.

Abstract We evaluate deconvolution methods, which infer levels of immune infiltration from bulk expression of tumor samples, through a community-wide DREAM Challenge. We assess six published and 22 community-contributed methods using in vitro and in silico transcriptional profiles of admixed cancer and healthy immune cells. Several published methods predict most cell types well, though they either were not trained to evaluate all functional CD8+ T cell states or do so with low accuracy. Several community-contributed methods address this gap, including a deep learning-based approach, whose strong performance establishes the applicability of this paradigm to deconvolution. Despite being developed largely using immune cells from healthy tissues, deconvolution methods predict levels of tumor-derived immune cells well. Our admixed and purified transcriptional profiles will be a valuable resource for developing deconvolution methods, including in response to common challenges we observe across methods, such as sensitive identification of functional CD4+ T cell states.

Abstract Image-guided percutaneous cryoablation is an established minimally invasive oncologic treatment. We hypothesized that cryoablation may modify the immune microenvironment through direct modulation of the tumor, thereby generating an anti-tumor response in tumors refractory to immune checkpoint inhibition (ICI). In this non-randomized phase II single-center study (NCT03290677), subjects with unresectable melanoma progressing on ICI underwent cryoablation of an enlarging metastasis, and ICI was continued for a minimum of two additional cycles. The primary endpoints were safety, feasibility and tumor response in non-ablated lesions. From May 2018 through July 2020, 17 patients were treated on study. The study met its primary endpoints with the combination strategy found to be safe and feasible with an objective response rate of 23.5% and disease control rate of 41% (4 partial response, 3 stable disease). Our data support further study of this synergistic therapeutic approach.

Abstract The anterior cingulate cortex gyrus (ACCg) has been implicated in prosocial behaviors and reasoning about social cues. While this indicates that ACCg is involved in social behavior, it remains unclear whether ACCg neurons also encode social information during goal-directed actions without social consequences. To address this, we assessed how social information is processed by ACCg neurons in a reward localization task. Here we show that neurons in the ACCg of female rhesus monkeys differentiate the identities of conspecifics in task images, even when identity was task-irrelevant. This was in contrast to the prearcuate cortex (PAC), which has not been strongly linked to social behavior, where neurons differentiated identities in both social and nonsocial images. Many neurons in the ACCg also categorically distinguished social from nonsocial trials, but this encoding was only slightly more common in ACCg compared to the PAC. Together, our results suggest that ACCg neurons are uniquely sensitive to social information that differentiates individuals, which may underlie its role in complex social reasoning.

Abstract Security of modern classical data encryption often relies on computationally hard problems, which can be trivialized with the advent of quantum computers. A potential remedy for this is quantum communication which takes advantage of the laws of quantum physics to provide secure exchange of information. Here, quantum key distribution (QKD) represents a powerful tool, allowing for unconditionally secure quantum communication between remote parties. At the same time, microwave quantum communication is set to play an important role in future quantum networks because of its natural frequency compatibility with superconducting quantum processors and modern near-distance communication standards. To this end, we present an experimental realization of a continuous-variable QKD protocol based on propagating displaced squeezed microwave states. We use superconducting parametric devices for generation and single-shot quadrature detection of these states. We demonstrate unconditional security in our experimental microwave QKD setting. The security performance is shown to be improved by adding finite trusted noise on the preparation side. Our results indicate feasibility of secure microwave quantum communication with the currently available technology in both open-air (up to ~ 80 m) and cryogenic (over 1000 m) conditions.

Abstract Marine phosphatization events cause episodic carbonate fluorapatite (CFA) precipitation on seamounts, and are commonly linked to growth hiatuses in ferromanganese (Fe-Mn) crusts. However, the complete record of these events and their paleoenvironmental significance remains poorly understood, in large part due to poor age constraints. Here, we apply U-Pb dating to CFA in Fe-Mn crusts from Western Pacific seamounts. These data exhibit good alignment with Sr isotope ages, revealing six potential phosphatization events. This established CFA chronology tightens the timespan of phosphatization events and refines the age framework of Fe-Mn crusts. We subsequently utilize a multiproxy approach to demonstrate that the phosphatization events occurred coeval with the expansion of oceanic oxygen minimum zones. The Western Pacific Fe-Mn crusts thus document major perturbations in global oceanic phosphorus cycling, which appear to have been driven by climate-induced increases in primary productivity linked to changes in global ocean circulation.

