A survival guide to Landsat preprocessing Young, Nicholas E.; Anderson, Ryan S.; Chignell, Stephen M. ...
Ecology,
April 2017, Letnik:
98, Številka:
4
Journal Article
Recenzirano
Odprti dostop
Landsat data are increasingly used for ecological monitoring and research. These data often require preprocessing prior to analysis to account for sensor, solar, atmospheric, and topographic effects. ...However, ecologists using these data are faced with a literature containing inconsistent terminology, outdated methods, and a vast number of approaches with contradictory recommendations. These issues can, at best, make determining the correct preprocessing workflow a difficult and time-consuming task and, at worst, lead to erroneous results. We address these problems by providing a concise overview of the Landsat missions and sensors and by clarifying frequently conflated terms and methods. Preprocessing steps commonly applied to Landsat data are differentiated and explained, including georeferencing and co-registration, conversion to radiance, solar correction, atmospheric correction, topographic correction, and relative correction. We then synthesize this information by presenting workflows and a decision tree for determining the appropriate level of imagery preprocessing given an ecological research question, while emphasizing the need to tailor each workflow to the study site and question at hand. We recommend a parsimonious approach to Landsat preprocessing that avoids unnecessary steps and recommend approaches and data products that are well tested, easily available, and sufficiently documented. Our focus is specific to ecological applications of Landsat data, yet many of the concepts and recommendations discussed are also appropriate for other disciplines and remote sensing platforms.
While inhibitors of BCL-2 family proteins (BH3 mimetics) have shown promise as anti-cancer agents, the various dependencies or co-dependencies of diverse cancers on BCL-2 genes remain poorly ...understood. Here we develop a drug screening approach to define the sensitivity of cancer cells from ten tissue types to all possible combinations of selective BCL-2, BCL-X
, and MCL-1 inhibitors and discover that most cell lines depend on at least one combination for survival. We demonstrate that expression levels of BCL-2 genes predict single mimetic sensitivity, whereas EMT status predicts synergistic dependence on BCL-X
+MCL-1. Lastly, we use a CRISPR/Cas9 screen to discover that BFL-1 and BCL-w promote resistance to all tested combinations of BCL-2, BCL-X
, and MCL-1 inhibitors. Together, these results provide a roadmap for rationally targeting BCL-2 family dependencies in diverse human cancers and motivate the development of selective BFL-1 and BCL-w inhibitors to overcome intrinsic resistance to BH3 mimetics.
Media coverage on coronavirus disease 2019 (COVID-19) has been extensive, yet large gaps remain in our understanding of the role of social media platforms during worldwide health crisis. The purpose ...of this study was to assess the most viewed YouTube videos on COVID-19 for medical content. We coded video characteristics, source, and medical content of the 113 most-widely viewed videos about COVID-19. Seventy-nine (69.9%) videos were classified as useful, and 10 (8.8%) videos were classified as misleading. Independent users were more likely to post misleading videos than useful videos (60.0% vs 21.5%, P = 0.009). News agencies were more likely to post useful videos than misleading videos (72.2% vs 40.0%, P = 0.039). Useful videos were more likely to present any information on prevalence or incidence (79.7% vs 20.0%, P < 0.001), as well as information on outcomes or prognosis (84.8% vs 30.0%, P < 0.001) compared to misleading videos. The World Health Organization contributed one useful video (1.3%), while no videos from the Center for Disease Control were included. Although YouTube generally is a useful source of medical information on the COVID-19 pandemic, increased efforts to disseminate accurate information from reputable sources is desired to help mitigate disease spread and decrease unnecessary panic in the general population.
Global estimates of forest aboveground biomass and carbon storage have major discrepancies linked to limitations in tree-level biomass estimates. Robust allometric equations can improve biomass ...estimates; however, destructive sampling to measure single-tree biomass is expensive, challenging, and prone to measurement error. We present a method to efficiently and non-destructively estimate single-tree biomass from terrestrial LiDAR scan data and test the approach on 21 destructively-sampled lodgepole pine (Pinus contorta) trees. The approach estimates branch and foliage volume using voxelization and estimates trunk volume using a method developed in this study called the Outer Hull Model (OHM). The OHM iteratively fits convex hulls, accurately handles noisy scan data, and fits the true shape of the trunk rather than forcing a cylindrical fit. Volume from the LiDAR scans is converted to biomass using density values from the literature and from field sampling to assess model sensitivity to density values. Whole-tree aboveground biomass estimates derived from the LiDAR scans were nearly unbiased and agreed strongly with destructive sampling data (R2=0.98, RMSE=20.4kg). Estimation of the trunk component biomass (R2=0.99, RMSE=12.3kg) was stronger than foliage and needle component estimates (R2=0.54, RMSE=21.4kg). The approach presented in this study accurately and non-destructively estimated the aboveground biomass of needleleaf trees with minimal user input. The promising performance on coniferous trees advances efficient sampling of single-tree biomass.
