QCD with Chemical Potential in a Small Hyperspherical Box

To leading order in perturbation theory, we solve QCD, defined on a small three sphere in the large N and Nf limit, at finite chemical potential and map out the phase diagram in the (mu,T) plane. The action of QCD is complex in the presence of a non-zero quark chemical potential which results in the sign problem for lattice simulations. In the large N theory, which at low temperatures becomes a conventional unitary matrix model with a complex action, we find that the dominant contribution to the functional integral comes from complexified gauge field configurations. For this reason the eigenvalues of the Polyakov line lie off the unit circle on a contour in the complex plane. We find at low temperatures that as mu passes one of the quark energy levels there is a third-order Gross-Witten transition from a confined to a deconfined phase and back again giving rise to a rich phase structure. We compare a range of physical observables in the large N theory to those calculated numerically in the theory with N=3. In the latter case there are no genuine phase transitions in a finite volume but nevertheless the observables are remarkably similar to the large N theory.Comment: 44 pages, 18 figures, jhep3 format. Small corrections and clarifications added in v3. Conclusions cleaned up. Published versio

Measuring every particle's size from three-dimensional imaging experiments

Often experimentalists study colloidal suspensions that are nominally monodisperse. In reality these samples have a polydispersity of 4-10%. At the level of an individual particle, the consequences of this polydispersity are unknown as it is difficult to measure an individual particle size from microscopy. We propose a general method to estimate individual particle radii within a moderately concentrated colloidal suspension observed with confocal microscopy. We confirm the validity of our method by numerical simulations of four major systems: random close packing, colloidal gels, nominally monodisperse dense samples, and nominally binary dense samples. We then apply our method to experimental data, and demonstrate the utility of this method with results from four case studies. In the first, we demonstrate that we can recover the full particle size distribution {\it in situ}. In the second, we show that accounting for particle size leads to more accurate structural information in a random close packed sample. In the third, we show that crystal nucleation occurs in locally monodisperse regions. In the fourth, we show that particle mobility in a dense sample is correlated to the local volume fraction.Comment: 7 pages, 5 figure

Disposition of Federally Owned Surpluses

PDZ domains are scaffolding modules in protein-protein interactions that mediate numerous physiological functions by interacting canonically with the C-terminus or non-canonically with an internal motif of protein ligands. A conserved carboxylate-binding site in the PDZ domain facilitates binding via backbone hydrogen bonds; however, little is known about the role of these hydrogen bonds due to experimental challenges with backbone mutations. Here we address this interaction by generating semisynthetic PDZ domains containing backbone amide-to-ester mutations and evaluating the importance of individual hydrogen bonds for ligand binding. We observe substantial and differential effects upon amide-to-ester mutation in PDZ2 of postsynaptic density protein 95 and other PDZ domains, suggesting that hydrogen bonding at the carboxylate-binding site contributes to both affinity and selectivity. In particular, the hydrogen-bonding pattern is surprisingly different between the non-canonical and canonical interaction. Our data provide a detailed understanding of the role of hydrogen bonds in protein-protein interactions

Does electronic clinical microbiology results reporting influence medical decision making: a pre- and post-interview study of medical specialists

Background: Clinicians view the accuracy of test results and the turnaround time as the two most important service aspects of the clinical microbiology laboratory. Because of the time needed for the culturing of infectious agents, final hardcopy culture results will often be available too late to have a significant impact on early antimicrobial therapy decisions, vital in infectious disease management. The clinical microbiologist therefore reports to the clinician clinically relevant preliminary results at any moment during the diagnostic process, mostly by telephone. Telephone reporting is error prone, however. Electronic reporting of culture results instead of reporting on paper may shorten the turnaround time and may ensure correct communication of results. The purpose of this study was to assess the impact of the implementation of electronic reporting of final microbiology results on medical decision making. Methods. In a pre- and post-interview study using a semi-structured design we asked medical specialists in our hospital about their use and appreciation of clinical microbiology results reporting before and after the implementation of an electronic reporting system. Results: Electronic reporting was highly appreciated by all interviewed clinicians. Major advantages were reduction of hardcopy handling and the possibility to review results in relation to other patient data. Use and meaning of microbiology reports differ significantly between medical specialties. Most clinicians need preliminary results for therapy decisions quickly. Therefore, after the implementation of electronic reporting, telephone consultation between clinician and microbiologist remained the key means of communication. Conclusions: Overall, electronic reporting increased the workflow efficiency of the medical specialists, but did not have an impact on their decision-making

A hybrid approach to protein folding problem integrating constraint programming with local search

