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Cooperation among kin is common in animal societies. Kin groups may form by individuals directly discriminating relatives based on kin recognition cues, or form passively through natal philopatry and limited dispersal. We describe the genetic landscape for a primitively eusocial wasp, Polistes dominula, and ask whether individuals choose cooperative partners that are nearby and/or that are genetic relatives. Firstly, we genotyped an entire sub-population of 1361 wasps and found genetic structuring on an extremely fine scale: the probability of finding genetic relatives decreases exponentially within just a few meters of an individual’s nest. At the same time, however, we found a lack of genetic structuring between natural nest aggregations within the population. Secondly, in a separate dataset where ~2000 wasps were genotyped, we show that wasps forced experimentally to make a new nest choice tended to choose new nests near to their original nests, and that these nests tended to contain some full sisters. However, a significant fraction of wasps chose nests that did not contain sisters, despite sisters being present in nearby nests. Although we cannot rule out a role for direct kin recognition or natal nest-mate recognition, our data suggest that kin groups may form via a philopatric rule-of-thumb, whereby wasps simply select groups and nesting sites that are nearby. The result is that most subordinate helpers obtain indirect fitness benefits by breeding cooperatively. [ABSTRACT FROM AUTHOR]

Creativity is a complex, multi-faceted concept encompassing a variety of related aspects, abilities, properties and behaviours. If we wish to study creativity scientifically, then a tractable and well-articulated model of creativity is required. Such a model would be of great value to researchers investigating the nature of creativity and in particular, those concerned with the evaluation of creative practice. This paper describes a unique approach to developing a suitable model of how creative behaviour emerges that is based on the words people use to describe the concept. Using techniques from the field of statistical natural language processing, we identify a collection of fourteen key components of creativity through an analysis of a corpus of academic papers on the topic. Words are identified which appear significantly often in connection with discussions of the concept. Using a measure of lexical similarity to help cluster these words, a number of distinct themes emerge, which collectively contribute to a comprehensive and multi-perspective model of creativity. The components provide an ontology of creativity: a set of building blocks which can be used to model creative practice in a variety of domains. The components have been employed in two case studies to evaluate the creativity of computational systems and have proven useful in articulating achievements of this work and directions for further research. [ABSTRACT FROM AUTHOR]

Wang et al. proposed a method for obtaining elliptic curves with embedding degree 1 for securing critical infrastructures, and presented several elliptic curves generated by their method with torsion points of 160 bits and 189 bits orders. They also presented some experimental results and claimed that their implementation of an elliptic curve generated with their method is faster than an implementation for embedded devices presented by Bertoni et al. In this paper, we point out that the security and efficiency claims given by Wang et al. are flawed. Specifically, we show that it is possible to solve finite field discrete logarithm problems defined over their elliptic curves in practice. On the elliptic curves with torsion points of 160 bits orders generated by Wang et al., their instances of finite field discrete logarithm problems are solved in around 4 hours by using a standard desktop PC. On the torsion points of 189 bits orders, their instances are solved in around 10 days by using two standard desktop PCs. The hardness of the finite field discrete logarithm problems is one of the most important bases of security; therefore, their elliptic curves should not be used for cryptographic purposes. [ABSTRACT FROM AUTHOR]

Introduction: In this paper we perform a replication analysis of “Effect of a cash transfer programme for schooling on prevalence of HIV and herpes simplex type 2 in Malawi: a cluster randomised trial” by Sarah Baird and others published in “The Lancet” in 2012. The original study was a two-year cluster randomized intervention trial of never married girls aged 13–22 in Malawi. Enumeration areas were randomized to either an intervention involving cash transfer (conditional or unconditional of school enrollment) or control. The study included 1708 Malawian girls, who were enrolled at baseline and had biological testing for HIV and herpes simplex virus type 2 (HSV-2) at 18 months. The original findings showed that in the cohort of girls enrolled in school at baseline, the intervention had an effect on school enrollment, sexual outcomes, and HIV and HSV-2 prevalence. However, in the baseline school dropout cohort, the original study showed no intervention effect on HIV and HSV-2 prevalence. Methods: We performed a replication of the study to investigate the consistency and robustness of key results reported. A pre-specified replication plan was approved and published online. Cleaned data was obtained from the original authors. A pure replication was conducted by reading the methods section and reproducing the results and tables found in the original paper. Robustness of the results were examined with alternative analysis methods in a measurement and estimation analysis (MEA) approach. A theory of change analysis was performed testing a causal pathway, the effect of intervention on HIV awareness, and whether the intervention effect depended on the wealth of the individual. Results: The pure replication found that other than a few minor discrepancies, the original study was well replicated. However, the randomization and sampling weights could not be verified due to the lack of access to raw data and a detailed sample selection plan. Therefore, we are unable to determine how sampling influenced the results, which could be highly dependent on the sample. In MEA it was found that the intervention effect on HIV prevalence in the baseline schoolgirls cohort was somewhat sensitive to model choice, with a non-significant intervention effect for HIV depending on the statistical model used. The intervention effect on HSV-2 prevalence was more robust in terms of statistical significance, however, the odds ratios and confidence intervals differed from the original result by more than 10%. A theory of change analysis showed no effect of intervention on HIV awareness. In a causal pathway analysis, several variables were partial mediators, or potential mediators, indicating that the intervention could be working through its effect on school enrollment or selected sexual behaviors. Conclusions: The effect of intervention on HIV prevalence in the baseline schoolgirls was sensitive to the model choice; however, HSV-2 prevalence results were confirmed. We recommend that the results from the original published analysis indicating the impact of cash transfers on HIV prevalence be treated with caution. [ABSTRACT FROM AUTHOR]

This paper investigates a well-known complex combinatorial problem known as the vehicle routing problem with time windows (VRPTW). Unlike the standard vehicle routing problem, each customer in the VRPTW is served within a given time constraint. This paper solves the VRPTW using an improved artificial bee colony (IABC) algorithm. The performance of this algorithm is improved by a local optimization based on a crossover operation and a scanning strategy. Finally, the effectiveness of the IABC is evaluated on some well-known benchmarks. The results demonstrate the power of IABC algorithm in solving the VRPTW. [ABSTRACT FROM AUTHOR]

Classical null hypothesis significance tests are not appropriate in corpus linguistics, because the randomness assumption underlying these testing procedures is not fulfilled. Nevertheless, there are numerous scenarios where it would be beneficial to have some kind of test in order to judge the relevance of a result (e.g. a difference between two corpora) by answering the question whether the attribute of interest is pronounced enough to warrant the conclusion that it is substantial and not due to chance. In this paper, I outline such a test. [ABSTRACT FROM AUTHOR]

