Nest Structure Research Articles

Morphological characteristics of beak-like tooth in spotted knifejaw (Oplegnathus punctatus) and mechanisms of dental development regulation by the Wnt, BMP, FGF and SHH signalling pathways

Oplegnathus punctatus is a fish species with beak-like tooth that feeds on algae, oysters, sea urchins, and other organisms attached to rocks. Currently, there are no research reports on the development and regulatory mechanisms of O. punctatus beak-like tooth. This present study firstly elucidated the nesting structure pattern of the beak-like tooth with dental formula (4, 15–16, 10–1) for O. punctatus. Four critical periods during early beak-like tooth development (28dph, 40dph, 50dph, 60dph) were also identified. In addition, 11 key genes (bmp2, bmpr2, smad1, wnt5a, msx, axin2, fgfr1a, fgfr2, pitx2, ptch1, cyp27a1) closely related to the development of beak-like tooth were discovered, with the highest expression levels in the initial stages of functional teeth and replacement teeth development, and expression in the mesenchymal and epithelial tissues of the teeth. Further research found that the cyp27a1 gene, related to vitamin D metabolism and calcium accumulation, was expressed in the maxilla and base of the tooth in O. punctatus. This study provides support for the biological theory of tooth development and healing and provides a reference for the adaptive evolution of tooth healing in special habitats.

Detecting and generating overlapping nested communities

Nestedness has been observed in a variety of networks but has been primarily viewed in the context of bipartite networks. Numerous metrics quantify nestedness and some clustering methods identify fully nested parts of graphs, but all with similar limitations. Clustering approaches also fail to uncover the overlap between fully nested subgraphs, as they assign vertices to a single group only. In this paper, we look at the nestedness of a network through an auxiliary graph, in which a directed edge represents a nested relationship between the two corresponding vertices of the network. We present an algorithm that recovers this so-called community graph, and finds the overlapping fully nested subgraphs of a network. We also introduce an algorithm for generating graphs with such nested structure, given by a community graph. This algorithm can be used to test a nested community detection algorithm of this kind, and potentially to evaluate different metrics of nestedness as well. Finally, we evaluate our nested community detection algorithm on a large variety of networks, including bipartite and non-bipartite ones, too. We derive a new metric from the community graph to quantify the nestedness of both bipartite and non-bipartite networks.

Characteristics Morphology and Morphometry Lepidotrigona terminata (Hymenoptera: Meliponini) in Central Sulawesi

Stingless bees are eusocial bees belonging to the Apidae family and the Meliponini subfamily. This study aims to describe the morphological and morphometric and nest structure characteristics of Stingless bee Lepidotrigona terminata from Parigi Moutong Regency. This study used the roaming method with a purposive sampling technique. Obtained morphological and morphometry data were analyzed using the Principal Component Analysis (PCA) method with PAST4 software. The morphological characters of Lepidotrigona terminata had a dominant black body, on the thorax, black scutum and scutellum covered with brown hair and yellow packaging on the edges. The tegula is brown, the tibia on the legs is black, the hind tibia is slightly hairy (plumose), antennae with 11 flagellomeres, the number of hamuli is 8. The most dominant character in the formation of seven groups of stingless bees in this study were Hamuli Number (HN), Fore Wing Length (FWL), and Length of Forewing Including Tegula (WL1). There are differences in character size compared to the same or different species in other areas.

Identifying current practices in modeling multi-year student achievement data: a systematic methodological review

ABSTRACT Assessing student achievement over multiple years is complicated by students’ memberships in shifting upper-level nesting structures. These structures are manifested in (1) annual matriculation to different classrooms and (2) mobility between schools. Failure to model these shifting upper-level nesting structures may bias the inferences researchers make about predictors of student achievement. The current study is a systematic methodological review of 59 multi-year elementary education studies that examine student achievement growth. The review focuses on studies from the previous decade with the hope of better understanding current practices in modeling student growth in multiyear educational research, the extent to which researchers account for shifting upper-level nesting structures, and the percent of variability attributed to different levels. Findings indicate that approaches to address shifting upper-level nesting structures are not consistently applied. Further, many researchers fail to recognize shifting upper-level nesting structures as a potential threat to the validity of their findings. Finally, evidence is presented that suggests even when schools are included in a model additional variability is attributed to classrooms beyond what is attributed to schools. Accordingly, it may be necessary to include multiple classroom memberships, where such data exist, in models that seek to understand contributors to student achievement.

