On inverse subsemigroups of the semigroup of orientation-preserving or orientation-reversing transformations

It is well-known [16] that the semigroup Tn of all total transformations of a given n-element set Xn is covered by its inverse subsemigroups. This note provides a short and direct proof, based on properties of digraphs of transformations, that every inverse subsemigroup of order-preserving transformations on a finite chain Xn is a semilattice of idempotents, and so the semigroup of all order-preserving transformations of Xn is not covered by its inverse subsemigroups. This result is used to show that the semigroup of all orientation-preserving transformations and the semigroup of all orientation-preserving or orientation-reversing transformations of the chain Xn are covered by their inverse subsemigroups precisely when n≤3

Methodological criteria for the assessment of moderators in systematic reviews of randomised controlled trials : a consensus study

Background: Current methodological guidelines provide advice about the assessment of sub-group analysis within RCTs, but do not specify explicit criteria for assessment. Our objective was to provide researchers with a set of criteria that will facilitate the grading of evidence for moderators, in systematic reviews. Method: We developed a set of criteria from methodological manuscripts (n = 18) using snowballing technique, and electronic database searches. Criteria were reviewed by an international Delphi panel (n = 21), comprising authors who have published methodological papers in this area, and researchers who have been active in the study of sub-group analysis in RCTs. We used the Research ANd Development/University of California Los Angeles appropriateness method to assess consensus on the quantitative data. Free responses were coded for consensus and disagreement. In a subsequent round additional criteria were extracted from the Cochrane Reviewers’ Handbook, and the process was repeated. Results: The recommendations are that meta-analysts report both confirmatory and exploratory findings for subgroups analysis. Confirmatory findings must only come from studies in which a specific theory/evidence based apriori statement is made. Exploratory findings may be used to inform future/subsequent trials. However, for inclusion in the meta-analysis of moderators, the following additional criteria should be applied to each study: Baseline factors should be measured prior to randomisation, measurement of baseline factors should be of adequate reliability and validity, and a specific test of the interaction between baseline factors and interventions must be presented. Conclusions: There is consensus from a group of 21 international experts that methodological criteria to assess moderators within systematic reviews of RCTs is both timely and necessary. The consensus from the experts resulted in five criteria divided into two groups when synthesising evidence: confirmatory findings to support hypotheses about moderators and exploratory findings to inform future research. These recommendations are discussed in reference to previous recommendations for evaluating and reporting moderator studies

Semigroups with operation-compatible Green’s quasiorders

We call a semigroup on which the Green’s quasiorder ≤ J (≤ L, ≤ R) is operation-compatible, a ≤ J-compatible (≤ L-compatible, ≤ R-compatible) semigroup. We study the classes of ≤ J-compatible, ≤ L-compatible and ≤ R-compatible semigroups, using the smallest operation-compatible quasiorders containing Green’s quasiorders as a tool. We prove a number of results, including the following. The class of ≤ L-compatible (≤ R-compatible) semigroups is closed under taking homomorphic images. A regular periodic semigroup is ≤ J-compatible if and only if it is a semilattice of simple semigroups. Every negatively orderable semigroup can be embedded into a negatively orderable ≤ J-compatible semigroup

