On the excursions of reflected local time processes and stochastic fluid queues

This paper extends previous work by the authors. We consider the local time process of a strong Markov process, add negative drift, and reflect it \`a la Skorokhod. The resulting process is used to model a fluid queue. We derive an expression for the joint law of the duration of an excursion, the maximum value of the process on it, and the time distance between successive excursions. We work with a properly constructed stationary version of the process. Examples are also given in the paper.Comment: 29 pages, 4 figure

Roughening of Fracture Surfaces: the Role of Plastic Deformations

Post mortem analysis of fracture surfaces of ductile and brittle materials on the $\mu$m-mm and the nm scales respectively, reveal self affine graphs with an anomalous scaling exponent $\zeta\approx 0.8$. Attempts to use elasticity theory to explain this result failed, yielding exponent $\zeta\approx 0.5$ up to logarithms. We show that when the cracks propagate via plastic void formations in front of the tip, followed by void coalescence, the voids positions are positively correlated to yield exponents higher than 0.5.Comment: 4 pages, 6 figure

Analysis of stochastic fluid queues driven by local time processes

We consider a stochastic fluid queue served by a constant rate server and driven by a process which is the local time of a certain Markov process. Such a stochastic system can be used as a model in a priority service system, especially when the time scales involved are fast. The input (local time) in our model is always singular with respect to the Lebesgue measure which in many applications is ``close'' to reality. We first discuss how to rigorously construct the (necessarily) unique stationary version of the system under some natural stability conditions. We then consider the distribution of performance steady-state characteristics, namely, the buffer content, the idle period and the busy period. These derivations are much based on the fact that the inverse of the local time of a Markov process is a L\'evy process (a subordinator) hence making the theory of L\'evy processes applicable. Another important ingredient in our approach is the Palm calculus coming from the point process point of view.Comment: 32 pages, 6 figure

Reducing CSF Partial Volume Effects to Enhance Diffusion Tensor Imaging Metrics of Brain Microstructure

Technological advances over recent decades now allow for in vivo observation of human brain tissue through the use of neuroimaging methods. While this field originated with techniques capable of capturing macrostructural details of brain anatomy, modern methods such as diffusion tensor imaging (DTI) that are now regularly implemented in research protocols have the ability to characterize brain microstructure. DTI has been used to reveal subtle micro-anatomical abnormalities in the prodromal phase ofº various diseases and also to delineate “normal” age-related changes in brain tissue across the lifespan. Nevertheless, imaging artifact in DTI remains a significant limitation for identifying true neural signatures of disease and brain-behavior relationships. Cerebrospinal fluid (CSF) contamination of brain voxels is a main source of error on DTI scans that causes partial volume effects and reduces the accuracy of tissue characterization. Several methods have been proposed to correct for CSF artifact though many of these methods introduce new limitations that may preclude certain applications. The purpose of this review is to discuss the complexity of signal acquisition as it relates to CSF artifact on DTI scans and review methods of CSF suppression in DTI. We will then discuss a technique that has been recently shown to effectively suppress the CSF signal in DTI data, resulting in fewer errors and improved measurement of brain tissue. This approach and related techniques have the potential to significantly improve our understanding of “normal” brain aging and neuropsychiatric and neurodegenerative diseases. Considerations for next-level applications are discussed

Travertine precipitation in the Paleoproterozoic Kuetsjärvi Sedimentary Formation, Pechenga Greenstone Belt, NE Fennoscandian Shield

PES was supported by Väisälä Foundation (Finnish Academy of Science and Letters) and the Finnish Doctoral Program in Geology. ATB was supported by NERC grant NE/G00398X/1. VAM was supported by NFR grant 191530/V30 (projects 331000 and 802795). This is a contribution (paper) # 18 to the ICDP FAR-DEEP project.Peer reviewedPublisher PD

Cyclase-associated protein 1 (CAP1) promotes cofilin-induced actin dynamics in mammalian nonmuscle cells

Cyclase-associated proteins (CAPs) are highly conserved actin monomer binding proteins present in all eukaryotes. However, the mechanism by which CAPs contribute to actin dynamics has been elusive. In mammals, the situation is further complicated by the presence of two CAP isoforms whose differences have not been characterized. Here, we show that CAP1 is widely expressed in mouse nonmuscle cells, whereas CAP2 is the predominant isoform in developing striated muscles. In cultured NIH3T3 and 1316171 cells, CAP1 is a highly abundant protein that colocalizes with cofilin-1 to dynamic regions of the cortical actin cytoskeleton. Analysis of CAP1 knockdown cells demonstrated that this protein promotes rapid actin filament depolymerization and is important for cell morphology, migration, and endocytosis. Interestingly, depletion of CAP1 leads to an accumulation of cofilin-1 into abnormal cytoplasmic aggregates and to similar cytoskeletal defects to those seen in cofilin-1 knockdown cells, demonstrating that CAP1 is required for proper subcellular localization and function of ADF/cofilin. Together, these data provide the first direct in vivo evidence that CAP promotes rapid actin dynamics in conjunction with ADF/cofilin and is required for several central cellular processes in mammals

