Search

Controversy has surrounded realist explanations of the causes of Russia's war against Ukraine, particularly John Mearsheimer's charge of western responsibility. This article seeks to clarify and contextualize his argument, situating it within the broader paradigm. Realism, and even its narrower offensive sub-school, offers a wide range of contrasting interpretations, depending on which major actors are studied and what characteristics they are endowed with. Like its classical predecessor, structural realism is premised on implicit views of human nature. In an effort to explicate some of these assumptions about the behavioural micro-foundations of states and their leaders, the article investigates main components of structural theory—including power differentials, 'rational' interests and states as unitary actors—and connects these concepts to base emotions like fear and anger. It argues that realists do well to differentiate between the aspirations of states and individual leaders' quest for power and status. In the same vein, reference to Russian security concerns may be emblematic of elites' perceived challenges of cultural subordination, and Putin's personal fears for the stability of his regime. Engagement with realist thought is essential, in part because of its continuing influence on policy-making (particularly in Russia) and in order to forestall improper co-option of caricaturized versions of realist arguments. [ABSTRACT FROM AUTHOR]

Motivation ChIP-seq detects protein–DNA interactions within chromatin, such as that of chromatin structural components and transcription machinery. ChIP-seq profiles are often noisy and variable across replicates, posing a challenge to the development of effective algorithms to accurately detect differential peaks. Methods have recently been designed for this purpose but sometimes yield conflicting results that are inconsistent with the underlying biology. Most existing algorithms perform well on limited datasets. To improve differential analysis of ChIP-seq, we present a novel Diff erential analysis method for ChIP -seq based on L imma (DiffChIPL). Results DiffChIPL is adaptive to asymmetrical or symmetrical data and can accurately report global differences. We used simulated and real datasets for transcription factors (TFs) and histone modification marks to validate and benchmark our algorithm. DiffChIPL shows superior performance in sensitivity and false positive rate in different simulations and control datasets. DiffChIPL also performs well on real ChIP-seq, CUT&RUN, CUT&Tag and ATAC-seq datasets. DiffChIPL is an accurate and robust method, exhibiting better performance in differential analysis for a variety of applications including TF binding, histone modifications and chromatin accessibility. Availability and implementation https://github.com/yancychy/DiffChIPL. Supplementary information Supplementary data are available at Bioinformatics online. [ABSTRACT FROM AUTHOR]

Motivation Pathway analyses have led to more insight into the underlying biological functions related to the phenotype of interest in various types of omics data. Pathway-based statistical approaches have been actively developed, but most of them do not consider correlations among pathways. Because it is well known that there are quite a few biomarkers that overlap between pathways, these approaches may provide misleading results. In addition, most pathway-based approaches tend to assume that biomarkers within a pathway have linear associations with the phenotype of interest, even though the relationships are more complex. Results To model complex effects including non-linear effects, we propose a new approach, Hierarchical structural CoMponent analysis using Kernel (HisCoM-Kernel). The proposed method models non-linear associations between biomarkers and phenotype by extending the kernel machine regression and analyzes entire pathways simultaneously by using the biomarker-pathway hierarchical structure. HisCoM-Kernel is a flexible model that can be applied to various omics data. It was successfully applied to three omics datasets generated by different technologies. Our simulation studies showed that HisCoM-Kernel provided higher statistical power than other existing pathway-based methods in all datasets. The application of HisCoM-Kernel to three types of omics dataset showed its superior performance compared to existing methods in identifying more biologically meaningful pathways, including those reported in previous studies. Availability and implementation The HisCoM-Kernel software is freely available at http://statgen.snu.ac.kr/software/HisCom-Kernel/. The RNA-seq data underlying this article are available at https://xena.ucsc.edu/ , and the others will be shared on reasonable request to the corresponding author. Supplementary information Supplementary data are available at Bioinformatics online. [ABSTRACT FROM AUTHOR]

The photosynthetic efficiency of plants in different environments is controlled by stomata, hydraulics, biochemistry, and mesophyll conductance (g m). Recently, g m was demonstrated to be the key limitation of photosynthesis in gymnosperms. Values of g m across gymnosperms varied over 20-fold, but this variation was poorly explained by robust structure-bound integrated traits such as leaf dry mass per area. Understanding how the component structural traits control g m is central for identifying the determinants of variability in g m across plant functional and phylogenetic groups. Here, we investigated the structural traits responsible for g m in 65 diverse gymnosperms. Although the integrated morphological traits, shape, and anatomical characteristics varied widely across species, the distinguishing features of all gymnosperms were thick mesophyll cell walls and low chloroplast area exposed to intercellular airspace (S c/ S) compared with angiosperms. S c/ S and cell wall thickness were the fundamental traits driving variations in g m across gymnosperm species. Chloroplast thickness was the strongest limitation of g m among liquid-phase components. The variation in leaf dry mass per area was not correlated with the key ultrastructural traits determining g m. Thus, given the absence of correlating integrated easy-to-measure traits, detailed knowledge of underlying component traits controlling g m across plant taxa is necessary to understand the photosynthetic limitations across ecosystems. [ABSTRACT FROM AUTHOR]

