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Abstract The cerebral cortex extends axonal projections to several subcortical brain regions, including the striatum, thalamus, superior colliculus, and pontine nuclei. Experimental tract-tracing studies have shown that these subcortical projections are topographically organized, reflecting the spatial organization of sensory surfaces and body parts. Several public collections of mouse- and rat- brain tract-tracing data are available, with the Allen mouse brain connectivity atlas being most prominent. There, a large body of image data can be inspected, but it is difficult to combine data from different experiments and compare spatial distribution patterns. To enable co-visualization and comparison of topographical organization in mouse brain cortico-subcortical projections across experiments, we represent axonal labelling data as point data in a common 3D brain atlas space. We here present a collection of point-cloud data representing spatial distribution of corticostriatal, corticothalamic, corticotectal, and corticopontine projections in mice and exemplify how these spatially integrated point data can be used as references for experimental investigations of topographic organization in transgenic mice, and for cross-species comparison with corticopontine projections in rats.

Abstract SABRE is emerging as a fast, simple and low-cost hyperpolarization method because of its ability to regenerate enhanced NMR signals. Generally, SABRE hyperpolarization has been performed predominantly manually, leading to variations in reproducibility and efficiency. Recent advances in SABRE include the development of automated shuttling systems to address previous inconsistencies. However, the operational complexity of such systems and the challenges of integration with existing workflows hinder their widespread adoption. This work presents a fully automated lab workstation based on a benchtop NMR spectrometer, specifically designed to facilitate SABRE of different nuclei across different polarization fields. We demonstrated the capability of this system through a series of routine SABRE experimental protocols, including consecutive SABRE hyperpolarization with high reproducibility (average standard deviation of 1.03%), optimization polarization of 13C nuclei respect to the polarization transfer field, and measurement of polarization buildup rate or decay time across a wide range of magnetic fields. Furthermore, we have iteratively optimized the durations for pulsed SABRE-SHEATH 13C pyruvate. The constructed SABRE workstation offers full automation, high reproducibility, and functional diversification, making it a practical tool for conducting routine SABRE hyperpolarization experiments. It provides a robust platform for high-throughput and reliable SABRE and X-SABRE hyperpolarization studies.

Background: After pylorus-resecting pancreatoduodenectomy (PrPD), delayed gastric emptying (DGE) might partially be attributed to biliary reflux. We investigated whether the incidence of primary DGE is reduced after Roux-en-Y instead of Billroth-II reconstruction. Methods: Patients undergoing PrPD from 2016 to 2019 at a high-volume center were identified. Excluding causes of secondary DGE, we matched patients with Roux-en-Y and Billroth-II reconstruction in a 1:2 ratio and compared primary DGE. Results: In 24 vs. 48 (Roux-en-Y vs. Billroth-II) patients, DGE (grade B/C) incidence (20.8 % vs. 18.8 %; P = 1.000), nasogastric tube requirement (median 2 vs. 2 days; P = 0.844) and time to solid food intake (7 vs. 7 days; P = 0.933) were comparable. Univariable logistic regression showed no association between DGE and Roux-en-Y reconstruction (OR 1.47; P = 0.524), in contrast to age (1.08; P = 0.030) and pancreatic biochemical leak (4.98; P = 0.007). Conclusions: Primary DGE did not differ between Roux-en-Y and Billroth-II reconstruction after PrPD. Instead, age and postoperative pancreatic biochemical leak were associated with higher DGE risk.

Abstract One approach to increasing nuclear magnetic resonance measurement sample throughput is to implement multiple, independent detection sites. However, the presence of radio frequency interference poses a challenge in multi-detector systems, particularly in unshielded coil arrays lacking sufficient electrical isolation. This issue can lead to unwanted coupling of inductive coils, resulting in excitation pulse interference and signal transfer among multiple detection sites. Here we propose a theoretical framework that combines electromagnetic simulation with spin-dynamic calculations. This framework enables the evaluation of coil coupling effects, the design of parallel pulse sequences to mitigate inter-channel coupling, and the separation of composite free induction decays obtained from multiple detectors. The parallel pulse compensation scheme was validated by a 2-channel parallel spectroscopy experiment. These results provide valuable insights for the design of parallel nuclear magnetic resonance hardware and for exploring the limits of parallelization capacity within a fixed magnet system.

Abstract This paper presents a topology optimization approach for the surface flows on variable design domains. Via this approach, the matching between the pattern of a surface flow and the 2-manifold used to define the pattern can be optimized, where the 2-manifold is implicitly defined on another fixed 2-manifold named as the base manifold. The fiber bundle topology optimization approach is developed based on the description of the topological structure of the surface flow by using the differential geometry concept of the fiber bundle. The material distribution method is used to achieve the evolution of the pattern of the surface flow. The evolution of the implicit 2-manifold is realized via a homeomorphous map. The design variable of the pattern of the surface flow and that of the implicit 2-manifold are regularized by two sequentially implemented surface-PDE filters. The two surface-PDE filters are coupled, because they are defined on the implicit 2-manifold and base manifold, respectively. The surface Navier-Stokes equations, defined on the implicit 2-manifold, are used to describe the surface flow. The fiber bundle topology optimization problem is analyzed using the continuous adjoint method implemented on the first-order Sobolev space. Several numerical examples have been provided to demonstrate this approach, where the combination of the viscous dissipation and pressure drop is used as the design objective.

IntroductionAnti-GABABR encephalitis is a rare disease reported to be often associated with tumors. The current study aims to summarize the clinical characteristics, imaging features, treatments, outcomes and explore the potential prognosis risk factors of patients with anti-GABABR encephalitis.MethodsPatients tested positive for anti-GABABR were retrospective studied from a single medical center in China over a period of 3 years. They were followed up for a maximum period of 18 months. Clinical data were summarized and prognostic factors including demographic characteristics, laboratory tests, and neurological functions were compared between survived and deceased patients at 18 months follow-up.ResultsTwenty-six patients, 10 females (38.5%) and 16 males (61.5%), diagnosed with anti-GABABR encephalitis were studied. The median age was 58 years. Of the 23 cases with complete clinical data, their main manifestations were epileptic seizures (65%), mental and behavioral abnormalities (52%), and cognitive impairment (48%). 7 (30.4%) cases had tumors: 5 small cell lung cancer (SCLC), 1 rectum adenocarcinoma (moderately differentiated) and 1 esophageal squamous cell carcinoma. MRI showed 5 (22%) cases had T2 FLAIR increased signals in cortex but with different regions affected. One of the two patients scanned for PET-CT showed hypermetabolism in the left temporal lobe region. The disease course ranged from 5 days to 3 years. 2 patients (one had esophageal carcinoma) without immunotherapy and 3 patients (one had SCLC) that did not response to immunotherapy died soon after diagnosis. 18 patients improved after immunotherapy while 3 (all had SCLC) died after relapses. The prevalence of epileptic seizures and malignancies was significantly lower in the survival group than in the deceased group at 18-months follow-up, the same as the admission mRs score. Serum fibrinogen, cerebrospinal fluid immunoglobulin G quotient, and 24-hour intrathecal synthesis rate were significantly lower in the survival groups as well.ConclusionsCortex T2 FLAIR abnormalities were only observed in a small proportion of anti-GABABR encephalitis patients with heterogeneous MRI phenotypes. High mRS score at admission, epileptic seizures and the presence of a tumor indicated a poor prognosis, while the underlying mechanism of the later two factors should be investigated further.