In this paper we investigate the changes in the functional connectivity intensity, and some related properties, in healthy people, across the life span and at resting state. For the explicit computation of the functional connectivity we exploit a recently proposed model, that bases not only on the correlations data provided by the acquisition equipment, but also on different parameters, such as the anatomical distances between nodes and their degrees. The leading purpose of the paper is to show that the proposed approach is able to recover the main aspects of resting state condition known from the available literature, as well as to suggest new insights, perspectives and speculations from a neurobiological point of view. Our study involves 133 subjects, both males and females of different ages, with no evidence of neurological diseases or systemic disorders. First, we show how the model applies to the sample, where the subjects are grouped into 28 different groups (14 of males and 14 of females), according to their age. This leads to the construction of two graphs (one for males and one for females), that can be realistically interpreted as representative of the neural network during the resting state. Second, following the idea that the brain network is better understood by focusing on specific nodes having a kind of centrality, we refine the two output graphs by introducing a new metric that favours the selection of nodes having higher degrees. As a third step, we extensively comment and discuss the obtained results. In particular, it is remarkable that, despite a great overlapping exists between the outcomes concerning males and females, some intriguing differences appear. This motivates a deeper local investigation, which represents the fourth part of the paper, carried out through a thorough statistical analysis. As a result, we are enabled to support that, for two special age groups, a few links contribute in differentiating the behaviour of males and females. In addition, we performed an average-based comparison between the proposed model and the traditional statistical correlation-based approach, then discussing and commenting the main outlined discrepancies. [ABSTRACT FROM AUTHOR]

The problem of finding an optimum within a set of possibilities that represent the varying successfulness of numerous subjects competing with one another is highly relevant in the field of ecosystem interactions. We propose a method for solving this problem by the application of the Nash equilibrium concept, which is frequently used in ecology. The proposed model is based on the transformation of the initial payoff vectors of subjects that interact in different situations into a statistical set of symmetrical game matrices that consist of permutations of payoff values. The equilibrium solution is expressed as values of the probability of Nash equilibrium occurrence with uniform distribution over all possible permutations based on uncertainty of positions of payoff values in the matrix. We assume that this equilibrium solution provides information on the distribution of the degree of stability among individual situations and interacting subjects. In this paper, we validate this assumption and demonstrate its application to a dataset that represents interspecies interactions in plant ecology. We propose that the use of the Nash equilibrium in the analysis of datasets formalized according to the Pareto optimality scheme is applicable in numerous other contexts. [ABSTRACT FROM AUTHOR]

Two critical tasks in multi-criteria group decision making (MCGDM) are to describe criterion values and to aggregate the described information to generate a ranking of alternatives. A flexible and superior tool for the first task is q-rung orthopair fuzzy number (qROFN) and an effective tool for the second task is aggregation operator. So far, nearly thirty different aggregation operators of qROFNs have been presented. Each operator has its distinctive characteristics and can work well for specific purpose. However, there is not yet an operator which can provide desirable generality and flexibility in aggregating criterion values, dealing with the heterogeneous interrelationships among criteria, and reducing the influence of extreme criterion values. To provide such an aggregation operator, Muirhead mean operator, power average operator, partitioned average operator, and Archimedean T-norm and T-conorm operations are concurrently introduced into q-rung orthopair fuzzy sets, and an Archimedean power partitioned Muirhead mean operator of qROFNs and its weighted form are presented and a MCGDM method based on the weighted operator is proposed in this paper. The generalised expressions of the two operators are firstly defined. Their properties are explored and proved and their specific expressions are constructed. On the basis of the specific expressions, a method for solving the MCGDM problems based on qROFNs is then designed. Finally, the feasibility and effectiveness of the method is demonstrated via a numerical example, a set of experiments, and qualitative and quantitative comparisons. [ABSTRACT FROM AUTHOR]

Alzheimer’s disease (AD) affects millions of people and is a major rising problem in health care worldwide. Recent research suggests that AD could have different subtypes, presenting differences in how the disease develops. Characterizing those subtypes could be key to deepen the understanding of this complex disease. In this paper, we used a multivariate, non-supervised clustering method over blood-based markers to find subgroups of patients defined by distinctive blood marker profiles. Our analysis on ADNI database identified 4 possible subgroups, each with a different blood profile. More importantly, we show that subgroups with different profiles have a different relationship between brain phenotypes detected in magnetic resonance imaging and disease condition. [ABSTRACT FROM AUTHOR]

Objectives: Professional sporting organisations invest considerable resources collecting and analysing data in order to better understand the factors that influence performance. Recent advances in non-invasive technologies, such as global positioning systems (GPS), mean that large volumes of data are now readily available to coaches and sport scientists. However analysing such data can be challenging, particularly when sample sizes are small and data sets contain multiple highly correlated variables, as is often the case in a sporting context. Multicollinearity in particular, if not treated appropriately, can be problematic and might lead to erroneous conclusions. In this paper we present a novel ‘leave one variable out’ (LOVO) partial least squares correlation analysis (PLSCA) methodology, designed to overcome the problem of multicollinearity, and show how this can be used to identify the training load (TL) variables that influence most ‘end fitness’ in young rugby league players. Methods: The accumulated TL of sixteen male professional youth rugby league players (17.7 ± 0.9 years) was quantified via GPS, a micro-electrical-mechanical-system (MEMS), and players’ session-rating-of-perceived-exertion (sRPE) over a 6-week pre-season training period. Immediately prior to and following this training period, participants undertook a 30–15 intermittent fitness test (30-15IFT), which was used to determine a players ‘starting fitness’ and ‘end fitness’. In total twelve TL variables were collected, and these along with ‘starting fitness’ as a covariate were regressed against ‘end fitness’. However, considerable multicollinearity in the data (VIF >1000 for nine variables) meant that the multiple linear regression (MLR) process was unstable and so we developed a novel LOVO PLSCA adaptation to quantify the relative importance of the predictor variables and thus minimise multicollinearity issues. As such, the LOVO PLSCA was used as a tool to inform and refine the MLR process. Results: The LOVO PLSCA identified the distance accumulated at very-high speed (>7 m·s-1) as being the most important TL variable to influence improvement in player fitness, with this variable causing the largest decrease in singular value inertia (5.93). When included in a refined linear regression model, this variable, along with ‘starting fitness’ as a covariate, explained 73% of the variance in v30-15IFT ‘end fitness’ (p<0.001) and eliminated completely any multicollinearity issues. Conclusions: The LOVO PLSCA technique appears to be a useful tool for evaluating the relative importance of predictor variables in data sets that exhibit considerable multicollinearity. When used as a filtering tool, LOVO PLSCA produced a MLR model that demonstrated a significant relationship between ‘end fitness’ and the predictor variable ‘accumulated distance at very-high speed’ when ‘starting fitness’ was included as a covariate. As such, LOVO PLSCA may be a useful tool for sport scientists and coaches seeking to analyse data sets obtained using GPS and MEMS technologies. [ABSTRACT FROM AUTHOR]

