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Studies indicate that the evaluation of animal welfare in birds may be carried out with the measurement of the stress-related hormone corticosterone in feathers. However a standardized procedure for corticosterone measurements in feathers is lacking, a validation needs to be carried out for each new species before implementation. The aim of the present study was to establish a valid method to measure corticosterone concentrations in feathers of laying hens in a precise and repeatable manner using an established and commercially available ELISA. Validation was performed with feather pools of tail and interscapular feathers of commercial Lohmann Brown laying hens. Assessment groups, consisting of 5 replicates, were created. All replicates of an assessment group were processed at the same time. Each replicate was run in 4 repetitions by ELISA. Intra-assay and interassay CV was 7.5 and 6.4%, respectively. The serial dilution showed linearity and parallelism. Examining the hormone extraction efficiency by using different methanol volumes resulted in no statistical differences (P > 0.05). Pulverized feathers showed higher corticosterone values than minced feathers (P > 0.05). Differences were shown between 2 feather types (tail vs. interscapular feathers; P 0.05). With the present study, a valid protocol, feasible for analyzing feather pools of laying hens, was developed. It may provide fundamentals for further investigations on corticosterone in feathers as a noninvasive indicator to evaluate aspects of animal welfare.

Abstract Fibrosis contributes to tissue repair, but excessive fibrosis disrupts organ function. Alagille syndrome (ALGS, caused by mutations in JAGGED1) results in liver disease and characteristic fibrosis. Here, we show that Jag1 Ndr/Ndr mice, a model for ALGS, recapitulate ALGS-like fibrosis. Single-cell RNA-seq and multi-color flow cytometry of the liver revealed immature hepatocytes and paradoxically low intrahepatic T cell infiltration despite cholestasis in Jag1 Ndr/Ndr mice. Thymic and splenic regulatory T cells (Tregs) were enriched and Jag1 Ndr/Ndr lymphocyte immune and fibrotic capacity was tested with adoptive transfer into Rag1 −/− mice, challenged with dextran sulfate sodium (DSS) or bile duct ligation (BDL). Transplanted Jag1 Ndr/Ndr lymphocytes were less inflammatory with fewer activated T cells than Jag1 +/+ lymphocytes in response to DSS. Cholestasis induced by BDL in Rag1 −/− mice with Jag1 Ndr/Ndr lymphocytes resulted in periportal Treg accumulation and three-fold less periportal fibrosis than in Rag1 −/− mice with Jag1 +/+ lymphocytes. Finally, the Jag1 Ndr/Ndr hepatocyte expression profile and Treg overrepresentation were corroborated in patients’ liver samples. Jag1-dependent hepatic and immune defects thus interact to determine the fibrotic process in ALGS.

Abstract Upon infecting its vertebrate host, the malaria parasite initially invades the liver where it undergoes massive replication, whilst remaining clinically silent. The coordination of host responses across the complex liver tissue during malaria infection remains unexplored. Here, we perform spatial transcriptomics in combination with single-nuclei RNA sequencing over multiple time points to delineate host-pathogen interactions across Plasmodium berghei-infected liver tissues. Our data reveals significant changes in spatial gene expression in the malaria-infected tissues. These include changes related to lipid metabolism in the proximity to sites of Plasmodium infection, distinct inflammation programs between lobular zones, and regions with enrichment of different inflammatory cells, which we term ‘inflammatory hotspots’. We also observe significant upregulation of genes involved in inflammation in the control liver tissues of mice injected with mosquito salivary gland components. However, this response is considerably delayed compared to that observed in P. berghei-infected mice. Our study establishes a benchmark for investigating transcriptome changes during host-parasite interactions in tissues, it provides informative insights regarding in vivo study design linked to infection and offers a useful tool for the discovery and validation of de novo intervention strategies aimed at malaria liver stage infection.

To facilitate the translation of immunotherapies from bench to bedside, predictive preclinical models are essential. We developed the in vivo immuno-oncology Hollow Fiber Assay (HFA) to bridge the gap between simpler cell-based in vitro assays and more complex mouse models for immuno-oncology drug evaluation. The assay involves co-culturing human cancer cell lines or primary patient-derived cancer cells with human immune cells inside semipermeable hollow fibers. Implanted intraperitoneally in mice, the fibers captured treatment-induced immune cell-mediated cancer cell killing following treatments with aCD3 and/or IL-2, demonstrating the feasibility of the assay. Traditional models require lengthy observation periods to monitor tumor growth and treatment response. The immuno-oncology HFA enables a rapid initial in vivo evaluation of immunological agents on cancer and immune cells of human origin, addressing two of the 3Rs — reduction and refinement — in animal research.

