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

Genomic Resources for Phylogenetics, Species Delimitation, and Geographic Localization of Neotropical Tree Species Cedrela odorata L. (Meliaceae)

Biodiversity loss is of global concern, and is due in part to deforestation and high consumer demand for wood and wood products. The neotropical tree species Cedrela odorata (“Spanish cedar” or “cedro”) is economically valuable for its wood and faces threats of overexploitation. Due to strong similarities in wood features across species, overlapping geographic distributions, and taxonomic uncertainty, other Cedrela species may be intentionally or mistakenly substituted for C. odorata in trade. This pressure is expected to make these species more vulnerable if current logging practices proceed unchecked. This dissertation focuses on the development of genomic resources for C. odorata and five closely allied species in the genus Cedrela. Each chapter describes how the implementation of genomic data can be used to better understand and protect this historically overexploited plant group. Chapter 2 presents a C. odorata leaf transcriptome, chloroplast genome, and a set of probes that can be used to enrich target regions (genes) of the nuclear genome for DNA sequence analysis. I demonstrated that these “target capture” probes efficiently sampled thousands of genes from C. odorata specimens (~ 7,900 genes at 10X depth), the four Cedrela species included (3,000-9,500 genes), closely related and endangered Swietenia mahagoni (Caribbean mahogany; 4,000 genes), and distantly related Guarea guidonia (muskwood; 750 genes) and Trichilia tuberculata (550 genes). This list of genes adds significantly to the available genomic resources for these species (most are currently represented by fewer than 20 genes), and makes a large contribution to genomic resources for the mahogany family (Meliaceae). In Chapter 3, I used the target capture probes to sample the genomes of 168 Cedrela trees representing six co-occurring species, with the goal of determining whether named species can be verified as distinct genetic entities based on robust genomic sampling. Of particular interest was the possibility that C. odorata may contain multiple genetic lineages that are morphologically similar or identical (i.e., cryptic species). I inferred the phylogenetic relationships among C. odorata and closely allied species with nuclear SNPs and chloroplast genomes. I found that C. odorata was clearly represented as two lineages: one in Mesoamerica, and one in South America that included allied species C. fissilis, C. nebulosa, and C. saltensis. I compared seven species delimitation schemes to current taxonomy (i.e., models combining individuals identified as distinct species under the same taxonomic name and/or separating previously grouped individuals). In all cases, species definitions showing simplified taxonomy (fewer species) were better representations of the data than current taxonomy. The best model supported: (i) the separation of Mesoamerican C. odorata sensu stricto and South American C. odorata into distinct taxa, and (ii) combining two previously described species (C. nebulosa and C. saltensis) with South American C. odorata into a single species. If these findings were adopted for Cedrela taxonomy, they would result in reduced taxonomic uncertainty in this genus, and would help streamline documentation of Cedrela in trade. In Chapter 4, I developed and tested a single nucleotide polymorphism (“SNP”) genotyping assay for geographic source validation of C. odorata, a critical need for law enforcement. I demonstrated that array SNPs and resulting genotypes accurately estimate C. odorata geographic origin at the scale of Central vs. South America, and that SNPs provided a median prediction error of 188.7 km from the true origin. This approach has promise for assigning geographic origin of C. odorata wood, and provides useful information for enforcing restrictions on the harvest and trade of C. odorata across its range in the Neotropics. Chapter 5 provides a review the major findings presented in this dissertation, and presents unresolved areas of research that may benefit from these genomic resources. For example, the presented data and methods may provide a starting point for future phylogenetic studies of Cedrela that consider the entire genus. The genomic depth obtained with the probe set should also be adequate to investigate the role of hybridization in the genus Cedrela

Accounts from developers of generic health state utility instruments explain why they produce different QALYs: a qualitative study