Objective: Hysterectomy is one of the most common gynaecological procedures. All-cause mortality within 30 days is an important indicator of care quality.The primary objectives of this quality project were to study all-cause 30-day mortality following hysterectomy in Sweden and the impact of age, ASA class, and malignant indication on outcomes. Population and methods: All hysterectomy procedures documented in the Swedish Perioperative Register (SPOR) were included from 2015 to 01-01 until 2021-12-31. Patient demographics and perioperative observations were collected and analysed. Main outcome measure: All-cause 30-day mortality. Results: The study cohort consisted of 25,391 patients with a mean age of 55.0 ± 13.8, and 54 % of patients were ASA I-II. All-cause 30-day mortality was low: only 1 patient died within the first 24 h, and 23 deaths were noted within 30 days among 25,391 procedures studied; equal to a perioperative mortality rate (POMR) 0.09 %. Higher age, higher ASA class, malignant indication, and combined general and neuraxial anaesthesia increased numerical POMR. Elderly (>65-years) and ASA III-IV were associated with significant increased un- and adjusted Odds Ratio for death within 30-days at 4.3 (95%CI 1.3–14.3, p = 0.02) and 15.3 (95%CI 4.8–84.4, p = 0.001) respectively. Conclusions: All-cause 30-day mortality associated with hysterectomy in Sweden during recent years is low with a POMR of 0.09 %. Higher age and more pronounced higher ASA class increased the odds ratio for all-cause 30-day mortality. Further efforts to optimise the perioperative care of elderly and frail patients are important.

Abstract Background Despite progress understanding the mechanisms underlying tumor spread, metastasis remains a clinical challenge. We identified the choline-producing glycerophosphodiesterase, EDI3 and reported its association with metastasis-free survival in endometrial cancer. We also observed that silencing EDI3 slowed cell migration and other cancer-relevant phenotypes in vitro. Recent work demonstrated high EDI3 expression in ER-HER2+ breast cancer compared to the other molecular subtypes. Silencing EDI3 in ER-HER2+ cells significantly reduced cell survival in vitro and decreased tumor growth in vivo. However, a role for EDI3 in tumor metastasis in this breast cancer subtype was not explored. Therefore, in the present work we investigate whether silencing EDI3 in ER-HER2+ breast cancer cell lines alters phenotypes linked to metastasis in vitro, and metastasis formation in vivo using mouse models of experimental metastasis. Methods To inducibly silence EDI3, luciferase-expressing HCC1954 cells were transduced with lentiviral particles containing shRNA oligos targeting EDI3 under the control of doxycycline. The effect on cell migration, adhesion, colony formation and anoikis was determined in vitro, and significant findings were confirmed in a second ER-HER2+ cell line, SUM190PT. Doxycycline-induced HCC1954-luc shEDI3 cells were injected into the tail vein or peritoneum of immunodeficient mice to generate lung and peritoneal metastases, respectively and monitored using non-invasive bioluminescence imaging. Metabolite levels in cells and tumor tissue were analyzed using targeted mass spectrometry and MALDI mass spectrometry imaging (MALDI-MSI), respectively. Results Inducibly silencing EDI3 reduced cell adhesion and colony formation, as well as increased susceptibility to anoikis in HCC1954-luc cells, which was confirmed in SUM190PT cells. No influence on cell migration was observed. Reduced luminescence was seen in lungs and peritoneum of mice injected with cells expressing less EDI3 after tail vein and intraperitoneal injection, respectively, indicative of reduced metastasis. Importantly, mice injected with EDI3-silenced cells survived longer. Closer analysis of the peritoneal organs revealed that silencing EDI3 had no effect on metastatic organotropism but instead reduced metastatic burden. Finally, metabolic analyses revealed significant changes in choline and glycerophospholipid metabolites in cells and in pancreatic metastases in vivo. Conclusions Reduced metastasis upon silencing supports EDI3’s potential as a treatment target in metastasizing ER-HER2+ breast cancer.

Abstract Electron paramagnetic resonance (EPR) spectroscopy stands out as a powerful analytical technique with extensive applications in the fields of biology, chemistry, physics, and material sciences. It proves invaluable for investigating the molecular structure and reaction mechanisms of substances containing unpaired electrons, such as metal complexes, organic and inorganic radicals, and intermediate states in chemical reactions. However, despite their remarkable capabilities, EPR systems face significant limitations in terms of sample throughput, as current commercial systems only target the analysis of one sample at a time. Here we introduce a novel scheme for conducting ultra-high frequency continuous-wave EPR (CW EPR) targeting the EPR spectroscopy of multiple microliter volume samples in parallel. Our proof-of-principle prototype involves two decoupled detection cells equipped with high qualty factor $$Q=104$$ Q = 104 solenoidal coils tuned to 488 and 589 MHz, ensuring a significant frequency gap for effective radio frequency (RF) decoupling between the channels. To further enhance electromagnetic decoupling, an orthogonal alignment of the coils was adopted. The paper further presents an innovative radiofrequency circuit concept that utilizes a single physical RF channel to simultaneously conduct parallel EPR on up to eight cells. Parallel EPR experiments on two BDPA samples, each with a sample volume of 18.3 μL, registered signal-to-noise ratios of 255 and 252 for the two EPR measurement cells, with no observable coupling. The showcased prototype, built using cost-effective commercially available fabrication technology, is readily scalable and represents an initial step with promising potential for advancing sample screening with high-throughput parallel EPR.

Abstract Alzheimer’s disease (AD) is broadly characterized by neurodegeneration, pathology accumulation, and cognitive decline. There is considerable variation in the progression of clinical symptoms and pathology in humans, highlighting the importance of genetic diversity in the study of AD. To address this, we analyze cell composition and amyloid-beta deposition of 6- and 14-month-old AD-BXD mouse brains. We utilize the analytical QUINT workflow- a suite of software designed to support atlas-based quantification, which we expand to deliver a highly effective method for registering and quantifying cell and pathology changes in diverse disease models. In applying the expanded QUINT workflow, we quantify near-global age-related increases in microglia, astrocytes, and amyloid-beta, and we identify strain-specific regional variation in neuron load. To understand how individual differences in cell composition affect the interpretation of bulk gene expression in AD, we combine hippocampal immunohistochemistry analyses with bulk RNA-sequencing data. This approach allows us to categorize genes whose expression changes in response to AD in a cell and/or pathology load-dependent manner. Ultimately, our study demonstrates the use of the QUINT workflow to standardize the quantification of immunohistochemistry data in diverse mice, - providing valuable insights into regional variation in cellular load and amyloid deposition in the AD-BXD model.

Abstract With the nationwide introduction of wastewater treatment the overall water quality improved significantly, but challenges remain, including diffuse pollution, historical sediment contamination and the presence of a multitude of anthropogenic chemical species. The implementation of several EU directives in the twenty-first century led to a stronger focus on improving water and sediment quality and the sustainable management of sediments at river basin scale. Hence, in the last 25 years, not only have the regulatory frameworks significantly changed, but also the scientific backbone of our products, delivered to Germany’s federal ministries, practitioners from the German Waterways and Shipping Administration, German federal states and the public. In this respect, approaches such as non-target screening, multi-element analysis, effect-based methods, novel approaches in microplastic and nanoparticle analysis and the benefits from the increase in digitalization and automation are key methods and processes to face future challenges, especially those connected to the global climate crisis.

Abstract Chronic liver diseases are worldwide on the rise. Due to the rapidly increasing incidence, in particular in Western countries, metabolic dysfunction-associated steatotic liver disease (MASLD) is gaining importance as the disease can develop into hepatocellular carcinoma. Lipid accumulation in hepatocytes has been identified as the characteristic structural change in MASLD development, but molecular mechanisms responsible for disease progression remained unresolved. Here, we uncover in primary hepatocytes from a preclinical model fed with a Western diet (WD) an increased basal MET phosphorylation and a strong downregulation of the PI3K-AKT pathway. Dynamic pathway modeling of hepatocyte growth factor (HGF) signal transduction combined with global proteomics identifies that an elevated basal MET phosphorylation rate is the main driver of altered signaling leading to increased proliferation of WD-hepatocytes. Model-adaptation to patient-derived hepatocytes reveal patient-specific variability in basal MET phosphorylation, which correlates with patient outcome after liver surgery. Thus, dysregulated basal MET phosphorylation could be an indicator for the health status of the liver and thereby inform on the risk of a patient to suffer from liver failure after surgery.

