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Abstract Dogs in shelters are faced with the challenge of adapting to a kennel after relinquishment and to a novel home after adoption. To measure adaptability of dogs, more feasible behavioural and physiological parameters need to be validated in different contexts. To evaluate nocturnal activity as an indicator of adaptability, we compared nocturnal activity, urinary cortisol:creatinine ratio (UCCR), and body weight changes of sheltered dogs the first period after intake in the shelter and after adoption. Nocturnal activity and UCCRs were significantly lower the first days after adoption than in the shelter. After adoption, nocturnal activity was significantly lower on night 2 than night 1, but not on night 3 and 4, suggesting a form of ‘rebound of resting’ during night 2 in the new home. UCCRs significantly decreased 7 days after adoption. Body weight decreased in the shelter but increased again after adoption. These findings suggest that overall, dogs rest better in a novel home than in a novel shelter but, in both contexts, some form of adaptation takes place. Nocturnal activity measured by an accelerometer differentiated well between shelter and home environments, and corresponded to UCCR responses, which supports usefulness of the method to monitor canine adaptability to novel environments.

Abstract The accumulation of erythrocyte membranes within an atherosclerotic plaque may contribute to the deposition of free cholesterol and thereby the enlargement of the necrotic core. Erythrocyte membranes can be visualized and quantified in the plaque by immunostaining for the erythrocyte marker glycophorin C. Hence, we theorized that the accumulation of erythrocytes quantified by glycophorin C could function as a marker for plaque vulnerability, possibly reflecting intraplaque hemorrhage (IPH), and offering predictive value for pre-procedural neurological symptoms. We employed the CellProfiler-integrated slideToolKit workflow to visualize and quantify glycophorin C, defined as the total plaque area that is positive for glycophorin C, in single slides of culprit lesions obtained from the Athero-Express Biobank of 1819 consecutive asymptomatic and symptomatic patients who underwent carotid endarterectomy. Our assessment included the evaluation of various parameters such as lipid core, calcifications, collagen content, SMC content, and macrophage burden. These parameters were evaluated using a semi-quantitative scoring method, and the resulting data was dichotomized as predefined criteria into categories of no/minor or moderate/heavy staining. In addition, the presence or absence of IPH was also scored. The prevalence of IPH and pre-procedural neurological symptoms were 62.4% and 87.1%, respectively. The amount of glycophorin staining was significantly higher in samples from men compared to samples of women (median 7.15 (IQR:3.37, 13.41) versus median 4.06 (IQR:1.98, 8.32), p

Fusion magnets made from high temperature superconducting ReBCO CORC® cables are typically protected with quench detection systems that use voltage or temperature measurements to trigger current extraction processes. Although small coils with low inductances have been demonstrated, magnet protection remains a challenge and magnets are typically operated with little knowledge of the intrinsic performance parameters. We propose a protection framework based on current distribution monitoring in fusion cables with limited inter-cable current sharing. By employing inverse Biot-Savart techniques to distributed Hall probe arrays around CORC® Cable-In-Conduit-Conductor (CICC) terminations, individual cable currents are recreated and used to extract the parameters of a predictive model. These parameters are shown to be of value for detecting conductor damage and defining safe magnet operating limits. The trained model is then used to predict cable current distributions in real-time, and departures between predictions and inverse Biot-Savart recreated current distributions are used to generate quench triggers. The methodology shows promise for quality control, operational planning and real-time quench detection in bundled CORC® cables for compact fusion reactors.

Abstract Tissue segmentation of histology whole-slide images (WSI) remains a critical task in automated digital pathology workflows for both accurate disease diagnosis and deep phenotyping for research purposes. This is especially challenging when the tissue structure of biospecimens is relatively porous and heterogeneous, such as for atherosclerotic plaques. In this study, we developed a unique approach called ‘EntropyMasker’ based on image entropy to tackle the fore- and background segmentation (masking) task in histology WSI. We evaluated our method on 97 high-resolution WSI of human carotid atherosclerotic plaques in the Athero-Express Biobank Study, constituting hematoxylin and eosin and 8 other staining types. Using multiple benchmarking metrics, we compared our method with four widely used segmentation methods: Otsu’s method, Adaptive mean, Adaptive Gaussian and slideMask and observed that our method had the highest sensitivity and Jaccard similarity index. We envision EntropyMasker to fill an important gap in WSI preprocessing, machine learning image analysis pipelines, and enable disease phenotyping beyond the field of atherosclerosis.

