Most methods for modeling species distributions from occurrence records require additional data representing the range of environmental conditions in the modeled region. These data, called background ...or pseudo-absence data, are usually drawn at random from the entire region, whereas occurrence collection is often spatially biased toward easily accessed areas. Since the spatial bias generally results in environmental bias, the difference between occurrence collection and background sampling may lead to inaccurate models. To correct the estimation, we propose choosing background data with the same bias as occurrence data. We investigate theoretical and practical implications of this approach. Accurate information about spatial bias is usually lacking, so explicit biased sampling of background sites may not be possible. However, it is likely that an entire target group of species observed by similar methods will share similar bias. We therefore explore the use of all occurrences within a target group as biased background data. We compare model performance using target-group background and randomly sampled background on a comprehensive collection of data for 226 species from diverse regions of the world. We find that target-group background improves average performance for all the modeling methods we consider, with the choice of background data having as large an effect on predictive performance as the choice of modeling method. The performance improvement due to target-group background is greatest when there is strong bias in the target-group presence records. Our approach applies to regression-based modeling methods that have been adapted for use with occurrence data, such as generalized linear or additive models and boosted regression trees, and to Maxent, a probability density estimation method. We argue that increased awareness of the implications of spatial bias in surveys, and possible modeling remedies, will substantially improve predictions of species distributions.
MaxEnt is a program for modelling species distributions from presence-only species records. This paper is written for ecologists and describes the MaxEnt model from a statistical perspective, making ...explicit links between the structure of the model, decisions required in producing a modelled distribution, and knowledge about the species and the data that might affect those decisions. To begin we discuss the characteristics of presence-only data, highlighting implications for modelling distributions. We particularly focus on the problems of sample bias and lack of information on species prevalence. The keystone of the paper is a new statistical explanation of MaxEnt which shows that the model minimizes the relative entropy between two probability densities (one estimated from the presence data and one, from the landscape) defined in covariate space. For many users, this viewpoint is likely to be a more accessible way to understand the model than previous ones that rely on machine learning concepts. We then step through a detailed explanation of MaxEnt describing key components (e.g. covariates and features, and definition of the landscape extent), the mechanics of model fitting (e.g. feature selection, constraints and regularization) and outputs. Using case studies for a Banksia species native to south-west Australia and a riverine fish, we fit models and interpret them, exploring why certain choices affect the result and what this means. The fish example illustrates use of the model with vector data for linear river segments rather than raster (gridded) data. Appropriate treatments for survey bias, unprojected data, locally restricted species, and predicting to environments outside the range of the training data are demonstrated, and new capabilities discussed. Online appendices include additional details of the model and the mathematical links between previous explanations and this one, example code and data, and further information on the case studies.
While numerous studies have addressed changes in climate extremes, analyses of concurrence of climate extremes are scarce, and climate change effects on joint extremes are rarely considered. This ...study assesses the occurrence of joint (concurrent) monthly continental precipitation and temperature extremes in Climate Research Unit (CRU) and University of Delaware (UD) observations, and in 13 Coupled Model Intercomparison Project Phase 5 (CMIP5) global climate simulations. The joint occurrences of precipitation and temperature extremes simulated by CMIP5 climate models are compared with those derived from the CRU and UD observations for warm/wet, warm/dry, cold/wet, and cold/dry combinations of joint extremes. The number of occurrences of these four combinations during the second half of the 20th century (1951-2004) is assessed on a common global grid. CRU and UD observations show substantial increases in the occurrence of joint warm/dry and warm/wet combinations for the period 1978-2004 relative to 1951-1977. The results show that with respect to the sign of change in the concurrent extremes, the CMIP5 climate model simulations are in reasonable overall agreement with observations. However, the results reveal notable discrepancies between regional patterns and the magnitude of change in individual climate model simulations relative to the observations of precipitation and temperature.
High rates of mental illness among students and discontinuation with university studies are regularly reported. The current study sought to explore relationships between motivation, university ...adaptation and indicators of mental health and well-being and academic performance of 184 first-year university students (73% female, mean age = 19.3 years). As expected, intrinsic motivation was associated with greater subjective well-being, meaning in life and academic performance. Extrinsic motivations showed few relationships to outcome variables, while amotivation was consistently associated with poor outcomes. Hierarchical regression revealed that after accounting for adjustment, motivational orientations provided a small, though significant, contribution to the prediction of outcomes. These results are discussed in relation to Self-Determination Theory, the eudaimonic/hedonic dichotomy and implications for career counselling and teaching.
