Recent spatial gene expression technologies enable comprehensive measurement of transcriptomic profiles while retaining spatial context. However, existing analysis methods do not address the limited ...resolution of the technology or use the spatial information efficiently. Here, we introduce BayesSpace, a fully Bayesian statistical method that uses the information from spatial neighborhoods for resolution enhancement of spatial transcriptomic data and for clustering analysis. We benchmark BayesSpace against current methods for spatial and non-spatial clustering and show that it improves identification of distinct intra-tissue transcriptional profiles from samples of the brain, melanoma, invasive ductal carcinoma and ovarian adenocarcinoma. Using immunohistochemistry and an in silico dataset constructed from scRNA-seq data, we show that BayesSpace resolves tissue structure that is not detectable at the original resolution and identifies transcriptional heterogeneity inaccessible to histological analysis. Our results illustrate BayesSpace's utility in facilitating the discovery of biological insights from spatial transcriptomic datasets.
Full text
Available for:
GEOZS, IJS, IMTLJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBMB, UL, UM, UPUK, ZAGLJ
This paper summarizes a strategy for supplying ecosystem services in urban areas through a participatory planning process targeting multifunctional green infrastructure. We draw from the literature ...on landscape multifunctionality, which has primarily been applied to agricultural settings, and propose opportunities to develop urban green infrastructure that could contribute to the sustainable social and ecological health of the city. Thinking in terms of system resilience, strategies might focus on the potential for green infrastructure to allow for adaptation and even transformation in the face of future challenges such as climate change, food insecurity, and limited resources. Because planning for multiple functions can be difficult when many diverse stakeholders are involved, we explored decision support tools that could be applied to green infrastructure planning in the early stages, to engage the public and encourage action toward implementing a preferred solution. Several specific ecosystem services that could be relevant for evaluating current and future urban green spaces include: plant biodiversity, food production, microclimate control, soil infiltration, carbon sequestration, visual quality, recreation, and social capital. Integrating such ecosystem services into small-scale greening projects could allow for creativity and local empowerment that would inspire broader transformation of green infrastructure at the city level. Those cities committing to such an approach by supporting greening projects are likely to benefit in the long run through the value of ecosystem services for urban residents and the broader public.
Full text
Available for:
EMUNI, NUK, SBMB, SBNM, UL, UPUK
► Extraction of urban agriculture sites from Google Earth images is highly accurate. ► Urban agriculture is an extensive land use type in Chicago. ► Much of the production area has been previously ...undocumented. ► A small percentage of Chicago sites reported to be community gardens produce food. ► Home gardens constitute the majority of existing food production area in Chicago.
Although always a part of city life, urban agriculture has recently attracted increased attention from diverse groups in the United States, which promote it as a strategy for stimulating economic development, increasing food security and access, and combatting obesity and diabetes, among other goals. Developing effective policies and programs at the city or neighborhood level demands as a first step the accurate mapping of existing urban agriculture sites. Mapping efforts in major U.S. cities have been limited in their focus and methodology. Focusing on public sites of food production, such as community gardens, they have overlooked the actual and potential contribution of private spaces, including home food gardens, to local food systems. This paper describes a case study of urban agriculture in Chicago which used the manual analysis of high-resolution aerial images in Google Earth in conjunction with ArcGIS to identify and map public and private spaces of food production. The resulting spatial dataset demonstrates that urban agriculture is an extensive land use type with wide variations in the distribution of sites across the city. Only 13% of sites reported to be community gardening projects by nongovernment organizations and government agencies were determined, through image analysis, to be sites of food production. The production area of home gardens identified by the study is almost threefold that of community gardens. Study results suggest opportunities may exist for scaling up existing production networks—including home food gardens—and enhancing community food sovereignty by leveraging local knowledges of urban agriculture.
Full text
Available for:
GEOZS, IJS, IMTLJ, KILJ, KISLJ, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UL, UM, UPCLJ, UPUK
Occupant behavior is one of the major factors influencing building energy consumption and contributing to uncertainty in building energy use prediction and simulation. Currently the understanding of ...occupant behavior is insufficient both in building design, operation and retrofit, leading to incorrect simplifications in modeling and analysis. This paper introduced the most recent advances and current obstacles in modeling occupant behavior and quantifying its impact on building energy use. The major themes include advancements in data collection techniques, analytical and modeling methods, and simulation applications which provide insights into behavior energy savings potential and impact. There has been growing research and applications in this field, but significant challenges and opportunities still lie ahead.
Full text
Available for:
GEOZS, IJS, IMTLJ, KILJ, KISLJ, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UL, UM, UPCLJ, UPUK, ZRSKP
Targeting PP2A in cancer: Combination therapies Mazhar, Sahar; Taylor, Sarah E.; Sangodkar, Jaya ...
Biochimica et biophysica acta. Molecular cell research,
01/2019, Volume:
1866, Issue:
1
Journal Article
Peer reviewed
Open access
The serine/threonine phosphatase PP2A regulates a vast portion of the phosphoproteome including pathways involved in apoptosis, proliferation and DNA damage response and PP2A inactivation is a vital ...step in malignant transformation. Many groups have explored the therapeutic venue of combining PP2A reactivation with kinase inhibition to counteract the very changes in tumor suppressors and oncogenes that lead to cancer development. Conversely, inhibition of PP2A to complement chemotherapy and radiation-induced cancer cell death is also an area of active investigation. Here we review the studies that utilize PP2A targeted agents as combination therapy in cancer. A potential role for PP2A in tumor immunity is also highlighted.