Abstract Background NGAL and Cystatin C (CysC) as biomarkers for the early detection of AKI are subject to both pathophysiological, as well as patient related heterogeneity. The aim of this study was to investigate the timeline of plasma levels of NGAL and CysC during the first seven days of ICU admission in a mixed ICU population and to relate these to AKI severity during ICU stay. Via these means we aimed to bring clarity to the previously reported heterogeneity of these renal biomarkers. Methods Prospective Observation Cohort. Consecutive patients admitted to adult ICU at an academic hospital in the Netherlands between 18-02-2014 and 31-03-2014 were included. Urine output, serum creatinine, plasma NGAL and CysC were recorded during the first seven days of ICU admission. Biomarker expression was analyzed based on KDIGO score and time of AKI diagnosis. Results 335 patients were included, 110 met KDIGO criteria for AKI. NGAL and CysC plasma levels were higher in AKI patients compared to non-AKI, high variability in individual values resulted in 56% of AKI patients having a false negative, and 32% of non-AKI patients having a false positive. Individual biomarker levels were variable, and no pattern based on KDIGO score was observed. Conclusions Plasma NGAL and CysC as biomarkers for the early AKI detection may be subject to pathophysiological, and patient related heterogeneity. Further understanding of individual biomarker profiles may help in their application amongst mixed ICU populations. Trial Registration The need for informed consent was waived by the Institutional Ethical Review Board of the University Medical Center Groningen (METc 2013 − 174) by Prof. dr. W.A. Kamps on May 17th 2013.

Abstract A Lenz lens is an electrically passive conductive element that, when placed in a time-varying magnetic field, acts as a magnetic flux concentrator or a magnetic lens. In the realm of nuclear magnetic resonance (NMR), Lenz lenses have been exploited as electrically passive metallic radiofrequency interposers placed between a sample and a tuned or untuned NMR detector in order to focus the $${B}_1$$ B 1 -field of the detector onto a smaller sample space. Here we explore a novel embodiment of the Lenz lens, which acts as a non-resonant stripline interposer, i.e., the $${B}_1$$ B 1 -field acts along the longitudinal volume of a sample container, such as a capillary or other microfluidic channel that is coincident with the axis of the stripline. The almost vanishing self-resonance of the stripline Lenz lens, at frequencies relevant for NMR, leads to a desirable $${B}_1$$ B 1 -field amplitude that is nearly perfectly uniform across the sample and hence lacking a characteristic sinusoidal modal shape. The action of Lenz’ law ensures that no stray $${B}_1$$ B 1 -field is found outside of the stripline’s active volume. Because the stripline Lenz lens does not rely on its own geometry to achieve resonance, its frequency response is thus widely broadband for field enhancements up to a factor of 11, with only the external driving resonator properties governing the overall resonant behaviour. We explore the use of the stripline Lenz lens with a sub-nanolitre sample volume, readily detecting 4 isotopes with resonances ranging from 125.76 to 500 MHz. The concept holds potential for the NMR study of thin films, small biological samples, as well as the in situ study of battery materials.

Abstract Background Access to HIV testing is crucial for detection, linkage to treatment, and prevention. In less urbanised areas, reliance on general practitioners (GPs) for HIV testing is probable, as sexual health centres (SHC) are mostly located within urbanised areas. Limited insight into individuals undergoing HIV testing stems from sparse standard registration of demographics at GPs. This cross-sectional study aims (1) to assess and compare HIV testing at the GP and SHC, and (2) to assess population- and provider-specific HIV incidence. Methods Individual HIV testing data of GPs and SHC were linked to population register data (aged ≥ 15 years, Rotterdam area, 2015–2019). We reported the proportion HIV tested, and compared GP and SHC testing rates with negative binomial generalised additive models. Data on new HIV diagnoses (2015–2019) from the Dutch HIV Monitoring Foundation relative to the population were used to assess HIV incidence. Results The overall proportion HIV tested was 1.14% for all residents, ranging from 0.41% for ≥ 40-year-olds to 4.70% for Antilleans. The GP testing rate was generally higher than the SHC testing rate with an overall rate ratio (RR) of 1.61 (95% CI: 1.56–1.65), but not for 15-24-year-olds (RR: 0.81, 95% CI: 0.74–0.88). Large differences in HIV testing rate (1.36 to 39.47 per 1,000 residents) and GP-SHC ratio (RR: 0.23 to 7.24) by geographical area were observed. The GPs’ contribution in HIV testing was greater for GP in areas further away from the SHC. In general, population groups that are relatively often tested are also the groups with most diagnoses and highest incidence (e.g., men who have sex with men, non-western). The overall incidence was 10.55 per 100,000 residents, varying from 3.09 for heterosexual men/women to 24.04 for 25–29-year-olds. Conclusions GPs have a pivotal role in HIV testing in less urbanised areas further away from the SHC, and among some population groups. A relatively high incidence often follows relatively high testing rates. Opportunities to improve HIV testing have been found for migrants, lower-educated individuals, in areas less urbanised areas and further away from GP/SHC. Strategies include additional targeted testing, via for example SHC branch locations and outreach activities.

The mechanisms underlying the remarkable capacity of the liver to regenerate are still not completely understood. Particularly, the cross-talk between cytokines and cellular components of the process is of utmost importance because they represent potential avenues for diagnostics and therapeutics. WNT1-inducible-signaling pathway protein 1 (WISP1) is a cytokine member of the CCN family, a family of proteins that play many different roles in liver pathophysiology. WISP1 also belongs to the earliest and strongest upregulated genes in mouse livers after CCl4 intoxication and has recently been shown to be secreted by tumor cells and to bind to type 1 collagen to cause its linearization in vitro and in tumor tissue in vivo. We show that WISP1 expression is strongly induced by TGFβ, a critical cytokine in wound healing processes. Additionally, secretion of WISP1 protein by hepatic stellate is increased in cells upon TGFβ stimulation (~seven-fold increase). Furthermore, WISP1 facilitates the migration of mouse hepatic stellate cells through collagen in vitro. However, in WISP1 knockout mice, no difference in stellate cell accumulation in damaged liver tissue and no influence on fibrosis was obtained, probably because the knockout of WISP1 was compensated by other factors in vivo.

Jimson weed (Datura stramonium L.) is a toxic weed that is occasionally found in fields with common bean (Phaseolus vulgaris L.) for the processing industry. Common bean growers are required to manually remove toxic weeds. If toxic weed plants remain, the standing crop will be rejected. Hence, the implementation of an automatic weed detection system aiding the farmers is badly needed. The overall goal of this study was to investigate if D. stramonium can be located in common bean fields using an unmanned aerial vehicle (UAV)-based ten-band multispectral camera. Therefore four objectives were defined: (I) assessing the spectral discriminative capacity between common bean and D. stramonium by the development and application of logistic regression models; (II) examining the influence of ground sampling distance (GSD) on model performance; and improving model generalization by (III) incorporating the use of vegetation indices and cumulative distribution function (CDF) matching and by (IV) combining spectral data from multiple common bean fields with the use of leave-one-group-out cross-validation (LOGO CV). Logistic regression models were created using data from fields at four different locations in Belgium. Based on the results, it was concluded that common bean and D. stramonium are separable based on multispectral information. A model trained and tested on the data of one location obtained a validation true positive rate and true negative rate of 99% and 95%, respectively. In this study, where D. stramonium had a mean plant size of 0.038 m2 (σ = 0.020), a GSD of 2.1 cm was found to be appropriate. However, the results proved to be location dependent as the model was not able to reliably distinguish D. stramonium in two other datasets. Finally, the use of a LOGO CV obtained the best results. Although small D. stramonium plants were still systematically overlooked and classified as common bean, the model was capable of detecting large D. stramonium plants on three of the four fields. This study emphasizes the variability in reflectance data among different common bean fields and the importance of an independent dataset to test model generalization.

