Interactive data exploration with targeted projection pursuit

Data exploration is a vital, but little considered, part of the scientific process; but few visualisation tools can cope with truly complex data. Targeted Projection Pursuit (TPP) is an interactive data exploration technique that provides an intuitive and transparent interface for data exploration. A prototype has been evaluated quantitatively and found to outperform algorithmic techniques on standard visual analysis tasks

Node-attribute graph layout for small-world networks

Small-world networks are a very commonly occurring type of graph in the real-world, which exhibit a clustered structure that is not well represented by current graph layout algorithms. In many cases we also have information about the nodes in such graphs, which are typically depicted on the graph as node colour, shape or size. Here we demonstrate that these attributes can instead be used to layout the graph in high-dimensional data space. Then using a dimension reduction technique, targeted projection pursuit, the graph layout can be optimised for displaying clustering. The technique out-performs force-directed layout methods in cluster separation when applied to a sample, artificially generated, small-world network

Understanding Visualization: A formal approach using category theory and semiotics

This article combines the vocabulary of semiotics and category theory to provide a formal analysis of visualization. It shows how familiar processes of visualization fit the semiotic frameworks of both Saussure and Peirce, and extends these structures using the tools of category theory to provide a general framework for understanding visualization in practice, including: relationships between systems, data collected from those systems, renderings of those data in the form of representations, the reading of those representations to create visualizations, and the use of those visualizations to create knowledge and understanding of the system under inspection. The resulting framework is validated by demonstrating how familiar information visualization concepts (such as literalness, sensitivity, redundancy, ambiguity, generalizability, and chart junk) arise naturally from it and can be defined formally and precisely. This article generalizes previous work on the formal characterization of visualization by, inter alia, Ziemkiewicz and Kosara and allows us to formally distinguish properties of the visualization process that previous work does not

Shared decision-making experiences in child long-term ventilation : a systematic review

INTRODUCTION: Recent decades have seen an increase in children receiving long-term ventilation. To ensure that long-term ventilation decisions incorporate the perspectives of stakeholders, it is vital that empirical evidence is gathered to substantiate frameworks and guidance on shared decision-making for long-term ventilation. This systematic review and qualitative evidence synthesis aimed to clarify what shared decision-making constitutes in relation to long-term ventilation initiation for children and young people (<21 years). METHODS: A systematic review of qualitative research was undertaken. Searches were conducted in MEDLINE, Embase, CINAHL, PsycINFO and Web of Science. RESULTS: Findings from 13 studies were included representative of 363 caregivers and 143 healthcare professional experiences. Components that support shared decision-making included acknowledging the unique positionality of caregivers and ensuring caregivers were informed about the implications of long-term ventilation. Beneficial qualities of engagement between stakeholders included honest, clear and timely dialogue using lay, tactful and sensitive language. CONCLUSION: Our findings clarify components and approaches supportive of shared decision-making in discussions about long-term ventilation. This review therefore provides a valuable resource to implement shared decision-making practices in the context of long-term ventilation decisions for children and young people

Rapid antiretroviral therapy initiation in the Botswana Combination Prevention Project: a quasi-experimental before and after study.

BACKGROUND: Ensuring that individuals who are living with HIV rapidly initiate antiretroviral therapy (ART) is an essential step in meeting the 90-90-90 targets. We evaluated the feasibility and outcomes of rapid ART initiation in the Botswana Combination Prevention Project (BCPP). We aimed to establish whether simplified ART initiation with the offer of same-day treatment could increase uptake and reduce time from clinic linkage to treatment initiation, while maintaining rates of retention in care and viral suppression. METHODS: We did a quasi-experimental before and after study with use of data from the BCPP. The BCPP was a community-randomised HIV-prevention trial done in 30 communities across Botswana from Oct 1, 2013, to June 30, 2018. Participants in the 15 intervention clusters, who were HIV-positive and not already taking ART were offered universal HIV-treatment and same-day ART with a dolutegravir-based regimen at first clinic visit. This rapid ART intervention was implemented mid-way through the trial on June 1, 2016, enabling us to determine the effect of rapid ART guidelines on time to ART initiation and rates of retention in care and viral suppression at 1 year in the BCPP intervention group. FINDINGS: We assessed 1717 adults linked to study clinics before rapid ART introduction and 800 after rapid ART introduction. During the rapid ART period, 457 (57·1%, 95% CI 53·7-60·6) individuals initiated ART within 1 day of linkage, 589 (73·7%, 70·6-76·7) of 799 within 1 week, 678 (84·9%, 82·4-87·3) of 799 within 1 month, and 744 (93·5%, 91·6-95·1) of 796 within 1 year. Before the introduction of rapid ART, 163 (9·5%, 95% CI 8·2-11·0) individuals initiated ART within 1 day of linkage, 276 (16·1%, 14·4-17·9) within 1 week, 839 (48·9%, 46·5-51·3) within 1 month, and 1532 (89·2%, 87·7-90·6) within 1 year. 1 year after ART initiation, 1472 (90·5%, 87·4-92·8) of 1627 individuals who linked in the standard ART period were in care and had a viral load of less than 400 copies per mL, compared with 578 (91·6%, 88·1-94·1) of 631 in the rapid ART period (risk ratio 1·01, 95% CI 0·92-1·11). INTERPRETATION: Our findings provide support for the WHO recommendations for rapid ART initiation, and add to the accumulating evidence showing the feasibility, acceptability, and safety of rapid ART initiation in low-income and middle-income country settings. FUNDING: US President's Emergency Plan for AIDS Relief

Advanced HIV disease in the Botswana combination prevention project: prevalence, risk factors, and outcomes.

