While the use of deep learning is a valuable technology for automatic detection systems for medical data and images, the biofouling community is still lacking an analytical tool for the detection and ...counting of diatoms on samples after short-term field exposure. In this work, a fully convolutional neural network was implemented as a fast and simple approach to detect diatoms on two-channel (fluorescence and phase-contrast) microscopy images by predicting bounding boxes. The developed approach performs well with only a small number of trainable parameters and a F1 score of 0.82. Counting diatoms was evaluated on a data set of 600 microscopy images of three different surface chemistries (hydrophilic and hydrophobic) and is very similar to counting by humans while demanding only a fraction of the analysis time.
Biofouling is a major challenge for sustainable shipping, filter membranes, heat exchangers, and medical devices. The development of fouling-resistant coatings requires the evaluation of their ...effectiveness. Such an evaluation is usually based on the assessment of fouling progression after different exposure times to the target medium (e.g. salt water). The manual assessment of macrofouling requires expert knowledge about local fouling communities due to high variances in phenotypical appearance, has single-image sampling inaccuracies for certain species, and lacks spatial information. Here an approach for automatic image-based macrofouling analysis was presented. A dataset with dense labels prepared from field panel images was made and a convolutional network (adapted U-Net) for the semantic segmentation of different macrofouling classes was proposed. The establishment of macrofouling localization allows for the generation of a successional model which enables the determination of direct surface attachment and in-depth epibiotic studies.
Polyelectrolyte multilayer (PEM) assembly is a versatile tool to construct low-fouling coatings. For application in the marine environment, their structure needs to be stabilized by covalent linkage. ...Here, we introduce an approach for spin coating of silane-based sol–gel chemistries using layer-by-layer assembly of polysaccharide-based hybrid polymer coatings (LBLHPs). The silane sol–gel chemistry allows the films to be cross-linked under water-based and mild reaction conditions. Two different silanes were used for this purpose, a conventional triethoxymethyl silane and a de novo synthesized zwitterionic silane. The polysaccharide–silane hybrid polymer coatings were thoroughly characterized with spectroscopic ellipsometry, water contact angle (WCA) goniometry, attenuated total reflection–Fourier transform infrared spectroscopy, and atomic force microscopy. The coatings showed good stability in seawater, smooth surfaces, a high degree of hydration, and WCAs below or close to the Berg limit. LBLHPs showed low-fouling properties in biological assays against nonspecific protein adsorption, attachment of the diatom Navicula perminuta, and settlement of zoospores of the macroalga Ulva linza.
Biofouling is a major challenge for sustainable shipping, filter membranes, heat exchangers, and medical devices. The development of fouling-resistant coatings requires the evaluation of their ...effectiveness. Such an evaluation is usually based on the assessment of fouling progression after different exposure times to the target medium (e.g., salt water). The manual assessment of macrofouling requires expert knowledge about local fouling communities due to high variances in phenotypical appearance, has single-image sampling inaccuracies for certain species, and lacks spatial information. Here we present an approach for automatic image-based macrofouling analysis. We created a dataset with dense labels prepared from field panel images and propose a convolutional network (adapted U-Net) for the semantic segmentation of different macrofouling classes. The establishment of macrofouling localization allows for the generation of a successional model which enables the determination of direct surface attachment and in-depth epibiotic studies.
Mesenteric infection by the parasitic blood fluke Schistosoma bovis is a common veterinary problem in Africa and the Middle East and occasionally in the Mediterranean Region. The species also has the ...ability to form interspecific hybrids with the human parasite S. haematobium with natural hybridisation observed in West Africa, presenting possible zoonotic transmission. Additionally, this exchange of alleles between species may dramatically influence disease dynamics and parasite evolution. We have generated a 374 Mb assembly of the S. bovis genome using Illumina and PacBio-based technologies. Despite infecting different hosts and organs, the genome sequences of S. bovis and S. haematobium appeared strikingly similar with 97% sequence identity. The two species share 98% of protein-coding genes, with an average sequence identity of 97.3% at the amino acid level. Genome comparison identified large continuous parts of the genome (up to several 100 kb) showing almost 100% sequence identity between S. bovis and S. haematobium. It is unlikely that this is a result of genome conservation and provides further evidence of natural interspecific hybridization between S. bovis and S. haematobium. Our results suggest that foreign DNA obtained by interspecific hybridization was maintained in the population through multiple meiosis cycles and that hybrids were sexually reproductive, producing viable offspring. The S. bovis genome assembly forms a highly valuable resource for studying schistosome evolution and exploring genetic regions that are associated with species-specific phenotypic traits.
