Deep learning-based classification of breast cancer molecular subtypes from H&E whole-slide images.

Classifying breast cancer molecular subtypes is crucial for tailoring treatment strategies. While immunohistochemistry (IHC) and gene expression profiling are standard methods for molecular subtyping, IHC can be subjective, and gene profiling is costly and not widely accessible in many regions. Previous approaches have highlighted the potential application of deep learning models on hematoxylin and eosin (H&E)-stained whole-slide images (WSIs) for molecular subtyping, but these efforts vary in their methods, datasets, and reported performance.

Using machine learning methods to predict all-cause somatic hospitalizations in adults: A systematic review.

Aim: In this review, we investigated how Machine Learning (ML) was utilized to predict all-cause somatic hospital admissions and readmissions in adults.

Methods: We searched eight databases (PubMed, Embase, Web of Science, CINAHL, ProQuest, OpenGrey, WorldCat, and MedNar) from their inception date to October 2023, and included records that predicted all-cause somatic hospital admissions and readmissions of adults using ML methodology. We used the CHARMS checklist for data extraction, PROBAST for bias and applicability assessment, and TRIPOD for reporting quality.

"Using network analysis modularity to group health code systems and decrease dimensionality in machine learning models".

Background: Machine learning (ML) prediction models in healthcare and pharmacy-related research face challenges with encoding high-dimensional Healthcare Coding Systems (HCSs) such as ICD, ATC, and DRG codes, given the trade-off between reducing model dimensionality and minimizing information loss.

Objectives: To investigate using Network Analysis modularity as a method to group HCSs to improve encoding in ML models.

Methods: The MIMIC-III dataset was utilized to create a multimorbidity network in which ICD-9 codes are the nodes and the edges are the number of patients sharing the same ICD-9 code pairs.

Social robots in research on social and cognitive development in infants and toddlers: A scoping review.

There is currently no systematic review of the growing body of literature on using social robots in early developmental research. Designing appropriate methods for early childhood research is crucial for broadening our understanding of young children's social and cognitive development. This scoping review systematically examines the existing literature on using social robots to study social and cognitive development in infants and toddlers aged between 2 and 35 months.

Publicly available datasets of breast histopathology H&E whole-slide images: A scoping review.

Advancements in digital pathology and computing resources have made a significant impact in the field of computational pathology for breast cancer diagnosis and treatment. However, access to high-quality labeled histopathological images of breast cancer is a big challenge that limits the development of accurate and robust deep learning models. In this scoping review, we identified the publicly available datasets of breast H&E-stained whole-slide images (WSIs) that can be used to develop deep learning algorithms.

An individually adjusted approach for communicating epidemiological results on health and lifestyle to patients.

If scientific research on modifiable risk factors was more accessible to the general population there is a potential to prevent disease and promote health. Mobile applications can automatically combine individual characteristics and statistical models of health to present scientific information as individually tailored visuals, and thus there is untapped potential in incorporating scientific research into apps aimed at promoting healthier lifestyles. As a proof-of-concept, we develop a statistical model of the relationship between Self-rated-health (SRH) and lifestyle-related factors, and a simple app for conveying its effects through a visualisation that sets the individual as the frame of reference.

Algorithm for predicting valvular heart disease from heart sounds in an unselected cohort.

Objective: This study aims to assess the ability of state-of-the-art machine learning algorithms to detect valvular heart disease (VHD) from digital heart sound recordings in a general population that includes asymptomatic cases and intermediate stages of disease progression.

Methods: We trained a recurrent neural network to predict murmurs from heart sound audio using annotated recordings collected with digital stethoscopes from four auscultation positions in 2,124 participants from the Tromsø7 study. The predicted murmurs were used to predict VHD as determined by echocardiography.

Social network analysis of Staphylococcus aureus carriage in a general youth population.

Objectives: Staphylococcus aureus carriage increases the risk of infection. We used social network analysis to evaluate whether contacts have the same S. aureus genotype indicating direct transmission or whether contagiousness is an indirect effect of contacts sharing the same lifestyle or characteristics.

A Pragmatic Machine Learning Approach to Quantify Tumor-Infiltrating Lymphocytes in Whole Slide Images.

Increased levels of tumor-infiltrating lymphocytes (TILs) indicate favorable outcomes in many types of cancer. The manual quantification of immune cells is inaccurate and time-consuming for pathologists. Our aim is to leverage a computational solution to automatically quantify TILs in standard diagnostic hematoxylin and eosin-stained sections (H&E slides) from lung cancer patients.

