Spatial microsimulation of osteoarthritis prevalence at the small area level in England – Constraint selection for a 2-stage microsimulation process

The presence of identical benchmark/constraint variables in both geographic and survey datasets is a principal requirement for static spatial microsimulation models, particularly in the field of medicine and health sciences. This is also a as key limitation of static spatial models because geographical datasets rarely contain all variables required to realistically simulate an outcome. We believe this challenge can be overcome by a multilevel approach to spatial microsimulation using a case study of estimating the small area level prevalence of knee osteoarthritis in England. In the paper, we describe constraint selection and demonstrate a novel two-stage spatial microsimulation procedure using SimObesity, a static deterministic combinatorial spatial microsimulation model. We also present the validation parameters of our synthetic data, important areas for consideration and avenues for future research. Our findings demonstrate that important benchmark variables absent from the geographical dataset can be incorporated into spatial microsimulation models without compromising model robustness

La recherche australienne en maîtrise de l'information 2000-2005

Le sens prêté au concept de maîtrise de l’information a évolué ces dernières années en Australie ; les contextes et les approches de recherche se sont diversifiés. Malgré la prédominance des projets à visée éducative, la recherche concerne aussi le monde du travail ou le secteur associatif. On note un début d’intérêt pour les contextes culturels différents, attesté par le démarrage de recherches sur les thématiques transculturelles et les influences culturelles. [The meaning given to the concept of information literacy in Australia has evolved in recent years; contexts and approaches in research have diversified. Despite the predominance of projects with educational aims, research also concerns the world of work or the associative sector. An awakening interest has been observed in different cultural contexts, demonstrated by the beginnings of research into cross-cultural themes and cultural influences.

Trans-Pacific doctoral success: A collaborative cohort model

The San Jose Gateway PhD program is a doctoral partnership between the School of Information at San Jose State University (SJSU) in the USA, and the Information Systems School at the Queensland University of Technology (QUT) in Australia. Because of Californian legislation, SJSU has not been able to offer PhD degrees. The Gateway Program therefore provides a research pathway for SJSU’s coursework students. It also helps the School to grow the research capacity of academic staff. For QUT, the Program provides the opportunity to advance research agendas and to build strong international connections and partnerships. The Program began in 2008. It is a distance-delivered cohort-based scheme with new students commencing in August of each year. All students are enrolled as part-time students in QUT’s Doctor of Philosophy. Each student is assigned supervisors from both universities. In addition to individual and group supervisory meetings, all students and supervisors meet in a virtual meeting space once a month. The online monthly meetings are supplemented by two residential events each year: (i) a one week face to face residential in August at San Jose State University, and; (ii) an online residential in March. This paper will critically reflect upon this unique Program, which has led to high quality research outcomes, rapid completions, and noteworthy graduate employments. Critical consideration of the challenges and future proofing of the approach will also be explored

Johns Hopkins Medicine responds to COVID-19: Adjusting patient- family- and staff-centered care

The extraordinary impact of the novel coronavirus disease 2019 (COVID-19) on the health care industry included a major, nearly immediate paradigm shift in the visitation policy for Johns Hopkins Medicine. This large health system, comprising six hospitals, a home care group, community physician practices and satellite outpatient sites moved from essentially open visitation to no visitation, creating an entirely new set of needs for our staff, patients and their loved ones. We developed new ways of communicating and connecting staff members, staff and patients, staff and the patient’s loved ones, and patients and their loved ones. Our intent was to maintain our commitment to patient- and family-centered care, to alleviate the anxiety and stress from this devastating pandemic to the extent possible. This article describes approaches taken by the health system’s Patient Experience leadership team and others to develop resources that educate patients, loved ones and staff about the process changes and facilitate incorporation of these new ways of communicating and connecting. The content is organized into three areas: including staff resources, consumer resources and resources that support consumer engagement. Many of the changes have been well received, enhancing our pre-COVID-19 ability to connect with one another and will be assimilated into our culture for the long term. We plan to develop objective measures of the effectiveness for approaches that outlive COVID-19 and enhance patient-centered care. Experience Framework This article is associated with the Patient, Family & Community Engagement lens of The Beryl Institute Experience Framework. (http://bit.ly/ExperienceFramework) Access other PXJ articles related to this lens. Access other resources related to this lens

Do trialists endorse clinical trial registration? Survey of a Pubmed sample

<p>Abstract</p> <p>Introduction</p> <p>Despite intense interest in trial registration, there is a wide gap between theoretical postulates on trial registration and its implementation worldwide.</p> <p>Objective</p> <p>We aimed to evaluate trialists views about current international guidelines on trial registration, including the World Health Organization's (WHO) International Clinical Trials Registry Platform (ICTRP) policies and the Ottawa Statement, as well as their intention to register any future clinical trials they conduct.</p> <p>Methods</p> <p>We identified all 40,158 PUBMED-indexed clinical trials published from May 2005 to May 2006 using an advanced search strategy. From a random sample of 500 confirmed clinical trials, corresponding authors with e-mail contact addresses were surveyed.</p> <p>Results</p> <p>A total of 275 (60%) questionnaires from 45 countries were completed. 31% of the respondents had received only nonindustry funding during the past ten years, while 5% and 61% had received only industry or mixed funding respectively. Approximately two third of participants supported registration of all 20 WHO Data Set items, and endorsed the Ottawa Statement part 1 and part 2. Delayed public disclosure of some essential data in instances where they may be considered sensitive for competitive commercial reasons was supported by 30% of the participants, whereas immediate disclosure was supported by 53%. Only 21% of participants had registered all of their ongoing trials since 2005, while 47% stated that they would provide the 20 WHO Data Set items to a publicly accessible register for all their future clinical trials; a significantly higher proportion of participants who received only nonindustry funding (62%) was found among those who would always provide the 20 WHO items for future trials, compared to 42% of participants who received mixed or only industry funding. Among those who were undecided about endorsing registration. One third of participants expressed a lack of sufficient knowledge as the primary reason.</p> <p>Conclusion</p> <p>Although disagreement was apparent on certain issues, our findings illustrate that trial registration is gradually becoming part of the current research paradigm internationally. Our results also suggest that researchers require more knowledge to inform their decision to comply with the International standards at this early stage of voluntary trial registration.</p

