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

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.

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

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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

Establishing the Relationship Between Nonhuman Primates and Mangrove Forests at the Global, National, and Local Scales

Global and spatially explicit information about the interaction between habitat and wildlife species is critical to enhancing conservation efforts. Despite the recognized importance of mangrove forests to non-human primates, the relationship between the two lacks understanding. To counter this, we created the MangPrim-21 database to map and measure the locations of interactions between all non-human primates and all mangrove forests globally. We report our findings across the global, national, and local scales for all inventoried non-human primates and all inventoried mangrove forests. Globally, we find that half of all non-primates potentially use mangrove forests, and more than half of the global mangrove forest falls within the delineated range of at least one non-human primate species. Nationally, we find that Indonesia, Madagascar, Brazil, Cameroon, and Malaysia likely have the most non-human primate and mangrove forest interactions. At the subnational level, we find that several discrete locations in Kalimantan are critical to both mangrove forests and non-human primates. The MangPrim-21 database provides a globally consistent and locally applicable database of non-human primate and mangrove forest interactions. The results presented have broader implications for non-human primate and mangrove conservation and global actions to protect both. Additionally, our results raise questions about the idea that non-human primates primarily use mangrove forests as a refuge from human encroachment and habitat degradation

Evaluation of an oral vaccination program to control raccoon rabies in a suburbanized landscape

We evaluated the efficacy of an oral rabies vaccination (ORV) program conducted in Erie County, New York, from July through September, 2002–2005. Ingress of the raccoon (Procyon lotor) rabies variant first occurred along the southern border of Erie County, New York, during 1992 and began to spread northward at a velocity of 31 km/year. Fixed-wing aircraft dropped ORV baits in rural landscapes; helicopters, hand baiting, and bait stations distributed baits in suburban landscapes (&#;x bait densities ranged 59–118 baits/km2). Our study objectives were to quantify rabies case densities, evaluate efficacy of intervention efforts, and determine biological, census, geographical, and weather variables potentially affecting oralrabies vaccination of raccoons in Erie County. Overall, 16% and 9% of the raccoons in Erie County tested positive for virus-neutralizing antibodies (VNA) at the 0.125 and 0.5 international units (IU)/ml levels, respectively. We found no differences between baiting strategies and frequencies of antibody-positive raccoons. However, adult males generally consumed baits most often, and the probability of seropositivity increased with raccoon age. Seroprevalence of VNA differed among raccoon sex and age classes, and vaccination year. A post-hoc kernel density estimation of rabies-positive raccoons and skunks (Mephitis mephitis) from 1992– 2006 (n = 364) revealed clustering in northeastern Erie County. Our results should help ORV managers maximize limited resources

Logistic regression parameters for Japanese knotweed and mugwort.

<p>The parameters b and b* are the regression and standardized regression coefficients <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0001635#pone.0001635-Menard1" target="_blank">[30]</a>, respectively, and |b*| is the absolute value of the standardized regression coefficient.</p><p>Variables with a dagger (†) are log₁₀ transformed.</p

Spatial clustering of invaded counties throughout the invasion history.

<p>Join count z-score test statistic values at each decadal interval since initial introduction for the contiguous US (A,D), and east (B,E) and west (C,F) of the 90^th meridian for Japanese knotweed (left column) and mugwort (right column). The bold line (1,1) represents adjoining counties both with a Japanese knotweed or mugwort record, the solid line (0,1) represents adjoining counties where one county has a weed record and the other does not, and the dashed line (0,0) represents adjoining counties where neither contain a weed record. Horizontal red bars show positive and negative Z-score thresholds at <i>P</i> = 0.05.</p

Habitat suitability of Japanese knotweed.

<p>Model predictions of habitat suitability based on the environmental and anthropogenic factors in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0001635#pone-0001635-t001" target="_blank">Table 1</a>.</p