•PP2A is a tumor suppressor that negatively regulates numerous proliferative and survival pathways.•PP2A reactivation in combination with oncogenic kinase inhibition harbors therapeutic potential.•PP2A inhibition has also been shown to have tumoricidal effects, particularly when combined with DNA damaging agents.
Full text
Available for:
GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
Tourism development is a key feature of the neoliberal economic development model. Through a mix of state and private investment, Indigenous communities in Mexico are encouraged to transform local ...cultural and environmental resources into tourist consumption sites. The process results in a shift toward reliance on tourism, in place of farming, leaving households with few alternative earning strategies amidst fluctuating tourist arrivals and income, confounding the relationship between tourism and sustainability and questioning the utility of tourism as a sustainable tool for development. This article analyses a community-based Indigenous tourism project in a rural Maya village in Mexico's Yucatan, and discusses strategies employed at household level to navigate the arrival of tourism. Funding agencies assessed this project based on a triple bottom line metric that accounts for ecological health, financial sustainability, and its relationship to local social capital; however, these fail to account for differences between local and non-local conceptions of authenticity, indigeneity, and success. From a social perspective, the project has exacerbated existing tensions and has arguably widened the gap between the politically and economically powerful and less powerful, marginalized families in the community. Questions about policy, governance systems, and elite domination and kin group control are raised.
Full text
Available for:
BFBNIB, NUK, PILJ, SAZU, UL, UM, UPUK
Regeneration of human cartilage is inherently inefficient; an abundant autologous source, such as human induced pluripotent stem cells (hiPSCs), is therefore attractive for engineering cartilage. We ...report a growth factor‐based protocol for differentiating hiPSCs into articular‐like chondrocytes (hiChondrocytes) within 2 weeks, with an overall efficiency >90%. The hiChondrocytes are stable and comparable to adult articular chondrocytes in global gene expression, extracellular matrix production, and ability to generate cartilage tissue in vitro and in immune‐deficient mice. Molecular characterization identified an early SRY (sex‐determining region Y) box (Sox)9low cluster of differentiation (CD)44lowCD140low prechondrogenic population during hiPSC differentiation. In addition, 2 distinct Sox9‐regulated gene networks were identified in the Sox9low and Sox9high populations providing novel molecular insights into chondrogenic fate commitment and differentiation. Our findings present a favorable method for generating hiPSC‐derived articular‐like chondrocytes. The hiChondrocytes are an attractive cell source for cartilage engineering because of their abundance, autologous nature, and potential to generate articular‐like cartilage rather than fibrocartilage. In addition, hiChondrocytes can be excellent tools for modeling human musculoskeletal diseases in a dish and for rapid drug screening.—Lee, J., Taylor, S. E. B., Smeriglio, P., Lai, J., Maloney, W. J., Yang, F., Bhutani, N. Early induction of a prechondrogenic population allows efficient generation of stable chondrocytes from human induced pluripotent stem cells. FASEB J. 29, 3399‐3410 (2015). www.fasebj.org
Full text
Available for:
BFBNIB, FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SAZU, SBCE, SBMB, UL, UM, UPUK
Human milk provides not only ideal nutrition for infant development but also immunologic factors to protect from infection and inflammation. For the newborn preterm infant, the natural delivery of ...milk is not attainable, and instead pumped maternal milk, donor human milk, and human milk fortification are mainstays of clinical care. Current research demonstrates a decreased risk of necrotizing enterocolitis with maternal milk and donor human milk when individually compared to formula and with a complete human milk diet of maternal milk supplemented with donor human milk. The incidence of severe retinopathy of prematurity is decreased with an exclusive human milk diet, and this decrease is more pronounced with human milk-based compared to bovine milk-based human milk fortifier. The incidence of other morbidities such as late-onset sepsis and bronchopulmonary dysplasia is decreased with higher dose of human milk though significant differences are not apparent in exclusive human milk diet studies.
Full text
Available for:
GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
Abstract
Small pelagic fisheries provide food security, livelihood support and economic stability for East African coastal communities—a region of least developed countries. Using remotely- sensed ...and field observations together with modelling, we address the biophysical drivers of this important resource. We show that annual variations of fisheries yield parallel those of chlorophyll-a (an index of phytoplankton biomass). While enhanced phytoplankton biomass during the Northeast monsoon is triggered by wind-driven upwelling, during the Southeast monsoon, it is driven by two current induced mechanisms: coastal “dynamic uplift” upwelling; and westward advection of nutrients. This biological response to the Southeast monsoon is greater than that to the Northeast monsoon. For years unaffected by strong
El-Niño
/
La-Niña
events, the Southeast monsoon wind strength over the south tropical Indian Ocean is the main driver of year-to-year variability. This has important implications for the predictability of fisheries yield, its response to climate change, policy and resource management.
Full text
Available for:
IZUM, KILJ, NUK, PILJ, PNG, SAZU, UL, UM, UPUK
PDF