Clinical pharmacologists and toxicologists are often faced with predicting equivalent dosages for humans from biological observations in laboratory animals. Allometric scaling has been used ...extensively as the basis for extrapolation of drug dosage that might be expected to produce the equivalent biological effects. Allometry is the study of size and its consequences and it is based on the anatomical, physiological, and biochemical similarities between animals. In this review, retrospective analyses have been performed based on data reported in the literature in an attempt to determine the utility of allometric scaling for human dose projections from pre-clinical data for compounds that are delivered by inhalation. The limited pre-clinical efficacy data available on inhaled drugs that are also used clinically supports the current method of scaling using a fixed allometric exponent of 0.67. An example of the utility of the human inhaled dose projections for planning inhaled toxicology studies is also presented.
Adipose-resident T cells (ARTs) regulate metabolic and inflammatory responses in obesity, but ART activation signals are poorly understood. Here, we describe class II major histocompatibility complex ...(MHCII) as an important component of high-fat-diet (HFD)-induced obesity. Microarray analysis of primary adipocytes revealed that multiple genes involved in MHCII antigen processing and presentation increased in obese women. In mice, adipocyte MHCII increased within 2 weeks on HFD, paralleling increases in proinflammatory ART markers and decreases in anti-inflammatory ART markers, and preceding adipose tissue macrophage (ATM) accumulation and proinflammatory M1 polarization. Mouse 3T3-L1 and primary adipocytes activated T cells in an antigen-specific, contact-dependent manner, indicating that adipocyte MHCII is functional. HFD-fed MHCII−/− mice developed less adipose inflammation and insulin resistance than did wild-type mice, despite developing similar adiposity. These investigations uncover a mechanism whereby a HFD-induced adipocyte/ART dialog involving MHCII instigates adipose inflammation and, together with ATM MHCII, escalates its progression.
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► Obesity enhances MHCII expression in primary human and mouse adipocytes ► Adipocytes activate CD4+ ARTs via MHCII and leptin to induce adipose inflammation ► Macrophage changes in adipose follow adipocyte and T cell interactions during HFD ► Adaptive immune mechanisms are essential to obesity-induced adipose inflammation
Antitumoral immunity requires organized, spatially nuanced interactions between components of the immune tumor microenvironment (iTME). Understanding this coordinated behavior in effective versus ...ineffective tumor control will advance immunotherapies. We re-engineered co-detection by indexing (CODEX) for paraffin-embedded tissue microarrays, enabling simultaneous profiling of 140 tissue regions from 35 advanced-stage colorectal cancer (CRC) patients with 56 protein markers. We identified nine conserved, distinct cellular neighborhoods (CNs)—a collection of components characteristic of the CRC iTME. Enrichment of PD-1+CD4+ T cells only within a granulocyte CN positively correlated with survival in a high-risk patient subset. Coupling of tumor and immune CNs, fragmentation of T cell and macrophage CNs, and disruption of inter-CN communication was associated with inferior outcomes. This study provides a framework for interrogating how complex biological processes, such as antitumoral immunity, occur through concerted actions of cells and spatial domains.
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•FFPE-CODEX multiplexed tissue imaging of 56 markers in 140 tissues of 35 CRC patients•Cellular neighborhoods reveal spatial organization of the tumor microenvironment•Altered organization of tumor and immune components in low- versus high-risk patients•Local enrichment of PD-1+CD4+ T cells correlates with survival in high-risk patients
A multiplexed tissue imaging and computational analysis framework applied to colorectal cancer allows interrogation of how spatial organization of the immune tumor microenvironment is linked to clinical outcomes.
The Electric and Magnetic Field Instrument and Integrated Science (EMFISIS) investigation on the NASA Radiation Belt Storm Probes (now named the Van Allen Probes) mission provides key wave and very ...low frequency magnetic field measurements to understand radiation belt acceleration, loss, and transport. The key science objectives and the contribution that EMFISIS makes to providing measurements as well as theory and modeling are described. The key components of the instruments suite, both electronics and sensors, including key functional parameters, calibration, and performance, demonstrate that EMFISIS provides the needed measurements for the science of the RBSP mission. The EMFISIS operational modes and data products, along with online availability and data tools provide the radiation belt science community with one the most complete sets of data ever collected.
The megaphone effect refers to the fact that the web makes a mass audience potentially available to ordinary consumers. The article focuses on fashion bloggers who acquire an audience by iterated ...displays of aesthetic discrimination applied to the selection and combination of clothing. The authors offer a theoretical account of bloggers’ success in terms of the accumulation of cultural capital via public displays of taste and describe how the exercise of taste produces economic rewards and social capital for these bloggers. The article situates fashion blogging as one instance of a larger phenomenon that includes online reviews and user-generated content and extends to the consumption of food and home decor as well as clothing. In these instances of the megaphone effect, a select few ordinary consumers are able to acquire an audience without the institutional mediation historically required.
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