Abstract Genome-wide association studies have identified over five hundred loci that contribute to variation in type 2 diabetes (T2D), an established risk factor for many diseases. However, the mechanisms and extent through which these loci contribute to subsequent outcomes remain elusive. We hypothesized that combinations of T2D-associated variants acting on tissue-specific regulatory elements might account for greater risk for tissue-specific outcomes, leading to diversity in T2D disease progression. We searched for T2D-associated variants acting on regulatory elements and expression quantitative trait loci (eQTLs) in nine tissues. We used T2D tissue-grouped variant sets as genetic instruments to conduct 2-Sample Mendelian Randomization (MR) in ten related outcomes whose risk is increased by T2D using the FinnGen cohort. We performed PheWAS analysis to investigate whether the T2D tissue-grouped variant sets had specific predicted disease signatures. We identified an average of 176 variants acting in nine tissues implicated in T2D, and an average of 30 variants acting on regulatory elements that are unique to the nine tissues of interest. In 2-Sample MR analyses, all subsets of regulatory variants acting in different tissues were associated with increased risk of the ten secondary outcomes studied on similar levels. No tissue-grouped variant set was associated with an outcome significantly more than other tissue-grouped variant sets. We did not identify different disease progression profiles based on tissue-specific regulatory and transcriptome information. Bigger sample sizes and other layers of regulatory information in critical tissues may help identify subsets of T2D variants that are implicated in certain secondary outcomes, uncovering system-specific disease progression.

The identification of disease hotspots is an increasingly important public health problem. While geospatial modeling offers an opportunity to predict the locations of hotspots using suitable environmental and climatological data, little attention has been paid to optimizing the design of surveys used to inform such models. Here we introduce an adaptive sampling scheme optimized to identify hotspot locations where prevalence exceeds a relevant threshold. Our approach incorporates ideas from Bayesian optimization theory to adaptively select sample batches. We present an experimental simulation study based on survey data of schistosomiasis and lymphatic filariasis across four countries. Results across all scenarios explored show that adaptive sampling produces superior results and suggest that similar performance to random sampling can be achieved with a fraction of the sample size.

Abstract Data on the clinical validity of DNA copy number variants (CNVs) in spermatogenic failure (SPGF) is limited. This study analyzed the genome-wide CNV profile in 215 men with idiopathic SPGF and 62 normozoospermic fertile men, recruited at the Andrology Clinic, Tartu University Hospital, Estonia. A two-fold higher representation of > 1 Mb CNVs was observed in men with SPGF (13%, n = 28) compared to controls (6.5%, n = 4). Seven patients with SPGF were identified as carriers of microdeletions (1q21.1; 2.4 Mb) or microduplications (3p26.3, 1.1 Mb; 7p22.3-p22.2, 1.56 Mb; 10q11.22, 1.42 Mb, three cases; Xp22.33; 2.3 Mb) linked to severe congenital conditions. Large autosomal CNV carriers had oligozoospermia, reduced or low-normal bitesticular volume (22–28 ml). The 7p22.3-p22.2 microduplication carrier presented mild intellectual disability, neuropsychiatric problems, and short stature. The Xp22.33 duplication at the PAR1/non-PAR boundary, previously linked to uterine agenesis, was detected in a patient with non-obstructive azoospermia. A novel recurrent intragenic deletion in testis-specific LRRC69 was significantly overrepresented in patients with SPGF compared to the general population (3.3% vs. 0.85%; χ2 test, OR = 3.9 [95% CI 1.8–8.4], P = 0.0001). Assessment of clinically valid CNVs in patients with SPGF will improve their management and counselling for general and reproductive health, including risk of miscarriage and congenital disorders in future offspring.

Abstract Fusion magnets made from high temperature superconducting ReBCO CORC® cables are typically protected with quench detection systems that use voltage or temperature measurements to trigger current extraction processes. Although small coils with low inductances have been demonstrated, magnet protection remains a challenge and magnets are typically operated with little knowledge of the intrinsic performance parameters. We propose a protection framework based on current distribution monitoring in fusion cables with limited inter-cable current sharing. By employing inverse Biot-Savart techniques to distributed Hall probe arrays around CORC® Cable-In-Conduit-Conductor (CICC) terminations, individual cable currents are recreated and used to extract the parameters of a predictive model. These parameters are shown to be of value for detecting conductor damage and defining safe magnet operating limits. The trained model is then used to predict cable current distributions in real-time, and departures between predictions and inverse Biot-Savart recreated current distributions are used to generate quench triggers. The methodology shows promise for quality control, operational planning and real-time quench detection in bundled CORC® cables for compact fusion reactors.