Challenges in assessing the sunscreen-melanoma association

Source at https://doi.org/10.1002/ijc.31997.Whether sunscreen use affects melanoma risk has been widely studied with contradictory results. To answer this question we performed a systematic review of all published studies, accounting for sources of heterogeneity and bias. We searched for original articles investigating the sunscreen‐melanoma association in humans to February 28, 2018. We then used random‐effects meta‐analysis to combine estimates of the association, stratified by study design. Stratified meta‐analysis and meta‐regression were used to identify sources of heterogeneity. We included 21,069 melanoma cases from 28 studies published 1979–2018: 23 case–control (11 hospital‐based, 12 population‐based), 1 ecological, 3 cohort and 1 randomised controlled trial (RCT). There was marked heterogeneity across study designs and among case–control studies but adjustment for confounding by sun exposure, sunburns and phenotype systematically moved estimates toward decreased melanoma risk among sunscreen users. Ever‐ vs. never‐use of sunscreen was inversely associated with melanoma in hospital‐based case–control studies (adjusted odds ratio (OR) = 0.57, 95%confidence interval (CI) 0.37–0.87, Pheterogeneity Pheterogeneity Pheterogeneity = 0.236). The association differed by latitude (Pinteraction = 0.042), region (Pinteraction = 0.008), adjustment for naevi/freckling (Pinteraction = 0.035), and proportion of never‐sunscreen‐users (Pinteraction = 0·012). Evidence from observational studies on sunscreen use and melanoma risk was weak and heterogeneous, consistent with the challenges of controlling for innate confounding by indication. The only RCT showed a protective effect of sunscreen

Repetitive arm functional tasks after stroke (RAFTAS): a pilot randomised controlled trial

Background Repetitive functional task practise (RFTP) is a promising treatment to improve upper limb recovery following stroke. We report the findings of a study to determine the feasibility of a multi-centre randomised controlled trial to evaluate this intervention. Methods A pilot randomised controlled trial was conducted. Patients with new reduced upper limb function were recruited within 14 days of acute stroke from three stroke units in North East England. Participants were randomised to receive a four week upper limb RFTP therapy programme consisting of goal setting, independent activity practise, and twice weekly therapy reviews in addition to usual post stroke rehabilitation, or usual post stroke rehabilitation. The recruitment rate; adherence to the RFTP therapy programme; usual post stroke rehabilitation received; attrition rate; data quality; success of outcome assessor blinding; adverse events; and the views of study participants and therapists about the intervention were recorded. Results Fifty five eligible patients were identified, 4-6% of patients screened at each site. Twenty four patients participated in the pilot study. Two of the three study sites met the recruitment target of 1-2 participants per month. The median number of face to face therapy sessions received was 6 [IQR 3-8]. The median number of daily repetitions of activities recorded was 80 [IQR 39-80]. Data about usual post stroke rehabilitation were available for 18/24 (75%). Outcome data were available for 22/24 (92%) at one month and 20/24 (83%) at three months. Outcome assessors were unblinded to participant group allocation for 11/22 (50%) at one month and 6/20 (30%) at three months. Four adverse events were considered serious as they resulted in hospitalisation. None were related to study treatment. Feedback from patients and local NHS therapists about the RFTP programme was mainly positive. Conclusions A multi-centre randomised controlled trial to evaluate an upper limb RFTP therapy programme provided early after stroke is feasible and acceptable to patients and therapists, but there are issues which needed to be addressed when designing a Phase III study. A Phase III study will need to monitor and report not only recruitment and attrition but also adherence to the intervention, usual post stroke rehabilitation received, and outcome assessor blinding

Green's relations and stability for subsemigroups

We prove new results on inheritance of Green's relations by subsemigroups in the presence of stability of elements. We provide counterexamples in other cases to show in particular that not all right-stable semigroups are embeddable in left-stable semigroups. This is carried out in the context of a survey of the various closely related notions of stability and minimality of Green's classes that have appeared in the literature over the last sixty years, and which have sometimes been presented in different forms

