Community structure is one of the main structural features of networks, revealing both their internal organization and the similarity of their elementary units. Despite the large variety of methods ...proposed to detect communities in graphs, there is a big need for multi-purpose techniques, able to handle different types of datasets and the subtleties of community structure. In this paper we present OSLOM (Order Statistics Local Optimization Method), the first method capable to detect clusters in networks accounting for edge directions, edge weights, overlapping communities, hierarchies and community dynamics. It is based on the local optimization of a fitness function expressing the statistical significance of clusters with respect to random fluctuations, which is estimated with tools of Extreme and Order Statistics. OSLOM can be used alone or as a refinement procedure of partitions/covers delivered by other techniques. We have also implemented sequential algorithms combining OSLOM with other fast techniques, so that the community structure of very large networks can be uncovered. Our method has a comparable performance as the best existing algorithms on artificial benchmark graphs. Several applications on real networks are shown as well. OSLOM is implemented in a freely available software (http://www.oslom.org), and we believe it will be a valuable tool in the analysis of networks.
This is the 4th edition of the highly acclaimed monograph on Extended Irreversible Thermodynamics, a theory that goes beyond the classical theory of irreversible processes. In contrast to the ...classical approach, the basic variables describing the system are complemented by non-equilibrium quantities. The claims made for extended thermodynamics are confirmed by the kinetic theory of gases and statistical mechanics. The book covers a wide spectrum of applications, and also contains a thorough discussion of the foundations and the scope of the current theories on non-equilibrium thermodynamics. For this new edition, the authors critically revised existing material while taking into account the most recent developments in fast moving fields such as heat transport in micro- and nanosystems or fast solidification fronts in materials sciences. Several fundamental chapters have been revisited emphasizing physics and applications over mathematical derivations. Also, fundamental questions on the definition of non-equilibrium temperature, entropy, fluctuations of fluxes and boundary conditions are revisited and presented in a modern way. Detailed solutions for more than 130 problem sets presented in this book, as well as a wide bibliography on extended irreversible thermodynamics are accessible at the http://telemaco.uab.es site.
When applied to structured data, conventional random cross‐validation techniques can lead to underestimation of prediction error, and may result in inappropriate model selection.
We present the r ...package blockCV, a new toolbox for cross‐validation of species distribution modelling. Although it has been developed with species distribution modelling in mind, it can be used for any spatial modelling.
The package can generate spatially or environmentally separated folds. It includes tools to measure spatial autocorrelation ranges in candidate covariates, providing the user with insights into the spatial structure in these data. It also offers interactive graphical capabilities for creating spatial blocks and exploring data folds.
Package blockCV enables modellers to more easily implement a range of evaluation approaches. It will help the modelling community learn more about the impacts of evaluation approaches on our understanding of predictive performance of species distribution models.
Foreign Language
هنگامی که روش اعتبارسنجی متقاطع بر روی دادههای دارای ساختار (مکانی٬ محیطی …) اعمال میشود٬ میتواند منجر به تخمین نادرست خطای پیشبینی و در نتیجه اشتباه در انتخاب مدلها شود.
در اینجا کتابخانه blockCV در نرمافزار برنامهنویسی R را بعنوان یک ابزار جدید برای اعتبارسنجی متقاطع مدلهای توزیع گونهها ارائه میدهیم. گرچه این کتابخانه با ایدهی مدلسازی توزیع گونهها توسعه داده شده است اما میتواند برای انواع مدلسازیهای مکانی نیز مورد استفاده قرار گیرد.
این کتابخانه توانایی ساخت زیرمجموعههای مجزای مکانی و محیطی از دادهها را دارد و همچنین شامل ابزاری برای اندازهگیری دامنه تاثیر خودهمبستگی مکانی در متغیرهای پیشبینیکننده میباشد که به کاربر دیدگاه بهتری از ساختار مکانی این دادهها را میدهد. این کتابخانه دارای ابزارهای گرافیکی برای بررسی و ساخت بلاکهای مکانی نیز میباشد.
کتابخانه blockCV مدلسازان را قادر میسازد که دامنه وسیعتری از روشهای اعتبارسنجی را بکار گیرند و همچنین درباره تاثیرات روشهای مختلف اعتبارسنجی بر درک بهتر ما از قدرت پیشبینی مدلهای توزیع گونهها کمک میکند.
