Search

Objective: Non-alcoholic fatty liver disease (NAFLD) is the most common chronic liver disease and is associated with an enhanced risk for liver and cardiovascular diseases and mortality. NAFLD can progress from simple hepatic steatosis to non-alcoholic steatohepatitis (NASH). However, the mechanisms predisposing to this progression remain undefined. Notably, hepatic mitochondrial dysfunction is a common finding in patients with NASH. Due to a lack of appropriate experimental animal models, it has not been evaluated whether this mitochondrial dysfunction plays a causative role for the development of NASH. Methods: To determine the effect of a well-defined mitochondrial dysfunction on liver physiology at baseline and during dietary challenge, C57BL/6J-mtFVB/N mice were employed. This conplastic inbred strain has been previously reported to exhibit decreased mitochondrial respiration likely linked to a non-synonymous gene variation (nt7778 G/T) of the mitochondrial ATP synthase protein 8 (mt-ATP8). Results: At baseline conditions, C57BL/6J-mtFVB/N mice displayed hepatic mitochondrial dysfunction characterized by decreased ATP production and increased formation of reactive oxygen species (ROS). Moreover, genes affecting lipid metabolism were differentially expressed, hepatic triglyceride and cholesterol levels were changed in these animals, and various acyl-carnitines were altered, pointing towards an impaired mitochondrial carnitine shuttle. However, over a period of twelve months, no spontaneous hepatic steatosis or inflammation was observed. On the other hand, upon dietary challenge with either a methionine and choline deficient diet or a western-style diet, C57BL/6J-mtFVB/N mice developed aggravated steatohepatitis as characterized by lipid accumulation, ballooning of hepatocytes and infiltration of immune cells. Conclusions: We observed distinct metabolic alterations in mice with a mitochondrial polymorphism associated hepatic mitochondrial dysfunction. However, a second hit, such as dietary stress, was required to cause hepatic steatosis and inflammation. This study suggests a causative role of hepatic mitochondrial dysfunction in the development of experimental NASH. Keywords: NAFLD, Steatohepatitis, Mitochondrial gene polymorphism, Mitochondrial dysfunction, Lipid metabolism, TNFα

Laser Metal Deposition (LMD) offers new perspectives for the fabrication of metal matrix nanocomposites (MMnCs). Current methods to produce MMnCs by LMD systematically involve the premixing of the nanopowders and the micropowders or require in-situ strategies, thereby restricting the possibilities to adjust the nature, content and location of the nano-reinforcement during printing. The objective of this study is to overcome such restrictions and propose a new process approach by direct injection of nanoparticles into a metallic matrix. Alumina (n-Al2O3) nanoparticles were introduced into a titanium matrix by using two different direct dry injection modes in order to locally increase the hardness. Energy dispersive X-ray spectroscopy (EDS) analyses validate the successful incorporation of the n-Al2O3 at chosen locations. Optical and high resolution transmission electron microscopic (HR-TEM) observations as well as X-ray diffraction (XRD) analyses indicate that n-Al2O3 powders are partly or totally dissolved into the Ti melted pool leading to the in-situ formation of a composite consisting of fine α2 lamellar microstructure within a Ti matrix and a solid solution with oxygen. Mechanical tests show a significant increase in hardness with the increase of injected n-Al2O3 amount. A maximum of 620 HV was measured that is almost 4 times higher than the pure LMD-printed Ti structure.

Enteroendocrine cells (EEC) produce neuropeptides, which are crucially involved in the maintenance of the intestinal barrier. Hence, EEC dysfunction is suggested to be involved in the complex pathophysiology of inflammatory bowel disease (IBD), which is characterized by decreased intestinal barrier function. However, the underlying mechanisms for EEC dysfunction are not clear and suitable models for a better understanding are lacking. Here, we demonstrate that Carboxypeptidase E (CPE) is specifically expressed in EEC of the murine colon and ileum and that its deficiency is associated with reduced intestinal levels of Neuropeptide Y (NPY) and Peptide YY (PYY), which are both produced by EEC. Moreover, cpe-/- mice exhibit an aggravated course of DSS-induced chronic colitis compared to wildtype littermates. In addition, we observed elevated mucosal IL-6 and KC transcript levels already at baseline conditions in cpe-/- mice. Moreover, supernatants obtained from isolated intestinal crypts of cpe-/- mice lead to increased IL-6 and KC expression in MODE-K cells in the presence of LPS. This effect was reversible by co-administration of recombinant NPY, suggesting a CPE mediated immunosuppressive effect in the intestines by influencing the processing of specific neuropeptides. In this context, the chemotaxis of bone marrow derived macrophages towards respective supernatants was enhanced. In conclusion, our data point to an anti-inflammatory role of CPE in the intestine by influencing local cytokine levels and thus regulating the migration of myeloid immune cells into the mucosa. These findings highlight the importance of EEC for intestinal homeostasis and propose EEC as potential therapeutic targets in IBD.

