Standardization, calibration and innovation: a special issue on lithic microwear method

YesThis paper introduces a special issue of the Journal of Archaeological Science that considers the current state and future directions in lithic microwear analysis. There is considerable potential for lithic microwear analysis to reconstruct past human behaviour as it can provide direct insight into past activities. Consequently, it is a technique worthy of significant additional investment and continued development. To further the cause of methodological maturation within microwear analysis and to promote standardization, calibration, and innovation, the following collection of papers present various approaches and perspectives on how greater methodological refinement and increased reliability of results can and should be achieved. Many of these papers were part of a session held at the 2011 Society for American Archaeology Meeting (SAA) in Sacramento, California, while others were selected from the 2012 International Conference on Use-Wear Analysis in Faro, Portugal. The purpose of the SAA session and this special themed issue is essentially two-fold. The first is to promote awareness of the need for methodological standardization, calibration, and continuing innovation. The second is to open a serious dialogue about how these aims could be pursued and achieved.AAE was supported by the AHRC (AH/J007935/1). HJL was supported by L’Équipe Archéometrie at the Laboratoires d’ Archéologie, a part of the Centre Interuniversitaire d’Études sur les Lettres, les Arts et les Traditions (CELAT) at Université Laval. DAM was supported by Fondation Fyssen and the University of Toronto. WJS was supported by Faculty Development Grant from Keene State College

Vascular dysfunction in the pathogenesis of Alzheimer's disease - A review of endothelium-mediated mechanisms and ensuing vicious circles

Late-onset dementia is a major health concern in the ageing population. Alzheimer's disease (AD) accounts for the largest proportion (65-70%) of dementia cases in the older population. Despite considerable research effort, the pathogenesis of late-onset AD remains unclear. Substantial evidence suggests that the neurodegenerative process is initiated by chronic cerebral hypoperfusion (CCH) caused by ageing and cardiovascular conditions. CCH causes reduced oxygen, glucose and other nutrient supply to the brain, with direct damage not only to the parenchymal cells, but also to the blood-brain barrier (BBB), a key mediator of cerebral homeostasis. BBB dysfunction mediates the indirect neurotoxic effects of CCH by promoting oxidative stress, inflammation, paracellular permeability, and dysregulation of nitric oxide, a key regulator of regional blood flow. As such, BBB dysfunction mediates a vicious circle in which cerebral perfusion is reduced further and the neurodegenerative process is accelerated. Endothelial interaction with pericytes and astrocytes could also play a role in the process. Reciprocal interactions between vascular dysfunction and neurodegeneration could further contribute to the development of the disease.A comprehensive overview of the complex scenario of interacting endothelium-mediated processes is currently lacking, and could prospectively contribute to the identification of adequate therapeutic interventions. This study reviews the current literature of in vitro and ex vivo studies on endothelium-mediated mechanisms underlying vascular dysfunction in AD pathogenesis, with the aim of presenting a comprehensive overview of the complex network of causative relationships. Particular emphasis is given to vicious circles which can accelerate the process of neurovascular degeneration

Prepotential and Instanton Corrections in N=2 Supersymmetric SU(N_1)xSU(N_2) Yang Mills Theories

In this paper we analyse the non-hyperelliptic Seiberg-Witten curves derived from M-theory that encode the low energy solution of N=2 supersymmetric theories with product gauge groups. We consider the case of a SU(N_1)xSU(N_2) gauge theory with a hypermultiplet in the bifundamental representation together with matter in the fundamental representations of SU(N_1) and SU(N_2). By means of the Riemann bilinear relations that hold on the Riemann surface defined by the Seiberg--Witten curve, we compute the logarithmic derivative of the prepotential with respect to the quantum scales of both gauge groups. As an application we develop a method to compute recursively the instanton corrections to the prepotential in a straightforward way. We present explicit formulas for up to third order on both quantum scales. Furthermore, we extend those results to SU(N) gauge theories with a matter hypermultiplet in the symmetric and antisymmetric representation. We also present some non-trivial checks of our results.Comment: 21 pages, 2 figures, minor changes and references adde

Diffeomorphism, kappa transformations and the theory of non-linear realisations

We will show how the theory of non-linear realisations can be used to naturally incorporate world line diffeomorphisms and kappa transformations for the point particle and superpoint particle respectively. Similar results also hold for a general p-brane and super p-brane, however, we must in these cases include an additional Lorentz transformation.Comment: 19pages, no figure. References are added and typos are correcte

Application of the broadband collision-induced dissociation (bbCID) mass spectrometry approach for protein glycosylation and phosphorylation analysis

Rationale Analysis of post‐translationally modified peptides by mass spectrometry (MS) remains incomplete, in part due to incomplete sampling of all peptides which is inherent to traditional data‐dependent acquisition (DDA). An alternative MS approach, data‐independent acquisition (DIA), enables comprehensive recording of all detectable precursor and product ions, independent of precursor intensity. The use of broadband collision‐induced dissociation (bbCID), a DIA method, was evaluated for the identification of protein glycosylation and phosphorylation. Methods bbCID was applied to identify glycopeptides and phosphopeptides generated from standard proteins using a high‐resolution Bruker maXis 3G mass spectrometer. In bbCID, precursor and product ion spectra were obtained by alternating low and high collision energy. Precursor ions were assigned manually based on the detection of diagnostic ions specific to either glycosylation or phosphorylation. The composition of the glycan modification was resolved in the positive ion mode, while the level of phosphorylation was investigated in the negative ion mode. Results The results demonstrate for the first time that the use of a bbCID approach is suitable for the identification of glycopeptides and phosphopeptides based on the detection of specific diagnostic and associated precursor ions. The novel use of bbCID in negative ion mode allowed the discrimination of singly and multiply phosphorylated peptides based on the detection of phosphate diagnostic ions. The results also demonstrate the ability of this approach to allow the identification of glycan composition in N‐ and O‐linked glycopeptides, in positive ion mode. Conclusions We contend that bbCID is a valuable addition to the existing toolkit for PTM discovery. Moreover, this technique could be employed to direct targeted proteomics methods, particularly where there is no a priori information on glycosylation or phosphorylation status. This technique is immediately relevant to the characterisation of individual proteins or biological samples of low complexity, as demonstrated for the analysis of the glycosylation status of a therapeutic protein

