Variability analysis of LC-MS experimental factors and their impact on machine learning

Abstract Background Machine learning (ML) technologies, especially deep learning (DL), have gained increasing attention in predictive mass spectrometry (MS) for enhancing the data-processing pipeline from raw data analysis to end-user predictions and rescoring. ML models need large-scale datasets for training and repurposing, which can be obtained from a range of public data repositories. However, applying ML to public MS datasets on larger scales is challenging, as they vary widely in terms of data acquisition methods, biological systems, and experimental designs. Results We aim to facilitate ML efforts in MS data by conducting a systematic analysis of the potential sources of variability in public MS repositories. We also examine how these factors affect ML performance and perform a comprehensive transfer learning to evaluate the benefits of current best practice methods in the field for transfer learning. Conclusions Our findings show significantly higher levels of homogeneity within a project than between projects, which indicates that it is important to construct datasets most closely resembling future test cases, as transferability is severely limited for unseen datasets. We also found that transfer learning, although it did increase model performance, did not increase model performance compared to a non-pretrained model

Genetic newborn screening and digital technologies: A project protocol based on a dual approach to shorten the rare diseases diagnostic path in Europe.

Since 72% of rare diseases are genetic in origin and mostly paediatrics, genetic newborn screening represents a diagnostic "window of opportunity". Therefore, many gNBS initiatives started in different European countries. Screen4Care is a research project, which resulted of a joint effort between the European Union Commission and the European Federation of Pharmaceutical Industries and Associations. It focuses on genetic newborn screening and artificial intelligence-based tools which will be applied to a large European population of about 25.000 infants. The neonatal screening strategy will be based on targeted sequencing, while whole genome sequencing will be offered to all enrolled infants who may show early symptoms but have resulted negative at the targeted sequencing-based newborn screening. We will leverage artificial intelligence-based algorithms to identify patients using Electronic Health Records (EHR) and to build a repository "symptom checkers" for patients and healthcare providers. S4C will design an equitable, ethical, and sustainable framework for genetic newborn screening and new digital tools, corroborated by a large workout where legal, ethical, and social complexities will be addressed with the intent of making the framework highly and flexibly translatable into the diverse European health systems

Prion protein-specific antibodies that detect multiple TSE agents with high sensitivity

This paper describes the generation, characterisation and potential applications of a panel of novel anti-prion protein monoclonal antibodies (mAbs). The mAbs were generated by immunising PRNP null mice, using a variety of regimes, with a truncated form of recombinant ovine prion protein spanning residues 94–233. Epitopes of specific antibodies were mapped using solid-phase Pepscan analysis and clustered to four distinct regions within the PrP molecule. We have demonstrated the utility of these antibodies by use of Western blotting and immunohistochemistry in tissues from a range of different species affected by transmissible spongiform encephalopathy (TSE). In comparative tests against extensively-used and widely-published, commercially available antibodies, similar or improved results can be obtained using these new mAbs, specifically in terms of sensitivity of detection. Since many of these antibodies recognise native PrPC, they could also be applied to a broad range of immunoassays such as flow cytometry, DELFIA analysis or immunoprecipitation. We are using these reagents to increase our understanding of TSE pathogenesis and for use in potential diagnostic screening assays

Prion peptide uptake in microglial cells--the effect of naturally occurring autoantibodies against prion protein.

In prion disease, a profound microglial activation that precedes neurodegeneration has been observed in the CNS. It is still not fully elucidated whether microglial activation has beneficial effects in terms of prion clearance or whether microglial cells have a mainly detrimental function through the release of pro-inflammatory cytokines. To date, no disease-modifying therapy exists. Several immunization attempts have been performed as one therapeutic approach. Recently, naturally occurring autoantibodies against the prion protein (nAbs-PrP) have been detected. These autoantibodies are able to break down fibrils of the most commonly used mutant prion variant PrP106-126 A117V and prevent PrP106-126 A117V-induced toxicity in primary neurons. In this study, we examined the phagocytosis of the prion peptide PrP106-126 A117V by primary microglial cells and the effect of nAbs-PrP on microglia. nAbs-PrP considerably enhanced the uptake of PrP106-126 A117V without inducing an inflammatory response in microglial cells. PrP106-126 A117V uptake was at least partially mediated through scavenger receptors. Phagocytosis of PrP106-126 A117V with nAbs-PrP was inhibited by wortmannin, a potent phosphatidylinositol 3-kinase inhibitor, indicating a separate uptake mechanism for nAbs-PrP mediated phagocytosis. These data suggest the possible mechanisms of action of nAbs-PrP in prion disease

Nonpalpable breast lesions: Association of mammographic abnormalities with diagnosis after needle-directed biopsy

AB colon; We reviewed the experience with needle-directed breast biopsies (NDBB) in a military medical center. In 195 patients, 207 NDBBs were done; 49 of these biopsies (24%) rendered a diagnosis of malignancy. The majority of patients (78%) had invasive cancer; 44% of them were found to have associated malignant axillary adenopathy. Mammographic indications were examined; 65% of the biopsies were done for microcalcifications with or without an associated mass/density. Approximately one third of these lesions harbored malignancy or high-risk hyperplasia. Discrete nodular densities had a low rate of malignancy (7%), while spiculated/stellate masses proved almost uniformly to be invasive cancer. NDBB should be considered in all women with mammographic abnormalities. The associated risk of malignancy may vary depending on the specific mammographic appearance of the lesion. Unfortunately, a significant number of women may have relatively advanced malignancy when first seen, despite having nonpalpable disease

Inhibition of PrP106-126 A117V uptake by specific blockers.

<p>Phagocytosis assay was performed following pre-treatment of microglial cells with (A) cytochalasin D (10 µM, 30 minutes), (B) fucoidan (500 µg/ml, 30 minutes), (C) wortmannin (10 µM, 60 minutes) and (D) co-incubation with fucoidan and wortmannin. All experiments were performed at least three times independently, and values are normalized to PrP106-126 A117V fibril uptake.</p

Inhibition of uptake of nAbs-PrP and ft-PrP by specific blockers.

<p>Western blot analysis of antibody uptake in microglial cells was performed following pre-treatment with cytochalasin D, fucoidan or wortmannin or the co-administration of fucoidan and wortmannin. Cells were co-incubated with PrP106-126 A117V and nAbs-PrP or ft-PrP (A) or with nAbs-PrP or ft-PrP alone (B). One representative experiment out of three is shown.</p

nAbs-PrP block fibril formation of PrP106-126 A117V.

<p>PrP106-126 A117V peptide (150 µM) was incubated with or without nAbs-PrP and ft-PrP at a ratio of 1∶60 at 37°C for 48 hours. The ThT Assay was performed to measure fibril formation. Fibril formation of PrP106-126 A117V was referred to as 100%. Experiments were performed at least three times independently.</p

Effect of PrP106-126 A117V on microglia.

<p>Following treatment for 24 hours with 10 µM PrP106-126 A117V with or without nAbs-PrP or ft-PrP, the MTT assay was performed to measure the mitochondrial activity of microglial cells. Values are normalized to untreated cells (A). The vitality of treated cells was verified by staining microglia with fluorescein diacetate/propidium iodide, and values are normalized to untreated cells (B). Supernatants of the cells were subjected to cytokine ELISA (C) and Griess assay (D) with LPS (1 µg/ml) as the positive control. (E) Conditioned supernatant of microglial cells was administered to primary neurons for 24 hours, and the MTT assay was performed. Values are normalized to untreated cells. All experiments were performed at least three times independently.</p