In this paper, the synchronization problem for a class of discrete-time complex-valued neural networks with time-varying delays is investigated. Compared with the previous work, the time delay and parameters are assumed to be time-varying. By separating the real part and imaginary part, the discrete-time model of complex-valued neural networks is derived. Moreover, by using the complex-valued Lyapunov-Krasovskii functional method and linear matrix inequality as tools, sufficient conditions of the synchronization stability are obtained. In numerical simulation, examples are presented to show the effectiveness of our method. [ABSTRACT FROM AUTHOR]

This paper considers the DCSK system under jamming environment. We consider both fast and slow switching pulse jamming (PJ). We derive approximations of the system bit error rates (BERs) in analytic expressions containing only well-known special functions, from which we show that for both jamming cases increasing the spreading factor can enhance the BER. In addition, we reveal that under the fast switching PJ, the BER does not depend on the jamming duty cycle ρ when ρ ≤ 0.5, however when ρ > 0.5, increasing its value degrades the BER. Moreover, we find out that under the slow switching PJ, increasing ρ may either enhance or degrade the BER. [ABSTRACT FROM AUTHOR]

In this paper, a unique and more distinctive encryption algorithm is proposed. This is based on the complexity of highly nonlinear S box in Flesnelet domain. The nonlinear pattern is transformed further to enhance the confusion in the dummy data using Fresnelet technique. The security level of the encrypted image boosts using the algebra of Galois field in Fresnelet domain. At first level, the Fresnelet transform is used to propagate the given information with desired wavelength at specified distance. It decomposes given secret data into four complex subbands. These complex sub-bands are separated into two components of real subband data and imaginary subband data. At second level, the net subband data, produced at the first level, is deteriorated to non-linear diffused pattern using the unique S-box defined on the Galois field . In the diffusion process, the permuted image is substituted via dynamic algebraic S-box substitution. We prove through various analysis techniques that the proposed scheme enhances the cipher security level, extensively. [ABSTRACT FROM AUTHOR]

Managing the biodiversity extinction crisis requires wise decision-making processes able to account for the limited resources available. In most decision problems in conservation biology, several conflicting objectives have to be taken into account. Most methods used in conservation either provide suboptimal solutions or use strong assumptions about the decision-maker’s preferences. Our paper reviews some of the existing approaches to solve multi-objective decision problems and presents new multi-objective linear programming formulations of two multi-objective optimization problems in conservation, allowing the use of a reference point approach. Reference point approaches solve multi-objective optimization problems by interactively representing the preferences of the decision-maker with a point in the criteria (objectives) space, called the reference point. We modelled and solved the following two problems in conservation: a dynamic multi-species management problem under uncertainty and a spatial allocation resource management problem. Results show that the reference point method outperforms classic methods while illustrating the use of an interactive methodology for solving combinatorial problems with multiple objectives. The method is general and can be adapted to a wide range of ecological combinatorial problems. [ABSTRACT FROM AUTHOR]

The 3D orientation of clasts within a deposit are known to be informative on processes that formed that deposit. In archaeological sites, a portion of the clasts in the deposit are introduced by non-geological processes, and these are typically systematically recorded in archaeological excavations with total stations. By recording a second point on elongated clasts it is possible to quickly and precisely capture their orientation. The statistical and graphical techniques for analyzing these data are well published, and there is a growing set of actualistic and archaeological comparative data to help with the interpretation of the documented patterns. This paper advances this area of research in presenting methods to address some shortcomings in current methodologies. First, a method for calculating confidence intervals on orientation statistics is presented to help address the question of how many objects are needed to assess the formation of a deposit based on orientations. Second, a method for assessing the probability that two assemblages have different orientations is presented based on permutations testing. This method differs from existing ones in that it considers three-dimensional orientations rather than working separately with the two-dimensional bearing and plunge components. Third, a method is presented to examine spatial variability in orientations based on a moving windows approach. The raw data plus the R code to build this document and to implement these methods plus those already described by McPherron are included to help further their use in assessing archaeological site formation processes. [ABSTRACT FROM AUTHOR]

Background: DSC is used to determine thermally-induced conformational changes of biomolecules within a blood plasma sample. Recent research has indicated that DSC curves (or thermograms) may have different characteristics based on disease status and, thus, may be useful as a monitoring and diagnostic tool for some diseases. Since thermograms are curves measured over a range of temperature values, they are considered functional data. In this paper we apply functional data analysis techniques to analyze differential scanning calorimetry (DSC) data from individuals from the Lupus Family Registry and Repository (LFRR). The aim was to assess the effect of lupus disease status as well as additional covariates on the thermogram profiles, and use FD analysis methods to create models for classifying lupus vs. control patients on the basis of the thermogram curves. Methods: Thermograms were collected for 300 lupus patients and 300 controls without lupus who were matched with diseased individuals based on sex, race, and age. First, functional regression with a functional response (DSC) and categorical predictor (disease status) was used to determine how thermogram curve structure varied according to disease status and other covariates including sex, race, and year of birth. Next, functional logistic regression with disease status as the response and functional principal component analysis (FPCA) scores as the predictors was used to model the effect of thermogram structure on disease status prediction. The prediction accuracy for patients with Osteoarthritis and Rheumatoid Arthritis but without Lupus was also calculated to determine the ability of the classifier to differentiate between Lupus and other diseases. Data were divided 1000 times into separate 2/3 training and 1/3 test data for evaluation of predictions. Finally, derivatives of thermogram curves were included in the models to determine whether they aided in prediction of disease status. Results: Functional regression with thermogram as a functional response and disease status as predictor showed a clear separation in thermogram curve structure between cases and controls. The logistic regression model with FPCA scores as the predictors gave the most accurate results with a mean 79.22% correct classification rate with a mean sensitivity = 79.70%, and specificity = 81.48%. The model correctly classified OA and RA patients without Lupus as controls at a rate of 75.92% on average with a mean sensitivity = 79.70% and specificity = 77.6%. Regression models including FPCA scores for derivative curves did not perform as well, nor did regression models including covariates. Conclusion: Changes in thermograms observed in the disease state likely reflect covalent modifications of plasma proteins or changes in large protein-protein interacting networks resulting in the stabilization of plasma proteins towards thermal denaturation. By relating functional principal components from thermograms to disease status, our Functional Principal Component Analysis model provides results that are more easily interpretable compared to prior studies. Further, the model could also potentially be coupled with other biomarkers to improve diagnostic classification for lupus. [ABSTRACT FROM AUTHOR]

