Infiltrating lymphocytes and human papillomavirus‐16–associated oropharyngeal cancer

Objectives/Hypothesis: Human papillomavirus‐16 (HPV‐16)–associated carcinoma of the oropharynx has a favorable prognosis. Such patients have elevated CD8+ T‐lymphocyte levels that correlate with response to chemotherapy and survival. Tumor‐infiltrating lymphocyte (TIL) subpopulations were assessed in pretreatment biopsies from a prospective patient cohort to determine if TIL subsets differed by HPV status, clinical factors, or patient outcome or correlated with peripheral blood T‐cell levels. Study Design: Retrospective immunological correlative study of patients entered in a prospective Phase 2 clinical trial. Methods: Measured were CD8, CD4, CD68, and Treg (FoxP3) lymphocytes by immunohistochemistry in a tissue microarray created from patients (n = 46) with advanced oropharyngeal cancer. Correlations with peripheral blood levels, HPV status, expression of epidermal growth factor receptor (EGFR), clinical tumor, and patient characteristics and outcome were determined. Median follow‐up was 6.6 years. Results: HPV‐16–positive patients had improved survival ( P = .016). Degree of T‐cell infiltration did not differ by HPV status but was significantly related to disease‐specific survival (DSS) and overall survival (OS). Even after adjusting for HPV status, we found that CD8, FoxP3, and total T cells were significantly associated with DSS ( P = .0236, P = .0040, and P = .0197, respectively) and OS ( P = .0137, P = .0158, and P = .0115, respectively). Less T‐cell infiltration ( P = .0130) and CD4 cells in particular ( P = .0792) were associated with higher EGFR expression. Conclusions: Improved outcomes are associated with increased TILs independent of HPV status and suggest the local immune response may be more related to factors such as tumor size, EGFR expression, or performance status than HPV status. Further study of larger numbers of patients and infiltrates combined with functional analysis of individual subsets may be necessary to detect significant differences in local immunity in HPV‐16–related cancers.Laryngoscope, 122:121–127, 2012Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/89454/1/22133_ftp.pd

TRY plant trait database - enhanced coverage and open access

Plant traits-the morphological, anatomical, physiological, biochemical and phenological characteristics of plants-determine how plants respond to environmental factors, affect other trophic levels, and influence ecosystem properties and their benefits and detriments to people. Plant trait data thus represent the basis for a vast area of research spanning from evolutionary biology, community and functional ecology, to biodiversity conservation, ecosystem and landscape management, restoration, biogeography and earth system modelling. Since its foundation in 2007, the TRY database of plant traits has grown continuously. It now provides unprecedented data coverage under an open access data policy and is the main plant trait database used by the research community worldwide. Increasingly, the TRY database also supports new frontiers of trait-based plant research, including the identification of data gaps and the subsequent mobilization or measurement of new data. To support this development, in this article we evaluate the extent of the trait data compiled in TRY and analyse emerging patterns of data coverage and representativeness. Best species coverage is achieved for categorical traits-almost complete coverage for 'plant growth form'. However, most traits relevant for ecology and vegetation modelling are characterized by continuous intraspecific variation and trait-environmental relationships. These traits have to be measured on individual plants in their respective environment. Despite unprecedented data coverage, we observe a humbling lack of completeness and representativeness of these continuous traits in many aspects. We, therefore, conclude that reducing data gaps and biases in the TRY database remains a key challenge and requires a coordinated approach to data mobilization and trait measurements. This can only be achieved in collaboration with other initiatives

A theory for ecological survey methods to map individual distributions

Spatially explicit approaches are widely recommended for ecosystem management. The quality of the data, such as presence/absence or habitat maps, affects the management actions recommended and is, therefore, key to management success. However, available data are often biased and incomplete. Previous studies have advanced ways to resolve data bias and missing data, but questions remain about how we design ecological surveys to develop a dataset through field surveys. Ecological surveys may have multiple spatial scales, including the spatial extent of the target ecosystem (observation window), the resolution for mapping individual distributions (mapping unit), and the survey area within each mapping unit (sampling unit). We developed an ecological survey method for mapping individual distributions by applying spatially explicit stochastic models. We used spatial point processes to describe individual spatial placements using either random or clustering processes. We then designed ecological surveys with different spatial scales and individual detectability. We found that the choice of mapping unit affected the presence mapped fraction, and the fraction of the total individuals covered by the presence mapped patches. Tradeoffs were found between these quantities and the map resolution, associated with equivalent asymptotic behaviors for both metrics at sufficiently small and large mapping unit scales. Our approach enabled consideration of the effect of multiple spatial scales in surveys, and estimation of the survey outcomes such as the presence mapped fraction and the number of individuals situated in the presence detected units. The developed theory may facilitate management decision-making and inform the design of monitoring and data gathering