Abstract Background High-throughput screening (HTS) of small molecule drug libraries has greatly facilitated the discovery of new cancer drugs. However, most phenotypic screening platforms used in the field of oncology are based solely on cancer cell populations and do not allow for the identification of immunomodulatory agents. Methods We developed a phenotypic screening platform based on a miniaturized co-culture system with human colorectal cancer- and immune cells, providing a model that recapitulates part of the tumor immune microenvironment (TIME) complexity while simultaneously being compatible with a simple image-based readout. Using this platform, we screened 1,280 small molecule drugs, all approved by the Food and Drug Administration (FDA), and identified statins as enhancers of immune cell-induced cancer cell death. Results The lipophilic statin pitavastatin had the most potent anti-cancer effect. Further analysis demonstrated that pitavastatin treatment induced a pro-inflammatory cytokine profile as well as an overall pro-inflammatory gene expression profile in our tumor-immune model. Conclusion Our study provides an in vitro phenotypic screening approach for the identification of immunomodulatory agents and thus addresses a critical gap in the field of immuno-oncology. Our pilot screen identified statins, a drug family gaining increasing interest as repurposing candidates for cancer treatment, as enhancers of immune cell-induced cancer cell death. We speculate that the clinical benefits described for cancer patients receiving statins are not simply caused by a direct effect on the cancer cells but rather are dependent on the combined effect exerted on both cancer and immune cells.

Abstract Spontaneous bleeds are a leading cause of death in the pediatric JAG1‐related liver disease Alagille syndrome (ALGS). We asked whether there are sex differences in bleeding events in patients, whether Jag1Ndr/Ndr mice display bleeds or vascular defects, and whether discovered vascular pathology can be confirmed in patients non‐invasively. We performed a systematic review of patients with ALGS and vascular events following PRISMA guidelines, in the context of patient sex, and found significantly more girls than boys reported with spontaneous intracranial hemorrhage. We investigated vascular development, homeostasis, and bleeding in Jag1Ndr/Ndr mice, using retina as a model. Jag1Ndr/Ndr mice displayed sporadic brain bleeds, a thin skull, tortuous blood vessels, sparse arterial smooth muscle cell coverage in multiple organs, which could be aggravated by hypertension, and sex‐specific venous defects. Importantly, we demonstrated that retinographs from patients display similar characteristics with significantly increased vascular tortuosity. In conclusion, there are clinically important sex differences in vascular disease in ALGS, and retinography allows non‐invasive vascular analysis in patients. Finally, Jag1Ndr/Ndr mice represent a new model for vascular compromise in ALGS.

Environmental sensors are crucial for monitoring weather conditions and the impacts of climate change. However, it is challenging to place sensors in a way that maximises the informativeness of their measurements, particularly in remote regions like Antarctica. Probabilistic machine learning models can suggest informative sensor placements by finding sites that maximally reduce prediction uncertainty. Gaussian process (GP) models are widely used for this purpose, but they struggle with capturing complex non-stationary behaviour and scaling to large datasets. This paper proposes using a convolutional Gaussian neural process (ConvGNP) to address these issues. A ConvGNP uses neural networks to parameterise a joint Gaussian distribution at arbitrary target locations, enabling flexibility and scalability. Using simulated surface air temperature anomaly over Antarctica as training data, the ConvGNP learns spatial and seasonal non-stationarities, outperforming a non-stationary GP baseline. In a simulated sensor placement experiment, the ConvGNP better predicts the performance boost obtained from new observations than GP baselines, leading to more informative sensor placements. We contrast our approach with physics-based sensor placement methods and propose future steps towards an operational sensor placement recommendation system. Our work could help to realise environmental digital twins that actively direct measurement sampling to improve the digital representation of reality.

Global transcriptional differences across lobular units in the liver remain unknown. Here the authors perform spatial transcriptomics of liver tissue to delineate transcriptional differences in physical space, confirm lobular zonation along transcriptional gradients and suggest the presence of previously uncharacterized structures within liver tissue.