Abstract Background Network theory is largely applied in real-world systems to assess landscape connectivity using empirical or theoretical networks. Empirical networks are usually built from discontinuous individual movement trajectories without knowing the effect of relocation frequency on the assessment of landscape connectivity while theoretical networks generally rely on simple movement rules. We investigated the combined effects of relocation sampling frequency and landscape fragmentation on the assessment of landscape connectivity using simulated trajectories and empirical high-resolution (1 Hz) trajectories of Alpine ibex (Capra ibex). We also quantified the capacity of commonly used theoretical networks to accurately predict landscape connectivity from multiple movement processes. Methods We simulated forager trajectories from continuous correlated biased random walks in simulated landscapes with three levels of landscape fragmentation. High-resolution ibex trajectories were reconstructed using GPS-enabled multi-sensor biologging data and the dead-reckoning technique. For both simulated and empirical trajectories, we generated spatial networks from regularly resampled trajectories and assessed changes in their topology and information loss depending on the resampling frequency and landscape fragmentation. We finally built commonly used theoretical networks in the same landscapes and compared their predictions to actual connectivity. Results We demonstrated that an accurate assessment of landscape connectivity can be severely hampered (e.g., up to 66% of undetected visited patches and 29% of spurious links) when the relocation frequency is too coarse compared to the temporal dynamics of animal movement. However, the level of landscape fragmentation and underlying movement processes can both mitigate the effect of relocation sampling frequency. We also showed that network topologies emerging from different movement behaviours and a wide range of landscape fragmentation were complex, and that commonly used theoretical networks accurately predicted only 30–50% of landscape connectivity in such environments. Conclusions Very high-resolution trajectories were generally necessary to accurately identify complex network topologies and avoid the generation of spurious information on landscape connectivity. New technologies providing such high-resolution datasets over long periods should thus grow in the movement ecology sphere. In addition, commonly used theoretical models should be applied with caution to the study of landscape connectivity in real-world systems as they did not perform well as predictive tools.

Abstract Onoceroids are a rare family of triterpenes. One representative onoceroid is ambrein, which is the main component of ambergris used as a traditional medicine. We have previously identified the onoceroid synthase, BmeTC, in Bacillus megaterium and succeeded in creating ambrein synthase by introducing mutations into BmeTC. Owing to the structural similarity of ambrein to vitamin D, a molecule with diverse biological activities, we hypothesized that some of the activities of ambergris may be induced by the binding of ambrein to the vitamin D receptor (VDR). We demonstrated the VDR binding ability of ambrein. By comparing the structure–activity relationships of triterpenes with both the VDR affinity and osteoclastic differentiation-promoting activity, we observed that the activity of ambrein was not induced via the VDR. Therefore, some of the activities of ambergris, but not all, can be attributed to its VDR interaction. Additionally, six unnatural onoceroids were synthesized using the BmeTC reactions, and these compounds exhibited higher VDR affinity than that of ambrein. Enzymatic syntheses of onoceroid libraries will be valuable in creating a variety of bioactive compounds beyond ambergris.

The integration of deep learning-based tools into diagnostic workflows is increasingly prevalent due to their efficiency and reproducibility in various settings. We investigated the utility of automated nuclear morphometry for assessing nuclear pleomorphism (NP), a criterion of malignancy in the current grading system in canine pulmonary carcinoma (cPC), and its prognostic implications. We developed a deep learning-based algorithm for evaluating NP (variation in size, i.e., anisokaryosis and/or shape) using a segmentation model. Its performance was evaluated on 46 cPC cases with comprehensive follow-up data regarding its accuracy in nuclear segmentation and its prognostic ability. Its assessment of NP was compared to manual morphometry and established prognostic tests (pathologists’ NP estimates (n = 11), mitotic count, histological grading, and TNM-stage). The standard deviation (SD) of the nuclear area, indicative of anisokaryosis, exhibited good discriminatory ability for tumor-specific survival, with an area under the curve (AUC) of 0.80 and a hazard ratio (HR) of 3.38. The algorithm achieved values comparable to manual morphometry. In contrast, the pathologists’ estimates of anisokaryosis resulted in HR values ranging from 0.86 to 34.8, with slight inter-observer reproducibility (k = 0.204). Other conventional tests had no significant prognostic value in our study cohort. Fully automated morphometry promises a time-efficient and reproducible assessment of NP with a high prognostic value. Further refinement of the algorithm, particularly to address undersegmentation, and application to a larger study population are required.

To gain insights into phosphorus (P) dynamics in soils and the ability to predict soil responses to varying fertilizer inputs, mass balance models prove to be valuable tools. In this study, a new dynamic mass balance model, PBalD8, was used to describe the change in extracted P in the A horizon of soils subjected to diverse fertilizer treatments over a period of 50 to 60 years in five soil fertility experiments. The model employed a Freundlich equation to describe soil-solution partitioning of P and assumed that acid-lactate-extractable P represented a labile pool of P in instant equilibrium with soil solution P. Additionally, oxalate-extractable inorganic P was presumed to comprise the sum of the labile and stable pools of P, with mass flux to and from the latter described by Fick’s first law. The model was evaluated using results from extractions and P K-edge XANES spectroscopy. Notably, organic P, as revealed by P K-edge XANES, did not substantially contribute to long-term changes in soil P content and was therefore excluded from consideration. In general, the model offered reasonable fits to the extracted P concentrations. However, for the P-depleted treatments, a prerequisite was that the P removal through harvest was lower compared to measurements. Conversely, in three of the soils, the modelled fertilizer inputs needed to be reduced to 70 % to 85 % of the known additions. These discrepancies may be attributed to the involvement of deeper soil horizons, including deep crop uptake and mixing with lower soil layers, although other factors such as lateral dispersion and inaccuracies in estimating applied fertilizers cannot be discounted. These results underscore the necessity of gaining a more comprehensive understanding of how deeper soil horizons influence P mass balances in agricultural soils. In one of the soils, Fjärdingslöv, P K-edge XANES results demonstrated the formation of calcium phosphate over time in the highest fertilization treatment, consistent with the model. Additionally, in two soils, Kungsängen and the P-depleted Vreta Kloster soil, the model predicted a significant contribution from mineral weathering. However, the PBalD8 model also projected higher P leaching rates than those observed, suggesting that the model may not fully capture this P output term.

