Probing the Origins of Increased Activity of the E22Q “Dutch” Mutant Alzheimer's β-Amyloid Peptide

AbstractThe amyloid peptide congener Aβ(10–35)-NH2 is simulated in an aqueous environment in both the wild type (WT) and E22Q “Dutch” mutant forms. The origin of the noted increase in deposition activity resulting from the Dutch mutation is investigated. Multiple nanosecond time scale molecular dynamics trajectories were performed and analyzed using a variety of measures of the peptide's average structure, hydration, conformational fluctuations, and dynamics. The results of the study support the conclusions that 1) the E22Q mutant and WT peptide are both stable in “collapsed coil” conformations consistent with the WT structure of Zhang et al. (2000, J. Struct. Biol. 130:130–141); 2) the E22Q peptide is more flexible in solution, supporting early claims that its equilibrium structural fluctuations are larger than those of the WT peptide; and 3) the local E22Q mutation leads to a change in the first solvation layer in the region of the peptide's “hydrophobic patch,” resulting in a more hydrophobic solvation of the mutant peptide. The simulation results support the view that the noted increase in activity due to the Dutch mutation results from an enhancement of the desolvation process that is an essential step in the aggregation of the peptide

Learning Signal Representations for EEG Cross-Subject Channel Selection and Trial Classification

EEG technology finds applications in several domains. Currently, most EEG systems require subjects to wear several electrodes on the scalp to be effective. However, several channels might include noisy information, redundant signals, induce longer preparation times and increase computational times of any automated system for EEG decoding. One way to reduce the signal-to-noise ratio and improve classification accuracy is to combine channel selection with feature extraction, but EEG signals are known to present high inter-subject variability. In this work we introduce a novel algorithm for subject-independent channel selection of EEG recordings. Considering multi-channel trial recordings as statistical units and the EEG decoding task as the class of reference, the algorithm (i) exploits channel-specific 1D-Convolutional Neural Networks (1D-CNNs) as feature extractors in a supervised fashion to maximize class separability; (ii) it reduces a high dimensional multi-channel trial representation into a unique trial vector by concatenating the channels' embeddings and (iii) recovers the complex inter-channel relationships during channel selection, by exploiting an ensemble of AutoEncoders (AE) to identify from these vectors the most relevant channels to perform classification. After training, the algorithm can be exploited by transferring only the parametrized subgroup of selected channel-specific 1D-CNNs to new signals from new subjects and obtain low-dimensional and highly informative trial vectors to be fed to any classifier

A Deep Survival EWAS approach estimating risk profile based on pre-diagnostic DNA methylation: An application to breast cancer time to diagnosis

Previous studies for cancer biomarker discovery based on pre-diagnostic blood DNA methylation (DNAm) profiles, either ignore the explicit modeling of the Time To Diagnosis (TTD), or provide inconsistent results. This lack of consistency is likely due to the limitations of standard EWAS approaches, that model the effect of DNAm at CpG sites on TTD independently. In this work, we aim to identify blood DNAm profiles associated with TTD, with the aim to improve the reliability of the results, as well as their biological meaningfulness. We argue that a global approach to estimate CpG sites effect profile should capture the complex (potentially non-linear) relationships interplaying between sites. To prove our concept, we develop a new Deep Learning-based approach assessing the relevance of individual CpG Islands (i.e., assigning a weight to each site) in determining TTD while modeling their combined effect in a survival analysis scenario. The algorithm combines a tailored sampling procedure with DNAm sites agglomeration, deep non-linear survival modeling and SHapley Additive exPlanations (SHAP) values estimation to aid robustness of the derived effects profile. The proposed approach deals with the common complexities arising from epidemiological studies, such as small sample size, noise, and low signal-to-noise ratio of blood-derived DNAm. We apply our approach to a prospective case-control study on breast cancer nested in the EPIC Italy cohort and we perform weighted gene-set enrichment analyses to demonstrate the biological meaningfulness of the obtained results. We compared the results of Deep Survival EWAS with those of a traditional EWAS approach, demonstrating that our method performs better than the standard approach in identifying biologically relevant pathways

Dual adversarial deconfounding autoencoder for joint batch-effects removal from multi-center and multi-scanner radiomics data

