Grain transportation and consumption reshapes the α-HCH exposure picture of China

Socio-economic activities like food trade can increase the uncertainty of human risk of persistent organic pollutants (POPs). We compared the change in model predicted α-hexachlorocyclohexane (α-HCH) cancer risk (CR) with and without grain trade in mainland China. In scenario without grain logistics, α-HCH moved fast away from southern and southeastern China via northward atmospheric transport. However, the grain logistics from northeastern China delivers the α-HCH previously accumulated in northeastern sink back to densely populated areas in recent years, which enhance CR by >50 % in the southern seaboard of China. The northward movement of grain production center and recent grain deficiency in southern provinces induced by dietary pattern changes is identified as the major driving factors of the reversed transport of α-HCH. The finding highlights the potential of socio-economic activities that can otherwise offset the risk reduction effect of the geochemical cycle of POPs.

Estimation of aboveground biomass of senescence grassland in China's arid region using multi-source data

Aboveground Biomass (AGB) in the grassland senescence period is a key indicator for assessing grassland fire risk and autumnal pasture carrying capacity. Despite the advancement of remote sensing in rapid monitoring of AGB on a regional scale, accurately monitoring AGB during the senescence period in vast arid areas remains a major challenge. Using remote sensing, environmental data, and 356 samples of grassland senescence period AGB data, this study utilizes the Gram-Schmidt Pan Sharpening (GS) method, multivariate selection methods, and machine learning algorithms (RF, SVM, and BP_ANN) to construct a model for AGB during senescence grassland, and applies the optimal model to analyze spatio-temporal pattern changes in AGB from 2000 to 2021 in arid regions. The results indicate that the GS method effectively enhances the correlation between measured AGB and vegetation indices, reducing model error to some extent; The accuracy of grassland AGB inversion models based on a single vegetation index is low (0.03 ≤ |R| ≤ 0.63), while the RF model constructed with multiple variables selected by the Boruta algorithm is the optimal model for estimating AGB in arid regions during the senescence period (R2 = 0.71, RMSE = 519.74 kg/ha); In the span of 22 years, the annual average AGB in the senescence period of arid regions was 1413.85 kg/ha, with regions of higher AGB primarily located in the northeast and southwest of the study area. The area experiencing an increase in AGB during the senescence period (79.97 %) was significantly larger than that with decreased AGB (20.03 %).

Evaluating a mass balance model for soil trace metals using the historical data from the King's Kitchen Garden (Versailles, France)

The mass balance of reconstituted Cd, Cu, Pb and Zn fluxes from 1683 to 2021 was compared to the current levels of the soil used only for vegetable production in the King's Kitchen Garden in Versailles (France). This comparison was made on the basis of 4 scenarios of organic matter application in the 18th and 19th centuries and by an uncertainty analysis over the entire period. The topsoil contamination falls within that of French kitchen gardens. Modelling of past fluxes predicted the correct trend (an increase) and order of magnitude of the soil metal contents. It produced a relatively accurate evaluation of the Cu and Zn contents. The model underestimated the Pb contents by about 80%, revealing a large and unknown source of soil contamination by this metal. The calculation overestimated the current Cd levels by about 100%, probably due to various biases, for example on atmospheric fallout or the composition of organic amendments. This assessment shows that modelling the mass balance of trace metal fluxes can be used to predict the long-term trend in the levels of these elements in cultivated soils, providing the input data are chosen according to realistic scenarios.

Assessing the performance of QSP models: biology as the driver for validation

Validation of a quantitative model is a critical step in establishing confidence in the model's suitability for whatever analysis it was designed. While processes for validation are well-established in the statistical sciences, the field of quantitative systems pharmacology (QSP) has taken a more piecemeal approach to defining and demonstrating validation. Although classical statistical methods can be used in a QSP context, proper validation of a mechanistic systems model requires a more nuanced approach to what precisely is being validated, and what role said validation plays in the larger context of the analysis. In this review, we summarize current thoughts of QSP validation in the scientific community, contrast the aims of statistical validation from several contexts (including inference, pharmacometrics analysis, and machine learning) with the challenges faced in QSP analysis, and use examples from published QSP models to define different stages or levels of validation, any of which may be sufficient depending on the context at hand.