•A novel algorithm is presented to estimate individual tree biomass from TLS data.•The algorithm uses the shape of the tree rather than forcing a cylinder to fit.•TLS biomass estimates were validated with destructive sampling data.•Estimates of whole-tree and trunk biomass were accurate.•The method advances efficient single-tree biomass estimation, improving allometry.
Phenology, by controlling the seasonal activity of vegetation on the land surface, plays a fundamental role in regulating photosynthesis and other ecosystem processes, as well as competitive ...interactions and feedbacks to the climate system. We conducted an analysis to evaluate the representation of phenology, and the associated seasonality of ecosystem‐scale CO2 exchange, in 14 models participating in the North American Carbon Program Site Synthesis. Model predictions were evaluated using long‐term measurements (emphasizing the period 2000–2006) from 10 forested sites within the AmeriFlux and Fluxnet‐Canada networks. In deciduous forests, almost all models consistently predicted that the growing season started earlier, and ended later, than was actually observed; biases of 2 weeks or more were typical. For these sites, most models were also unable to explain more than a small fraction of the observed interannual variability in phenological transition dates. Finally, for deciduous forests, misrepresentation of the seasonal cycle resulted in over‐prediction of gross ecosystem photosynthesis by +160 ± 145 g C m−2 yr−1 during the spring transition period and +75 ± 130 g C m−2 yr−1 during the autumn transition period (13% and 8% annual productivity, respectively) compensating for the tendency of most models to under‐predict the magnitude of peak summertime photosynthetic rates. Models did a better job of predicting the seasonality of CO2 exchange for evergreen forests. These results highlight the need for improved understanding of the environmental controls on vegetation phenology and incorporation of this knowledge into better phenological models. Existing models are unlikely to predict future responses of phenology to climate change accurately and therefore will misrepresent the seasonality and interannual variability of key biosphere–atmosphere feedbacks and interactions in coupled global climate models.
•Body temperature fluctuations in ground squirrels demonstrate a large core temperature range during seasonal hibernation.•Proteins responsible for calcium handling in skeletal muscle are at their ...lowest annual level during hibernation.•Sarcolipin gene expression in thirteen-lined and Arctic ground squirrels shows pronounced decrease during torpor.•Sarcolipin protein levels in SR vesicles are significantly reduced during torpor compared to active (post-arousal) animals in April.•New model showing seasonal profile of non-shivering thermogenic capacity from skeletal muscle via sarcolipin and brown adipose tissue.
Hibernation in mammals is a whole-body phenotype that involves profound reductions in oxygen consumption, metabolic reactions, core body temperature, neural activity and heart rate. An important aspect of mammalian hibernation is the ability to reverse this state of hypothermic torpor by rewarming and subsequent arousal. Brown adipose tissue (BAT) and skeletal muscle shivering have been characterized as the predominant driving forces for thermogenesis during arousal. Conversely, the thermogenic contribution of these organs needs to be minimized as hibernating mammals enter torpor. Because skeletal muscle accounts for approximately 40% of the dry mass of the typical mammalian body, we aim to broaden the spotlight to include the importance of down-regulating skeletal muscle non-shivering thermogenesis during hibernation to allow for whole-body cooling and long-term maintenance of a depressed core body temperature when the animal is in torpor. This minireview will briefly describe the current understanding of thermoregulation in hibernating mammals and present new preliminary data on the importance of skeletal muscle and the micro-peptide sarcolipin as a major thermogenic target.
The translation of basic research into improved therapies for breast cancer patients requires relevant preclinical models that incorporate spontaneous metastasis. We have completed a functional and ...molecular characterisation of a new isogenic C57BL/6 mouse model of breast cancer metastasis, comparing and contrasting it with the established BALB/c 4T1 model. Metastatic EO771.LMB tumours were derived from poorly metastatic parental EO771 mammary tumours. Functional differences were evaluated using both in vitro assays and spontaneous metastasis assays in mice. Results were compared to non-metastatic 67NR and metastatic 4T1.2 tumours of the 4T1 model. Protein and transcript levels of markers of human breast cancer molecular subtypes were measured in the four tumour lines, as well as p53 (Tp53) tumour-suppressor gene status and responses to tamoxifen in vivo and in vitro. Array-based expression profiling of whole tumours identified genes and pathways that were deregulated in metastatic tumours. EO771.LMB cells metastasised spontaneously to lung in C57BL/6 mice and displayed increased invasive capacity compared with parental EO771. By immunohistochemical assessment, EO771 and EO771.LMB were basal-like, as was the 4T1.2 tumour, whereas 67NR had a luminal phenotype. Primary tumours from all lines were negative for progesterone receptor, Erb-b2/Neu and cytokeratin 5/6, but positive for epidermal growth factor receptor (EGFR). Only 67NR displayed nuclear estrogen receptor alpha (ERα) positivity. EO771 and EO771.LMB expressed mutant p53, whereas 67NR and 4T1.2 were p53-null. Integrated molecular analysis of both the EO771/EO771.LMB and 67NR/4T1.2 pairs indicated that upregulation of matrix metalloproteinase-3 (MMP-3), parathyroid hormone-like hormone (Pthlh) and S100 calcium binding protein A8 (S100a8) and downregulation of the thrombospondin receptor (Cd36) might be causally involved in metastatic dissemination of breast cancer.