Abstract The past decade has yielded more biodiversity observations from community science than the past century of traditional scientific collection. This rapid influx of data is promising for overcoming critical biodiversity data shortfalls, but we also have vast untapped resources held in undigitized natural history collections. Yet, the ability of these undigitized collections to fill data gaps, especially compared against the constant accumulation of community science data, remains unclear. Here, we compare how well community science (iNaturalist) observations and digitized herbarium specimens represent the diversity, distributions, and modeling needs of vascular plants in Canada. We find that, despite having only a third as many records, herbarium specimens capture more taxonomic, phylogenetic, and functional diversity and more efficiently capture species’ environmental niches. As such, the digitization of Canada’s 7.3M remaining specimens has the potential to more than quintuple our ability to model biodiversity. In contrast, it would require over 27M more iNaturalist observations to produce similar benefits. Our findings indicate that digitizing Earth’s remaining herbarium specimens is likely an efficient, feasible, and potentially critical investment when it comes to improving our ability to predict and protect biodiversity into the future.

Abstract Deep-water formation in the eastern Subpolar North Atlantic Ocean (eSPNA) and Nordic Seas is crucial for maintaining the lower limb of the Atlantic Meridional Overturning Circulation (AMOC), of consequence for global climate. However, it is still uncertain which processes determine the deep-water formation and how much Atlantic and Arctic waters respectively contribute to the lower limb. To address this, here we used Lagrangian trajectories to diagnose a global eddy-resolving ocean model that agrees well with recent observations highlighting the eSPNA as a primary source of the AMOC lower limb. Comprised of 72% Atlantic waters and 28% Arctic waters, the density and depth of the AMOC lower limb is critically dependent on Atlantic-Arctic mixing, primarily in the vicinity of Denmark Strait. In contrast, Atlantic waters gaining density through air-sea interaction along the eastern periphery of Nordic Seas and not entering the Arctic Ocean make a negligible contribution to the lower limb.

Abstract While recent technical breakthroughs have enabled advances in the description of reefs down to 150 m, the structure and depth zonation of deep-reef communities below 150 m remains largely unknown. Here, we present results from over 10 years of deep-reef fish surveys using human-occupied submersibles at four locations across the Caribbean Sea, constituting one of the only continuous reef-fish surveys from 10 to 480 m (1 site) and 40 to 300 m (3 sites). We identify four vertically stratified deep-reef fish communities between 40 and 300 m bordered by an altiphotic (0–10 m) and a deep-sea (300–480 m) community. We found a strong faunal break around 150 m that separates mesophotic and rariphotic zones and secondary breaks at ~ 70 to 90 m and ~ 180 to 200 m subdividing these zones into upper and lower communities. From 300 to 480 m in Roatán, we found a single fish community dominated by deep-sea families, indicating that the lower boundary of the reef-fish realm occurs at 300 m. No differences were found between communities ranging from 20 to 60 m, suggesting that fishes from the lower altiphotic and upper mesophotic form an ecological continuum. While some variability was observed across sites, the overall depth zonation and key species characterizing depth zones were consistent. Most deep-reef species observed were depth specialists restricted to a single depth zone, but many shallow-reef species extended down to mesophotic depths. Depth segregation among species of a genus was found across ten reef-fish genera and likely constitutes one of the mechanisms driving community distinctiveness and thereby fish diversity across depths.

Abstract Tuberculous meningitis (TBM)—the extrapulmonary form of tuberculosis, is the most severe complication associated with tuberculosis, particularly in infants and children. The gold standard for the diagnosis of TBM requires cerebrospinal fluid (CSF) through lumbar puncture—an invasive sample collection method, and currently available CSF assays are often not sufficient for a definitive TBM diagnosis. Urine is metabolite-rich and relatively unexplored in terms of its potential to diagnose neuroinfectious diseases. We used an untargeted proton magnetic resonance (1H-NMR) metabolomics approach to compare the urine from 32 patients with TBM (stratified into stages 1, 2 and 3) against that from 39 controls in a South African paediatric cohort. Significant spectral bins had to satisfy three of our four strict cut-off quantitative statistical criteria. Five significant biological metabolites were identified—1-methylnicotinamide, 3-hydroxyisovaleric acid, 5-aminolevulinic acid, N-acetylglutamine and methanol—which had no correlation with medication metabolites. ROC analysis revealed that methanol lacked diagnostic sensitivity, but the other four metabolites showed good diagnostic potential. Furthermore, we compared mild (stage 1) TBM and severe (stages 2 and 3) TBM, and our multivariate metabolic model could successfully classify severe but not mild TBM. Our results show that urine can potentially be used to diagnose severe TBM.

