Effect of paper quality on the response rate to a postal survey: A randomised controlled trial. [ISRCTN32032031]

BACKGROUND: Response rates to surveys are declining and this threatens the validity and generalisability of their findings. We wanted to determine whether paper quality influences the response rate to postal surveys METHODS: A postal questionnaire was sent to all members of the British Society of Gynaecological Endoscopy (BSGE). Recipients were randomised to receiving the questionnaire printed on standard quality paper or high quality paper. RESULTS: The response rate for the recipients of high quality paper was 43/195 (22%) and 57/194 (29%) for standard quality paper (relative rate of response 0.75, 95% CI 0.33–1.05, p = 0.1 CONCLUSION: The use of high quality paper did not increase response rates to a questionnaire survey of gynaecologists affiliated to an endoscopic society

Test-retest reliability of FreeSurfer automated hippocampal subfield segmentation within and across scanners

The human hippocampus is vulnerable to a range of degenerative conditions and as such, accurate in vivo measurement of the hippocampus and hippocampal substructures via neuroimaging is of great interest for understanding mechanisms of disease as well as for use as a biomarker in clinical trials of novel therapeutics. Although total hippocampal volume can be measured relatively reliably, it is critical to understand how this reliability is affected by acquisition on different scanners, as multiple scanning platforms would likely be utilized in large-scale clinical trials. This is particularly true for hippocampal subregional measurements, which have only relatively recently been measurable through common image processing platforms such as FreeSurfer. Accurate segmentation of these subregions is challenging due to their small size, magnetic resonance imaging (MRI) signal loss in medial temporal regions of the brain, and lack of contrast for delineation from standard neuroimaging procedures. Here, we assess the test-retest reliability of the FreeSurfer automated hippocampal subfield segmentation procedure using two Siemens model scanners (a Siemens Trio and Prismafit Trio upgrade). T1-weighted images were acquired for 11 generally healthy younger participants (two scans on the Trio and one scan on the Prismafit). Each scan was processed through the standard cross-sectional stream and the recently released longitudinal pipeline in FreeSurfer v6.0 for hippocampal segmentation. Test-retest reliability of the volumetric measures was examined for individual subfields as well as percent volume difference and Dice overlap among scans and intra-class correlation coefficients (ICC). Reliability was high in the molecular layer, dentate gyrus, and whole hippocampus with the inclusion of three time points with mean volume differences among scans less than 3%, overlap greater than 80%, and ICC >0.95. The parasubiculum and hippocampal fissure showed the least improvement in reliability with mean volume difference greater than 5%, overlap less than 70%, and ICC scores ranging from 0.78 to 0.89. Other subregions, including the CA regions, were stable in their mean volume difference and overlap (75% respectively) and showed improvement in reliability with the inclusion of three scans (ICC ​> ​0.9). Reliability was generally higher within scanner (Trio-Trio), however, Trio-Prismafit reliability was also high and did not exhibit an obvious bias. These results suggest that the FreeSurfer automated segmentation procedure is a reliable method to measure total as well as hippocampal subregional volumes and may be useful in clinical applications including as an endpoint for future clinical trials of conditions affecting the hippocampus

The Symmetry of Partner Modelling

© 2016, International Society of the Learning Sciences, Inc. Collaborative learning has often been associated with the construction of a shared understanding of the situation at hand. The psycholinguistics mechanisms at work while establishing common grounds are the object of scientific controversy. We postulate that collaborative tasks require some level of mutual modelling, i.e. that each partner needs some model of what the other partners know/want/intend at a given time. We use the term “some model” to stress the fact that this model is not necessarily detailed or complete, but that we acquire some representations of the persons we interact with. The question we address is: Does the quality of the partner model depend upon the modeler’s ability to represent his or her partner? Upon the modelee’s ability to make his state clear to the modeler? Or rather, upon the quality of their interactions? We address this question by comparing the respective accuracies of the models built by different team members. We report on 5 experiments on collaborative problem solving or collaborative learning that vary in terms of tasks (how important it is to build an accurate model) and settings (how difficult it is to build an accurate model). In 4 studies, the accuracy of the model that A built about B was correlated with the accuracy of the model that B built about A, which seems to imply that the quality of interactions matters more than individual abilities when building mutual models. However, these findings do not rule out the fact that individual abilities also contribute to the quality of modelling process