TRY plant trait database - enhanced coverage and open access

Plant traits—the morphological, anatomical, physiological, biochemical and phenological characteristics of plants—determine how plants respond to environmental factors, affect other trophic levels, and influence ecosystem properties and their benefits and detriments to people. Plant trait data thus represent the basis for a vast area of research spanning from evolutionary biology, community and functional ecology, to biodiversity conservation, ecosystem and landscape management, restoration, biogeography and earth system modelling. Since its foundation in 2007, the TRY database of plant traits has grown continuously. It now provides unprecedented data coverage under an open access data policy and is the main plant trait database used by the research community worldwide. Increasingly, the TRY database also supports new frontiers of trait‐based plant research, including the identification of data gaps and the subsequent mobilization or measurement of new data. To support this development, in this article we evaluate the extent of the trait data compiled in TRY and analyse emerging patterns of data coverage and representativeness. Best species coverage is achieved for categorical traits—almost complete coverage for ‘plant growth form’. However, most traits relevant for ecology and vegetation modelling are characterized by continuous intraspecific variation and trait–environmental relationships. These traits have to be measured on individual plants in their respective environment. Despite unprecedented data coverage, we observe a humbling lack of completeness and representativeness of these continuous traits in many aspects. We, therefore, conclude that reducing data gaps and biases in the TRY database remains a key challenge and requires a coordinated approach to data mobilization and trait measurements. This can only be achieved in collaboration with other initiatives

Biocrust landscape-scale spatial distribution is strongly controlled by terrain attributes: Topographic thresholds for colonization in a semiarid badland system

Biological soil crust, or biocrust communities, are the dominating life form in many extreme habitats, such as arid and semiarid badlands, where water scarcity and highly erodible substrates limit vegetation cover. While climate, soil and biotic factors have been described as environmental filters influencing biocrust distribution in such biomes, little is known about the effect of terrain attributes on creating specific microhabitats that promote or restrict biocrust colonization. This study aimed to identify the main terrain attributes controlling biocrust distribution in the driest badland system in Europe, the Tabernas Badlands (SE Spain). To do this, we analysed the influence of different terrain attributes related to landscape stability and microclimate formation on the spatial distribution of lichen and cyanobacteria, using field measurements and topographical information from a LiDAR survey. Our results showed that the spatial distribution of cyanobacteria-dominated biocrusts, which are physiologically and morphologically adapted to extreme drought and high UVA radiation, was mostly associated with areas of high potential incoming solar radiation. The exception was bare south-aspect hillslopes with very high sediment transport potential, where bare physically crusted soils were the dominant ground cover. Lichen-dominated biocrusts, in contrast, colonized near the top of north-aspect hillslopes, characterized by low potential incoming solar radiation and potential evapotranspiration, and their cover decreased downstream, as conditions became good enough for vascular plants. © 2019 John Wiley & Sons, Ltd

Plant functional types and traits as biodiversity indicators for tropical forests: two biogeographically separated case studies including birds, mammals and termites

Multi-taxon surveys were conducted in species-rich, lowland palaeotropical and neotropical forested landscapes in Sumatra, Indonesia and Mato Grosso, Brazil. Gradient-directed transects (gradsects) were sampled across a range of forested land use mosaics, using a uniform protocol to simultaneously record vegetation (vascular plant species, plant functional types (PFTs) and vegetation structure), vertebrates (birds, mammals) and invertebrates (termites), in addition to measuring site and soil properties, including carbon stocks. At both sites similar correlations were detected between major components of structure (mean canopy height, woody basal area and litter depth) and the diversities of plant species and PFTs. A plant species to PFT ratio [spp.:PFTs] was the best overall predictor of animal diversity, especially termite species richness in Sumatra. To a notable extent vegetation structure also correlated with animal diversity. These surrogates demonstrate generic links between habitat structural elements, carbon stocks and biodiversity. They may also offer practical low-cost indicators for rapid assessment in tropical forest landscapes