Formative-reflective scheme for the assessment of tourism destination competitiveness: an analysis of Italian municipalities

In this article, we propose a formative-reflective scheme for the assessment of Tourism Destination Competitiveness (TDC) based on a combined use of Partial Least Squares-Path Modelling (PLS-PM) and the method recently proposed by Fattore, Pelagatti, and Vittadini (FPV). TDC is conceived as a construct reflecting the tourism performance of a destination, and several determinants are considered, including endowed resources, created resources, and supporting factors. The proposed scheme is applied to a case study on 1575 Italian municipalities for which the Italian National Institute of Statistics released data on tourist flows. Our contribution is innovative for three aspects: (i) the consistency of the formative-reflective scheme for TDC assessment is discussed on a theoretical basis; (ii) an empirical comparison between PLS-PM and the FPV method is performed; (iii) data with higher granularity than most studies on TDC assessment are employed. Our findings highlight that endowed resources are the primary driver of TDC, followed by created resources and supporting factors, and emphasize that the best ranked destinations are big cities with a multifaceted tourism alongside sea and mountain destinations with cultural attractions.

Towards a comprehensive assessment of QSP models: what would it take?

Quantitative Systems Pharmacology (QSP) has emerged as a powerful ensemble of approaches aiming at developing integrated mathematical and computational models elucidating the complex interactions between pharmacology, physiology, and disease. As the field grows and matures its applications expand beyond the boundaries of research and development and slowly enter the decision making and regulatory arenas. However, widespread acceptance and eventual adoption of a new modeling approach requires assessment criteria and quantifiable metrics that establish credibility and increase confidence in model predictions. QSP aims to provide an integrated understanding of pathology in the context of therapeutic interventions. Because of its ambitious nature and the fact that QSP emerged in an uncoordinated manner as a result of activities distributed across organizations and academic institutions, high entropy characterizes the tools, methods, and computational methodologies and approaches used. The eventual acceptance of QSP model predictions as supporting material for an application to a regulatory agency will require that two key aspects are considered: (1) increase confidence in the QSP framework, which drives standardization and assessment; and (2) careful articulation of the expectations. Both rely heavily on our ability to rigorously and consistently assess QSP models. In this manuscript, we wish to discuss the meaning and purpose of such an assessment in the context of QSP model development and elaborate on the differentiating features of QSP that render such an endeavor challenging. We argue that QSP establishes a conceptual, integrative framework rather than a specific and well-defined computational methodology. QSP elicits the use of a wide variety of modeling and computational methodologies optimized with respect to specific applications and available data modalities, which exceed the data structures employed by chemometrics and PK/PD models. While the range of options fosters creativity and promises to substantially advance our ability to design pharmaceutical interventions rationally and optimally, our expectations of QSP models need to be clearly articulated and agreed on, with assessment emphasizing the scope of QSP studies rather than the methods used. Nevertheless, QSP should not be considered an independent approach, rather one of many in the broader continuum of computational models.

Spatiotemporal dynamics of grassland aboveground biomass and its driving factors in North China over the past 20 years

Although remote sensing has enabled rapid monitoring of grassland aboveground biomass (AGB) at a regional scale, it is still a difficult challenge to construct an accurate estimation model of grassland AGB in a vast region to support the AGB dynamics analysis over a long time series. In this study, extensive grassland AGB measurements (collected in North China during the grassland growing season of 2000-2019), MODIS data, and environmental factors (climate, topography and soil) were employed to construct the grassland AGB models using four machine learning algorithms (random forest, support vector machine, artificial neural network and extreme learning machine) combined with four variable selections. The spatial distributions of annual grassland AGB from 2000 to 2019 were simulated based on the optimal AGB model. The temporal change and future trend of AGB series from 2000 to 2019 were comprehensively analyzed by the slope model and Hurst exponent. The influences of natural and anthropogenic factors on grassland AGB dynamics were explored quantitatively using the Geodetector model. The results showed that (1) the random forest model constructed from the variables selected by the successive projections algorithm is the optimal grassland AGB model. (2) The 20-year average grassland AGB in North China showed an overall spatial distribution of being low in the central and western parts and high in the southeastern part. (3) The annual maximum grassland AGB in most regions (82.71%) showed an increasing trend during 2000-2019; and most of the grasslands with a decreasing trend of AGB were located in regions with low AGB values and arid climates. (4) The future trend of grassland AGB after the study period may be optimistic, as reflected by more grassland AGB was predicted to increase rather than decrease (70.38% vs. 29.62%). (5) The main driving factors of spatiotemporal dynamics of grassland AGB were precipitation, soil type, and livestock density; the interactive influence of two drivers on AGB showed mutual enhancement.