Abstract Interactions between the gut microbiota and the immune system may be involved in vaccine and infection responses. In the present study, we studied the interactions between caecal microbiota composition and parameters describing the immune response in six experimental inbred chicken lines harboring different MHC haplotypes. Animals were challenge-infected with the infectious bronchitis virus (IBV), and half of them were previously vaccinated against this pathogen. We explored to what extent the gut microbiota composition and the genetic line could be related to the immune response, evaluated through flow cytometry. To do so, we characterized the caecal bacterial communities with a 16S rRNA gene amplicon sequencing approach performed one week after the IBV infectious challenge. We observed significant effects of both the vaccination and the genetic line on the microbiota after the challenge infection with IBV, with a lower bacterial richness in vaccinated chickens. We also observed dissimilar caecal community profiles among the different lines, and between the vaccinated and non-vaccinated animals. The effect of vaccination was similar in all the lines, with a reduced abundance of OTU from the Ruminococcacea UCG-014 and Faecalibacterium genera, and an increased abundance of OTU from the Eisenbergiella genus. The main association between the caecal microbiota and the immune phenotypes involved TCRϒδ expression on TCRϒδ + T cells. This phenotype was negatively associated with OTU from the Escherichia-Shigella genus that were also less abundant in the lines with the highest responses to the vaccine. We proved that the caecal microbiota composition is associated with the IBV vaccine response level in inbred chicken lines, and that the TCRϒδ + T cells (judged by TCRϒδ expression) may be an important component involved in this interaction, especially with bacteria from the Escherichia-Shigella genus. We hypothesized that bacteria from the Escherichia-Shigella genus increased the systemic level of bacterial lipid antigens, which subsequently mitigated poultry γδ T cells.

Abstract Shelter dogs are exposed to a variety of stressors. Among non-invasive techniques, hair cortisol concentration (HCC) is suggested an easy to collect biomarker for giving insight into long-term stress responses. We evaluated HCC as an indicator of long-term cortisol responses in dogs in an animal shelter over different chronological time points during sheltering and after adoption. Hair samples were collected from the neck region following a shave/re-shave protocol of shelter dogs (total n = 52) at four different time periods: T1 intake at shelter (pre-shelter period, n = 51); T2 after 6 weeks in the shelter (n = 23); T3 6 weeks after adoption (n = 24); T4 6 months after adoption (n = 22). HCC at T2 was significantly higher than HCC at T1, T3 and T4 (effect of sample collection moment: F3,41 = 12.78, p

Abstract No single reliable parameter exists to assess liver graft function of extended criteria donors during ex-vivo normothermic machine perfusion (NMP). The liver maximum capacity (LiMAx) test is a clinically validated cytochromal breath test, measuring liver function based on 13CO2 production. As an innovative concept, we aimed to integrate the LiMAx breath test with NMP to assess organ function. Eleven human livers were perfused using NMP. After one hour of stabilization, LiMAx testing was performed. Injury markers (ALT, AST, miR-122, FMN, and Suzuki-score) and lactate clearance were measured and related to LiMAx values. LiMAx values ranged between 111 and 1838 µg/kg/h, and performing consecutive LiMAx tests during longer NMP was feasible. No correlation was found between LiMAx value and miR-122 and FMN levels in the perfusate. However, a significant inverse correlation was found between LiMAx value and histological injury (Suzuki-score, R = − 0.874, P

Abstract The diagnosis of kidney allograft rejection is based on late histological and clinical markers. Early, specific and minimally-invasive biomarkers may improve rejection diagnosis. Endothelial cells (EC) are one of the earliest targets in kidney transplant rejection. We investigated whether circulating EC (cEC) could serve as an earlier and less invasive biomarker for allograft rejection. Blood was collected from a cohort of 51 kidney transplant recipients before and at multiple timepoints after transplantation, including during a for cause biopsy. The number and phenotype of EC was assessed by flow-cytometric analysis. Unbiased selection of EC was done using principal component (PCA) analysis. Paired analysis revealed a transient cEC increase of 2.1-fold on the third day post-transplant, recovering to preoperative levels at seventh day post-transplant and onwards. Analysis of HLA subtype demonstrated that cEC mainly originate from the recipient. cEC levels were not associated with allograft rejection, allograft function or other allograft pathologies. However, cEC in patients with allograft rejection and increased levels of cEC showed elevated levels of KIM-1 (kidney injury marker-1). These findings indicate that cEC numbers and phenotype are affected after kidney transplantation but may not improve rejection diagnosis.

