Integrating Open Source GIS Software in Undergraduate Curriculum, Research, and Outreach - Recent Experiences at Salisbury University

The Department of Geography and Geosciences at Salisbury University has a long tradition of teaching geographic information science. Until recently, most of the courses and research activities focused on commercial software offerings. However, the Department recently integrated Free and Open Source Software for GIS (FOSSG) into its curriculum, research, and outreach. Curriculum changes included introducing students to FOSSG in traditional GIS courses using QGIS, and creating two entirely new courses in Enterprise GIS and GIS Programming using PostGIS, GDAL, and Spatial Lite. Through a competitive National Science Foundation (NSF) Research Experience for Undergraduates grant (REU), students participated in cutting edge research projects in parallel processing with Hadoop and spatial Hadoop for cluster computing, and CUDA for GPGPU calculation on embarrassingly parallel processes for raster data. Finally, undergraduate interns working in the Department\u27s Eastern Shore Regional GIS Cooperative (ESRGC) developed geodashboards using node.js, PostGIS, and Leaflet, while a special topics course developed a GIS based iphone and Android application used by 4,000 participants in the annual Sea Gull Century bike ride using GeoJSON, Leaflet, and javascript. In addition to highlighting the successes of these activities, this paper will discuss the process we used to make the necessary changes in our curriculum, secure the necessary funding for external projects, and the training approach we used to get our computer science students proficient in programming with FOSSG tools

Revealing Historic Invasion Patterns and Potential Invasion Sites for Two Non-Native Plant Species

The historical spatio-temporal distribution of invasive species is rarely documented, hampering efforts to understand invasion dynamics, especially at regional scales. Reconstructing historical invasions through use of herbarium records combined with spatial trend analysis and modeling can elucidate spreading patterns and identify susceptible habitats before invasion occurs. Two perennial species were chosen to contrast historic and potential phytogeographies: Japanese knotweed (Polygonum cuspidatum), introduced intentionally across the US; and mugwort (Artemisia vulgaris), introduced largely accidentally to coastal areas. Spatial analysis revealed that early in the invasion, both species have a stochastic distribution across the contiguous US, but east of the 90th meridian, which approximates the Mississippi River, quickly spread to adjacent counties in subsequent decades. In contrast, in locations west of the 90th meridian, many populations never spread outside the founding county, probably a result of encountering unfavorable environmental conditions. Regression analysis using variables categorized as environmental or anthropogenic accounted for 24% (Japanese knotweed) and 30% (mugwort) of the variation in the current distribution of each species. Results show very few counties with high habitat suitability (≥80%) remain un-invaded (5 for Japanese knotweed and 6 for mugwort), suggesting these perennials are reaching the limits of large-scale expansion. Despite differences in initial introduction loci and pathways, Japanese knotweed and mugwort demonstrate similar historic patterns of spread and show declining rates of regional expansion. Invasion mitigation efforts should be concentrated on areas identified as highly susceptible that border invaded regions, as both species demonstrate secondary expansion from introduction loci

Antiinflammatory Therapy with Canakinumab for Atherosclerotic Disease

Background: Experimental and clinical data suggest that reducing inflammation without affecting lipid levels may reduce the risk of cardiovascular disease. Yet, the inflammatory hypothesis of atherothrombosis has remained unproved. Methods: We conducted a randomized, double-blind trial of canakinumab, a therapeutic monoclonal antibody targeting interleukin-1β, involving 10,061 patients with previous myocardial infarction and a high-sensitivity C-reactive protein level of 2 mg or more per liter. The trial compared three doses of canakinumab (50 mg, 150 mg, and 300 mg, administered subcutaneously every 3 months) with placebo. The primary efficacy end point was nonfatal myocardial infarction, nonfatal stroke, or cardiovascular death. RESULTS: At 48 months, the median reduction from baseline in the high-sensitivity C-reactive protein level was 26 percentage points greater in the group that received the 50-mg dose of canakinumab, 37 percentage points greater in the 150-mg group, and 41 percentage points greater in the 300-mg group than in the placebo group. Canakinumab did not reduce lipid levels from baseline. At a median follow-up of 3.7 years, the incidence rate for the primary end point was 4.50 events per 100 person-years in the placebo group, 4.11 events per 100 person-years in the 50-mg group, 3.86 events per 100 person-years in the 150-mg group, and 3.90 events per 100 person-years in the 300-mg group. The hazard ratios as compared with placebo were as follows: in the 50-mg group, 0.93 (95% confidence interval [CI], 0.80 to 1.07; P = 0.30); in the 150-mg group, 0.85 (95% CI, 0.74 to 0.98; P = 0.021); and in the 300-mg group, 0.86 (95% CI, 0.75 to 0.99; P = 0.031). The 150-mg dose, but not the other doses, met the prespecified multiplicity-adjusted threshold for statistical significance for the primary end point and the secondary end point that additionally included hospitalization for unstable angina that led to urgent revascularization (hazard ratio vs. placebo, 0.83; 95% CI, 0.73 to 0.95; P = 0.005). Canakinumab was associated with a higher incidence of fatal infection than was placebo. There was no significant difference in all-cause mortality (hazard ratio for all canakinumab doses vs. placebo, 0.94; 95% CI, 0.83 to 1.06; P = 0.31). Conclusions: Antiinflammatory therapy targeting the interleukin-1β innate immunity pathway with canakinumab at a dose of 150 mg every 3 months led to a significantly lower rate of recurrent cardiovascular events than placebo, independent of lipid-level lowering. (Funded by Novartis; CANTOS ClinicalTrials.gov number, NCT01327846.

