Optimizing multi-dimensional terahertz imaging analysis for colon cancer diagnosis

Peer reviewedPublisher PD

DichroMatch: a website for similarity searching of circular dichroism spectra

Circular dichroism (CD) spectroscopy is a widely used method for examining the structure, folding and conformational changes of proteins. A new online CD analysis server (DichroMatch) has been developed for identifying proteins with similar spectral characteristics by detecting possible structurally and functionally related proteins and homologues. DichroMatch includes six different methods for determining the spectral nearest neighbours to a query protein spectrum and provides metrics of how similar these spectra are and, if corresponding crystal structures are available for the closest matched proteins, information on their secondary structures and fold classifications. By default, DichroMatch uses all the entries in the Protein Circular Dichroism Data Bank (PCDDB) for its comparison set, providing the broadest range of publicly available protein spectra to match with the unknown protein. Alternatively, users can download or create their own specialized data sets, thereby enabling comparisons between the structures of related proteins such as wild-type versus mutants or homologues or a series of spectra of the same protein under different conditions. The DichroMatch server is freely available at http://dichromatch.cryst.bbk.ac.uk

Adiabatic and Non-Adiabatic Contributions to the Free Energy from the Electron-Phonon Interaction for Na, K, Al, and Pb

We calculate the adiabatic contributions to the free energy due to the electron--phonon interaction at intermediate temperatures, $0 \leqslant k_{B} T < \epsilon_{F}$ for the elemental metals Na, K, Al, and Pb. Using our previously published results for the nonadiabatic contributions we show that the adiabatic contribution, which is proportional to $T^{2}$ at low temperatures and goes as $T^{3}$ at high temperatures, dominates the nonadiabatic contribution for temperatures above a cross--over temperature, $T_{c}$, which is between 0.5 and 0.8 $T_{m}$, where $T_{m}$ is the melting temperature of the metal. The nonadiabatic contribution falls as $T^{-1}$ for temperatures roughly above the average phonon frequency.Comment: Updated versio

The Distribution of Metallicity in the IGM at z~2.5: OVI and CIV Absorption in the Spectra of 7 QSOs

We present a direct measurement of the metallicity distribution function for the high redshift intergalactic medium. We determine the shape of this function using survival statistics, which account for both detections and non-detections of OVI and CIV associated with HI absorption in quasar spectra. Our OVI sample probes the metal content of ~50% of all baryons at z~2.5. We find a median intergalactic abundance of [O,C/H]=-2.82; the differential abundance distribution is approximately lognormal with mean ~-2.85 and \sigma=0.75 dex. Some 60-70% the Lya forest lines are enriched to observable levels ([O,C/H]>-3.5) while the remaining ~30% of the lines have even lower abundances. Thus we have not detected a universal metallicity floor as has been suggested for some Population III enrichment scenaria. In fact, we argue that the bulk of the intergalactic metals formed later than the first stars that are thought to have triggered reionization. We do not observe a significant trend of decreasing metallicity toward the lower density IGM, at least within regions that would be characterized as filaments in numerical simulations. However, an [O/H] enhancement may be present at somewhat high densities. We estimate that roughly half of all baryons at these redshifts have been enriched to [O/H]>=-3.5. We develop a simple model for the metallicity evolution of the IGM, to estimate the chemical yield of galaxies formed prior to z~2.5. We find that the typical galaxy recycled 0.1-0.4% of its mass back into the IGM as heavy elements in the first 3 Gyr after the Big Bang.Comment: 23 pages in emulateapj, 19 figures. Accepted to ApJ, pending review of new changes. Revised comparison between our results and Schaye et al (2003

The Rules of Human T Cell Fate in vivo.

