Out-of-the-box calving-front detection method using deep learning

Glaciers across the globe react to the changing climate. Monitoring the transformation of glaciers is essential for projecting their contribution to global mean sea level rise. The delineation of glacier-calving fronts is an important part of the satellite-based monitoring process. This work presents a calving-front extraction method based on the deep learning framework nnU-Net, which stands for no new U-Net. The framework automates the training of a popular neural network, called U-Net, designed for segmentation tasks. Our presented method marks the calving front in synthetic aperture radar (SAR) images of glaciers. The images are taken by six different sensor systems. A benchmark dataset for calving-front extraction is used for training and evaluation. The dataset contains two labels for each image. One label denotes a classic image segmentation into different zones (glacier, ocean, rock, and no information available). The other label marks the edge between the glacier and the ocean, i.e., the calving front. In this work, the nnU-Net is modified to predict both labels simultaneously. In the field of machine learning, the prediction of multiple labels is referred to as multi-task learning (MTL). The resulting predictions of both labels benefit from simultaneous optimization. For further testing of the capabilities of MTL, two different network architectures are compared, and an additional task, the segmentation of the glacier outline, is added to the training. In the end, we show that fusing the label of the calving front and the zone label is the most efficient way to optimize both tasks with no significant accuracy reduction compared to the MTL neural-network architectures. The automatic detection of the calving front with an nnU-Net trained on fused labels improves from the baseline mean distance error (MDE) of 753±76 to 541±84 m. The scripts for our experiments are published on GitHub (https://github.com/ho11laqe/nnUNet_calvingfront_detection, last access: 20 November 2023). An easy-access version is published on Hugging Face (https://huggingface.co/spaces/ho11laqe/nnUNet_calvingfront_detection, last access: 20 November 2023).</p

Out-of-the-box calving front detection method using deep-learning

Abstract. Glaciers across the globe react to the changing climate. Monitoring the transformation of glaciers is essential for projecting their contribution to global mean sea level (GMSL) rise. The delineation of glacier-calving fronts is an important part of the satellite-based monitoring process. This work presents a calving front extraction method based on the deep learning framework nnU-Net, which stands for no new U-Net. The framework automates the training of a popular neural network, called 5 U-Net, designed for segmentation tasks. Our presented method marks the calving front in Synthetic Aperture Radar (SAR) images of glaciers. The images are taken by six different sensor systems. A benchmark dataset for calving front extraction is used for training and evaluation. The dataset contains two labels for each image. One label denotes a classic image segmentation into different zones (glacier, ocean, rock, and no information available). The other label marks the edge between the glacier and the ocean, i. e., the calving front. In this work, the nnU-Net is modified to predict both labels simultaneously. In the field 10 of machine learning, the prediction of multiple labels is referred to as Multi-Task-Learning (MTL). The resulting predictions of both labels benefit from simultaneous optimization. For further testing of the capabilities of MTL, two different network architectures are compared, and an additional task, the segmentation of the glacier outline, is added to the training. In the end, we show that fusing the label of the calving front and the zone label is the most efficient way to optimize both tasks with no significant accuracy reduction compared to the MTL neural network architectures. The automatic detection of the calving front 15 with a nnU-Net trained on fused labels improves from the baselineMean Distance Error (MDE) of 753 ± 76mto 541 ± 84m. The scripts for our experiments are published on Gitlab (https://gitlab.cs.fau.de/ho11laqe/nnunet_glacer.git)

A decellularized human corneal scaffold for anterior corneal surface reconstruction

Abstract Allogenic transplants of the cornea are prone to rejection, especially in repetitive transplantation and in scarred or highly vascularized recipient sites. Patients with these ailments would particularly benefit from the possibility to use non-immunogenic decellularized tissue scaffolds for transplantation, which may be repopulated by host cells in situ or in vitro. So, the aim of this study was to develop a fast and efficient decellularization method for creating a human corneal extracellular matrix scaffold suitable for repopulation with human cells from the corneal limbus. To decellularize human donor corneas, sodium deoxycholate, deoxyribonuclease I, and dextran were assessed to remove cells and nuclei and to control tissue swelling, respectively. We evaluated the decellularization effects on the ultrastructure, optical, mechanical, and biological properties of the human cornea. Scaffold recellularization was studied using primary human limbal epithelial cells, stromal cells, and melanocytes in vitro and a lamellar transplantation approach ex vivo. Our data strongly suggest that this approach allowed the effective removal of cellular and nuclear material in a very short period of time while preserving extracellular matrix proteins, glycosaminoglycans, tissue structure, and optical transmission properties. In vitro recellularization demonstrated good biocompatibility of the decellularized human cornea and ex vivo transplantation revealed complete epithelialization and stromal repopulation from the host tissue. Thus, the generated decellularized human corneal scaffold could be a promising biological material for anterior corneal reconstruction in the treatment of corneal defects

