Invasion percolation and critical transient in the Barabási Model of human dynamics

We introduce an exact probabilistic description for L=2 of the Barabási model for the dynamics of a list of L tasks. This permits us to study the problem out of the stationary state and to solve explicitly the extremal limit case where a critical behavior for the waiting time distribution is observed. This behavior deviates at any finite time from that of the stationary state. We study also the characteristic relaxation time for finite time deviations from stationarity in all cases showing that it diverges in the extremal limit, confirming that these deviations are important at all time

How Xenopus laevis embryos replicate reliably: investigating the random-completion problem

DNA synthesis in \textit{Xenopus} frog embryos initiates stochastically in time at many sites (origins) along the chromosome. Stochastic initiation implies fluctuations in the time to complete and may lead to cell death if replication takes longer than the cell cycle time ($\approx 25$ min). Surprisingly, although the typical replication time is about 20 min, \textit{in vivo} experiments show that replication fails to complete only about 1 in 300 times. How is replication timing accurately controlled despite the stochasticity? Biologists have proposed two solutions to this "random-completion problem." The first solution uses randomly located origins but increases their rate of initiation as S phase proceeds, while the second uses regularly spaced origins. In this paper, we investigate the random-completion problem using a type of model first developed to describe the kinetics of first-order phase transitions. Using methods from the field of extreme-value statistics, we derive the distribution of replication-completion times for a finite genome. We then argue that the biologists' first solution to the problem is not only consistent with experiment but also nearly optimizes the use of replicative proteins. We also show that spatial regularity in origin placement does not alter significantly the distribution of replication times and, thus, is not needed for the control of replication timing.Comment: 16 pages, 9 figures, submitted to Physical Review

Iterative approximation of k-limited polling systems

The present paper deals with the problem of calculating queue length distributions in a polling model with (exhaustive) k-limited service under the assumption of general arrival, service and setup distributions. The interest for this model is fueled by an application in the field of logistics. Knowledge of the queue length distributions is needed to operate the system properly. The multi-queue polling system is decomposed into single-queue vacation systems with k-limited service and state-dependent vacations, for which the vacation distributions are computed in an iterative approximate manner. These vacation models are analyzed via matrix-analytic techniques. The accuracy of the approximation scheme is verified by means of an extensive simulation study. The developed approximation turns out be accurate, robust and computationally efficient

Paired plasma lipidomics and proteomics analysis in the conversion from mild cognitive impairment to Alzheimer's disease.

Alzheimer's disease (AD) is a neurodegenerative condition for which there is currently no available medication that can stop its progression. Previous studies suggest that mild cognitive impairment (MCI) is a phase that precedes the disease. Therefore, a better understanding of the molecular mechanisms behind MCI conversion to AD is needed. Here, we propose a machine learning-based approach to detect the key metabolites and proteins involved in MCI progression to AD using data from the European Medical Information Framework for Alzheimer's Disease Multimodal Biomarker Discovery Study. Proteins and metabolites were evaluated separately in multiclass models (controls, MCI and AD) and together in MCI conversion models (MCI stable vs converter). Only features selected as relevant by 3/4 algorithms proposed were kept for downstream analysis. Multiclass models of metabolites highlighted nine features further validated in an independent cohort (0.726 mean balanced accuracy). Among these features, one metabolite, oleamide, was selected by all the algorithms. Further in-vitro experiments in rodents showed that disease-associated microglia excreted oleamide in vesicles. Multiclass models of proteins stood out with nine features, validated in an independent cohort (0.720 mean balanced accuracy). However, none of the proteins was selected by all the algorithms. Besides, to distinguish between MCI stable and converters, 14 key features were selected (0.872 AUC), including tTau, alpha-synuclein (SNCA), junctophilin-3 (JPH3), properdin (CFP) and peptidase inhibitor 15 (PI15) among others. This omics integration approach highlighted a set of molecules associated with MCI conversion important in neuronal and glia inflammation pathways

Multivariate GWAS of Alzheimer’s disease CSF biomarker profiles implies GRIN2D in synaptic functioning