Predicting breast cancer metastasis from whole-blood transcriptomic measurements.

Objective: In this exploratory work we investigate whether blood gene expression measurements predict breast cancer metastasis. Early detection of increased metastatic risk could potentially be life-saving. Our data comes from the Norwegian Women and Cancer epidemiological cohort study.

Reproduction study using public data of: Development and validation of a deep learning algorithm for detection of diabetic retinopathy in retinal fundus photographs.

We have attempted to reproduce the results in Development and validation of a deep learning algorithm for detection of diabetic retinopathy in retinal fundus photographs, published in JAMA 2016; 316(22), using publicly available data sets. We re-implemented the main method in the original study since the source code is not available. The original study used non-public fundus images from EyePACS and three hospitals in India for training.

Norwegian e-Infrastructure for Life Sciences (NeLS).

The Norwegian e-Infrastructure for Life Sciences (NeLS) has been developed by ELIXIR Norway to provide its users with a system enabling data storage, sharing, and analysis in a project-oriented fashion. The system is available through easy-to-use web interfaces, including the Galaxy workbench for data analysis and workflow execution. Users confident with a command-line interface and programming may also access it through Secure Shell (SSH) and application programming interfaces (APIs).

META-pipe Authorization service.

We describe the design, implementation, and use of the META-pipe Authorization service. META-pipe is a complete workflow for the analysis of marine metagenomics data. We will provide META-pipe as a web based data analysis service for ELIXIR users.

META-pipe cloud setup and execution.

META-pipe is a complete service for the analysis of marine metagenomic data. It provides assembly of high-throughput sequence data, functional annotation of predicted genes, and taxonomic profiling. The functional annotation is computationally demanding and is therefore currently run on a high-performance computing cluster in Norway.

Interactions between the tumor and the blood systemic response of breast cancer patients.

Although systemic immunity is critical to the process of tumor rejection, cancer research has largely focused on immune cells in the tumor microenvironment. To understand molecular changes in the patient systemic response (SR) to the presence of BC, we profiled RNA in blood and matched tumor from 173 patients. We designed a system (MIxT, Matched Interactions Across Tissues) to systematically explore and link molecular processes expressed in each tissue.

The metagenomic data life-cycle: standards and best practices.

Metagenomics data analyses from independent studies can only be compared if the analysis workflows are described in a harmonized way. In this overview, we have mapped the landscape of data standards available for the description of essential steps in metagenomics: (i) material sampling, (ii) material sequencing, (iii) data analysis, and (iv) data archiving and publishing. Taking examples from marine research, we summarize essential variables used to describe material sampling processes and sequencing procedures in a metagenomics experiment.

ELIXIR pilot action: Marine metagenomics - towards a domain specific set of sustainable services.

Metagenomics, the study of genetic material recovered directly from environmental samples, has the potential to provide insight into the structure and function of heterogeneous microbial communities.  There has been an increased use of metagenomics to discover and understand the diverse biosynthetic capacities of marine microbes, thereby allowing them to be exploited for industrial, food, and health care products. This ELIXIR pilot action was motivated by the need to establish dedicated data resources and harmonized metagenomics pipelines for the marine domain, in order to enhance the exploration and exploitation of marine genetic resources.

Kvik: three-tier data exploration tools for flexible analysis of genomic data in epidemiological studies.

Kvik is an open-source framework that we developed for explorative analysis of functional genomics data from large epidemiological studies. Creating such studies requires a significant amount of time and resources. It is therefore usual to reuse the data from one study for several research projects.

Targeted exploration and analysis of large cross-platform human transcriptomic compendia.

We present SEEK (search-based exploration of expression compendia; http://seek.princeton.edu/), a query-based search engine for very large transcriptomic data collections, including thousands of human data sets from many different microarray and high-throughput sequencing platforms.

Functional knowledge transfer for high-accuracy prediction of under-studied biological processes.

A key challenge in genetics is identifying the functional roles of genes in pathways. Numerous functional genomics techniques (e.g.

IMP: a multi-species functional genomics portal for integration, visualization and prediction of protein functions and networks.

Integrative multi-species prediction (IMP) is an interactive web server that enables molecular biologists to interpret experimental results and to generate hypotheses in the context of a large cross-organism compendium of functional predictions and networks. The system provides a framework for biologists to analyze their candidate gene sets in the context of functional networks, as they expand or focus these sets by mining functional relationships predicted from integrated high-throughput data. IMP integrates prior knowledge and data collections from multiple organisms in its analyses.