comspat: an R package to analyze within-community spatial organization using species combinations

The diversity of species combinations observable in sampling units reflects a species' uneven distribution and preference for specific abiotic and biotic conditions – a phenomenon most commonly expressed in terms of ecological assembly rules of plant communities and other sessile organisms (e.g. subtidal algae, invertebrates and coral reefs). We present comspat, a new R package that uses grid or transect data sets to measure the number of realized (observed) species combinations (NRC) and the Shannon diversity of realized species combinations (compositional diversity; CD) as a function of spatial scale. NRC and CD represent two measures from a model family developed by Pál Juhász-Nagy based on information theory. Classical Shannon diversity measures biodiversity based on the number and relative abundance of species, whereas the specific version of Shannon diversity presented here characterizes biodiversity and provides information on species coexistence relationships; both measures operate at fine-scale within the sampling unit or within the community. comspat offers two commonly applied null models, complete spatial randomness and random shift, to disentangle the textural, intraspecific and interspecific effects on the observed spatial patterns. Combined, these models assist users in detecting and interpreting spatial associations and inferring assembly mechanisms. Our open-sourced package provides a vignette that describes the method and reproduces the figures from this paper to help users contextualize and apply functions to their data

Intraspecific phenotypic variability of plant functional traits in contrasting mountain grasslands habitats

Empirical studies that link plants intraspecific variation to environmental conditions are almost lacking, despite their relevance in understanding mechanisms of plant adaptation, in predicting the outcome of environmental change and in conservation. Here, we investigate intraspecific trait variation of four grassland species along with abiotic environmental variation at high spatial resolution (n = 30 samples per species trait and environmental factor per site) in two contrasting grassland habitats in Central Apennines (Italy). We test for phenotypic adaptation between habitats, intraspecific trait-environment relationships within habitats, and the extent of trait and environmental variation. We considered whole plant, clonal, leaf, and seed traits. Differences between habitats were tested using ANOVA and ANCOVA. Trait-environment relationships were assessed using multiple regression models and hierarchical variance partitioning. The extent of variation was calculated using the coefficient of variation. Significant intraspecific differences in trait attributes between the contrasting habitats indicate phenotypic adaptation to in situ environmental conditions. Within habitats, light, soil temperature, and the availability of nitrate, ammonium, magnesium and potassium were the most important factors driving intraspecific trait-environment relationships. Leaf traits and height growth show lower variability than environment being probably more regulated by plants than clonal traits which show much higher variability. We show the adaptive significance of key plant traits leading to intraspecific adaptation of strategies providing insights for conservation of extant grassland communities. We argue that protecting habitats with considerable medium- and small-scale environmental heterogeneity is important to maintain large intraspecific variability within local populations that finally can buffer against uncertainty of future climate and land use scenarios

Context-dependent assembly rules and the role of dominating grasses in semi-natural abandoned sub-Mediterranean grasslands

We investigated fine-scale patterns of trait-based community assembly in calcareous grasslands of the Central Apennines, Italy. We used the habitat template of environmentally contrasting north-facing and south-facing slopes of a mountain valley to understand mechanisms that contribute to species coexistence (i.e. the persistence of diversity) after cessation of previous land use practices. Firstly, we tested late successional dominating grasses (Sesleria nitida, Brachypodium rupestre and Bromopsis erectus) for their ability to serve as biotic filtering effects on the diversity of subordinate species in plant communities. Secondly, we analyzed fine-scale trait-based (i.e. species-level traits related to competition, regeneration, establishment, dispersal, and flowering) community assembly of subordinate species in absence of dominant grass. We found that assembly rules for traits related to the same life-history process were mostly consistent within habitats. Further we established that within habitats the traits related to different lifehistory processes can show different assembly rules. For example, while generative regeneration traits (seed mass) may show convergence pattern, divergence was inferred for the vegetative (clonal) regeneration traits. Depending on traits, the assembly rules can be similar or contrasting in different habitats. We conclude that our finding of non-random assembly in the majority of investigated traits emphasizes the importance of hierarchical exclusion of strong biotic filters when searching for trait-based assembly rules in abandoned grasslands. Thus, for nature conservation purposes, disturbance appears to be the process that is most important in driving the survival of subordinate species by the exclusion of biotic filters. Subsequently, a multitude of trait-based mechanisms allow for coexistence of the subordinate species. These mechanisms depend on habitats and traits and thus may vary from community to community, indicating that heterogeneous landscapes might support multiple processes of coexistence

Finite Element Analysis of Various Osteotomies Used in the Treatment of Developmental Hip Dysplasia in Children

Late-discovered developmental hip dysplasia deformities often necessitate complex surgical treatments and meticulous preoperative planning. The selection of osteotomies is contingent upon the patient’s age and the specific structural deformity of the hip. In our anatomical hip model, derived from the data of a 12-year-old patient, we performed virtual osteotomies that are commonly recommended for such cases. We precisely constructed geometric models for various osteotomies, including the Dega, Pemberton, Tönnis, Ganz, Chiari pelvic, and Pauwels femoral osteotomies. We employed Autodesk Inventor for the finite element analysis of the hip joint and the corrective osteotomies. In comparing one-stage osteotomies, we noted that the Dega and Ganz pelvic osteotomies, especially when combined with the Pauwels femoral osteotomy, yielded the most favorable outcomes. These combinations led to enhanced femoral head coverage and reduced intra-articular pressure. Furthermore, we calculated the femoral head-to-acetabulum volume ratio for both the Dega and Pauwels osteotomies. The encouraging results we obtained advocate for the integration of finite element analysis in virtual osteotomies of the pelvis and femur as a preoperative tool in the management of developmental hip dysplasia

