Grassland and breeding bird use of moist-soil wetlands managed for waterfowl

Many species of breeding birds are declining in the United States, and grassland birds are among those experiencing the steepest declines. One of the most widely accepted reasons for decreasing populations is habitat loss. For grassland birds in the midwestern United States during the spring and summer, a major concern is the loss of breeding habitat. Illinois has retained less than 1% of native prairie from the early 1800s due to the expansion of agriculture and urban development. Birds that historically relied on prairies for breeding must use alternate vegetative communities to fulfill their needs. Seasonally dewatered wetlands (e.g., moist-soil wetlands) provide vegetation structure similar to grasslands and may provide breeding habitat for birds during the summer when dewatered. I quantified avian use of dewatered moist-soil wetlands in the Illinois River Valley and used environmental variables to predict measures of avian density, avian conservation significance (ACS), nest density, and nest success. Nest densities were greater in grasslands (0.13 nests/ha, SE = 0.02) than in moist-soil wetlands (0.09 nests/ha, SE = 0.01), but habitat did not have a strong effect on avian density (grassland �� = 13.5 birds/ha, SE = 3.5; moist-soil wetland �� = 10.2 birds/ha, SE = 1.1) or ACS (grassland �� = 218.6, SE = 27.8; moist-soil wetland �� = 214.2, SE = 15.9). The percent cover of woody vegetation had a positive relationship with ACS, and the percent cover of forbs had a negative relationship with avian density. Sites that were disconnected from the river had greater avian conservation significance than partially connected sites. Wetland size and the proximity to the Illinois River were poor predictors of nest density. I observed many grassland birds using moist-soil wetlands, including nesting dickcissels (Spiza americana, a generalist-grassland nester) and grasshopper sparrows (Ammodramus savannarum, an obligate-grassland nester). I also observed the state endangered northern harrier (Circus cyaneus), common gallinule (Gallinula galaeta), and Forster's tern (Sterna forsteri) in moist-soil wetlands. Dewatered moist-soil wetlands provide useful breeding habitat for grassland birds, but wetlands that are partially connected to the Illinois River pose a risk to nesting birds if they are flooded during the breeding season. I recommend that moist-soil managers conduct a mid-season or late drawdown of wetlands that are at a high risk of flooding to avoid creating an ecological trap for breeding birds. In moist-soil wetlands that are disconnected from the Illinois River and less likely to flood, I recommend an early drawdown to allow moist-soil vegetation to grow and provide habitat for grassland birds

Comparison of species classification models of mass spectrometry data : kernel discriminant analysis vs. random forest : a case study of Afrormosia (Pericopsis elata (Harms) Meeuwen)

Rationale: The genus Pericopsis includes four tree species of which only Pericopsis elata (Harms) Meeuwen is of commercial interest. Enforcement officers might have difficulties discerning this CITES-listed species from some other tropical African timber species. Therefore, we tested several methods to separate and identify these species rapidly in order to enable customs officials to uncover illegal trade. In this study, two classification methods using Direct Analysis in Real Time (DART) ionization coupled with Time-of-Flight Mass Spectrometry (DART-TOFMS) data to discern between several species are presented. Methods: Metabolome profiles were collected using DART ionization coupled with TOFMS analysis of heartwood specimens of all four Pericopsis species and Haplormosia monophylla (Harms) Harms, Dalbergia melanoxylon Guill. & Perr. Harms, and Milicia excelsa (Welw.) C.C. Berg. In total, 95 specimens were analysed and the spectra evaluated. Kernel Discriminant Analysis (KDA) and Random Forest classification were used to discern the species. Results: DART-TOFMS spectra obtained from wood slivers and post-processing analysis using KDA and Random Forest classification separated Pericopsis elata from the other Pericopsis taxa and its lookalike timbers Haplormosia monophylla, Milicia excelsa, and Dalbergia melanoxylon. Only 50 ions were needed to achieve the highest accuracy. Conclusions: DART-TOFMS spectra of the taxa were reproducible and the results of the chemometric analysis provided comparable accuracy. Haplormosia monophylla was visually distinguished based on the heatmap and was excluded from further analysis. Both classification methods, KDA and Random Forest, were capable of distinguishing Pericopsis elata from the other Pericopsis taxa, Milicia excelsa, and Dalbergia melanoxylon, timbers that are commonly traded

Dataset for genomic resources for the neotropical tree genus Cedrela (Meliaceae) and its relatives

This dataset is available as supplement for a research article submitted in 2018 and accepted in 2019. Genomic resources for the Neotropical tree genus Cedrela (Meliaceae) and its relatives. By Kristen N. Finch, B.A.; F. Andrew Jones, Ph.D.; Richard Cronn, Ph.D. Tree species in the genus Cedrela are threatened by timber overexploitation across the Neotropics. Genetic identification of processed timber can be used to supplement wood anatomy to assist in the taxonomic and source validation of protected species and populations of Cedrela. However, few genetic resources exist that enable both species and source identification of Cedrela timber products. We developed several genomic resources including a leaf transcriptome, chloroplast genome, and diagnostic single nucleotide polymorphisms (SNPs) that may assist the classification of Cedrela specimens to species and geographic origin. In this supplementary directory, we share the assembled transcriptome reference, hybridization capture probe sequences, and the chloroplast genome reference for a single specimen, CEOD_NYBG (C. odorata from the living collection at the New York Botanical Garden). We also include: chloroplast genome sequences for each of the 43 specimens screened in our diversity panel (as separate files and as a combined file, aligned and unaligned), the VCF file containing SNPs for species and origin prediction for Cedrela, and data sets to replicate our statistical analysis using R. By sharing these resources, we hope to enable future research on this widespread Neotropical tree genus

