Results and Lessons Learned from the sbv IMPROVER Metagenomics Diagnostics for Inflammatory Bowel Disease Challenge

in Scientific Reports (2023), in press

A growing body of evidence links gut microbiota changes with inflammatory bowel disease (IBD), raising the potential benefit of exploiting metagenomics data for non-invasive IBD diagnostics. The sbv ... [more ▼]

A growing body of evidence links gut microbiota changes with inflammatory bowel disease (IBD), raising the potential benefit of exploiting metagenomics data for non-invasive IBD diagnostics. The sbv IMPROVER Metagenomics Diagnosis for Inflammatory Bowel Disease Challenge (MEDIC) investigated computational metagenomics methods for discriminating IBD and nonIBD subjects. Participants in this challenge were given independent training and test metagenomics data from IBD and nonIBD subjects, which could be wither either raw read data (sub-challenge 1, SC1) or processed taxonomy- and function-based profiles (sub-challenge 2, SC2). A total of 81 anonymized submissions were received between September 2019 and March 2020. Most participants’ predictions performed better than random predictions in classifying IBD vs nonIBD, Ulcerative Colitis (UC) vs nonIBD, and Crohn’s Disease (CD) vs nonIBD. However, discrimination between UC and CD remains challenging, with the classification quality similar to the set of random predictions. We analyzed the class prediction accuracy, the metagenomics features by the teams, and computational methods used. These results will be openly shared with the scientific community to help advance IBD research and illustrate the application of a range of computational methodologies for effective metagenomic classification. [less ▲]

Contactless radar-based breathing monitoring of premature infants in the neonatal intensive care unit

in Scientific Reports (2022), 12(1), 1--15

Vital sign monitoring systems are essential in the care of hospitalized neonates. Due to the immaturity of their organs and immune system, premature infants require continuous monitoring of their vital ... [more ▼]

Vital sign monitoring systems are essential in the care of hospitalized neonates. Due to the immaturity of their organs and immune system, premature infants require continuous monitoring of their vital parameters and sensors need to be directly attached to their fragile skin. Besides mobility restrictions and stress, these sensors often cause skin irritation and may lead to pressure necrosis. In this work, we show that a contactless radar-based approach is viable for breathing monitoring in the Neonatal intensive care unit (NICU). For the first time, different scenarios common to the NICU daily routine are investigated, and the challenges of monitoring in a real clinical setup are addressed through different contributions in the signal processing framework. Rather than just discarding measurements under strong interference, we present a novel random body movement mitigation technique based on the time-frequency decomposition of the recovered signal. In addition, we propose a simple and accurate frequency estimator which explores the harmonic structure of the breathing signal. As a result, the proposed radar-based solution is able to provide reliable breathing frequency estimation, which is close to the reference cabled device values most of the time. Our findings shed light on the strengths and limitations of this technology and lay the foundation for future studies toward a completely contactless solution for vital signs monitoring. [less ▲]

No evidence for intervention-associated DNA methylation changes in monocytes of patients with posttraumatic stress disorder.

in Scientific reports (2022), 12(1), 17347

DNA methylation patterns can be responsive to environmental influences. This observation has sparked interest in the potential for psychological interventions to influence epigenetic processes. Recent ... [more ▼]

DNA methylation patterns can be responsive to environmental influences. This observation has sparked interest in the potential for psychological interventions to influence epigenetic processes. Recent studies have observed correlations between DNA methylation changes and therapy outcome. However, most did not control for changes in cell composition. This study had two aims: first, we sought to replicate therapy-associated changes in DNA methylation of commonly assessed candidate genes in isolated monocytes from 60 female patients with post-traumatic stress disorder (PTSD). Our second, exploratory goal was to identify novel genomic regions with substantial pre-to-post intervention DNA methylation changes by performing whole-genome bisulfite sequencing (WGBS) in two patients with PTSD. Equivalence testing and Bayesian analyses provided evidence against physiologically meaningful intervention-associated DNA methylation changes in monocytes of PTSD patients in commonly investigated target genes (NR3C1, FKBP5, SLC6A4, OXTR). Furthermore, WGBS yielded only a limited set of candidate regions with suggestive evidence of differential DNA methylation pre- to post-therapy. These differential DNA methylation patterns did not prove replicable when investigated in the entire cohort. We conclude that there is no evidence for major, recurrent intervention-associated DNA methylation changes in the investigated genes in monocytes of patients with PTSD. [less ▲]

Magnetostructural coupling in RFeO3 (R = Nd, Tb, Eu and Gd)

in SCIENTIFIC REPORTS (2022), 12(1), 9697-14

We investigate the interplay of magnetization and lattice vibrations in rare-earth orthoferrites RFeO3, with a specific focus on non-symmetry-breaking anomalies. To do so, we study the magnetization ... [more ▼]

We investigate the interplay of magnetization and lattice vibrations in rare-earth orthoferrites RFeO3, with a specific focus on non-symmetry-breaking anomalies. To do so, we study the magnetization, magnon excitations and lattice dynamics as a function of temperature in NdFeO3, TbFeO3, EuFeO3 and GdFeO3. The magnetization shows distinct temperature anomalous behavior for all investigated rare-earth orthoferrites, even in the compounds with no phase transitions occurring at those temperatures. Through spin-phonon coupling, these magnetic changes are mirrored by the FeO6 rotation mode for all the studied RFeO3, revealing a common magnetostructural effect associated with the octahedra rotations. The R3+ oscillation modes evidence a Fe3+/R3+ spins cross-talk for the NdFeO3 and TbFeO3 cases. Our work sheds light into the common magnetostructural coupling in rare-earth orthoferrites, and the important role of magnetic anisotropy and spin-orbit coupling strength of the R-Fe interactions on the spin-reorientation transition at high temperatures. [less ▲]