LYVE-1+ macrophages form a collaborative CCR5-dependent perivascular niche that influences chemotherapy responses in murine breast cancer

Tumor-associated macrophages (TAMs) are a heterogeneous population of cells that facilitate cancer progression. However, our knowledge of the niches of individual TAM subsets and their development and function remain incomplete. Here, we describe a population of lymphatic vessel endothelial hyaluronan receptor-1 (LYVE-1)-expressing TAMs, which form coordinated multi-cellular "nest" structures that are heterogeneously distributed proximal to vasculature in tumors of a spontaneous murine model of breast cancer. We demonstrate that LYVE-1+ TAMs develop in response to IL-6, which induces their expression of the immune-suppressive enzyme heme oxygenase-1 and promotes a CCR5-dependent signaling axis, which guides their nest formation. Blocking the development of LYVE-1+ TAMs or their nest structures, using gene-targeted mice, results in an increase in CD8+ Tcell recruitment to the tumor and enhanced response to chemotherapy. This study highlights an unappreciated collaboration of a TAM subset to form a coordinated niche linked to immune exclusion and resistance to anti-cancer therapy.

Can nesting behaviour allow reptiles to adapt to climate change?

A range of abiotic parameters within a reptile nest influence the viability and attributes (including sex, behaviour and body size) of hatchlings that emerge from that nest. As a result of that sensitivity, a reproducing female can manipulate the phenotypic attributes of her offspring by laying her eggs at times and in places that provide specific conditions. Nesting reptiles shift their behaviour in terms of timing of oviposition, nest location and depth of eggs beneath the soil surface across spatial and temporal gradients. Those maternal manipulations affect mean values and variances of both temperature and soil moisture, and may modify the vulnerability of embryos to threats such as predation and parasitism. By altering thermal and hydric conditions in reptile nests, climate change has the potential to dramatically modify the developmental trajectories and survival rates of embryos, and the phenotypes of hatchlings. Reproducing females buffer such effects by modifying the timing, location and structure of nests in ways that enhance offspring viability. Nonetheless, our understanding of nesting behaviours in response to climate change remains limited in reptiles. Priority topics for future studies include documenting climate-induced changes in the nest environment, the degree to which maternal behavioural shifts can mitigate climate-related deleterious impacts on offspring development, and ecological and evolutionary consequences of maternal nesting responses to climate change. This article is part of the theme issue 'The evolutionary ecology of nests: a cross-taxon approach'.

Foraging behaviour affects nest architecture in a cross-species comparison of ant nests.

Animals construct and inhabit nests that can exhibit dramatic intra- and interspecific variation due to differences in behaviour, the biotic and abiotic environment, and evolutionary history. In ants, variation in nest architecture reflects both differences in ecology and in the collective behaviour of the colonies that live in the nests. Each component of the nest (such as depth, and the number, size and connectivity of chambers) reflects selective pressures for different functions, or structural constraints that are imposed by the environment or evolutionary history. To determine potential drivers of nest structure variation in subterranean nests, we performed a meta-analysis of measures of published ant nests to compare different structural elements within and across species. We complemented this survey with 42 nest casts of two closely related species. We quantified nest features that can potentially impact ant foraging behaviour and examined whether phylogeny or foraging strategy are better explanatory variables for the variation we observed. We found that foraging strategy better explained nest features than evolutionary history. Our work reveals the importance of ecology in shaping nest structure and provides an important foundation for future investigations into the selective pressures that have shaped ant nest architecture. This article is part of the theme issue 'The evolutionary ecology of nests: a cross-taxon approach'.

Long-term environmental stability does not erode plasticity in nest building responses to changing ambient conditions.

The primary function of animal nests is to protect developing offspring from hostile and fluctuating environments. Animal builders have been shown to adjust nest construction in response to changes in their environment. However, the extent of this plasticity, and its dependence on an evolutionary history of environmental variability, is not well understood. To test whether an evolutionary history with flowing water impacts male ability to adjust nests in response to flow regime, we collected three-spined sticklebacks (Gasterosteus aculeatus) from three lakes and three rivers, and brought them into reproductive condition in controlled laboratory aquaria. Males were then allowed to nest under both flowing and static conditions. Nest building behaviour, nest structure and nest composition were all recorded. In comparison to males building nests under static conditions, males building in flowing water took longer to construct their nests and invested more in nesting behaviour. Moreover, nests built in flowing water contained less material, were smaller, more compact, neater and more elongated than nests built under static conditions. Whether males came from rivers or lakes had little impact on nesting activities, or male capacity to adjust behaviours in response to flow treatment. Our findings suggest that aquatic animals which have experienced a stable environment over a long period of time retain plasticity in nest-building behaviours that allow them to adjust nests to ambient flow conditions. This ability may prove crucial in coping with the increasingly unpredictable flow regimes found in anthropogenically altered waterways and those resulting from global climate change. This article is part of the theme issue 'The evolutionary ecology of nests: a cross-taxon approach'.