Unravelling mechanisms of short-term vegetation dynamics in complex coppice forest systems

The silvicultural management of coppicing has been very common in deciduous forests in many European countries. After decades of decline of this practice, socio-economic changes might induce a revival valuing the biomass as a resource. New insights in the ecological processes that regulate plant diversity are relevant for a sustainable forest management. While studies on long-term changes are available, the short-term dynamics of the coppice forest understorey has not yet been explored. In this context, it is interesting to evaluate the species compositional changes, including the processes of species turnover and species impoverishment (nestedness) and to investigate the role of plant functional traits. For this purpose, we resampled a chronosequence of complex coppice beech forests of the Central Apennines (Italy) monitoring the short-time species dynamics of five years (i.e. from 2006 to 2011) in three age classes, i.e. post-logged, recovering and old coppice stands (0–16, 17–31 and > 32 years, respectively). In contrast to our expectation, declining species richness appeared only in the recovering stands, while the landscape scale (between-stand) heterogeneity, except for post-logged and recovering stands in 2011, did not change over five years. Significant temporal nestedness was found in each stage of succession. However, the rate of species turnover and species impoverishment do not significantly differ among the three age classes, indicating their constant importance along the forest regeneration after disturbance. Only in the early stage of forest regeneration after coppicing, species compositional changes are reflected by functional changes with surviving understorey species having clonal regeneration traits. Our results suggest an overall landscape-scale stability (and sustainability) of this coppice forest system. We conclude with management indications, highlighting the importance of maintaining the traditional local approach (coppicing with standards in small 0.5–1.0 ha sized management units with a ca 30-year rotation cycle) where active coppice parcels are interspersed by abandoned stands. © 2017 Institute of Botany, Academy of Sciences of the Czech Republi

Finite Element Analysis of Normal and Dysplastic Hip Joints in Children

From a surgical point of view, quantification cannot always be achieved in the developmental deformity in hip joints, but finite element analysis can be a helpful tool to compare normal joint architecture with a dysplastic counterpart. CT scans from the normal right hip of an 8-year-old boy and the dysplastic left hip of a 12-year-old girl were used to construct our geometric models. In a three-dimensional model construction, distinctions were made between the cortical bone, trabecular bone, cartilage, and contact nonlinearities of the hip joint. The mathematical model incorporated the consideration of the linear elastic and isotropic properties of bony tissue in children, separately for the cortical bone, trabecular bone, and articular cartilage. Hexahedral elements were used in Autodesk Inventor software version 2022 (“Ren”) for finite element analysis of the two hips in the boundary conditions of the single-leg stance. In the normal hip joint on the cartilaginous surfaces of the acetabulum, we found a kidney-shaped stress distribution in a 471,672 mm2 area. The measured contact pressure values were between 3.0 and 4.3 MPa. In the dysplastic pediatric hip joint on a patch of 205,272 mm2 contact area, the contact pressure values reached 8.5 MPa. Furthermore, the acetabulum/femur head volume ratio was 20% higher in the dysplastic hip joint. We believe that the knowledge gained from the normal and dysplastic pediatric hip joints can be used to develop surgical treatment methods and quantify and compare the efficiency of different surgical treatments used in children with hip dysplasia

Comparative Analysis of Zearalenone Effects on Thyroid Receptor Alpha (TRα) and Beta (TRβ) Expression in Rat Primary Cerebellar Cell Cultures

Thyroid receptors play an important role in postnatal brain development. Zearalenone (ZEN), a major mycotoxin of Fusarium fungi, is well known to cause serious health problems in animals and humans through various mechanisms, including the physiological pathways of thyroid hormone (TH). In the present study, we aimed to investigate the expression of thyroid receptors α (TRα) and β (TRβ) in primary cerebellar neurons in the presence or absence of glia and following ZEN treatment, using quantitative reverse transcription-polymerase chain reaction (qRT-PCR) and Western blot. Primary cerebellar granule cells were treated with low doses of ZEN (0.1 nM) in combination with physiologically relevant concentrations of l-thyroxine (T4), 3,3′,5-triiodo-l-thyronine (T3) and 17β-estradiol (E2). Expression levels of TRα and TRβ at mRNA and protein levels were slightly modified by ZEN administered alone; however, along with thyroid and steroid hormones, modelling the physiological conditions, expression levels of TRs varied highly depending on the given treatment. Gene expression levels were also highly modulated by the presence or absence of glial cells, with mostly contrasting effects. Our results demonstrate divergent transcriptional and translational mechanisms involved in the expression of TRs implied by ZEN and hormonal milieu, as well as culturing conditions