Abstract This study addresses the question of the lateral preference of the National Hockey League players. The shooting preference, left or right, was analysed as a function of the origin of four groups of players that are from the USA, Canada, Europe, or Russia. The analysis reveals that the players from the USA are more likely to shoot right than players from other countries. Also, compared to defense players from other groups, defense players from the USA have a higher number of shots per game and a higher goal-to-assist ratio. The study also shows that for wingers shooting left, those playing on the right wing have more goals or points per game than those playing on the left wing; and that European forward players have a better differential (+/−) than American and Canadian forward players. The study reveals the influence of the players’ origin on the preference in a bimanual asymmetric task and the impact of this preference on ice hockey performances.

Abstract 3D printing technologies such as fused filament fabrication (FFF) offer great opportunities to enable the fabrication of complex geometries without access to a workshop or knowledge of machining. By adding filler materials to the raw filaments used for FFF, the material properties of the plastic can be adapted. With the addition of neutron absorbing particles, filaments can be created that enable 3D printing of neutron shielding with arbitrary geometry. Two materials for FFF are presented with different mixing ratios of hexagonal Boron nitride (h-BN) and Polylactic acid (PLA). BNPLA25 with 25 %wt h-BN and BNPLA35 with 35 %wt h-BN are compared to the commercially available Addbor N25 material. To qualify the applicability of BNPLA25 and BNPLA35 as shielding material for neutron instrumentation, such as neutron imaging, we investigated the overall neutron attenuation, the influence of non-optimized print settings, as well as characterized the incoherent neutron scattering and the microstructure using neutron imaging, and time-of-flight small-angle-neutron-scattering. Finally, the tensile strength of the material was determined in standardized tensile tests. The measured neutron attenuation shows excellent agreement with analytical calculations, thus validating both the material composition and the calculation method. Approximately 6 mm (8 mm) BNPLA35 are needed for $$1\times 10^{-3}$$ 1 × 10 - 3 transmission of a cold (thermal) neutron beam. Lack of extrusion due to suboptimal print settings can be compensated by increased thickness, clearly visible defects can be mitigated by 11–18% increase in thickness. Incoherent scattering is shown to be strongly reduced compared to pure PLA. The tensile strength of the material is shown not to be impacted by the h-BN filler. The good agreement between the measured attenuation and calculation, combined with the adoption of safety factor enables the quick and easy development as well as the performance estimation of shielding components. BNPLA is uniquely suited for 3D printing neutron shielding because of the combination of non-abrasive h-BN particles in standard PLA, which results in a filament that can be printed with almost any off-the-shelf printer and virtually no prior experience in 3D printing. This mitigates the slightly lower attenuation observed as compared to filaments containing $${\hbox {B}_{4}}\hbox {C}$$ B 4 C , which is highly abrasive and requires extensive additive manufacturing experience.

Abstract Anelloviruses are nonpathogenic viruses that comprise a major portion of the human virome. Despite being ubiquitous in the human population, anelloviruses (ANVs) remain poorly understood. Basic features of the virus, such as the identity of its capsid protein and the structure of the viral particle, have been unclear until now. Here, we use cryogenic electron microscopy to describe the first structure of an ANV-like particle. The particle, formed by 60 jelly roll domain-containing ANV capsid proteins, forms an icosahedral particle core from which spike domains extend to form a salient part of the particle surface. The spike domains come together around the 5-fold symmetry axis to form crown-like features. The base of the spike domain, the P1 subdomain, shares some sequence conservation between ANV strains while a hypervariable region, forming the P2 subdomain, is at the spike domain apex. We propose that this structure renders the particle less susceptible to antibody neutralization by hiding vulnerable conserved domains while exposing highly diverse epitopes as immunological decoys, thereby contributing to the immune evasion properties of anelloviruses. These results shed light on the structure of anelloviruses and provide a framework to understand their interactions with the immune system.