Code-based cryptography is one of few alternatives supposed to be secure in a post-quantum world. Meanwhile, identity-based identification and signature (IBI/IBS) schemes are two of the most fundamental cryptographic primitives, so several code-based IBI/IBS schemes have been proposed. However, with increasingly profound researches on coding theory, the security reduction and efficiency of such schemes have been invalidated and challenged. In this paper, we construct provably secure IBI/IBS schemes from code assumptions against impersonation under active and concurrent attacks through a provably secure code-based signature technique proposed by Preetha, Vasant and Rangan (PVR signature), and a security enhancement Or-proof technique. We also present the parallel-PVR technique to decrease parameter values while maintaining the standard security level. Compared to other code-based IBI/IBS schemes, our schemes achieve not only preferable public parameter size, private key size, communication cost and signature length due to better parameter choices, but also provably secure. [ABSTRACT FROM AUTHOR]

Muirhead mean (MM) is a well-known aggregation operator which can consider interrelationships among any number of arguments assigned by a variable vector. Besides, it is a universal operator since it can contain other general operators by assigning some special parameter values. However, the MM can only process the crisp numbers. Inspired by the MM’ advantages, the aim of this paper is to extend MM to process the intuitionistic fuzzy numbers (IFNs) and then to solve the multi-attribute group decision making (MAGDM) problems. Firstly, we develop some intuitionistic fuzzy Muirhead mean (IFMM) operators by extending MM to intuitionistic fuzzy information. Then, we prove some properties and discuss some special cases with respect to the parameter vector. Moreover, we present two new methods to deal with MAGDM problems with the intuitionistic fuzzy information based on the proposed MM operators. Finally, we verify the validity and reliability of our methods by using an application example, and analyze the advantages of our methods by comparing with other existing methods. [ABSTRACT FROM AUTHOR]

In a general (k, n) scalable secret image sharing (SSIS) scheme, the secret image is shared by n participants and any k or more than k participants have the ability to reconstruct it. The scalability means that the amount of information in the reconstructed image scales in proportion to the number of the participants. In most existing SSIS schemes, the size of each image shadow is relatively large and the dealer does not has a flexible control strategy to adjust it to meet the demand of differen applications. Besides, almost all existing SSIS schemes are not applicable under noise circumstances. To address these deficiencies, in this paper we present a novel SSIS scheme based on a brand-new technique, called compressed sensing, which has been widely used in many fields such as image processing, wireless communication and medical imaging. Our scheme has the property of flexibility, which means that the dealer can achieve a compromise between the size of each shadow and the quality of the reconstructed image. In addition, our scheme has many other advantages, including smooth scalability, noise-resilient capability, and high security. The experimental results and the comparison with similar works demonstrate the feasibility and superiority of our scheme. [ABSTRACT FROM AUTHOR]

In this paper we present a three-dimensional (3D) morphometrical assessment of human tibia sexual dimorphism based on whole bone digital representation. To detect shape–size and shape differences between sexes, we used geometric morphometric tools and colour-coded surface deviation maps. The surface-based methodology enabled analysis of sexually dimorphic features throughout the shaft and articular ends of the tibia. The overall study dataset consisted of 183 3D models of adult tibiae from three Czech population subsets, dating to the early medieval (9–10th century) (N = 65), early 20th century (N = 61) and 21st-century (N = 57). The time gap between the chronologically most distant and contemporary datasets was more than 1200 years. The results showed that, in all three datasets, sexual dimorphism was pronounced. There were some sex-dimorphic characteristics common to all three samples, such as tuberosity protrusion, anteriorly bowed shaft and relatively larger articular ends in males. Diachronic comparisons also revealed substantial shape variation related to the most dimorphic area. Male/female distinctions showed a consistent temporal trend regarding the location of dimorphic areas (shifting distally with time), while the maximal deviation between male and female digitized surfaces fluctuated and reached the lowest level in the 21st-century sample. Sex determination on a whole-surface basis yielded the lowest return of correct sex assignment in the 20th-century group, which represented the lowest socioeconomic status. The temporal variation could be attributed to changes in living conditions, the decreasing lower limb loading/labour division in the last 12 centuries having the greatest effect. Overall, the results showed that a surface-based approach is successful for analysing complex long bone geometry. [ABSTRACT FROM AUTHOR]

Data analysis and model-data comparisons in the environmental sciences require diagnostic measures that quantify time series dynamics and structure, and are robust to noise in observational data. This paper investigates the temporal dynamics of environmental time series using measures quantifying their information content and complexity. The measures are used to classify natural processes on one hand, and to compare models with observations on the other. The present analysis focuses on the global carbon cycle as an area of research in which model-data integration and comparisons are key to improving our understanding of natural phenomena. We investigate the dynamics of observed and simulated time series of Gross Primary Productivity (GPP), a key variable in terrestrial ecosystems that quantifies ecosystem carbon uptake. However, the dynamics, patterns and magnitudes of GPP time series, both observed and simulated, vary substantially on different temporal and spatial scales. We demonstrate here that information content and complexity, or Information Theory Quantifiers (ITQ) for short, serve as robust and efficient data-analytical and model benchmarking tools for evaluating the temporal structure and dynamical properties of simulated or observed time series at various spatial scales. At continental scale, we compare GPP time series simulated with two models and an observations-based product. This analysis reveals qualitative differences between model evaluation based on ITQ compared to traditional model performance metrics, indicating that good model performance in terms of absolute or relative error does not imply that the dynamics of the observations is captured well. Furthermore, we show, using an ensemble of site-scale measurements obtained from the FLUXNET archive in the Mediterranean, that model-data or model-model mismatches as indicated by ITQ can be attributed to and interpreted as differences in the temporal structure of the respective ecological time series. At global scale, our understanding of C fluxes relies on the use of consistently applied land models. Here, we use ITQ to evaluate model structure: The measures are largely insensitive to climatic scenarios, land use and atmospheric gas concentrations used to drive them, but clearly separate the structure of 13 different land models taken from the CMIP5 archive and an observations-based product. In conclusion, diagnostic measures of this kind provide data-analytical tools that distinguish different types of natural processes based solely on their dynamics, and are thus highly suitable for environmental science applications such as model structural diagnostics. [ABSTRACT FROM AUTHOR]

