Modeling and solving staff scheduling with partial weighted maxSAT.

Employee scheduling is a well known problem that appears in a wide range of different areas including health care, air lines, transportation services, and basically any organization that has to deal with workforces. In this paper we model a collection of challenging staff scheduling instances as a weighted partial Boolean maximum satisfiability (maxSAT) problem. Using our formulation we conduct a comparison of four different cardinality constraint encodings and analyze their applicability on this problem. Additionally, we measure the performance of two leading solvers from the maxSAT evaluation 2015 in a series of benchmark experiments and compare their results to state of the art solutions. In the process we also generate a number of challenging maxSAT instances that are publicly available and can be used as benchmarks for the development and verification of modern SAT solvers.

Mathematical analysis of the influence of brain metabolism on the BOLD signal in Alzheimer's disease.

Blood oxygen level-dependent functional magnetic resonance imaging (BOLD-fMRI) is a standard clinical tool for the detection of brain activation. In Alzheimer's disease (AD), task-related and resting state fMRI have been used to detect brain dysfunction. It has been shown that the shape of the BOLD response is affected in early AD. To correctly interpret these changes, the mechanisms responsible for the observed behaviour need to be known. The parameters of the canonical hemodynamic response function (HRF) commonly used in the analysis of fMRI data have no direct biological interpretation and cannot be used to answer this question. We here present a model that allows relating AD-specific changes in the BOLD shape to changes in the underlying energy metabolism. According to our findings, the classic view that differences in the BOLD shape are only attributed to changes in strength and duration of the stimulus does not hold. Instead, peak height, peak timing and full width at half maximum are sensitive to changes in the reaction rate of several metabolic reactions. Our systems-theoretic approach allows the use of patient-specific clinical data to predict dementia-driven changes in the HRF, which can be used to improve the results of fMRI analyses in AD patients.

Cooperative gene regulation by microRNA pairs and their identification using a computational workflow.

MicroRNAs (miRNAs) are an integral part of gene regulation at the post-transcriptional level. Recently, it has been shown that pairs of miRNAs can repress the translation of a target mRNA in a cooperative manner, which leads to an enhanced effectiveness and specificity in target repression. However, it remains unclear which miRNA pairs can synergize and which genes are target of cooperative miRNA regulation. In this paper, we present a computational workflow for the prediction and analysis of cooperating miRNAs and their mutual target genes, which we refer to as RNA triplexes. The workflow integrates methods of miRNA target prediction; triplex structure analysis; molecular dynamics simulations and mathematical modeling for a reliable prediction of functional RNA triplexes and target repression efficiency. In a case study we analyzed the human genome and identified several thousand targets of cooperative gene regulation. Our results suggest that miRNA cooperativity is a frequent mechanism for an enhanced target repression by pairs of miRNAs facilitating distinctive and fine-tuned target gene expression patterns. Human RNA triplexes predicted and characterized in this study are organized in a web resource at www.sbi.uni-rostock.de/triplexrna/.

Parameter identifiability and sensitivity analysis predict targets for enhancement of STAT1 activity in pancreatic cancer and stellate cells.

The present work exemplifies how parameter identifiability analysis can be used to gain insights into differences in experimental systems and how uncertainty in parameter estimates can be handled. The case study, presented here, investigates interferon-gamma (IFNγ) induced STAT1 signalling in two cell types that play a key role in pancreatic cancer development: pancreatic stellate and cancer cells. IFNγ inhibits the growth for both types of cells and may be prototypic of agents that simultaneously hit cancer and stroma cells. We combined time-course experiments with mathematical modelling to focus on the common situation in which variations between profiles of experimental time series, from different cell types, are observed. To understand how biochemical reactions are causing the observed variations, we performed a parameter identifiability analysis. We successfully identified reactions that differ in pancreatic stellate cells and cancer cells, by comparing confidence intervals of parameter value estimates and the variability of model trajectories. Our analysis shows that useful information can also be obtained from nonidentifiable parameters. For the prediction of potential therapeutic targets we studied the consequences of uncertainty in the values of identifiable and nonidentifiable parameters. Interestingly, the sensitivity of model variables is robust against parameter variations and against differences between IFNγ induced STAT1 signalling in pancreatic stellate and cancer cells. This provides the basis for a prediction of therapeutic targets that are valid for both cell types.

Cerebral amyloid-ß proteostasis is regulated by the membrane transport protein ABCC1 in mice.

In Alzheimer disease (AD), the intracerebral accumulation of amyloid-ß (Aß) peptides is a critical yet poorly understood process. Aß clearance via the blood-brain barrier is reduced by approximately 30% in AD patients, but the underlying mechanisms remain elusive. ABC transporters have been implicated in the regulation of Aß levels in the brain. Using a mouse model of AD in which the animals were further genetically modified to lack specific ABC transporters, here we have shown that the transporter ABCC1 has an important role in cerebral Aß clearance and accumulation. Deficiency of ABCC1 substantially increased cerebral Aß levels without altering the expression of most enzymes that would favor the production of Aß from the Aß precursor protein. In contrast, activation of ABCC1 using thiethylperazine (a drug approved by the FDA to relieve nausea and vomiting) markedly reduced Aß load in a mouse model of AD expressing ABCC1 but not in such mice lacking ABCC1. Thus, by altering the temporal aggregation profile of Aß, pharmacological activation of ABC transporters could impede the neurodegenerative cascade that culminates in the dementia of AD.