OBJECTIVE(S): To determine the proportion of individuals linking to HIV-care with advanced HIV-disease (CD4 cell counts ≤200 cells/μl) in the Botswana Combination Prevention Project, describe the characteristics of these individuals, and examine treatment outcomes. DESIGN: A subanalysis of a cluster-randomized HIV-prevention trial. HIV status was assessed in 16-64-year-olds through home and mobile testing. All HIV-positive persons not on antiretroviral therapy were referred to local Ministry of Health and Wellness clinics for treatment. METHODS: Analysis was restricted to the 15 intervention clusters. The proportion of individuals with advanced HIV disease was determined; associations between advanced HIV disease and sex and age explored; and rates of viral suppression determined at 1-year. Mortality and retention in care were compared between CD4 strata (CD4 cell counts ≤200 vs. >200 cells/μl). RESULTS: Overall, 17.2% [430/2499; 95% confidence interval (CI) 15.7-18.8%] of study participants had advanced HIV disease (CD4 cell counts ≤200 cells/μl) at time of clinic linkage. Men were significantly more likely to present with CD4 cell counts 200 cells/μl or less than women [23.7 vs. 13.4%, adjusted odds ratio 1.9, 95% CI 1.5-2.3]. The risk of advanced HIV disease increased with increasing age (adjusted odds ratio 2.2, 95% CI 1.4-3.2 >35 vs. <25 years). Patients with CD4 cell counts 200 cells/μl or less had significantly higher rates of attrition from care during follow-up (hazards ratio 1.47, 95% CI 1.1-2.1). CONCLUSION: Advanced HIV disease due to late presentation to or disengagement from antiretroviral therapy care remains common in the Treat All era in Botswana, calling for innovative testing, linkage, and treatment strategies to engage and retain harder-to-reach populations in care

Micro Methods for Megafauna: Novel Approaches to Late Quaternary Extinctions and Their Contributions to Faunal Conservation in the Anthropocene

Drivers of Late Quaternary megafaunal extinctions are relevant to modern conservation policy in a world of growing human population density, climate change, and faunal decline. Traditional debates tend toward global solutions, blaming either dramatic climate change or dispersals of Homo sapiens to new regions. Inherent limitations to archaeological and paleontological data sets often require reliance on scant, poorly resolved lines of evidence. However, recent developments in scientific technologies allow for more local, context-specific approaches. In the present article, we highlight how developments in five such methodologies (radiocarbon approaches, stable isotope analysis, ancient DNA, ancient proteomics, microscopy) have helped drive detailed analysis of specific megafaunal species, their particular ecological settings, and responses to new competitors or predators, climate change, and other external phenomena. The detailed case studies of faunal community composition, extinction chronologies, and demographic trends enabled by these methods examine megafaunal extinctions at scales appropriate for practical understanding of threats against particular species in their habitats today. </section

Great Lake Review Fall 2009

Great Lake Review is SUNY Oswego's student-edited literary and art magazine. Great Lake Review is published, in general, every semester, and contains primarily student art work, poetry, fiction, and other literary works.SUNY Oswego Student Associatio

Exome sequencing of 20,979 individuals with epilepsy reveals shared and distinct ultra-rare genetic risk across disorder subtypes

Identifying genetic risk factors for highly heterogeneous disorders like epilepsy remains challenging. Here, we present the largest whole-exome sequencing study of epilepsy to date, with >54,000 human exomes, comprising 20,979 deeply phenotyped patients from multiple genetic ancestry groups with diverse epilepsy subtypes and 33,444 controls, to investigate rare variants that confer disease risk. These analyses implicate seven individual genes, three gene sets, and four copy number variants at exome-wide significance. Genes encoding ion channels show strong association with multiple epilepsy subtypes, including epileptic encephalopathies, generalized and focal epilepsies, while most other gene discoveries are subtype-specific, highlighting distinct genetic contributions to different epilepsies. Combining results from rare single nucleotide/short indel-, copy number-, and common variants, we offer an expanded view of the genetic architecture of epilepsy, with growing evidence of convergence among different genetic risk loci on the same genes. Top candidate genes are enriched for roles in synaptic transmission and neuronal excitability, particularly postnatally and in the neocortex. We also identify shared rare variant risk between epilepsy and other neurodevelopmental disorders. Our data can be accessed via an interactive browser, hopefully facilitating diagnostic efforts and accelerating the development of follow-up studies