SSE: a nucleotide and amino acid sequence analysis platform

<p>Abstract</p> <p>Background</p> <p>There is an increasing need to develop bioinformatic tools to organise and analyse the rapidly growing amount of nucleotide and amino acid sequence data in organisms ranging from viruses to eukaryotes.</p> <p>Finding</p> <p>A simple sequence editor (SSE) was developed to create an integrated environment where sequences can be aligned, annotated, classified and directly analysed by a number of built-in bioinformatic programs. SSE incorporates a sequence editor for the creation of sequence alignments, a process assisted by integrated CLUSTAL/MUSCLE alignment programs and automated removal of indels. Sequences can be fully annotated and classified into groups and annotated of sequences and sequence groups and access to analytical programs that analyse diversity, recombination and RNA secondary structure. Methods for analysing sequence diversity include measures of divergence and evolutionary distances, identity plots to detect regions of nucleotide or amino acid homology, reconstruction of sequence changes, mono-, di- and higher order nucleotide compositional biases and codon usage.</p> <p>Association Index calculations, GroupScans, Bootscanning and TreeOrder scans perform phylogenetic analyses that reconcile group membership with tree branching orders and provide powerful methods for examining segregation of alleles and detection of recombination events. Phylogeny changes across alignments and scoring of branching order differences between trees using the Robinson-Fould algorithm allow effective visualisation of the sites of recombination events.</p> <p>RNA secondary and tertiary structures play important roles in gene expression and RNA virus replication. For the latter, persistence of infection is additionally associated with pervasive RNA secondary structure throughout viral genomic RNA that modulates interactions with innate cell defences. SSE provides several programs to scan alignments for RNA secondary structure through folding energy thermodynamic calculations and phylogenetic methods (detection of co-variant changes, and structure conservation between divergent sequences). These analyses complement methods based on detection of sequence constraints, such as suppression of synonymous site variability.</p> <p>For each program, results can be plotted in real time during analysis through an integrated graphics package, providing publication quality graphs. Results can be also directed to tabulated datafiles for import into spreadsheet or database programs for further analysis.</p> <p>Conclusions</p> <p>SSE combines sequence editor functions with analytical tools in a comprehensive and user-friendly package that assists considerably in bioinformatic and evolution research.</p

Updating a systematic review – what difference did it make? Case study of nicotine replacement therapy

AIMS: To examine the effect of updating a systematic review of nicotine replacement therapy on its contents and conclusions. METHODS: We examined the effects of regular updating of a systematic review of nicotine replacement therapy for smoking cessation. We considered two outcomes. First, we assessed the effect of adding new data to meta-analyses, comparing results in 2000 with the results in 1994. Second, we assessed qualitatively the ways inwhich the nature of the questions addressed by the review had changed between the two dates. For the first outcome, we compared the number of trials, the pooled estimate of effect using the odds ratio, and the results of pre-specified subgroup analyses, for nicotine gum and patch separately. Using a test for interaction, we assessed whether differences between estimates were statistically significant. RESULTS: There were ten new trials of nicotine gum between 1994 and 2000, and the meta-analytic effect changed little. For the nicotine patch the number of trials increased from 9 to 30, and the meta-analytic effect fell from 2.07 (95% CI 1.64 – 2.62) to 1.73 (95% CI 1.56 – 1.93). Apparent differences in relative effect in sub-groups found in 1994 were not found in 2000. The updated systematic review addressed a number of questions not identified in the original version. CONCLUSIONS: Updating the meta-analyses lead to a more precise estimate of the likely effect of the nicotine patch, but the clinical message was unchanged. Further placebo controlled NRT trials are not likely to add to the evidence base. It is questionable whether updating the meta-analyses to include them is worthwhile. The content of the systematic review has, however, changed, with the addition of data addressing questions not considered in the original review. There is a tension between the principle of identifying the important questions prior to conducting a review, and keeping the review up to date as primary research identifies new avenues of enquiry

Quantum physics meets biology

Quantum physics and biology have long been regarded as unrelated disciplines, describing nature at the inanimate microlevel on the one hand and living species on the other hand. Over the last decades the life sciences have succeeded in providing ever more and refined explanations of macroscopic phenomena that were based on an improved understanding of molecular structures and mechanisms. Simultaneously, quantum physics, originally rooted in a world view of quantum coherences, entanglement and other non-classical effects, has been heading towards systems of increasing complexity. The present perspective article shall serve as a pedestrian guide to the growing interconnections between the two fields. We recapitulate the generic and sometimes unintuitive characteristics of quantum physics and point to a number of applications in the life sciences. We discuss our criteria for a future quantum biology, its current status, recent experimental progress and also the restrictions that nature imposes on bold extrapolations of quantum theory to macroscopic phenomena.Comment: 26 pages, 4 figures, Perspective article for the HFSP Journa