Abstract The histone-like nucleoid structuring (H-NS) protein is a DNA binding factor, found in gammaproteobacteria, with functional equivalents in diverse microbes. Universally, such proteins are understood to silence transcription of horizontally acquired genes. Here, we identify transposon capture as a major overlooked function of H-NS. Using genome-scale approaches, we show that H-NS bound regions are transposition “hotspots”. Since H-NS often interacts with pathogenicity islands, such targeting creates clinically relevant phenotypic diversity. For example, in Acinetobacter baumannii, we identify altered motility, biofilm formation, and interactions with the human immune system. Transposon capture is mediated by the DNA bridging activity of H-NS and, if absent, more ubiquitous transposition results. Consequently, transcribed and essential genes are disrupted. Hence, H-NS directs transposition to favour evolutionary outcomes useful for the host cell.

Abstract Targeted antineoplastic immunotherapies have achieved remarkable clinical outcomes. However, resistance to these therapies due to target absence or antigen shedding limits their efficacy and excludes tumours from candidacy. To address this limitation, here we engineer an oncolytic rhabdovirus, vesicular stomatitis virus (VSVΔ51), to express a truncated targeted antigen, which allows for HER2-targeting with trastuzumab. The truncated HER2 (HER2T) lacks signaling capabilities and is efficiently expressed on infected cell surfaces. VSVΔ51-mediated HER2T expression simulates HER2-positive status in tumours, enabling effective treatment with the antibody-drug conjugate trastuzumab emtansine in vitro, ex vivo, and in vivo. Additionally, we combine VSVΔ51-HER2T with an oncolytic vaccinia virus expressing a HER2-targeted T-cell engager. This dual-virus therapeutic strategy demonstrates potent curative efficacy in vivo in female mice using CD3+ infiltrate for anti-tumour immunity. Our findings showcase the ability to tailor the tumour microenvironment using oncolytic viruses, thereby enhancing compatibility with “off-the-shelf” targeted therapies.

Abstract Alleviating water scarcity is at the core of Sustainable Development Goal 6. Yet the timing of water scarcity in its onset and possible relief in different regions of the world due to climate change and changing human population dynamics remains poorly investigated. Here we assess the timing of the first emergence of water scarcity (FirstWS) and disappearance of water scarcity (EndWS), by using ensembles of simulations with six Global Hydrological Models under two representative concentration pathways (i.e., RCP2.6, RCP6.0) combined with two shared socioeconomic pathways (i.e., SSP2, SSP3) for 1901–2090. Historically (1901–2020), FirstWS occurred predominantly in Asia (e.g., China and India) and Africa (e.g., East Africa); the peak time of emerging water scarcity began around the 1980s. Under all the four future RCPs-SSPs scenarios (2021–2090), FirstWS will likely occur mainly in some regions of Africa, for which the newly added area is double that in Asia. On the other hand, EndWS will mostly occur in China after 2050, primarily due to the projected declining population. We, therefore, call for specific attention and effort to adapt to the looming water scarcity in Africa.

Abstract Spatially resolved transcriptomics has revolutionized RNA studies by aligning RNA abundance with tissue structure, enabling direct comparisons between histology and gene expression. Traditional approaches to identifying signature genes often involve preliminary data grouping, which can overlook subtle expression patterns in complex tissues. We present Spatial Gradient Screening, an algorithm which facilitates the supervised detection of histology-associated gene expression patterns without prior data grouping. Utilizing spatial transcriptomic data along with single-cell deconvolution from injured mouse cortex, and TCR-seq data from brain tumors, we compare our methodology to standard differential gene expression analysis. Our findings illustrate both the advantages and limitations of cluster-free detection of gene expression, offering more profound insights into the spatial architecture of transcriptomes. The algorithm is embedded in SPATA2, an open-source framework written in R, which provides a comprehensive set of tools for investigating gene expression within tissue.

Abstract CRISPR/Cas-based transcriptional activators can be enhanced by intrinsically disordered regions (IDRs). However, the underlying mechanisms are still debatable. Here, we examine 12 well-known IDRs by fusing them to the dCas9-VP64 activator, of which only seven can augment activation, albeit independently of their phase separation capabilities. Moreover, modular domains (MDs), another class of multivalent molecules, though ineffective in enhancing dCas9-VP64 activity on their own, show substantial enhancement in transcriptional activation when combined with dCas9-VP64-IDR. By varying the number of gRNA binding sites and fusing dCas9-VP64 with different IDRs/MDs, we uncover that optimal, rather than maximal, cis-trans cooperativity enables the most robust activation. Finally, targeting promoter-enhancer pairs yields synergistic effects, which can be further amplified via enhancing chromatin interactions. Overall, our study develops a versatile platform for efficient gene activation and sheds important insights into CRIPSR-based transcriptional activators enhanced with multivalent molecules.

