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Background: Alternative splicing (AS) is a principal mode of genetic regulation and one of the most widely used mechanisms to generate structurally and functionally distinct mRNA and protein variants. Dysregulation of AS may result in aberrant transcription and protein products, leading to the emergence of human diseases. Although considered important for regulating gene expression, genome-wide AS dysregulation, underlying mechanisms, and clinical relevance in knee osteoarthritis (OA) remain unelucidated. Therefore, in this study, we elucidated and validated AS events and their regulatory mechanisms during OA progression. Results: In this study, we identified differentially expressed genes between human OA and healthy meniscus samples. Among them, the OA-associated genes were primarily enriched in biological pathways such as extracellular matrix organization and ossification. The predominant OA-associated regulated AS (RAS) events were found to be involved in apoptosis during OA development. The expression of the apoptosis-related gene BCL2L13, XAF1, and NF2 were significantly different between OA and healthy meniscus samples. The construction of a covariation network of RNA-binding proteins (RBPs) and RAS genes revealed that differentially expressed RBP genes LAMA2 and CUL4B may regulate the apoptotic genes XAF1 and BCL2L13 to undergo AS events during OA progression. Finally, RT-qPCR revealed that CUL4B expression was significantly higher in OA meniscus samples than in normal controls and that the AS ratio of XAF1 was significantly different between control and OA samples; these findings were consistent with their expected expression and regulatory relationships. Conclusions: Differentially expressed RBPs may regulate the AS of apoptotic genes during knee OA progression. XAF1 and its regulator, CUL4B, may serve as novel biomarkers and potential therapeutic targets for this disease. [ABSTRACT FROM AUTHOR]

The modular organization of tetrapod paired limbs and girdles, influenced by the expression of Hox genes is one of the primary driving forces of the evolution of animal locomotion. The increased morphological diversification of the paired limbs is correlated with reduced between‐limb covariation, while correlation within the elements is usually higher than between the elements. The tailed amphibians, such as Lissotriton newts, have a biphasic lifestyle with aquatic and terrestrial environments imposing different constraints on limb skeleton. By employing the methods of computerized microtomography and 3D geometric morphometrics, we explored the pattern of morphological variation, disparity, modularity and morphological integration in the proximal parts of the anterior limbs of six species of Eurasian small bodied newts. Although the species significantly differ in limb shape, there is a great overlap in morphology of scapula and humerus, and there are no differences in morphological disparity. For the scapula, the shape differences related to the duration of the aquatic period are in length, depth and curvature. The shape of the humerus is not affected by the length of aquatic period, and shape differences between the species are related to robustness of the body. The length of aquatic period has statistically supported phylogenetic signal. The scapula and humerus are structures of varying modularity. For the humerus, the strongest support on the phylogenetic level was for the capitulum/shaft hypothesis, which can also be interpreted as functional modularity. For the scapula, the greatest support was for the antero‐posterior hypothesis of modularity in case of Lissotriton vulgaris, which can be explained by different functional roles and muscle insertion patterns, while there was no phylogenetic modularity. The modularity patterns seem to correspond with the general tetrapod pattern, with modularity being more pronounced in the distal structure. The future research should include more salamandrid taxa with different habitat preferences and both adult and larval stages, in order to explore how size, phylogeny and ecology affect the morphology and covariation patterns of limbs. [ABSTRACT FROM AUTHOR]

Using a mixed methods approach, we explore a relationship between students' graph reasoning and graph selection via a fully online assessment. Our population includes 673 students enrolled in college algebra, an introductory undergraduate mathematics course, across four U.S. postsecondary institutions. The assessment is accessible on computers, tablets, and mobile phones. There are six items; for each, students are to view a video animation of a dynamic situation (e.g., a toy car moving along a square track), declare their understanding of the situation, select a Cartesian graph to represent a relationship between given attributes in the situation, and enter text to explain their graph choice. To theorize students' graph reasoning, we draw on Thompson's theory of quantitative reasoning, which explains students' conceptions of attributes as being possible to measure. To code students' written responses, we appeal to Johnson and colleagues' graph reasoning framework, which distinguishes students' quantitative reasoning about one or more attributes capable of varying (Covariation, Variation) from students' reasoning about observable elements in a situation (Motion, Iconic). Quantitizing those qualitative codes, we examine connections between the latent variables of students' graph reasoning and graph selection. Using structural equation modeling, we report a significant finding: Students' graph reasoning explains 40% of the variance in their graph selection (standardized regression weight is 0.64, p < 0.001). Furthermore, our results demonstrate that students' quantitative forms of graph reasoning (i.e., variational and covariational reasoning) influence the accuracy of their graph selection. [ABSTRACT FROM AUTHOR]

The paper deals with the estimation methodology for the α-stable periodic autoregressive (PAR) models. For the classical (Gaussian) PAR time series is cyclostationary systems the periodicity is manifested in the model characteristics. One of the most common characteristics used in this context is the autocovariance function. One of the methods of the PAR model estimation utilizes the Yule-Walker equations that contain the autocovariance function of the given process. However, for the infinite variance version of the PAR model (i.e., α-stable-distributed) it is expected that the autocovariance function is not properly defined. Thus, alternative measures need to be used. In this paper, we present the general idea of the modified Yule-Walker equations for the considered model. It is proposed to replace the classical dependency measure by the dependency measures properly defined for infinite variance models. We demonstrate two possible modifications based on the covariation and fractional lower order covariance. The first approach was recently proposed in the literature while the latter is a novel algorithm. We compare the effectiveness of both estimation methods for the considered model. Finally, the results are compared with the classical Yule-Walker approach. We demonstrate the limitations of the classical method for the considered model. The possible application for real data analysis is demonstrated. [ABSTRACT FROM AUTHOR]

An important pathogen of concern for Pacific oyster growers in the USA is ostreid herpesvirus 1 (OsHV‐1). Currently, oyster stocks exist that are tolerant to OsHV‐1; however, it is uncertain if a trade‐off exists between their tolerance to OsHV‐1 and their growth in different environments. To investigate any potential trade‐offs, Pacific oyster families with varying levels of OsHV‐1 tolerance were grown in a bay where OsHV‐1 is endemic (Tomales Bay, CA) and in a bay where OsHV‐1 is absent (Willapa Bay, WA). In Tomales Bay, we found that oysters from OsHV‐1 tolerant families grew faster than oysters from OsHV‐1 susceptible families, while in Willapa Bay, no statistically significant difference in growth was found between oyster families with different levels of OsHV‐1 tolerance observed in Tomales Bay. These findings indicate that Pacific oysters bred to be tolerant to OsHV‐1 would not be expected to have a longer time‐to‐market regardless of the presence of OsHV‐1 in the growing environment. [ABSTRACT FROM AUTHOR]

