Machine Learning Pipeline for Predicting Bone Marrow Edema Along the Sacroiliac Joints on Magnetic Resonance Imaging.

OBJECTIVE: We aimed to develop and validate a fully automated machine learning (ML) algorithm that predicts bone marrow edema (BME) on a quadrant level in sacroiliac (SI) joint magnetic resonance imaging (MRI). METHODS: A computer vision workflow automatically locates the SI joints, segments regions of interest (ilium and sacrum), performs objective quadrant extraction, and predicts presence of BME, suggestive of inflammatory lesions, on a quadrant level in semicoronal slices of T1/T2-weighted MRI scans. Ground truth was determined by consensus among human readers. The inflammation classifier was trained using a ResNet18 backbone and five-fold cross-validated on scans of patients with spondyloarthritis (SpA) (n = 279), postpartum individuals (n = 71), and healthy subjects (n = 114). Independent SpA patient MRI scans (n = 243) served as test data set. Patient-level predictions were derived from aggregating quadrant-level predictions, ie, at least one positive quadrant. RESULTS: The algorithm automatically detects the SI joints with a precision of 98.4% and segments ilium/sacrum with an intersection over union of 85.6% and 67.9%, respectively. The inflammation classifier performed well in cross-validation: area under the curve (AUC) 94.5%, balanced accuracy (B-ACC) 80.5%, and F1 score 64.1%. In the test data set, AUC was 88.2%, B-ACC 72.1%, and F1 score 50.8%. On a patient level, the model achieved a B-ACC of 81.6% and 81.4% in the cross-validation and test data set, respectively. CONCLUSION: We propose a fully automated ML pipeline that enables objective and standardized evaluation of BME along the SI joints on MRI. This method has the potential to screen large numbers of patients with (suspected) SpA and is a step closer towards artificial intelligence-assisted diagnosis and follow-up.

PERK recruits E-Syt1 at ER-mitochondria contacts for mitochondrial lipid transport and respiration.

The integrity of ER-mitochondria appositions ensures transfer of ions and phospholipids (PLs) between these organelles and exerts crucial effects on mitochondrial bioenergetics. Malfunctions within the ER-mitochondria contacts altering lipid trafficking homeostasis manifest in diverse pathologies, but the molecular effectors governing this process remain ill-defined. Here, we report that PERK promotes lipid trafficking at the ER-mitochondria contact sites (EMCS) through a non-conventional, unfolded protein response-independent, mechanism. PERK operates as an adaptor for the recruitment of the ER-plasma membrane tether and lipid transfer protein (LTP) Extended-Synaptotagmin 1 (E-Syt1), within the EMCS. In resting cells, the heterotypic E-Syt1-PERK interaction endorses transfer of PLs between the ER and mitochondria. Weakening the E-Syt1-PERK interaction or removing the lipid transfer SMP-domain of E-Syt1, compromises mitochondrial respiration. Our findings unravel E-Syt1 as a PERK interacting LTP and molecular component of the lipid trafficking machinery of the EMCS, which critically maintains mitochondrial homeostasis and fitness.

Sodium perturbs mitochondrial respiration and induces dysfunctional Tregs.

FOXP3+ regulatory T cells (Tregs) are central for peripheral tolerance, and their deregulation is associated with autoimmunity. Dysfunctional autoimmune Tregs display pro-inflammatory features and altered mitochondrial metabolism, but contributing factors remain elusive. High salt (HS) has been identified to alter immune function and to promote autoimmunity. By investigating longitudinal transcriptional changes of human Tregs, we identified that HS induces metabolic reprogramming, recapitulating features of autoimmune Tregs. Mechanistically, extracellular HS raises intracellular Na+, perturbing mitochondrial respiration by interfering with the electron transport chain (ETC). Metabolic disturbance by a temporary HS encounter or complex III blockade rapidly induces a pro-inflammatory signature and FOXP3 downregulation, leading to long-term dysfunction in vitro and in vivo. The HS-induced effect could be reversed by inhibition of mitochondrial Na+/Ca2+ exchanger (NCLX). Our results indicate that salt could contribute to metabolic reprogramming and that short-term HS encounter perturb metabolic fitness and long-term function of human Tregs with important implications for autoimmunity.