ObjectiveWe apply the superiorization methodology to the constrained intensity-modulated radiation therapy (IMRT) treatment planning problem. Superiorization combines a feasibility-seeking projection algorithm with objective function reduction: The underlying projection algorithm is perturbed with gradient descent steps to steer the algorithm towards a solution with a lower objective function value compared to one obtained solely through feasibility-seeking.ApproachWithin the open-source inverse planning toolkit matRad, we implement a prototypical algorithmic framework for superiorization using the well-established Agmon, Motzkin, and Schoenberg (AMS) feasibility-seeking projection algorithm and common nonlinear dose optimization objective functions. Based on this prototype, we apply superiorization to intensity-modulated radiation therapy treatment planning and compare it with (i) bare feasibility-seeking (i.e., without any objective function) and (ii) nonlinear constrained optimization using first-order derivatives. For these comparisons, we use the TG119 water phantom, the head-and-neck and the prostate patient of the CORT dataset.Main resultsBare feasibility-seeking with AMS confirms previous studies, showing it can find solutions that are nearly equivalent to those found by the established piece-wise least-squares optimization approach. The superiorization prototype solved the linearly constrained planning problem with similar dosimetric performance to that of a general-purpose nonlinear constrained optimizer while showing smooth convergence in both constraint proximity and objective function reduction.SignificanceSuperiorization is a useful alternative to constrained optimization in radiotherapy inverse treatment planning. Future extensions with other approaches to feasibility-seeking, e.g., with dose-volume constraints and more sophisticated perturbations, may unlock its full potential for high performant inverse treatment planning.

A method to isolate and sequence individual nuclei from human and mouse muscle biopsies provides further insight into the mechanisms of dystrophin loss and repair, in the context of Duchenne muscular dystrophy.

Introduction: In the Belgian part of the North Sea, sand for beach and foreshore nourishments is extracted from the Hinder Banks, about 40 km offshore. The extraction is not screened for shells and other very coarse material, as is the case for sand extraction for industrial use. Intermittent but intensive sand extraction took place from 2012 to 2019 on the Oosthinder, and since 2019 on the Noordhinder.Methods: To better understand sediment variability during human-induced disturbance of the seabed, both sandbanks have been monitored using multibeam bathymetry and backscatter, and Reineck box cores on board of the Research Vessel Belgica A962. Acoustic and sediment data were preferably jointly collected within a one-week period to substantiate the interrelationships.Result: Very well-sorted medium sands with low backscatter values (−28 to −33 dB) are detected near the top of the sandbank, while (moderately) well-sorted coarser sands and shell fragments with high backscatter values (−20 to −24 dB) are detected in the deeper parts of the sandbank slope. Although natural conditions such as sandwave movement and storms may mask early sediment changes, 7 years of intermittent and intensive sand extraction on the upper parts of a gentle sandbank slope caused a seabed deepening of at least 2 m, a backscatter decrease between 5 and 8 dB, a reduction in carbonate content by 1%–5% and an increase in organic matter content by 1%–2%. Two years after the cessation of the operations, the carbonate content increased and organic matter content decreased by 1%–2%.Discussion: Natural variability of sediments remains dependent on depth and geomorphology in both undisturbed, as well as recently and longer disturbed sandbank systems. However, a spreading of the more homogeneous, very well-sorted medium sands with limited carbonate content from the sandbank crest to the upper parts of the sandbank slope was observed, as sand extraction progressed. Subsequently, possible first signs of a slow return to the original sediment characteristics were detected.

Duchenne Muscular Dystrophy (DMD)’s complex multi-system pathophysiology, coupled with the cost-prohibitive logistics of multi-year drug screening and follow-up, has hampered the pursuit of new therapeutic approaches. Here we conducted a systematic historical and text mining-based pilot feasibility study to explore the potential of established or previously tested drugs as prospective DMD therapeutic agents. Our approach utilized a Swanson linking-inspired method to uncover meaningful yet largely hidden deep semantic connections between pharmacologically significant DMD targets and drugs developed for unrelated diseases. Specifically, we focused on molecular target-based MeSH terms and categories as high-yield bioinformatic proxies, effectively tagging relevant literature with categorical metadata. To identify promising leads, we comprehensively assembled published reports from 2011 and sampling from subsequent years. We then determined the earliest year when distinct MeSH terms or category labels of the relevant cellular target were referenced in conjunction with the drug, as well as when the pertinent target itself was first conclusively identified as holding therapeutic value for DMD. By comparing the earliest year when the drug was identifiable as a DMD treatment candidate with that of the first actual report confirming this, we computed an Index of Delayed Discovery (IDD), which serves as a metric of Swanson-linked latent knowledge. Using these findings, we identified data from previously unlinked articles subsetted via MeSH-derived Swanson linking or from target classes within the DrugBank repository. This enabled us to identify new but untested high-prospect small-molecule candidates that are of particular interest in repurposing for DMD and warrant further investigations.

