Structure motivator: a tool for exploring small three-dimensional elements in proteins

<br>Background: Protein structures incorporate characteristic three-dimensional elements defined by some or all of hydrogen bonding, dihedral angles and amino acid sequence. The software application, Structure Motivator, allows interactive exploration and analysis of such elements, and their resolution into sub-classes.</br> <br>Results: Structure Motivator is a standalone application with an embedded relational database of proteins that, as a starting point, can furnish the user with a palette of unclassified small peptides or a choice of pre-classified structural motifs. Alternatively the application accepts files of data generated externally. After loading, the structural elements are displayed as two-dimensional plots of dihedral angles (φ/ψ, φ/χ1 or in combination) for each residue, with visualization options to allow the conformation or amino acid composition at one residue to be viewed in the context of that at other residues. Interactive selections may then be made and structural subsets saved to file for further sub-classification or external analysis. The application has been applied both to classical motifs, such as the β-turn, and ‘non-motif’ structural elements, such as specific segments of helices.</br> <br>Conclusions: Structure Motivator allows structural biologists, whether or not they possess computational skills, to subject small structural elements in proteins to rapid interactive analysis that would otherwise require complex programming or database queries. Within a broad group of structural motifs, it facilitates the identification and separation of sub-classes with distinct stereochemical properties.</br&gt

The Glasgow raspberry pi cloud: a scale model for cloud computing infrastructures

Data Centers (DC) used to support Cloud services often consist of tens of thousands of networked machines under a single roof. The significant capital outlay required to replicate such infrastructures constitutes a major obstacle to practical implementation and evaluation of research in this domain. Currently, most research into Cloud computing relies on either limited software simulation, or the use of a testbed environments with a handful of machines. The recent introduction of the Raspberry Pi, a low-cost, low-power single-board computer, has made the construction of a miniature Cloud DCs more affordable. In this paper, we present the Glasgow Raspberry Pi Cloud (PiCloud), a scale model of a DC composed of clusters of Raspberry Pi devices. The PiCloud emulates every layer of a Cloud stack, ranging from resource virtualisation to network behaviour, providing a full-featured Cloud Computing research and educational environment

Quantum Distillation Of Position Entanglement With The Polarization Degrees Of Freedom

Sources of entangled photon pairs using two parametric down-converters are capable of generating interchangeable entanglement in two different degrees of freedom. The connection between these two degrees of freedom allows the control of the entanglement properties of one, by acting on the other degree of freedom. We demonstrate experimentally, the quantum distillation of the position entanglement using polarization analyzers.Comment: Submitted for publication in Optics Communication

The β-link motif in protein architecture

The β-link is a composite protein motif consisting of a G1β β-bulge and a type II β-turn, and is generally found at the end of two adjacent strands of antiparallel β-sheet. The 1,2-positions of the β-bulge are also the 3,4-positions of the β-turn, with the result that the N-terminal portion of the polypeptide chain is orientated at right angles to the β-sheet. Here, it is reported that the β-link is frequently found in certain protein folds of the SCOPe structural classification at specific locations where it connects a β-sheet to another area of a protein. It is found at locations where it connects one β-sheet to another in the β-sandwich and related structures, and in small (four-, five- or six-stranded) β-barrels, where it connects two β-strands through the polypeptide chain that crosses an open end of the barrel. It is not found in larger (eight-stranded or more) β-barrels that are straightforward β-meanders. In some cases it initiates a connection between a single β-sheet and an α-helix. The β-link also provides a framework for catalysis in serine proteases, where the catalytic serine is part of a conserved β-link, and in cysteine proteases, including Mpro of human SARS-CoV-2, in which two residues of the active site are located in a conserved β-link

Domestic Rivalry and Export Performance: Theory and Evidence from International Airline Markets

The much-studied relationship between domestic rivalry and export performance consists of those supporting a national-champion rationale, and those supporting a rivalry rationale. While the empirical literature generally supports the positive effects of domestic rivalry, the national-champion rationale actually rests on firmer theoretical ground. We address this inconsistency by providing a theoretical framework that illustrates three paths via which domestic rivalry translates into enhanced international exports. Furthermore, empirical tests on the world airline industry elicit the existence of one particular path - an enhanced firm performance effect - that connects domestic rivalry with improved international exports