Identifying causal relations from time series is the first step to understanding the behavior of complex systems. Although many methods have been proposed, few papers have applied multiple methods together to detect causal relations based on time series generated from coupled nonlinear systems with some unobserved parts. Here we propose the combined use of three methods and a majority vote to infer causality under such circumstances. Two of these methods are proposed here for the first time, and all of the three methods can be applied even if the underlying dynamics is nonlinear and there are hidden common causes. We test our methods with coupled logistic maps, coupled Rössler models, and coupled Lorenz models. In addition, we show from ice core data how the causal relations among the temperature, the CH4 level, and the CO2 level in the atmosphere changed in the last 800,000 years, a conclusion also supported by irregularly sampled data analysis. Moreover, these methods show how three regions of the brain interact with each other during the visually cued, two-choice arm reaching task. Especially, we demonstrate that this is due to bottom up influences at the beginning of the task, while there exist mutual influences between the posterior medial prefrontal cortex and the presupplementary motor area. Based on our results, we conclude that identifying causality with an appropriate ensemble of multiple methods ensures the validity of the obtained results more firmly. [ABSTRACT FROM AUTHOR]

The joint analysis of multiple traits has recently become popular since it can increase statistical power to detect genetic variants and there is increasing evidence showing that pleiotropy is a widespread phenomenon in complex diseases. Currently, most of existing methods use all of the traits for testing the association between multiple traits and a single variant. However, those methods for association studies may lose power in the presence of a large number of noise traits. In this paper, we propose an “optimal” maximum heritability test (MHT-O) to test the association between multiple traits and a single variant. MHT-O includes a procedure of deleting traits that have weak or no association with the variant. Using extensive simulation studies, we compare the performance of MHT-O with MHT, Trait-based Association Test uses Extended Simes procedure (TATES), SUM_SCORE and MANOVA. Our results show that, in all of the simulation scenarios, MHT-O is either the most powerful test or comparable to the most powerful test among the five tests we compared. [ABSTRACT FROM AUTHOR]

Graphlets are small subgraphs, usually containing up to five vertices, that can be found in a larger graph. Identification of the graphlets that a vertex in an explored graph touches can provide useful information about the local structure of the graph around that vertex. Actually finding all graphlets in a large graph can be time-consuming, however. As the graphlets grow in size, more different graphlets emerge and the time needed to find each graphlet also scales up. If it is not needed to find each instance of each graphlet, but knowing the number of graphlets touching each node of the graph suffices, the problem is less hard. Previous research shows a way to simplify counting the graphlets: instead of looking for the graphlets needed, smaller graphlets are searched, as well as the number of common neighbors of vertices. Solving a system of equations then gives the number of times a vertex is part of each graphlet of the desired size. However, until now, equations only exist to count graphlets with 4 or 5 nodes. In this paper, two new techniques are presented. The first allows to generate the equations needed in an automatic way. This eliminates the tedious work needed to do so manually each time an extra node is added to the graphlets. The technique is independent on the number of nodes in the graphlets and can thus be used to count larger graphlets than previously possible. The second technique gives all graphlets a unique ordering which is easily extended to name graphlets of any size. Both techniques were used to generate equations to count graphlets with 4, 5 and 6 vertices, which extends all previous results. Code can be found at and . [ABSTRACT FROM AUTHOR]

This paper presents a high payload watermarking scheme for High Efficiency Video Coding (HEVC). HEVC is an emerging video compression standard that provides better compression performance as compared to its predecessor, i.e. H.264/AVC. Considering that HEVC may will be used in a variety of applications in the future, the proposed algorithm has a high potential of utilization in applications involving broadcast and hiding of metadata. The watermark is embedded into the Quantized Transform Coefficients (QTCs) during the encoding process. Later, during the decoding process, the embedded message can be detected and extracted completely. The experimental results show that the proposed algorithm does not significantly affect the video quality, nor does it escalate the bitrate. [ABSTRACT FROM AUTHOR]

This paper proposes a statistical generalized species-area model (GSAM) to represent various patterns of species-area relationship (SAR), which is one of the fundamental patterns in ecology. The approach enables the generalization of many preliminary models, as power-curve model, which is commonly used to mathematically describe the SAR. The GSAM is applied to simulated data set of species diversity in areas of different sizes and a real-world data of insects of Hymenoptera order has been modeled. We show that the GSAM enables the identification of the best statistical model and estimates the number of species according to the area. [ABSTRACT FROM AUTHOR]

The evolutionary history of certain species such as polyploids are modeled by a generalization of phylogenetic trees called multi-labeled phylogenetic trees, or MUL trees for short. One problem that relates to inferring a MUL tree is how to construct the smallest possible MUL tree that is consistent with a given set of rooted triplets, or SMRT problem for short. This problem is NP-hard. There is one algorithm for the SMRT problem which is exact and runs in time, where is the number of taxa. In this paper, we show that the SMRT does not seem to be an appropriate solution from the biological point of view. Indeed, we present a heuristic algorithm named MTRT for this problem and execute it on some real and simulated datasets. The results of MTRT show that triplets alone cannot provide enough information to infer the true MUL tree. So, it is inappropriate to infer a MUL tree using triplet information alone and considering the minimum number of duplications. Finally, we introduce some new problems which are more suitable from the biological point of view. [ABSTRACT FROM AUTHOR]

In biological systems, the dynamic analysis method has gained increasing attention in the past decade. The Boolean network is the most common model of a genetic regulatory network. The interactions of activation and inhibition in the genetic regulatory network are modeled as a set of functions of the Boolean network, while the state transitions in the Boolean network reflect the dynamic property of a genetic regulatory network. A difficult problem for state transition analysis is the finding of attractors. In this paper, we modeled the genetic regulatory network as a Boolean network and proposed a solving algorithm to tackle the attractor finding problem. In the proposed algorithm, we partitioned the Boolean network into several blocks consisting of the strongly connected components according to their gradients, and defined the connection between blocks as decision node. Based on the solutions calculated on the decision nodes and using a satisfiability solving algorithm, we identified the attractors in the state transition graph of each block. The proposed algorithm is benchmarked on a variety of genetic regulatory networks. Compared with existing algorithms, it achieved similar performance on small test cases, and outperformed it on larger and more complex ones, which happens to be the trend of the modern genetic regulatory network. Furthermore, while the existing satisfiability-based algorithms cannot be parallelized due to their inherent algorithm design, the proposed algorithm exhibits a good scalability on parallel computing architectures. [ABSTRACT FROM AUTHOR]

The reconcilability of actions and beliefs in inter-country relationships, either in business or politics, is of vital importance as incorrect beliefs on foreigners’ behavior can have serious implications. We study a typical inter-country interaction by means of a controlled laboratory investment game experiment in Germany, Israel and Palestine involving 400 student participants in total. An investor has to take a risky decision in a foreign country that involves transferring money to an investee/allocator. We found a notable constellation of calibrated and un-calibrated beliefs. Within each country, transfer standards exist, which investees correctly anticipate within their country. However, across countries these standards differ. By attributing the standard of their own environment to the other countries investees are remarkably bad in predicting foreign investors’ behavior. The tendency to ignore this potential difference can be a source of misinterpreting motives in cross-country interaction. Foreigners might perceive behavior as unfavorable or favorable differentiation, even though—unknown to them—investors actually treat fellow-country people and foreigners alike. [ABSTRACT FROM AUTHOR]

