Rescuing and Sharing Historical Vegetation Data for Ecological Analysis: The California Vegetation Type Mapping Project

Research efforts that synthesize historical and contemporary ecological data with modeling approaches improve our understanding of the complex response of species, communities, and landscapes to changing biophysical conditions through time and in space. Historical ecological data are particularly important in this respect. There are remaining barriers that limit such data synthesis, and technological improvements that make multiple diverse datasets more readily available for integration and synthesis are needed. This paper presents one case study of the Wieslander Vegetation Type Mapping project in California and highlights the importance of rescuing, digitizing and sharing historical datasets. We review the varied ecological uses of the historical collection: the vegetation maps have been used to understand legacies of land use change and plan for the future; the plot data have been used to examine changes to chaparral and forest communities around the state and to predict community structure and shifts under a changing climate; the photographs have been used to understand changing vegetation structure; and the voucher specimens in combination with other specimen collections have been used for large scale distribution modeling efforts. The digitization and sharing of the data via the web has broadened the scope and scale of the types of analysis performed. Yet, additional research avenues can be pursued using multiple types of VTM data, and by linking VTM data with contemporary data. The digital VTM collection is an example of a data infrastructure that expands the potential of large scale research through the integration and synthesis of data drawn from numerous data sources; its journey from analog to digital is a cautionary tale of the importance of finding historical data, digitizing it with best practices, linking it with other datasets, and sharing it with the research community

Small food stores and availability of nutritious foods: a comparison of database and in-store measures, Northern California, 2009.

IntroductionSmall food stores are prevalent in urban neighborhoods, but the availability of nutritious food at such stores is not well known. The objective of this study was to determine whether data from 3 sources would yield a single, homogenous, healthful food store category that can be used to accurately characterize community nutrition environments for public health research.MethodsWe conducted in-store surveys in 2009 on store type and the availability of nutritious food in a sample of nonchain food stores (n = 102) in 6 predominantly urban counties in Northern California (Alameda, Contra Costa, Marin, Sacramento, San Francisco, and Santa Clara). We compared survey results with commercial database information and neighborhood sociodemographic data by using independent sample t tests and classification and regression trees.ResultsSampled small food stores yielded a heterogeneous group of stores in terms of store type and nutritious food options. Most stores were identified as convenience (54%) or specialty stores (22%); others were small grocery stores (19%) and large grocery stores (5%). Convenience and specialty stores were smaller and carried fewer nutritious and fresh food items. The availability of nutritious food and produce was better in stores in neighborhoods that had a higher percentage of white residents and a lower population density but did not differ significantly by neighborhood income.ConclusionCommercial databases alone may not adequately categorize small food stores and the availability of nutritious foods. Alternative measures are needed to more accurately inform research and policies that seek to address disparities in diet-related health conditions

From the Field to the Cloud: A Review of Three Approaches to Sharing Historical Data From Field Stations Using Principles From Data Science

Historical data play an important role in our understanding of environmental change and ecosystem dynamics. By lengthening the temporal scale of scientific inquiry, historical data reveal insights into the dynamic nature of ecosystems. However, most historical data has yet to make a full contribution, remaining “dark” and out of reach to the broader scientific community. This article responds to several calls stressing the importance of empirical historical materials and urges their preservation and accessibility. Despite the importance of historical data collections, few standards have emerged to integrate historical dark data into the larger digital data landscape. To encourage greater use of historical data across scientific disciplines it is vital to make data findable, accessible, interoperable, and reusable (e.g., the FAIR principles). In this paper we discuss the potential of historical dark data to contribute to the modern digital ecological data landscape. We do this by focusing on three cases from the University of California field and research stations and the groups that have worked to make historical dark data discoverable. Despite the common goal of maximizing the potential use of these data collections, each case and the methods employed are unique, and showcase varying levels of success in achieving the FAIR principles and shepherding historical data into the twenty-first century

Obesity and the food environment: income and ethnicity differences among people with diabetes: the Diabetes Study of Northern California (DISTANCE).

