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Amino acids that are in close contact in a protein structure tend to co-evolve, which gives rise to sequence correlations. Direct coupling analysis (DCA) is a method for predicting such contacts directly from sequence correlations, without assuming any prior knowledge of structures. To this end, sequence correlations are modeled using an Ising-like ansatz, whose couplings are determined through an

We define a mathematical method that, given the form of an interaction network, defines an energy as a function of the state of the network. When combined with a suitable entropy, it yields a free energy that gives rise to the dynamics of the network, allowing solutions and optimal paths to be efficiently found. This is done primarily with the gene regulatory networks governing cell reprogramming

The recently introduced capsule networks have already shown much success on image classification tasks. In this thesis, capsule networks are described and applied to a binary classification task, namely that of classifying hotspots from bone scintigraphy scans. The performance of capsule networks on this task is compared to that of convolutional neural networks. The results indicate that there is

The generation of induced pluripotent stem (iPS) cells from differentiated cells is a process of great scientific interest due to the medical potential of such cells. This process (called 'reprogramming' of cells) is however notoriously inefficient and still not very well understood. Therefore studies that can help us understand the interactions and mechanisms governing the reprogramming p

Artificial Neural Networks (ANNs) are widely used information processing algorithms based roughly on biological neural networks. These networks can be trained to find complex patterns in datasets and to produce certain output signals given a set of input signals. A key element of ANNs are their so-called activation functions, which control the signal strengths between the artificial neurons in a n

Artificial neural networks have been used to solve different problems, one being survival analysis of medical data. For survival analysis, the main interest is often how samples become sorted by their outputs, which makes survival analysis a rank based problem. A rank based error function lacks a gradient, which makes gradient descent based training difficult. A genetic training algorithm, based o

Convolutional Neural Networks (CNNs) and pre-trained word embeddings have revolutionized the field of Natural Language Processing (NLP) during the last years. In this project, CNNs are used on top of the Word2Vec word representation for a sentence classification task on medical research articles. Both individual networks for each category as well as a combined classification network are optimized

In the field of computational biology, fluorescence microscopy images often constitute the input source of information. The process of binarization of raw images to delineate interesting objects requires image segmentation into signal and background pixels. Several methods to perform image segmentation exist, the Otsu method being a popular unsupervised example. The Otsu method's lack of pro

During the last few years, crowding effects on the physics of proteins has become an increasingly popular topic of research. This is is because most biological processes involving proteins naturally take place in a crowded environment, e.g. in the cellular environment where macromolecules may occupy 30% of the volume. One such biological process would be the formation of amyloid aggregates, which

The North Atlantic region is a key component of the climate system via large-scale atmosphere and ocean circulation. Climate field reconstructions can provide a long-term context for ongoing climate change and contribute to our understanding of climate dynamics, impact of external forcings, and act as references for model evaluation and baseline for natural variability. There are distinct differen

Regulation of intracellular levels of reactive oxygen species (ROS) remains poorly understood. Aquaporin 3 (AQP3) facilitates the membrane transport of hydrogen peroxide (H2O2), a key ROS signaling molecule. Here we elucidate the molecular mechanism of AQP3 and show that its regulatory properties are both pH dependent and autoregulated by H2O2. Using single particle cryo-electron microscopy, we pr

In 1634, silver was found in inland Sápmi, on the present border between Norway and Sweden. The Swedish Crown had the ore extracted and a works for refining the silver was established in Silbojokk the following year. During the coming decades, two more works and many mines were opened in Sápmi. Sámi, Swedish and Dutch/German migrant workers were employed under restrictive conditions and in a harsh

China plans expanding 49.5 million hectares of new forests by 2050 to strengthen carbon sequestration. However, estimates of the carbon benefits from this expansion rarely consider the effect of 'forest edge', where tree mortality increases under intensified stress from wind, drought, pests, and fire. Here we show that proximity to forest edges substantially reduces biomass carbon storage, and dev

Wood density is a crucial anatomical trait influencing forest carbon storage. However, dynamic global vegetation models (DGVMs) typically assume a fixed species-level wood density, neglecting environment-driven variability. In this proof-of-concept study, we explore the potential impact of dynamic wood density on tree- and forest-level carbon storage by integrating a simple temperature-response fu

Quasi-experimental study of effects of an organizational intervention on staff and patients over a 8 year perspective; Before, under and after an organizational change. Effects on staff are staff-turnover, fatigue and burnout (n=268) on Three wards including the intervention ward. Independent variables are staff demographics, education, experience, job status, sick-leave and responses on a burn-ou

We investigated whether aminoguanidine (AG), an inhibitor of advanced glycated end product formation, or probucol (PB), a free radical scavenger, could influence signs of glomerular and distal tubular function and morphological changes in kidneys of male Wistar rats after 6 months of streptozocin (STZ)-induced diabetes. Diabetic rats had a higher kidney weight/body weight ratio (P<.001), but neith

Uniform electroporation of the heterogeneous structure of spinach leaf cross section is a technological challenge that is addressed in this investigation. Three dimensional models were created with cells arranged in specific tissue types, considering a leaf with its air fraction and a leaf where the air fraction was replaced by a solution of known properties using vacuum impregnation. The models w

This paper suggests an extension of an existing, clinically evaluated, closed-loop drug delivery system for hypnotic depth control using propofol. The extension introduces closed-loop administration of the analgesic drug remifentanil, thus forming a multiple input–single output (MISO) control system. Remifentanil acts and is metabolized at a significantly faster time scale than propofol. Direct co