The bioaccumulation of Potentially Toxic Elements (PTEs) by benthic invertebrates in estuarine sediments is poorly understood. We sampled and analysed PTEs in sediments and benthic invertebrates from five sites in the Skeena Estuary (British Columbia, Canada), including sites adjacent to an abandoned cannery and a decommissioned papermill. Our aim was to elucidate baseline levels of PTE concentrations at sites that may be recovering from disturbance associated with prior industrial development and identify organisms that could be used to biomonitor the impact of future industrial developments. There was no indication that sediments of the salmon cannery were polluted, but acidic sediments adjacent to the papermill contained elevated concentrations of Cd, Cr, Hg and Pb. Benthic invertebrate community assemblages confirm that sediments have mostly recovered from prior industrial development associated with discharge of papermill sludge. Overall, we did not observe any relationship between PTE concentrations in the sediment and PTE concentrations in invertebrate tissues. However, we did observe a negative relationship between sediment pH and the Biota-Sediment Accumulation Factor (BSAF) of most PTEs for Oregon pill bugs (Gnorimosphaeroma oregonensis). G. oregonensis, observed at all sites, feeds on the fibers associated with the papermill discharge. Thus, G. oregonensis is a useful biomonitors for quantifying the impact of the decommissioned papermill, and are candidate biomonitors for assessing the impact of similar industrial development projects on intertidal ecosystems. [ABSTRACT FROM AUTHOR]

Downscaled climate projections need to be linked to downscaled projections of population and economic growth to fully develop implications for land, natural resources, and ecosystems for future scenarios. We develop an empirical spatiotemporal approach for jointly projecting population and income at the county scale in the United States that is consistent with neoclassical economic growth theory and overlapping labor markets and that accounts for labor migration and spatial spillovers. Downscaled projections generated for the five Shared Socioeconomic Pathways used to support global scenario analysis generally show growth focused around relatively few centers especially in the southeast and western regions, with some areas in the Midwest and northeast experiencing population declines. Results are consistent with economic growth theory and with historical trends in population change and convergence of per capita personal income across US counties. [ABSTRACT FROM AUTHOR]

The Complexity-entropy causality plane (CECP) is a parsimonious representation space for time series. It has only two dimensions: normalized permutation entropy () and Jensen-Shannon complexity () of a time series. This two-dimensional representation allows for detection of slow or rapid drifts in the condition of mechanical components monitored through sensor measurements. The CECP representation can be used for both predictive analytics and visual monitoring of changes in component condition. This method requires minimal pre-processing of raw signals. Furthermore, it is insensitive to noise, stationarity, and trends. These desirable properties make CECP a good candidate for machine condition monitoring and fault diagnostics. In this work we study the effectiveness of CECP on three rotary component condition assessment applications. We use CECP representation of vibration signals to differentiate various machine component health conditions for rotary machine components, namely roller bearing and gears. The results confirm that the CECP representation is able to detect, with high accuracy, changes in underlying dynamics of machine component degradation states. From class separability perspective, the CECP representation is able to generate linearly separable classes for the classification of different fault states. This classification performance improves with increasing signal length. For signal length of 16,384 data points, the fault classification accuracy varies from 90% to 100% for bearing applications, and from 85% to 100% for gear applications. We observed that the optimum parameter for CECP representatino depends on the application. For bearing applications we found that embedding dimension D = 4, 5, 6, and embedding delay τ = 1, 2, 3 are suitable for good fault classification. For gear applications we find that embedding dimension D = 4, 5, and embedding delay τ = 1, 5 are suitable for fault classification. [ABSTRACT FROM AUTHOR]

While prediction errors (PE) have been established to drive learning through adaptation of internal models, the role of model-compliant events in predictive processing is less clear. Checkpoints (CP) were recently introduced as points in time where expected sensory input resolved ambiguity regarding the validity of the internal model. Conceivably, these events serve as on-line reference points for model evaluation, particularly in uncertain contexts. Evidence from fMRI has shown functional similarities of CP and PE to be independent of event-related surprise, raising the important question of how these event classes relate to one another. Consequently, the aim of the present study was to characterise the functional relationship of checkpoints and prediction errors in a serial pattern detection task using electroencephalography (EEG). Specifically, we first hypothesised a joint P3b component of both event classes to index recourse to the internal model (compared to non-informative standards, STD). Second, we assumed the mismatch signal of PE to be reflected in an N400 component when compared to CP. Event-related findings supported these hypotheses. We suggest that while model adaptation is instigated by prediction errors, checkpoints are similarly used for model evaluation. Intriguingly, behavioural subgroup analyses showed that the exploitation of potentially informative reference points may depend on initial cue learning: Strict reliance on cue-based predictions may result in less attentive processing of these reference points, thus impeding upregulation of response gain that would prompt flexible model adaptation. Overall, present results highlight the role of checkpoints as model-compliant, informative reference points and stimulate important research questions about their processing as function of learning und uncertainty. [ABSTRACT FROM AUTHOR]

In this note we present a robust bootstrap test with good Type I error control for testing the general hypothesis H0: ρ = ρ0. In order to carry out this test we use what is termed a surrogate bootstrap distribution. The test was inspired by the studentized permutation for testing H0: ρ = 0, which was proven to be exact in certain scenarios and asymptotically correct overall. We show that the bootstrap based test is robust to a variety of distributional scenarios in terms of proper Type I error control. [ABSTRACT FROM AUTHOR]

China's rapid urbanization and high traffic accident frequency have received many researchers’ attention. It is important to reveal how urban infrastructures and other risk factors affects the traffic accident frequency. A growing amount of research has examined the local risk factors impact on traffic accident frequency at certain time. Some studies considered these spatial influences but overlooked the temporal correlation/heterogeneity of traffic accidents and related risk factors. This study explores risk factors’ influence on urban traffic accidents frequency while considering both the spatial and temporal correlation/heterogeneity of traffic accidents. The study area is split into 100 equally sized rectangle traffic analysis zones (TAZs), and the urban traffic accident frequency and attributes in each TAZ are extracted. The linear regression model, spatial lag model (SLM), spatial error model (SEM) and time-fixed effects error model (T-FEEM) are established and compared respectively. The proposed methodologies are illustrated using ten-month traffic accident data from the urban area of Guiyang City, China. The results reveal that the time-fixed effects error model, which considers both spatial and temporal correlation/heterogeneity of traffic accidents, is superior to other models. More traffic accidents will happen in those TAZs that have more hospitals or schools. Moreover, hospitals have a greater influence on traffic accidents than schools. Because of the location in the margin of the city, those TAZs that have passenger stations have more traffic accidents. This study provides policy makers with more detailed characterization about the impact of related risk factors on traffic accident frequencies, and it is suggested that not only the spatial correlation/heterogeneity but also the temporal correlation/heterogeneity should be taken into account in guiding traffic accident control of urban area. [ABSTRACT FROM AUTHOR]