Variation in nest-building behaviour in birds: a multi-species approach.

Researchers have long suggested that animals with greater behavioural flexibility will be more likely to survive in face of environmental changes. However, it is unknown how this varies across species. Nest building is a behaviour directly related to the reproduction and survival of species by conferring protection from external environmental conditions. The study of nests offers a window into the behaviour of birds, and variation in nest morphology is necessarily linked to variation in building behaviours. We test whether variation in nest morphology is phylogenetically conserved by using data on nest morphology from 55 passerine species (>700 specimens) and measuring intraspecific variability in nest structure. We found that species mean and within-species variation in nest morphology are phylogenetically conserved, and that species with domed nests presented higher levels of nest morphology variation than cup nest species. We also revealed that the capacity of species to present innovative behaviours is not linked with how they vary nest morphology. Moreover, we revealed that nests from species with larger variation in clutch size and that are built by single parents are more variable. Our results help in the understanding of how behaviour and extended phenotypes evolve, and highlight the importance of exploring the phylogenetic history of behavioural flexibility when trying to predict the capacity of species to respond to novel challenges. This article is part of the theme issue 'The evolutionary ecology of nests: a cross-taxon approach'.

The evolution of nest site use and nest architecture in modern birds and their ancestors.

The evolution of nest site use and nest architecture in the non-avian ancestors of birds remains poorly understood because nest structures do not preserve well as fossils. Nevertheless, the evidence suggests that the earliest dinosaurs probably buried eggs below ground and covered them with soil so that heat from the substrate fuelled embryo development, while some later dinosaurs laid partially exposed clutches where adults incubated them and protected them from predators and parasites. The nests of euornithine birds-the precursors to modern birds-were probably partially open and the neornithine birds-or modern birds-were probably the first to build fully exposed nests. The shift towards smaller, open cup nests has been accompanied by shifts in reproductive traits, with female birds having one functioning ovary in contrast to the two ovaries of crocodilians and many non-avian dinosaurs. The evolutionary trend among extant birds and their ancestors has been toward the evolution of greater cognitive abilities to construct in a wider diversity of sites and providing more care for significantly fewer, increasingly altricial, offspring. The highly derived passerines reflect this pattern with many species building small, architecturally complex nests in open sites and investing significant care into altricial young. This article is part of the theme issue 'The evolutionary ecology of nests: a cross-taxon approach'.

Doubly coupled nested tensor decompositions with application to multirelay multicarrier MIMO communication networks

Coupled tensor decompositions have emerged as a promising approach to analyze large dimensional datasets in the context of signal processing applications. In this paper, the general concept of doubly coupled decomposition (DCD) for high-order tensors is first proposed, extending the idea of coupled decompositions to doubly coupled nested structures which result from the contraction of two sets of tensors, each set depending on a specific mode. Two new decompositions are defined, the so-called doubly coupled nested Tucker decomposition (DCNTD) and doubly coupled nested PARAFAC decomposition (DCNPD). Uniqueness of these DCDs is analyzed. In a second part, we show how these DCDs can be used to model multirelay multicarrier MIMO cooperative communication networks with two different tensor codings at the source and relay nodes. Exploiting the multilinear structure of the received signals and assuming the coding tensors are known at the destination, semi-blind closed-form receivers are developed for jointly estimating the channels and transmitted symbols. The proposed receivers use Khatri-Rao and Kronecker product factorization algorithms. Identifiability conditions for system parameter estimation and design of the tensor codes are also addressed. Monte Carlo simulation results illustrate the performance improvement of the proposed DCD-based systems over existing state-of-the-art ones.

Nest complexity correlates with larger brain size but smaller body mass across bird species.

Amniotes differ substantially in absolute and relative brain size after controlling for allometry, and numerous hypotheses have been proposed to explain brain size evolution. Brain size is thought to correlate with processing capacity and the brain's ability to support complex manipulation such as nest-building skills. The increased complexity of nest structure is supposed to be a measure of an ability to manipulate nesting material into the required shape. The degree of nest-structure complexity is also supposed to be associated with body mass, partly because small species lose heat faster and delicate and insulated nests are more crucial for temperature control of eggs during incubation by small birds. Here, we conducted comparative analyses to test these hypotheses by investigating whether the complexity of species-typical nest structure can be explained by brain size and body mass (a covariate also to control for allometric effects on brain size) across 1353 bird species from 147 families. Consistent with these hypotheses, our results revealed that avian brain size increases as the complexity of the nest structure increases after controlling for a significant effect of body size, and also that a negative relationship exists between nest complexity and body mass.