The Photodetector Array Camera and Spectrometer (PACS) is one of the three science instruments on ESA's far infrared and submillimetre observatory. It employs two Ge:Ga photoconductor arrays ...(stressed and unstressed) with 16×25 pixels, each, and two filled silicon bolometer arrays with 16×32 and 32×64 pixels, respectively, to perform integral-field spectroscopy and imaging photometry in the 60–210 μm wavelength regime. In photometry mode, it simultaneously images two bands, 60–85 μm or 85–125 μm and 125–210 μm, over a field of view of ~1.75'× 3.5', with close to Nyquist beam sampling in each band. In spectroscopy mode, it images a field of 47” × 47”, resolved into 5×5 pixels, with an instantaneous spectral coverage of ~1500 km s-1 and a spectral resolution of ~175 km s-1. We summarise the design of the instrument, describe observing modes, calibration, and data analysis methods, and present our current assessment of the in-orbit performance of the instrument based on the performance verification tests. PACS is fully operational, and the achieved performance is close to or better than the pre-launch predictions.
There is increasing interest in the potential contribution of the gut microbiome to autism spectrum disorder (ASD). However, previous studies have been underpowered and have not been designed to ...address potential confounding factors in a comprehensive way. We performed a large autism stool metagenomics study (n = 247) based on participants from the Australian Autism Biobank and the Queensland Twin Adolescent Brain project. We found negligible direct associations between ASD diagnosis and the gut microbiome. Instead, our data support a model whereby ASD-related restricted interests are associated with less-diverse diet, and in turn reduced microbial taxonomic diversity and looser stool consistency. In contrast to ASD diagnosis, our dataset was well powered to detect microbiome associations with traits such as age, dietary intake, and stool consistency. Overall, microbiome differences in ASD may reflect dietary preferences that relate to diagnostic features, and we caution against claims that the microbiome has a driving role in ASD.
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•Limited autism-microbiome associations from stool metagenomics of n = 247 children•Romboutsia timonensis was the only taxa associated with autism diagnosis•Autistic traits such as restricted interests are associated with less-diverse diet•Less-diverse diet, in turn, is associated with lower microbiome alpha-diversity
Large autism stool metagenomics study finds limited direct autism associations, in contrast to strong relationships with dietary traits, stool consistency, and age, suggestive of a model whereby genetic and phenotypic measures of the autism spectrum promote a less-diverse diet that reduces microbiome diversity.
Little is known about the composition of intrahepatic immune cells and their contribution to the pathogenesis of primary sclerosing cholangitis (PSC). Herein, we aimed to create an atlas of ...intrahepatic T cells and thereby perform an in-depth characterization of T cells in inflamed human liver.
Different single-cell RNA sequencing methods were combined with in silico analyses on intrahepatic and peripheral T cells from patients with PSC (n = 11) and healthy donors (HDs, n = 4). Multi-parameter flow cytometry and functional in vitro experiments were conducted on samples from patients with PSC (n = 24), controls with other liver diseases and HDs.
We identified a population of intrahepatic naive-like CD4+ T cells, which was present in all liver diseases tested, but particularly expanded in PSC. This population had a transcriptome and T cell receptor repertoire similar to circulating naive T cells but expressed a set of genes associated with tissue residency. Their periductal location supported the concept of tissue-resident naive-like T cells in livers of patients with PSC. Trajectory inference suggested that these cells had the developmental propensity to acquire a T helper 17 (TH17) polarization state. Functional and chromatin accessibility experiments revealed that circulating naive T cells in patients with PSC were predisposed to polarize towards TH17 cells.
We report the first atlas of intrahepatic T cells in PSC, which led to the identification of a previously unrecognized population of tissue-resident naive-like T cells in the inflamed human liver and to the finding that naive CD4+ T cells in PSC harbour the propensity to develop into TH17 cells.