Species distribution models (SDMs) constitute the most common class of models across ecology, evolution and conservation. The advent of ready‐to‐use software packages and increasing availability of ...digital geoinformation have considerably assisted the application of SDMs in the past decade, greatly enabling their broader use for informing conservation and management, and for quantifying impacts from global change. However, models must be fit for purpose, with all important aspects of their development and applications properly considered. Despite the widespread use of SDMs, standardisation and documentation of modelling protocols remain limited, which makes it hard to assess whether development steps are appropriate for end use. To address these issues, we propose a standard protocol for reporting SDMs, with an emphasis on describing how a study's objective is achieved through a series of modeling decisions. We call this the ODMAP (Overview, Data, Model, Assessment and Prediction) protocol, as its components reflect the main steps involved in building SDMs and other empirically‐based biodiversity models. The ODMAP protocol serves two main purposes. First, it provides a checklist for authors, detailing key steps for model building and analyses, and thus represents a quick guide and generic workflow for modern SDMs. Second, it introduces a structured format for documenting and communicating the models, ensuring transparency and reproducibility, facilitating peer review and expert evaluation of model quality, as well as meta‐analyses. We detail all elements of ODMAP, and explain how it can be used for different model objectives and applications, and how it complements efforts to store associated metadata and define modelling standards. We illustrate its utility by revisiting nine previously published case studies, and provide an interactive web‐based application to facilitate its use. We plan to advance ODMAP by encouraging its further refinement and adoption by the scientific community.
In this study, growth‐dependent changes in the mechanical properties of the tomato (Solanum lycopersicum) cuticle during fruit development were investigated in two cultivars with different patterns ...of cuticle growth and accumulation. The mechanical properties were determined in uniaxial tensile tests using strips of isolated cuticles. Changes in the functional groups of the cuticle chemical components were analysed by attenuated total reflectance–Fourier transform infrared (ATR‐FTIR). The early stages of fruit growth are characterized by an elastic cuticle, and viscoelastic behaviour only appeared at the beginning of cell enlargement. Changes in the cutin:polysaccharide ratio during development affected the strength required to achieve viscoelastic deformation. The increase in stiffness and decrease in extensibility during ripening, related to flavonoid accumulation, were accompanied by an increase in cutin depolymerization as a result of a reduction in the overall number of ester bonds. Quantitative changes in cuticle components influence the elastic/viscoelastic behaviour of the cuticle. The cutin:polysaccharide ratio modulates the stress required to permanently deform the cuticle and allow cell enlargement. Flavonoids stiffen the elastic phase and reduce permanent viscoelastic deformation. Ripening is accompanied by a chemical cleavage of cutin ester bonds. An infrared (IR) band related to phenolic accumulation can be used to monitor changes in the cutin esterification index.
Species distribution modeling (SDM) is widely used in ecology and conservation. Currently, the most available data for SDM are species presence‐only records (available through digital databases). ...There have been many studies comparing the performance of alternative algorithms for modeling presence‐only data. Among these, a 2006 paper from Elith and colleagues has been particularly influential in the field, partly because they used several novel methods (at the time) on a global data set that included independent presence–absence records for model evaluation. Since its publication, some of the algorithms have been further developed and new ones have emerged. In this paper, we explore patterns in predictive performance across methods, by reanalyzing the same data set (225 species from six different regions) using updated modeling knowledge and practices. We apply well‐established methods such as generalized additive models and MaxEnt, alongside others that have received attention more recently, including regularized regressions, point‐process weighted regressions, random forests, XGBoost, support vector machines, and the ensemble modeling framework biomod. All the methods we use include background samples (a sample of environments in the landscape) for model fitting. We explore impacts of using weights on the presence and background points in model fitting. We introduce new ways of evaluating models fitted to these data, using the area under the precision‐recall gain curve, and focusing on the rank of results. We find that the way models are fitted matters. The top method was an ensemble of tuned individual models. In contrast, ensembles built using the biomod framework with default parameters performed no better than single moderate performing models. Similarly, the second top performing method was a random forest parameterized to deal with many background samples (contrasted to relatively few presence records), which substantially outperformed other random forest implementations. We find that, in general, nonparametric techniques with the capability of controlling for model complexity outperformed traditional regression methods, with MaxEnt and boosted regression trees still among the top performing models. All the data and code with working examples are provided to make this study fully reproducible.
