Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell

Gene duplication is a crucial mechanism of evolutionary innovation. A substantial fraction of eukaryotic genomes consists of paralogous gene families. We assess the extent of ancestral paralogy, which dates back to the last common ancestor of all eukaryotes, and examine the origins of the ancestral paralogs and their potential roles in the emergence of the eukaryotic cell complexity. A parsimonious reconstruction of ancestral gene repertoires shows that 4137 orthologous gene sets in the last eukaryotic common ancestor (LECA) map back to 2150 orthologous sets in the hypothetical first eukaryotic common ancestor (FECA) [paralogy quotient (PQ) of 1.92]. Analogous reconstructions show significantly lower levels of paralogy in prokaryotes, 1.19 for archaea and 1.25 for bacteria. The only functional class of eukaryotic proteins with a significant excess of paralogous clusters over the mean includes molecular chaperones and proteins with related functions. Almost all genes in this category underwent multiple duplications during early eukaryotic evolution. In structural terms, the most prominent sets of paralogs are superstructure-forming proteins with repetitive domains, such as WD-40 and TPR. In addition to the true ancestral paralogs which evolved via duplication at the onset of eukaryotic evolution, numerous pseudoparalogs were detected, i.e. homologous genes that apparently were acquired by early eukaryotes via different routes, including horizontal gene transfer (HGT) from diverse bacteria. The results of this study demonstrate a major increase in the level of gene paralogy as a hallmark of the early evolution of eukaryotes

Inelastic neutron and x-ray scattering as probes of the sign structure of the Fe-pnictide superconducting gap

Neutron spin-flip scattering observations of a resonance in the superconducting state is often taken as evidence of an unconventional superconducting state in which the gap changes sign $\Delta(k+Q)=-\Delta(k)$ for momentum transfers $Q$ which play an important role in the pairing. Recently questions regarding this identification for the Fe-pnictide superconductors have been raised and it has been suggested that $\Delta(k+Q)=\Delta(k)$. Here we propose that inelastic neutron or x-ray scattering measurements of the spectral weight of a phonon of momentum $Q$ can distinguish between these two pairing scenarios.Comment: 4 pages, 4 figure

Evidence-based practice 'on-the-go': using ViaTherapy as a tool to enhance clinical decision making in upper limb rehabilitation after stroke, a quality improvement initiative.

Recovery of upper limb function after stroke is currently sub-optimal, despite good quality evidence showing that interventions enabling repetitive practice of task-specific activity are effective in improving function. Therapists need to access and engage with such evidence to optimise outcomes with people with stroke, but this is challenging in fast-paced stroke rehabilitation services. This quality improvement project aimed to investigate acceptability and service impact of a new, international tool for accessing evidence on upper limb rehabilitation after stroke-'ViaTherapy'-in a team of community rehabilitation therapists. Semi-structured interviews were undertaken at baseline to determine confidence in, and barriers to, evidence-based practice (EBP) to support clinical decision making. Reported barriers included time, lack of access to evidence and a research-practice disconnect. The clinicians then integrated use of 'ViaTherapy' into their practice for 4 weeks. Follow-up interviews explored the accessibility of the tool in community rehabilitation practice, and its impact on clinician confidence, treatment planning and provision. Clinicians found the tool, used predominantly in mobile device app format, to be concise and simple to use, providing evidence 'on-the-go'. Confidence in accessing and using EBP grew by 22% from baseline. Clinicans reported changes in intensity of delivery of interventions, as rapid access to recommended doses via the tool was available. Following this work, the participating health and social care service provider changed provision of therapists' technology to enable use of apps. Barriers to use of EBP in stroke rehabilitation persist; the baseline situation here supported the need for more accessible means of integrating best evidence into clinical processes. This quality improvement project successfully integrated ViaTherapy into clinical practice, and found that the tool has potential to underpin positive changes in upper limb therapy service delivery after stroke, by increasing accessibility to, use of and confidence in EBP. Definitive evaluation is now indicated

Unital Quantum Channels - Convex Structure and Revivals of Birkhoff's Theorem

The set of doubly-stochastic quantum channels and its subset of mixtures of unitaries are investigated. We provide a detailed analysis of their structure together with computable criteria for the separation of the two sets. When applied to O(d)-covariant channels this leads to a complete characterization and reveals a remarkable feature: instances of channels which are not in the convex hull of unitaries can return to it when either taking finitely many copies of them or supplementing with a completely depolarizing channel. In these scenarios this implies that a channel whose noise initially resists any environment-assisted attempt of correction can become perfectly correctable.Comment: 31 page