Insect community structure covaries with host plant chemistry but is not affected by prior herbivory

By feeding on plant tissue, insect herbivores can change several characteristics of their hosts. These changes have the potential to alter the quality of the plant for other herbivore species, potentially altering the structure of the community of species attacking the plant at a later point in time. We tested whether herbivory early in the season changes host plant performance, polyphenol chemistry, and the community structure of sessile herbivores later in the season. We experimentally manipulated densities of early‐season moth caterpillars on a set of young oak trees and measured tree growth, reproduction, leaf chemistry, and the abundance and community composition of leafmining and galling species later in the season. The experimental manipulations of early‐season herbivores did not affect late‐season leaf chemistry or tree performance. Early‐season herbivores had a weak negative effect on the abundance of gallers and a positive, tree‐dependent effect on the overall diversity of late‐season sessile herbivores. The chemical composition of leaves covaried with the species composition of the late‐season leafmining and galling community. Both the chemical composition of the host tree and the late‐season insect community structure were strongly affected by the growth location of the tree. Our results suggest that plant‐mediated indirect effects between herbivores might play a limited role in this system, whereas the underlying variation in plant chemistry is an important factor structuring the associated insect community. Our results emphasize that factors other than prior herbivory can be important determinants of plant chemistry and the community composition of herbivores

Reducing CSF partial volume effects to enhance diffusion tensor imaging metrics of brain microstructure

Technological advances over recent decades now allow for in vivo observation of human brain tissue through the use of neuroimaging methods. While this field originated with techniques capable of capturing macrostructural details of brain anatomy, modern methods such as diffusion tensor imaging (DTI) that are now regularly implemented in research protocols have the ability to characterize brain microstructure. DTI has been used to reveal subtle micro-anatomical abnormalities in the prodromal phase ofº various diseases and also to delineate “normal” age-related changes in brain tissue across the lifespan. Nevertheless, imaging artifact in DTI remains a significant limitation for identifying true neural signatures of disease and brain-behavior relationships. Cerebrospinal fluid (CSF) contamination of brain voxels is a main source of error on DTI scans that causes partial volume effects and reduces the accuracy of tissue characterization. Several methods have been proposed to correct for CSF artifact though many of these methods introduce new limitations that may preclude certain applications. The purpose of this review is to discuss the complexity of signal acquisition as it relates to CSF artifact on DTI scans and review methods of CSF suppression in DTI. We will then discuss a technique that has been recently shown to effectively suppress the CSF signal in DTI data, resulting in fewer errors and improved measurement of brain tissue. This approach and related techniques have the potential to significantly improve our understanding of “normal” brain aging and neuropsychiatric and neurodegenerative diseases. Considerations for next-level applications are discussed

The Newick utilities: high-throughput phylogenetic tree processing in the Unix shell

Summary: We present a suite of Unix shell programs for processing any number of phylogenetic trees of any size. They perform frequently-used tree operations without requiring user interaction. They also allow tree drawing as scalable vector graphics (SVG), suitable for high-quality presentations and further editing, and as ASCII graphics for command-line inspection. As an example we include an implementation of bootscanning, a procedure for finding recombination breakpoints in viral genomes

Topological organization of whole-brain white matter in HIV infection

Infection with human immunodeficiency virus (HIV) is associated with neuroimaging alterations. However, little is known about the topological organization of whole-brain networks and the corresponding association with cognition. As such, we examined structural whole-brain white matter connectivity patterns and cognitive performance in 29 HIV+ young adults (mean age = 25.9) with limited or no HIV treatment history. HIV+ participants and demographically similar HIV− controls (n = 16) residing in South Africa underwent magnetic resonance imaging (MRI) and neuropsychological testing. Structural network models were constructed using diffusion MRI-based multifiber tractography and T(1)-weighted MRI-based regional gray matter segmentation. Global network measures included whole-brain structural integration, connection strength, and structural segregation. Cognition was measured using a neuropsychological global deficit score (GDS) as well as individual cognitive domains. Results revealed that HIV+ participants exhibited significant disruptions to whole-brain networks, characterized by weaker structural integration (characteristic path length and efficiency), connection strength, and structural segregation (clustering coefficient) than HIV− controls (p < 0.05). GDSs and performance on learning/recall tasks were negatively correlated with the clustering coefficient (p < 0.05) in HIV+ participants. Results from this study indicate disruption to brain network integrity in treatment-limited HIV+ young adults with corresponding abnormalities in cognitive performance