Species distribution models (SDMs) are widely used to explain and predict species ranges and environmental niches. They are most commonly constructed by inferring species' occurrence–environment ...relationships using statistical and machine-learning methods. The variety of methods that can be used to construct SDMs (e.g. generalized linear/additive models, tree-based models, maximum entropy, etc.), and the variety of ways that such models can be implemented, permits substantial flexibility in SDM complexity. Building models with an appropriate amount of complexity for the study objectives is critical for robust inference. We characterize complexity as the shape of the inferred occurrence–environment relationships and the number of parameters used to describe them, and search for insights into whether additional complexity is informative or superfluous. By building ‘under fit’ models, having insufficient flexibility to describe observed occurrence–environment relationships, we risk misunderstanding the factors shaping species distributions. By building ‘over fit’ models, with excessive flexibility, we risk inadvertently ascribing pattern to noise or building opaque models. However, model selection can be challenging, especially when comparing models constructed under different modeling approaches. Here we argue for a more pragmatic approach: researchers should constrain the complexity of their models based on study objective, attributes of the data, and an understanding of how these interact with the underlying biological processes. We discuss guidelines for balancing under fitting with over fitting and consequently how complexity affects decisions made during model building. Although some generalities are possible, our discussion reflects differences in opinions that favor simpler versus more complex models. We conclude that combining insights from both simple and complex SDM building approaches best advances our knowledge of current and future species ranges.
It has long been suspected that the rate of mutation varies across the human genome at a large scale based on the divergence between humans and other species. However, it is now possible to directly ...investigate this question using the large number of de novo mutations (DNMs) that have been discovered in humans through the sequencing of trios. We investigate a number of questions pertaining to the distribution of mutations using more than 130,000 DNMs from three large datasets. We demonstrate that the amount and pattern of variation differs between datasets at the 1MB and 100KB scales probably as a consequence of differences in sequencing technology and processing. In particular, datasets show different patterns of correlation to genomic variables such as replication time. Never-the-less there are many commonalities between datasets, which likely represent true patterns. We show that there is variation in the mutation rate at the 100KB, 1MB and 10MB scale that cannot be explained by variation at smaller scales, however the level of this variation is modest at large scales-at the 1MB scale we infer that ~90% of regions have a mutation rate within 50% of the mean. Different types of mutation show similar levels of variation and appear to vary in concert which suggests the pattern of mutation is relatively constant across the genome. We demonstrate that variation in the mutation rate does not generate large-scale variation in GC-content, and hence that mutation bias does not maintain the isochore structure of the human genome. We find that genomic features explain less than 40% of the explainable variance in the rate of DNM. As expected the rate of divergence between species is correlated to the rate of DNM. However, the correlations are weaker than expected if all the variation in divergence was due to variation in the mutation rate. We provide evidence that this is due the effect of biased gene conversion on the probability that a mutation will become fixed. In contrast to divergence, we find that most of the variation in diversity can be explained by variation in the mutation rate. Finally, we show that the correlation between divergence and DNM density declines as increasingly divergent species are considered.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
The monthly Extended Reconstructed Sea Surface Temperature (ERSST) dataset, available on global 2° × 2° grids, has been revised herein to version 4 (v4) from v3b. Major revisions include updated and ...substantially more complete input data from the International Comprehensive Ocean–Atmosphere Data Set (ICOADS) release 2.5; revised empirical orthogonal teleconnections (EOTs) and EOT acceptance criterion; updated sea surface temperature (SST) quality control procedures; revised SST anomaly (SSTA) evaluation methods; updated bias adjustments of ship SSTs using the Hadley Centre Nighttime Marine Air Temperature dataset version 2 (HadNMAT2); and buoy SST bias adjustment not previously made in v3b.