Investigation of Electric Field–Induced Structural Changes at Fe-Doped SrTiO3 Anode Interfaces by Second Harmonic Generation

We report on the detection of electric field–induced second harmonic generation (EFISHG) from the anode interfaces of reduced and oxidized Fe-doped SrTiO3 (Fe:STO) single crystals. For the reduced crystal, we observe steady enhancements of the susceptibility components as the imposed dc-voltage increases. The enhancements are attributed to a field-stabilized electrostriction, leading to Fe:Ti-O bond stretching and bending in Fe:Ti-O6 octahedra. For the oxidized crystal, no obvious structural changes are observed below 16 kV/cm. Above 16 kV/cm, a sharp enhancement of the susceptibilities occurs due to local electrostrictive deformations in response to oxygen vacancy migrations away from the anode. Differences between the reduced and oxidized crystals are explained by their relative oxygen vacancy and free carrier concentrations which alter internal electric fields present at the Pt/Fe:STO interfaces. Our results show that the optical SHG technique is a powerful tool for detecting structural changes near perovskite-based oxide interfaces due to field-driven oxygen vacancy migration

Experimental Test of Connector Rotation during DNA Packaging into Bacteriophage ϕ29 Capsids

The bacteriophage ϕ29 generates large forces to compact its double-stranded DNA genome into a protein capsid by means of a portal motor complex. Several mechanical models for the generation of these high forces by the motor complex predict coupling of DNA translocation to rotation of the head-tail connector dodecamer. Putative connector rotation is investigated here by combining the methods of single-molecule force spectroscopy with polarization-sensitive single-molecule fluorescence. In our experiment, we observe motor function in several packaging complexes in parallel using video microscopy of bead position in a magnetic trap. At the same time, we follow the orientation of single fluorophores attached to the portal motor connector. From our data, we can exclude connector rotation with greater than 99% probability and therefore answer a long-standing mechanistic question

Zafirlukast Is a Dual Modulator of Human Soluble Epoxide Hydrolase and Peroxisome Proliferator-Activated Receptor γ

Cysteinyl leukotriene receptor 1 antagonists (CysLT1RA) are frequently used as add-on medication for the treatment of asthma. Recently, these compounds have shown protective effects in cardiovascular diseases. This prompted us to investigate their influence on soluble epoxide hydrolase (sEH) and peroxisome proliferator activated receptor (PPAR) activities, two targets known to play an important role in CVD and the metabolic syndrome. Montelukast, pranlukast and zafirlukast inhibited human sEH with IC50 values of 1.9, 14.1, and 0.8 μM, respectively. In contrast, only montelukast and zafirlukast activated PPARγ in the reporter gene assay with EC50 values of 1.17 μM (21.9% max. activation) and 2.49 μM (148% max. activation), respectively. PPARα and δ were not affected by any of the compounds. The activation of PPARγ was further investigated in 3T3-L1 adipocytes. Analysis of lipid accumulation, mRNA and protein expression of target genes as well as PPARγ phosphorylation revealed that montelukast was not able to induce adipocyte differentiation. In contrast, zafirlukast triggered moderate lipid accumulation compared to rosiglitazone and upregulated PPARγ target genes. In addition, we found that montelukast and zafirlukast display antagonistic activities concerning recruitment of the PPARγ cofactor CBP upon ligand binding suggesting that both compounds act as PPARγ modulators. In addition, zafirlukast impaired the TNFα triggered phosphorylation of PPARγ2 on serine 273. Thus, zafirlukast is a novel dual sEH/PPARγ modulator representing an excellent starting point for the further development of this compound class

Association of candidate pharmacogenetic markers with platinum-induced ototoxicity:PanCareLIFE dataset

Genetic association studies suggest a genetic predisposi- tion for cisplatin-induced ototoxicity. Among other candidate genes, thiopurine methyltransferase ( TPMT ) is considered a critical gene for susceptibility to cisplatin-induced hearing loss in a pharmacogenetic guideline. The PanCareLIFE cross- sectional cohort study evaluated the genetic associations in a large pan-European population and assessed the diagnos- tic accuracy of the genetic markers. 1,112 pediatric cancer survivors who had provided biomaterial for genotyping were screened for participation in the pharmacogenetic association study. 900 participants qualified for inclusion. Based on the assessment of original audiograms, patients were assigned to three phenotype categories: no, minor, and clinically relevant hearing loss. Fourteen variants in eleven candidate genes ( ABCC3, OTOS, TPMT, SLC22A2, NFE2L2, SLC16A5, LRP2, GSTP1, SOD2, WFS1, and ACYP2 ) were genotyped. The genotype and phenotype data represent a resource for conducting meta- analyses to derive a more precise pooled estimate of the ef- fects of genes on the risk of hearing loss due to platinum treatment