<p>Abstract</p> <p>Background</p> <p>The protein folding problem remains one of the most challenging open problems in computational biology. Simplified models in terms of lattice structure and energy function have been proposed to ease the computational hardness of this optimization problem. Heuristic search algorithms and constraint programming are two common techniques to approach this problem. The present study introduces a novel hybrid approach to simulate the protein folding problem using constraint programming technique integrated within local search.</p> <p>Results</p> <p>Using the face-centered-cubic lattice model and 20 amino acid pairwise interactions energy function for the protein folding problem, a constraint programming technique has been applied to generate the neighbourhood conformations that are to be used in generic local search procedure. Experiments have been conducted for a few small and medium sized proteins. Results have been compared with both pure constraint programming approach and local search using well-established local move set. Substantial improvements have been observed in terms of final energy values within acceptable runtime using the hybrid approach.</p> <p>Conclusion</p> <p>Constraint programming approaches usually provide optimal results but become slow as the problem size grows. Local search approaches are usually faster but do not guarantee optimal solutions and tend to stuck in local minima. The encouraging results obtained on the small proteins show that these two approaches can be combined efficiently to obtain better quality solutions within acceptable time. It also encourages future researchers on adopting hybrid techniques to solve other hard optimization problems.</p

STAT-HI: A Socio-Technical Assessment Tool for Health Informatics Implementations

This paper proposes a socio-technical assessment tool (STAT-HI) for health informatics implementations. We explore why even projects allegedly using sound methodologies repeatedly fail to give adequate attention to socio-technical issues, and we present an initial draft of a structured assessment tool for health informatics implementation that encapsulates socio-technical good practice. Further work is proposed to enrich and validate the proposed instrument. This proposal was presented for discussion at a meeting of the UK Faculty of Health Informatics in December 2009

The Concept of Transparency in International Relations: towards a critical approach

Transparency is an important concept in International Relations. The possibility of realizing transparency in practice operates as a central analytical axis defining distinct positions on core theoretical problems within the field, from the security dilemma to the function of international institutions and beyond. As a political practice the pursuit of transparent governance is a dominant feature of global politics, promoted by a wide range of actors across a vast range of issue areas, from nuclear proliferation to Internet governance to the politics of foreign aid. Yet, despite its importance, precisely what transparency means or how the concept is understood is frequently ill-defined by academics and policy-makers alike. As a result, the epistemological and ontological underpinnings of approaches to transparency in IR often sit in tension with their wider theoretical commitments. This article will examine the three primary understandings of transparency used in IR in order to unpack these commitments. It finds that while transparency is often explicitly conceptualized as a property of information, particularly within rationalist scholarship, this understanding rests upon an unarticulated set of sociological assumptions. This analysis suggests that conceptualizing ‘transparency-as-information’ without a wider sociology of knowledge production is highly problematic, potentially obscuring our ability to recognize transparent practices in global governance. Understanding transparency as dialogue, as a social practice rooted in shared cognitive capacities and epistemic frameworks, provides a firmer analytical ground from which to examine transparency in International Relations

βA3/A1-Crystallin controls anoikis-mediated cell death in astrocytes by modulating PI3K/AKT/mTOR and ERK survival pathways through the PKD/Bit1-signaling axis

During eye development, apoptosis is vital to the maturation of highly specialized structures such as the lens and retina. Several forms of apoptosis have been described, including anoikis, a form of apoptosis triggered by inadequate or inappropriate cell–matrix contacts. The anoikis regulators, Bit1 (Bcl-2 inhibitor of transcription-1) and protein kinase-D (PKD), are expressed in developing lens when the organelles are present in lens fibers, but are downregulated as active denucleation is initiated. We have previously shown that in rats with a spontaneous mutation in the Cryba1 gene, coding for βA3/A1-crystallin, normal denucleation of lens fibers is inhibited. In rats with this mutation (Nuc1), both Bit1 and PKD remain abnormally high in lens fiber cells. To determine whether βA3/A1-crystallin has a role in anoikis, we induced anoikis in vitro and conducted mechanistic studies on astrocytes, cells known to express βA3/A1-crystallin. The expression pattern of Bit1 in retina correlates temporally with the development of astrocytes. Our data also indicate that loss of βA3/A1-crystallin in astrocytes results in a failure of Bit1 to be trafficked to the Golgi, thereby suppressing anoikis. This loss of βA3/A1-crystallin also induces insulin-like growth factor-II, which increases cell survival and growth by modulating the phosphatidylinositol-3-kinase (PI3K)/AKT/mTOR and extracellular signal-regulated kinase pathways. We propose that βA3/A1-crystallin is a novel regulator of both life and death decisions in ocular astrocytes