The composition of intrahepatic immune cells in primary sclerosing cholangitis (PSC) and their contribution to disease pathogenesis is widely unknown. We analysed intrahepatic T cells and identified a previously uncharacterized population of liver-resident CD4+ T cells which are expanded in the livers of patients with PSC compared to healthy liver tissue and other liver diseases. These cells are likely to contribute to the pathogenesis of PSC and could be targeted in novel therapeutic approaches.
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•First single-cell atlas of intrahepatic T cell landscape in PSC.•Identification of tissue-resident naive-like CD4+ T cells in human liver which are expanded in livers of patients with PSC.•Trajectory inference suggested a developmental propensity of these cells to acquire a TH17 polarization state.•Functional experiments, using circulating naive CD4+ T cells, support the inferred propensity to acquire a TH17 polarization state.•Chromatin accessibility studies revealed imprinting of naive CD4+ T cells towards effector function in PSC.
The phylogenetic structure of the microbial community residing in a fermentation sample from a production-scale biogas plant fed with maize silage, green rye and liquid manure was analysed by an ...integrated approach using clone library sequences and metagenome sequence data obtained by 454-pyrosequencing. Sequencing of 109 clones from a bacterial and an archaeal 16S-rDNA amplicon library revealed that the obtained nucleotide sequences are similar but not identical to 16S-rDNA database sequences derived from different anaerobic environments including digestors and bioreactors. Most of the bacterial 16S-rDNA sequences could be assigned to the phylum
Firmicutes with the most abundant class
Clostridia and to the class
Bacteroidetes, whereas most archaeal 16S-rDNA sequences cluster close to the methanogen
Methanoculleus bourgensis. Further sequences of the archaeal library most probably represent so far non-characterised species within the genus
Methanoculleus. A similar result derived from phylogenetic analysis of
mcrA clone sequences. The
mcrA gene product encodes the α-subunit of methyl-coenzyme-M reductase involved in the final step of methanogenesis. BLASTn analysis applying stringent settings resulted in assignment of 16S-rDNA metagenome sequence reads to 62 16S-rDNA amplicon sequences thus enabling frequency of abundance estimations for 16S-rDNA clone library sequences. Ribosomal Database Project (RDP) Classifier processing of metagenome 16S-rDNA reads revealed abundance of the phyla
Firmicutes,
Bacteroidetes and
Euryarchaeota and the orders
Clostridiales,
Bacteroidales and
Methanomicrobiales. Moreover, a large fraction of 16S-rDNA metagenome reads could not be assigned to lower taxonomic ranks, demonstrating that numerous microorganisms in the analysed fermentation sample of the biogas plant are still unclassified or unknown.
The incidence of esophageal adenocarcinoma (EAC) has risen significantly over recent decades. Although survival has improved, cure rates remain poor, with <20% of patients surviving 5 years. This is ...the first study to explore methylome, transcriptome and ENCODE data to characterize the role of methylation in EAC. We investigate the genome-wide methylation profile of 250 samples including 125 EAC, 19 Barrett's esophagus (BE), 85 squamous esophagus and 21 normal stomach. Transcriptome data of 70 samples (48 EAC, 4 BE and 18 squamous esophagus) were used to identify changes in methylation associated with gene expression. BE and EAC showed similar methylation profiles, which differed from squamous tissue. Hypermethylated sites in EAC and BE were mainly located in CpG-rich promoters. A total of 18575 CpG sites associated with 5538 genes were differentially methylated, 63% of these genes showed significant correlation between methylation and mRNA expression levels. Pathways involved in tumorigenesis including cell adhesion, TGF and WNT signaling showed enrichment for genes aberrantly methylated. Genes involved in chromosomal segregation and spindle formation were aberrantly methylated. Given the recent evidence that chromothripsis may be a driver mechanism in EAC, the role of epigenetic perturbation of these pathways should be further investigated. The methylation profiles revealed two EAC subtypes, one associated with widespread CpG island hypermethylation overlapping H3K27me3 marks and binding sites of the Polycomb proteins. These subtypes were supported by an independent set of 89 esophageal cancer samples. The most hypermethylated tumors showed worse patient survival.
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