Geographical variation in animals’ acoustic signals has received much attention. However, few studies have compared the patterns and underlying selective forces driving geographical divergence of vocalizations with similar and different functions within the same species. Also, the social consequences of geographical divergence in acoustic signals are still rather poorly understood. Here we recorded three types of social calls of male great Himalayan leaf-nosed bats (Hipposideros armiger) across eight colonies in China. Two calls share similar functions and the third has a function distinct from the other two. We examined the patterns and causes of geographical variation of each of these calls. We found that all three calls had significant geographic variation with similar patterns of spatial variation. Only one of the two social calls with similar functions was found to be affected by genetic drift, while the other two calls were not affected by selection, drift, or morphological constraints. Furthermore, we found that bats could discriminate between vocalizations of their own colony and those of an allopatric colony. Overall, these results suggest that acoustic signals with similar functions may be shaped by different driving forces and acoustic signals with different functions may exhibit similar geographical patterns. This study expands our limited knowledge of the patterns of geographical variation of vocalizations emitted at different emotional states and highlights the importance of comparing simultaneously patterns and causes of geographical divergence of vocalizations with similar and different functions.Significance statement: This study provides the empirical evidence suggesting that calls with a similar function may fail to co-vary and alternatively calls with a different function may co-vary. Moreover, we show that bats can discriminate between calls of their own colony from those of a foreign colony. These results expand our limited knowledge of the patterns of geographical variation of vocalizations uttered under different emotional states and the nature of functional drivers that influence the evolution of communicative systems. [ABSTRACT FROM AUTHOR]

Facial approximation (FA) provides a promising means of generating the possible facial appearance of a deceased person. It facilitates exploration of the evolutionary forces driving anatomical changes in ancestral humans and can capture public attention. Despite the recent progress made toward improving the performance of FA methods, a limited understanding of detailed quantitative craniofacial relationships between facial bone and soft tissue morphology may hinder their accuracy, and hence subjective experience and artistic interpretation are required. In this study, we explored craniofacial relationships among human populations based upon average facial soft tissue thickness depths (FSTDs) and covariations between hard and soft tissues of the nose and mouth using geometric morphometrics. Furthermore, we proposed a computerized method to assign the learned craniofacial relationships to generate a probable facial appearance of Homo sapiens, reducing human intervention. A smaller resemblance comparison (an average Procrustes distance was 0.0258 and an average Euclidean distance was 1.79 mm) between approximated and actual faces and a greater recognition rate (91.67%) tested by a face pool indicated that average dense FSTDs contributed to raising the accuracy of approximated faces. Results of partial least squares (PLS) analysis showed that nasal and oral hard tissues have an effect on their soft tissues separately. However, relatively weaker RV correlations (<0.4) and greater approximation errors suggested that we need to be cautious about the accuracy of the approximated nose and mouth soft tissue shapes from bony structures. Overall, the proposed method can facilitate investigations of craniofacial relationships and potentially improve the reliability of the approximated faces for use in numerous applications in forensic science, archaeology, and anthropology. [ABSTRACT FROM AUTHOR]

Spatial growth constraints in the head region can lead to coordinated patterns of morphological variation that pleiotropically modify genetically defined phenotypes as the tissues compete for space. Here we test for such architectural modifications during rhesus macaque (Macaca mulatta) postnatal ontogeny. We captured cranium and brain shape from 153 MRI datasets spanning 13 to 1090 postnatal days and tested for patterns of covariation with measurements of relative brain, eyeball, and masseter muscle size as well as callosal tract length. We find that the shape of the infant (<365 days) macaque cranium was most closely aligned to masseter muscle and brain size measured relative to face size. Infant brain and juvenile (365–1090 days) cranium shape were more closely linked with brain size relative to basicranium and face size. Meanwhile, the juvenile macaque brain shape was dominated by the size of the brain relative to that of the basicranium. Associations with relative eyeball size and commissural tract lengths were weaker. Our results are consistent with a spatial‐packing regime operating during postnatal macaque ontogeny, in which relative growth of the masseter, face and basicranium have a greater influence than brain growth on the overall shape of the cranium and brain. [ABSTRACT FROM AUTHOR]

The biological significance of behavioural predictability (environment-independent within-individual behavioural variation) became accepted recently as an important part of an individual's behavioural strategy besides behavioural type (individual mean behaviour). However, we do not know how behavioural type and predictability evolve. Here, we tested different evolutionary scenarios: (i) the two traits evolve independently (lack of correlations) and (ii) the two traits' evolution is constrained (abundant correlations) due to either (ii/a) proximate constraints (direction of correlations is similar) or (ii/b) local adaptations (direction of correlations is variable). We applied a set of phylogenetic meta-analyses based on 93 effect sizes across 44 vertebrate and invertebrate species, focusing on activity and risk-taking. The general correlation between behavioural type and predictability did not differ from zero. Effect sizes for correlations showed considerable heterogeneity, with both negative and positive correlations occurring. The overall absolute (unsigned) effect size was high (Zr = 0.58), and significantly exceeded the null expectation based on randomized data. Our results support the adaptive scenario: correlations between behavioural type and predictability are abundant in nature, but their direction is variable. We suggest that the evolution of these behavioural components might be constrained in a system-specific way.

