Neuro-explicit semantic segmentation of the diffusion cloud chamber.

For decades, in diffusion cloud chambers, different types of subatomic particle tracks from radioactive sources or cosmic radiation had to be identified with the naked eye which limited the amount of data that could be processed. In order to allow these classical particle detectors to enter the digital era, we successfully developed a neuro-explicit artificial intelligence model that, given an image from the cloud chamber, automatically annotates most of the particle tracks visible in the image according to the type of particle or process that created it. To achieve this goal, we combined the attention U-Net neural network architecture with methods that model the shape of the detected particle tracks. Our experiments show that the model effectively detects particle tracks and that the neuro-explicit approach decreases the misclassification rate of rare particles by 73% compared with solely using the attention U-Net.

Abundant toxin-related genes in the genomes of beneficial symbionts from deep-sea hydrothermal vent mussels.

Bathymodiolus mussels live in symbiosis with intracellular sulfur-oxidizing (SOX) bacteria that provide them with nutrition. We sequenced the SOX symbiont genomes from two Bathymodiolus species. Comparison of these symbiont genomes with those of their closest relatives revealed that the symbionts have undergone genome rearrangements, and up to 35% of their genes may have been acquired by horizontal gene transfer. Many of the genes specific to the symbionts were homologs of virulence genes. We discovered an abundant and diverse array of genes similar to insecticidal toxins of nematode and aphid symbionts, and toxins of pathogens such as Yersinia and Vibrio. Transcriptomics and proteomics revealed that the SOX symbionts express the toxin-related genes (TRGs) in their hosts. We hypothesize that the symbionts use these TRGs in beneficial interactions with their host, including protection against parasites. This would explain why a mutualistic symbiont would contain such a remarkable 'arsenal' of TRGs.

ICT-based system to predict and prevent falls (iStoppFalls): results from an international multicenter randomized controlled trial.

BACKGROUND: Falls and fall-related injuries are a serious public health issue. Exercise programs can effectively reduce fall risk in older people. The iStoppFalls project developed an Information and Communication Technology-based system to deliver an unsupervised exercise program in older people's homes. The primary aims of the iStoppFalls randomized controlled trial were to assess the feasibility (exercise adherence, acceptability and safety) of the intervention program and its effectiveness on common fall risk factors. METHODS: A total of 153 community-dwelling people aged 65+ years took part in this international, multicentre, randomized controlled trial. Intervention group participants conducted the exercise program for 16 weeks, with a recommended duration of 120 min/week for balance exergames and 60 min/week for strength exercises. All intervention and control participants received educational material including advice on a healthy lifestyle and fall prevention. Assessments included physical and cognitive tests, and questionnaires for health, fear of falling, number of falls, quality of life and psychosocial outcomes. RESULTS: The median total exercise duration was 11.7 h (IQR = 22.0) over the 16-week intervention period. There were no adverse events. Physiological fall risk (Physiological Profile Assessment, PPA) reduced significantly more in the intervention group compared to the control group (F1,127 = 4.54, p = 0.035). There was a significant three-way interaction for fall risk assessed by the PPA between the high-adherence (>90 min/week; n = 18, 25.4 %), low-adherence (<90 min/week; n = 53, 74.6 %) and control group (F2,125 = 3.12, n = 75, p = 0.044). Post hoc analysis revealed a significantly larger effect in favour of the high-adherence group compared to the control group for fall risk (p = 0.031), postural sway (p = 0.046), stepping reaction time (p = 0.041), executive functioning (p = 0.044), and quality of life (p for trend = 0.052). CONCLUSIONS: The iStoppFalls exercise program reduced physiological fall risk in the study sample. Additional subgroup analyses revealed that intervention participants with better adherence also improved in postural sway, stepping reaction, and executive function. TRIAL REGISTRATION: Australian New Zealand Clinical Trials Registry Trial ID: ACTRN12614000096651 International Standard Randomised Controlled Trial Number: ISRCTN15932647.

TGF-ß1-dependent induction and nuclear translocation of FHL2 promotes keratin expression in pilomatricoma.