ObjectiveIt is unknown whether any association between neighborhood food environment and obesity varies according to individual income and/or race/ethnicity. The objectives of this study were to test whether there was an association between food environments and obesity among adults with diabetes and whether this relationship differed according to individual income or race/ethnicity.Research design and methodsSubjects (n = 16,057) were participants in the Diabetes Study of Northern California survey. Kernel density estimation was used to create a food environment score for each individual's residence address that reflected the mix of healthful and unhealthful food vendors nearby. Logistic regression models estimated the association between the modeled food environment and obesity, controlling for confounders, and testing for interactions between food environment and race/ethnicity and income.ResultsThe authors found that more healthful food environments were associated with lower obesity in the highest income groups (incomes 301-600% and >600% of U.S. poverty line) among whites, Latinos, and Asians. The association was negative, but smaller and not statistically significant, among high-income blacks. On the contrary, a more healthful food environment was associated with higher obesity among participants in the lowest-income group (<100% poverty threshold), which was statistically significant for black participants in this income category.ConclusionsThese findings suggest that the availability of healthful food environments may have different health implications when financial resources are severely constrained

EXOESQUELETO NA ASSISTÊNCIA A MARCHA HUMANA

A marcha humana representa um indicador de qualidade de vida importante. O déficit de marcha é um dos desafios enfrentados pelos indivíduos afetados por qualquer transtorno neurológico, como lesão da medula espinhal, acidente vascular cerebral, entre outros. O treinamento de marcha para pacientes com distúrbios neurológicos é de grande interesse para os pesquisadores envolvidos no desenvolvimento de tecnologias assistivas, bem como para fisioterapeutas empenhados na reabilitação desses pacientes. Exoesqueletos já foram apresentados nos filmes de ficção científica como Alien, Matrix e Avatar. Este é um típico caso em que a vida imita o vídeo. Exoesqueletos como aqueles têm sido desenvolvidos pelas forças armadas para auxiliar em tarefas militares e agora estão sendo empregados na saúde. Há grande expectativa acerca dos benefícios desse tipo de dispositivo para obtenção da funcionalidade e independência de pessoas com dificuldades na marcha, bem como para compreensão dos comprometimentos clínicos e funcionais através da pesquisa. Entretanto, para a realidade brasileira, é uma tecnologia de custo elevado e disponível, no caso do Keeogo, apenas no Canadá. Já o Exo-H2 possui distribuidores na Espanha, Itália, Chile, Colômbia, Coreia e outros.Palavras-chave: Exoesqueleto energizado. Marcha. Reabilitação.

Assessing Threats and Conservation Status of Historical Centers of Oak Richness in California

Oak trees are emblematic of California landscapes, they serve as keystone cultural and ecological species and as indicators of natural biological diversity. As historically undeveloped landscapes are increasingly converted to urban environments, endemic oak woodland extent is reduced, which underscores the importance of strategic placement and reintroduction of oaks and woodland landscape for the maintenance of biodiversity and reduction of habitat fragmentation. This paper investigated the effects of human urban development on oak species in California by first modeling historical patterns of richness for eight oak tree species using historical map and plot data from the California Vegetation Type Mapping (VTM) collection. We then examined spatial intersections between hot spots of historical oak richness and modern urban and conservation lands and found that impacts from development and conservation vary by both species and richness. Our findings suggest that the impact of urban development on oaks has been small within the areas of highest oak richness but that areas of highest oak richness are also poorly conserved. Third, we argue that current policy measures are inadequate to conserve oak woodlands and suggest regions to prioritize acquisition of conservation lands as well as examine urban regions where historic centers of oak richness were lost as potential frontiers for oak reintroduction. We argue that urban planning could benefit from the adoption of historical data and modern species distribution modelling techniques primarily used in natural resources and conservation fields to better locate hot spots of species richness, understand where habitats and species have been lost historically and use this evidence as incentive to recover what was lost and preserve what still exists. This adoption of historical data and modern techniques would then serve as a paradigm shift in the way Urban Planners recognize, quantify, and use landscape history in modern built environments

Bartonella quintana Endocarditis in Dogs

TOC summary line: PCR and sequencing provide the first evidence that B. quintana can be pathogenic in dogs

Evaluating Tidal Marsh Sustainability in the Face of Sea-Level Rise: A Hybrid Modeling Approach Applied to San Francisco Bay