Background and Aims Few studies of angiosperms have focused on androecial evolution in conjunction with evolutionary shifts in corolla morphology and pollinator relationships. The Western Hemisphere clade of Justiciinae (Acanthaceae) presents the rare opportunity to examine remarkable diversity in staminal morphology. We took a phylogenetically informed approach to examine staminal diversity in this hypervariable group and asked whether differences in anther thecae separation is associated with phylogenetically informed patterns of variation in corolla morphology. We further discuss evidence for associations between anther diversity and pollinators in this lineage. Methods For the Dianthera / Sarotheca / Plagiacanthus (DSP) clade of Western Hemisphere Justiciinae, we characterized floral diversity based on a series of corolla measurements and using a model-based clustering approach. We then tested for correlations between anther thecae separation and corolla traits, and for shifts in trait evolution, including evidence for convergence. Key Results There is evolutionary vagility in corolla and anther traits across the DSP clade with little signal of phylogenetic constraint. Floral morphology clusters into four distinct groups that are, in turn, strongly associated with anther thecae separation, a novel result in Acanthaceae and, to our knowledge, across flowering plants. These cluster groups are marked by floral traits that strongly point to associations with pollinating animals. Specifically, species that are known or likely to be hummingbird pollinated have stamens with parallel thecae, whereas those that are likely bee or fly pollinated have stamens with offset, divergent thecae. Conclusions Our results suggest that anther thecae separation is likely under selection in concert with other corolla characters. Significant morphological shifts detected by our analyses corresponded to putative shifts from insect to hummingbird pollination. Results from this study support the hypothesis that floral structures function in an integrated manner and are likely subject to selection as a suite. Further, these changes can be hypothesized to represent adaptive evolution. [ABSTRACT FROM AUTHOR]

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The time series with periodic behavior, such as the periodic autoregressive (PAR) models belonging to the class of the periodically correlated processes, are present in various real applications. In the literature, such processes were considered in different directions, especially with the Gaussian-distributed noise. However, in most of the applications, the assumption of the finite-variance distribution seems to be too simplified. Thus, one can consider the extensions of the classical PAR model where the non-Gaussian distribution is applied. In particular, the Gaussian distribution can be replaced by the infinite-variance distribution, e.g. by the α -stable distribution. In this paper, we focus on the multidimensional α -stable PAR time series models. For such models, we propose a new estimation method based on the Yule-Walker equations. However, since for the infinite-variance case the covariance does not exist, thus it is replaced by another measure, namely the covariation. In this paper we propose to apply two estimators of the covariation measure. The first one is based on moment representation (moment-based) while the second one—on the spectral measure representation (spectral-based). The validity of the new approaches are verified using the Monte Carlo simulations in different contexts, including the sample size and the index of stability of the noise. Moreover, we compare the moment-based covariation-based method with spectral-based covariation-based technique. Finally, the real data analysis is presented. [ABSTRACT FROM AUTHOR]

Abstract Background Improving the prediction of structures, especially those containing pseudoknots (structures with crossing base pairs) is an ongoing challenge. Homology-based methods utilize structural similarities within a family to predict the structure. However, their prediction is limited to the consensus structure, and by the quality of the alignment. Minimum free energy (MFE) based methods, on the other hand, do not rely on familial information and can predict structures of novel RNA molecules. Their prediction normally suffers from inaccuracies due to their underlying energy parameters. Results We present a new method for prediction of RNA pseudoknotted secondary structures that combines the strengths of MFE prediction and alignment-based methods. KnotAli takes a multiple RNA sequence alignment as input and uses covariation and thermodynamic energy minimization to predict possibly pseudoknotted secondary structures for each individual sequence in the alignment. We compared KnotAli’s performance to that of three other alignment-based programs, two that can handle pseudoknotted structures and one control, on a large data set of 3034 RNA sequences with varying lengths and levels of sequence conservation from 10 families with pseudoknotted and pseudoknot-free reference structures. We produced sequence alignments for each family using two well-known sequence aligners (MUSCLE and MAFFT). Conclusions We found KnotAli’s performance to be superior in 6 of the 10 families for MUSCLE and 7 of the 10 for MAFFT. While both KnotAli and Cacofold use background noise correction strategies, we found KnotAli’s predictions to be less dependent on the alignment quality. KnotAli can be found online at the Zenodo image: https://doi.org/10.5281/zenodo.5794719

Residues in proteins that are in close spatial proximity are more prone to covariate as their interactions are likely to be preserved due to structural and evolutionary constraints. If we can detect and quantify such covariation, physical contacts may then be predicted in the structure of a protein solely from the sequences that decorate it. To carry out such predictions, and following the work of others, we have implemented a multivariate Gaussian model to analyze correlation in multiple sequence alignments. We have explored and tested several numerical encodings of amino acids within this model. We have shown that 1D encodings based on amino acid biochemical and biophysical properties, as well as higher dimensional encodings computed from the principal components of experimentally derived mutation/substitution matrices, do not perform as well as a simple twenty dimensional encoding with each amino acid represented with a vector of one along its own dimension and zero elsewhere. The optimum obtained from representations based on substitution matrices is reached by using 10 to 12 principal components; the corresponding performance is less than the performance obtained with the 20-dimensional binary encoding. We highlight also the importance of the prior when constructing the multivariate Gaussian model of a multiple sequence alignment.

This paper focuses on the importance of covariational reasoning within the processes of mathematics teaching and learning. Despite the internationally recognized relevance of covariation, research shows that only a small percentage of students and teachers is able to adopt covariational reasoning and the majority of mathematics curricula do not contain explicit references to covariational skills. In particular, when covariational reasoning manifests as conceptual knowledge, it becomes challenging to assess, and the need for innovative methods of assessment emerges; there is a need for suitable assessment to highlight the characteristics of covariation and capture the various features that characterize conceptual understanding. Comparative judgement (CJ) is an innovative assessment method based on collective expert judgements of students' work rather than requiring scoring rubrics. Due to its holistic approach, CJ is particularly suitable for assessing complex mathematical competencies, and, as we shall see in this study, it proved to be appropriate for the covariation's assessment. In details, our study aims to investigate the perception and relevance attributed by mathematics teachers to covariation as a theoretical construct and the way CJ can help in the assessment of covariational reasoning skills underlying a less structured modelling task. [ABSTRACT FROM AUTHOR]