Learning in Medicine: The Importance of Statistical Thinking

In many fields, including medicine and biology, there has been in the last years an increasing diffusion and availability of complex data from different sources. Examples include biological experiments or data from health care providers. These data encompass information that can potentially enhance therapeutic advancement and constitute the core of modern system medicine. When analyzing these complex data, it is important to appropriately quantify uncertainty, avoiding using only algorithmic and automated approaches, which are not always appropriate. Improper application of algorithmic approaches, which ignore domain knowledge, could result in filling the literature with imprecise and/or misleading conclusions. In this chapter, we highlight the importance of statistical thinking when leveraging complex data and models to enhance science progress. In particular, we discuss the reproducibility and replicability issues, the importance of uncertainty quantification, and some common pitfalls in the analysis of big data.

A community effort to assess and improve computerized interpretation of 12-lead resting electrocardiogram

Computerized interpretation of electrocardiogram plays an important role in daily cardiovascular healthcare. However, inaccurate interpretations lead to misdiagnoses and delay proper treatments. In this work, we built a high-quality Chinese 12-lead resting electrocardiogram dataset with 15,357 records, and called for a community effort to improve the performances of CIE through the China ECG AI Contest 2019. This dataset covers most types of ECG interpretations, including the normal type, 8 common abnormal types, and the other type which includes both uncommon abnormal and noise signals. Based on the Contest, we systematically assessed and analyzed a set of top-performing methods, most of which are deep neural networks, with both their commonalities and characteristics. This study establishes the benchmarks for computerized interpretation of 12-lead resting electrocardiogram and provides insights for the development of new methods.

Graphical Abstract

Detection of hidden model errors by combining single and multi-criteria calibration

Environmental models aim to reproduce landscape processes with mathematical equations. Observations are used for validation. The performance and uncertainties are quantified either by single or multi-criteria model assessment. In a case-study, we combine both approaches. We use a coupled hydro-biogeochemistry landscape-scale model to simulate 14 target values on discharge, stream nitrate as well as soil moisture, soil temperature and trace gas emissions (N₂O, CO₂) from different land uses. We reveal typical mistakes that happen during both, single and multi-criteria model assessment. Such as overestimated uncertainty in multi-criteria and ignored wrong model processes in single-criterion calibration. These mistakes can mislead the development of water quality and in general all environmental models. Only the combination of both approaches reveals the five types of posterior probability distributions for model parameters. Each type allocates a specific type of error. We identify and locate mismatched parameter values, obsolete parameters, flawed model structures and wrong process representations. The presented method can guide model users and developers to the so far hidden errors in their models. We emphasize to include observations from physical, chemical, biological and ecological processes in the model assessment, rather than the typical discipline specific assessments.

Protein Structure Modeling with MODELLER

Genome sequencing projects have resulted in a rapid increase in the number of known protein sequences. In contrast, only about one-hundredth of these sequences have been characterized at atomic resolution using experimental structure determination methods. Computational protein structure modeling techniques have the potential to bridge this sequence-structure gap. In the following chapter, we present an example that illustrates the use of MODELLER to construct a comparative model for a protein with unknown structure. Automation of a similar protocol has resulted in models of useful accuracy for domains in more than half of all known protein sequences.

Comparing Aachen Minipigs and Pietrain Piglets as Models of Experimental Pediatric Urology to Human Reference Data

INTRODUCTION

Swine had special roles in the development of minimally invasive procedures to treat vesicoureteral reflux, and minipigs have been gaining ground in recent years in experimental pediatric urology as they combine small size with less vulnerable adult physiology, but their suitability as a model has never been assessed. We therefore compared a landrace piglet with a juvenile minipig to elucidate comparability.

METHODS

We evaluated five 3-week old Pietrain piglets and five 3-month old Aachen Minipigs as representatives of landrace and minipig models based on their expected bodyweight being similar to a newborn human. We compared renal weight, volume - via the ellipsoid formula - and ureteral length. In addition, we calculated porcine renal function via Gasthuys' formula. In order to compare the groups with previously published values for infants, we used resampling techniques to allow comparison to humans.

RESULTS

Renal weight was higher in humans than in Pietrain piglets (ΔL = 7.6 g; ΔR = 5.4 g) and Aachen Minipigs (ΔL = 11 g; ΔR = 9.4 g). Renal volumes in humans were higher than in both Pietrain piglets (ΔL = 5.6 mL, p < 0.001; ΔR = 3.7 mL, p = 0.004) and Aachen Minipigs (ΔL = 8.1 mL; ΔR = 6.6 mL; both p < 0.001). Ureteral lengths in humans and both pig breeds were comparable as were estimated renal functions between both pig breeds.