Background: Therapeutic drug monitoring of biological Tumor Necrosis Factor (TNF)-alpha inhibitors is of critical importance. In this study, the performance of practically advantageous chemiluminescent immunoassays of Theradiag, assessing Infliximab and Adalimumab serum concentrations and anti-drug antibodies (ADA) against these biologics, were compared to the Enzyme-Linked Immuno-Sorbent Assays (ELISAs) from Sanquin Diagnostics. Methods: Leftover serum samples (n = 80 for each parameter) from patients treated with Infliximab or Adalimumab were collected. Correlation and agreement analyses for serum concentration and ADAs, respectively, were performed. Both Theradiag ADA assays, an assay targeting both free and bound ADAs and an assay targeting solely free ADAs, were investigated and compared to the Sanquin Diagnostics ADA assay, targeting both free and bound ADAs. Results: Strong positive correlations were observed between the biologic concentration assessment of Infliximab (Spearman’s Rho = 0.91) and Adalimumab (Spearman’s Rho = 0.94). However, there appeared to be significant bias in the Theradiag assay when compared to Sanquin (Infliximab median (Confidence Interval (CI)) = 2.1 (1.7–2.6) µg/mL; Adalimumab median (CI) = 0.8 (0.5–0.9) µg/mL). Agreement analyses showed moderate to good agreement for the Theradiag and Sanquin Diagnostics ADA assays, when detecting both free and bound ADAs, for Infliximab (Cohen’s k = 0.717) and Adalimumab (Cohen’s k = 0.802). In contrast, the Theradiag ADA assay detecting solely free ADAs had zero to poor agreement for Infliximab (Cohen’s k = 0.458) and Adalimumab (Cohen’s k = 0.119), respectively. Conclusions: This study demonstrated strong correlations and good agreement between the Theradiag and Sanquin Diagnostics assays measuring Infliximab and Adalimumab serum concentrations and ADAs, both free and bound, against these biologics. Discordance analyses showed significantly decreased drug concentrations in the solely free assays, indicating that the combined detection of free and bound ADAs better aligns with drug levels.

Alternaria solani is the second most devastating foliar pathogen of potato crops worldwide, causing premature defoliation of the plants. This disease is currently prevented through the regular application of detrimental crop protection products and is guided by early warnings based on weather predictions and visual observations by farmers. To reduce the use of crop protection products, without additional production losses, it would be beneficial to be able to automatically detect Alternaria solani in potato fields. In recent years, the potential of deep learning in precision agriculture is receiving increasing research attention. Convolutional Neural Networks (CNNs) are currently the state of the art, but also come with challenges, especially regarding in-field robustness. This stems from the fact that they are often trained on datasets that are limited in size or have been recorded in controlled environments, not necessarily representative of real-world settings. We collected a dataset consisting of ultra-high-resolution modified RGB UAV-imagery of both symptomatic and non-symptomatic potato crops in the field during various years and disease stages to cover the great variability in agricultural data. We developed a convolutional neural network to perform in-field detection of Alternaria, defined as a binary classification problem. Our model achieves a similar accuracy as several state-of-the-art models for disease detection, but has a much lower inference time, which enhances its practical applicability. By using training data of three consecutive growing seasons (2019, 2020 and 2021) and test data of an independent fourth year (2022), an F1 score of 0.93 is achieved. Furthermore, we evaluate how different properties of the dataset such as its size and class imbalance impact the obtained accuracy.

Abstract Rapid drug development requires a high throughput screening technology. NMR could benefit from parallel detection but is hampered by technical obstacles. Detection sites must be magnetically shimmed to ppb uniformity, which for parallel detection is precluded by commercial shimming technology. Here we show that, by centering a separate shim system over each detector and employing deep learning to cope with overlapping non-orthogonal shimming fields, parallel detectors can be rapidly calibrated. Our implementation also reports the smallest NMR stripline detectors to date, based on an origami technique, facilitating further upscaling in the number of detection sites within the magnet bore.

Abstract The orbitofrontal, posterior parietal, and insular cortices are sites of higher-order cognitive processing implicated in a wide range of behaviours, including working memory, attention guiding, decision making, and spatial navigation. To better understand how these regions contribute to such functions, we need detailed knowledge about the underlying structural connectivity. Several tract-tracing studies have investigated specific aspects of orbitofrontal, posterior parietal and insular connectivity, but a digital resource for studying the cortical and subcortical projections from these areas in detail is not available. We here present a comprehensive collection of brightfield and fluorescence microscopic images of serial coronal sections from 49 rat brain tract-tracing experiments, in which discrete injections of the anterograde tracers biotinylated dextran amine and/or Phaseolus vulgaris leucoagglutinin were placed in the orbitofrontal, parietal, or insular cortex. The images are spatially registered to the Waxholm Space Rat brain atlas. The image collection, with corresponding reference atlas maps, is suitable as a reference framework for investigating the brain-wide efferent connectivity of these cortical association areas.

Abstract Registration of data to a common frame of reference is an essential step in the analysis and integration of diverse neuroscientific data. To this end, volumetric brain atlases enable histological datasets to be spatially registered and analyzed, yet accurate registration remains expertise-dependent and slow. In order to address this limitation, we have trained a neural network, DeepSlice, to register mouse brain histological images to the Allen Brain Common Coordinate Framework, retaining registration accuracy while improving speed by >1000 fold.

Commercial crocodilian farms face significant economic and livestock losses attributed to stress, which may be linked to their adopted husbandry practices. The development of appropriate and modernized husbandry guidelines, particularly those focused on stress mitigation, is impeded by the limited understanding of the crocodilian stress response. Fifteen grower Nile crocodiles were subjected to simulated acute transport stress, with blood samples collected at various intervals post-stress. Plasma levels of corticosterone (CORT), dehydroepiandrosterone (DHEA), adrenaline, and noradrenaline were determined using high-performance liquid chromatography. Glucose and lactate were measured using portable meters and the heterophil-to-lymphocyte ratio (HLR) was determined via differential leucocyte counts. Significant differences were elicited after the stressor, with acute fluctuations observed in the fast-acting catecholamines (adrenaline and noradrenaline) when compared to the baseline. Downstream effects of these catecholamines and CORT appear to be associated with a persistent increase in plasma glucose and HLR. Lactate also showed acute fluctuations over time but returned to the baseline by the final measurement. DHEA, which is used in a ratio with CORT, showed fluctuations over time with an inverted release pattern to the catecholamines. The study highlights the temporal dynamics of physiological markers under acute stress, contributing to our understanding of crocodilian stress and potentially informing improved farming practices for conservation and sustainable management.

Urinary bladder cancer, a smoking and occupation related disease, was subject of several genome-wide association studies (GWAS). However, studies on the course of the disease based on GWAS findings differentiating between muscle invasive bladder cancer (MIBC) and non-muscle invasive bladder cancer (NMIBC) are rare. Thus we investigated 4 single nucleotide polymorphisms (SNPs) detected in GWAS, related to the genes coding for TACC3 (transforming, acidic coiled-coil containing protein 3), for FGFR3 (fibroblast growth factor receptor 3), for PSCA (prostate stem cell antigen) and the genes coding for CBX6 (chromobox homolog 6) and APOBEC3A (apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3A). This study is based on 712 bladder cancer patients and 875 controls from 3 different case control studies in Germany. The 4 SNPs of interest (PSCA rs2294008 and rs2978974, FGFR3-TACC3 rs798766, and CBX6-APOBEC3A rs1014971) were determined by real-time polymerase chain reaction. The distribution of the 4 SNPs does not vary significantly between cases and controls in the entire study group and in the 3 local subgroups, including two former highly industrialized areas and a region without such history. Also, no significant differences in the bladder cancer subgroups of MIBC and NMIBC were observed. The 4 investigated SNPs do not noticeably contribute differently to the bladder cancer risk for the bladder cancer subgroups of MIBC and NMIBC.

