FamLink2 - A comprehensive tool for likelihood computations in pedigrees analyses involving linked DNA markers accounting for genotype uncertainties.

There is an increasing demand for software that can handle an arbitrary number of linked markers in forensic genetics; primarily with application to inference of relationships and direct matching but also in applications such as ancestry inference and mixture interpretation. With the emergence of sequencing technologies, denser sets of SNP markers are generated and analyzed. Additionally, sequence data of low quality and quantity DNA generate uncertainty about the underlying true genotype.

Improved computations for relationship inference using low-coverage sequencing data.

Pedigree inference, for example determining whether two persons are second cousins or unrelated, can be done by comparing their genotypes at a selection of genetic markers. When the data for one or more of the persons is from low-coverage next generation sequencing (lcNGS), currently available computational methods either ignore genetic linkage or do not take advantage of the probabilistic nature of lcNGS data, relying instead on first estimating the genotype. We provide a method and software (see familias.

Pharmacodynamic Model-Based Safety Management of Eribulin-Induced Myelosuppression in Patients With Breast Cancer.

Background: Neutropenia is a major dose-limiting toxicity of cancer chemotherapy. Semimechanistic mathematical models have been applied to describe the time course of neutrophil counts. The objectives of this study were to develop a mathematical model describing changes in neutrophil counts during eribulin treatment, to apply the empirical Bayes method to predict the probability of developing neutropenia ≥ grade 3 during eribulin treatment in each patient, and to propose the implementation of this mathematical tool in clinical practice for individual safety management.

Diversity strengthens competing teams.

How does the composition of a collection of individuals affect its outcome in competition with other collections of individuals? Assuming that individuals can be different, we develop a model to interpolate between individual-level interactions and collective-level consequences. Rooted in theoretical mathematics, the model is not constrained to any specific context. Potential applications include research, education, sports, politics, ecology, agriculture, algorithms and finance.

Combining dense and sparse labeling in optical DNA mapping.

Optical DNA mapping (ODM) is based on fluorescent labeling, stretching and imaging of single DNA molecules to obtain sequence-specific fluorescence profiles, DNA barcodes. These barcodes can be mapped to theoretical counterparts obtained from DNA reference sequences, which in turn allow for DNA identification in complex samples and for detecting structural changes in individual DNA molecules. There are several types of DNA labeling schemes for ODM and for each labeling type one or several types of match scoring methods are used.

Detection of structural variations in densely-labelled optical DNA barcodes: A hidden Markov model approach.

Large-scale genomic alterations play an important role in disease, gene expression, and chromosome evolution. Optical DNA mapping (ODM), commonly categorized into sparsely-labelled ODM and densely-labelled ODM, provides sequence-specific continuous intensity profiles (DNA barcodes) along single DNA molecules and is a technique well-suited for detecting such alterations. For sparsely-labelled barcodes, the possibility to detect large genomic alterations has been investigated extensively, while densely-labelled barcodes have not received as much attention.

Marked point process analysis of epidermal nerve fibres.

Epidermal nerve fibre (ENF) density and summed length of ENFs per epidermal surface area are reduced, and ENFs may appear more clustered within the epidermis in subjects suffering from diabetic neuropathy compared to healthy subjects. Therefore, it is important to understand the spatial behaviour of ENFs in healthy and neuropathy subjects. By using confocal microscopy data , we study the spatial structure of epidermal nerves by regarding the nerve tree locations as realizations of marked point processes .

Methodological approach for measuring the effects of organisational-level interventions on employee withdrawal behaviour.

Background: Theoretical frameworks have recommended organisational-level interventions to decrease employee withdrawal behaviours such as sickness absence and employee turnover. However, evaluation of such interventions has produced inconclusive results. The aim of this study was to investigate if mixed-effects models in combination with time series analysis, process evaluation, and reference group comparisons could be used for evaluating the effects of an organisational-level intervention on employee withdrawal behaviour.

New Characterization Measures of Pore Shape and Connectivity Applied to Coatings used for Controlled Drug Release.

Pore geometry characterization-methods are important tools for understanding how pore structure influences properties such as transport through a porous material. Bottlenecks can have a large influence on transport and related properties. However, existing methods only catch certain types of bottleneck effects caused by variations in pore size.

Cell polarisation in a bulk-surface model can be driven by both classic and non-classic Turing instability.

The GTPase Cdc42 is the master regulator of eukaryotic cell polarisation. During this process, the active form of Cdc42 is accumulated at a particular site on the cell membrane called the pole. It is believed that the accumulation of the active Cdc42 resulting in a pole is driven by a combination of activation-inactivation reactions and diffusion.

Point process models for sweat gland activation observed with noise.

The aim of this article is to construct spatial models for the activation of sweat glands for healthy subjects and subjects suffering from peripheral neuropathy by using videos of sweating recorded from the subjects. The sweat patterns are regarded as realizations of spatial point processes and two point process models for the sweat gland activation and two methods for inference are proposed. Several image analysis steps are needed to extract the point patterns from the videos and some incorrectly identified sweat gland locations may be present in the data.

New Conceptual Toxicokinetic Model to Assess Synergistic Mixture Effects between the Aromatic Hydrocarbon β-Naphthoflavone and the Azole Nocodazole on the CYP1A Biomarker in a Fish Cell Line.

Toxicokinetic interactions with catabolic cytochrome P450 (CYP) enzymes can inhibit chemical elimination pathways and cause synergistic mixture effects. We have created a mathematical bottom-up model for a synergistic mixture effect where we fit a multidimensional function to a given data set using an auxiliary nonadditive approach. The toxicokinetic model is based on the data from a previous study on a fish cell line, where the CYP1A enzyme activity was measured over time after exposure to various combinations of the aromatic hydrocarbon β-naphthoflavone and the azole nocodazole.