Muscle damage and fibro-fatty replacement of skeletal muscles is a main pathologic feature of Duchenne muscular dystrophy (DMD) with more proximal muscles affected earlier and more distal affected later in the disease course, suggesting that different skeletal muscle groups possess distinctive characteristics that influence their susceptibility to disease. To explore transcriptomic factors driving differential gene expression and modulating DMD skeletal muscle severity, we characterized the transcriptome of vastus lateralis (VL), a more proximal and susceptible muscle, relative to tibialis anterior (TA), a more distal and protected muscle, in 15 healthy individuals using bulk RNA sequencing to identify gene expression differences that may mediate their relative susceptibility to damage with loss of dystrophin. Matching single nuclei RNA sequencing data was generated for 3 of the healthy individuals, to infer cell composition in the bulk RNA sequencing dataset and to improve mapping of differentially expressed genes to their cell source of expression. A total of 3,410 differentially expressed genes were identified and mapped to cell type using single nuclei RNA sequencing of muscle, including long non-coding RNAs and protein coding genes. There was an enrichment of genes involved in calcium release from the sarcoplasmic reticulum, particularly in the myofibers and these myofiber genes were higher in the VL. There was an enrichment of genes in “Collagen-Containing Extracellular Matrix” expressed by fibroblasts, endothelial, smooth muscle and pericytes, with most genes higher in the TA, as well as genes in “Regulation Of Apoptotic Process” expressed across all cell types. Previously reported genetic modifiers were also enriched within the differentially expressed genes. We also identify 6 genes with differential isoform usage between the VL and TA. Lastly, we integrate our findings with DMD RNA sequencing data from the TA, and identify “Collagen-Containing Extracellular Matrix” and “Negative Regulation Of Apoptotic Process” as differentially expressed between DMD compared to healthy. Collectively, these findings propose novel candidate mechanisms that may mediate differential muscle susceptibility in muscular dystrophies and provide new insight into potential therapeutic targets.

Acute scrotal pain (ASP) requiring surgical exploration is common in the pediatric population, but little has been reported on this subject with regard to the adult population. The aim of this study was to investigate the demographic and clinical characteristics and outcomes of scrotal explorations performed on adult patients. Patients over 21 years of age who underwent surgical exploration for ASP with suspected testicular torsion (TT) at 14 French hospitals between January 2005 and December 2019 were included in this study. The main outcome measures were demographic characteristics, pathology found during scrotal exploration, and perioperative outcomes. Logistic regression was used to perform univariate and multivariate analyses to identify predictors of TT. Data for 1329 men were analyzed. The median age was 30 (interquartile range [IQR]: 25–35; range: 21–89) years. Regarding the clinical examination, 867 (65.2%) patients presented with an elevation of the testicle, 613 (46.1%) patients with scrotal edema or erythema, and 211 (15.9%) patients with nausea or vomiting. Operative findings identified TT in only 684 (51.5%) patients, epididymo-orchitis in 112 (8.4%) patients, a tumor in 16 (1.2%) patients, and no causes in 475 (35.7%) patients. Orchiectomy for nonviable testes was required in 101 (7.6%) patients. In multivariate analysis, an elevation of the testicle, erythema/swelling, and the presence of nausea/vomiting were found to be associated with the occurrence of TT. Testicular torsion is not exclusive to children and adolescents, so must be considered in males of any age with acute scrotal findings. However, one-third of scrotal explorations in adults did not lead to a diagnosis.

Abstract Background Tissue-nonspecific alkaline phosphatase (TNSALP) encoded by the ALPL gene is of particular importance for bone mineralization. Mutation in the ALPL gene can lead to persistent low ALP activity resulting in the rare disease Hypophosphatasia (HPP) that is characterized by disturbed bone and dental mineralization. While severe forms are extremely rare with an estimated prevalence of 1/100.000, recent studies suggest that moderate form caused by heterozygous mutations are much more frequent with an estimated prevalence of 1/508. The purpose of this study was to estimate the prevalence of low AP levels in the population based on laboratory measurements. Methods In this study, the prevalence of low AP activity and elevated pyridoxal-5-phosphate (PLP) levels was analyzed in 6.918.126 measurements from 2011 to 2016 at a single laboratory in northern Germany. Only laboratory values of subjects older than 18 years of age were included. Only the first measurement was included, all repeated values were excluded. Results In total, 8.46% of the measurements of a total of 6.918.126 values showed a value

Generalisations in narrative texts typically do not or not exclusively serve to devise the narrated world, but provide information about the narrative instance, the meaning of what is told or the real world. The paper contributes to the linguistic-literary description of generalisations, develops a tagset for their identification and classification, and presents the results of their collaborative annotation in a diachronic corpus (1616–1930). Finally, the paper presents a rule-based and a statistical tagger for the automatic recognition of generalisations that allow users to access a variety of examples of the phenomenon and can be used in the analysis of the functions of generalisations and the associated narratological phenomena.