AI is a viable alternative to high throughput screening: a 318-target study

: High throughput screening (HTS) is routinely used to identify bioactive small molecules. This requires physical compounds, which limits coverage of accessible chemical space. Computational approaches combined with vast on-demand chemical libraries can access far greater chemical space, provided that the predictive accuracy is sufficient to identify useful molecules. Through the largest and most diverse virtual HTS campaign reported to date, comprising 318 individual projects, we demonstrate that our AtomNet® convolutional neural network successfully finds novel hits across every major therapeutic area and protein class. We address historical limitations of computational screening by demonstrating success for target proteins without known binders, high-quality X-ray crystal structures, or manual cherry-picking of compounds. We show that the molecules selected by the AtomNet® model are novel drug-like scaffolds rather than minor modifications to known bioactive compounds. Our empirical results suggest that computational methods can substantially replace HTS as the first step of small-molecule drug discovery

Effect of aliskiren on post-discharge outcomes among diabetic and non-diabetic patients hospitalized for heart failure: insights from the ASTRONAUT trial

Aims The objective of the Aliskiren Trial on Acute Heart Failure Outcomes (ASTRONAUT) was to determine whether aliskiren, a direct renin inhibitor, would improve post-discharge outcomes in patients with hospitalization for heart failure (HHF) with reduced ejection fraction. Pre-specified subgroup analyses suggested potential heterogeneity in post-discharge outcomes with aliskiren in patients with and without baseline diabetes mellitus (DM). Methods and results ASTRONAUT included 953 patients without DM (aliskiren 489; placebo 464) and 662 patients with DM (aliskiren 319; placebo 343) (as reported by study investigators). Study endpoints included the first occurrence of cardiovascular death or HHF within 6 and 12 months, all-cause death within 6 and 12 months, and change from baseline in N-terminal pro-B-type natriuretic peptide (NT-proBNP) at 1, 6, and 12 months. Data regarding risk of hyperkalaemia, renal impairment, and hypotension, and changes in additional serum biomarkers were collected. The effect of aliskiren on cardiovascular death or HHF within 6 months (primary endpoint) did not significantly differ by baseline DM status (P = 0.08 for interaction), but reached statistical significance at 12 months (non-DM: HR: 0.80, 95% CI: 0.64-0.99; DM: HR: 1.16, 95% CI: 0.91-1.47; P = 0.03 for interaction). Risk of 12-month all-cause death with aliskiren significantly differed by the presence of baseline DM (non-DM: HR: 0.69, 95% CI: 0.50-0.94; DM: HR: 1.64, 95% CI: 1.15-2.33; P < 0.01 for interaction). Among non-diabetics, aliskiren significantly reduced NT-proBNP through 6 months and plasma troponin I and aldosterone through 12 months, as compared to placebo. Among diabetic patients, aliskiren reduced plasma troponin I and aldosterone relative to placebo through 1 month only. There was a trend towards differing risk of post-baseline potassium ≥6 mmol/L with aliskiren by underlying DM status (non-DM: HR: 1.17, 95% CI: 0.71-1.93; DM: HR: 2.39, 95% CI: 1.30-4.42; P = 0.07 for interaction). Conclusion This pre-specified subgroup analysis from the ASTRONAUT trial generates the hypothesis that the addition of aliskiren to standard HHF therapy in non-diabetic patients is generally well-tolerated and improves post-discharge outcomes and biomarker profiles. In contrast, diabetic patients receiving aliskiren appear to have worse post-discharge outcomes. Future prospective investigations are needed to confirm potential benefits of renin inhibition in a large cohort of HHF patients without D