Abstract Hypoxia is prevalent in atherosclerotic plaques, promoting plaque aggravation and subsequent cardiovascular disease (CVD). Transmembrane protein carbonic anhydrase IX (CAIX) is hypoxia-induced and can be shed into the circulation as soluble CAIX (sCAIX). As plaque macrophages are hypoxic, we hypothesized a role for CAIX in macrophage function, and as biomarker of hypoxic plaque burden and CVD. As tumor patients with probable CVD are treated with CAIX inhibitors, this study will shed light on their safety profile. CAIX co-localized with macrophages (CD68) and hypoxia (pimonidazole), and correlated with lipid core size and pro-inflammatory iNOS+ macrophages in unstable human carotid artery plaques. Although elevated pH and reduced lactate levels in culture medium of CAIX knock-out (CAIXko) macrophages confirmed its role as pH-regulator, only spare respiratory capacity of CAIXko macrophages was reduced. Proliferation, apoptosis, lipid uptake and expression of pro- and anti-inflammatory genes were not altered. Plasma sCAIX levels and plaque-resident CAIX were below the detection threshold in 50 and 90% of asymptomatic and symptomatic cases, respectively, while detectable levels did not associate with primary or secondary events, or intraplaque hemorrhage. Initial findings show that CAIX deficiency interferes with macrophage metabolism. Despite a correlation with inflammatory macrophages, plaque-resident and sCAIX expression levels are too low to serve as biomarkers of future CVD.

Abstract The development, homeostasis, and repair of intrahepatic and extrahepatic bile ducts are thought to involve distinct mechanisms including proliferation and maturation of cholangiocyte and progenitor cells. This study aimed to characterize human extrahepatic cholangiocyte organoids (ECO) using canonical Wnt-stimulated culture medium previously developed for intrahepatic cholangiocyte organoids (ICO). Paired ECO and ICO were derived from common bile duct and liver tissue, respectively. Characterization showed both organoid types were highly similar, though some differences in size and gene expression were observed. Both ECO and ICO have cholangiocyte fate differentiation capacity. However, unlike ICO, ECO lack the potential for differentiation towards a hepatocyte-like fate. Importantly, ECO derived from a cystic fibrosis patient showed no CFTR channel activity but normal chloride channel and MDR1 transporter activity. In conclusion, this study shows that ECO and ICO have distinct lineage fate and that ECO provide a competent model to study extrahepatic bile duct diseases like cystic fibrosis.

Abstract Fluorescent nanodiamonds (FNDs) are promising nanoprobes, owing to their stable and magnetosensitive fluorescence. Therefore they can probe properties as magnetic resonances, pressure, temperature or strain. The unprecedented sensitivity of diamond defects can detect the faint magnetic resonance of a single electron or even a few nuclear spins. However, these sensitivities are only achieved if the diamond probe is close to the molecules that need to be detected. In order to utilize its full potential for biological applications, the diamond particle has to enter the cell. Some model systems, like HeLa cells, readily ingest particles. However, most cells do not show this behavior. In this article we show for the first time generally applicable methods, which are able to transport fluorescent nanodiamonds into cells with a thick cell wall. Yeast cells, in particular Saccharomyces cerevisiae, are a favored model organism to study intracellular processes including aging on a cellular level. In order to introduce FNDs in these cells, we evaluated electrical transformation and conditions of chemical permeabilization for uptake efficiency and viability. 5% DMSO (dimethyl sulfoxide) in combination with optimized chemical transformation mix leads to high uptake efficiency in combination with low impact on cell biology. We have evaluated all steps in the procedure.

Abstract An expansive collateral artery network is correlated with improved survival in case of adverse cardiac episodes. We aimed to identify cellular microRNAs (miRNA; miR) important for collateral artery growth. Chronic total occlusion (CTO) patients (n = 26) were dichotomized using pressure-derived collateral flow index (CFIp) measurements; high collateral capacity (CFIp > 0.39; n = 14) and low collateral (CFIp

Abstract Chiral magnets are promising materials for the realisation of high-density and low-power spintronic memory devices. For these future applications, a key requirement is the synthesis of appropriate materials in the form of thin films ordering well above room temperature. Driven by the Dzyaloshinskii-Moriya interaction, the cubic compound FeGe exhibits helimagnetism with a relatively high transition temperature of 278 K in bulk crystals. We demonstrate that this temperature can be enhanced significantly in thin films. Using x-ray scattering and ferromagnetic resonance techniques, we provide unambiguous experimental evidence for long-wavelength helimagnetic order at room temperature and magnetic properties similar to the bulk material. We obtain α intr = 0.0036 ± 0.0003 at 310 K for the intrinsic damping parameter. We probe the dynamics of the system by means of muon-spin rotation, indicating that the ground state is reached via a freezing out of slow dynamics. Our work paves the way towards the fabrication of thin films of chiral magnets that host certain spin whirls, so-called skyrmions, at room temperature and potentially offer integrability into modern electronics.