Summary Animal studies for embryotoxicity evaluation of potential therapeutics and environmental factors are complex, costly, and time-consuming. Often, studies are not of human relevance because of species differences. In the present study, we recapitulated the process of cardiomyogenesis in human induced pluripotent stem cells (hiPSCs) by modulation of the Wnt signaling pathway to identify a key cardiomyogenesis gene signature that can be applied to identify compounds and/or stress factors compromising the cardiomyogenesis process. Among the 23 tested teratogens and 16 non-teratogens, we identified three retinoids including 13-cis-retinoic acid that completely block the process of cardiomyogenesis in hiPSCs. Moreover, we have identified an early gene signature consisting of 31 genes and associated biological processes that are severely affected by the retinoids. To predict the inhibitory potential of teratogens and non-teratogens in the process of cardiomyogenesis we established the “Developmental Cardiotoxicity Index” (CDI31g) that accurately differentiates teratogens and non-teratogens to do or do not affect the differentiation of hiPSCs to functional cardiomyocytes.

Abstract Brain atlases are important reference resources for accurate anatomical description of neuroscience data. Open access, three-dimensional atlases serve as spatial frameworks for integrating experimental data and defining regions-of-interest in analytic workflows. However, naming conventions, parcellation criteria, area definitions, and underlying mapping methodologies differ considerably between atlases and across atlas versions. This lack of standardized description impedes use of atlases in analytic tools and registration of data to different atlases. To establish a machine-readable standard for representing brain atlases, we identified four fundamental atlas elements, defined their relations, and created an ontology model. Here we present our Atlas Ontology Model (AtOM) and exemplify its use by applying it to mouse, rat, and human brain atlases. We discuss how AtOM can facilitate atlas interoperability and data integration, thereby increasing compliance with the FAIR guiding principles. AtOM provides a standardized framework for communication and use of brain atlases to create, use, and refer to specific atlas elements and versions. We argue that AtOM will accelerate analysis, sharing, and reuse of neuroscience data.

Abstract The human liver has a remarkable capacity to regenerate and thus compensate over decades for fibrosis caused by toxic chemicals, drugs, alcohol, or malnutrition. To date, no protective mechanisms have been identified that help the liver tolerate these repeated injuries. In this study, we revealed dysregulation of lipid metabolism and mild inflammation as protective mechanisms by studying longitudinal multi-omic measurements of liver fibrosis induced by repeated CCl4 injections in mice (n = 45). Based on comprehensive proteomics, transcriptomics, blood- and tissue-level profiling, we uncovered three phases of early disease development—initiation, progression, and tolerance. Using novel multi-omic network analysis, we identified multi-level mechanisms that are significantly dysregulated in the injury-tolerant response. Public data analysis shows that these profiles are altered in human liver diseases, including fibrosis and early cirrhosis stages. Our findings mark the beginning of the tolerance phase as the critical switching point in liver response to repetitive toxic doses. After fostering extracellular matrix accumulation as an acute response, we observe a deposition of tiny lipid droplets in hepatocytes only in the Tolerant phase. Our comprehensive study shows that lipid metabolism and mild inflammation may serve as biomarkers and are putative functional requirements to resist further disease progression.

Abstract Fatty liver disease or the accumulation of fat in the liver, has been reported to affect the global population. This comes with an increased risk for the development of fibrosis, cirrhosis, and hepatocellular carcinoma. Yet, little is known about the effects of a diet containing high fat and alcohol towards epigenetic aging, with respect to changes in transcriptional and epigenomic profiles. In this study, we took up a multi-omics approach and integrated gene expression, methylation signals, and chromatin signals to study the epigenomic effects of a high-fat and alcohol-containing diet on mouse hepatocytes. We identified four relevant gene network clusters that were associated with relevant pathways that promote steatosis. Using a machine learning approach, we predict specific transcription factors that might be responsible to modulate the functionally relevant clusters. Finally, we discover four additional CpG loci and validate aging-related differential CpG methylation. Differential CpG methylation linked to aging showed minimal overlap with altered methylation in steatosis.

Abstract In grating-based X-ray Talbot interferometry, the wave nature of X-ray radiation is exploited to generate phase contrast images of objects that do not generate sufficient contrast in conventional X-ray imaging relying on X-ray absorption. The phase sensitivity of this interferometric technique is proportional to the interferometer length and inversely proportional to the period of gratings. However, the limited spatial coherency of X-rays limits the maximum interferometer length, and the ability to obtain smaller-period gratings is limited by the manufacturing process. Here, we propose a new optical configuration that employs a combination of a converging parabolic micro-lens array and a diverging micro-lens array, instead of a binary phase grating. Without changing the grating period or the interferometer length, the phase signal is enhanced because the beam deflection by a sample is amplified through the array of converging-diverging micro-lens pairs. We demonstrate that the differential phase signal detected by our proposed set-up is twice that of a Talbot interferometer, using the same binary absorption grating, and with the same overall inter-grating distance.

Abstract Primary sclerosing cholangitis (PSC) is a chronic cholestatic liver disease characterized by chronic inflammation and progressive fibrosis of the biliary tree. The majority of PSC patients suffer from concomitant inflammatory bowel disease (IBD), which has been suggested to promote disease development and progression. However, the molecular mechanisms by which intestinal inflammation may aggravate cholestatic liver disease remain incompletely understood. Here, we employ an IBD-PSC mouse model to investigate the impact of colitis on bile acid metabolism and cholestatic liver injury. Unexpectedly, intestinal inflammation and barrier impairment improve acute cholestatic liver injury and result in reduced liver fibrosis in a chronic colitis model. This phenotype is independent of colitis-induced alterations of microbial bile acid metabolism but mediated via hepatocellular NF-κB activation by lipopolysaccharide (LPS), which suppresses bile acid metabolism in-vitro and in-vivo. This study identifies a colitis-triggered protective circuit suppressing cholestatic liver disease and encourages multi-organ treatment strategies for PSC.

Neuroscientists employ a range of methods and generate increasing amounts of data describing brain structure and function. The anatomical locations from which observations or measurements originate represent a common context for data interpretation, and a starting point for identifying data of interest. However, the multimodality and abundance of brain data pose a challenge for efforts to organize, integrate, and analyze data based on anatomical locations. While structured metadata allow faceted data queries, different types of data are not easily represented in a standardized and machine-readable way that allow comparison, analysis, and queries related to anatomical relevance. To this end, three-dimensional (3D) digital brain atlases provide frameworks in which disparate multimodal and multilevel neuroscience data can be spatially represented. We propose to represent the locations of different neuroscience data as geometric objects in 3D brain atlases. Such geometric objects can be specified in a standardized file format and stored as location metadata for use with different computational tools. We here present the Locare workflow developed for defining the anatomical location of data elements from rodent brains as geometric objects. We demonstrate how the workflow can be used to define geometric objects representing multimodal and multilevel experimental neuroscience in rat or mouse brain atlases. We further propose a collection of JSON schemas (LocareJSON) for specifying geometric objects by atlas coordinates, suitable as a starting point for co-visualization of different data in an anatomical context and for enabling spatial data queries.