The processes governing lymphocyte fate (division, differentiation, and death), are typically assumed to be independent of cell age. This assumption has been challenged by a series of elegant studies which clearly show that, for murine cells in vitro, lymphocyte fate is age-dependent and that younger cells (i.e., cells which have recently divided) are less likely to divide or die. Here we investigate whether the same rules determine human T cell fate in vivo. We combined data from in vivo stable isotope labeling in healthy humans with stochastic, agent-based mathematical modeling. We show firstly that the choice of model paradigm has a large impact on parameter estimates obtained using stable isotope labeling i.e., different models fitted to the same data can yield very different estimates of T cell lifespan. Secondly, we found no evidence in humans in vivo to support the model in which younger T cells are less likely to divide or die. This age-dependent model never provided the best description of isotope labeling; this was true for naïve and memory, CD4+ and CD8+ T cells. Furthermore, this age-dependent model also failed to predict an independent data set in which the link between division and death was explored using Annexin V and deuterated glucose. In contrast, the age-independent model provided the best description of both naïve and memory T cell dynamics and was also able to predict the independent dataset

Implications of Student and Instructor Involvement in the Basic Course

The purpose of the study is to test the notion that students in the basic course who possess high levels of communication competence will perform better in and subsequently will be more satisfied with the course than their counterparts with low levels of competence. Results show no support for the initial hypothesis. Further analysis, however, showed that the level of instructor competence has a significant effect on student evaluation of instructors

“Free Will and Affirmation: Assessing Honderich’s Third Way”

In the third and final part of his A Theory of Determinism (TD) Ted Honderich addresses the fundamental question concerning “the consequences of determinism.” The critical question he aims to answer is what follows if determinism is true? This question is, of course, intimately bound up with the problem of free will and, in particular, with the question of whether or not the truth of determinism is compatible or incompatible with the sort of freedom required for moral responsibility. It is Honderich’s aim to provide a solution to “the problem of the consequences of determinism” and a key element of this is his articulation and defence of an alternative response to the implications of determinism that collapses the familiar Compatibilist/Incompatibilist dichotomy. Honderich offers us a third way – the response of “Affirmation” (HFY 125-6). Although his account of Affirmation has application and relevance to issues and features beyond freedom and responsibility, my primary concern in this essay will be to examine Honderich’s theory of “Affirmation” as it concerns the free will problem

High-efficiency biolistic co-transformation and regeneration of 'Chardonnay' ( Vitis vinifera L.) containing npt-II and antimicrobial peptide genes

A reliable and efficient system for transformation and regeneration of 'Chardonnay' (Vitis vinifera L.) plants via microprojectile bombardment was developed. Improvements over the previous biolistic transformation system included: (1) the use of gold particles for bombardment; (2) step-wise selection at 10 then 15mg/l kanamycin; and (3) embryo induction at 27°C. Embryogenic cell cultures were either bombarded with pBI426, which contains the reporter gene gus (uidA) coding for β-glucuronidase (GUS), or were co-bombarded with pSAN237 carrying the npt-II (neomycin phosphotransferase II) selectable marker gene, and a second plasmid with an antimicrobial peptide gene. A large number of transient (7,883±1,928) and stable (46±32) blue spots per plate at 2 and 95days after bombardment, respectively, were obtained according to GUS expression analyses. A total of 447 putative transgenic embryos was harvested from 84 bombarded plates. From these embryos, 242 (54%) were regenerated into plants within the first year of the experiment. Southern blot analyses confirmed integration of the transgenes into the grape genome. Co-transformation was tested with four separate antimicrobial constructs. The co-transformation frequency of unlinked genes was 48% as measured by polymerase chain reaction (PCR), and 56% as estimated by dot blot hybridization. Expression of the gus gene, and PCR and Southern blot analyses of npt-II and antimicrobial genes from regenerated plants document stable transformation of 'Chardonnay' and establish the parameters for highly-efficient biolistic transformation in V. vinifer

Globalization, the ambivalence of European integration and the possibilities for a post-disciplinary EU studies

Using the work of Manuel Castells as a starting point, this article explores the ambivalent relationship between globalization and European integration and the variety of ways in which the mainstream political science of the EU has attempted to deal with this issue. The analysis here suggests that various 'mainstreaming' disciplinary norms induce types of work that fail to address fully the somewhat paradoxical and counter-intuitive range of possible relationships between globalization and European integration. The article explores critically four possible analytical ways out of this paradox—abandonment of the concept of globalization, the development of definition precision in globalization studies, the reorientation of work to focus on globalization as discourse, and inter- and post-disciplinarity. The argument suggests that orthodox discussions of the relationship require a notion of social geography that sits at odds with much of the literature on globalization and while greater dialogue between disciplines is to be welcomed, a series of profound epistemological questions need to be confronted if studies of the interplay between global and social process are to be liberated from their disciplinary chains