Abstract Determining sex-bias in brain structure is of great societal interest to improve diagnostics and treatment of brain-related disorders. So far, studies on sex-bias in brain structure predominantly focus on macro-scale measures, and often ignore factors determining this bias. Here we study sex-bias in cortical and hippocampal microstructure in relation to sex hormones. Investigating quantitative intracortical profiling in-vivo using the T1w/T2w ratio in 1093 healthy females and males of the cross-sectional Human Connectome Project young adult sample, we find that regional cortical and hippocampal microstructure differs between males and females and that the effect size of this sex-bias varies depending on self-reported hormonal status in females. Microstructural sex-bias and expression of sex hormone genes, based on an independent post-mortem sample, are spatially coupled. Lastly, sex-bias is most pronounced in paralimbic areas, with low laminar complexity, which are predicted to be most plastic based on their cytoarchitectural properties. Albeit correlative, our study underscores the importance of incorporating sex hormone variables into the investigation of brain structure and plasticity.

Abstract A large-scale biophysical network model for the isolated striatal body is developed to optimise potential intrastriatal deep brain stimulation applied to, e.g. obsessive-compulsive disorder. The model is based on modified Hodgkin–Huxley equations with small-world connectivity, while the spatial information about the positions of the neurons is taken from a detailed human atlas. The model produces neuronal spatiotemporal activity patterns segregating healthy from pathological conditions. Three biomarkers were used for the optimisation of stimulation protocols regarding stimulation frequency, amplitude and localisation: the mean activity of the entire network, the frequency spectrum of the entire network (rhythmicity) and a combination of the above two. By minimising the deviation of the aforementioned biomarkers from the normal state, we compute the optimal deep brain stimulation parameters, regarding position, amplitude and frequency. Our results suggest that in the DBS optimisation process, there is a clear trade-off between frequency synchronisation and overall network activity, which has also been observed during in vivo studies.

Abstract Adenoid cystic carcinoma (AdCC) is a salivary gland neoplasm that infrequently appears in the sinonasal region. The aim of this study was to evaluate the outcome and clinicopathological parameters of sinonasal AdCC. A retrospective analysis was conducted on all cases of AdCC affecting the nasal cavity or paranasal sinuses between 2000 and 2018 at the University Hospital Zurich. Tumor material was examined for morphological features and analyzed for molecular alterations. A total of 14 patients were included. Mean age at presentation was 57.7 years. Sequencing revealed MYB::NFIB gene fusion in 11/12 analyzable cases. Poor prognostic factors were solid variant (p 30%), high-grade transformation, and sphenoid sinus involvement are negative prognostic factors for sinonasal AdCC. A high prevalence of MYB::NFIB gene fusion may help to correctly classify diagnostically challenging (e.g. metatypical) cases.

Abstract While magnetomyography (MMG) using optically pumped magnetometers (OPMs) is a promising method for non-invasive investigation of the neuromuscular system, it has almost exclusively been performed in magnetically shielded rooms (MSRs) to date. MSRs provide extraordinary conditions for biomagnetic measurements but limit the widespread adoption of measurement methods due to high costs and extensive infrastructure. In this work, we address this issue by exploring the feasibility of mobile OPM-MMG in a setup of commercially available components. From field mapping and simulations, we find that the employed zero-field OPM can operate within a large region of the mobile shield, beyond which residual magnetic fields and perturbations become increasingly intolerable. Moreover, with digital filtering and moderate averaging a signal quality comparable to that in a heavily shielded MSR is attained. These findings facilitate practical and cost-effective implementations of OPM-MMG systems in clinical practice and research.

Abstract Our prototype system designed for clinical data acquisition and recording of studies is a novel electronic data capture (EDC) software for simple and lightweight data capture in clinical research. Existing software tools are either costly or suffer from very limited features. To overcome these shortcomings, we designed an EDC software together with a mobile client. We aimed at making it easy to set-up, modifiable, scalable and thereby facilitating research. We wrote the software in R using a modular approach and implemented existing data standards along with a meta data driven interface and database structure. The prototype is an adaptable open-source software, which can be installed locally or in the cloud without advanced IT-knowledge. A mobile web interface and progressive web app for mobile use and desktop computers is added. We show the software’s capability, by demonstrating four clinical studies with over 1600 participants and 679 variables per participant. We delineate a simple deployment approach for a server-installation and indicate further use-cases. The software is available under the MIT open-source license. Conclusively the software is versatile, easily deployable, highly modifiable, and extremely scalable for clinical studies. As an open-source R-software it is accessible, open to community-driven development and improvement in the future.