Extreme enriched and heterogeneous ⁸⁷Sr/⁸⁶Sr ratios recorded in magmatic plagioclase from the Samoan hotspot

We report the major-element, trace-element, and 87Sr/86Sr compositions of six plagioclase crystals from two Samoan lavas with extreme EM2 isotopic compositions (ALIA-115-18 with whole-rock 87Sr/86Sr of 0.718592, and ALIA-115-21 with whole-rock 87Sr/86Sr of 0.720469). We employed laser-ablation split-stream mass spectrometry (LASS) to simultaneously measure 87Sr/86Sr ratios, major-element concentrations, and trace-element concentrations in the same plagioclase crystal volume. We find that two plagioclase crystals have extreme 87Sr/86Sr heterogeneity in excess of 5000 ppm (where ppm of 87Sr/Sr variability86=106⋅[Sr/8687Srmax−87Sr/86Srmin]/87Sr/86Sravg). In two of the plagioclase crystals, we identify the highest 87Sr/86Sr ratios (0.7224) ever measured in any fresh, mantle-derived ocean island basalt (OIB) or OIB-hosted mineral phase.We find that in 87Sr/86Sr-versus-Sr concentration space, the six plagioclase crystals overlap in a “common component” region with higher 87Sr/86Sr than has been previously identified in whole-rock Samoan lavas or mineral separates. We use the occurrence of olivine mineral inclusions (Fo=74.5±0.8, 2 SD) in the high-87Sr/86Sr zone of one plagioclase crystal to infer the bulk composition (Mg#=46.8±0.8, 2 SD) of the extreme EM2 magma from which the olivine and high-87Sr/86Sr plagioclase crystallized. We argue that a relatively evolved EM2 endmember magma mixed with at least one lower-87Sr/86Sr melt to generate the observed intra-crystal plagioclase isotopic heterogeneity.By inferring that subducted terrigenous sediment gives rise to EM2 signatures in Samoan lavas, we estimate that the quantity of sediment necessary to generate the most-elevated 87Sr/86Sr ratios observed in the Samoan plagioclase is ∼7% of the mantle source. We also estimate that sediment subduction into the mantle over geologic time has generated a sediment domain that constitutes 0.02% of the mass of the mantle, a much lower proportion than required in the EM2 mantle source. Even if subducted sediment is concentrated in large low-shear-velocity provinces (LLSVPs) at the base of the mantle (which constitute up to 7.7% of the mantle's mass), then only 0.25% of the LLSVPs are composed of sediment. This requires that the distribution of subducted sediment in the mantle is heterogeneous, and the high relative abundance of sediment in the Samoan EM2 mantle is an anomalous relic of ancient subduction that has survived convective attenuation

Phenotypic microarrays suggest Escherichia coli ST131 is not a metabolically distinct lineage of extra-intestinal pathogenic E. coli

Extraintestinal pathogenic E. coli (ExPEC) are the major aetiological agent of urinary tract infections (UTIs) in humans. The emergence of the CTX-M producing clone E. coli ST131 represents a major challenge to public health worldwide. A recent study on the metabolic potential of E. coli isolates demonstrated an association between the E. coli ST131 clone and enhanced utilisation of a panel of metabolic substrates. The studies presented here investigated the metabolic potential of ST131 and other major ExPEC ST isolates using 120 API test reagents and found that ST131 isolates demonstrated a lower metabolic activity for 5 of 120 biochemical tests in comparison to non-ST131 ExPEC isolates. Furthermore, comparative phenotypic microarray analysis showed a lack of specific metabolic profile for ST131 isolates countering the suggestion that these bacteria are metabolically fitter and therefore more successful human pathogens

Scandinavian Flagship Universities: an Appraisal of Leading National Universities in the European Context

In the immediate post-Sputnik era, Clark Kerr saw America’s breed of universities as “multiversities,” characterized by growing enrollment, an increasingly diversified academic community, and as the emerging driver of knowledge production and innovation (Kerr 2001: xi). This is now a widely shared vision throughout the world. Governments have provided additional funding, fueling further growth in academic programs and attracting talent. One result: the number of perceived stakeholders has increased, along with their expectations