Intrinsically disordered regions (IDRs) can function as autoregulators of folded enzymes to which they are tethered. One example is the bacterial cell division protein FtsZ. This includes a folded core and a C-terminal tail (CTT) that encompasses a poorly conserved, disordered C-terminal linker (CTL) and a well-conserved 17-residue C-terminal peptide (CT17). Sites for GTPase activity of FtsZs are formed at the interface between GTP binding sites and T7 loops on cores of adjacent subunits within dimers. Here, we explore the basis of autoregulatory functions of the CTT in Bacillus subtilis FtsZ (Bs-FtsZ). Molecular simulations show that the CT17 of Bs-FtsZ makes statistically significant CTL-mediated contacts with the T7 loop. Statistical coupling analysis of more than 1,000 sequences from FtsZ orthologs reveals clear covariation of the T7 loop and the CT17 with most of the core domain, whereas the CTL is under independent selection. Despite this, we discover the conservation of nonrandom sequence patterns within CTLs across orthologs. To test how the nonrandom patterns of CTLs mediate CTT–core interactions and modulate FtsZ functionalities, we designed Bs-FtsZ variants by altering the patterning of oppositely charged residues within the CTL. Such alterations disrupt the core–CTT interactions, lead to anomalous assembly and inefficient GTP hydrolysis in vitro and protein degradation, aberrant assembly, and disruption of cell division in vivo. Our findings suggest that viable CTLs in FtsZs are likely to be IDRs that encompass nonrandom, functionally relevant sequence patterns that also preserve three-way covariation of the CT17, the T7 loop, and core domain. [ABSTRACT FROM AUTHOR]

A long‐standing question in comparative biology is how the evolution of biomechanical systems influences morphological evolution. The need for functional fidelity implies that the evolution of such systems should be associated with tighter morphological covariation, which may promote or dampen rates of morphological evolution. I examine this question across multiple evolutionary origins of the trap‐jaw mechanism in the genus Strumigenys. Trap‐jaw ants have latch‐mediated, spring‐actuated systems that amplify the power output of their mandibles. I use Bayesian estimates of covariation and evolutionary rates to test the hypotheses that the evolution of this high‐performance system is associated with tighter morphological covariation in the head and mandibles relative to nontrap‐jaw forms and that this leads to shifts in rates of morphological evolution. Contrary to these hypotheses, there is no evidence of a large‐scale shift to higher covariation in trap‐jaw forms, while different traits show both increased and decreased evolutionary rates between forms. These patterns may be indicative of many‐to‐one mapping and/or mechanical sensitivity in the trap‐jaw LaMSA system. Overall, it appears that the evolution of trap‐jaw forms in Strumigenys did not require a correlated increase in morphological covariation, partly explaining the proclivity with which the system has evolved. [ABSTRACT FROM AUTHOR]

Abstract Background Mammalian mandible and cranium are well-established model systems for studying canalization and developmental stability (DS) as two elements of developmental homeostasis. Nematode infections are usually acquired in early life and increase in intensity with age, while canalization and DS of rodent skulls could vary through late postnatal ontogeny. We aimed to estimate magnitudes and describe patterns of mandibular and cranial canalization and DS related to age and parasite intensity (diversity) in adult yellow-necked mice (Apodemus flavicollis). Results We found the absence of age-related changes in the levels of canalization for mandibular and cranial size and DS for mandibular size. However, individual measures of mandibular and cranial shape variance increased, while individual measures of mandibular shape fluctuating asymmetry (FA) decreased with age. We detected mandibular and cranial shape changes during postnatal ontogeny, but revealed no age-related dynamics of their covariance structure among and within individuals. Categories regarding parasitism differed in the level of canalization for cranial size and the level of DS for cranial shape. We observed differences in age-related dynamics of the level of canalization between non-parasitized and parasitized animals, as well as between yellow-necked mice parasitized by different number of nematode species. Likewise, individual measures of mandibular and cranial shape FA decreased with age for the mandible in the less parasitized category and increased for the cranium in the most parasitized category. Conclusions Our age-related results partly agree with previous findings. However, no rodent study so far has explored age-related changes in the magnitude of FA for mandibular size or mandibular and cranial FA covariance structure. This is the first study dealing with the nematode parasitism-related canalization and DS in rodents. We showed that nematode parasitism does not affect mandibular and cranial shape variation and covariance structure among and within individuals. However, parasite intensity (diversity) is related to ontogenetic dynamics of the levels of canalization and DS. Overall, additional studies on animals from natural populations are required before drawing some general conclusions.

Are causal explanations (e.g., “she switched careers because of the COVID pandemic”) treated differently from the corresponding claims that one factor caused another (e.g., “the COVID pandemic caused her to switch careers”)? We examined whether explanatory and causal claims diverge in their responsiveness to two different types of information: covariation strength and mechanism information. We report five experiments with 1,730 participants total, showing that compared to judgments of causal strength, explanatory judgments tend to be more sensitive to mechanism and less sensitive to covariation – even though explanatory judgments respond to both types of information. We also report exploratory comparisons to judgments of understanding, and discuss implications of our findings for theories of explanation, understanding, and causal attribution. These findings shed light on the potentially unique role of explanation in cognition.

Summary: A trait coordination network is constructed through intercorrelations of functional traits, which reflect trait‐based adaptive strategies. However, little is known about how these networks change across spatial scales, and what drivers and mechanisms mediate this change.This study bridges that gap by integrating functional traits related to plant carbon gain and water economy into the coordination network of Siberian elm (Ulmus pumila), a eurybiont that survives along a 3800 km environmental gradient from humid forest to arid desert.Our results demonstrated that both stomatal density and stomatal size reached a physiological threshold at which adjustments in these traits were not sufficient to cope with the increased environmental stress. Network analysis further revealed that the mechanism for overcoming this threshold, the stomatal opening ratio, gratio, was represented by the highest values for centrality across different spatial scales, and therefore mediated the changes in the trait coordination network along environmental gradients. The mediating roles manifested as creating the highest maximum theoretical stomatal conductance (gsmax) but lowest possible gratio for pathogen defense in humid regions, while maintaining the gratio 'sweet spot' (c. 20% in this region) for highest water use efficiency in semihumid regions, and having the lowest gsmax and highest gratio for gas exchange and leaf cooling in arid regions.These results suggested that the stomatal traits related to control of stomatal movement play fundamental roles in balancing gas exchange, leaf cooling, embolism resistance and pathogen defense. These insights will allow more accurate model parameterization for different regions, and therefore better predictions of species' responses to global change. [ABSTRACT FROM AUTHOR]

