Multiple structural alignment for distantly related all b structures using TOPS pattern discovery and simulated annealing

Topsalign is a method that will structurally align diverse protein structures, for example, structural alignment of protein superfolds. All proteins within a superfold share the same fold but often have very low sequence identity and different biological and biochemical functions. There is often signi®cant structural diversity around the common scaffold of secondary structure elements of the fold. Topsalign uses topological descriptions of proteins. A pattern discovery algorithm identi®es equivalent secondary structure elements between a set of proteins and these are used to produce an initial multiple structure alignment. Simulated annealing is used to optimize the alignment. The output of Topsalign is a multiple structure-based sequence alignment and a 3D superposition of the structures. This method has been tested on three superfolds: the b jelly roll, TIM (a/b) barrel and the OB fold. Topsalign outperforms established methods on very diverse structures. Despite the pattern discovery working only on b strand secondary structure elements, Topsalign is shown to align TIM (a/b) barrel superfamilies, which contain both a helices and b strands

Compassion on University Degree Programmes at a UK University: The Neuroscience of Effective Group work

This article is published under the Creative Commons Attribution (CC BY 4.0) licence. Anyone may reproduce, distribute, translate and create derivative works of this article (for both commercial and non-commercial purposes), subject to full attribution to the original publication and authors. The full terms of this licence may be seen at http://creativecommons.org/ licences/by/4.0/legalcodePurpose The purpose of this paper is to explore the neuroscience that underpins the psychology of compassion as a competency. We explain why this cognitive competency is now taught and assessed on modules of different degree subjects in a UK university. Design/methodology/approach The paper is divided into first, an exploration of recent psychology and neuroscience literature that illuminates the differences, and relationship, between empathy and compassion for safeness building in teams. Within that, the role of oxytocin in achieving social and intellectual rewards though the exercise of cognitive flexibility, working memory and impulsive inhibitory control (Zelazo, et al, 2016) is also identified. The literature findings are compared against relevant qualitative data from the above university’s, so far, nine years of mixed methods action research on compassion-focused pedagogy (CfP). Findings These are that the concept and practice of embedding compassion as a cognitive competency into assessed university group work is illuminated and rationalised by research findings in neuroscience. Research limitations/implications The limitations of the study are that, so far, fMRI research methods have not been used to investigate student subjects involved in the compassion-focused pedagogy now in use. Practical implications The paper has implications for theory, policy and practice in relation to managing the increasing amount of group work that accompanies widening participation in Higher Education. Originality/value A review of this kind specifically for student assessed group and its implications for student academic achievement and mental health has not, apparently, been publishedPeer reviewe

Candida albicans in Urinary Tract or in Seminal Sac

A case of urinary tract infection due to Candida albicans and responding to fluconazole is presente

A survey of the prevalence of Schistosomiasis among pupils in Apata and Laranto areas in Jos, Plateau State

Prevalence of Schistosomiasis in apparently healthy primary school pupils in Apata and Laranto areas of Jos was surveyed using 300 samples of stool and 300 samples of urine. The stool samples were processed using formol ether concentration techniques while the urine samples were processed by ordinary centrifugal sedimentation technique. The overall prevalence of urinary (Schistosoma haematobium) and intestinal (Schistosoma mansoni) schistosomiasis was 0.67%, with three samples (1% prevalence) positive for intestinal (Schistosoma mansoni) and one sample (0.33% prevalence) positive for urinary (Schistosoma haematobium) schistosomiasis respectively. Two of the three cases positive for Schistosoma mansoni were males in the age group of 11–15 years and the one positive for Schistosoma haematobium was a male patient. Prevalence in the studied area is therefore very low and immigration, sex and age dependen

Combinatorial Bounds and Characterizations of Splitting Authentication Codes

We present several generalizations of results for splitting authentication codes by studying the aspect of multi-fold security. As the two primary results, we prove a combinatorial lower bound on the number of encoding rules and a combinatorial characterization of optimal splitting authentication codes that are multi-fold secure against spoofing attacks. The characterization is based on a new type of combinatorial designs, which we introduce and for which basic necessary conditions are given regarding their existence.Comment: 13 pages; to appear in "Cryptography and Communications

Resolution requirements for numerical simulations of transition

The resolution requirements for direct numerical simulations of transition to turbulence are investigated. A reliable resolution criterion is determined from the results of several detailed simulations of channel and boundary-layer transition

Reflexive-insensitive Modal Logics

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)We analyze a class of modal logics rendered insensitive to reflexivity by way of a modification to the semantic definition of the modal operator. We explore the extent to which these logics can be characterized, and prove a general completeness theorem on the basis of a translation between normal modal logics and their reflexive-insensitive counterparts. Lastly, we provide a sufficient semantic condition describing when a similarly general soundness result is also available.9167180CAPES (Coordination for the Improvement of Higher Education Personnel) in BrazilFAPESP (Sao Paulo Research Foundation) [2013/25095-4]Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP

Annual variation in the levels of transcripts of sex-specific genes in the mantle of the common mussel, Mytilus edulis

Mytilus species are used as sentinels for the assessment of environmental health but sex or stage in the reproduction cycle is rarely considered even though both parameters are likely to influence responses to pollution. We have validated the use of a qPCR assay for sex identification and related the levels of transcripts to the reproductive cycle. A temporal study of mantle of Mytilus edulis found transcripts of male-specific vitelline coat lysin (VCL) and female-specific vitelline envelope receptor for lysin (VERL) could identify sex over a complete year. The levels of VCL/VERL were proportional to the numbers of sperm/ova and are indicative of the stage of the reproductive cycle. Maximal levels of VCL and VERL were found in February 2009 declining to minima between July - August before increasing and re-attaining a peak in February 2010. Water temperature may influence these transitions since they coincide with minimal water temperature in February and maximal temperature in August. An identical pattern of variation was found for a cryptic female-specific transcript (H5) but a very different pattern was observed for oestrogen receptor 2 (ER2). ER2 varied in a sex-specific way with male > female for most of the cycle, with a female maxima in July and a male maxima in December. Using artificially spawned animals, the transcripts for VCL, VERL and H5 were shown to be present in gametes and thus their disappearance from mantle is indicative of spawning. VCL and VERL are present at equivalent levels in February and July-August but during gametogenesis (August to January) and spawning (March to June) VCL is present at lower relative amounts than VERL. This may indicate sex-specific control mechanisms for these processes and highlight a potential pressure point leading to reduced reproductive output if environmental factors cause asynchrony to gamete maturation or release

Re-imagining professional learning for teachers: A reflection on the transformative experience of an organic inquiry.

Challenged, frustrated and motivated by my observation and sense that learning experiences are often designed and facilitated with an emphasis on criticality over creativity, I engaged in PhD studies to explore the question, How can expanding my understanding of creativity and its connection to learning assist me to re-imagine professional learning for teachers so that their learning experiences are enhanced? In this article I discuss how my practice as a professional learning facilitator for teachers transformed through this study. In particular I describe my experiences and findings from my open exploration of creativity as a phenomenon and how the organic inquiry approach adopted for this study engendered deeply reflective and reflexive experiences that brought to light the importance of connecting to the imaginal as a generative source of creativity and possibility. I also describe how for myself and participants in this study, storytelling and engaging with stories of creativity gave access to a place of openness for seeing phenomena (creativity and learning) in a new light