In this study, we describe the approach taken by the International Council for the Exploration of the Seas Irish Sea benchmark working group (WKIrish), to co-create diet information for six commercial species using fishers' and scientists knowledge and incorporate it into an existing Ecopath food web model of the Irish Sea. To understand how the co-created diet information changed the model we compared a suite of food web indicators before and after the addition of fishers' knowledge (FK). Of the 80 predator–prey interactions suggested by fishers during workshops, 50 were already included in the model. Although the small number of changes made to the model structure had an insignificant impact on the ecosystem-level indicators, indicators of species hierarchical importance and mixed trophic impacts were significantly changed, particularly for commercial species. FK heightened the importance of discards as a source of food for rays, plaice, and whiting and reduced the importance of cod, toothed whales, and plaice as structural components of the food web. FK therefore led to changes which will influence pairwise advice derived from the model. We conclude by providing lessons from WKIrish which we believe were key to the positive co-production experience and development of integrated management. [ABSTRACT FROM AUTHOR]

The universe in large scales is structured as a network known as cosmic web. Filaments are one of the structural components of this web, which can be introduced as a novel probe to study the formation and evolution of structures and as a probe to study the cosmological models and to address the missing baryon problem. The aim of this work is to introduce an analytical framework to study the statistics of filaments such as number density of them and also to obtain the length-mass relation. For this objective, we model filaments as collapsed objects which have an extension in one direction, accordingly we use the ellipsoidal collapse to study the evolution of an over-dense region via gravitational instability. We find that the non-linear density of filaments in the epoch of formation is almost mass independent and is in order of ∼30. By introducing filament's extended condition , we find a fitting function for length-mass relation. For the statistics of filaments, we propose a novel framework named excursion set of saddle points. In this approach, we count the saddle points of the density field Hessian matrix, and relate it to the count of filaments. In addition, we addressed the filament in filament problem with up-crossing approximation. [ABSTRACT FROM AUTHOR]

Integration is an essential feature of complex biomechanical systems, with coordination and covariation occurring among and within structural components at time scales that vary from microseconds to deep evolutionary time. Integration has been suggested to both promote and constrain morphological evolution, and the effects of integration on the evolution of structure likely vary by system, clade, historical contingency, and time scale. In this introduction to the 2019 symposium "Multifunctional Structures and Multistructural Functions," we discuss the role of integration among structures in the context of functional integration and multifunctionality. We highlight articles from this issue of Integrative and Comparative Biology that explore integration within and among kinematics, sensory and motor systems, physiological systems, developmental processes, morphometric dimensions, and biomechanical functions. From these myriad examples it is clear that integration can exist at multiple levels of organization that can interact with adjacent levels to result in complex patterns of structural and functional phenotypes. We conclude with a synthesis of major themes and potential future directions, particularly with respect to using multifunctionality, itself, as a trait in evolutionary analyses. [ABSTRACT FROM AUTHOR]

Recently-developed, molecularly-based phylogenies of geckos have provided the basis for reassessing the number of times adhesive toe-pads have arisen within the Gekkota. At present both a single origin and multiple origin hypotheses prevail, each of which has consequences that relate to explanations about digit form and evolutionary transitions underlying the enormous variation in adhesive toe pad structure among extant, limbed geckos (pygopods lack pertinent features). These competing hypotheses result from mapping the distribution of toe pads onto a phylogenetic framework employing the simple binary expedient of whether such toe pads are present or absent. It is evident, however, that adhesive toe pads are functional complexes that consist of a suite of integrated structural components that interact to bring about adhesive contact with the substratum and release from it. We evaluated the competing hypotheses about toe pad origins using 34 features associated with digit structure (drawn from the overall form of the digits; the presence and form of adhesive scansors; the proportions and structure of the phalanges; aspects of digital muscular and tendon morphology; presence and form of paraphalangeal elements; and the presence and form of substrate compliance-enhancing structures). We mapped these onto a well-supported phylogeny to reconstruct their evolution. Nineteen of these characters proved to be informative for all extant, limbed geckos, allowing us to assess which of them exhibit co-occurrence and/or clade-specificity. We found the absence of adhesive toe pads to be the ancestral state for the extant Gekkota as a whole, and our data to be consistent with independent origins of adhesive toe pads in the Diplodactylidae, Sphaerodactylidae, Phyllodactylidae, and Gekkonidae, with a strong likelihood of multiple origins in the latter three families. These findings are consistent with recently-published evidence of the presence of adhesively-competent digits in geckos generally regarded as lacking toe pads. Based upon morphology we identify other taxa at various locations within the gekkotan tree that are promising candidates for the expression of the early phases of adhesively-assisted locomotion. Investigation of functionally transitional forms will be valuable for enhancing our understanding of what is necessary and sufficient for the transition to adhesively-assisted locomotion, and for those whose objectives are to develop simulacra of the gekkotan adhesive system for biotechnological applications. [ABSTRACT FROM AUTHOR]

