A Flexible Tool to Correct Superimposed Mass Isotopologue Distributions in GC-APCI-MS Flux Experiments

The investigation of metabolic fluxes and metabolite distributions within cells by means of tracer molecules is a valuable tool to unravel the complexity of biological systems. Technological advances in mass spectrometry (MS) technology such as atmospheric pressure chemical ionization (APCI) coupled with high resolution (HR), not only allows for highly sensitive analyses but also broadens the usefulness of tracer-based experiments, as interesting signals can be annotated de novo when not yet present in a compound library. However, several effects in the APCI ion source, i.e., fragmentation and rearrangement, lead to superimposed mass isotopologue distributions (MID) within the mass spectra, which need to be corrected during data evaluation as they will impair enrichment calculation otherwise. Here, we present and evaluate a novel software tool to automatically perform such corrections. We discuss the different effects, explain the implemented algorithm, and show its application on several experimental datasets. This adjustable tool is available as an R package from CRAN.SALSA (School of Analytical Sciences Adlershof, Albert-Einstein-Straße 5, 12489 Berlin, Germany)Peer Reviewe

A Call to Reflect on Evaluation Practices for Failure Detection in Image Classification

Reliable application of machine learning-based decision systems in the wild is one of the major challenges currently investigated by the field. A large portion of established approaches aims to detect erroneous predictions by means of assigning confidence scores. This confidence may be obtained by either quantifying the model's predictive uncertainty, learning explicit scoring functions, or assessing whether the input is in line with the training distribution. Curiously, while these approaches all state to address the same eventual goal of detecting failures of a classifier upon real-life application, they currently constitute largely separated research fields with individual evaluation protocols, which either exclude a substantial part of relevant methods or ignore large parts of relevant failure sources. In this work, we systematically reveal current pitfalls caused by these inconsistencies and derive requirements for a holistic and realistic evaluation of failure detection. To demonstrate the relevance of this unified perspective, we present a large-scale empirical study for the first time enabling benchmarking confidence scoring functions w.r.t all relevant methods and failure sources. The revelation of a simple softmax response baseline as the overall best performing method underlines the drastic shortcomings of current evaluation in the abundance of publicized research on confidence scoring. Code and trained models are at https://github.com/IML-DKFZ/fd-shifts

Secreted Klotho and FGF23 in chronic kidney disease Stage 1 to 5: a sequence suggested from a cross-sectional study

Background Klotho and fibroblast growth factor 23 (FGF23) are key regulators of mineral metabolism in renal insufficiency. FGF23 levels have been shown to increase early in chronic kidney disease (CKD); however, the corresponding soluble Klotho levels at the different CKD stages are not known. Methods Soluble Klotho, FGF23, parathyroid hormone (PTH), 1,25-dihydroxy vitamin D3 (1,25D) and other parameters of mineral metabolism were measured in an observational cross-sectional study in 87 patients. Locally weighted scatter plot smoothing function of these parameters were plotted versus estimated glomerular filtration rate (eGFR) to illustrate the pattern of the relationship. Linear and non-linear regression analyses were performed to estimate changes in mineral metabolism parameters per 1mL/min/1.73 m2 decline. Results In CKD 1-5, Klotho and 1,25D linearly decreased, whereas both FGF23 and PTH showed a baseline at early CKD stages and then a curvilinear increase. Crude mean Klotho level declined by 4.8 pg/mL (95% CI 3.5-6.2 pg/mL, P < 0.0001) and 1,25D levels by 0.30 ng/L (95% CI 0.18-0.41 ng/L, P < 0.0001) as GFR declined by 1 mL/min/1.73 m2. After adjustment for age, gender, serum 25-hydroxyvitamin D levels and concomitant medications (calcium, supplemental vitamin D and calcitriol), we estimated that the mean Klotho change was 3.2 pg/mL (95% CI 1.2-5.2 pg/mL, P = 0.0019) for each 1 mL/min/1.73 m2 GFR change. FGF23 departed from the baseline at an eGFR of 47 mL/min/1.73 m2 (95% CI 39-56 mL/min/1.73 m2), whereas PTH departed at an eGFR of 34 mL/min/1.73 m2 (95% CI 19-50 mL/min/1.73 m2). Conclusions Soluble Klotho and 1,25D levels decrease and FGF23 levels increase at early CKD stages, whereas PTH levels increase at more advanced CKD stage

cOOpD: Reformulating COPD classification on chest CT scans as anomaly detection using contrastive representations