Purpose and setting: Despite the label generic health state utility instruments (HSUIs), empirical evidence shows that different HSUIs generate different estimates of Health-Related Quality of Life (HRQoL) in the same person. Once a HSUI is used to generate a QALY, the difference between HSUIs is often ignored, and decision-makers act as if \u27a QALY is a QALY is a QALY\u27. Complementing evidence that different generic HSUIs produce different empirical values, this study addresses an important gap by exploring how HSUIs differ, and processes that produced this difference. 15 developers of six generic HSUIs used for estimating the QOL component of QALYs: Quality of Well-Being (QWB) scale; 15 Dimension instrument (15D); Health Utilities Index (HUI); EuroQol EQ-5D; Short Form-6 Dimension (SF-6D), and the Assessment of Quality of Life (AQoL) were interviewed in 2012-2013. Principal findings: We identified key factors involved in shaping each instrument, and the rationale for similarities and differences across measures. While HSUIs have a common purpose, they are distinctly discrete constructs. Developers recalled complex developmental processes, grounded in unique histories, and these backgrounds help to explain different pathways taken at key decision points during the HSUI development. The basis for the HSUIs was commonly not equivalent conceptually: differently valued concepts and goals drove instrument design and development, according to each HSUI\u27s defined purpose. Developers drew from different sources of knowledge to develop their measure depending on their conceptualisation of HRQoL. Major conclusions/contribution to knowledge: We generated and analysed first-hand accounts of the development of the HSUIs to provide insight, beyond face value, about how and why such instruments differ. Findings enhance our understanding of why the six instruments developed the way they did, from the perspective of key developers of those instruments. Importantly, we provide additional, original explanation for why a QALY is not a QALY is not a QALY

Progress in Understanding the Toxicity of Gasoline and Diesel Engine Exhaust Emissions

To help guide heavy vehicle engine, fuel, and exhaust after-treatment technology development, the U.S. Department of Energy and the Lovelace Respiratory Research Institute are conducting research not addressed elsewhere on aspects of the toxicity of particulate engine emissions. Advances in these technologies that reduce diesel particulate mass emissions may result in changes in particle composition, and there is concern that the number of ultrafine (<0.1 micron) particles may increase. All present epidemiological and laboratory data on the toxicity of diesel emissions were derived from emissions of older-technology engines. New, short-term toxicity data are needed to make health-based choices among diesel technologies and to compare the toxicity of diesel emissions to those of other engine technologies. This research program has two facets: (1) development and use of short-term in vitro and in vivo toxicity assays for comparing the toxicities of gasoline and diesel exhaust emissions; and (2) determination of the disposition of inhaled ultrafine particles deposited in the lung. Responses of cultured cells, cultured lung slices, and rodent lungs to various types of particles were compared to develop an improved short-term toxicity screening capability. To date, chemical toxicity indicators of cultured human A549 cells and early inflammatory and cytotoxic indicators of rat lungs have given the best distinguishing capability. A study is now underway to determine the relative toxicities of exhaust samples from in-use diesel and gasoline engines. The samples are being collected under the direction of the National Renewable Energy Laboratory with support from DOE's Office of Heavy Vehicle Technologies. The ability to generate solid ultrafine particles and to trace their movement in the body as particles and soluble material was developed. Data from rodents suggest that ultrafine particles can move from the lung to the liver in particulate form. The quantitative disposition of inhaled ultrafine particles will be determined in rodents and nonhuman primates

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

Dataset for predicting the geographic origin of Spanish Cedar (Cedrela odorata L.) based on DNA variation

The legality of wood products in trade often depends on their geographic origin, creating a need for forensic tools that can verify claims of provenance for wood and wood products. Cedrela odorata L. or Spanish cedar is a target of illegal logging. We developed a 140 SNP Agena™ MassARRAY® assay for geographic assignment of C. odorata specimens to their origin. Hybridization capture, target enrichment, and short-read sequencing of 192 Cedrela specimens allowed us to identify 140 spatially informative SNPs that differentiate C. odorata specimens by latitude, temperature, and precipitation. These SNPs were validated using 356 Cedrela specimens from eight species, and genetic clusters from discriminant analysis of principal components corresponded roughly to species groups. We used random forest classification and the R package SPASIBA to perform discrete and continuous spatial assignment of C. odorata sensu stricto specimens and to evaluate classification error. In this supplementary directory, a reduced representation nuclear genome reference for C. odorata, a VCF file containing 144,083 high quality SNPs for C. odorata which may be used to further refine out SNP genotyping assay for geographic assignment or other purposes, 140 SNP primers used for the Agena™ MassARRAY®, 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.Keywords: Logging; Cedrela; Forensic biology; Plants; Mahogany--South America; Meliaceae; Spanish ceda