Abstract Balenine possesses some of carnosine’s and anserine’s functions, yet it appears more resistant to the hydrolysing CN1 enzyme. The aim of this study was to elucidate the stability of balenine in the systemic circulation and its bioavailability in humans following acute supplementation. Two experiments were conducted in which (in vitro) carnosine, anserine and balenine were added to plasma to compare degradation profiles and (in vivo) three increasing doses (1–4–10 mg/kg) of balenine were acutely administered to 6 human volunteers. Half-life of balenine (34.9 ± 14.6 min) was respectively 29.1 and 16.3 times longer than that of carnosine (1.20 ± 0.36 min, p = 0.0044) and anserine (2.14 ± 0.58 min, p = 0.0044). In vivo, 10 mg/kg of balenine elicited a peak plasma concentration (Cmax) of 28 µM, which was 4 and 18 times higher than with 4 (p = 0.0034) and 1 mg/kg (p = 0.0017), respectively. CN1 activity showed strong negative correlations with half-life (ρ = − 0.829; p = 0.0583), Cmax (r = − 0.938; p = 0.0372) and incremental area under the curve (r = − 0.825; p = 0.0433). Overall, balenine seems more resistant to CN1 hydrolysis resulting in better in vivo bioavailability, yet its degradation remains dependent on enzyme activity. Although a similar functionality as carnosine and anserine remains to be demonstrated, opportunities arise for balenine as nutraceutical or ergogenic aid.

Abstract The ability of Timm’s sulphide silver method to stain zincergic terminal fields has made it a useful neuromorphological marker. Beyond its roles in zinc-signalling and neuromodulation, zinc is involved in the pathophysiology of ischemic stroke, epilepsy, degenerative diseases and neuropsychiatric conditions. In addition to visualising zincergic terminal fields, the method also labels transition metals in neuronal perikarya and glial cells. To provide a benchmark reference for planning and interpretation of experimental investigations of zinc-related phenomena in rat brains, we have established a comprehensive repository of serial microscopic images from a historical collection of coronally, horizontally and sagittally oriented rat brain sections stained with Timm’s method. Adjacent Nissl-stained sections showing cytoarchitecture, and customised atlas overlays from a three-dimensional rat brain reference atlas registered to each section image are included for spatial reference and guiding identification of anatomical boundaries. The Timm-Nissl atlas, available from EBRAINS, enables experimental researchers to navigate normal rat brain material in three planes and investigate the spatial distribution and density of zincergic terminal fields across the entire brain.

Abstract Background Patients infrequently mobilize at the surgical ward after cardiac surgery. Inactivity results in prolonged hospital stay, readmissions and increased cardiovascular mortality. Next, the course of in-hospital mobilization activities for patients is unclear. The aim was to evaluate early mobilization after heart surgery with a mobilization poster on the Activity Classification Guide for Inpatient Activities score from the American College for Sports Medicine (ACSM). Second, to develop a Thorax Centrum Twente (TCT) score to assess distinctive activities performed. Methods A poster was developed for the Moving is Improving! study to stimulate hospital mobilization after heart surgery. In this sequential-group study at a cardiothoracic surgery ward, 32 patients were included in the usual care group and 209 patients in the poster mobilization group. Change of ACSM and TCT scores over time were both defined as primary endpoints. Secondary endpoints included length of stay and survival. A subgroup analysis for coronary artery bypass grafting (CABG) was performed. Results ACSM score increased during hospital stay (p

Abstract Introduction Soil degradation coupled with poor access to organic nutrient resources remains a major constraint in increased crop productivity in sub‐Saharan Africa, thus hindering the continent's efforts in achieving the United Nations' Sustainable Development Goals, particularly goals 1 (end poverty), 2 (zero hunger) and 3 (improve human health). Water treatment residual (WTR), a by‐product of clean water treatment, has been identified as an alternative organic nutrient resource for crop production. However, there are some inconsistences in soil phosphorus (P) dynamics following aluminium WTR (Al‐WTR) application. Materials & Methods A laboratory experiment was conducted to evaluate the P sorption of a sandy soil amended with 10% Al‐WTR, 10% compost (C) as a quasi‐control, 10% C + 10% Al‐WTR (10% coamendment) and 5% C + 5% Al‐WTR (5% coamendment) under varying levels of pH, particle size and P concentration. We calculated crop P fertilizer requirements under different amendments. Results The results demonstrated that all amendments exceeded the minimum of 0.2 mg P L−1 needed in soil solution at equilibrium to maintain plant growth. However, the maximum P sorption capacity was higher for 10% Al‐WTR single amendment, ranging from 770 to 1000 mg P Kg−1, and from 714 to 1000 mg P Kg−1 and 555 to 909 mg P Kg−1 for 10% and 5% coamendments, respectively, across a range of pH and soil particle size fractions. The coamendments showed a reduction in crop P fertilizer requirements by ranges of 30–60% and 60–70% for the 10% and 5% coamendment levels, respectively, across different pH and particle sizes, relative to 10% Al‐WTR. Conclusion Results show that the use of 5% coamendment in sandy soils increases P availability sufficiently to improve crop yields. The results provide scope for using Al‐WTR coamendments to rebuild soil health in sandy soils in urban agriculture and increase macronutrient provision in crops to support human health.

Precancerous cells in the oral cavity may appear as oral potentially malignant disorders, but they may also present as dysplasia without visual manifestation in tumor-adjacent tissue. As it is currently not possible to prevent the malignant transformation of these oral precancers, new treatments are urgently awaited. Here, we generated precancer culture models using a previously established method for the generation of oral keratinocyte cultures and incorporated CRISPR/Cas9 editing. The generated cell lines were used to investigate the efficacy of a set of small molecule inhibitors. Tumor-adjacent mucosa and oral leukoplakia biopsies were cultured and genetically characterized. Mutations were introduced in CDKN2A and TP53 using CRISPR/Cas9 and combined with the ectopic activation of telomerase to generate cell lines with prolonged proliferation. The method was tested in normal oral keratinocytes and tumor-adjacent biopsies and subsequently applied to a large set of oral leukoplakia biopsies. Finally, a subset of the immortalized cell lines was used to assess the efficacy of a set of small molecule inhibitors. Culturing and genomic engineering was highly efficient for normal and tumor-adjacent oral keratinocytes, but success rates in oral leukoplakia were remarkably low. Knock-out of CDKN2A in combination with either the activation of telomerase or knock-out of TP53 seemed a prerequisite for immortalization. Prolonged culturing was accompanied by additional genetic aberrations in these cultures. The generated cell lines were more sensitive than normal keratinocytes to small molecule inhibitors of previously identified targets. In conclusion, while very effective for normal keratinocytes and tumor-adjacent biopsies, the success rate of oral leukoplakia cell culturing methods was very low. Genomic engineering enabled the prolonged culturing of OL-derived keratinocytes but was associated with acquired genetic changes. Further studies are required to assess to what extent the immortalized cultures faithfully represent characteristics of the cells in vivo.

This work presents anodically electrodeposited copper (Cu)/chitosan gel as a novel precursor for synthesizing a Cu/carbon nanocomposite through laser-induced carbonization. Metal/carbon nanocomposites offering advantageous properties compared to their individual counterparts stand out in various applications, particularly in those involving electrochemical phenomena. However, their synthesis often suffers from complicated and time-consuming synthesis procedures. Here, we integrate anodic electrodeposition and laser-induced carbonization to yield a rapid, simple, and inexpensive procedure for synthesizing metal/carbon nanocomposite. A precursor composite involving Cu-coordinated chitosan film is achieved through anodic electrodeposition on a copper anode. Irradiation by an infrared laser with optimized parameters results in the thermochemical decomposition of the Cu/chitosan composite, rapidly forming a nanocomposite material featuring highly graphitized and porous carbon materials. Elemental mapping confirms the formation of the nanocomposite, although no crystalline phases of copper are observed during X-ray diffraction. This can be attributed to the rapid nature of the laser-carbonization process. The nanocomposite material is further demonstrated for electrochemical sensing of hydrogen peroxide (H2O2), exhibiting a sensitivity of 2.65 mM−1 for concentrations ranging from 0.01 mM to 0.1 mM H2O2, and 0.01 ± 0.01 mM−1 for concentrations from 0.1 to 10 mM H2O2. These sensitivities are comparable to other non-enzymatic H2O2 biosensors. The finding of this work signifies a rapid and facile method for synthesizing metal/carbon nanocomposites with strong implications for the field of biosensors.

