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

PocketMatch: A new algorithm to compare binding sites in protein structures

Background: Recognizing similarities and deriving relationships among protein molecules is a fundamental
requirement in present-day biology. Similarities can be present at various levels which can be detected through comparison of protein sequences or their structural folds. In some cases similarities obscure at these levels could be present merely in the substructures at their binding sites. Inferring functional similarities between protein molecules by comparing their binding sites is still largely exploratory and not as yet a routine protocol. One of
the main reasons for this is the limitation in the choice of appropriate analytical tools that can compare binding sites with high sensitivity. To benefit from the enormous amount of structural data that is being rapidly accumulated, it is essential to have high throughput tools that enable large scale binding site comparison.

Results: Here we present a new algorithm PocketMatch for comparison of binding sites in a frame invariant
manner. Each binding site is represented by 90 lists of sorted distances capturing shape and chemical nature of the site. The sorted arrays are then aligned using an incremental alignment method and scored to obtain PMScores for pairs of sites. A comprehensive sensitivity analysis and an extensive validation of the algorithm have been carried out. Perturbation studies where the geometry of a given site was retained but the residue types were changed randomly, indicated that chance similarities were virtually non-existent. Our analysis also demonstrates that shape information alone is insufficient to discriminate between diverse binding sites, unless
combined with chemical nature of amino acids.

Conclusions: A new algorithm has been developed to compare binding sites in accurate, efficient and
high-throughput manner. Though the representation used is conceptually simplistic, we demonstrate that along
with the new alignment strategy used, it is sufficient to enable binding comparison with high sensitivity. Novel methodology has also been presented for validating the algorithm for accuracy and sensitivity with respect to geometry and chemical nature of the site. The method is also fast and takes about 1/250th second for one comparison on a single processor. A parallel version on BlueGene has also been implemented

Female economic dependence and the morality of promiscuity

This article is made available through the Brunel Open Access Publishing Fund. Copyright @ The Author(s) 2014.In environments in which female economic dependence on a male mate is higher, male parental investment is more essential. In such environments, therefore, both sexes should value paternity certainty more and thus object more to promiscuity (because promiscuity undermines paternity certainty). We tested this theory of anti-promiscuity morality in two studies (N = 656 and N = 4,626) using U.S. samples. In both, we examined whether opposition to promiscuity was higher among people who perceived greater female economic dependence in their social network. In Study 2, we also tested whether economic indicators of female economic dependence (e.g., female income, welfare availability) predicted anti-promiscuity morality at the state level. Results from both studies supported the proposed theory. At the individual level, perceived female economic dependence explained significant variance in anti-promiscuity morality, even after controlling for variance explained by age, sex, religiosity, political conservatism, and the anti-promiscuity views of geographical neighbors. At the state level, median female income was strongly negatively related to anti-promiscuity morality and this relationship was fully mediated by perceived female economic dependence. These results were consistent with the view that anti-promiscuity beliefs may function to promote paternity certainty in circumstances where male parental investment is particularly important

Identification of a novel type of spacer element required for imprinting in fission yeast

Asymmetrical segregation of differentiated sister chromatids is thought to be important for cellular differentiation in higher eukaryotes. Similarly, in fission yeast, cellular differentiation involves the asymmetrical segregation of a chromosomal imprint. This imprint has been shown to consist of two ribonucleotides that are incorporated into the DNA during laggingstrand synthesis in response to a replication pause, but the underlying mechanism remains unknown. Here we present key novel discoveries important for unravelling this process. Our data show that cis-acting sequences within the mat1 cassette mediate pausing of replication forks at the proximity of the imprinting site, and the results suggest that this pause dictates specific priming at the position of imprinting in a sequence-independent manner. Also, we identify a novel type of cis-acting spacer region important for the imprinting process that affects where subsequent primers are put down after the replication fork is released from the pause. Thus, our data suggest that the imprint is formed by ligation of a not-fullyprocessed Okazaki fragment to the subsequent fragment. The presented work addresses how differentiated sister chromatids are established during DNA replication through the involvement of replication barriers

Elevated expression of polymorphonuclear leukocyte elastase in breast cancer tissue is associated with tamoxifen failure in patients with advanced disease