Tests show that the impacts of the revisions to ship SST bias adjustment in ERSST.v4 are dominant among all revisions and updates. The effect is to make SST 0.1°–0.2°C cooler north of 30°S but 0.1°–0.2°C warmer south of 30°S in ERSST.v4 than in ERSST.v3b before 1940. In comparison with the Met Office SST product the Hadley Centre Sea Surface Temperature dataset, version 3 (HadSST3), the ship SST bias adjustment in ERSST.v4 is 0.1°–0.2°C cooler in the tropics but 0.1°–0.2°C warmer in the midlatitude oceans both before 1940 and from 1945 to 1970. Comparisons highlight differences in long-term SST trends and SSTA variations at decadal time scales among ERSST.v4, ERSST.v3b, HadSST3, and Centennial Observation-Based Estimates of SST version 2 (COBE-SST2), which is largely associated with the difference of bias adjustments in these SST products. The tests also show that, when compared with v3b, SSTAs in ERSST.v4 can substantially better represent the El Niño/La Niña behavior when observations are sparse before 1940. Comparisons indicate that SSTs in ERSST.v4 are as close to satellite-based observations as other similar SST analyses.
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BFBNIB, DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Observations of sea surface and land–near-surface merged temperature anomalies are used to monitor climate variations and to evaluate climate simulations; therefore, it is important to make analyses ...of these data as accurate as possible. Analysis uncertainty occurs because of data errors and incomplete sampling over the historical period. This manuscript documents recent improvements in NOAA’s merged global surface temperature anomaly analysis, monthly, in spatial 5° grid boxes. These improvements allow better analysis of temperatures throughout the record, with the greatest improvements in the late nineteenth century and since 1985. Improvements in the late nineteenth century are due to improved tuning of the analysis methods. Beginning in 1985, improvements are due to the inclusion of bias-adjusted satellite data. The old analysis (version 2) was documented in 2005, and this improved analysis is called version 3.
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BFBNIB, DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
The uncertainty in Extended Reconstructed SST (ERSST) version 4 (v4) is reassessed based upon 1) reconstruction uncertainties and 2) an extended exploration of parametric uncertainties. The ...reconstruction uncertainty (Ur
) results from using a truncated (130) set of empirical orthogonal teleconnection functions (EOTs), which yields an inevitable loss of information content, primarily at a local level. The Ur
is assessed based upon 32 ensemble ERSST.v4 analyses with the spatially complete monthly Optimum Interpolation SST product. The parametric uncertainty (Up
) results from using different parameter values in quality control, bias adjustments, and EOT definition etc. The Up
is assessed using a 1000-member ensemble ERSST.v4 analysis with different combinations of plausible settings of 24 identified internal parameter values. At the scale of an individual grid box, the SST uncertainty varies between 0.3° and 0.7°C and arises from both Ur
and Up
. On the global scale, the SST uncertainty is substantially smaller (0.03°–0.14°C) and predominantly arises from Up
. The SST uncertainties are greatest in periods and locales of data sparseness in the nineteenth century and relatively small after the 1950s. The global uncertainty estimates in ERSST.v4 are broadly consistent with independent estimates arising from the Hadley Centre SST dataset version 3 (HadSST3) and Centennial Observation-Based Estimates of SST version 2 (COBE-SST2). The uncertainty in the internal parameter values in quality control and bias adjustments can impact the SST trends in both the long-term (1901–2014) and “hiatus” (2000–14) periods.
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BFBNIB, DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Described herein is the parametric and structural uncertainty quantification for the monthly Extended Reconstructed Sea Surface Temperature (ERSST) version 4 (v4). A Monte Carlo ensemble approach was ...adopted to characterize parametric uncertainty, because initial experiments indicate the existence of significant nonlinear interactions. Globally, the resulting ensemble exhibits a wider uncertainty range before 1900, as well as an uncertainty maximum around World War II. Changes at smaller spatial scales in many regions, or for important features such as Niño-3.4 variability, are found to be dominated by particular parameter choices.