Combinatorial inhibition of effector and feedback pathways is a promising treatment strategy for KRAS mutant cancers. However, the particular pathways that should be targeted to optimize therapeutic ...responses are unclear. Using CRISPR/Cas9, we systematically mapped the pathways whose inhibition cooperates with drugs targeting the KRAS effectors MEK, ERK, and PI3K. By performing 70 screens in models of KRAS mutant colorectal, lung, ovarian, and pancreas cancers, we uncovered universal and tissue-specific sensitizing combinations involving inhibitors of cell cycle, metabolism, growth signaling, chromatin regulation, and transcription. Furthermore, these screens revealed secondary genetic modifiers of sensitivity, yielding a SRC inhibitor-based combination therapy for KRAS/PIK3CA double-mutant colorectal cancers (CRCs) with clinical potential. Surprisingly, acquired resistance to combinations of growth signaling pathway inhibitors develops rapidly following treatment, but by targeting signaling feedback or apoptotic priming, it is possible to construct three-drug combinations that greatly delay its emergence.
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•Scalable CRISPR screening identifies combination therapies for KRAS-driven cancers•Identification of tissue-specific and secondary modifiers of sensitivity•Clinical promise of combined MAPK and SRC inhibition in KRAS/PIK3CA mutant CRC•Key strategies to control the rapid evolution of resistance to two-body combinations
Anderson et al. develop a screening approach to rapidly uncover potent and durable combination therapies in KRAS-driven cancers. This scalable approach can be applied to diverse cancer types for the discovery of potent treatment strategies. Furthermore, they describe rational methods to engineer higher-order therapies to control tumor evolution.
Abstract
MiR-21 was identified as a gene whose expression correlated with the extent of metastasis of murine mammary tumours. Since miR-21 is recognised as being associated with poor prognosis in ...cancer, we investigated its contribution to mammary tumour growth and metastasis in tumours with capacity for spontaneous metastasis. Unexpectedly, we found that suppression of miR-21 activity in highly metastatic tumours resulted in regression of primary tumour growth in immunocompetent mice but did not impede growth in immunocompromised mice. Analysis of the immune infiltrate of the primary tumours at the time when the tumours started to regress revealed an influx of both CD4
+
and CD8
+
activated T cells and a reduction in PD-L1
+
infiltrating monocytes, providing an explanation for the observed tumour regression. Loss of anti-tumour immune suppression caused by decreased miR-21 activity was confirmed by transcriptomic analysis of primary tumours. This analysis also revealed reduced expression of genes associated with cell cycle progression upon loss of miR-21 activity. A second activity of miR-21 was the promotion of metastasis as shown by the loss of metastatic capacity of miR-21 knockdown tumours established in immunocompromised mice, despite no impact on primary tumour growth. A proteomic analysis of tumour cells with altered miR-21 activity revealed deregulation of proteins known to be associated with tumour progression. The development of therapies targeting miR-21, possibly via targeted delivery to tumour cells, could be an effective therapy to combat primary tumour growth and suppress the development of metastatic disease.
An individual's spatial behavior is shaped by social and environmental factors and provides critical information about population processes to inform conservation and management actions. ...Heterogeneity in spatial overlap among conspecifics can be evaluated using estimates of home ranges and core areas and used to understand factors influencing space use and territoriality. To understand and test predictions about spatial behavior in an invasive large mammal, the wild pig (Sus scrofa), we examined variation in space use between sexes and seasons. We predicted that if animals were territorial that there would be a reduction in space-use overlap when comparing overlap of home ranges (HR-HR), to home ranges and core areas (HR-CA), and in-turn between core areas (CA-CA). Home ranges and core areas were estimated for 54 wild pigs at Buck Island Ranch, FL from GPS telemetry data. Overlap indices were calculated to estimate the strength (space-use overlap) and number of potential interactions within three wet seasons (June-October) and two dry seasons (December-April). Among sexes, home range size did not vary seasonally, and males exhibited larger home ranges compared to females (M = 10.36 ± 0.79 km
(± SE), F = 3.21 ± 0.16 km
). Strength of overlap varied by season with wild pig home ranges overlapping more during the dry season. Males interacted with a greater number of individuals of both sexes, compared to females, and exhibited greater strength of overlap during the dry season. Consistent with our predictions, wild pigs appeared to exhibit territorial behavior, where strength of overlap decreased when comparing HR-HR to HR-CA and HR-CA to CA-CA. Our framework can be used to understand patterns of space use and territoriality in populations, which has important implications in understanding intraspecific interactions and population processes, such as how pathogens and parasites might spread within and among populations.
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