The Interrelationships of Land Plants and the Nature of the Ancestral Embryophyte

The evolutionary emergence of land plant body plans transformed the planet. However, our understanding of this formative episode is mired in the uncertainty associated with the phylogenetic relationships among bryophytes (hornworts, liverworts, and mosses) and tracheophytes (vascular plants). Here we attempt to clarify this problem by analyzing a large transcriptomic dataset with models that allow for compositional heterogeneity between sites. Zygnematophyceae is resolved as sister to land plants, but we obtain several distinct relationships between bryophytes and tracheophytes. Concatenated sequence analyses that can explicitly accommodate site-specific compositional heterogeneity give more support for a mosses-liverworts clade, "Setaphyta," as the sister to all other land plants, and weak support for hornworts as the sister to all other land plants. Bryophyte monophyly is supported by gene concatenation analyses using models explicitly accommodating lineage-specific compositional heterogeneity and analyses of gene trees. Both maximum-likelihood analyses that compare the fit of each gene tree to proposed species trees and Bayesian supertree estimation based on gene trees support bryophyte monophyly. Of the 15 distinct rooted relationships for embryophytes, we reject all but three hypotheses, which differ only in the position of hornworts. Our results imply that the ancestral embryophyte was more complex than has been envisaged based on topologies recognizing liverworts as the sister lineage to all other embryophytes. This requires many phenotypic character losses and transformations in the liverwort lineage, diminishes inconsistency between phylogeny and the fossil record, and prompts re-evaluation of the phylogenetic affinity of early land plant fossils, the majority of which are considered stem tracheophytes

Ortho2ExpressMatrix—a web server that interprets cross-species gene expression data by gene family information

<p>Abstract</p> <p>Background</p> <p>The study of gene families is pivotal for the understanding of gene evolution across different organisms and such phylogenetic background is often used to infer biochemical functions of genes. Modern high-throughput experiments offer the possibility to analyze the entire transcriptome of an organism; however, it is often difficult to deduct functional information from that data.</p> <p>Results</p> <p>To improve functional interpretation of gene expression we introduce Ortho2ExpressMatrix, a novel tool that integrates complex gene family information, computed from sequence similarity, with comparative gene expression profiles of two pre-selected biological objects: gene families are displayed with two-dimensional matrices. Parameters of the tool are object type (two organisms, two individuals, two tissues, etc.), type of computational gene family inference, experimental meta-data, microarray platform, gene annotation level and genome build. Family information in Ortho2ExpressMatrix bases on computationally different protein family approaches such as EnsemblCompara, InParanoid, SYSTERS and Ensembl Family. Currently, respective all-against-all associations are available for five species: human, mouse, worm, fruit fly and yeast. Additionally, microRNA expression can be examined with respect to miRBase or TargetScan families. The visualization, which is typical for Ortho2ExpressMatrix, is performed as matrix view that displays functional traits of genes (differential expression) as well as sequence similarity of protein family members (BLAST e-values) in colour codes. Such translations are intended to facilitate the user's perception of the research object.</p> <p>Conclusions</p> <p>Ortho2ExpressMatrix integrates gene family information with genome-wide expression data in order to enhance functional interpretation of high-throughput analyses on diseases, environmental factors, or genetic modification or compound treatment experiments. The tool explores differential gene expression in the light of orthology, paralogy and structure of gene families up to the point of ambiguity analyses. Results can be used for filtering and prioritization in functional genomic, biomedical and systems biology applications. The web server is freely accessible at <url>http://bioinf-data.charite.de/o2em/cgi-bin/o2em.pl</url>.</p

Think globally, measure locally: The MIREN standardized protocol for monitoring plant species distributions along elevation gradients

Climate change and other global change drivers threaten plant diversity in mountains worldwide. A widely documented response to such environmental modifications is for plant species to change their elevational ranges. Range shifts are often idiosyncratic and difficult to generalize, partly due to variation in sampling methods. There is thus a need for a standardized monitoring strategy that can be applied across mountain regions to assess distribution changes and community turnover of native and non-native plant species over space and time. Here, we present a conceptually intuitive and standardized protocol developed by the Mountain Invasion Research Network (MIREN) to systematically quantify global patterns of native and non-native species distributions along elevation gradients and shifts arising from interactive effects of climate change and human disturbance. Usually repeated every five years, surveys consist of 20 sample sites located at equal elevation increments along three replicate roads per sampling region. At each site, three plots extend from the side of a mountain road into surrounding natural vegetation. The protocol has been successfully used in 18 regions worldwide from 2007 to present. Analyses of one point in time already generated some salient results, and revealed region-specific elevational patterns of native plant species richness, but a globally consistent elevational decline in non-native species richness. Non-native plants were also more abundant directly adjacent to road edges, suggesting that disturbed roadsides serve as a vector for invasions into mountains. From the upcoming analyses of time series, even more exciting results can be expected, especially about range shifts. Implementing the protocol in more mountain regions globally would help to generate a more complete picture of how global change alters species distributions. This would inform conservation policy in mountain ecosystems, where some conservation policies remain poorly implemented