Substantial differences in parametric uncertainty estimates are found between ERSST.v4 and the independently derived Hadley Centre SST version 3 (HadSST3) product. The largest uncertainties are over the mid and high latitudes in ERSST.v4 but in the tropics in HadSST3. Overall, in comparison with HadSST3, ERSST.v4 has larger parametric uncertainties at smaller spatial and shorter time scales and smaller parametric uncertainties at longer time scales, which likely reflects the different sources of uncertainty quantified in the respective parametric analyses. ERSST.v4 exhibits a stronger globally averaged warming trend than HadSST3 during the period of 1910–2012, but with a smaller parametric uncertainty. These global-mean trend estimates and their uncertainties marginally overlap.
Several additional SST datasets are used to infer the structural uncertainty inherent in SST estimates. For the global mean, the structural uncertainty, estimated as the spread between available SST products, is more often than not larger than the parametric uncertainty in ERSST.v4. Neither parametric nor structural uncertainties call into question that on the global-mean level and centennial time scale, SSTs have warmed notably.
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BFBNIB, DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Human exposure to green space and vegetation is widely recognized to result in physical and mental health benefits; however, to date, the specific effects of tree cover, diversity, and species ...composition on student academic performance have not been investigated. We compiled standardized performance scores in Grades 3 and 6 for the collective student body in 387 schools across the Toronto District School Board (TDSB), and examined variation in relation to tree cover, tree diversity, and tree species composition based on comprehensive inventories of trees on school properties combined with aerial-photo-based assessments of tree cover. Analyses accounted for variation due to socioeconomic factors using the learning opportunity index (LOI), a regional composite index of external challenges to learning that incorporates income and other factors, such as students with English as a second language. As expected, LOI had the greatest influence on student academic performance; however, the proportion of tree cover, as distinct from other types of "green space" such as grass, was found to be a significant positive predictor of student performance, accounting for 13% of the variance explained in a statistical model predicting mean student performance assessments. The effects of tree cover and species composition were most pronounced in schools that showed the highest level of external challenges, suggesting the importance of urban forestry investments in these schools.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
B cells are important in the pathogenesis of many, and perhaps all, immune-mediated diseases. Each B cell expresses a single B cell receptor (BCR)
, and the diverse range of BCRs expressed by the ...total B cell population of an individual is termed the 'BCR repertoire'. Our understanding of the BCR repertoire in the context of immune-mediated diseases is incomplete, and defining this could provide new insights into pathogenesis and therapy. Here, we compared the BCR repertoire in systemic lupus erythematosus, anti-neutrophil cytoplasmic antibody (ANCA)-associated vasculitis, Crohn's disease, Behçet's disease, eosinophilic granulomatosis with polyangiitis, and immunoglobulin A (IgA) vasculitis by analysing BCR clonality, use of immunoglobulin heavy-chain variable region (IGHV) genes and-in particular-isotype use. An increase in clonality in systemic lupus erythematosus and Crohn's disease that was dominated by the IgA isotype, together with skewed use of the IGHV genes in these and other diseases, suggested a microbial contribution to pathogenesis. Different immunosuppressive treatments had specific and distinct effects on the repertoire; B cells that persisted after treatment with rituximab were predominately isotype-switched and clonally expanded, whereas the inverse was true for B cells that persisted after treatment with mycophenolate mofetil. Our comparative analysis of the BCR repertoire in immune-mediated disease reveals a complex B cell architecture, providing a platform for understanding pathological mechanisms and designing treatment strategies.
Epidemiology of Posttraumatic Osteoarthritis Thomas, Abbey C; Hubbard-Turner, Tricia; Wikstrom, Erik A ...
Journal of athletic training,
06/2017, Letnik:
52, Številka:
6
Journal Article
Recenzirano
Odprti dostop
Osteoarthritis is a leading cause of disability whose prevalence and incidence continue to increase. History of joint injury represents an important risk factor for posttraumatic osteoarthritis and ...is a significant contributor to the rapidly growing percentage of the population with osteoarthritis. This review will present the epidemiology associated with posttraumatic osteoarthritis, with particular emphasis on the knee and ankle joints. It is important to understand the effect of posttraumatic osteoarthritis on the population so that sufficient resources can be devoted to countering the disease and promoting optimal long-term health for patients after joint injury.
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