Simple Summary: The origin of complex morphological structures is explained mainly by direct pathways fusing adjacent modules, while the independent effect of parallel pathways acting on different areas of a morphogenetic field is less well-known. The palimpsest model that explains the cephalothoracic structural complexity of decapod crustaceans is composed of two hox-regulatory parallel pathways that tagmatize the anterior metameres early, followed by a direct pathway that fuses the tagmata forming the developmental modules. The cephalothoracic geometry of Aegla araucaniensis shows a marked sexual dimorphism; its adaptive causes also promote dimorphic variations in the evolvability of developmental modularity. We found areas of instability in the variance of the asymmetry in both developmental modules. The direct pathway presents intermediate levels of canalization in the covariation of the developmental modules, although significantly higher in males. This low restrictive potential promotes expressions of gonadic modularity in females and agonistic modularity in males, which differ significantly from developmental modularity. The cephalothoracic palimpsest model of decapods allows studying modularity in an explicit evo–devo context. The integration of complex structures is proportional to the intensity of the structural fusion; its consequences are better known than the covariational effects under less restrictive mechanisms. The synthesis of a palimpsest model based on two early parallel pathways and a later direct pathway explains the cephalothoracic complexity of decapod crustaceans. Using this model, we tested the evolvability of the developmental modularity in Aegla araucaniensis, an anomuran crab with an evident adaptive sexual dimorphism. The asymmetric patterns found on the landmark configurations suggest independent perturbations of the parallel pathways in each module and a stable asymmetry variance near the fusion by canalization of the direct pathway, which was more intense in males. The greater covariational flexibility imposed by the parallel pathways promotes the expression of gonadic modularity that favors the reproductive output in females and agonistic modularity that contributes to mating success in males. Under these divergent expressions of evolvability, the smaller difference between developmental modularity and agonistic modularity in males suggests higher levels of canalization due to a relatively more intense structural fusion. We conclude that: (1) the cephalothorax of A. araucaniensis is an evolvable structure, where parallel pathways promote sexual disruptions in the expressions of functional modularity, which are more restricted in males, and (2) the cephalothoracic palimpsest of decapods has empirical advantages in studying the developmental causes of evolution of complex structures. [ABSTRACT FROM AUTHOR]

Links between contrasting ecological conditions and evolutionary shifts in neurosensory components, such as brain and eye size, are accumulating. Whether selection operates in a different manner on these traits between sexes is unclear. Trinidadian killifish (Anablepsoides hartii) are found in sites with and without predators. Male killifish from sites without predators have evolved larger brains and eyes than males from sites with predators. These differences in brain size are present early in life but disappear in adult size classes. Here, we evaluated female brain growth allometries to determine whether females exhibit similar size-specific differences in brain size between sites that differ in predation intensity. We also quantified brain size and structure and eye size to determine whether these structures co-evolved in a sex-specific manner. We found that female brain growth allometries did not differ across populations. Yet, female killifish from sites without predators exhibited a larger cerebellum, optic tectum and dorsal medulla early in life (before maturation), although such differences disappeared in larger size classes. Females from sites with predators exhibited similar patterns in brain growth to males in those sites; therefore, shifts in brain size and structure are driven by differences between sexes in sites without predators. We also found evidence for covariation between brain and eye size in both sexes despite different levels of variation in both structures, suggesting that these structures might covary to fluctuating degrees in sex-specific ways. We conclude that differential investment in brain tissue in sites without predators might be linked to varying reproductive and cognitive demands between the sexes. [ABSTRACT FROM AUTHOR]

The evolution of the hominoid lineage is characterized by pervasive homoplasy, notably in regions such as the vertebral column, which plays a central role in body support and locomotion. Few isolated and fewer associated vertebrae are known for most fossil hominoid taxa, but identified specimens indicate potentially high levels of convergence in terms of both form and number. Homoplasy thus complicates attempts to identify the anatomy of the last common ancestor of hominins and other taxa and stymies reconstructions of evolutionary scenarios. One way to clarify the role of homoplasy is by investigating constraints via phenotypic integration, which assesses covariation among traits, shapes evolutionary pathways, and itself evolves in response to selection. We assessed phenotypic integration and evolvability across the subaxial (cervical, thoracic, lumbar, sacral) vertebral column of macaques (n = 96), gibbons (n = 77), chimpanzees (n = 92), and modern humans (n = 151). We found a mid-cervical cluster that may have shifted cranially in hominoids, a persistent thoracic cluster that is most marked in chimpanzees, and an expanded lumbosacral cluster in hominoids that is most expanded in gibbons. Our results highlight the highly conserved nature of the vertebral column. Taxa appear to exploit existing patterns of integration and ontogenetic processes to shift, expand, or reduce cluster boundaries. Gibbons appear to be the most highly derived taxon in our sample, possibly in response to their highly specialized locomotion. • Phenotypic integration can reveal areas under particular evolutionary constraints. • Macaques and hominoids display conserved patterns of integration and evolvability. • Hominoids include the sacrum in the cluster corresponding to lumbar elements. • Gibbons display a specialized thoracolumbar clusters. [ABSTRACT FROM AUTHOR]

Research on covariational reasoning has continued to evolve as researchers learn more about how students coordinate two (or more) quantities' values as covarying. In this study, I examine the connection between students' covariational reasoning and how they interpret the value of a rate of change. The findings suggest that attending to students' quantifications of a rate of change can provide insight into their covariational reasoning and how we might better support students in reasoning at higher levels. Additionally, this manuscript provides an update to the Carlson et al. (2002) Covariation Framework that includes two additional categories of student reasoning and an additional dimension that describes students' interpretation of a rate value at each level of the framework. [ABSTRACT FROM AUTHOR]

We analyse variation in vowel production within monologues produced by speakers in a quiet, well-controlled environment. Using principal component analysis (PCA) and generalized additive mixed models (GAMMs), applied to a large corpus of naturalistic recordings of New Zealand English speakers, we show that the first formant of monophthongs varies significantly with variation in a speaker's relative amplitude. We also find that amplitude variation is used, potentially agentively, to mark the beginning and ending of topical sections within single-speaker monologues. These results have significant methodological consequences for the study of vocalic variation in the context of research on speaker style and language variation and change. While laboratory research has shown a connection between variation in F1 and amplitude in loud environments or with distant interlocutors, this has not been seen in quiet environments with unscripted speech of the sort often used in sociolinguistcs. We argue that taking account of this variation is an important challenge for both within-speaker investigation of stylistic covariation and across-speaker investigation. In the latter case we recommend, as a minimal step, the inclusion of a measure of relative amplitude within regression models. [ABSTRACT FROM AUTHOR]