A Miniaturised, Fully Integrated NDIR CO2 Sensor On-Chip.

In this paper, we present a fully integrated Non-dispersive Infrared (NDIR) CO2 sensor implemented on a silicon chip. The sensor is based on an integrating cylinder with access waveguides. A mid-IR LED is used as the optical source, and two mid-IR photodiodes are used as detectors. The fully integrated sensor is formed by wafer bonding of two silicon substrates. The fabricated sensor was evaluated by performing a CO2 concentration measurement, showing a limit of detection of ∼750 ppm. The cross-sensitivity of the sensor to water vapor was studied both experimentally and numerically. No notable water interference was observed in the experimental characterizations. Numerical simulations showed that the transmission change induced by water vapor absorption is much smaller than the detection limit of the sensor. A qualitative analysis on the long term stability of the sensor revealed that the long term stability of the sensor is subject to the temperature fluctuations in the laboratory. The use of relatively cheap LED and photodiodes bare chips, together with the wafer-level fabrication process of the sensor provides the potential for a low cost, highly miniaturized NDIR CO2 sensor.

Osteopontin Expression Identifies a Subset of Recruited Macrophages Distinct from Kupffer Cells in the Fatty Liver.

Metabolic-associated fatty liver disease (MAFLD) represents a spectrum of disease states ranging from simple steatosis to non-alcoholic steatohepatitis (NASH). Hepatic macrophages, specifically Kupffer cells (KCs), are suggested to play important roles in the pathogenesis of MAFLD through their activation, although the exact roles played by these cells remain unclear. Here, we demonstrated that KCs were reduced in MAFLD being replaced by macrophages originating from the bone marrow. Recruited macrophages existed in two subsets with distinct activation states, either closely resembling homeostatic KCs or lipid-associated macrophages (LAMs) from obese adipose tissue. Hepatic LAMs expressed Osteopontin, a biomarker for patients with NASH, linked with the development of fibrosis. Fitting with this, LAMs were found in regions of the liver with reduced numbers of KCs, characterized by increased Desmin expression. Together, our data highlight considerable heterogeneity within the macrophage pool and suggest a need for more specific macrophage targeting strategies in MAFLD.

An interactive ImageJ plugin for semi-automated image denoising in electron microscopy.

The recent advent of 3D in electron microscopy (EM) has allowed for detection of nanometer resolution structures. This has caused an explosion in dataset size, necessitating the development of automated workflows. Moreover, large 3D EM datasets typically require hours to days to be acquired and accelerated imaging typically results in noisy data. Advanced denoising techniques can alleviate this, but tend to be less accessible to the community due to low-level programming environments, complex parameter tuning or a computational bottleneck. We present DenoisEM: an interactive and GPU accelerated denoising plugin for ImageJ that ensures fast parameter tuning and processing through parallel computing. Experimental results show that DenoisEM is one order of magnitude faster than related software and can accelerate data acquisition by a factor of 4 without significantly affecting data quality. Lastly, we show that image denoising benefits visualization and (semi-)automated segmentation and analysis of ultrastructure in various volume EM datasets.

On-Chip Non-Dispersive Infrared CO2 Sensor Based On an Integrating Cylinder.

In this paper, we propose a novel, miniaturized non-dispersive infrared (NDIR) CO2 sensor implemented on a silicon chip. The sensor has a simple structure, consisting of a hollow metallic cylindrical cavity along with access waveguides. A detailed analysis of the proposed sensor is presented. Simulation with 3D ray tracing shows that an integrating cylinder with 4 mm diameter gives an equivalent optical path length of 3 . 5 cm. The sensor is fabricated using Deep Reactive Ion Etching (DRIE) and wafer bonding. The fabricated sensor was evaluated by performing a CO2 concentration measurement, showing a limit of detection of ∼100 ppm. The response time of the sensor is only ∼2.8 s, due to its small footprint. The use of DRIE-based waveguide structures enables mass fabrication, as well as the potential co-integration of flip-chip integrated midIR light-emitting diodes (LEDs) and photodetectors, resulting in a compact, low-power, and low-cost NDIR CO2 sensor.

Image Degradation in Microscopic Images: Avoidance, Artifacts, and Solutions.