Recent studies have revealed the dynamic and complex evolution of CLCA1 gene homologues in and between mammals and birds with a particularly high diversity in mammals. In contrast, CLCA2 has only been found as a single copy gene in mammals, to date. Furthermore, CLCA2 has only been investigated in few mammalian species but not in birds. Here, we established core genomic, protein biochemical and expressional properties of CLCA2 in several bird species and compared them with mammalian CLCA2. Chicken, turkey, quail and ostrich CLCA2 were compared to their mammalian orthologues using in silico, biochemical and expressional analyses. CLCA2 was found highly conserved not only at the level of genomic and exon architecture but also in terms of the canonical CLCA2 protein domain organization. The putatively prototypical galline CLCA2 (gCLCA2) was cloned and immunoblotting as well as immunofluorescence analyses of heterologously expressed gCLCA2 revealed protein cleavage, glycosylation patterns and anchoring in the plasma membrane similar to those of most mammalian CLCA2 orthologues. Immunohistochemistry found highly conserved CLCA2 expression in epidermal keratinocytes in all birds and mammals investigated. Our results suggest a highly conserved and likely evolutionarily indispensable role of CLCA2 in keratinocyte function. Its high degree of conservation on the genomic, biochemical and expressional levels stands in contrast to the dynamic structural complexities and proposed functional diversifications between mammalian and avian CLCA1 homologues, insinuating a significant degree of negative selection of CLCA2 orthologues among birds and mammals. Finally, and again in contrast to CLCA1, the high conservation of CLCA2 makes it a strong candidate for studying basic properties of the functionally still widely unresolved CLCA gene family.

Background: Gastric per oral endoscopic esophageal myotomy (G-POEM) is a promising procedure to treat refractory gastroparesis. The safety profile of G-POEM is an important topic because gastroparesis is a functional pathology, with a procedure whose effectiveness is between 50 and 65% depending on the studies. Objectives: We present this retrospective multicenter study, with the aim of establishing a safety profile, focusing on serious adverse events (AEs). Design: This was a multicenter observational cohort study conducted in five French expert centers. Methods: All patients who underwent G-POEM for refractory gastroparesis between 2015 and 2021 were included for analysis. AEs were classified into per endoscopic, early postoperative, and late postoperative, up to 1 month. Their severity was assessed using Dindo–Clavien and American Society for Gastrointestinal Endoscopy classification. The primary objective was to evaluate the rate of G-POEM severe AEs. Secondary objectives were to document other postoperative AEs, and to identify predictive factors. Results: In all, 217 patients were included: 81 men and 136 women, mean age 52 ± 17 years. The average procedural time was 44 ± 14 min (12–78). The average hospital stay was 3.7 ± 2.3 days. The AEs rate classified as Clavien–Dindo ⩾3 was 0.4% (one delayed bleeding requiring blood transfusion and endoscopic management). There were no deaths or patients admitted to intensive care unit. The rates of mucosotomy and capnoperitoneum were 3.7 and 1.8%, respectively, without clinical consequences. Most patients (81.5%) did not experience any AE. Three cases of dumping syndrome occurred, quickly managed by dietary measures. Conclusion: Our study confirms the safety of G-POEM with less than 0.5% of serious AEs, medically managed. This outcome makes this a procedure to have a good benefit–risk ratio.

Abstract Emerging and promising therapeutic interventions for Duchenne muscular dystrophy (DMD) are confounded by the challenges of quantifying dystrophin. Current approaches have poor precision, require large amounts of tissue, and are difficult to standardize. This paper presents an immuno-mass spectrometry imaging method using gadolinium (Gd)-labeled anti-dystrophin antibodies and laser ablation-inductively coupled plasma-mass spectrometry to simultaneously quantify and localize dystrophin in muscle sections. Gd is quantified as a proxy for the relative expression of dystrophin and was validated in murine and human skeletal muscle sections following k-means clustering segmentation, before application to DMD patients with different gene mutations where dystrophin expression was measured up to 100 µg kg−1 Gd. These results demonstrate that immuno-mass spectrometry imaging is a viable approach for pre-clinical to clinical research in DMD. It rapidly quantified relative dystrophin in single tissue sections, efficiently used valuable patient resources, and may provide information on drug efficacy for clinical translation.

The etching of high aspect ratio structures in silicon via the Bosch process is essential in modern technologies such as microelectromechanical systems (MEMS) and through‑silicon vias (TSV) fabrication. The process can be very demanding on the mask selectivity due to long etching times, and it has been shown that an Al2O3 hard mask is very suitable in this regard, as it offers significantly higher selectivity compared to the conventional SiO2 or resist masks. In this work, we employ a combination of Scanning Electron Microscopy (SEM), Spectroscopic Ellipsometry (SE) and X-Ray Photoelectron Spectroscopy (XPS) depth profiling to scrutinize the Al2O3 mask etching mechanism and therefore the origin of the extraordinary high selectivity. We demonstrate that by increasing the passivation step time, a thicker fluorocarbon polymer layer is formed on the Al2O3, and Al2O3 is then removed with a minuscule average etch rate of ~0.01 nm/min. XPS depth profiling reveals that during Deep Reactive Ion Etching (DRIE) using the Bosch process, an AlFx layer is formed between the polymer and Al2O3. As AlFx is non-volatile, it requires sputtering to be removed. If the polymer layer is thick enough to attenuate the incoming ions such that their energy is not sufficient to lead to desorption of AlFx, such as when using a longer passivation time, the mask is not eroded. By investigating the surface after different amounts of DRIE cycles, we also obtained information about the formation rate of AlFx and the changes in the Al2O3 and polymer thicknesses over the course of a DRIE process. These findings further expand the knowledge of DRIE and can help process engineers to tailor the processes accordingly.