Rationale: Liver cirrhosis is known to affect drug pharmacokinetics, but the functional assessment of the underlying pathophysiological alterations in drug metabolism is difficult.Methods: Cirrhosis in mice was induced by repeated treatment with carbon tetrachloride for 12 months. A cocktail of six drugs was administered, and parent compounds as well as phase I and II metabolites were quantified in blood, bile, and urine in a time-dependent manner. Pharmacokinetics were modeled in relation to the altered expression of metabolizing enzymes. In discrepancy with computational predictions, a strong increase of glucuronides in blood was observed in cirrhotic mice compared to vehicle controls.Results: The deviation between experimental findings and computational simulations observed by analyzing different hypotheses could be explained by increased sinusoidal export and corresponded to increased expression of export carriers (Abcc3 and Abcc4). Formation of phase I metabolites and clearance of the parent compounds were surprisingly robust in cirrhosis, although the phase I enzymes critical for the metabolism of the administered drugs in healthy mice, Cyp1a2 and Cyp2c29, were downregulated in cirrhotic livers. RNA-sequencing revealed the upregulation of numerous other phase I metabolizing enzymes which may compensate for the lost CYP isoenzymes. Comparison of genome-wide data of cirrhotic mouse and human liver tissue revealed similar features of expression changes, including increased sinusoidal export and reduced uptake carriers.Conclusion: Liver cirrhosis leads to increased blood concentrations of glucuronides because of increased export from hepatocytes into the sinusoidal blood. Although individual metabolic pathways are massively altered in cirrhosis, the overall clearance of the parent compounds was relatively robust due to compensatory mechanisms.

The recent development of high-throughput workflows in genomics and transcriptomics revealed that efficient annotation of such results is essential for researchers to draw conclusions from obtained results. Although some tools are available, their functionality is limited. Here, we present AGouTI-a universal tool for flexible annotation of any genomic or transcriptomic coordinates using known genomic features deposited in different publicly available databases in the form of GTF or GFF files. In contrast to currently available tools, AGouTI is designed to provide a flexible selection of genomic features overlapping or adjacent to annotated intervals and can be used on custom column-based text files obtained from different data analysis pipelines. Although providing many unique options, AGouTI is straightforward in installation and usage, enabling effortless integration into existing data analysis workflows.

IntroductionDespite optimal treatment, patients with chronic coronary artery disease (CAD) and diabetes mellitus (DM) are at high risk of cardiovascular events, emphasizing the need for new treatment options. The Low-Dose Colchicine 2 (LoDoCo2) trial demonstrated that colchicine reduces cardiovascular risk in patients with chronic CAD. This analysis determines the efficacy of colchicine in patients with chronic CAD and DM as well as the effect of colchicine on the development of new-onset type 2 diabetes mellitus (T2DM).MethodsThe LoDoCo2 trial randomized 5,522 patients to placebo or colchicine 0.5 mg once daily, with a median follow-up of 28.6 months. The primary composite endpoint was cardiovascular death, spontaneous myocardial infarction, ischemic stroke, or ischemia-driven revascularization. The effect of its treatment in patients with and without DM was evaluated by including an interaction term in the model.ResultsA total of 1,007 participants (18.2%) had T2DM at baseline. The adjusted hazard ratio (HR) [(95% confidence interval (CI)] for the primary endpoint in the T2DM group was 1.52 (1.15–2.01, p

We report on a portable dielectrophoresis manipulation platform, for the positioning and immobilization of small dielectric objects, such as cells or microbes, using a circular array of up to six symmetrically arranged and independently controllable micro-electrodes. The system’s micro-controller-instructed electronic drivers can be operated in three distinct modes. We demonstrate the system’s function by actuating bacterial cells to specific locations and orientations within a region of interest. Using a deep learning approach, we map voltage phase combinations of the six electrodes to geometrical trap position locations, thereby facilitating smooth trajectory planning.

The design methods for gradient coils are mostly based on discrete extrinsic methods (e.g., the Biot–Savart integration calculation), for which the surface normal vector strongly influences any numerical calculation of the discretized surface. Previous studies are mostly based on regular or analytical surfaces, which allow normal vectors to be expressed analytically. For certain applications, design methods for extending current-carrying surfaces from developable or analytic geometries to arbitrary surfaces generated from a scanned point cloud are required. The key task is to correctly express the discretized normal vectors to ensure geometrical accuracy of the designed coils. Mathematically, it has been proven that applying a Delaunay triangulation to approximate a smooth surface can result in the discrete elemental normal vectors converging to those of the original surface. Accordingly, this article uses Delaunay triangulation to expand upon previous design methods so that they encompass arbitrary piecewise continuous surfaces. Two design methods, the stream function and the so-called solid isotropic material with penalization (SIMP) method, are used to design circumvolute and noncircumvolute gradient coils on general surfaces.

Abstract The experience of adversity in childhood has been associated with poor health outcomes in adulthood. In search of the biological mechanisms underlying these effects, research so far focused on alterations of DNA methylation or shifts in transcriptomic profiles. The level of protein, however, has been largely neglected. We utilized mass spectrometry to investigate the proteome of CD14+ monocytes in healthy adults reporting childhood adversity and a control group before and after psychosocial stress exposure. Particular proteins involved in (i) immune processes, such as neutrophil-related proteins, (ii) protein metabolism, or (iii) proteins related to mitochondrial biology, such as those involved in energy production processes, were upregulated in participants reporting exposure to adversity in childhood. This functional triad was further corroborated by protein interaction- and co-expression analyses, was independent of stress exposure, i.e. observed at both pre- and post-stress time points, and became evident especially in females. In line with the mitochondrial allostatic load model, our findings provide evidence for the long-term effects of childhood adversity on mitochondrial biology.

Abstract Background Intrinsic or acquired resistance to HER2-targeted therapy is often a problem when small molecule tyrosine kinase inhibitors or antibodies are used to treat patients with HER2 positive breast cancer. Therefore, the identification of new targets and therapies for this patient group is warranted. Activated choline metabolism, characterized by elevated levels of choline-containing compounds, has been previously reported in breast cancer. The glycerophosphodiesterase EDI3 (GPCPD1), which hydrolyses glycerophosphocholine to choline and glycerol-3-phosphate, directly influences choline and phospholipid metabolism, and has been linked to cancer-relevant phenotypes in vitro. While the importance of choline metabolism has been addressed in breast cancer, the role of EDI3 in this cancer type has not been explored. Methods EDI3 mRNA and protein expression in human breast cancer tissue were investigated using publicly-available Affymetrix gene expression microarray datasets (n = 540) and with immunohistochemistry on a tissue microarray (n = 265), respectively. A panel of breast cancer cell lines of different molecular subtypes were used to investigate expression and activity of EDI3 in vitro. To determine whether EDI3 expression is regulated by HER2 signalling, the effect of pharmacological inhibition and siRNA silencing of HER2, as well as the influence of inhibiting key components of signalling cascades downstream of HER2 were studied. Finally, the influence of silencing and pharmacologically inhibiting EDI3 on viability was investigated in vitro and on tumour growth in vivo. Results In the present study, we show that EDI3 expression is highest in ER-HER2 + human breast tumours, and both expression and activity were also highest in ER-HER2 + breast cancer cell lines. Silencing HER2 using siRNA, as well as inhibiting HER2 signalling with lapatinib decreased EDI3 expression. Pathways downstream of PI3K/Akt/mTOR and GSK3β, and transcription factors, including HIF1α, CREB and STAT3 were identified as relevant in regulating EDI3 expression. Silencing EDI3 preferentially decreased cell viability in the ER-HER2 + cells. Furthermore, silencing or pharmacologically inhibiting EDI3 using dipyridamole in ER-HER2 + cells resistant to HER2-targeted therapy decreased cell viability in vitro and tumour growth in vivo. Conclusions Our results indicate that EDI3 may be a potential novel therapeutic target in patients with HER2-targeted therapy-resistant ER-HER2 + breast cancer that should be further explored.