The goal of modern microscopy is to acquire high-quality image based data sets. A typical microscopy workflow is set up in order to address a specific biological question and involves different steps. The first step is to precisely define the biological question, in order to properly come to an experimental design for sample preparation and image acquisition. A better object representation allows biological users to draw more reliable scientific conclusions. Image restoration can manipulate the acquired data in an effort to reduce the impact of artifacts (spurious results) due to physical and technical limitations, resulting in a better representation of the object of interest. However, precise usage of these algorithms is necessary so as to avoid further artifacts that might influence the data analysis and bias the conclusions. It is essential to understand image acquisition, and how it introduces artifacts and degradations in the acquired data, so that their effects on subsequent analysis can be minimized. This paper provides an overview of the fundamental artifacts and degradations that affect many micrographs. We describe why artifacts appear, in what sense they impact overall image quality, and how to mitigate them by first improving the acquisition parameters and then applying proper image restoration techniques.

Bayesian deconvolution of scanning electron microscopy images using point-spread function estimation and non-local regularization.

Microscopy is one of the most essential imaging techniques in life sciences. High-quality images are required in order to solve (potentially life-saving) biomedical research problems. Many microscopy techniques do not achieve sufficient resolution for these purposes, being limited by physical diffraction and hardware deficiencies. Electron microscopy addresses optical diffraction by measuring emitted or transmitted electrons instead of photons, yielding nanometer resolution. Despite pushing back the diffraction limit, blur should still be taken into account because of practical hardware imperfections and remaining electron diffraction. Deconvolution algorithms can remove some of the blur in post-processing but they depend on knowledge of the point-spread function (PSF) and should accurately regularize noise. Any errors in the estimated PSF or noise model will reduce their effectiveness. This paper proposes a new procedure to estimate the lateral component of the point spread function of a 3D scanning electron microscope more accurately. We also propose a Bayesian maximum a posteriori deconvolution algorithm with a non-local image prior which employs this PSF estimate and previously developed noise statistics. We demonstrate visual quality improvements and show that applying our method improves the quality of subsequent segmentation steps.

Development and evaluation of a TaqMan duplex real-time PCR quantification method for reliable enumeration of Candidatus Microthrix.

Candidatus Microtrhix parvicella is one of the most common filamentous bacteria reported to be involved in bulking and foaming problems in activated sludge plants worldwide. In order to detect and quantify both M. parvicella and Microthrix calida by quantitative PCR (qPCR), primers targeting 16S rDNA genes were designed. The qPCR reaction was optimized by using the TaqMan technology and an internal positive control was included to ensure the absence of PCR inhibitors. A total of 29 samples originating from different wastewater treatment plants were analyzed and the results were compared by using conventional microscopy, fluorescent in situ hybridization and an existing SYBR Green-based assay. Our assay showed a 100% specificity for both M. parvicella and M. calida, a sensitivity of 2.93×10(9) to 29 copy numbers/reaction, an amplification efficiency of 93% and no PCR inhibition. By performing a spiking experiment including different Microthrix concentrations, recovery rates ranging from 65 to 98% were obtained. A positive correlation with the SYBR Green assay (R(2)=0.85) was found and most of the samples were in accordance with the microscopical observation. In comparison with SYBR Green assay, the probe-based TaqMan assay had a much lower detection limit. Compared with microscopy, some samples had a lower or higher enumeration when using qPCR. In conclusion, a qPCR method is forwarded here that could be useful as an early warning tool for fast and reliable detection of Microthrix in for instance sludge bulking events.

Tunable optical forces between nanophotonic waveguides.

The confinement of light in components with nanoscale cross-sections in nanophotonic circuits significantly enhances the magnitude of the optical forces experienced by these components. Here we demonstrate optical gradient forces between two nanophotonic waveguides, and show that the sign of the force can be tuned from attractive to repulsive by controlling the relative phase of the optical fields injected into the waveguides. The optical gradient force could have applications in optically tunable microphotonic devices and nanomechanical systems.

Combustive approach for measuring total volatile phosphorus content in landfill gas.