Decisions and disease: a mechanism for the evolution of cooperation.

In numerous contexts, individuals may decide whether they take actions to mitigate the spread of disease, or not. Mitigating the spread of disease requires an individual to change their routine behaviours to benefit others, resulting in a 'disease dilemma' similar to the seminal prisoner's dilemma. In the classical prisoner's dilemma, evolutionary game dynamics predict that all individuals evolve to 'defect.

Symmetry structures in dynamic models of biochemical systems.

Understanding the complex interactions of biochemical processes underlying human disease represents the holy grail of systems biology. When processes are modelled in ordinary differential equation (ODE) fashion, the most common tool for their analysis is linear stability analysis where the long-term behaviour of the model is determined by linearizing the system around its steady states. However, this asymptotic behaviour is often insufficient for completely determining the structure of the underlying system.

Cultivation-Free Typing of Bacteria Using Optical DNA Mapping.

A variety of pathogenic bacteria can infect humans, and rapid species identification is crucial for the correct treatment. However, the identification process can often be time-consuming and depend on the cultivation of the bacterial pathogen(s). Here, we present a stand-alone, enzyme-free, optical DNA mapping assay capable of species identification by matching the intensity profiles of large DNA molecules to a database of fully assembled bacterial genomes (>10 000).

Symmetries of Post-Galilean Expansions.

In this Letter we study an infinite extension of the Galilei symmetry group in any dimension that can be thought of as a nonrelativistic or post-Galilean expansion of the Poincaré symmetry. We find an infinite-dimensional vector space on which this generalized Galilei group acts and usual Minkowski space can be modeled by our construction. We also construct particle and string actions that are invariant under these transformations.

Synergistic effects of repair, resilience and retention of damage determine the conditions for replicative ageing.

Accumulation of damaged proteins is a hallmark of ageing, occurring in organisms ranging from bacteria and yeast to mammalian cells. During cell division in Saccharomyces cerevisiae, damaged proteins are retained within the mother cell, resulting in an ageing mother while a new daughter cell exhibits full replicative potential. The cell-specific features determining the ageing remain elusive.

The mobile FOX AmpC beta-lactamases originated in Aeromonas allosaccharophila.

Objective: It is important to understand the origins of antibiotic resistance genes so that risks associated with the emergence of novel resistance genes can be assessed and managed. The chromosomal ampC gene (CAV-1) of Aeromonas caviae (A. caviae) has been reported as the origin of mobile FOX cephalosporinases.

Predicting verbal memory decline following temporal lobe resection for epilepsy.

Objectives: The aim of the study was to develop a prediction model for verbal memory decline after temporal lobe resection (TLR) for epilepsy. The model will be used in the preoperative counselling of patients to give individualized information about risk for verbal memory decline.

Materials And Methods: A sample of 110 consecutive patients who underwent TLR for epilepsy at Sahlgrenska University Hospital between 1987 and 2011 constituted the basis for the prediction model.

A Bayesian hierarchical point process model for epidermal nerve fiber patterns.

We introduce the Thomas process in a Bayesian hierarchical setting as a model for point pattern data with a nested structure. This model is applied to a nerve fiber data set which consists of several point patterns of nerve entry points from 47 subjects divided into 3 groups, where the grouping is based on the diagnosed severity of a certain nerve disorder. The modeling assumption is that each point pattern is a realization of a Thomas process, with parameter values specific to the subject.

Effect of liraglutide on anthropometric measurements, sagittal abdominal diameter and adiponectin levels in people with type 2 diabetes treated with multiple daily insulin injections: evaluations from a randomized trial (MDI-liraglutide study 5).

Aim: Use of the glucagon-like peptide 1 receptor agonist liraglutide has been shown to reduce weight. Different types of anthropometric measurements can be used to measure adiposity. This study evaluated the effect of liraglutide on sagittal abdominal diameter, waist circumference, waist-to-hip ratio and adiponectin levels in people with type 2 diabetes (T2D) treated with multiple daily insulin injections (MDI).

CMY-1/MOX-family AmpC β-lactamases MOX-1, MOX-2 and MOX-9 were mobilized independently from three Aeromonas species.

Objectives: To investigate the origin of CMY-1/MOX-family β-lactamases.

Methods: Publicly available genome assemblies were screened for CMY-1/MOX genes. The loci of CMY-1/MOX genes were compared with respect to synteny and nucleotide identity, and subjected to phylogenetic analysis.

Cardiac troponin T concentrations and patient-specific risk of myocardial infarction using the novel PALfx parameter.

Background: Myocardial infarction (MI) is more likely if the heart damage biomarker cardiac troponin T (cTnT) is elevated in a blood sample from a patient with chest pain. There is no conventional method to estimate the risk of MI at a specific cTnT concentration. The purpose of this study was to evaluate the performance of a novel method that converts cTnT concentrations to patient-specific risks of MI.

PER extended-spectrum β-lactamases originate from Pararheinheimera spp.

To investigate the origin of PER extended-spectrum β-lactamases, publicly available sequence databases were searched for bla genes. Three genomes from Pararheinheimera, a genus associated with water and soil environments, were found to carry bla genes but lacked the ISCR1/ISPa12/ISPa13 insertion sequences commonly associated with bla in clinical isolates. Sequence analysis revealed 78-96% nucleotide identity and conserved synteny between the clinical mobile genetic elements (MGEs) encoding bla and the bla locus in the Pararheinheimera genomes.

A Polyakov Formula for Sectors.

We consider finite area convex Euclidean circular sectors. We prove a variational Polyakov formula which shows how the zeta-regularized determinant of the Laplacian varies with respect to the opening angle. Varying the angle corresponds to a conformal deformation in the direction of a conformal factor with a logarithmic singularity at the origin.