Tidal marshes will be threatened by increasing rates of sea-level rise (SLR) over the next century. Managers seek guidance on whether existing and restored marshes will be resilient under a range of potential future conditions, and on prioritizing marsh restoration and conservation activities.Building upon established models, we developed a hybrid approach that involves a mechanistic treatment of marsh accretion dynamics and incorporates spatial variation at a scale relevant for conservation and restoration decision-making. We applied this model to San Francisco Bay, using best-available elevation data and estimates of sediment supply and organic matter accumulation developed for 15 Bay subregions. Accretion models were run over 100 years for 70 combinations of starting elevation, mineral sediment, organic matter, and SLR assumptions. Results were applied spatially to evaluate eight Bay-wide climate change scenarios.Model results indicated that under a high rate of SLR (1.65 m/century), short-term restoration of diked subtidal baylands to mid marsh elevations (-0.2 m MHHW) could be achieved over the next century with sediment concentrations greater than 200 mg/L. However, suspended sediment concentrations greater than 300 mg/L would be required for 100-year mid marsh sustainability (i.e., no elevation loss). Organic matter accumulation had minimal impacts on this threshold. Bay-wide projections of marsh habitat area varied substantially, depending primarily on SLR and sediment assumptions. Across all scenarios, however, the model projected a shift in the mix of intertidal habitats, with a loss of high marsh and gains in low marsh and mudflats.Results suggest a bleak prognosis for long-term natural tidal marsh sustainability under a high-SLR scenario. To minimize marsh loss, we recommend conserving adjacent uplands for marsh migration, redistributing dredged sediment to raise elevations, and concentrating restoration efforts in sediment-rich areas. To assist land managers, we developed a web-based decision support tool (www.prbo.org/sfbayslr)

Sustained expansion of NKT cells and antigen-specific T cells after injection of α-galactosyl-ceramide loaded mature dendritic cells in cancer patients

Natural killer T (NKT) cells are distinct glycolipid reactive innate lymphocytes that are implicated in the resistance to pathogens and tumors. Earlier attempts to mobilize NKT cells, specifically, in vivo in humans met with limited success. Here, we evaluated intravenous injection of monocyte-derived mature DCs that were loaded with a synthetic NKT cell ligand, α-galactosyl-ceramide (α-GalCer; KRN-7000) in five patients who had advanced cancer. Injection of α-GalCer–pulsed, but not unpulsed, dendritic cells (DCs) led to >100-fold expansion of several subsets of NKT cells in all patients; these could be detected for up to 6 mo after vaccination. NKT activation was associated with an increase in serum levels of interleukin-12 p40 and IFN-γ inducible protein-10. In addition, there was an increase in memory CD8(+) T cells specific for cytomegalovirus in vivo in response to α-GalCer–loaded DCs, but not unpulsed DCs. These data demonstrate the feasibility of sustained expansion of NKT cells in vivo in humans, including patients who have advanced cancer, and suggest that NKT activation might help to boost adaptive T cell immunity in vivo

Coastal and Inland Aquatic Data Products for the Hyperspectral Infrared Imager (HyspIRI)

The HyspIRI Aquatic Studies Group (HASG) has developed a conceptual list of data products for the HyspIRI mission to support aquatic remote sensing of coastal and inland waters. These data products were based on mission capabilities, characteristics, and expected performance. The topic of coastal and inland water remote sensing is very broad. Thus, this report focuses on aquatic data products to keep the scope of this document manageable. The HyspIRI mission requirements already include the global production of surface reflectance and temperature. Atmospheric correction and surface temperature algorithms, which are critical to aquatic remote sensing, are covered in other mission documents. Hence, these algorithms and their products were not evaluated in this report. In addition, terrestrial products (e.g., land use land cover, dune vegetation, and beach replenishment) were not considered. It is recognized that coastal studies are inherently interdisciplinary across aquatic and terrestrial disciplines. However, products supporting the latter are expected to already be evaluated by other components of the mission. The coastal and inland water data products that were identified by the HASG, covered six major environmental and ecological areas for scientific research and applications: wetlands, shoreline processes, the water surface, the water column, bathymetry and benthic cover types. Accordingly, each candidate product was evaluated for feasibility based on the HyspIRI mission characteristics and whether it was unique and relevant to the HyspIRI science objectives