A technique was developed to measure the total gaseous phosphorus content in biogas. The amount of air needed for a neutral to oxidising flame was mixed with the biogas. The gas mixture was burnt in a closed quartz burner and the combustion gasses were bubbled through a nitric acid solution. The phosphate content in the bubbling liquid was determined with sector field ICP-MS. The technique was validated in the lab with phosphine. Afterwards the set-up was installed on a landfill. The total gaseous phosphorus content in the landfill gas, measured with the combustive technique, ranged from 1.65 to 4.44 microg P/m3. At the same time the phosphine concentration in the landfill gas was determined gas chromatographically (GC). The phosphine (PH3) content measured with GC ranged from 7.6 to 16.7 microg PH3-P/m3. Since the phosphine-P content (GC) was consistently higher than the total gaseous phosphorus content (burner/ICP-MS), the hypothesised presence of highly toxic gaseous phosphorus compounds other than phosphine could not be demonstrated.

Microbially mediated phosphine emission.

There is still a lot of controversy in literature concerning the question whether a biochemical system exists enabling micro-organisms to reduce phosphate to phosphine gas. The search for so-called 'de novo synthesised' phosphine is complicated by the fact that soils, slurries, sludges, etc., which are often used as inocula, usually contain matrix bound phosphine (MBP). Matrix bound phosphine is a general term used to indicate non-gaseous reduced phosphorus compounds that are transformed into phosphine gas upon reaction with bases or acids. A study was carried out to compare the different digestion methods, used to transform matrix bound phosphine into phosphine gas. It was demonstrated that caustic and acidic digestion methods should be used to measure the matrix bound phosphine of the inoculum prior to inoculation to avoid false positive results concerning de novo synthesis. This is especially true if anthropogenically influenced inocula possibly containing minute steel or aluminium particles are used. The comparative study on different digestion methods also revealed that the fraction of phosphorus in mild steel, converted to phosphine during acid corrosion depended on the temperature. Following these preliminary studies, anaerobic growth experiments were set up using different inocula and media to study the emission of phosphine gas. Phosphine was detected in the headspace gases and its quantity and timeframe of emission depended on the medium composition, suggesting microbially mediated formation of the gas. The amount of phosphine emitted during the growth experiments never exceeded the bound phosphine present in inocula, prior to inoculation. Hence, de novo synthesis of phosphine from phosphate could not be demonstrated. Yet, microbially mediated conversion to phosphine of hitherto unknown reduced phosphorus compounds in the inoculum was evidenced.

Occurrence and origin of phosphine in landfill gas.

A landfill (Hooge Maey, Flanders, Belgium) was subjected to an in-depth study in order to explain the origin of phosphine detected in high amounts in landfill gas, in comparison with biogas from other sources, during a previous study. The spatial and temporal variability of the phosphine concentration in landfill gas was assessed. Twenty-four wells were monitored and differences in phosphine concentration up to one log unit were observed (3.2-32.4 microg/m(3)). The phosphine concentration in each well was constant in time over a period of 4 months. No correlation was found between the phosphine concentration and methane, carbon dioxide, hydrogen sulfide, ethene or ethane concentration. In a series of laboratory tests, it was shown that phosphine was emitted during batch fermentation tests inoculated with landfill leachate when Fe(0) or Al(0) specimens were added. Conditions favouring corrosion of iron gave rise to higher emissions of phosphine. The phosphine concentration in the headspace of a batch test rose to 1.43 mg/m(3) after 27 days of incubation. Weight loss of corroding steel coupons correlated with phosphine emission. Calculations showed that all phosphine emitted from the 0.005 km(3) landfill (160 g/year) could be attributed to corrosion of metals. No evidence of de novo synthesis could be established.

Determination of phosphine in biogas and sludge at ppt-levels with gas chromatography-thermionic specific detection.

A gas chromatographic (GC) system to measure free phosphine in biogas and matrix bound phosphine in manure and sludge is presented. The system consists of a sample preconcentration trap filled with glass beads, connected with a capillary GC equipped with a thermionic specific detector. With a trap temperature as low as -155 degrees C, a sampling flow of 20 ml/min and a typical total sample volume of 100 ml, free phosphine concentrations in the low ng/m3 range and matrix bound phosphine in the low ng/kg dry matter range, can be accurately and reproducibly determined.