Mathematical Modelling of Optical Coherence Tomography

In this chapter a general mathematical model of Optical Coherence Tomography (OCT) is presented on the basis of the electromagnetic theory. OCT produces high resolution images of the inner structure of biological tissues. Images are obtained by measuring the time delay and the intensity of the backscattered light from the sample considering also the coherence properties of light. The scattering problem is considered for a weakly scattering medium located far enough from the detector. The inverse problem is to reconstruct the susceptibility of the medium given the measurements for different positions of the mirror. Different approaches are addressed depending on the different assumptions made about the optical properties of the sample. This procedure is applied to a full field OCT system and an extension to standard (time and frequency domain) OCT is briefly presented.Comment: 28 pages, 5 figures, book chapte

Focal brain trauma in the cryogenic lesion model in mice

The method to induce unilateral cryogenic lesions was first described in 1958 by Klatzo. We describe here an adaptation of this model that allows reliable measurement of lesion volume and vasogenic edema by 2, 3, 5-triphenyltetrazolium chloride-staining and Evans blue extravasation in mice. A copper or aluminium cylinder with a tip diameter of 2.5 mm is cooled with liquid nitrogen and placed on the exposed skull bone over the parietal cortex (coordinates from bregma: 1.5 mm posterior, 1.5 mm lateral). The tip diameter and the contact time between the tip and the parietal skull determine the extent of cryolesion. Due to an early damage of the blood brain barrier, the cryogenic cortical injury is characterized by vasogenic edema, marked brain swelling, and inflammation. The lesion grows during the first 24 hours, a process involving complex interactions between endothelial cells, immune cells, cerebral blood flow, and the intracranial pressure. These contribute substantially to the damage from the initial injury. The major advantage of the cryogenic lesion model is the circumscribed and highly reproducible lesion size and location

t2prhd: a tool to study the patterns of repeat evolution

BACKGROUND: The models developed to characterize the evolution of multigene families (such as the birth-and-death and the concerted models) have also been applied on the level of sequence repeats inside a gene/protein. Phylogenetic reconstruction is the method of choice to study the evolution of gene families and also sequence repeats in the light of these models. The characterization of the gene family evolution in view of the evolutionary models is done by the evaluation of the clustering of the sequences with the originating loci in mind. As the locus represents positional information, it is straightforward that in the case of the repeats the exact position in the sequence should be used, as the simple numbering according to repeat order can be misleading. RESULTS: We have developed a novel rapid visual approach to study repeat evolution, that takes into account the exact repeat position in a sequence. The "pairwise repeat homology diagram" visualizes sequence repeats detected by a profile HMM in a pair of sequences and highlights their homology relations inferred by a phylogenetic tree. The method is implemented in a Perl script (t2prhd) available for downloading at http://t2prhd.sourceforge.net and is also accessible as an online tool at http://t2prhd.brc.hu. The power of the method is demonstrated on the EGF-like and fibronectin-III-like (Fn-III) domain repeats of three selected mammalian Tenascin sequences. CONCLUSION: Although pairwise repeat homology diagrams do not carry all the information provided by the phylogenetic tree, they allow a rapid and intuitive assessment of repeat evolution. We believe, that t2prhd is a helpful tool with which to study the pattern of repeat evolution. This method can be particularly useful in cases of large datasets (such as large gene families), as the command line interface makes it possible to automate the generation of pairwise repeat homology diagrams with the aid of script

Fast Inhibition of Glutamate-Activated Currents by Caffeine

Background: Caffeine stimulates calcium-induced calcium release (CICR) in many cell types. In neurons, caffeine stimulates CICR presynaptically and thus modulates neurotransmitter release. Methodology/Principal Findings: Using the whole-cell patch-clamp technique we found that caffeine (20 mM) reversibly increased the frequency and decreased the amplitude of miniature excitatory postsynaptic currents (mEPSCs) in neocortical neurons. The increase in mEPSC frequency is consistent with a presynaptic mechanism. Caffeine also reduced exogenously applied glutamate-activated currents, confirming a separate postsynaptic action. This inhibition developed in tens of milliseconds, consistent with block of channel currents. Caffeine (20 mM) did not reduce currents activated by exogenous NMDA, indicating that caffeine block is specific to non-NMDA type glutamate receptors. Conclusions/Significance: Caffeine-induced inhibition of mEPSC amplitude occurs through postsynaptic block of non-NMDA type ionotropic glutamate receptors. Caffeine thus has both pre and postsynaptic sites of action at excitatory synapses

‘Lower than a Snake’s Belly’ : Discursive Constructions of Dignity and Heroism in Low-Status Garbage Work