Systems biology via redescription and ontologies (I): finding phase changes with applications to malaria temporal data

Biological systems are complex and often composed of many subtly interacting components. Furthermore, such systems evolve through time and, as the underlying biology executes its genetic program, the relationships between components change and undergo dynamic reorganization. Characterizing these relationships precisely is a challenging task, but one that must be undertaken if we are to understand these systems in sufficient detail. One set of tools that may prove useful are the formal principles of model building and checking, which could allow the biologist to frame these inherently temporal questions in a sufficiently rigorous framework. In response to these challenges, GOALIE (Gene ontology algorithmic logic and information extractor) was developed and has been successfully employed in the analysis of high throughput biological data (e.g. time-course gene-expression microarray data and neural spike train recordings). The method has applications to a wide variety of temporal data, indeed any data for which there exist ontological descriptions. This paper describes the algorithms behind GOALIE and its use in the study of the Intraerythrocytic Developmental Cycle (IDC) of Plasmodium falciparum, the parasite responsible for a deadly form of chloroquine resistant malaria. We focus in particular on the problem of finding phase changes, times of reorganization of transcriptional control

Glucocorticoids with different chemical structures but similar glucocorticoid receptor potency regulate subsets of common and unique genes in human trabecular meshwork cells

<p>Abstract</p> <p>Background</p> <p>In addition to their well-documented ocular therapeutic effects, glucocorticoids (GCs) can cause sight-threatening side-effects including ocular hypertension presumably via morphological and biochemical changes in trabecular meshwork (TM) cells. In the present study, we directly compared the glucocorticoid receptor (GR) potency for dexamethasone (DEX), fluocinolone acetonide (FA) and triamcinolone acetonide (TA), examined the expression of known GRα and GRβ isoforms, and used gene expression microarrays to compare the effects of DEX, FA, and TA on the complete transcriptome in two primary human TM cell lines.</p> <p>Methods</p> <p>GR binding affinity for DEX, FA, and TA was measured by a cell-free competitive radio-labeled GR binding assay. GR-mediated transcriptional activity was assessed using the GeneBLAzer beta-lactamase reporter gene assay. Levels of GRα and GRβ isoforms were assessed by Western blot. Total RNA was extracted from TM 86 and TM 93 cells treated with 1 μM DEX, FA, or TA for 24 hr and used for microarray gene expression analysis. The microarray experiments were repeated three times. Differentially expressed genes were identified by Rosetta Resolver Gene Expression Analysis System.</p> <p>Results</p> <p>The GR binding affinity (IC₅₀) for DEX, FA, and TA was 5.4, 2.0, and 1.5 nM, respectively. These values are similar to the GR transactivation EC₅₀of 3.0, 0.7, and 1.5 nM for DEX, FA, and TA, respectively. All four GRα translational isoforms (A-D) were expressed in TM 86 and TM 93 total cell lysates, however, the C and D isoforms were more highly expressed relative to A and B. All four GRβ isoforms (A-D) were also detected in TM cells, although GRβ-D isoform expression was lower compared to that of the A, B, or C isoforms. Microarray analysis revealed 1,968 and 1,150 genes commonly regulated by DEX, FA, and TA in TM 86 and TM 93, respectively. These genes included RGC32, OCA2, ANGPTL7, MYOC, FKBP5, SAA1 and ZBTB16. In addition, each GC specifically regulated a unique set of genes in both TM cell lines. Using Ingenuity Pathway Analysis (IPA) software, analysis of the data from TM 86 cells showed that DEX significantly regulated transcripts associated with RNA post-transcriptional modifications, whereas FA and TA modulated genes involved in lipid metabolism and cell morphology, respectively. In TM 93 cells, DEX significantly regulated genes implicated in histone methylation, whereas FA and TA altered genes associated with cell cycle and cell adhesion, respectively.</p> <p>Conclusion</p> <p>Human trabecular meshwork cells in culture express all known GRα and GRβ translational isoforms, and GCs with similar potency but subtly different chemical structure are capable of regulating common and unique gene subsets and presumably biologic responses in these cells. These GC structure-dependent effects appear to be TM cell-lineage dependent.</p