Background Recent studies suggest that acute-combined carnosine and anserine supplementation has the potential to improve the performance of certain cycling protocols. Yet, data on optimal dose, timing of ingestion, effective exercise range, and mode of action are lacking. Three studies were conducted to establish dosing and timing guidelines concerning carnosine and anserine intake and to unravel the mechanism underlying the ergogenic effects. Methods First, a dose response study A was conducted in which 11 men randomly received placebo, 10, 20, or 30 mg.kg−1 of both carnosine and anserine. They performed 3x maximal voluntary isometric contractions (MVC), followed by a 5 x 6 s repeated cycling sprint ability test (RSA), once before the supplement and 30 and 60 minutes after. In a second study, 15 men performed 3x MVCs with femoral nerve electrical stimulation, followed by an RSA test, once before 30 mg.kg−1 carnosine and anserine and 60 minutes after. Finally, in study C, eight men performed a high intensity cycling training after randomly ingesting 30 mg.kg−1 of carnosine and anserine, a placebo or antihistamines (reduce post-exercise blood flow) to investigate effects on muscle perfusion. Results Study A showed a 3% peak power (p = 0.0005; 95% CI = 0.07 to 0.27; ES = 0.91) and 4.5% peak torque (p = 0.0006; 95% CI = 0.12 to 0.50; ES = 0.87) improvement on RSA and MVC, with 30 mg.kg−1 carnosine + anserine ingestion 60 minutes before the performance yielding the best results. Study B found no performance improvement on group level; however, a negative correlation (r = −0.54; p = 0.0053; 95% CI = −0.77 to −0.19) was found between carnosinase enzyme activity (responsible for carnosine and anserine breakdown) and performance improvement. No effect of the supplement on neuromuscular function nor on muscle perfusion was found. Conclusions These studies reveal that acute ingestion of 30 mg.kg−1 of both carnosine and anserine, 60 minutes before a high intensity exercise, can potentially improve performance, such as short cycling sprints or maximal muscle contractions. Subjects with lower carnosinase activity, and thus a slower breakdown of circulating dipeptides, appear to benefit more from this ergogenic effect. Finally, neither the involvement of a direct effect on neuromuscular function, nor an indirect effect on recovery through increased muscle perfusion could be confirmed as potential mechanism of action. The ergogenic mechanism therefore remains elusive.

Abstract Sarcoidosis is a multisystem inflammatory granulomatous disease of unknown cause that most commonly affects lungs and lymph nodes, with frequent yet asymptomatic cardiac involvement. The epidemiologically associated cardiovascular risk suggests an underlying prothrombotic state and endothelial dysfunction, currently understudied in the available literature. Therefore, we aimed to investigate prothrombotic plasma properties together with selected echocardiographic and laboratory biomarkers of cardiovascular injury in that disease. N = 53 patients with pulmonary sarcoidosis in clinical remission and N = 66 matched controls were assessed for inflammatory and endothelial injury biomarkers, plasma thrombin generation profile, and echocardiographic and lung function parameters. Sarcoidosis cases had impaired systolic and diastolic left ventricular function, higher concentrations of inflammatory markers, D-dimer and factor VIII activity compared to the controls. The coexistence of extrapulmonary disease was associated with elevated circulating vascular cell adhesion molecule 1, while cases with hypercalcemia had higher thrombomodulin concentration. Sarcoidosis was characterized by the unfavorably altered thrombin generation profile, reflected by the 16% higher endogenous thrombin potential (ETP), 24% increased peak thrombin concentration, and 12% shorter time to thrombin peak in comparison to the control group. ETP was higher in cases with proxies of pulmonary restriction, extrapulmonary–extracutaneous manifestation, and need for corticosteroids use. Despite the clinical remission, sarcoidosis is related to prothrombotic plasma properties and signs of endothelial injury, likely contributing to the higher risk of cardiovascular events. In addition, subclinical cardiac involvement may play an additional role, although further clinical and experimental studies are needed to verify these findings.

Dolutegravir is a highly potent HIV integrase strand transfer inhibitor that is recommended for first-line anti-retroviral treatment in all major treatment guidelines. A recent study has shown that people taking this class of anti-retroviral treatment have a substantially higher risk of early-onset cardiovascular disease, a condition shown previously to be associated with increased platelet reactivity. To date, few studies have explored the effects of dolutegravir on platelet activation. Accordingly, the current study was undertaken with the primary objective of investigating the effects of dolutegravir on the reactivity of human platelets in vitro. Platelet-rich plasma, isolated platelets, or buffy coat cell suspensions prepared from the blood of healthy adults were treated with dolutegravir (2.5–10 µg/ml), followed by activation with adenosine 5’-diphosphate (ADP), thrombin, or a thromboxane A2 receptor agonist U46619. Expression of platelet CD62P (P-selectin), formation of heterotypic neutrophil:platelet aggregates, and calcium (Ca2+) fluxes were measured using flow cytometry and fluorescence spectrometry, respectively. Dolutegravir caused dose-related potentiation of ADP-, thrombin- and U46619-activated expression of CD62P by platelets, as well as a significant increases in formation of neutrophil:platelet aggregates. These effects were paralleled by a spontaneous, receptor-independent elevation in cytosolic Ca2+ that appears to underpin the mechanism by which the antiretroviral agent augments the responsiveness of these cells to ADP, thrombin and U46619. The most likely mechanism of dolutegravir-mediated increases in platelet cytosolic Ca2+ relates to a combination of lipophilicity and divalent/trivalent metal-binding and/or chelating properties of the anti-retroviral agent. These properties are likely to confer ionophore-type activities on dolutegravir that would promote movement of Ca2+ across the plasma membrane, delivering the cation to the cytosol where it would augment Ca2+-dependent intracellular signaling mechanisms. These effects of dolutegravir may lead to hyper-activation of platelets which, if operative in vivo, may contribute to an increased risk for cardiometabolic co-morbidities.

Abstract Background Non-resectability is common in patients with pancreatic ductal adenocarcinoma (PDAC) due to local invasion or distant metastases. Then, biliary or gastroenteric bypasses or both are often established despite associated morbidity and mortality. The current study explores outcomes after palliative bypass surgery in patients with non-resectable PDAC. Methods From the prospectively maintained German StuDoQ|Pancreas registry, all patients with histopathologically confirmed PDAC who underwent non-resective pancreatic surgery between 2013 and 2018 were retrospectively identified, and the influence of the surgical procedure on morbidity and mortality was analyzed. Results Of 389 included patients, 127 (32.6%) underwent explorative surgery only, and a biliary, gastroenteric or double bypass was established in 92 (23.7%), 65 (16.7%) and 105 (27.0%). After exploration only, patients had a significantly shorter stay in the intensive care unit (mean 0.5 days [SD 1.7] vs. 1.9 [3.6], 2.0 [2.8] or 2.1 [2.8]; P