Level Sets of the Takagi Function: Local Level Sets

The Takagi function \tau : [0, 1] \to [0, 1] is a continuous non-differentiable function constructed by Takagi in 1903. The level sets L(y) = {x : \tau(x) = y} of the Takagi function \tau(x) are studied by introducing a notion of local level set into which level sets are partitioned. Local level sets are simple to analyze, reducing questions to understanding the relation of level sets to local level sets, which is more complicated. It is known that for a "generic" full Lebesgue measure set of ordinates y, the level sets are finite sets. Here it is shown for a "generic" full Lebesgue measure set of abscissas x, the level set L(\tau(x)) is uncountable. An interesting singular monotone function is constructed, associated to local level sets, and is used to show the expected number of local level sets at a random level y is exactly 3/2.Comment: 32 pages, 2 figures, 1 table. Latest version has updated equation numbering. The final publication will soon be available at springerlink.co

Quantifying endothelial cell proliferation in the zebrafish embryo

Introduction: Endothelial cell (EC) proliferation is a fundamental determinant of vascular development and homeostasis, and contributes to cardiovascular disease by increasing vascular permeability to blood-borne lipoproteins. Rodents have been traditionally used to analyse EC proliferation mechanisms in vascular health and disease; however, alternative models such as the zebrafish embryo allow researchers to conduct small scale screening studies in a physiologically relevant vasculature whilst reducing the use of mammals in biomedical research. In vitro models of EC proliferation are valuable but do not fully recapitulate the complexity of the in vivo situation. Several groups have used zebrafish embryos for vascular biology research because they offer the advantages of an in vivo model in terms of complexity but are also genetically manipulable and optically transparent. Methods: Here we investigated whether zebrafish embryos can provide a suitable model for the study of EC proliferation. We explored the use of antibody, DNA labelling, and time-lapse imaging approaches. Results: Antibody and DNA labelling approaches were of limited use in zebrafish due to the low rate of EC proliferation combined with the relatively narrow window of time in which they can label proliferating nuclei. By contrast, time-lapse imaging of fluorescent proteins localised to endothelial nuclei was a sensitive method to quantify EC proliferation in zebrafish embryos. Discussion: We conclude that time-lapse imaging is suitable for analysis of endothelial cell proliferation in zebrafish, and that this method is capable of capturing more instances of EC proliferation than immunostaining or cell labelling alternatives. This approach is relevant to anyone studying endothelial cell proliferation for screening genes or small molecules involved in EC proliferation. It offers greater biological relevance than existing in vitro models such as HUVECs culture, whilst reducing the overall number of animals used for this type of research

Phosphopeptide enrichment for phosphoproteomic analysis - a tutorial and review of novel materials

Significant technical advancements in phosphopeptide enrichment have enabled the identification of thousands of p-peptides (mono and multiply phosphorylated) in a single experiment. However, it is still not possible to enrich all p-peptide species in a single step. A range of new techniques and materials has been developed, with the potential to provide a step-change in phosphopeptide enrichment. The first half of this review contains a tutorial for new potential phosphoproteomic researchers; discussing the key steps of a typical phosphoproteomic experiment used to investigate canonical phosphorylation sites (serine, threonine and tyrosine). The latter half then show-cases the latest developments in p-peptide enrichment including: i) Strategies to mitigate non-specific binding in immobilized metal ion affinity chromatography and metal oxide affinity chromatography protocols; ii) Techniques to separate multiply phosphorylated peptides from monophosphorylated peptides (including canonical from non-canonical phosphorylated peptides), or to simultaneously co-enrich other post-translational modifications; iii) New hybrid materials and methods directed towards enhanced selectivity and efficiency of metal-based enrichment; iv) Novel materials that hold promise for enhanced phosphotyrosine enrichment. A combination of well-understood techniques and materials is much more effective than any technique in isolation; but the field of phosphoproteomics currently requires benchmarking of novel materials against current methodologies to fully evaluate their utility in peptide based proteoform analysis

A particle-based model for endothelial cell migration under flow conditions

Endothelial cells (ECs) play a major role in the healing process following angioplasty to inhibit excessive neointima. This makes the process of EC healing after injury, in particular EC migration in a stented vessel, important for recovery of normal vessel function. In that context, we present a novel particle-based model of EC migration and validate it against in vitro experimental data. We have developed a particle-based model of EC migration under flow conditions in an in vitro vessel with obstacles. Cell movement in the model is a combination of random walks and directed movement along the local flow velocity vector. For model calibration, a set of experimental data for cell migration in a similarly shaped channel has been used. We have calibrated the model for a baseline case of a channel with no obstacles and then applied it to the case of a channel with ridges on the bottom surface, representative of stent strut geometry. We were able to closely reproduce the cell migration speed and angular distribution of their movement relative to the flow direction reported in vitro. The model also reproduces qualitative aspects of EC migration, such as entrapment of cells downstream from the flow-disturbing ridge. The model has the potential, after more extensive in vitro validation, to study the effect of variation in strut spacing and shape, through modification of the local flow, on EC migration. The results of this study support the hypothesis that EC migration is strongly affected by the direction and magnitude of local wall shear stress