A Realization of N=1 SW(3/2,2){\cal SW}(3/2,2) Algebras with Wolf Spaces

We find out that some unitary minimal models of the N=1 ${\cal SW}(3/2,2)$ superconformal algebra can be realized as the level one coset models based on the Wolf spaces $SU(n)/(SU(n-2)\times SU(2))$. We obtain the expression of the fermionic current with the conformal weight 5/2 in the algebra. Then, these models are twisted to give the topological conformal field theories.Comment: 7 pages, references added, published versio

M-theory on `toric' G_2 cones and its type II reduction

We analyze a class of conical G_2 metrics admitting two commuting isometries, together with a certain one-parameter family of G_2 deformations which preserves these symmetries. Upon using recent results of Calderbank and Pedersen, we write down the explicit G_2 metric for the most general member of this family and extract the IIA reduction of M-theory on such backgrounds, as well as its type IIB dual. By studying the asymptotics of type II fields around the relevant loci, we confirm the interpretation of such backgrounds in terms of localized IIA 6-branes and delocalized IIB 5-branes. In particular, we find explicit, general expressions for the string coupling and R-R/NS-NS forms in the vicinity of these objects. Our solutions contain and generalize the field configurations relevant for certain models considered in recent work of Acharya and Witten.Comment: 45 pages, references adde

Laser Cooling of Trapped Fermi Gases deeply below the Fermi Temperature

We study the collective Raman cooling of a polarized trapped Fermi gas in the Festina Lente regime, when the heating effects associated with photon reabsorptions are suppressed. We predict that by adjusting the spontaneous Raman emission rates and using appropriately designed anharmonic traps, temperatures of the order of 2.7% of the Fermi temperature can be achieved in 3D.Comment: 4 pages, 3 figures; final versio

Localization of electromagnetic waves in a two dimensional random medium

Motivated by previous investigations on the radiative effects of the electric dipoles embedded in structured cavities, localization of electromagnetic waves in two dimensions is studied {\it ab initio} for a system consisting of many randomly distributed two dimensional dipoles. A set of self-consistent equations, incorporating all orders of multiple scattering of the electromagnetic waves, is derived from first principles and then solved numerically for the total electromagnetic field. The results show that spatially localized electromagnetic waves are possible in such a simple but realistic disordered system. When localization occurs, a coherent behavior appears and is revealed as a unique property differentiating localization from either the residual absorption or the attenuation effects

Diffusive and localization behavior of electromagnetic waves in a two-dimensional random medium

In this paper, we discuss the transport phenomena of electromagnetic waves in a two-dimensional random system which is composed of arrays of electrical dipoles, following the model presented earlier by Erdogan, et al. (J. Opt. Soc. Am. B {\bf 10}, 391 (1993)). A set of self-consistent equations is presented, accounting for the multiple scattering in the system, and is then solved numerically. A strong localization regime is discovered in the frequency domain. The transport properties within, near the edge of and nearly outside the localization regime are investigated for different parameters such as filling factor and system size. The results show that within the localization regime, waves are trapped near the transmitting source. Meanwhile, the diffusive waves follow an intuitive but expected picture. That is, they increase with travelling path as more and more random scattering incurs, followed by a saturation, then start to decay exponentially when the travelling path is large enough, signifying the localization effect. For the cases that the frequencies are near the boundary of or outside the localization regime, the results of diffusive waves are compared with the diffusion approximation, showing less encouraging agreement as in other systems (Asatryan, et al., Phys. Rev. E {\bf 67}, 036605 (2003).)Comment: 8 pages 9 figure

Quantum optics in the phase space - A tutorial on Gaussian states

In this tutorial, we introduce the basic concepts and mathematical tools needed for phase-space description of a very common class of states, whose phase properties are described by Gaussian Wigner functions: the Gaussian states. In particular, we address their manipulation, evolution and characterization in view of their application to quantum information.Comment: Tutorial. 23 pages, 1 figure. Updated version accepted for publication in EPJ - ST devoted to the memory of Federico Casagrand