Effect of angiotensin-converting enzyme inhibitor and angiotensin receptor blocker initiation on organ support-free days in patients hospitalized with COVID-19

IMPORTANCE Overactivation of the renin-angiotensin system (RAS) may contribute to poor clinical outcomes in patients with COVID-19. Objective To determine whether angiotensin-converting enzyme (ACE) inhibitor or angiotensin receptor blocker (ARB) initiation improves outcomes in patients hospitalized for COVID-19. DESIGN, SETTING, AND PARTICIPANTS In an ongoing, adaptive platform randomized clinical trial, 721 critically ill and 58 non–critically ill hospitalized adults were randomized to receive an RAS inhibitor or control between March 16, 2021, and February 25, 2022, at 69 sites in 7 countries (final follow-up on June 1, 2022). INTERVENTIONS Patients were randomized to receive open-label initiation of an ACE inhibitor (n = 257), ARB (n = 248), ARB in combination with DMX-200 (a chemokine receptor-2 inhibitor; n = 10), or no RAS inhibitor (control; n = 264) for up to 10 days. MAIN OUTCOMES AND MEASURES The primary outcome was organ support–free days, a composite of hospital survival and days alive without cardiovascular or respiratory organ support through 21 days. The primary analysis was a bayesian cumulative logistic model. Odds ratios (ORs) greater than 1 represent improved outcomes. RESULTS On February 25, 2022, enrollment was discontinued due to safety concerns. Among 679 critically ill patients with available primary outcome data, the median age was 56 years and 239 participants (35.2%) were women. Median (IQR) organ support–free days among critically ill patients was 10 (–1 to 16) in the ACE inhibitor group (n = 231), 8 (–1 to 17) in the ARB group (n = 217), and 12 (0 to 17) in the control group (n = 231) (median adjusted odds ratios of 0.77 [95% bayesian credible interval, 0.58-1.06] for improvement for ACE inhibitor and 0.76 [95% credible interval, 0.56-1.05] for ARB compared with control). The posterior probabilities that ACE inhibitors and ARBs worsened organ support–free days compared with control were 94.9% and 95.4%, respectively. Hospital survival occurred in 166 of 231 critically ill participants (71.9%) in the ACE inhibitor group, 152 of 217 (70.0%) in the ARB group, and 182 of 231 (78.8%) in the control group (posterior probabilities that ACE inhibitor and ARB worsened hospital survival compared with control were 95.3% and 98.1%, respectively). CONCLUSIONS AND RELEVANCE In this trial, among critically ill adults with COVID-19, initiation of an ACE inhibitor or ARB did not improve, and likely worsened, clinical outcomes. TRIAL REGISTRATION ClinicalTrials.gov Identifier: NCT0273570

Spatial SQL

1_t3bh2uq

How Do I Do This in ArcGIS/Manifold?: Illustrating Classic GIS Tasks

A print on demand of these books and articles can be obtained from Cornell Business Services (CBS) Digital Services by sending e-mail to [email protected] or calling 607.255.2524. In the body of the message include the identifier.uri for the book or article, and ask to be contacted regarding payment.In 1988, the United States Geological Survey (USGS) created a classic document titled "The Process for Selecting Geographic Information Systems" (Guptil, et. al., 1988). The document provided an overview of the process for selecting geographic information systems, in addition to a checklist of functions that a GIS should include. The functions were broken into five separate categories: user interface, database management, database creation, data manipulation and analysis, and data display and presentation. The document became required reading for those involved in the selection of GIS, and was often used as a supplementary checklist in competitive benchmarks of GIS software. Although the document is over 15 years old, many of the functions listed are still relevant today, and represent some of the most commonly used features within GIS. In fact, the document was so forward thinking that most GIS software products are still unable to perform all the tasks listed. Therefore, this document attempts to illustrate the GIS processes listed in the USGS document using two popular GIS software systems: ArcGIS 8.3 and Manifold 6.0. While the document does illustrate the steps required to complete the classic GIS tasks in a side-by-side format, it is not meant to be a comparison or an endorsement of either product (they just happen to be the two most popular products in our lab). Rather, it is meant to serve as a cheat-sheet for GIS professionals needing some direction in performing classic GIS functions. Many individuals are beginning to experiment with Manifold GIS, and the large user base of ArcView 3.x user continues to migrate to ArcGIS