Pilomatricoma is a tumour derived from hair matrix cells, which shows progressive keratin expression. Tumorigenesis is frequently associated with activating mutations in ß-catenin gene inducing nuclear expression of ß-catenin protein. The present study analysed the role of transforming growth factor-ß1 (TGF-ß1) and four-and-a-half LIM domain protein 2 (FHL2) in pilomatricoma in synopsis with their expression patterns in human anagen hair. Human anagen hair showed TGF-ß1 and nuclear FHL2 expression in the outer root sheath layer separated from nuclear ß-catenin staining, which was observed in cells of matrix and inner root sheath layers. Correspondingly, 41 out of 50 pilomatricomas showed co-labelling of TGF-ß1 and nuclear FHL2 in tumour cells, which mostly lacked nuclear ß-catenin expression. Tumoural proliferation (ki67) was associated with nuclear ß-catenin staining but not with expression of nuclear FHL2. In early pilomatricomas, TGF-ß1 expression was observed in few peripheral tumour cells showing absent or faint nuclear FHL2 co-staining. TGF-ß1 expression extended in growing tumours going along with strong nuclear FHL2 co-labelling as well as progressive keratin 14 and keratin 1 expression. In vitro, cultured human keratinocytes showed weak to marked autocrine TGF-ß1 expression; in case of enhanced TGF-ß1 expression associated with keratin 10 staining. TGF-ß1-treatment of cultured human keratinocytes induced nuclear and cytoplasmatic FHL2 staining as well as keratin 14 staining. Accordingly, siRNA-mediated FHL2 knockdown of TGF-ß1-stimulated keratinocytes reduced keratin 14 staining. In conclusion, tumoural TGF-ß1 secretion seems to induce nuclear translocation of co-factor FHL2 mediating progressive keratin expression in pilomatricoma.

Hydrogen is an energy source for hydrothermal vent symbioses.

The discovery of deep-sea hydrothermal vents in 1977 revolutionized our understanding of the energy sources that fuel primary productivity on Earth. Hydrothermal vent ecosystems are dominated by animals that live in symbiosis with chemosynthetic bacteria. So far, only two energy sources have been shown to power chemosynthetic symbioses: reduced sulphur compounds and methane. Using metagenome sequencing, single-gene fluorescence in situ hybridization, immunohistochemistry, shipboard incubations and in situ mass spectrometry, we show here that the symbionts of the hydrothermal vent mussel Bathymodiolus from the Mid-Atlantic Ridge use hydrogen to power primary production. In addition, we show that the symbionts of Bathymodiolus mussels from Pacific vents have hupL, the key gene for hydrogen oxidation. Furthermore, the symbionts of other vent animals such as the tubeworm Riftia pachyptila and the shrimp Rimicaris exoculata also have hupL. We propose that the ability to use hydrogen as an energy source is widespread in hydrothermal vent symbioses, particularly at sites where hydrogen is abundant.

MetaBar - a tool for consistent contextual data acquisition and standards compliant submission.

BACKGROUND: Environmental sequence datasets are increasing at an exponential rate; however, the vast majority of them lack appropriate descriptors like sampling location, time and depth/altitude: generally referred to as metadata or contextual data. The consistent capture and structured submission of these data is crucial for integrated data analysis and ecosystems modeling. The application MetaBar has been developed, to support consistent contextual data acquisition. RESULTS: MetaBar is a spreadsheet and web-based software tool designed to assist users in the consistent acquisition, electronic storage, and submission of contextual data associated to their samples. A preconfigured Microsoft Excel spreadsheet is used to initiate structured contextual data storage in the field or laboratory. Each sample is given a unique identifier and at any stage the sheets can be uploaded to the MetaBar database server. To label samples, identifiers can be printed as barcodes. An intuitive web interface provides quick access to the contextual data in the MetaBar database as well as user and project management capabilities. Export functions facilitate contextual and sequence data submission to the International Nucleotide Sequence Database Collaboration (INSDC), comprising of the DNA DataBase of Japan (DDBJ), the European Molecular Biology Laboratory database (EMBL) and GenBank. MetaBar requests and stores contextual data in compliance to the Genomic Standards Consortium specifications. The MetaBar open source code base for local installation is available under the GNU General Public License version 3 (GNU GPL3). CONCLUSION: The MetaBar software supports the typical workflow from data acquisition and field-sampling to contextual data enriched sequence submission to an INSDC database. The integration with the megx.net marine Ecological Genomics database and portal facilitates georeferenced data integration and metadata-based comparisons of sampling sites as well as interactive data visualization. The ample export functionalities and the INSDC submission support enable exchange of data across disciplines and safeguarding contextual data.