Entanglement Creation Using Quantum Interrogation

We present some applications of high efficiency quantum interrogation ("interaction free measurement") for the creation of entangled states of separate atoms and of separate photons. The quantum interrogation of a quantum object in a superposition of object-in and object-out leaves the object and probe in an entangled state. The probe can then be further entangled with other objects in subsequent quantum interrogations. By then projecting out those cases were the probe is left in a particular final state, the quantum objects can themselves be left in various entangled states. In this way we show how to generate two-, three-, and higher qubit entanglement between atoms and between photons. The effect of finite efficiency for the quantum interrogation is delineated for the various schemes.Comment: 7 pages, 13 figures, Submitted to PR

Breast cancer and exposure to tobacco smoke during potential windows of susceptibility

Purpose: An association between smoking and breast cancer is unresolved, although a higher risk from exposure during windows of susceptibility has been proposed. The objective of this prospective study was to evaluate the association between tobacco smoke and breast cancer with a focus on timing of exposure, especially during early life. Methods: Sister study participants (n = 50,884) aged 35–74 were enrolled from 2003 to 2009. Women in the United States and Puerto Rico were eligible if they were breast cancer-free but had a sister with breast cancer. Participants completed questionnaires on smoking and environmental tobacco smoke (ETS) exposure. Cox regression was used to estimate adjusted hazard ratios (HRs) and 95% confidence intervals (95% CIs) for breast cancer risk. Results: During follow-up (mean = 6.4 years), 1,843 invasive breast cancers were diagnosed. Neither active smoking nor adult ETS was associated with breast cancer risk. However, never smoking women exposed to ETS throughout their childhood had a 17% higher risk of breast cancer (95% CI 1.00–1.36) relative to those with no exposure. In utero ETS exposure was also associated with breast cancer (HR = 1.16, 95% CI 1.01–1.32) and the HR was most elevated for women born in earlier birth cohorts (<1940, HR = 1.44, 95% CI 1.02–2.02; 1940–1949, HR = 1.28, 95% CI 1.01–1.62). Conclusion: In utero ETS and ETS exposure during childhood and adolescence were associated with increased risk of breast cancer and associations varied by birth cohort

Adult physical activity and breast cancer risk in women with a family history of breast cancer

Background: Recreational physical activity has been consistently associated with reduced breast cancer risk. Less is known about how family history of breast cancer affects the association and whether it varies by menopausal status. Methods: The Sister Study is a cohort of 50,884 women who had a sister with breast cancer but no prior breast cancer themselves at enrollment. Women reported all recreational sport/exercise activities they participated in over the past 12 months. Hours/week and MET-hours/week of physical activity were considered in association with breast cancer risk. Hazard ratios (HR) and 95% confidence intervals (CI) were calculated with Cox regression. Extent of family history, examined as a modifier, was characterized by a Bayesian score incorporating characteristics of the family structure. Results: During follow-up (average 8.4 years), 3,023 cases were diagnosed. Higher hours/week (HR ≥7vs&lt;1 = 0.77; 95% CI, 0.66–0.90) and MET-hours/week (HR quartile4vs1 = 0.75; 95% CI, 0.67–0.85) of physical activity were associated with reduced postmenopausal breast cancer risk. Hours/week and MET-hours/week were associated with suggestively increased premenopausal breast cancer risk (MET-hours/week HR quartile4vs1 = 1.25; 95% CI, 0.98–1.60). Associations did not vary with extent of family history. However, the increased risk in premenopausal women may be limited to those with stronger family history. Conclusions: In women with a family history of breast cancer, physical activity was associated with reduced postmenopausal, but not premenopausal, breast cancer risk and was not modified by extent of family history. Impact: This was the first study to examine the association between physical activity and breast cancer risk in a large population with a family history of breast cancer