In vitro models of patient-derived muscle allow for more efficient development of genetic medicines for the muscular dystrophies, which often present mutation-specific pathologies. One popular strategy to generate patient-specific myotubes involves reprogramming dermal fibroblasts to a muscle lineage through MyoD induction. However, creating physiologically relevant, reproducible tissues exhibiting multinucleated, aligned myotubes with organized striations is dependent on the introduction of physicochemical cues that mimic the native muscle microenvironment. Here, we engineered patient-specific control and dystrophic muscle tissues in vitro by culturing and differentiating MyoD–directly reprogrammed fibroblasts isolated from one healthy control subject, three patients with Duchenne muscular dystrophy (DMD), and two Limb Girdle 2A/R1 (LGMD2A/R1) patients on micromolded gelatin hydrogels. Engineered DMD and LGMD2A/R1 tissues demonstrated varying levels of defects in α-actinin expression and organization relative to control, depending on the mutation. In genetically relevant DMD tissues amenable to mRNA reframing by targeting exon 44 or 45 exclusion, exposure to exon skipping antisense oligonucleotides modestly increased myotube coverage and alignment and rescued dystrophin protein expression. These findings highlight the value of engineered culture substrates in guiding the organization of reprogrammed patient fibroblasts into aligned muscle tissues, thereby extending their value as tools for exploration and dissection of the cellular and molecular basis of genetic muscle defects, rescue, and repair.

Literary narratives regularly contain passages that different readers attribute to different speakers: a character, the narrator, or the author. Since literary narratives are highly ambiguous constructs, it is often impossible to decide between diverging attributions of a specific passage by hermeneutic means. Instead, we hypothesise that attribution decisions are often influenced by annotator bias, in particular an annotator's literary preferences and beliefs. We present first results on the correlation between the literary attitudes of an annotator and their attribution choices. In a second set of experiments, we present a neural classifier that is capable of imitating individual annotators as well as a common-sense annotator, and reaches accuracies of up to 88% (which improves the majority baseline by 23%).

Caffeine is by far the most ubiquitous psychostimulant worldwide found in tea, coffee, cocoa, energy drinks, and many other beverages and food. Caffeine is almost exclusively metabolized in the liver by the cytochrome P-450 enzyme system to the main product paraxanthine and the additional products theobromine and theophylline. Besides its stimulating properties, two important applications of caffeine are metabolic phenotyping of cytochrome P450 1A2 (CYP1A2) and liver function testing. An open challenge in this context is to identify underlying causes of the large inter-individual variability in caffeine pharmacokinetics. Data is urgently needed to understand and quantify confounding factors such as lifestyle (e.g., smoking), the effects of drug-caffeine interactions (e.g., medication metabolized via CYP1A2), and the effect of disease. Here we report the first integrative and systematic analysis of data on caffeine pharmacokinetics from 141 publications and provide a comprehensive high-quality data set on the pharmacokinetics of caffeine, caffeine metabolites, and their metabolic ratios in human adults. The data set is enriched by meta-data on the characteristics of studied patient cohorts and subjects (e.g., age, body weight, smoking status, health status), the applied interventions (e.g., dosing, substance, route of application), measured pharmacokinetic time-courses, and pharmacokinetic parameters (e.g., clearance, half-life, area under the curve). We demonstrate via multiple applications how the data set can be used to solidify existing knowledge and gain new insights relevant for metabolic phenotyping and liver function testing based on caffeine. Specifically, we analyzed 1) the alteration of caffeine pharmacokinetics with smoking and use of oral contraceptives; 2) drug-drug interactions with caffeine as possible confounding factors of caffeine pharmacokinetics or source of adverse effects; 3) alteration of caffeine pharmacokinetics in disease; and 4) the applicability of caffeine as a salivary test substance by comparison of plasma and saliva data. In conclusion, our data set and analyses provide important resources which could enable more accurate caffeine-based metabolic phenotyping and liver function testing.

Species-specific diversities are particular features of mammalian chloride channel regulator, calcium activated (CLCA) genes. In contrast to four complex gene clusters in mammals, only two CLCA genes appear to exist in chickens. CLCA2 is conserved in both, while only the galline CLCA1 (gCLCA1) displays close genetic distance to mammalian clusters 1, 3 and 4. In this study, sequence analyses and biochemical characterizations revealed that gCLCA1 as a putative avian prototype shares common protein domains and processing features with all mammalian CLCA homologues. It has a transmembrane (TM) domain in the carboxy terminal region and its mRNA and protein were detected in the alimentary canal, where the protein was localized in the apical membrane of enterocytes, similar to CLCA4. Both mammals and birds seem to have at least one TM domain containing CLCA protein with complex glycosylation in the apical membrane of enterocytes. However, some characteristic features of mammalian CLCA1 and 3 including entire protein secretion and expression in cell types other than enterocytes seem to be dispensable for chicken. Phylogenetic analyses including twelve bird species revealed that avian CLCA1 and mammalian CLCA3 form clades separate from a major branch containing mammalian CLCA1 and 4. Overall, our data suggest that gCLCA1 and mammalian CLCA clusters 1, 3 and 4 stem from a common ancestor which underwent complex gene diversification in mammals but not in birds.