DISCUSSION AND CONCLUSION

Both landrace piglets and juvenile minipigs are suitable models for experimental pediatric urology as parameters did not differ between them. In addition, the anatomic parameters are comparable or smaller than in infants. This might facilitate translational research as technical failure is less likely in larger organs. Additional research is necessary to cover higher age ranges than those included in the present pilot study.

On assessing binary regression models based on ungrouped data

Assessing a binary regression model based on ungrouped data is a commonly encountered but very challenging problem. Although tests, such as Hosmer-Lemeshow test and le Cessie-van Houwelingen test, have been devised and widely used in applications, they often have low power in detecting lack of fit and not much theoretical justification has been made on when they can work well. In this article, we propose a new approach based on a cross-validation voting system to address the problem. In addition to a theoretical guarantee that the probabilities of type I and II errors both converge to zero as the sample size increases for the new method under proper conditions, our simulation results demonstrate that it performs very well.

Selected aspects of prior and likelihood information for a Bayesian classifier in a road safety analysis

The development of the Bayesian logistic regression model classifying the road accident severity is discussed. The already exploited informative priors (method of moments, maximum likelihood estimation, and two-stage Bayesian updating), along with the original idea of a Boot prior proposal, are investigated when no expert opinion has been available. In addition, two possible approaches to updating the priors, in the form of unbalanced and balanced training data sets, are presented. The obtained logistic Bayesian models are assessed on the basis of a deviance information criterion (DIC), highest probability density (HPD) intervals, and coefficients of variation estimated for the model parameters. The verification of the model accuracy has been based on sensitivity, specificity and the harmonic mean of sensitivity and specificity, all calculated from a test data set. The models obtained from the balanced training data set have a better classification quality than the ones obtained from the unbalanced training data set. The two-stage Bayesian updating prior model and the Boot prior model, both identified with the use of the balanced training data set, outperform the non-informative, method of moments, and maximum likelihood estimation prior models. It is important to note that one should be careful when interpreting the parameters since different priors can lead to different models.

High-Dimensional Profiling for Computational Diagnosis

New technologies allow for high-dimensional profiling of patients. For instance, genome-wide gene expression analysis in tumors or in blood is feasible with microarrays, if all transcripts are known, or even without this restriction using high-throughput RNA sequencing. Other technologies like NMR finger printing allow for high-dimensional profiling of metabolites in blood or urine. Such technologies for high-dimensional patient profiling represent novel possibilities for molecular diagnostics. In clinical profiling studies, researchers aim to predict disease type, survival, or treatment response for new patients using high-dimensional profiles. In this process, they encounter a series of obstacles and pitfalls. We review fundamental issues from machine learning and recommend a procedure for the computational aspects of a clinical profiling study.

Protein Structure Modeling with MODELLER

Genome sequencing projects have resulted in a rapid increase in the number of known protein sequences. In contrast, only about one-hundredth of these sequences have been characterized at atomic resolution using experimental structure determination methods. Computational protein structure modeling techniques have the potential to bridge this sequence-structure gap. In the following chapter, we present an example that illustrates the use of MODELLER to construct a comparative model for a protein with unknown structure. Automation of a similar protocol has resulted in models of useful accuracy for domains in more than half of all known protein sequences.

Combined approaches to flexible fitting and assessment in virus capsids undergoing conformational change

Fitting of atomic components into electron cryo-microscopy (cryoEM) density maps is routinely used to understand the structure and function of macromolecular machines. Many fitting methods have been developed, but a standard protocol for successful fitting and assessment of fitted models has yet to be agreed upon among the experts in the field. Here, we created and tested a protocol that highlights important issues related to homology modelling, density map segmentation, rigid and flexible fitting, as well as the assessment of fits. As part of it, we use two different flexible fitting methods (Flex-EM and iMODfit) and demonstrate how combining the analysis of multiple fits and model assessment could result in an improved model. The protocol is applied to the case of the mature and empty capsids of Coxsackievirus A7 (CAV7) by flexibly fitting homology models into the corresponding cryoEM density maps at 8.2 and 6.1 Å resolution. As a result, and due to the improved homology models (derived from recently solved crystal structures of a close homolog – EV71 capsid – in mature and empty forms), the final models present an improvement over previously published models. In close agreement with the capsid expansion observed in the EV71 structures, the new CAV7 models reveal that the expansion is accompanied by ∼5° counterclockwise rotation of the asymmetric unit, predominantly contributed by the capsid protein VP1. The protocol could be applied not only to viral capsids but also to many other complexes characterised by a combination of atomic structure modelling and cryoEM density fitting.