Hepatitis B viruses (HBVs) are compact viruses with circular genomes of ∼3.2 kb in length. Four genes (HBx, Core, Surface, and Polymerase) generating seven products are encoded on overlapping reading frames. Ten HBV genotypes have been characterised (A–J), which may account for differences in transmission, outcomes of infection, and treatment response. However, HBV genotyping is rarely undertaken, and sequencing remains inaccessible in many settings. We set out to assess which amino acid (aa) sites in the HBV genome are most informative for determining genotype, using a machine learning approach based on random forest algorithms (RFA). We downloaded 5,496 genome-length HBV sequences from a public database, excluding recombinant sequences, regions with conserved indels, and genotypes I and J. Each gene was separately translated into aa, and the proteins concatenated into a single sequence (length 1,614 aa). Using RFA, we searched for aa sites predictive of genotype and assessed covariation among the sites with a mutual information–based method. We were able to discriminate confidently between genotypes A–H using ten aa sites. Half of these sites (5/10) sites were identified in Polymerase (Pol), of which 4/5 were in the spacer domain and one in reverse transcriptase. A further 4/10 sites were located in Surface protein and a single site in HBx. There were no informative sites in Core. Properties of the aa were generally not conserved between genotypes at informative sites. Among the highest co-varying pairs of sites, there were fifty-five pairs that included one of these 'top ten' sites. Overall, we have shown that RFA analysis is a powerful tool for identifying aa sites that predict the HBV lineage, with an unexpectedly high number of such sites in the spacer domain, which has conventionally been viewed as unimportant for structure or function. Our results improve ease of genotype prediction from limited regions of HBV sequences and may have future applications in understanding HBV evolution. [ABSTRACT FROM AUTHOR]

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Abstract Brain size, brain architecture, and eye size vary extensively in vertebrates. However, the extent to which the evolution of these components is intricately connected remains unclear. Trinidadian killifish, Anablepsoides hartii, are found in sites that differ in the presence and absence of large predatory fish. Decreased rates of predation are associated with evolutionary shifts in brain size; males from sites without predators have evolved a relatively larger brain and eye size than males from sites with predators. Here, we evaluated the extent to which the evolution of brain size, brain structure, and eye size covary in male killifish. We utilized wild‐caught and common garden‐reared specimens to determine whether specific components of the brain have evolved in response to differences in predation and to determine if there is covariation between the evolution of brain size, brain structure, and eye size. We observed consistent shifts in brain architecture in second generation common garden reared, but not wild caught preserved fish. Male killifish from sites that lack predators exhibited a significantly larger telencephalon, optic tectum, cerebellum, and dorsal medulla when compared with fish from sites with predators. We also found positive connections between the evolution of brain structure and eye size but not between overall brain size and eye size. These results provide evidence for evolutionary covariation between the components of the brain and eye size. Such results suggest that selection, directly or indirectly, acts upon specific regions of the brain, rather than overall brain size, to enhance visual capabilities.

This study aims at understanding the role of the tools chosen throughout the processes of solving a non-routine mathematical problem and communicating its solution. In assuming that problem-solving is a synchronous activity of mathematization and expression of mathematical thinking we take our proposed Mathematical Problem Solving with Technology (MPST) model to analyze the processes of solving-and-expressing-problems. Resorting to qualitative methods for data collection and analysis, we report on the case of an 8th grader working on a covariation problem to examine the role that paper-and-pencil and digital tools play in the development of a conceptual model of the situation. We found that the resources used throughout the solving-and-expressing activity influenced the depth of the conceptual model developed, within a process of progressive mathematization. Whereas paper-and-pencil led to the emergence of a conceptual model based on exploring particular cases, the digital transformation of the solution was triggered by the process of communicating its mathematical justification and expanded the previous model. Moreover, the complexity of this activity is evidenced by its multiple sequences of processes. Finally, the integration process seems crucial as the concomitant use of technological and mathematical resources precedes major advancements in the expansion of the conceptual model.

Background: Improving the prediction of structures, especially those containing pseudoknots (structures with crossing base pairs) is an ongoing challenge. Homology-based methods utilize structural similarities within a family to predict the structure. However, their prediction is limited to the consensus structure, and by the quality of the alignment. Minimum free energy (MFE) based methods, on the other hand, do not rely on familial information and can predict structures of novel RNA molecules. Their prediction normally suffers from inaccuracies due to their underlying energy parameters. Results: We present a new method for prediction of RNA pseudoknotted secondary structures that combines the strengths of MFE prediction and alignment-based methods. KnotAli takes a multiple RNA sequence alignment as input and uses covariation and thermodynamic energy minimization to predict possibly pseudoknotted secondary structures for each individual sequence in the alignment. We compared KnotAli's performance to that of three other alignment-based programs, two that can handle pseudoknotted structures and one control, on a large data set of 3034 RNA sequences with varying lengths and levels of sequence conservation from 10 families with pseudoknotted and pseudoknot-free reference structures. We produced sequence alignments for each family using two well-known sequence aligners (MUSCLE and MAFFT). Conclusions: We found KnotAli's performance to be superior in 6 of the 10 families for MUSCLE and 7 of the 10 for MAFFT. While both KnotAli and Cacofold use background noise correction strategies, we found KnotAli's predictions to be less dependent on the alignment quality. KnotAli can be found online at the Zenodo image: https://doi.org/10.5281/zenodo.5794719 [ABSTRACT FROM AUTHOR]

The function concept arose from analyzing the relationships between co-varying quantities to model change. From the covariation perspective of function, we analyzed the responses of 13 pre-service teachers to the tasks to interpret rates of change or reason the corresponding change of one quantity from the changes of the other using the given rate of change; by using the rate of change, a change of one quantity can be directly deduced from the given change of the other quantity. Most of the pre-service teachers reasoned the change correctly. However, a portion of pre-service teachers reflexively calculated the formula of the function and the difference between the two values of the function. In addition, some teachers revealed their insufficient understanding of the slope of the linear function. The conceptions of pre-service teachers help elucidate what and how students might learn and might not learn about functions from the school mathematics curriculum.