A new species of the paper wasp genus Ropalidia Guérin-Méneville, plebeja group (Hymenoptera, Vespidae, Polistinae), from Vietnam

A new species, Ropalidia daklak Bui, Mai & Nguyen, sp. nov., belonging to the plebeja-group of the genus Ropalidia Guérin-Méneville, 1831 is described and figured based on females and males from Vietnam. The nest structure of the new species is described, and an updated key is provided to all known species of the group.

Nested Named Entity Recognition as Building Local Hypergraphs

Named entity recognition is a fundamental task in natural language processing. Based on the sequence labeling paradigm for flat named entity recognition, multiple methods have been developed to handle the nested structures. However, they either require fixed recognition order or introduce complex hypergraphs. To tackle this problem, we propose a novel model named Local Hypergraph Builder Network (LHBN) that builds multiple simpler local hypergraphs to capture named entities instead of a single complex full-size hypergraph. The proposed model has three main properties: (1) The named entities that share boundaries are captured in the same local hypergraph. (2) The boundary information is enhanced by building local hypergraphs. (3) The hypergraphs can be built bidirectionally to take advantage of the identification direction preference of different named entities. Experiments illustrate that our model outperforms previous state-of-the-art methods on four widely used nested named entity recognition datasets: ACE04, ACE05, GENIA, and KBP17. The code is available at https://github.com/yanyk13/local-hypergraph-building-network.git.

The use of plastic litter as nesting material by the azure-winged magpie Cyanopica cyanus in an agricultural environment of South Korea.

In bird species, anthropogenic nesting materials have been known to have a negative effect on the survival of birds in general, but in some species, these can be used instead of natural materials, which can have a positive effect on the structural aspects of nests. Our study aims to investigate the type and amount of anthropogenic materials found in the nests of the colonial breeding azure-winged magpie (Cyanopica cyanus) in an agricultural area, as well as the characteristics of these used for each nest structure. We found that plastic litter was used in all of the azure-winged magpie breeding nests observed, and the types and amounts of plastic litter used differed between the cup and the outer. In all nests, soft, elastic, and insulating materials such as polyester fiber were mainly observed in the cup, and strings that weave and anchor branches and soil from nature were mostly found in the outer. The amount of plastic litter used in nests was related to the size of the nest. Plastic litter used in nests is thought to be collected from agricultural materials used in agricultural lands, vinyl greenhouses, and agricultural warehouses in our study site. Consequently, we expect that the phenomenon of azure-winged magpies using plastic litters for nest building may be common situation for the current agricultural environment where plastics are widespread.

Thin pyramidal cones in nematic liquid crystals.

The present study investigates the arrangement of hollow pyramidal cone shells and their interactions with degenerate planar anchoring on the inner and outer surfaces of particles within the nematic host. The shell thickness is in order of the nematic coherence length. The numerical behavior of colloids is determined by minimizing the Landau-de Gennes free energy in the presence of the Fournier surface energy and using the finite element method. Colloidal pyramidal cones can orient parallel and perpendicular with the far director orientation. In the parallel alignment, we found the splay director distortion into the pyramid with two boojum defects at the inner and outer tips. The director shows bending distortion without defect patterns when the pyramid is aligned perpendicularly. They induce long-range dipolar interaction and can form nested structures in close contact.

The effect of embedded structures on cognitive load for novice learners during block-based code comprehension

BackgroundCoding has become an integral part of STEM education. However, novice learners face difficulties in processing codes within embedded structures (also termed nested structures). This study aimed to investigate the cognitive mechanism underlying the processing of embedded coding structures based on hierarchical complexity theory, which suggests that more complex hierarchies are involved in embedded versus sequential coding structures. Hierarchical processing is expected to place a great load on the working memory system to maintain, update, and manipulate information. We therefore examined the difference in cognitive load induced by embedded versus sequential structures, and the relations between the difference in cognitive load and working memory capacity.ResultsThe results of Experiment 1 did not fully support our hypotheses, possibly due to the unexpected use of cognitive strategies and the way stimuli were presented. With these factors well controlled, a new paradigm was designed in Experiment 2. Results indicate that the cognitive load, as measured by the accuracy and response times of a code comprehension task, was greater in embedded versus sequential conditions. Additionally, the extra cognitive load induced by embedded coding structures was significantly related to working memory capacity.ConclusionsThe findings of these analyses suggest that processing embedded coding structures exerts great demands on the working memory system to maintain and manipulate hierarchical information. It is therefore important to provide scaffolding strategies to help novice learners process codes across different hierarchical levels within embedded coding structures.