Accurate seasonal forecasts of sea ice are highly valuable, particularly in the context of sea ice loss due to global warming. A new machine learning tool for sea ice forecasting offers a substantial increase in accuracy over current physics-based dynamical model predictions.

The role of automatic electrocardiogram (ECG) analysis in clinical practice is limited by the accuracy of existing models. In that context, the authors present a Deep Neural Network (DNN) that recognizes different abnormalities in ECG recordings which matches or outperform cardiology and emergency resident medical doctors.

Abstract In polymer‐based organic photovoltaic cells, the capability of charge extraction/injection of molybdenum trioxide (MoO3) is demonstrated as interface layer for polymer bulk heterojunction (BHJ). The present work determines the dipole formed at the MoO3 and conjugated poly [2,3‐bis (3‐octyloxyphenyl) quinoxaline‐5,8‐diyl‐alt‐thiophene‐2,5‐diyl] (TQ1):(6,6)‐Phenyl C71 butyric acid methyl ester (PC71BM) bulk heterojunction interface. This dipole has a major influence on the charge transport across the TQ1:PC71BM interface. The formation of the dipole is determined with electron spectroscopy and the depth profiling technique neutral impact collision ion scattering spectroscopy. Metastable induced electron and UV‐photoelectron spectroscopy is applied to determine the enclosed surface coverage of minimum 1.5 nm MoO3 and a maximized dipole strength of 2.4 eV with >2 nm MoO3 deposition on BHJ. It is also demonstrated that the air exposure reduces the dipole at the interface and leads to a decrease in cell performance providing evidence that the dipole formed at the interface is beneficial for the functioning of photovoltaic cells. The results indicate that the reduction in dipole might not be the only mechanism leading to cell performance degradation. The findings of the present work have relevance for other BHJ systems because MoO3 as high work function material is likely to interact with other organic materials in a similar way.

For several years CERN has been offering a centralised service for Elasticsearch, a popular distributed system for search and analytics of user provided data. The service offered by CERN IT is better described as a service of services, delivering centrally managed and maintained Elasticsearch instances to CERN users who have a justified need for it. This dynamic infrastructure currently consists of about 30 distinct and independent Elasticsearch installations, in the following referred to as Elasticsearch clusters, some of which are shared between different user communities. The service is used by several hundred users mainly for logs and service analytics. Due to its size and complexity, the installation produces a huge amount of internal monitoring data which can be difficult to process in real time with limited available person power. Early on, an idea was therefore born to process this data automatically, aiming to extract anomalies and possible issues building up in real time, allowing the experts to address them before they start to cause an issue for the users of the service. Both deep learning and traditional methods have been applied to analyse the data in order to achieve this goal. This resulted in the current deployment of an anomaly detection system based on a one layer multi dimensional LSTM neural network, coupled with applying a simple moving average to the data to validate the results. This paper will describe which methods were investigated and give an overview of the current system, including data retrieval, data pre-processing and analysis. In addition, reports on experiences gained when applying the system to actual data will be provided. Finally, weaknesses of the current system will be briefly discussed, and ideas for future system improvements will be sketched out.

Summary: Genetic loss and gain of function in mice have typically been studied by using knockout or knockin mice that take months to years to generate. To address this problem for the nervous system, we developed NEPTUNE (NEural Plate Targeting by in Utero NanoinjEction) to rapidly and flexibly transduce the neural plate with virus prior to neurulation, and thus manipulate the future nervous system. Stable integration in >95% of cells in the brain enabled long-term overexpression, and conditional expression was achieved by using cell-type-specific MiniPromoters. Knockdown of Olig2 by using NEPTUNE recapitulated the phenotype of Olig2−/− embryos. We used NEPTUNE to investigate Sptbn2, mutations in which cause spinocerebellar ataxia type 5. Sptbn2 knockdown induced dose-dependent defects in the neural tube, embryonic turning, and abdominal wall closure, previously unreported functions for Sptbn2. NEPTUNE thus offers a rapid and cost-effective technique to test gene function in the nervous system and can reveal phenotypes incompatible with life. Motivation: Current methods used to alter gene expression in mouse embryos to study brain development lack efficacy and are time consuming. NEPTUNE provides an addition to the molecular toolbox, allowing rapid and widespread manipulation of gene expression before neurulation in vivo. This technique can be adapted to specifically target central nervous system (CNS) cell subtypes such as neurons or glia. Functional analysis can be performed within days after injection. NEPTUNE can thus reduce the financial and ethical costs of animal research, while accelerating the process from hypothesis to results in vivo.