Synchronized oscillatory gamma-band activity (30-100Hz) has been suggested to constitute a key mechanism to dynamically orchestrate sensory information integration across multiple spatio-temporal scales. We here tested whether interhemispheric functional connectivity and ensuing auditory perception can selectively be modulated by high-density transcranial alternating current stimulation (HD-tACS). For this purpose, we applied multi-site HD-tACS at 40Hz bilaterally with a phase lag of 180° and recorded a 64-channel EEG to study the oscillatory phase dynamics at the source-space level during a dichotic listening (DL) task in twenty-six healthy participants. In this study, we revealed an oscillatory phase signature at 40Hz which reflects different temporal profiles of the phase asymmetries during left and right ear percept. Here we report that 180°-tACS did not affect the right ear advantage during DL at group level. However, a follow-up analysis revealed that the intrinsic phase asymmetries during sham-tACS determined the directionality of the behavioral modulations: While a shift to left ear percept was associated with augmented interhemispheric asymmetry (closer to 180°), a shift to right ear processing was elicited in subjects with lower asymmetry (closer to 0°). Crucially, the modulation of the interhemispheric network dynamics depended on the deviation of the tACS-induced phase-lag from the intrinsic phase asymmetry. Our characterization of the oscillatory network trends is giving rise to the importance of phase-specific gamma-band coupling during ambiguous auditory perception, and emphasizes the necessity to address the inter-individual variability of phase asymmetries in future studies by tailored stimulation protocols. [ABSTRACT FROM AUTHOR]

Commercial surrogacy in emerging countries such as India is often associated with exploitation of vulnerable women, the assumption being that it is performed by poor and uneducated women for rich intended parents. However, the hypothesis that surrogates are poor women has rarely been confronted with field data. The objective was to compare the socioeconomic characteristics of Indian surrogates interviewed in social studies with those of Indian women in the general population in order to provide preliminary data on whether surrogates have a specific profile and are indeed disadvantaged compared with their counterparts. The study analyzes the data from four cross-sectional studies carried out in India among surrogates between 2006 and 2014. Surrogates were recruited through clinics, agencies and agents. Data were collected during face-to-face interviews. The resulting convenience sample included 96 Indian surrogates. Their sociodemographic characteristics were compared with those of the general population extracted from Indian national surveys. The surrogates interviewed had their first child at a younger age than women in the general population, but they tended to have a smaller family. Their social situation tended to be better than that of the general population in terms of education, employment and family income. These results provide first empirical evidence moderating the common assumption that Indian surrogates are the poorest and least educated women. This does not mean, however, that exploitation does not exist. More studies are needed to confirm these results and to explore the issue in new international destinations for surrogacy. [ABSTRACT FROM AUTHOR]

We propose a set of family-based burden and kernel tests for censored traits (FamBAC and FamKAC). Here, censored traits refer to time-to-event outcomes, for instance, age-at-onset of a disease. To model censored traits in family-based designs, we used the frailty model, which incorporated not only fixed genetic effects of rare variants in a region of interest but also random polygenic effects shared within families. We first partitioned genotype scores of rare variants into orthogonal between- and within-family components, and then derived their corresponding efficient score statistics from the frailty model. Finally, FamBAC and FamKAC were constructed by aggregating the weighted efficient scores of the within-family components across rare variants and subjects. FamBAC collapsed rare variants within subject first to form a burden test that followed a chi-squared distribution; whereas FamKAC was a variant component test following a mixture of chi-squared distributions. For FamKAC, p-values can be computed by permutation tests or for computational efficiency by approximation methods. Through simulation studies, we showed that type I error was correctly controlled by FamBAC for various variant weighting schemes (0.0371 to 0.0527). However, FamKAC type I error rates based on approximation methods were deflated (max 0.0376) but improved by permutation tests. Our simulations also demonstrated that burden test FamBAC had higher power than kernel test FamKAC when high proportion (e.g. ≥ 80%) of causal variants had effects in the same direction. In contrast, when the effects of causal variants on the censored trait were in mixed directions, FamKAC outperformed FamBAC and had comparable or higher power than an existing method, RVFam. Our proposed framework has the flexibility to accommodate general nuclear families, and can be used to analyze sequence data for censored traits such as age-at-onset of a complex disease of interest. [ABSTRACT FROM AUTHOR]

We used an ensemble of statistical methods to build a model that predicts kidney transplant survival and identifies important predictive variables. The proposed model achieved better performance, measured by Harrell’s concordance index, than the Estimated Post Transplant Survival model used in the kidney allocation system in the U.S., and other models published recently in the literature. The model has a five-year concordance index of 0.724 (in comparison, the concordance index is 0.697 for the Estimated Post Transplant Survival model, the state of the art currently in use). It combines predictions from random survival forests with a Cox proportional hazards model. The rankings of importance for the model’s variables differ by transplant recipient age. Better survival predictions could eventually lead to more efficient allocation of kidneys and improve patient outcomes. [ABSTRACT FROM AUTHOR]

Pair bonds are often maintained through the reciprocal and coordinated exchange of communicative signals. The ability to recognize and appropriately respond to a partner’s signals will define a pair’s ability to reproduce. Individual variation in responsiveness, by shaping the formation and maintenance of strong pair bonds, will ultimately influence an individual’s reproductive output. Throughout the breeding period, female cowbirds (Molothrus ater) respond to male song displays using a vocalization known as the chatter. In this study, we investigated whether variation in chatters remained repeatable across years and predicted reproductive performance. A flock of cowbirds housed in a large aviary complex was observed during the spring of 2011 to 2012. We recorded courtship interactions, including singing behavior for males, and chatters and eggs laid by females. The rate with which females responded to song using chatters remained consistent across years, with some females predictably responding to more songs using chatters than others. During 2012, chattering predicted the number of eggs females laid and her paired status. Paired females were more likely to respond to songs with chatters, and there was a strong positive relationship between the number of eggs laid and the proportion of songs she responded to using chatters. Overall, these findings suggest that variation in female vocal behavior is associated with their reproductive success. [ABSTRACT FROM AUTHOR]