Analysis of the African coelacanth genome sheds light on tetrapod evolution

It was a zoological sensation when a living specimen of the coelacanth was first discovered in 1938, as this lineage of lobe-finned fish was thought to have gone extinct 70 million years ago. The modern coelacanth looks remarkably similar to many of its ancient relatives, and its evolutionary proximity to our own fish ancestors provides a glimpse of the fish that first walked on land. Here we report the genome sequence of the African coelacanth, Latimeria chalumnae. Through a phylogenomic analysis, we conclude that the lungfish, and not the coelacanth, is the closest living relative of tetrapods. Coelacanth protein-coding genes are significantly more slowly evolving than those of tetrapods, unlike other genomic features . Analyses of changes in genes and regulatory elements during the vertebrate adaptation to land highlight genes involved in immunity, nitrogen excretion and the development of fins, tail, ear, eye, brain, and olfaction. Functional assays of enhancers involved in the fin-to-limb transition and in the emergence of extra-embryonic tissues demonstrate the importance of the coelacanth genome as a blueprint for understanding tetrapod evolution

Outcomes of cerebral venous thrombosis due to vaccine-induced immune thrombotic thrombocytopenia after the acute phase

© 2022 American Heart Association, Inc.Background: Cerebral venous thrombosis (CVT) due to vaccine-induced immune thrombotic thrombocytopenia (VITT) is a severe condition, with high in-hospital mortality rates. Here, we report clinical outcomes of patients with CVT-VITT after SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) vaccination who survived initial hospitalization. Methods: We used data from an international registry of patients who developed CVT within 28 days of SARS-CoV-2 vaccination, collected until February 10, 2022. VITT diagnosis was classified based on the Pavord criteria. Outcomes were mortality, functional independence (modified Rankin Scale score 0–2), VITT relapse, new thrombosis, and bleeding events (all after discharge from initial hospitalization). Results: Of 107 CVT-VITT cases, 43 (40%) died during initial hospitalization. Of the remaining 64 patients, follow-up data were available for 60 (94%) patients (37 definite VITT, 9 probable VITT, and 14 possible VITT). Median age was 40 years and 45/60 (75%) patients were women. Median follow-up time was 150 days (interquartile range, 94–194). Two patients died during follow-up (3% [95% CI, 1%–11%). Functional independence was achieved by 53/60 (88% [95% CI, 78%–94%]) patients. No new venous or arterial thrombotic events were reported. One patient developed a major bleeding during follow-up (fatal intracerebral bleed). Conclusions: In contrast to the high mortality of CVT-VITT in the acute phase, mortality among patients who survived the initial hospitalization was low, new thrombotic events did not occur, and bleeding events were rare. Approximately 9 out of 10 CVT-VITT patients who survived the acute phase were functionally independent at follow-up.This study was funded by the Netherlands Organisation for Health Research and Development (ZonMw, grant number 10430072110005), the Dr. C.J. Vaillant Foundation, and Hospital District of Helsinki and Uusimaa (grant TYH2022223).info:eu-repo/semantics/publishedVersio

Phylogenomic analyses of malaria parasites and evolution of their exported proteins

<p>Abstract</p> <p>Background</p> <p><it>Plasmodium falciparum </it>is the most malignant agent of human malaria. It belongs to the taxon Laverania, which includes other ape-infecting <it>Plasmodium </it>species. The origin of the Laverania is still debated. <it>P. falciparum </it>exports pathogenicity-related proteins into the host cell using the <it>Plasmodium </it>export element (PEXEL). Predictions based on the presence of a PEXEL motif suggest that more than 300 proteins are exported by <it>P. falciparum</it>, while there are many fewer exported proteins in non-Laverania.</p> <p>Results</p> <p>A whole-genome approach was applied to resolve the phylogeny of eight <it>Plasmodium </it>species and four outgroup taxa. By using 218 orthologous proteins we received unanimous support for a sister group position of Laverania and avian malaria parasites. This observation was corroborated by the analyses of 28 exported proteins with orthologs present in all <it>Plasmodium </it>species. Most interestingly, several deviations from the <it>P. falciparum </it>PEXEL motif were found to be present in the orthologous sequences of non-Laverania.</p> <p>Conclusion</p> <p>Our phylogenomic analyses strongly support the hypotheses that the Laverania have been founded by a single <it>Plasmodium </it>species switching from birds to African great apes or <it>vice versa</it>. The deviations from the canonical PEXEL motif in orthologs may explain the comparably low number of exported proteins that have been predicted in non-Laverania.</p