GIO: Generating Efficient Matrix and Frame Readers for Custom Data Formats by Example

Data Scientists deal with a wide variety of file data formats and data representations. Probably the most difficult to handle are custom data formats that liberally define their own particular flat or nested structure with multiple custom delimiters, multi-line records, or undocumented semantics of attribute sequences, co-appearances, and repetitions. As a prerequisite for exploratory ML model training, data scientists need to map these data representations into regular frames or matrices. Unfortunately, existing tools and frameworks provide only limited support for aiding this process, which causes redundant manual efforts and unnecessary data quality issues. In this paper, we initiate work on automatic matrix and frame reader generation by example. A user provides a sample of raw text data and its mapped matrix or frame representation. Our GIO framework then first identifies the mapping rules from raw to structured data, and subsequently generates source code of an efficient, multi-threaded reader for reading full raw datasets of this format. In order to facilitate manual improvements, both the mapping rules, and generated reader can be modified as needed. Our experiments show that GIO is able to correctly identify the mapping rules for basic text formats like CSV, LibSVM, MatrixMarket; custom text formats from publishing, automotive, and health care; as well as various nested formats such as JSON and XML. Additionally, the automatically generated readers yield competitive performance compared to hand-coded readers and tuned libraries like RapidJSON.

Ecology and distribution of the European Roller <i>Coracias garrulus</i> in a recently recolonized area of Northern Italy

This study reports the first data on the ecology and distribution patterns of a population of Eurasian Roller Coracias garrulus breeding in the province of Alessandria in northwestern Italy. The research was conducted between 2017 and 2021. 13 pairs were found, 12 of which were confirmed to be breeding. The species primarily chose to nest in natural cavities in White poplar Populus alba, with nesting observed to a lesser extent in Black poplar Populus nigra, Turkey Oak Quercus cerris and in one case sandy river banks. The home range of each pair is mostly within pluriannual stable meadows and arable crops; on average it extends over 0,92 km2 with values that seems to oscillate according to the degree of fragmentation and isolation of patches of stable meadows: this can be explained by the lower availability of arthropods (consisting mostly of Orthoptera) found in mosaics of alternating meadows interspersed with annual crops. In such conditions, a low density of pairs was observed, along with an increase in territorial boundaries and greater distance between the nests. In the sectors characterised by large, multi-annual stable meadows, with more diverse and abundant entomofauna, supporting a higher number of breeding pairs, a significant contraction of home ranges is observed, with an increased concentration of nesting sites, and higher intraspecific tolerance. Between 2019 and 2021 a total of 17 artificial nest boxes were installed, 3 of which have been successfully occupied. Given the continuous anthropogenic transformation these territories are regularly facing, sometimes subtracting potential nesting or feeding sites due to crop rotation, coppicing, ex-novo construction of ground solar panel systems on agricultural land, etc., in order to protect and conserve this population of European Roller, it is desirable to put in place a greater number of artificial nest structures together with monitoring aimed at protecting the biodiversity of the territory.

Morphology, Morphometry, and Nest Structure of Tetragonula biroi (Hymenoptera: Meliponini) In Central Sulawesi

Stingless bees are social bees that live in colonies. Indonesia has a variety of stingless bee species that can be identified based on morphological, morphometric and nest structure characters. This study aims to describe the morphological, morphometric and nest structure characteristics of Stingless bee Tetragonula biroi from Sigi Regency. This study used the roaming method to find samples in nature, with a purposive sampling technique. Obtained morphological, morphometry and nest structure data were analyzed using the Principal Component Analysis (PCA) method with PAST4 software. The morphological characters of the worker bee Tetragonula biroi have a dominant black body, blackish brown abdomen, antennae with 11 flagellomeres, black thorax, black hair standing on the mesoscutum and mesoscutellum, brownish black mandibles, with 5 hamuli. The most dominant character in the formation of seven groups of stingless bees in this study, namely Hamuli Number (HN), Fore Wing Length (FWL), and Length of Forewing Including Tegula (WL1). The nest entrance hole of T. biroi is elliptical in shape with a width of 7.1 cm and a height of 2.8 cm and is light brown in color. The internal structure of the nest of T. biroi consists of honey cells, pollen cells and stem cells. The existence of size differences in the same specimen and from different places, can be influenced by several environmental factors and is also a form of morphological adaptation.