Population stratification is a well-known confounding factor in both common and rare variant association analyses. Rare variants tend to be more geographically clustered than common variants, because of their more recent origin. However, it is not yet clear if population stratification at a very fine scale (neighboring administrative regions within a country) would lead to statistical bias in rare variant analyses. As the inclusion of convenience controls from external studies is indeed a common procedure, in order to increase the power to detect genetic associations, this problem is important. We studied through simulation the impact of a fine scale population structure on different rare variant association strategies, assessing type I error and power. We showed that principal component analysis (PCA) based methods of adjustment for population stratification adequately corrected type I error inflation at the largest geographical scales, but not at finest scales. We also showed in our simulations that adding controls obviously increased power, but at a considerably lower level when controls were drawn from another population. [ABSTRACT FROM AUTHOR]

Oscillations of the brain’s local field potential (LFP) may coordinate neural ensembles and brain networks. It has been difficult to causally test this model or to translate its implications into treatments, because there are few reliable ways to alter LFP oscillations. We developed a closed-loop analog circuit to enhance brain oscillations by feeding them back into cortex through phase-locked transcranial electrical stimulation. We tested the system in a rhesus macaque with chronically implanted electrode arrays, targeting 8–15 Hz (alpha) oscillations. Ten seconds of stimulation increased alpha oscillatory power for up to 1 second after stimulation offset. In contrast, open-loop stimulation decreased alpha power. There was no effect in the neighboring 15–30 Hz (beta) LFP rhythm or on a neighboring array that did not participate in closed-loop feedback. Analog closed-loop neurostimulation might thus be a useful strategy for altering brain oscillations, both for basic research and the treatment of neuro-psychiatric disease. [ABSTRACT FROM AUTHOR]

Accurate assessment of the association between continuous variables such as gene expression and survival is a critical aspect of precision medicine. In this report, we provide a review of some of the available survival analysis and validation tools by referencing published studies that have utilized these tools. We have identified pitfalls associated with the assumptions inherent in those applications that have the potential to impact scientific research through their potential bias. In order to overcome these pitfalls, we have developed a novel method that enables the logrank test method to handle continuous variables that comprehensively evaluates survival association with derived aggregate statistics. This is accomplished by exhaustively considering all the cutpoints across the full expression gradient. Direct side-by-side comparisons, global ROC analysis, and evaluation of the ability to capture relevant biological themes based on current understanding of RAS biology all demonstrated that the new method shows better consistency between multiple datasets of the same disease, better reproducibility and robustness, and better detection power to uncover biological relevance within the selected datasets over the available survival analysis methods on univariate gene expression and penalized linear model-based methods. [ABSTRACT FROM AUTHOR]

Interval mapping approaches have been playing significant role for quantitative trait locus (QTL) mapping to discover genetic architecture of diseases or traits with molecular markers. Composite interval mapping (CIM) is one of the superior approaches of the interval mapping for discovering both linked and unlinked putative QTL positions. However, estimators of this approach are not robust against phenotypic outliers. As a result, it fails to detect true QTL positions in presence of outliers. In this study, we investigated the performance of β-Composite Interval Mapping (BetaCIM) for detecting both linked and unlinked important QTLs positions from the robustness points of views. Performance of this approach depends on the value of tuning parameter β. It reduces to the classical CIM approach for β →0. We described and formulated the cross-validation procedure for selecting trait specific optimum value of β. It was observed that the optimum value of β depends on both amount of contaminated observations and their scatteredness. BetaCIM approach discover similar QTL positions as classical IM/CIM in absence of phenotypic outliers, but gives better results in presence of phenotypic outliers in terms of detecting true QTLs and effects estimation. We formulated the generalized forms of robust QTL analysis and developed an R-package named “BetaCIM” by implementing this robust approach. Left and right kidney weight data sets of mouse intercross population (129 S1/SvlmJ × A/J) were analyzed by using BetaCIM, CIM, and IM approaches. For right kidney weight (RKW) CIM and BetaCIM provided similar LOD score profile, and both approaches identified 3 QTL positions. IM approach also identified 3 QTL positions. For left kidney weight (LKW), there was evidence of one outlying observation; and in this case the BetaCIM approach identified 2 QTL positions. However, none of the QTLs were significant by CIM and IM approaches at 5% level of significance. Gene expression ontology (GEO) search showed that the candidate genes (Otof and A330033J07Rik) of the identified QTLs for LKW were expressed in kidney. Both simulation and real data analysis results showed that BetaCIM approach improves the performance over the existing methods in presence of phenotypic outliers. Otherwise, it keeps almost equal performance. [ABSTRACT FROM AUTHOR]

We have identified nine highly connected and differentially expressed gene subnetworks between aggressive primary tumors and metastatic lesions in endometrial carcinomas. We implemented a novel pipeline combining gene set and network approaches, which here allows integration of protein-protein interactions and gene expression data. The resulting subnetworks are significantly associated with disease progression across tumor stages from complex atypical hyperplasia, primary tumors to metastatic lesions. The nine subnetworks include genes related to metastasizing features such as epithelial-mesenchymal transition (EMT), hypoxia and cell proliferation. TCF4 and TWIST2 were found as central genes in the subnetwork related to EMT. Two of the identified subnetworks display statistically significant association to patient survival, which were further supported by an independent validation in the data from The Cancer Genome Atlas data collection. The first subnetwork contains genes related to cell proliferation and cell cycle, while the second contains genes involved in hypoxia such as HIF1A and EGLN3. Our findings provide a promising context to elucidate the biological mechanisms of metastasis, suggest potential prognostic markers and further identify therapeutic targets. The pipeline R source code is freely available, including permutation tests to assess statistical significance of the identified subnetworks. [ABSTRACT FROM AUTHOR]

Comparing the functional performance of biological systems often requires comparing multiple mechanical properties. Such analyses, however, are commonly presented using orthogonal plots that compare N ≤ 3 properties. Here, we develop a multidimensional visualization strategy using permutated radar charts (radial, multi-axis plots) to compare the relative performance distributions of mechanical systems on a single graphic across N ≥ 3 properties. Leveraging the fact that radar charts plot data in the form of closed polygonal profiles, we use shape descriptors for quantitative comparisons. We identify mechanical property-function correlations distinctive to rigid, flexible, and damage-tolerant biological materials in the form of structural ties, beams, shells, and foams. We also show that the microstructures of dentin, bone, tendon, skin, and cartilage dictate their tensile performance, exhibiting a trade-off between stiffness and extensibility. Lastly, we compare the feeding versus singing performance of Darwin’s finches to demonstrate the potential of radar charts for multidimensional comparisons beyond mechanics of materials. [ABSTRACT FROM AUTHOR]