“New” cyanobacterial blooms are not new: two centuries of lake production are related to ice cover and land use

Recent cyanobacterial blooms in otherwise unproductive lakes may be warning signs of impending eutrophication in lakes important for recreation and drinking water, but little is known of their historical precedence or mechanisms of regulation. Here, we examined long-term sedimentary records of both general and taxon-specific trophic proxies from seven lakes of varying productivity in the northeastern United States to investigate their relationship to historical in-lake, watershed, and climatic drivers of trophic status. Analysis of fossil pigments (carotenoids and chlorophylls) revealed variable patterns of past primary production across lakes over two centuries despite broadly similar changes in regional climate and land use. Sediment abundance of the cyanobacterium Gloeotrichia, a large, toxic, nitrogen-fixing taxon common in recent blooms in this region, revealed that this was not a new taxon in the phytoplankton communities but rather had been present for centuries. Histories of Gloeotrichia abundance differed strikingly across lakes and were not consistently associated with most other sediment proxies of trophic status. Changes in ice cover most often coincided with changes in fossil pigments, and changes in watershed land use were often related to changes in Gloeotrichia abundance, although no single climatic or land-use factor was associated with proxy changes across all seven lakes. The degree to which changes in lake sediment records co-occurred with changes in the timing of ice-out or agricultural land use was negatively correlated with the ratio of watershed area to lake area. Thus, both climate and land management appeared to play key roles in regulation of primary production in these lakes, although the manner in which these factors influenced lakes was mediated by catchment morphometry. Improved understanding of the past interactions between climate change, land use, landscape setting, and water quality underscores the complexity of mechanisms regulating lake and cyanobacterial production and highlights the necessity of considering these interactions—rather than searching for a singular mechanism—when evaluating the causes of ongoing changes in low-nutrient lakes

Ecological homogenization of oil Properties in the American Residential Macrosystem

The conversion of native ecosystems to residential ecosystems dominated by lawns has been a prevailing land-use change in the United States over the past 70 years. Similar development patterns and management of residential ecosystems cause many characteristics of residential ecosystems to be more similar to each other across broad continental gradients than that of former native ecosystems. For instance, similar lawn management by irrigation and fertilizer applications has the potential to influence soil carbon (C) and nitrogen (N) pools and processes. We evaluated the mean and variability of total soil C and N stocks, potential net N mineralization and nitrification, soil nitrite (NO2−)/nitrate (NO3−) and ammonium (NH4+) pools, microbial biomass C and N content, microbial respiration, bulk density, soil pH, and moisture content in residential lawns and native ecosystems in six metropolitan areas across a broad climatic gradient in the United States: Baltimore, MD (BAL); Boston, MA (BOS); Los Angeles, CA (LAX); Miami, FL (MIA); Minneapolis–St. Paul, MN (MSP); and Phoenix, AZ (PHX). We observed evidence of higher N cycling in lawn soils, including significant increases in soil NO2−/NO3−, microbial N pools, and potential net nitrification, and significant decreases in NH4+ pools. Self-reported yard fertilizer application in the previous year was linked with increased NO2−/ NO3− content and decreases in total soil N and C content. Self-reported irrigation in the previous year was associated with decreases in potential net mineralization and potential net nitrification and with increases in bulk density and pH. Residential topsoil had higher total soil C than native topsoil, and microbial biomass C was markedly higher in residential topsoil in the two driest cities (LAX and PHX). Coefficients of variation for most biogeochemical metrics were higher in native soils than in residential soils across all cities, suggesting that residential development homogenizes soil properties and processes at the continental scale

Homogenization of Plant Diversity, Composition, and Structure in North American Urban Yards

Urban ecosystems are widely hypothesized to be more ecologically homogeneous than natural ecosystems. We argue that urban plant communities assemble from a complex mix of horticultural and regional species pools, and evaluate the homogenization hypothesis by comparing cultivated and spontaneously occurring urban vegetation to natural area vegetation across seven major U.S. cities. There was limited support for homogenization of urban diversity, as the cultivated and spontaneous yard flora had greater numbers of species than natural areas, and cultivated phylogenetic diversity was also greater. However, urban yards showed evidence of homogenization of composition and structure. Yards were compositionally more similar across regions than were natural areas, and tree density was less variable in yards than in comparable natural areas. This homogenization of biodiversity likely reflects similar horticultural source pools, homeowner preferences, and management practices across U.S. cities

Climate and lawn management interact to control C4 plant distribution in residential lawns across seven U.S. cities.

