Pymablock: an algorithm and a package for quasi-degenerate perturbation theory

A common technique in the study of complex quantum-mechanical systems is to reduce the number of degrees of freedom in the Hamiltonian by using quasi-degenerate perturbation theory. While the Schrieffer--Wolff transformation achieves this and constructs an effective Hamiltonian, its scaling is suboptimal, and implementing it efficiently is both challenging and error-prone. We introduce an algorithm for constructing an equivalent effective Hamiltonian as well as a Python package, Pymablock, that implements it. Our algorithm combines an optimal asymptotic scaling with a range of other improvements. The package supports numerical and analytical calculations of any order and it is designed to be interoperable with any other packages for specifying the Hamiltonian. We demonstrate how the package handles constructing a k.p model, analyses a superconducting qubit, and computes the low-energy spectrum of a large tight-binding model. We also compare its performance with reference calculations and demonstrate its efficiency.Comment: 21 pages, 5 figure

Dimerization of cAMP phosphodiesterase-4 (PDE4) in living cells requires interfaces located in both the UCR1 and catalytic unit domains

PDE4 family cAMP phosphodiesterases play a pivotal role in determining compartmentalised cAMP signalling through targeted cAMP breakdown. Expressing the widely found PDE4D5 isoform, as both bait and prey in a yeast 2-hybrid system, we demonstrated interaction consistent with the notion that long PDE4 isoforms form dimers. Four potential dimerization sites were uncovered using a scanning peptide array approach, where a recombinant purified PDE4D5 fusion protein was used to probe a 25-mer library of overlapping peptides covering the entire PDE4D5 sequence. Key residues involved in PDE4D5 dimerization were defined using a site-directed mutagenesis programme directed by an alanine scanning peptide array approach. Critical residues stabilising PDE4D5 dimerization were defined within the regulatory UCR1 region found in long, but not short, PDE4 isoforms, namely the Arg173, Asn174 and Asn175 (DD1) cluster. Disruption of the DD1 cluster was not sufficient, in itself, to destabilise PDE4D5 homodimers. Instead, disruption of an additional interface, located on the PDE4 catalytic unit, was also required to convert PDE4D5 into a monomeric form. This second dimerization site on the conserved PDE4 catalytic unit is dependent upon a critical ion pair interaction. This involves Asp463 and Arg499 in PDE4D5, which interact in a trans fashion involving the two PDE4D5 molecules participating in the homodimer. PDE4 long isoforms adopt a dimeric state in living cells that is underpinned by two key contributory interactions, one involving the UCR modules and one involving an interface on the core catalytic domain. We propose that short forms do not adopt a dimeric configuration because, in the absence of the UCR1 module, residual engagement of the remaining core catalytic domain interface provides insufficient free energy to drive dimerization. The functioning of PDE4 long and short forms is thus poised to be inherently distinct due to this difference in quaternary structure

Illness Beliefs Predict Mortality in Patients with Diabetic Foot Ulcers

Background - Patients’ illness beliefs have been associated with glycaemic control in diabetes and survival in other conditions. Objective - We examined whether illness beliefs independently predicted survival in patients with diabetes and foot ulceration. Methods - Patients (n = 169) were recruited between 2002 and 2007. Data on illness beliefs were collected at baseline. Data on survival were extracted on 1st November 2011. Number of days survived reflected the number of days from date of recruitment to 1st November 2011. Results - Cox regressions examined the predictors of time to death and identified ischemia and identity beliefs (beliefs regarding symptoms associated with foot ulceration) as significant predictors of time to death. Conclusions - Our data indicate that illness beliefs have a significant independent effect on survival in patients with diabetes and foot ulceration. These findings suggest that illness beliefs could improve our understanding of mortality risk in this patient group and could also be the basis for future therapeutic interventions to improve survival

"We're all the same here"—Investigating the rehabilitative climate of a re-rolled sexual offender prison: a qualitative longitudinal study

Understanding how individuals with sexual convictions experience prison and its environment is important because such experiences can impact on rehabilitation outcomes. This is the first qualitative longitudinal investigation that explores the experiences of prisoners in a prison exclusively for individuals with sexual convictions over time. The purpose of this research was to explore the rehabilitative and therapeutic climate of a recently re-rolled prison (a general prison turned into a prison only for individuals who have sexually offended) at two time points (T1 at reroll and T2 a year later). The study focuses on prisoners perspectives of the purpose of the prison, experience of prison life, relationships in the prison, and the prison regime over time. Twenty interviews were conducted across the time points and revealed two main superordinate themes “‘Being’ in a prison for individuals with sexual convictions” and “obstructions to change". This research adds to the emerging body of knowledge surrounding the importance of the wider prison environment on the rehabilitation of individuals with sexual convictions and on the benefits and risks of co-locating men who have committed sexual offences in the same prison site. It also has implications wider than rehabilitation of those convicted of sexual offences and has insights for the types of environment and prisoner-staff relationships that are conducive to rehabilitation

Chemical informatics uncovers a new role for moexipril as a novel inhibitor of cAMP phosphodiesterase-4 (PDE4)

PDE4 is one of eleven known cyclic nucleotide phosphodiesterase families and plays a pivotal role in mediating hydrolytic degradation of the important cyclic nucleotide second messenger, cyclic 3′5′ adenosine monophosphate (cAMP). PDE4 inhibitors are known to have anti-inflammatory properties, but their use in the clinic has been hampered by mechanism-associated side effects that limit maximally tolerated doses. In an attempt to initiate the development of better-tolerated PDE4 inhibitors we have surveyed existing approved drugs for PDE4-inhibitory activity. With this objective, we utilised a high-throughput computational approach that identified moexipril, a well tolerated and safe angiotensin-converting enzyme (ACE) inhibitor, as a PDE4 inhibitor. Experimentally we showed that moexipril and two structurally related analogues acted in the micro molar range to inhibit PDE4 activity. Employing a FRET-based biosensor constructed from the nucleotide binding domain of the type 1 exchange protein activated by cAMP, EPAC1, we demonstrated that moexipril markedly potentiated the ability of forskolin to increase intracellular cAMP levels. Finally, we demonstrated that the PDE4 inhibitory effect of moexipril is functionally able to induce phosphorylation of the Hsp20 by cAMP dependent protein kinase A. Our data suggest that moexipril is a bona fide PDE4 inhibitor that may provide the starting point for development of novel PDE4 inhibitors with an improved therapeutic window

Online distributed leadership: A content analysis of interaction and teacher reflections on computer-supported learning

This study performs a content analysis of the communication that develops in online educational situations. It focuses on two aspects of communication in a context in which we observe instructional leadership: how leadership is seen in the virtual classroom and how teachers view their role. The study attempts to answer the question of how teachers lead this methodological change, that is, instructional leadership at the service of distributed leadership. The study analyses the online interaction and teachers’ reflections on the communication between teachers and students in the process of virtual teaching, specifically in post compulsory secondary education in Spain.Study financed by an R&D project in the area of Education Sciences Management entitled ‘Learning-Focused Leadership and its Impact on Improvement: Practices and Results in Secondary Education’, under the Subprogram for basic, non-oriented research projects. National Plan for R&D, 2010 Competition