Illinois Waterfowl Surveys and Investigations W-43-R-63 Annual Progress Report FY2016 Period: 1 July 2015 – 30 June 2016

Objectives 1) Inventory abundance and distribution of waterfowl and other waterbirds (a minimum of 10 species and guilds) during autumn migration at a minimum of 30 sites along the Illinois and central Mississippi rivers of Illinois, 2) Estimate waterfowl and other waterbird population sizes (a minimum of 10 species and guilds) during autumn migration using an aerial quadrat survey along the central Illinois River for comparison with aerial inventories (Objective 1), 3) Investigate the ecology of up to 50 gadwall and 50 American green-winged teal during spring migration in and near the central Illinois River valley of Illinois, 4) Determine breeding bird use of and nest density in a minimum of 10 moist-soil wetlands managed for waterfowl during summer in central Illinois, 5) Investigate the breeding ecology of a minimum of 50 sandhill cranes during spring and summer in northeastern Illinois consistent with an ongoing research project, 6) Investigate movements and home range size of a minimum of 10 Canada geese during winter in and near the Greater Chicago Metropolitan Area of Illinois, and 7) Determine habitat quality of a minimum of 100 wetlands and deepwater habitats during spring, summer, and early autumn for migrating dabbling ducks, breeding wetland birds, and migrating shorebirds in Illinois.Illinois Department of Natural Resources, Division of Wildlife & U.S. Fish and Wildlife Service Contract Number: RC09-13FWUIUCunpublishednot peer reviewedOpe

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

Data from: A set of plastid loci for use in multiplex fragment length genotyping for intraspecific variation in Pinus (Pinaceae)

Premise of the study: Recently released Pinus plastome sequences support characterization of 15 plastid Simple Sequence Repeat (ptSSR) loci originally published for P. contorta and P. thunbergii. This allows selection of loci for single-tube PCR multiplexed genotyping in any subsection of the genus. Methods: Unique placement of primers and primer conservation across the genus were investigated, and a set of six loci were selected for single-tube multiplexing. We compare interspecific variation between ptSSRs and nucleotide sequences of ycf1 then test intraspecific variation for ptSSRs using 911 samples in the P. ponderosa species complex. Results: The ptSSR loci contain mononucleotide and complex repeats with additional length variation in flanking regions. They are not located in hypervariable regions and most primers are conserved across the genus. A single PCR per sample multiplexed for six loci yielded 45 alleles in 911 samples. Discussion: The protocol allows efficient genotyping of many samples. The ptSSR loci are too variable for Pinus phylogenies but are useful for the study of genetic structure within and among populations. The multiplex method could easily be extended to other plant groups by choosing primers for ptSSR loci in a plastome alignment for the target group

A Set of Plastid Loci for Use in Multiplex Fragment Length Genotyping for Intraspecific Variation in <i>Pinus</i> (Pinaceae)

Premise of the study: Recently released Pinus plastome sequences support characterization of 15 plastid simple sequence repeat (cpSSR) loci originally published for P. contorta and P. thunbergii. This allows selection of loci for single-tube PCR multiplexed genotyping in any subsection of the genus. Methods: Unique placement of primers and primer conservation across the genus were investigated, and a set of six loci were selected for single-tube multiplexing. We compared interspecific variation between cpSSRs and nucleotide sequences ofycf1 and tested intraspecific variation for cpSSRs using 911 samples in the P. ponderosa species complex. Results: The cpSSR loci contain mononucleotide and complex repeats with additional length variation in flanking regions. They are not located in hypervariable regions, and most primers are conserved across the genus. A single PCR per sample multiplexed for six loci yielded 45 alleles in 911 samples. Discussion: The protocol allows efficient genotyping of many samples. The cpSSR loci are too variable for Pinus phylogenies but are useful for the study of genetic structure within and among populations. The multiplex method could easily be extended to other plant groups by choosing primers for cpSSR loci in a plastome alignment for the target group

Estimating the international burden of sport-related death : A review of data sources

Introduction Despite detailed recommendations for sports injury data capture provided since the mid-1990s, international data collection efforts for sport-related death remains limited in scope. The purpose of this paper was to review the data sources available for studying sport-related death and describe their key features, coverage, accessibility and strengths and limitations. Methods The outcomes of interest for this review was death occurring as a result of participation in organised sport-related activity. Data sources used to enumerate death in sport were identified, drawing from the authors’ knowledge/experience and review of key references from international organisations. The general purpose, case identification, structure, strengths and limitations of each source in relation to collection of data for sport-related death were summarised, drawing on examples from the international published literature to illustrate this application. Results Seven types of resources were identified for capturing deaths in sport. Data sources varied considerably in their ability to identify: participant status, sport relatedness of the death, types of sport-related deaths they capture, level of detail provided about the circumstances and medical care received. The most detailed sources were those that were dedicated to sports surveillance. Sport relatedness and type of sport may not be reliably captured by systems not dedicated to sports injury surveillance. Only one source permitted international comparisons and was limited to one sport (soccer). Conclusion Data on sport-related death are currently collected across a wide variety of data sources. This review highlights the need for robust, comprehensive approaches with standardised methodologies enabling linkage between sources and international comparisons