Author Posting. © Ecological Society of America, 2019. This article is posted here by permission of Ecological Society of America for personal use, not for redistribution. The definitive version was published in Trammell, T. L. E., Pataki, D. E., Still, C. J., Ehleringer, J. R., Avolio, M. L., Bettez, N., Cavender-Bares, J., Groffman, P. M., Grove, M., Hall, S. J., Heffernan, J., Hobbie, S. E., Larson, K. L., Morse, J. L., Neill, C., Nelson, K. C., O'Neil-Dunne, J., Pearse, W. D., Chowdhury, R. R., Steele, M., & Wheeler, M. M. Climate and lawn management interact to control C4 plant distribution in residential lawns across seven U.S. cities. Ecological Applications, 29(4), (2019): e01884, doi: 10.1002/eap.1884.In natural grasslands, C4 plant dominance increases with growing season temperatures and reflects distinct differences in plant growth rates and water use efficiencies of C3 vs. C4 photosynthetic pathways. However, in lawns, management decisions influence interactions between planted turfgrass and weed species, leading to some uncertainty about the degree of human vs. climatic controls on lawn species distributions. We measured herbaceous plant carbon isotope ratios (δ13C, index of C3/C4 relative abundance) and C4 cover in residential lawns across seven U.S. cities to determine how climate, lawn plant management, or interactions between climate and plant management influenced C4 lawn cover. We also calculated theoretical C4 carbon gain predicted by a plant physiological model as an index of expected C4 cover due to growing season climatic conditions in each city. Contrary to theoretical predictions, plant δ13C and C4 cover in urban lawns were more strongly related to mean annual temperature than to growing season temperature. Wintertime temperatures influenced the distribution of C4 lawn turf plants, contrary to natural ecosystems where growing season temperatures primarily drive C4 distributions. C4 cover in lawns was greatest in the three warmest cities, due to an interaction between climate and homeowner plant management (e.g., planting C4 turf species) in these cities. The proportion of C4 lawn species was similar to the proportion of C4 species in the regional grass flora. However, the majority of C4 species were nonnative turf grasses, and not of regional origin. While temperature was a strong control on lawn species composition across the United States, cities differed as to whether these patterns were driven by cultivated lawn grasses vs. weedy species. In some cities, biotic interactions with weedy plants appeared to dominate, while in other cities, C4 plants were predominantly imported and cultivated. Elevated CO2 and temperature in cities can influence C3/C4 competitive outcomes; however, this study provides evidence that climate and plant management dynamics influence biogeography and ecology of C3/C4 plants in lawns. Their differing water and nutrient use efficiency may have substantial impacts on carbon, water, energy, and nutrient budgets across cities.This research was funded by a series of collaborative grants from the U.S. National Science Foundation Macrosystems Biology Program (EF‐1065548, 1065737, 1065740, 1065741, 1065772, 1065785, 1065831, 121238320). The authors thank La'Shaye Ervin, William Borrowman, Moumita Kundu, and Barbara Uhl for field and laboratory assistance

Climate and Lawn Management Interact to Control C\u3csub\u3e4\u3c/sub\u3e Plant Distribution in Residential Lawns Across Seven U.S. Cities

In natural grasslands, C4 plant dominance increases with growing season temperatures and reflects distinct differences in plant growth rates and water use efficiencies of C3 vs. C4 photosynthetic pathways. However, in lawns, management decisions influence interactions between planted turfgrass and weed species, leading to some uncertainty about the degree of human vs. climatic controls on lawn species distributions. We measured herbaceous plant carbon isotope ratios (δ13C, index of C3/C4 relative abundance) and C4 cover in residential lawns across seven U.S. cities to determine how climate, lawn plant management, or interactions between climate and plant management influenced C4 lawn cover. We also calculated theoretical C4carbon gain predicted by a plant physiological model as an index of expected C4 cover due to growing season climatic conditions in each city. Contrary to theoretical predictions, plant δ13C and C4 cover in urban lawns were more strongly related to mean annual temperature than to growing season temperature. Wintertime temperatures influenced the distribution of C4 lawn turf plants, contrary to natural ecosystems where growing season temperatures primarily drive C4 distributions. C4 cover in lawns was greatest in the three warmest cities, due to an interaction between climate and homeowner plant management (e.g., planting C4 turf species) in these cities. The proportion of C4 lawn species was similar to the proportion of C4 species in the regional grass flora. However, the majority of C4 species were nonnative turf grasses, and not of regional origin. While temperature was a strong control on lawn species composition across the United States, cities differed as to whether these patterns were driven by cultivated lawn grasses vs. weedy species. In some cities, biotic interactions with weedy plants appeared to dominate, while in other cities, C4 plants were predominantly imported and cultivated. Elevated CO2 and temperature in cities can influence C3/C4competitive outcomes; however, this study provides evidence that climate and plant management dynamics influence biogeography and ecology of C3/C4plants in lawns. Their differing water and nutrient use efficiency may have substantial impacts on carbon, water, energy, and nutrient budgets across cities