Abstract Medical imaging represents the primary tool for investigating and monitoring several diseases, including cancer. The advances in quantitative image analysis have developed towards the extraction of biomarkers able to support clinical decisions. To produce robust results, multi-center studies are often set up. However, the imaging information must be denoised from confounding factors—known as batch-effect—like scanner-specific and center-specific influences. Moreover, in non-solid cancers, like lymphomas, effective biomarkers require an imaging-based representation of the disease that accounts for its multi-site spreading over the patient’s body. In this work, we address the dual-factor deconfusion problem and we propose a deconfusion algorithm to harmonize the imaging information of patients affected by Hodgkin Lymphoma in a multi-center setting. We show that the proposed model successfully denoises data from domain-specific variability (p-value < 0.001) while it coherently preserves the spatial relationship between imaging descriptions of peer lesions (p-value = 0), which is a strong prognostic biomarker for tumor heterogeneity assessment. This harmonization step allows to significantly improve the performance in prognostic models with respect to state-of-the-art methods, enabling building exhaustive patient representations and delivering more accurate analyses (p-values < 0.001 in training, p-values < 0.05 in testing). This work lays the groundwork for performing large-scale and reproducible analyses on multi-center data that are urgently needed to convey the translation of imaging-based biomarkers into the clinical practice as effective prognostic tools. The code is available on GitHub at this https://github.com/LaraCavinato/Dual-ADAE

Circulating tumor cells detection and counting in uveal melanomas by a filtration-based method

Uveal melanoma is one of the most deadly diseases in ophthalmology for which markers able to predict the appearance of metastasis are needed. The study investigates the role of circulating tumor cells (CTC) as a prognostic factor in this disease. We report the detection of circulating tumor cells by Isolation by Size of Epithelial Tumor cells (ISET) in a cohort of 31 uveal melanoma patients: we identified single CTCs or clusters of cells in 17 patients, while the control population, subjects with choroidal nevi, showed no CTC in peripheral blood. The presence of CTCs did not correlate with any clinical and pathological parameter, such as tumor larger basal diameter (LBD), tumor height and TNM. By stratifying patients in groups on the basis of the number of CTC (lower or higher than 10 CTC per 10 mL blood) and the presence of CTC clusters we found a significant difference in LBD (p = 0.019), Tumor height (p = 0.048), disease-free and overall survival (p &lt; 0.05). In conclusion, we confirm the role of CTC as a negative prognostic marker in uveal melanoma patients after a long follow-up period. Further characterization of CTC will help understanding uveal melanoma metastasization and improve patient management. © 2014 by the authors; licensee MDPI, Basel, Switzerland

Aneurysm of the lateral marginal vein of the foot

Superficial venous aneurysms are a very rare pathology. This case report describes a 21-years-old male patient, who developed a soft, slow-growing mass, in the lateral part of the dorsal foot. Based on clinical examination and EcocolorDoppler ultrasound exam, the diagnosis of venous aneurysm of the lateral marginal vein was confirmed. The treatment proposed was ultrasound-guided foam sclerotherapy. The purpose of this work is to describe for the first time a venous superficial aneurysm localized in the lateral marginal vein of the foot. It is the first case reported in English literature

Protostellar Outflows at the EarliesT Stages (POETS). III. H2O masers tracing disk-winds and jets near luminous YSOs

The goal of the Protostellar Outflows at the EarliesT Stages (POETS) survey is to image the disk-outflow interface on scales of 10-100 au in a statistically significant sample (36) of luminous young stellar objects (YSO), targeting both the molecular and ionized components of the outflows. The outflow kinematics is studied at milliarcsecond scales through VLBI observations of the 22 GHz water masers. We employed the JVLA at 6, 13, and 22 GHz in the A- and B-Array configurations to determine the spatial structure and the spectral index of the radio continuum emission. In about half of the targets, the water masers observed at separation <= 1000 au from the YSOs trace either or both of these kinematic structures: 1) a spatially elongated distribution oriented at close angle with the direction of collimation of the maser proper motions (PM), and 2) a linear LSR velocity (Vlsr) gradient across the YSO position. The kinematic structure (1) is readily interpreted in terms of a protostellar jet, as confirmed in some targets via the comparison with independent observations of the YSO jets, in thermal (continuum and line) emissions, reported in the literature. The kinematic structure (2) is interpreted in terms of a disk-wind (DW) seen almost edge-on on the basis of several pieces of evidence: first, it is invariably directed perpendicular to the YSO jet; second, it agrees in orientation and polarity with the Vlsr gradient in thermal emissions (when reported in the literature) identifying the YSO disk at scales of <= 1000~au; third, the PMs of the masers delineating the Vlsr gradients hint at flow motions at a speed of 10-20 km/s directed at large angles with the disk midplane. In the remaining targets, the maser PMs are not collimated but rather tend to align along two almost perpendicular directions, and could originate in DW-jet systems slightly inclined (<= 30 deg) with respect to edge-on.Comment: 61 pages (Main: 13 pages, Appendix: 48 pages), 18 figures (5 + 13), 28 tables (1 + 27), accepted for publication in section 6. Interstellar and circumstellar matter of A&