BACKGROUND: Genome-wide association studies (GWAS) of Alzheimer's disease (AD) have identified several risk loci, but many remain unknown. Cerebrospinal fluid (CSF) biomarkers may aid in gene discovery and we previously demonstrated that six CSF biomarkers (β-amyloid, total/phosphorylated tau, NfL, YKL-40, and neurogranin) cluster into five principal components (PC), each representing statistically independent biological processes. Here, we aimed to (1) identify common genetic variants associated with these CSF profiles, (2) assess the role of associated variants in AD pathophysiology, and (3) explore potential sex differences. METHODS: We performed GWAS for each of the five biomarker PCs in two multi-center studies (EMIF-AD and ADNI). In total, 973 participants (n = 205 controls, n = 546 mild cognitive impairment, n = 222 AD) were analyzed for 7,433,949 common SNPs and 19,511 protein-coding genes. Structural equation models tested whether biomarker PCs mediate genetic risk effects on AD, and stratified and interaction models probed for sex-specific effects. RESULTS: Five loci showed genome-wide significant association with CSF profiles, two were novel (rs145791381 [inflammation] and GRIN2D [synaptic functioning]) and three were previously described (APOE, TMEM106B, and CHI3L1). Follow-up analyses of the two novel signals in independent datasets only supported the GRIN2D locus, which contains several functionally interesting candidate genes. Mediation tests indicated that variants in APOE are associated with AD status via processes related to amyloid and tau pathology, while markers in TMEM106B and CHI3L1 are associated with AD only via neuronal injury/inflammation. Additionally, seven loci showed sex-specific associations with AD biomarkers. CONCLUSIONS: These results suggest that pathway and sex-specific analyses can improve our understanding of AD genetics and may contribute to precision medicine

Synthesizing Systems with Optimal Average-Case Behavior for Ratio Objectives

We show how to automatically construct a system that satisfies a given logical specification and has an optimal average behavior with respect to a specification with ratio costs. When synthesizing a system from a logical specification, it is often the case that several different systems satisfy the specification. In this case, it is usually not easy for the user to state formally which system she prefers. Prior work proposed to rank the correct systems by adding a quantitative aspect to the specification. A desired preference relation can be expressed with (i) a quantitative language, which is a function assigning a value to every possible behavior of a system, and (ii) an environment model defining the desired optimization criteria of the system, e.g., worst-case or average-case optimal. In this paper, we show how to synthesize a system that is optimal for (i) a quantitative language given by an automaton with a ratio cost function, and (ii) an environment model given by a labeled Markov decision process. The objective of the system is to minimize the expected (ratio) costs. The solution is based on a reduction to Markov Decision Processes with ratio cost functions which do not require that the costs in the denominator are strictly positive. We find an optimal strategy for these using a fractional linear program.Comment: In Proceedings iWIGP 2011, arXiv:1102.374

TMEM106B and CPOX are genetic determinants of cerebrospinal fluid Alzheimer's disease biomarker levels

INTRODUCTION: Neurofilament light (NfL), chitinase-3-like protein 1 (YKL-40), and neurogranin (Ng) are biomarkers for Alzheimer's disease (AD) to monitor axonal damage, astroglial activation, and synaptic degeneration, respectively. METHODS: We performed genome-wide association studies (GWAS) using DNA and cerebrospinal fluid (CSF) samples from the EMIF-AD Multimodal Biomarker Discovery study for discovery, and the Alzheimer's Disease Neuroimaging Initiative study for validation analyses. GWAS were performed for all three CSF biomarkers using linear regression models adjusting for relevant covariates. RESULTS: We identify novel genome-wide significant associations between DNA variants in TMEM106B and CSF levels of NfL, and between CPOX and YKL-40. We confirm previous work suggesting that YKL-40 levels are associated with DNA variants in CHI3L1. DISCUSSION: Our study provides important new insights into the genetic architecture underlying interindividual variation in three AD-related CSF biomarkers. In particular, our data shed light on the sequence of events regarding the initiation and progression of neuropathological processes relevant in AD