Ecological homogenization of urban USA

Author Posting. © Ecological Society of America, 2014. This article is posted here by permission of Ecological Society of America for personal use, not for redistribution. The definitive version was published in Frontiers in Ecology and the Environment 12 (2014): 74-81, doi:10.1890/120374.A visually apparent but scientifically untested outcome of land-use change is homogenization across urban areas, where neighborhoods in different parts of the country have similar patterns of roads, residential lots, commercial areas, and aquatic features. We hypothesize that this homogenization extends to ecological structure and also to ecosystem functions such as carbon dynamics and microclimate, with continental-scale implications. Further, we suggest that understanding urban homogenization will provide the basis for understanding the impacts of urban land-use change from local to continental scales. Here, we show how multi-scale, multi-disciplinary datasets from six metropolitan areas that cover the major climatic regions of the US (Phoenix, AZ; Miami, FL; Baltimore, MD; Boston, MA; Minneapolis–St Paul, MN; and Los Angeles, CA) can be used to determine how household and neighborhood characteristics correlate with land-management practices, land-cover composition, and landscape structure and ecosystem functions at local, regional, and continental scales.We thank the MacroSystems Biology Program in the Emerging Frontiers Division of the Biological Sciences Directorate at NSF for support. The “Ecological Homogenization of Urban America” project was supported by a series of collaborative grants from this program (EF-1065548, 1065737, 1065740, 1065741, 1065772, 1065785, 1065831, 121238320). The work arose from research funded by grants from the NSF Long Term Ecological Research Program supporting work in Baltimore (DEB-0423476), Phoenix (BCS-1026865, DEB-0423704 and DEB-9714833), Plum Island (Boston) (OCE-1058747 and 1238212), Cedar Creek (Minneapolis–St Paul) (DEB-0620652), and Florida Coastal Everglades (Miami) (DBI-0620409)

Microduplications of 16p11.2 are associated with schizophrenia

Recurrent microdeletions and microduplications of a 600-kb genomic region of chromosome 16p11.2 have been implicated in childhood-onset developmental disorders1,2,3. We report the association of 16p11.2 microduplications with schizophrenia in two large cohorts. The microduplication was detected in 12/1,906 (0.63%) cases and 1/3,971 (0.03%) controls (P = 1.2 × 10−5, OR = 25.8) from the initial cohort, and in 9/2,645 (0.34%) cases and 1/2,420 (0.04%) controls (P = 0.022, OR = 8.3) of the replication cohort. The 16p11.2 microduplication was associated with a 14.5-fold increased risk of schizophrenia (95% CI (3.3, 62)) in the combined sample. A meta-analysis of datasets for multiple psychiatric disorders showed a significant association of the microduplication with schizophrenia (P = 4.8 × 10−7), bipolar disorder (P = 0.017) and autism (P = 1.9 × 10−7). In contrast, the reciprocal microdeletion was associated only with autism and developmental disorders (P = 2.3 × 10−13). Head circumference was larger in patients with the microdeletion than in patients with the microduplication (P = 0.0007)

Report on computational assessment of Tumor Infiltrating Lymphocytes from the International Immuno-Oncology Biomarker Working Group

Funder: U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI)Funder: National Center for Research Resources under award number 1 C06 RR12463-01, VA Merit Review Award IBX004121A from the United States Department of Veterans Affairs Biomedical Laboratory Research and Development Service, the DOD Prostate Cancer Idea Development Award (W81XWH-15-1-0558), the DOD Lung Cancer Investigator-Initiated Translational Research Award (W81XWH-18-1-0440), the DOD Peer Reviewed Cancer Research Program (W81XWH-16-1-0329), the Ohio Third Frontier Technology Validation Fund, the Wallace H. Coulter Foundation Program in the Department of Biomedical Engineering and the Clinical and Translational Science Award Program (CTSA) at Case Western Reserve University.Funder: Susan G Komen Foundation (CCR CCR18547966) and a Young Investigator Grant from the Breast Cancer Alliance.Funder: The Canadian Cancer SocietyFunder: Breast Cancer Research Foundation (BCRF), Grant No. 17-194Abstract: Assessment of tumor-infiltrating lymphocytes (TILs) is increasingly recognized as an integral part of the prognostic workflow in triple-negative (TNBC) and HER2-positive breast cancer, as well as many other solid tumors. This recognition has come about thanks to standardized visual reporting guidelines, which helped to reduce inter-reader variability. Now, there are ripe opportunities to employ computational methods that extract spatio-morphologic predictive features, enabling computer-aided diagnostics. We detail the benefits of computational TILs assessment, the readiness of TILs scoring for computational assessment, and outline considerations for overcoming key barriers to clinical translation in this arena. Specifically, we discuss: 1. ensuring computational workflows closely capture visual guidelines and standards; 2. challenges and thoughts standards for assessment of algorithms including training, preanalytical, analytical, and clinical validation; 3. perspectives on how to realize the potential of machine learning models and to overcome the perceptual and practical limits of visual scoring