Besides a variety of other proteases, polymorphonuclear leukocyte elastase (PMN-E) is also suggested to play a role in the processes of tumour cell invasion and metastasis. Yet, there is only limited data available on the relation between the tumour level of PMN-E and prognosis in patients with primary breast cancer, and no published information exists on its relation with the efficacy of response to systemic therapy in patients with advanced breast cancer. In the present study, we have measured with enzyme-linked immunosorbent assay the levels of total PMN-E in cytosolic extracts of 463 primary breast tumours, and have correlated their levels with the rate and duration of response on first-line tamoxifen therapy (387 patients) or chemotherapy (76 patients) in patients with locally advanced and/or distant metastatic breast cancer. Furthermore, the probabilities of progression-free survival and postrelapse survival were studied in relation to the tumour levels of PMN-E. Our results show that in logistic regression analysis for response to tamoxifen treatment in patients with advanced disease, high PMN-E tumour levels were associated with a poor rate of response compared with those with low PMN-E levels (odds ratio: OR, 0.40; 95% CI, 0.22-0.73; P = 0.003). After correction for the contribution of the traditional predictive factors in multivariate analysis, the tumour PMN-E status was an independent predictor of response (P = 0.01). Furthermore, a high tumour PMN-E level was related with a poor progression-free survival (P<0.001) and postrelapse survival (P = 0.002) in a time-dependent analysis. In contrast, the tumour level of PMN-E was not significantly related with the efficacy of response to first-line chemotherapy in patients with advanced breast cancer. Our present results suggest that PMN-E is an independent predictive marker for the efficacy of tamoxifen treatment in patients with advanced breast cancer

Selective scattering between Floquet-Bloch and Volkov states in a topological insulator

The coherent optical manipulation of solids is emerging as a promising way to engineer novel quantum states of matter. The strong time periodic potential of intense laser light can be used to generate hybrid photon-electron states. Interaction of light with Bloch states leads to Floquet-Bloch states which are essential in realizing new photo-induced quantum phases. Similarly, dressing of free electron states near the surface of a solid generates Volkov states which are used to study non-linear optics in atoms and semiconductors. The interaction of these two dynamic states with each other remains an open experimental problem. Here we use Time and Angle Resolved Photoemission Spectroscopy (Tr-ARPES) to selectively study the transition between these two states on the surface of the topological insulator Bi2Se3. We find that the coupling between the two strongly depends on the electron momentum, providing a route to enhance or inhibit it. Moreover, by controlling the light polarization we can negate Volkov states in order to generate pure Floquet-Bloch states. This work establishes a systematic path for the coherent manipulation of solids via light-matter interaction.Comment: 21 pages, 6 figures, final version to appear in Nature Physic

Post-supereruption recovery at Toba Caldera

Large calderas, or supervolcanoes, are sites of the most catastrophic and hazardous events on Earth, yet the temporal details of post-supereruption activity, or resurgence, remain largely unknown, limiting our ability to understand how supervolcanoes work and address their hazards. Toba Caldera, Indonesia, caused the greatest volcanic catastrophe of the last 100 kyr, climactically erupting ~74 ka. Since the supereruption, Toba has been in a state of resurgence but its magmatic and uplift history has remained unclear. Here we reveal that new 14 C, zircon U-Th crystallization and (U-Th)/He ages show resurgence commenced at 69.7±4.5 ka and continued until at least ~2.7 ka, progressing westward across the caldera, as reflected by post-caldera effusive lava eruptions and uplifted lake sediment. The major stratovolcano north of Toba, Sinabung, shows strong geochemical kinship with Toba, and zircons from recent eruption products suggest Toba's climactic magma reservoir extends beneath Sinabung and is being tapped during eruptions

Global ocean heat content in the Last Interglacial

The Last Interglacial (129-116 ka) represents one of the warmest climate intervals of the last 800,000 years and the most recent time when sea level was meters higher than today. However, the timing and magnitude of peak warmth varies between reconstructions, and the relative importance of individual sources contributing to elevated sea level (mass gain versus seawater expansion) during the Last Interglacial remains uncertain. Here we present the first mean ocean temperature record for this interval from noble gas measurements in ice cores and constrain the thermal expansion contribution to sea level. Mean ocean temperature reaches its maximum value of 1.1±0.3°C warmer-than-modern at the end of the penultimate deglaciation at 129 ka, resulting in 0.7±0.3m of elevated sea level, relative to present. However, this maximum in ocean heat content is a transient feature; mean ocean temperature decreases in the first several thousand years of the interglacial and achieves a stable, comparable-to-modern value by ~127 ka. The synchroneity of the peak in mean ocean temperature with proxy records of abrupt transitions in oceanic and atmospheric circulation suggests that the mean ocean temperature maximum is related to the accumulation of heat in the ocean interior during the preceding period of reduced overturning circulation