Biomass allocation plays a critical role in plant morphological formation and phenotypic plasticity, which greatly impact plant adaptability and competitiveness. While empirical studies on plant biomass allocation have focused on molecular biology and ecology approaches, detailed insight into the genetic basis of biomass allocation between leaf and stem growth is still lacking. Herein, we constructed a bivariate mapping model to identify covariation QTLs governing carbon (C) allocation between the leaves and stem as well as the covariation of traits within and between organs in a full-sib mapping population of C. bungei. A total of 123 covQTLs were detected for 23 trait pairs, including six leaf traits (leaf length, width, area, perimeter, length/width ratio and petiole length) and five stem traits (height, diameter at breast height, wood density, stemwood volume and stemwood biomass). The candidate genes were further identified in tissue-specific gene expression data, which provided insights into the genetic architecture underlying C allocation for traits or organs. The key QTLs related to growth and biomass allocation, which included UVH1, CLPT2, GAD/SPL, COG1 and MTERF4, were characterised and verified via gene function annotation and expression profiling. The integration of a bivariate Quantitative trait locus mapping model and gene expression profiling will enable the elucidation of genetic architecture underlying biomass allocation and covariation growth, in turn providing a theoretical basis for forest molecular marker-assisted breeding with specific C allocation strategies for adaptation to heterogeneous environments.

Individual animals vary in their behaviors. This is true even when they share the same genotype and were reared in the same environment. Clusters of covarying behaviors constitute behavioral syndromes, and an individual’s position along such axes of covariation is a representation of their personality. Despite these conceptual frameworks, the structure of behavioral covariation within a genotype is essentially uncharacterized and its mechanistic origins unknown. Passing hundreds of inbred Drosophila individuals through an experimental pipeline that captured hundreds of behavioral measures, we found sparse but significant correlations among small sets of behaviors. Thus, the space of behavioral variation has many independent dimensions. Manipulating the physiology of the brain, and specific neural populations, altered specific correlations. We also observed that variation in gene expression can predict an individual’s position on some behavioral axes. This work represents the first steps in understanding the biological mechanisms determining the structure of behavioral variation within a genotype.

The integration of complex structures is proportional to the intensity of the structural fusion; its consequences are better known than the covariational effects under less restrictive mechanisms. The synthesis of a palimpsest model based on two early parallel pathways and a later direct pathway explains the cephalothoracic complexity of decapod crustaceans. Using this model, we tested the evolvability of the developmental modularity in Aegla araucaniensis, an anomuran crab with an evident adaptive sexual dimorphism. The asymmetric patterns found on the landmark configurations suggest independent perturbations of the parallel pathways in each module and a stable asymmetry variance near the fusion by canalization of the direct pathway, which was more intense in males. The greater covariational flexibility imposed by the parallel pathways promotes the expression of gonadic modularity that favors the reproductive output in females and agonistic modularity that contributes to mating success in males. Under these divergent expressions of evolvability, the smaller difference between developmental modularity and agonistic modularity in males suggests higher levels of canalization due to a relatively more intense structural fusion. We conclude that: (1) the cephalothorax of A. araucaniensis is an evolvable structure, where parallel pathways promote sexual disruptions in the expressions of functional modularity, which are more restricted in males, and (2) the cephalothoracic palimpsest of decapods has empirical advantages in studying the developmental causes of evolution of complex structures.

Aim: Suicide is one of the leading causes of death globally, inherently linked with mental health conditions. Existing studies have also found a significant association between suicide and chronic health conditions such as human immunodeficiency virus (HIV). Although there have been enormous studies on these global health issues, knowledge about their co-existence is elusive. This paper examines the link between HIV and suicide in 186 countries using geospatial techniques and spatial statistics. Subject and methods: We used country-level suicide and HIV data obtained from the United Nations Development Program database. The local bivariate spatial association technique was used to determine the covariation of HIV and suicide, while autoregressive models were used to estimate the unexplained country-level variables in the model. Due to evidence of spatial dependencies, we applied multiscale geographically weighted regression (MGWR) to examine the spatial variation in the predictor variables. The local bivariate spatial association technique was used to determine the covariation of HIV and suicide. Results: Analysis indicated that HIV significantly covaried with suicide in regions of Africa and Europe. Our result suggests that HIV is a significant driver of suicide among females in sub-Saharan Africa while it drives suicide among males in many regions including the country of South Africa, Lesotho, Swaziland, Oceania, and Southeast Asia. MGWR indicated that HIV was negatively associated with suicide in the Americas and European countries, but positively associated with suicide in Africa, the Middle East, and Oceania. Conclusion: There is a double burden of HIV and suicide in sub-Saharan Africa. Therefore, investment in both mental healthcare and access to antiretroviral drugs is essential in reducing suicide at both global and local levels. [ABSTRACT FROM AUTHOR]

Abstract: The perception of social meanings and styles is dependent upon the contributions of a constellation of multiple covarying sociolinguistic variants. This suggests that listeners maintain associations between stylistically coherent variants and their social meanings in mental representation. The present paper expands upon this notion, aiming to gain converging evidence from production as a way to explore the cognitive representations of variants and their social meanings more deeply. To do this, four American English speakers were asked to produce sentences containing (ING) words (as in talking vs. talkin’), in their –in and –ing variants, in a laboratory setting. Productions were acoustically analyzed to evaluate whether the speakers also manipulated other stylistically-linked variables, even though prompted only to manipulate (ING). The variant –in has been shown to index a range of social meanings in American English, including Southern and casual. Results demonstrate that speakers indeed modulated other variables beyond (ING) in ways that align with the Southern and casual social meanings of –in. That producing one variant (–in) could lead to stylistically congruent realizations of other variables suggests that speakers not only hold indexical linkages between variants and styles in mental representation, but that variants are also linked to variants of other variables through associations with those styles. A better understanding of social meaning in cognition provides an important base upon which to advance research on sociolinguistic perception. Keywords: covariation; social meaning; cognitive representation; style. Resumo: A percepção de significados sociais e de estilos depende das constribuições de uma constelação de múltiplas variantes sociolinguísticas em covariação. Isto sugere que os falantes mantêm associações entre variantes estilisticamente coerentes e seus significados sociais numa representação mental. O presente trabalho expande essa noção, com o objetivo de ganhar evidências advindas da produção como meio de explorar mais profundamente as representações cognitivas de variantes e de seus significados sociais. Para isso, quatro falantes de inglês norte-americano foram convidados a produzir sentenças que contêm variantes de (ING) (como em talking vs. talkin’ ‘falando’), em contexto de laboratório. As produções foram acusticamente analisadas no sentido de avaliar se os falantes também manipularam estilisticamente outras variáveis, ainda que houvessem sido instruídos a manipular apenas (ING). Trabalhos anteriores já mostraram que a variante –in indicia uma grande extensão de significados sociais em inglês norte-americano, incluindo sotaque sulista e casualidade. Os resultados mostram que os falantes de fato modulam outras variáveis além de (ING) que se alinham a esses significados sociais de –in. O fato de que a produção de uma variante pode conduzir a realizações estilisticamente congruentes de variantes de outras variáveis sugere que os falantes não apenas detêm associações indiciais entre variantes e estilos em sua representação mental, mas também que variantes de diferentes variáveis estão ligadas entre si na sua associação a tais estilos. Entender melhor a significação social de múltiplas variáveis na cognição oferece uma base importante na qual deve avançar a pesquisa sobre percepção sociolinguística. Palavras-chave: covariação; significado social; representação cognitiva; estilo.