Abstract To develop a deep learning-based model capable of segmenting the left ventricular (LV) myocardium on native T1 maps from cardiac MRI in both long-axis and short-axis orientations. Models were trained on native myocardial T1 maps from 50 healthy volunteers and 75 patients using manual segmentation as the reference standard. Based on a U-Net architecture, we systematically optimized the model design using two different training metrics (Sørensen-Dice coefficient = DSC and Intersection-over-Union = IOU), two different activation functions (ReLU and LeakyReLU) and various numbers of training epochs. Training with DSC metric and a ReLU activation function over 35 epochs achieved the highest overall performance (mean error in T1 10.6 ± 17.9 ms, mean DSC 0.88 ± 0.07). Limits of agreement between model results and ground truth were from -35.5 to + 36.1 ms. This was superior to the agreement between two human raters (-34.7 to + 59.1 ms). Segmentation was as accurate for long-axis views (mean error T1: 6.77 ± 8.3 ms, mean DSC: 0.89 ± 0.03) as for short-axis images (mean error ΔT1: 11.6 ± 19.7 ms, mean DSC: 0.88 ± 0.08). Fully automated segmentation and quantitative analysis of native myocardial T1 maps is possible in both long-axis and short-axis orientations with very high accuracy.

Abstract Glucagon-like peptide 1 (GLP-1) stimulates insulin secretion and holds significant pharmacological potential. Nevertheless, the regulation of energy homeostasis by centrally-produced GLP-1 remains partially understood. Preproglucagon cells, known to release GLP-1, are found in the olfactory bulb (OB). We show that activating GLP-1 receptors (GLP-1R) in the OB stimulates insulin secretion in response to oral glucose in lean and diet-induced obese male mice. This is associated with reduced noradrenaline content in the pancreas and blocked by an α2-adrenergic receptor agonist, implicating functional involvement of the sympathetic nervous system (SNS). Inhibiting GABAA receptors in the paraventricular nucleus of the hypothalamus (PVN), the control centre of the SNS, abolishes the enhancing effect on insulin secretion induced by OB GLP-1R. Therefore, OB GLP-1-dependent regulation of insulin secretion relies on a relay within the PVN. This study provides evidence that OB GLP-1 signalling engages a top-down neural mechanism to control insulin secretion via the SNS.

Abstract The integration of extrinsic signaling with cell-intrinsic transcription factors can direct progenitor cells to differentiate into distinct cell fates. In the developing Drosophila eye, differentiation of photoreceptors R1–R7 requires EGFR signaling mediated by the transcription factor Pointed, and our single-cell RNA-Seq analysis shows that the same photoreceptors require the eye-specific transcription factor Glass. We find that ectopic expression of Glass and activation of EGFR signaling synergistically induce neuronal gene expression in the wing disc in a Pointed-dependent manner. Targeted DamID reveals that Glass and Pointed share many binding sites in the genome of developing photoreceptors. Comparison with transcriptomic data shows that Pointed and Glass induce photoreceptor differentiation through intermediate transcription factors, including the redundant homologs Scratch and Scrape, as well as directly activating neuronal effector genes. Our data reveal synergistic activation of a multi-layered transcriptional network as the mechanism by which EGFR signaling induces neuronal identity in Glass-expressing cells.

Abstract The yield of pearl millet, a resilient cereal crop crucial for African food security, is severely impacted by the root parasitic weed Striga hermonthica, which requires host-released hormones, called strigolactones (SLs), for seed germination. Herein, we identify four SLs present in the Striga-susceptible line SOSAT-C88-P10 (P10) but absent in the resistant 29Aw (Aw). We generate chromosome-scale genome assemblies, including four gapless chromosomes for each line. The Striga-resistant Aw lacks a 0.7 Mb genome segment containing two putative CARLACTONOIC ACID METHYLTRANSFERASE1 (CLAMT1) genes, which may contribute to SL biosynthesis. Functional assays show that P10CLAMT1b produces the SL-biosynthesis intermediate methyl carlactonoate (MeCLA) and that MeCLA is the precursor of P10-specific SLs. Screening a diverse pearl millet panel confirms the pivotal role of the CLAMT1 section for SL diversity and Striga susceptibility. Our results reveal a reason for Striga susceptibility in pearl millet and pave the way for generating resistant lines through marker-assisted breeding or direct genetic modification.