In this paper, we consider how dignity is discursively constructed in the context of work dominated by physicality and dirt. Based on semi-structured interviews with garbage workers, our analysis considers how the deprivations they experience are cast through discourses intended to construct their individual and collective worth. We consider the manner in which dignity maybe denied to such workers through popular repudiations of individuality and status. We demonstrate how this positioning arises from contact with physical dirt, and associations with socially dirty work based on ascriptions of servility, abuse and ambivalence. We go on to consider how garbage workers respond to this positioning through discourses of ‘everyday heroism’. Heroism is evoked through three interrelated narratives that speaks to a particular type of masculinity. The first takes the form of a classic process of reframing and recalibration through which workers not only renegotiate their public position and status, but also point to the inherent value to be had in working with dirt as part of that which we identify as a process of ‘affirmation’. The second narrative arises from the imposition of favourable social and occupational comparisons that effectively elevate garbage collectors’ social position. The third discourse—and previously unobserved in respect of garbage work—centres on paternalistic practices of care. Combined, these discourses disrupt the generally held view that dirty work is antithetical to heroism and wounds dignity

‘Lower than a snake’s belly’ : discursive constructions of dignity and heroism in low-status garbage work.

In this paper, we consider how dignity is discursively constructed in the context of work dominated by physicality and dirt. Based on semi-structured interviews with garbage workers, our analysis considers how the deprivations they experience are cast through discourses intended to construct their individual and collective worth. We consider the manner in which dignity maybe denied to such workers through popular repudiations of individuality and status. We demonstrate how this positioning arises from contact with physical dirt, and associations with socially dirty work based on ascriptions of servility, abuse and ambivalence. We go on to consider how garbage workers respond to this positioning through discourses of ‘everyday heroism’. Heroism is evoked through three inter-related narratives that speaks to a particular type of masculinity. The first takes the form of a classic process of reframing and recalibration through which workers not only renegotiate their public position and status, but also point to the inherent value to be had in working with dirt as part of that which we identify as a process of ‘affirmation’. The second narrative arises from the imposition of favourable social and occupational comparisons that effectively elevate garbage collectors’ social position. The third discourse—and previously unobserved in respect of garbage work—centres on paternalistic practices of care. Combined, these discourses disrupt the generally held view that dirty work is antithetical to heroism and wounds dignity

Brain energy metabolism: A roadmap for future research

Although we have learned much about how the brain fuels its functions over the last decades, there remains much still to discover in an organ that is so complex. This article lays out major gaps in our knowledge of interrelationships between brain metabolism and brain function, including biochemical, cellular, and subcellular aspects of functional metabolism and its imaging in adult brain, as well as during development, aging, and disease. The focus is on unknowns in metabolism of major brain substrates and associated transporters, the roles of insulin and of lipid droplets, the emerging role of metabolism in microglia, mysteries about the major brain cofactor and signaling molecule NAD+, as well as unsolved problems underlying brain metabolism in pathologies such as traumatic brain injury, epilepsy, and metabolic downregulation during hibernation. It describes our current level of understanding of these facets of brain energy metabolism as well as a roadmap for future research

Coevolution of Interacting Fertilization Proteins

Reproductive proteins are among the fastest evolving in the proteome, often due to the consequences of positive selection, and their rapid evolution is frequently attributed to a coevolutionary process between interacting female and male proteins. Such a process could leave characteristic signatures at coevolving genes. One signature of coevolution, predicted by sexual selection theory, is an association of alleles between the two genes. Another predicted signature is a correlation of evolutionary rates during divergence due to compensatory evolution. We studied female–male coevolution in the abalone by resequencing sperm lysin and its interacting egg coat protein, VERL, in populations of two species. As predicted, we found intergenic linkage disequilibrium between lysin and VERL, despite our demonstration that they are not physically linked. This finding supports a central prediction of sexual selection using actual genotypes, that of an association between a male trait and its female preference locus. We also created a novel likelihood method to show that lysin and VERL have experienced correlated rates of evolution. These two signatures of coevolution can provide statistical rigor to hypotheses of coevolution and could be exploited for identifying coevolving proteins a priori. We also present polymorphism-based evidence for positive selection and implicate recent selective events at the specific structural regions of lysin and VERL responsible for their species-specific interaction. Finally, we observed deep subdivision between VERL alleles in one species, which matches a theoretical prediction of sexual conflict. Thus, abalone fertilization proteins illustrate how coevolution can lead to reproductive barriers and potentially drive speciation

‘What Do I Get?’ Punk Objects as Meaningful and Valuable Souvenirs

Despite social scientists’ increasing interest on souvenirs in tourism, little has been written on the role and meanings of souvenirs within specific subcultures, such as punk subcultures. This chapter focuses on the exploration of punk objects as potential souvenirs in relation to “punk tourism” by investigating the meanings attached to subcultural artefacts as opposed to mass produced products. As part of an ethnographic fieldwork on punk tourism that the two authors have been conducting in Malaysia since 2016, in this chapter we focus on the role and meanings of punk souvenirs within the Malaysian punk scene. As the empirical material presented in this chapter shows, a DIY produced punk product has the advantage of channelling more than one value. While the value of souvenirs lies in their propensity to act as “mnemonic devices” related to a place visited, subcultural products like those produced by punks have the potential to fulfil additional values. In an age where authenticity and claims of appropriation of culture are placed under scrutiny, a punk object holds the potential of being a meaningful and valuable souvenir