We investigated the effect of adding p-anisaldehyde (AA) solvent to the ink containing poly[[2,60-4,8-di(5-ethylhexylthienyl)benzo[1,2-b:3,3-b]dithiophene][3-fluoro-2[(2-ethylhexyl)carbonyl]thieno[3,4-b]thiophenediyl]](PTB7-Th) and 3,9-bis(2-methylene-(3-(1,1-dicyanomethylene)-indanone))-5,5,11,11-tetrakis(4-hexylphenyl)-dithieno[2,3-d:20,30-d0]-s-indaceno[1,2-b:5,6-b0]-dithiophene(ITIC) on the morphology of the active layer. The present study focuses on determining the effect of the additive on the compositions at the surface of the PTB7-Th: ITIC composite and its morphology, forming one side of the interface of the blend with the MoOX electrode, and the influence of the structural change on the performance of devices. Studies of device performance show that the addition of the additive AA leads to an improvement in device performance. Upon the addition of AA, the concentration of PTB7-Th at the surface of the bulk heterojunction (BHJ) increases, causing an increase in surface roughness of the surface of the BHJ. This finding contributes to an understanding of the interaction between the donor material and high work function electrode/interface material. The implications for the interface are discussed.

We have developed two series of p-type conjugated polymers based on poly[2,3-bis-(3-octyloxyphenyl)quinoxaline-5,8-diyl-alt-thiophene-2,5-diyl] (TQ1) polymeric backbone utilizing polar pendant groups, i.e., tertiary amine and pyridine, to achieve switchable solubility in water and ethanol. By balancing the ratio between polar and non-polar side-groups, we could combine green-solvent processability with the manufacturing of functional photovoltaic devices. Due to the unavailability of water/alcohol soluble acceptors, the photovoltaic performance of these new polymers was evaluated using organic solvent by incorporating PC61BM. For water/alcohol soluble partial amine-based polymers, we achieve a maximum power conversion efficiency (PCE) of ∼0.8% whereas alcohol soluble partial pyridine-based polymers show enhanced PCE of ∼1.3% with inverted device structure. We propose that the enhancement in PCE is a result of the reduction in amino-group content and the lower basicity of pyridine, both of which decrease the interaction between functionalized polymers with the anode interface material and reduce the miscibility of the donor and acceptor. Further improvement of the photovoltaic performance, in particular the open-circuit voltage (Voc), was achieved by using an anode buffer layer to mitigate the unfavorable interaction of the amino/pyridine groups with the MoO3 electrode. Our work demonstrated the possibility of substituent modification for conjugated polymers using tertiary amine and pyridine groups to achieve water/alcohol soluble and functional donor materials.

Liver diseases constitute an important medical problem, and a number of these diseases, termed cholangiopathies, affect the biliary system of the liver. In this review, we describe the current understanding of the causes of cholangiopathies, which can be genetic, viral or environmental, and the few treatment options that are currently available beyond liver transplantation. We then discuss recent rapid progress in a number of areas relevant for decoding the disease mechanisms for cholangiopathies. This includes novel data from analysis of transgenic mouse models and organoid systems, and we outline how this information can be used for disease modeling and potential development of novel therapy concepts. We also describe recent advances in genomic and transcriptomic analyses and the importance of such studies for improving diagnosis and determining whether certain cholangiopathies should be viewed as distinct or overlapping disease entities. Keywords: Liver, Transplant, Cholangiocyte, Hepatocyte, Bile duct, Organoid, Alagille syndrome, Biliary atresia, Primary sclerosing cholangitis (PSC), Primary biliary cholangitis (PBC), Cystic fibrosis

Printing solar cell: yield enhanced by laminating the active layer The manufacturing yield of the flexible organic solar cells is enhanced with a new lamination method by solving the shunting problem due to conductive inks. A collaborative team led by Olle Inganäs from Linköping University, Sweden fabricates polymer: PCBM all-organic solar cells in ambient conditions using the active layer as the lamination adhesive. The team shows that reduced exposure to ambient is critical to achieve high device efficiency and suppress degradation. The degraded devices generate asymmetric photocurrent due to the electron traps in the active layer. The reported active layer lamination method not only solves the shunting problem in a number of different polymer: PCBM combinations, but also provides wide tenability and control of the composition and vertical phase separation of the active layer.