Analyses of Arabidopsis thaliana defense response to the damping-off oomycete pathogen Pythium irregulare show that resistance to P. irregulare requires a multicomponent defense strategy. Penetration ...represents a first layer, as indicated by the susceptibility of pen2 mutants, followed by recognition, likely mediated by ERECTA receptor-like kinases. Subsequent signaling of inducible defenses is predominantly mediated by jasmonic acid (JA), with insensitive coi1 mutants showing extreme susceptibility. In contrast with the generally accepted roles of ethylene and salicylic acid cooperating with or antagonizing, respectively, JA in the activation of defenses against necrotrophs, both are required to prevent disease progression, although much less so than JA. Meta-analysis of transcriptome profiles confirmed the predominant role of JA in activation of P. irregulare-induced defenses and uncovered abscisic acid (ABA) as an important regulator of defense gene expression. Analysis of cis-regulatory sequences also revealed an unexpected overrepresentation of ABA response elements in promoters of P. irregulare-responsive genes. Subsequent infections of ABA-related and callose-deficient mutants confirmed the importance of ABA in defense, acting partly through an undescribed mechanism. The results support a model for ABA affecting JA biosynthesis in the activation of defenses against this oomycete.
How Biology Handles Nitrite Maia, Luisa B; Moura, José J. G
Chemical reviews,
05/2014, Letnik:
114, Številka:
10
Journal Article
Recenzirano
Odprti dostop
Nitrogen's biochemistry and signaling pathways that are involved in nitrite chemisry were explored. In order to generate nitrite-dependent signaling nitrogen oxide, organisms reuse different ...metalloproteins in their cells.
Cis‐(+)‐12‐oxo‐phytodienoic acid (OPDA) is likely to play signaling roles in plant defense that do not depend on its further conversion to the phytohormone jasmonic acid. To elucidate the role of ...OPDA in Solanum lycopersicum (tomato) plant defense, we have silenced the 12‐oxophytodienoate reductase 3 (OPR3) gene. Two independent transgenic tomato lines (SiOPR3‐1 and SiOPR3‐2) showed significantly reduced OPR3 expression upon infection with the necrotrophic pathogen Botrytis cinerea. Moreover, SiOPR3 plants are more susceptible to this pathogen, and this susceptibility is accompanied by a significant decrease in OPDA levels and by the production of JA‐Ile being almost abolished. OPR3 silencing also leads to a major reduction in the expression of other genes of the jasmonic acid (JA) synthesis and signaling pathways after infection. These results confirm that in tomato plants, as in Arabidopsis, OPR3 determines OPDA availability for JA biosynthesis. In addition, we show that an intact JA biosynthetic pathway is required for proper callose deposition, as its pathogen‐induced accumulation is reduced in SiOPR3 plants. Interestingly, OPDA, but not JA, treatment restored basal resistance to B. cinerea and induced callose deposition in SiOPR3‐1 and SiOPR3‐2 transgenic plants. These results provide clear evidence that OPDA by itself plays a major role in the basal defense of tomato plants against this necrotrophic pathogen.
Aim
The idea of combining predictions from different models into an ensemble has gained considerable popularity in species distribution modelling, partly due to free and comprehensive software such ...as the R package BIOMOD. However, despite proliferation of ensemble models, we lack oversight of how and where they are used for modelling distributions, and how well they perform. Here, we present such an overview.
Location
Global.
Methods
Since BIOMOD is freely available and widely used by ensemble species distribution modellers, we focused on articles that apply BIOMOD, filtering the initial 852 papers identified in our structured literature search to a relevant final subset of 224 eligible peer‐reviewed journal articles.
Results
BIOMOD‐based ensembles are used across many taxa and locations, with terrestrial plants being the most represented group of species (n = 72) and Europe being the most represented continent (n = 106). These studies often focus on forecasting distributions in the future (n = 109), and commonly use presence‐only species data (n = 139) and climatic environmental predictors (n = 219). An average of six models are used in ensembles, and approximately half of ensembles weight contributions of models by their cross‐validation performance. However, discussion about choices made in the modelling process and unambiguous information on the performance of ensemble models versus individual models are limited. The use of independent data to validate model performance is particularly uncommon.
Main conclusions
We document the breadth of ensemble applications, but could not draw strong quantitative conclusions about the predictive performance of ensemble models, due to lack of unambiguous information reported. Understanding how and where ensembles are best used when modelling species distributions is important for enabling best choices for different applications. To enable this objective to be achieved, we provide recommendations for thorough reporting practices in a BIOMOD‐based ensemble workflow.
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