Systemic delivery of antisense oligonucleotides (AO) for DMD exon skipping has proven effective for reframing DMD mRNA, rescuing dystrophin expression, and slowing disease progression in animal models. In humans with Duchenne muscular dystrophy treated with AOs, low levels of dystrophin have been induced, and modest slowing of disease progression has been observed, highlighting the need for improved efficiency of human skipping drugs. Here, we demonstrate that dantrolene and Rycals S107 and ARM210 potentiate AO-mediated exon skipping of exon 44 or exon 45 in patient-derived myotube cultures with appropriate mutations. Further, dantrolene is shown to boost AO-mediated exon skipping in patient-derived, induced cardiomyocyte cultures. Our findings further validate the ryanodine receptors (RyR) as the likely target responsible for exon skip boosting and demonstrate potential applicability beyond exon 51 skipping. These data provide preclinical support of dantrolene trial as an adjuvant to AO-mediated exon-skipping therapy in humans and identify a novel Rycal, ARM210, for development as a potential exon-skipping booster. Further, they highlight the value of mutation-specific DMD culture models for basic discovery, preclinical drug screening and translation of personalized genetic medicines. Keywords: Duchenne muscular dystrophy, combination therapy, dantrolene, dystrophin, exon skipping, armgo, ARM210, muscle, therapy

The HfO2-based resistive random access memory (RRAM) is one of the most promising candidates for non-volatile memory applications. The detection and examination of the dynamic behavior of oxygen ions/vacancies are crucial to deeply understand the microscopic physical nature of the resistive switching (RS) behavior. By using synchrotron radiation based, non-destructive and bulk-sensitive hard X-ray photoelectron spectroscopy (HAXPES), we demonstrate an operando diagnostic detection of the oxygen ‘breathing’ behavior at the oxide/metal interface, namely, oxygen migration between HfO2 and TiN during different RS periods. The results highlight the significance of oxide/metal interfaces in RRAM, even in filament-type devices.

Abstract Background The aetiology and pathogenesis of primary bone marrow oedema syndrome (BMES) remain unclear. This retrospective cross-sectional study in a large cohort of patients with BMES was performed to characterise the overall skeletal status and turnover in patients with BMES, with the aim of identifying risk factors for this disease. Methods Patients who were diagnosed with BMES on the basis of clinical and radiological (magnetic resonance imaging) findings in our outpatient clinic were identified retrospectively. Patient history, co-existing metabolic disorders, bone metabolism parameters (serum calcium, phosphate, 25-OH-D3, bone-specific alkaline phosphatase, parathyroid hormone, and osteocalcin, and urinary deoxypyridinoline) and bone mineral density (as measured by dual-energy X-ray absorptiometry) were extracted from the medical records. Patients with secondary causes for BMES were excluded from the study. Results Of the 171 patients, 65 were identified without secondary cause for BMES. Of the 65 patients, 61.5% were female. The mean age was 49.5 ± 16.7 years, and age-related BMES prevalence showed two peaks, one in adolescence (11–20 years) and one at an older age (51–70 years). BMES predominantly affected the weight-bearing joints, namely, the ankle/foot (55.1%), knee (22.4%) and proximal femur (16.3%). Thyroid disorders and secondary hyperparathyroidism were highly prevalent (21.5 and 21.4%, respectively). On average, the cohort had elevated deoxypyridinoline levels and low 25-OH-D3 levels (19.0 ± 7.5 μg/l in patients without vitamin D supplementation). Osteopenia and osteoporosis were diagnosed in 47.4 and 17.5% of patients, respectively. Conclusions BMES is associated with high bone turnover. Patients who are diagnosed with BMES should be screened carefully for bone metabolism disorders and their potential risk factors.

The annotation guidelines for narrative levels and narrative acts have been developed in conjunction with my master thesis, the goal of which is to distinguish plot relevant settings from rather mentioned spaces in literary texts. For this, the determination of narrative levels is a requirement to precisely classify settings. Nevertheless, the guidelines itself were developed independently from the spatial classification task.

Abstract Background Impaired bone quality is associated with poor outcome of spinal surgery. The aim of the study was to assess the bone mineral status of patients scheduled to undergo spinal surgery and to report frequencies of bone mineral disorders. Methods We retrospectively analyzed the bone mineral status of 144 patients requiring spinal surgery including bone mineral density by dual-energy X-ray absorptiometry (DXA) as well as laboratory data with serum levels of 25-hydroxyvitamin D (25-OH-D), parathyroid hormone, calcium, bone specific alkaline phosphate, osteocalcin, and gastrin. High-resolution peripheral quantitative computed tomography (HR-pQCT) was additionally performed in a subgroup of 67 patients with T-Score below − 1.5 or history of vertebral fracture. Results Among 144 patients, 126 patients (87.5%) were older than 60 years. Mean age was 70.1 years. 42 patients (29.1%) had suffered from a vertebral compression fracture. 12 previously undiagnosed vertebral deformities were detected in 12 patients by vertebral fracture assessment (VFA). Osteoporosis was present in 39 patients (27.1%) and osteopenia in 63 patients (43.8%). Only 16 patients (11.1%) had received anti-osteoporotic therapy, while 54 patients (37.5%) had an indication for specific anti-osteoporotic therapy but had not received it yet. The majority of patients had inadequate vitamin D status (73.6%) and 34.7% of patients showed secondary hyperparathyroidism as a sign for a significant disturbed calcium homeostasis. In a subgroup of 67 patients, severe vertebral deformities were associated with stronger deficits in bone microarchitecture at the distal radius compared to the distal tibia. Conclusions This study shows that bone metabolism disorders are highly prevalent in elderly patients scheduled for spinal surgery. Vertebral deformities are associated with a predominant deterioration of bone microstructure at the distal radius. As impaired bone quality can compromise surgical outcome, we strongly recommend an evaluation of bone mineral status prior to operation and anti-osteoporotic therapy if necessary.