Tumor-Related Methylated Cell-Free DNA and Circulating Tumor Cells in Melanoma

Solid tumor release into the circulation cell-free DNA (cfDNA) and circulating tumor cells (CTCs) which represent promising biomarkers for cancer diagnosis. Circulating tumor DNA may be studied in plasma from cancer patients by detecting tumor specific alterations, such as genetic or epigenetic modifications. Ras association domain family 1 isoform A (RASSF1A) is a tumor suppressor gene silenced by promoter hypermethylation in a variety of human cancers including melanoma.The aim of the present study was to assess the diagnostic performance of a tumor-related methylated cfDNA marker in melanoma patients and to compare this parameter with the presence of CTCs.RASSF1A promoter methylation was quantified in cfDNA by qPCR in a consecutive series of 84 melanoma patients and 68 healthy controls. In a subset of 68 cases, the presence of CTCs was assessed by a filtration method (Isolation by Size of Epithelial Tumor Cells, ISET) as well as by an indirect method based on the detection of tyrosinase mRNA by RT-qPCR. The distribution of RASSF1A methylated cfDNA was investigated in cases and controls and the predictive capability of this parameter was assessed by means of the area under the ROC curve (AUC).The percentage of cases with methylated RASSF1A promoter in cfDNA was significantly higher in each class of melanoma patients (in situ, invasive and metastatic) than in healthy subjects (Pearson chi-squared test, p<0.001). The concentration of RASSF1A methylated cfDNA in the subjects with a detectable quantity of methylated alleles was significantly higher in melanoma patients than in controls. The biomarker showed a good predictive capability (in terms of AUC) in discriminating between melanoma patients and healthy controls. This epigenetic marker associated to cfDNA did not show a significant correlation with the presence of CTCs, but, when the two parameters are jointly considered, we obtain a higher sensitivity of the detection of positive cases in invasive and metastatic melanomas.Our data suggest that cell-free tumor DNA and CTCs represent two complementary aspects of the liquid biopsy which may improve the diagnosis and the clinical management of melanoma patients

In vitro antimicrobial activity of essential oils against salmonella enterica serotypes enteritidis and typhimurium strains isolated from poultry

Salmonella enterica serotype Enteritidis and S. enterica serotype Typhimurium are frequently present among poultry and are associated with outbreaks of human salmonellosis. The study investigated the in vitro antimicrobial activity of essential oils (EOs) obtained from Aloysia triphylla, Cinnamomum zeylanicum, Cymbopogon citratus, Litsea cubeba, Mentha piperita, Syzygium aromaticum against S. Enteritidis and S. Thyphimurium strains previously isolated from poultry. A 1:1 mixture of C. zeylanicum and S. aromaticum was also tested. The activity of all compounds was evaluated against the yeast Saccharomyces cerevisiae, commonly used as probiotic. The highest antibacterial activity was observed for C. zeylanicum (minimum inhibitory concentrations (MICs) ranging from 1.26 mg/mL to 0.63 mg/mL), S. aromaticum (MICs from 2.637 mg/mL to 0.164 mg/mL) and the mixture (MICs from 1.289 mg/mL to 0.322 mg/mL). No activity was recorded against S. cerevisiae. The results suggest a possible use of C. zeylanicum and S. aromaticum, alone or in combination, in the farm environment for disinfection and in poultry diet, combined with S. cerevisiae administration, for an integrated approach to avoid Salmonella intestinal colonization