Galaxies are complex systems made up of different structural components such as bulges, discs, and bars. Understanding galaxy evolution requires unveiling, independently, their history of stellar mass and metallicity assembly. We introduce c2d, a new algorithm to perform spectro-photometric multicomponent decompositions of integral field spectroscopy (IFS) datacubes. The galaxy surface-brightness distribution at each wavelength (quasi-monochromatic image) is fitted using GASP2D, a 2D photometric decomposition code. As a result, c2d provides both a characteristic one-dimensional spectra and a full datacube with all the spatial and spectral information for every component included in the fit. We show the basic steps of the c2d spectro-photometric fitting procedure, tests on mock datacubes demonstrating its reliability, and a first application of c2d to a sample of three early-type galaxies (ETGs) observed within the Calar Alto Legacy Integral Field Area survey. The resulting datacubes from c2d are processed through the Pipe3D pipeline obtaining both the stellar populations and ionized gas properties of bulges and discs. This paper presents an overview of the potential of c2d  +  Pipe3D to unveil the formation and evolution of galaxies. [ABSTRACT FROM AUTHOR]

Traditional approaches for genetic mapping are to simply associate the genotypes of a quantitative trait locus (QTL) with the phenotypic variation of a complex trait. A more mechanistic strategy has emerged to dissect the trait phenotype into its structural components and map specific QTLs that control the mechanistic and structural formation of a complex trait. We describe and assess such a strategy, called structural mapping, by integrating the internal structural basis of trait formation into a QTL mapping framework. Electrical impedance spectroscopy (EIS) has been instrumental for describing the structural components of a phenotypic trait and their interactions. By building robust mathematical models on circuit EIS data and embedding these models within a mixture model-based likelihood for QTL mapping, structural mapping implements the EM algorithm to obtain maximum likelihood estimates of QTL genotype-specific EIS parameters. The uniqueness of structural mapping is to make it possible to test a number of hypotheses about the pattern of the genetic control of structural components. We validated structural mapping by analyzing an EIS data collected for QTL mapping of frost hardiness in a controlled cross of jujube trees. The statistical properties of parameter estimates were examined by simulation studies. Structural mapping can be a powerful alternative for genetic mapping of complex traits by taking account into the biological and physical mechanisms underlying their formation. [ABSTRACT FROM AUTHOR]

ABSTRACT We present an analysis of the circumnuclear structure of NGC 1316 using both near-infrared imaging and stellar kinematics. 2D decomposition of the images suggests the presence of a structure that resembles inner gaseous spiral arms, at about 5-15 arcsec from the centre (≈500 to 1500 pc). We also find a disc-like stellar structure with radius less than 200 pc. Analysis of previously published SINFONI integral field kinematics data indicates a kinematically decoupled core in the same spatial scale, further evidence that indeed the nuclear stellar structure found is a kinematically cold stellar disc. We suggest that both newly found structural components are the result of a recent accretion of a companion galaxy. [ABSTRACT FROM AUTHOR]

A phylogenetic-like tree of structural fragments has been constructed to extract useful insights from a structural database of bitter molecules. The tree of structural fragments summarizes the substructural groups present in the molecules from the bitter database. These structural fragments are compared with a large number of random molecules to highlight substructures specific to bitter molecules. This organization of the structures enabled the detection of structure–activity relationships for the bitter molecules through the construction of R-tables. Key structural groups, able to distinguish between bitter and random molecules, were identified through an analysis of the tree. This information can be used to further understand which structural components are involved in producing a bitter taste. [ABSTRACT FROM AUTHOR]

The article discusses the synthesis of stereoisomers of trihydroxy unsaturated fatty acid by the key steps of evans asymmetric alkylation, sharpless kinetic resolution and diastereoselective reduction. It mentions that synthesis of stereoisomers employs building blocks of nigricanoside alpha chains by use of stereochemically flexible synthetic strategy. It also compares structural components present in nigricanosides with different components present in monogalactosyldiacylglycerols.