Abstract Primary production can determine the outcome of management actions on ecosystem properties, thereby defining sustainable management. Yet human agencies commonly overlook spatio-temporal variations in productivity by recommending fixed resource extraction thresholds. We studied the influence of forest productivity on habitat disturbance levels that boreal caribou – a threatened, late-seral ungulate under top-down control – should be able to withstand. Based on 10 years of boreal caribou monitoring, we found that adult survival and recruitment to populations decreased with landscape disturbance, but increased with forest productivity. This benefit of productivity reflected the net outcome of an increase in resources for apparent competitors and predators of caribou, and a more rapid return to the safety of mature conifer forests. We estimated 3-fold differences in forest harvesting levels that caribou populations could withstand due to variations in forest productivity. The adjustment of ecosystem provisioning services to local forest productivity should provide strong conservation and socio-economic advantages.

Long remained on the sidelines of research on the small towns, the ancient cities of the Massif Central have recently received a new analysis, conducted as part of a doctoral thesis. Thus, from a critical reading of the corpus of settlements obtained from the bibliographies, research conducted recently showed the diversity of cohousing medium mountain. In light of this work, it is possible to propose a classification of small towns and analyse their geography in the study areas. It shows a significant diffusion of the urban phenomenon, the distribution seems less influenced by the relief as communication channels which are however themselves very constrained by the topography. The chronological development of the urban framework shows a drop in enrollment began in the late 2th century but by no means a complete disappearance of the sites. However, this observation is greatly influenced by an incomplete documentation that remains largely silent for the 4th and 5th centuries is not to precisely characterise occupations. Finally, thematic analyses show contrasting settlements between highly urbanised sites and grouped habitats reduced to much simpler forms.

Osteoid osteoma (OO) is a benign bone tumor producing non-mineralized bone matrix (i.e., osteoid). While peritumoral edema is commonly found in OO, extensive bone marrow edema has been reported less frequently. Furthermore, the micro-morphological characteristics of the nidus and its central calcification remain unclear. In this study, a consecutive series of four patients suffering from extensive bone marrow edema triggered by intra-articular osteoid osteoma underwent clinical examination, magnetic resonance imaging (MRI) and computed tomography (CT) as well as dual-energy X-ray absorptiometry (DXA) and laboratory bone turnover analyses. The obtained resection specimens were processed by undecalcified histology and were subsequently analyzed by light microscopy and quantitative backscattered electron imaging (qBEI). We report an entity of intra-articular osteoid osteoma in the knee and foot, in which an extensive and persistent bone marrow edema syndrome masked the correct diagnosis. While metabolic bone diseases were excluded in all cases, the reassessment of the patients’ clinical history including pain characteristics (nocturnal, aspirin sensitivity) led us to perform additional CT, where the tumor was diagnosed. The micro-morphological analysis of the OO biopsies revealed that the nidus was surrounded by hyperosteoidosis, while central mineralization was detected in all cases. This mineralized area showed a significantly higher mineralization heterogeneity than the surrounding trabecular bone and more disorganized collagen fibers detected by qBEI and polarized light microscopy, respectively. Taken together, our results indicate that osteoid osteoma should be considered when persistent and extensive, peri-articular bone marrow edema is diagnosed. The central calcification that is found inside the nidus in conventional imaging was mirrored by bone matrix with a heterogeneous mineralization pattern. Keywords: Osteoid osteoma, Bone marrow edema, Joint pain, Bone tumor, MRI, qBEI

ABSTRACT The response to teriparatide has been described in very few cases of hypophosphatasia (HPP). In this cross‐sectional study, we report the prevalence of symptomatic bone marrow edema (BME) and fracture healing complications in a large cohort of childhood and adult HPP patients and discuss the results of teriparatide treatment in four cases. From 2016 to 2018, 51 patients with a diagnosis of HPP were seen at our institution. The diagnosis of HPP was established by low serum alkaline phosphatase (ALP), elevated serum pyridoxal‐5‐phosphate (PLP), at least one typical clinical symptom of HPP and supported by ALPL mutation analysis. In this study cohort, 28 (56%) and 14 (27%) patients had a history of fracture or a history of BME, respectively. Four patients, including middle‐aged to elderly women and men who all presented with persistent symptomatic BME or fracture healing complications, were treated with teriparatide. DXA was performed prior to treatment and laboratory values were measured on a regular basis during treatment. Treatment with teriparatide showed variable effects in terms of clinical and biochemical response. Although all four patients displayed a temporary increase in ALP activity, only two patients with a mild form of adult HPP and moderately increased PLP levels showed definite clinical and radiological improvement after teriparatide treatment. In conclusion, fracture healing complications and BME occur frequently in HPP patients. Teriparatide shows variable clinical and biochemical effects depending on the severity of the disease. PLP levels and the number of ALPL alleles might be good parameters to predict treatment outcomes. © 2019 The Authors. JBMR Plus Published by Wiley Periodicals, Inc. on behalf of the American Society for Bone and Mineral Research