Abstract
Multi-omics datasets represent distinct aspects of the central dogma of molecular biology. Such high-dimensional molecular profiles pose challenges to data interpretation and hypothesis generation. ActivePathways is an integrative method that discovers significantly enriched pathways across multiple datasets using statistical data fusion, rationalizes contributing evidence and highlights associated genes. As part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2658 cancers across 38 tumor types, we integrated genes with coding and non-coding mutations and revealed frequently mutated pathways and additional cancer genes with infrequent mutations. We also analyzed prognostic molecular pathways by integrating genomic and transcriptomic features of 1780 breast cancers and highlighted associations with immune response and anti-apoptotic signaling. Integration of ChIP-seq and RNA-seq data for master regulators of the Hippo pathway across normal human tissues identified processes of tissue regeneration and stem cell regulation. ActivePathways is a versatile method that improves systems-level understanding of cellular organization in health and disease through integration of multiple molecular datasets and pathway annotations. © 2020, The Author(s).

Abstract
AbstractTraditional detection of aquatic invasive species, via morphological identification is often time-consuming and can require a high level of taxonomic expertise, leading to delayed mitigation responses. Environmental DNA (eDNA) detection approaches of multiple species using Illumina-based sequencing technology have been used to overcome these hindrances, but sample processing is often lengthy. More recently, portable nanopore sequencing technology has become available, which has the potential to make molecular detection of invasive species more widely accessible and to substantially decrease sample turnaround times. However, nanopore-sequenced reads have a much higher error rate than those produced by Illumina platforms, which has so far hindered the adoption of this technology. We provide a detailed laboratory protocol and bioinformatic tools to increase the reliability of nanopore sequencing to detect invasive species, and we test its application using invasive bivalves. We sampled water from sites with pre-existing bivalve occurrence and abundance data, and contrasting bivalve communities, in Italy and Portugal. We extracted, amplified and sequenced eDNA with a turnaround of 3.5 days. The majority of processed reads were = 99 % identical to reference sequences. There were no taxa detected other than those known to occur. The lack of detections of some species at some sites could be explained by their known low abundances. This is the first reported use of MinION to detect aquatic invasive species from eDNA samples. The approach can be easily adapted for other metabarcoding applications, such as biodiversity assessment, ecosystem health assessment and diet studies.

Abstract
AbstractPurposePredicting outcomes after resection of primary melanoma remains crude, primarily based on tumour thickness. We explored gene expression signatures for their ability to better predict outcomes.MethodsDifferential expression analysis of 194 primary melanomas resected from patients who either developed distant metastasis (n=89) or did not (n=105) was performed. We identified 121 metastasis-associated genes that were included in our prognostic signature, “Cam_121”. Several machine learning classification models were trained using nested leave- one-out cross validation (LOOCV) to test the signature’s capacity to predict metastases, as well as regression models to predict survival. The prognostic accuracy was externally validated in two independent datasets.ResultsCam_121 performed significantly better in predicting distant metastases than any of the models trained with the clinical covariates alone (pAccuracy=4.92×10-3), as well as those trained with two published prognostic signatures. Cam_121 expression score was strongly associated with progression-free survival (HR=1.7, p=3.44×10-6), overall survival (HR=1.73, p=7.71×10-6) and melanoma-specific survival (HR=1.59, p=0.02). Cam_121 expression score also negatively correlated with measures of immune cell infiltration (?=-0.73, p<2.2×10-16), with a higher score representing reduced tumour lymphocytic infiltration and a higher absolute 5-year risk of death in stage II melanoma.ConclusionsThe Cam_121 primary melanoma gene expression signature outperformed currently available alternatives in predicting the risk of distant recurrence. The signature confirmed (using unbiased approaches) the central prognostic importance of immune cell infiltration in long-term patient outcomes and could be used to identify stage II melanoma patients at highest risk of metastases and poor survival who might benefit most from adjuvant therapies.Translational relevancePredicting outcomes after resection of primary melanoma is currently based on traditional histopathological staging, however survival outcomes within these disease stages varies markedly. Since adjuvant systemic therapies are now being used routinely, accurate prognostic information is needed to better risk stratify patients and avoid unnecessary use of high cost, potentially harmful drugs, as well as to inform future adjuvant strategies. The Cam_121 gene expression signature appears to have this capability and warrants evaluation in prospective clinical trials.

Abstract

Abstract
Missing data is a problem often found in real-world datasets and it can degrade the performance of most machine learning models. Several deep learning techniques have been used to address this issue, and one of them is the Autoencoder and its Denoising and Variational variants. These models are able to learn a representation of the data with missing values and generate plausible new ones to replace them. This study surveys the use of Autoencoders for the imputation of tabular data and considers 26 works published between 2014 and 2020. The analysis is mainly focused on discussing patterns and recommendations for the architecture, hyperparameters and training settings of the network, while providing a detailed discussion of the results obtained by Autoencoders when compared to other state-of-the-art methods, and of the data contexts where they have been applied. The conclusions include a set of recommendations for the technical settings of the network, and show that Denoising Autoencoders outperform their competitors, particularly the often used statistical methods.

Abstract
Background patients with palliative needs often experience high symptom burden which causes suffering to themselves and their families. Depression and psychological distress should not be considered a "normal event" in advanced disease patients and should be screened, diagnosed, acted on and followed-up. Psychological distress has been associated with greater physical symptom severity, suffering, and mortality in cancer patients. A holistic, but short measure should be used for physical and non-physical needs assessment. The Integrated Palliative care Outcome Scale is one such measure. This work aims to determine palliative needs of patients and explore screening accuracy of two items pertaining to psychological needs. Methods multi-centred observational study using convenience sampling. Data were collected in 9 Portuguese centres. Inclusion criteria: >= 18 years, mentally fit to give consent, diagnosed with an incurable, potentially life-threatening illness. Exclusion criteria: patient in distress ("unable to converse for a period of time"), cognitively impaired. Descriptive statistics used for demographics. Receiving Operator Characteristics curves and Area Under the Curve for anxiety and depression discriminant properties against the Hospital Anxiety and Depression Scale. Results 1703 individuals were screened between July 1st, 2015 and February 2016. A total of 135 (7.9%) were included. Main reason for exclusion was being healthy (75.2%). The primary care centre screened most individuals, as they have the highest rates of daily patients and the majority are healthy. Mean age is 66.8 years (SD 12.7), 58 (43%) are female. Most patients had a cancer diagnosis 109 (80.7%). Items scoring highest (=4) were: family or friends anxious or worried (36.3%); feeling anxious or worried about illness (13.3%); feeling depressed (9.6%). Using a cut-off score of 2/3, Area Under the Curve for depression and anxiety items were above 70%. Conclusions main palliative needs were psychological, family related and spiritual. This suggests that clinical teams may better manage physical issues and there is room for improvement regarding non-physical needs. Using the Integrated Palliative care Outcome Scale systematically could aid clinical teams screening patients for distressing needs and track their progress in assisting patients and families with those issues.