Classification of heterogeneous diseases is challenging due to their complexity, variability of symptoms and imaging findings. Chronic Obstructive Pulmonary Disease (COPD) is a prime example, being underdiagnosed despite being the third leading cause of death. Its sparse, diffuse and heterogeneous appearance on computed tomography challenges supervised binary classification. We reformulate COPD binary classification as an anomaly detection task, proposing cOOpD: heterogeneous pathological regions are detected as Out-of-Distribution (OOD) from normal homogeneous lung regions. To this end, we learn representations of unlabeled lung regions employing a self-supervised contrastive pretext model, potentially capturing specific characteristics of diseased and healthy unlabeled regions. A generative model then learns the distribution of healthy representations and identifies abnormalities (stemming from COPD) as deviations. Patient-level scores are obtained by aggregating region OOD scores. We show that cOOpD achieves the best performance on two public datasets, with an increase of 8.2% and 7.7% in terms of AUROC compared to the previous supervised state-of-the-art. Additionally, cOOpD yields well-interpretable spatial anomaly maps and patient-level scores which we show to be of additional value in identifying individuals in the early stage of progression. Experiments in artificially designed real-world prevalence settings further support that anomaly detection is a powerful way of tackling COPD classification

Distribution pattern following systemic mesenchymal stem cell injection depends on the age of the recipient and neuronal health

BACKGROUND: Mesenchymal stem cells (MSCs) show therapeutic efficacy in many different age-related degenerative diseases, including Alzheimer's disease. Very little is currently known about whether or not aging impacts the transplantation efficiency of MSCs. METHODS: In this study, we investigated the distribution of intravenously transplanted syngeneic MSCs derived from young and aged mice into young, aged, and transgenic APP/PS1 Alzheimer's disease mice. MSCs from male donors were transplanted into female mice and their distribution pattern was monitored by PCR using Y-chromosome specific probes. Biodistribution of transplanted MSCs in the brains of APP/PS1 mice was additionally confirmed by immunofluorescence and confocal microscopy. RESULTS: Four weeks after transplantation into young mice, young MSCs were found in the lung, axillary lymph nodes, blood, kidney, bone marrow, spleen, liver, heart, and brain cortex. In contrast, young MSCs that were transplanted into aged mice were only found in the brain cortex. In both young and aged mouse recipients, transplantation of aged MSCs showed biodistribution only in the blood and spleen. Although young transplanted MSCs only showed neuronal distribution in the brain cortex in young mice, they exhibited a wide neuronal distribution pattern in the brains of APP/PS1 mice and were found in the cortex, cerebellum, hippocampus, olfactory bulb, and brainstem. The immunofluorescent signal of both transplanted MSCs and resident microglia was robust in the brains of APP/PS1 mice. Monocyte chemoattractant-1 levels were lowest in the brain cortex of young mice and were significantly increased in APP/PS1 mice. Within the hippocampus, monocyte chemoattractant-1 levels were significantly higher in aged mice compared with younger and APP/PS1 mice. CONCLUSIONS: We demonstrate in vivo that MSC biodistribution post transplantation is detrimentally affected by aging and neuronal health. Aging of both the recipient and the donor MSCs used attenuates transplantation efficiency. Clinically, our data would suggest that aged MSCs should not be used for transplantation and that transplantation of MSCs into aged patients will be less efficacious

Fiber-orientation independent component of R2* obtained from single-orientation MRI measurements in simulations and a post-mortem human optic chiasm

The effective transverse relaxation rate (R2*) is sensitive to the microstructure of the human brain like the g-ratio which characterises the relative myelination of axons. However, the fibre-orientation dependence of R2* degrades its reproducibility and any microstructural derivative measure. To estimate its orientation-independent part (R2,iso*) from single multi-echo gradient-recalled-echo (meGRE) measurements at arbitrary orientations, a second-order polynomial in time model (hereafter M2) can be used. Its linear time-dependent parameter, β1, can be biophysically related to R2,iso* when neglecting the myelin water (MW) signal in the hollow cylinder fibre model (HCFM). Here, we examined the performance of M2 using experimental and simulated data with variable g-ratio and fibre dispersion. We found that the fitted β1 can estimate R2,iso* using meGRE with long maximum-echo time (TEmax ≈ 54 ms), but not accurately captures its microscopic dependence on the g-ratio (error 84%). We proposed a new heuristic expression for β1 that reduced the error to 12% for ex vivo compartmental R2 values. Using the new expression, we could estimate an MW fraction of 0.14 for fibres with negligible dispersion in a fixed human optic chiasm for the ex vivo compartmental R2 values but not for the in vivo values. M2 and the HCFM-based simulations failed to explain the measured R2*-orientation-dependence around the magic angle for a typical in vivo meGRE protocol (with TEmax ≈ 18 ms). In conclusion, further validation and the development of movement-robust in vivo meGRE protocols with TEmax ≈ 54 ms are required before M2 can be used to estimate R2,iso* in subjects