Background: Mammalian mandible and cranium are well-established model systems for studying canalization and developmental stability (DS) as two elements of developmental homeostasis. Nematode infections are usually acquired in early life and increase in intensity with age, while canalization and DS of rodent skulls could vary through late postnatal ontogeny. We aimed to estimate magnitudes and describe patterns of mandibular and cranial canalization and DS related to age and parasite intensity (diversity) in adult yellow-necked mice (Apodemus flavicollis). Results: We found the absence of age-related changes in the levels of canalization for mandibular and cranial size and DS for mandibular size. However, individual measures of mandibular and cranial shape variance increased, while individual measures of mandibular shape fluctuating asymmetry (FA) decreased with age. We detected mandibular and cranial shape changes during postnatal ontogeny, but revealed no age-related dynamics of their covariance structure among and within individuals. Categories regarding parasitism differed in the level of canalization for cranial size and the level of DS for cranial shape. We observed differences in age-related dynamics of the level of canalization between non-parasitized and parasitized animals, as well as between yellow-necked mice parasitized by different number of nematode species. Likewise, individual measures of mandibular and cranial shape FA decreased with age for the mandible in the less parasitized category and increased for the cranium in the most parasitized category. Conclusions: Our age-related results partly agree with previous findings. However, no rodent study so far has explored age-related changes in the magnitude of FA for mandibular size or mandibular and cranial FA covariance structure. This is the first study dealing with the nematode parasitism-related canalization and DS in rodents. We showed that nematode parasitism does not affect mandibular and cranial shape variation and covariance structure among and within individuals. However, parasite intensity (diversity) is related to ontogenetic dynamics of the levels of canalization and DS. Overall, additional studies on animals from natural populations are required before drawing some general conclusions. [ABSTRACT FROM AUTHOR]

This paper considers how 5- to 11-year-olds’ verbal reasoning about the causality underlying extended, dynamic natural processes links to various facets of their statistical thinking. Such continuous processes typically do not provide perceptually distinct causes and effect, and previous work suggests that spatial–temporal analysis, the ability to analyze spatial configurations that change over time, is a crucial predictor of reasoning about causal mechanism in such situations. Work in the Humean tradition to causality has long emphasized on the importance of statistical thinking for inferring causal links between distinct cause and effect events, but here we assess whether this is also viable for causal thinking about continuous processes. Controlling for verbal and non-verbal ability, two studies (N = 107; N = 124) administered a battery of covariation, probability, spatial–temporal, and causal measures. Results indicated that spatial–temporal analysis was the best predictor of causal thinking across both studies, but statistical thinking supported and informed spatial–temporal analysis: covariation assessment potentially assists with the identification of variables, while simple probability judgment potentially assists with thinking about unseen mechanisms. We conclude that the ability to find out patterns in data is even more widely important for causal analysis than commonly assumed, from childhood, having a role to play not just when causally linking already distinct events but also when analyzing the causal process underlying extended dynamic events without perceptually distinct components.

The free energy principle (FEP) is an information-theoretic approach to living systems. FEP characterizes life by living systems' resistance to the second law of thermodynamics: living systems do not randomly visit the possible states, but actively work to remain within a set of viable states. In FEP, this is modelled mathematically. Yet, the status of these models is typically unclear: are these models employed by organisms or strictly scientific tools of understanding? In this article, I argue for an instrumentalist take on models in FEP. I shall argue that models used as instruments for knowledge by scientists and models as implemented by organisms to navigate the world are being conflated, which leads to erroneous conclusions. I further argue that a realist position is unwarranted. First, it overgenerates models and thus trivializes the notion of modelling. Second, even when the mathematical mechanisms described by FEP are implemented in an organism, they do not constitute a model. They are covariational, not representational in nature, and precede the social practices that have shaped our scientific modelling practice. I finally argue that the above arguments do not affect the instrumentalist position. An instrumentalist approach can further add to conceptual clarity in the FEP literature. [ABSTRACT FROM AUTHOR]

Multiple sensory signals from visual, somatosensory and vestibular systems are used for human postural control. To maintain postural stability, the central nervous system keeps the center of mass (CoM) within the base of support. The influence of the stomatognathic motor system on postural control has been established under static conditions, but it has not yet been investigated during dynamic steady-state balance. The purpose of the study was to investigate the effects of controlled stomatognathic motor activity on the control and stability of the CoM during dynamic steady-state balance. A total of 48 physically active and healthy adults were assigned to three groups with different stomatognathic motor conditions: jaw clenching, tongue pressing and habitual stomatognathic behavior. Dynamic steady-state balance was assessed using an oscillating platform and the kinematic data were collected with a 3D motion capturing system. The path length (PL) of the 3D CoM trajectory was used for quantifying CoM sway. Temporal dynamics of the CoM movement was assessed with a detrended fluctuation analysis (DFA). An uncontrolled manifold (UCM) analysis was applied to assess the stability and control of the CoM with a subject-specific anthropometric 3D model. The statistical analysis revealed that the groups did not differ significantly in PL, DFA scaling exponents or UCM parameters. The results indicated that deliberate jaw clenching or tongue pressing did not seem to affect the sway, control or stability of the CoM on an oscillating platform significantly. Because of the task-specificity of balance, further research investigating the effects of stomatognathic motor activities on dynamic steady-state balance with different movement tasks are needed. Additionally, further analysis by use of muscle synergies or co-contractions may reveal effects on the level of muscles, which were not visible on the level of kinematics. This study can contribute to the understanding of postural control mechanisms, particularly in relation to stomatognathic motor activities and under dynamic conditions. [ABSTRACT FROM AUTHOR]