Gene-corrected p.A30P SNCA patient-derived isogenic neurons rescue neuronal branching and function

in Scientific Reports (2021), 11

Parkinson’s disease (PD) is characterised by the degeneration of A9 dopaminergic neurons and the pathological accumulation of alpha-synuclein. The p.A30P SNCA mutation generates the pathogenic form of the ... [more ▼]

Parkinson’s disease (PD) is characterised by the degeneration of A9 dopaminergic neurons and the pathological accumulation of alpha-synuclein. The p.A30P SNCA mutation generates the pathogenic form of the alpha-synuclein protein causing an autosomal-dominant form of PD. There are limited studies assessing pathogenic SNCA mutations in patient-derived isogenic cell models. Here we provide a functional assessment of dopaminergic neurons derived from a patient harbouring the p.A30P SNCA mutation. Using two clonal gene-corrected isogenic cell lines we identified image-based phenotypes showing impaired neuritic processes. The pathological neurons displayed impaired neuronal activity, reduced mitochondrial respiration, an energy deficit, vulnerability to rotenone, and transcriptional alterations in lipid metabolism. Our data describes for the first time the mutation-only effect of the p.A30P SNCA mutation on neuronal function, supporting the use of isogenic cell lines in identifying image-based pathological phenotypes that can serve as an entry point for future disease-modifying compound screenings and drug discovery strategies. [less ▲]

Towards global flood mapping onboard low cost satellites with machine learning

in Scientific Reports (2021), 11(7249 (2021)),

Spaceborne Earth observation is a key technology for flood response, offering valuable information to decision makers on the ground. Very large constellations of small, nano satellites— ’CubeSats’ are a ... [more ▼]

Spaceborne Earth observation is a key technology for flood response, offering valuable information to decision makers on the ground. Very large constellations of small, nano satellites— ’CubeSats’ are a promising solution to reduce revisit time in disaster areas from days to hours. However, data transmission to ground receivers is limited by constraints on power and bandwidth of CubeSats. Onboard processing offers a solution to decrease the amount of data to transmit by reducing large sensor images to smaller data products. The ESA’s recent PhiSat-1 mission aims to facilitate the demonstration of this concept, providing the hardware capability to perform onboard processing by including a power-constrained machine learning accelerator and the software to run custom applications. This work demonstrates a flood segmentation algorithm that produces flood masks to be transmitted instead of the raw images, while running efficiently on the accelerator aboard the PhiSat-1. Our models are trained on WorldFloods: a newly compiled dataset of 119 globally verified flooding events from disaster response organizations, which we make available in a common format. We test the system on independent locations, demonstrating that it produces fast and accurate segmentation masks on the hardware accelerator, acting as a proof of concept for this approach. [less ▲]

Interplay between success and patterns of human collaboration: case study of a Thai Research Institute

in Scientific Reports (2021)

Intraoperative discrimination of native meningioma and dura mater by Raman spectroscopy

in Scientific Reports (2021)

Gene expression profile of CD14+ blood monocytes following lifestyle-induced weight loss in individuals with metabolic syndrome.

in Scientific Reports (2020), 10(1), 17855

Lifestyle-induced weight loss is regarded as an efficient therapy to reverse metabolic syndrome (MetS) and to prevent disease progression. The objective of this study was to investigate whether lifestyle ... [more ▼]

Lifestyle-induced weight loss is regarded as an efficient therapy to reverse metabolic syndrome (MetS) and to prevent disease progression. The objective of this study was to investigate whether lifestyle-induced weight loss modulates gene expression in circulating monocytes. We analyzed and compared gene expression in monocytes (CD14+ cells) and subcutaneous adipose tissue biopsies by unbiased mRNA profiling. Samples were obtained before and after diet-induced weight loss in well-defined male individuals in a prospective controlled clinical trial (ICTRP Trial Number: U1111-1158-3672). The BMI declined significantly (- 12.6%) in the treatment arm (N = 39) during the 6-month weight loss intervention. This was associated with a significant reduction in hsCRP (- 45.84%) and circulating CD14+ cells (- 21.0%). Four genes were differentially expressed (DEG's) in CD14+ cells following weight loss (ZRANB1, RNF25, RB1CC1 and KMT2C). Comparative analyses of paired CD14+ monocytes and subcutaneous adipose tissue samples before and after weight loss did not identify common genes differentially regulated in both sample types. Lifestyle-induced weight loss is associated with specific changes in gene expression in circulating CD14+ monocytes, which may affect ubiquitination, histone methylation and autophagy [less ▲]

Great apes selectively retrieve relevant memories to guide action

in Scientific Reports (2020)

Memory allows us to draw on past experiences to inform behaviour in the present. However, memories rarely match the situation at hand exactly, and new situations regularly trigger multiple related ... [more ▼]

Memory allows us to draw on past experiences to inform behaviour in the present. However, memories rarely match the situation at hand exactly, and new situations regularly trigger multiple related memories where only some are relevant to act upon. The flexibility of human memory systems is largely attributed to the ability to disregard irrelevant, but salient, memories in favour of relevant ones. This is considered an expression of an executive function responsible for suppressing irrelevant memories, associated with the prefrontal cortex. It is unclear to what extent animals have access to this ability. Here, we demonstrate, in a series of tool-use tasks designed to evoke conflicting memories, that chimpanzees and an orangutan suffer from this conflict but overcome it in favour of a more relevant memory. Such mnemonic flexibility is among the most advanced expressions of executive function shown in animals to date and might explain several behaviours related to tool-use, innovation, planning and more. [less ▲]