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Interleukin-10 promoter polymorphisms and the outcome of hepatitis C virus infection.

The natural outcome and response to treatment in hepatitis C virus (HCV) infection varies between individuals. Whereas some variation may be attributable to viral and environmental variables, it is probable that host genetic background also plays a significant role. Interleukin (IL)-10 has a key function in the regulation of cellular immune responses and in the suppression of pro-inflammatory cytokine secretion. Functional polymorphisms in the IL-10 gene have been described. We investigated the role of these polymorphisms in the outcome of HCV infection, treatment response and development of fibrosis in a case-control association study. Self-limiting infection was associated with the IL-10 (-592) AA genotype (OR=2.05; P=0.028). Persistent infection was associated with the IL-10 (-1082) GG genotype (OR=0.48; P=0.018). Sustained response to interferon therapy was associated with the IL-10 (-1082) GG genotype (OR=2.28; P=0.005) and the haplotype GCC (OR=2.27; P=0.020). The IL-10 (-1082) AA genotype and the ATA/ATA and ACC/ACC homozygous haplotypes were more frequent among patients with rapid fibrosis. Furthermore, the microsatellites IL-10.R and IL-10.G were associated with interferon response with IL-10R.2 conveying susceptibility (OR=1.80; P=0.034), and IL-10R.3 and IL-10.G13 being protective (OR=0.47; P=0.003 and OR=0.59; P=0.042, respectively). We conclude that polymorphisms in the IL-10 promoter appear to have some influence on the outcome of HCV infection, treatment and development of fibrosis.

Disease Progression↗

Slipped capital femoral epiphysis. A report of 4 cases occurring in one family.

We describe slipped capital femoral epiphysis in 4 members of a black, obese family, who were all first-degree relatives. The aetiology of slipped capital femoral epiphysis is unknown, although it is thought to be multifactorial. Genetic predisposition and environmental factors have been associated with the condition. A familial incidence with at least two cases in the same family has been reported. In epidemiological studies, this incidence ranges from 3% to 35%. Our cases were investigated in an attempt to find a possible aetiological genetic factor. A genetic predisposition with an autosomal dominant pattern of transmission is suggested, although environmental variables must be considered as provocative factors.

Adolescent↗

Learning machines applied to potential forest distribution.

The clearing of forests to obtain land for pasture and agriculture and the replacement of autochthonous species by other faster-growing varieties of trees for timber have both led to the loss of vast areas of forest worldwide. At present, many developed countries are attempting to reverse these effects, establishing policies for the restoration of older woodland systems. Reforestation is a complex matter, planned and carried out by experts who need objective information regarding the type of forest that can be sustained in each area. This information is obtained by drawing up feasibility models constructed using statistical methods that make use of the information provided by morphological and environmental variables (height, gradient, rainfall, etc.) that partially condition the presence or absence of a specific kind of forestation in an area. The aim of this work is to construct a set of feasibility models for woodland located in the basin of the River Liébana (NW Spain), to serve as a support tool for the experts entrusted with carrying out the reforestation project. The techniques used are multilayer perceptron neural networks and support vector machines. Their results will be compared to the results obtained by traditional techniques (such as discriminant analysis and logistic regression) by measuring the degree of fit between each model and the existing distribution of woodlands. The interpretation and problems of the feasibility models are commented on in the Discussion section.

Artificial Intelligence↗

Harvesting in seasonal environments.

Most harvest theory is based on an assumption of a constant or stochastic environment, yet most populations experience some form of environmental seasonality. Assuming that a population follows logistic growth we investigate harvesting in seasonal environments, focusing on maximum annual yield (M.A.Y.) and population persistence under five commonly used harvest strategies. We show that the optimal strategy depends dramatically on the intrinsic growth rate of population and the magnitude of seasonality. The ordered effectiveness of these alternative harvest strategies is given for different combinations of intrinsic growth rate and seasonality. Also, for piecewise continuous-time harvest strategies (i.e., open/closed harvest, and pulse harvest) harvest timing is of crucial importance to annual yield. Optimal timing for harvests coincides with maximal rate of decline in the seasonally fluctuating carrying capacity. For large intrinsic growth rate and small environmental variability several strategies (i.e., constant exploitation rate, linear exploitation rate, and time-dependent harvest) are so effective that M.A.Y. is very close to maximum sustainable yield (M.S.Y.). M.A.Y. of pulse harvest can be even larger than M.S.Y. because in seasonal environments population size varies substantially during the course of the year and how it varies relative to the carrying capacity is what determines the value relative to optimal harvest rate. However, for populations with small intrinsic growth rate but subject to large seasonality none of these strategies is particularly effective with M.A.Y. much lower than M.S.Y. Finding an optimal harvest strategy for this case and to explore harvesting in populations that follow other growth models (e.g., involving predation or age structure) will be an interesting but challenging problem.

Animals↗

Gene-environment interactions differentially affect mouse strain behavioral parameters.

Systematic phenotyping of mouse strains and mutants generated through genome-wide mutagenesis programs promises to deliver a wealth of functional genetic information. To this end, the appropriation of a standard series of phenotyping protocols is desirable to produce data sets that are consistent within and across laboratories and across time. Standard phenotyping protocols such as EMPReSS (European Mouse Phenotyping Resource for Standardised Screens) provide a series of protocols aimed at phenotyping multiple body systems that could realistically be adopted and/or reproduced in any laboratory. This includes a series of neurologic and behavioral screens, bearing in mind that this class of phenotype is well represented in targeted mutants and mutagenesis screens. Having cross-validated screening batteries in a number of laboratories and in a number of commonly used inbred strains, our group was interested in establishing whether subtle changes in cage environment could affect behavioral test outcome. Aside from unavoidable quantitative differences in test outcome, we identified significant and distinct genotype-environment-test interactions. For example, specific strain order in open-field center entries and total distance traveled can be reversed depending on the form of enrichment used, while prepulse inhibition of the acoustic startle response is, even quantitatively, unaffected by the enrichment condition. Our findings argue that unless systematically recorded, behavioral studies conducted under subtle variations in cage environment may lead to data misinterpretation, although this could be limited to particular behaviors. Further investigations into the extent and limits of genetic and environmental variables are critical for the realization of both behavioral and functional genomics endpoints.

Animals↗

Seasonal cycle in vitamin A1/A2-based visual pigment composition during the life history of coho salmon (Oncorhynchus kisutch).

Microspectrophotometry of rod photoreceptors was used to follow variations in visual pigment vitamin A1/A2 ratio at various life history stages in coho salmon. Coho parr shifted their A1/A2 ratio seasonally with A2 increasing during winter and decreasing in summer. The cyclical pattern was statistically examined by a least-squares cosine model, fit to the 12-month data sets collected from different populations. A1/A2 ratio varied with temperature and day length. In 1+ (>12 month old) parr the A2 to A1 shift in spring coincided with smoltification, a metamorphic transition preceding seaward migration in salmonids. The coincidence of the shift from A2 to A1 with both the spring increase in temperature and day length, and with the timing of seaward migration presented a challenge for interpretation. Our data show a shift in A1/A2 ratio correlated with season, in both 0+ (<12 months old) coho parr that remained in fresh water for another year and in oceanic juvenile coho. These findings support the hypothesis that the A1/A2 pigment pair system in coho is an adaptation to seasonal variations in environmental variables rather than to a change associated with migration or metamorphosis.

Animals↗

Psychosocial functioning following surgical treatment for intractable epilepsy in childhood.

METHODS: Psychosocial functioning was examined in 13 children who had undergone surgical treatment for intractable epilepsy. The ratings of each child's social, emotional and behavioural problems were obtained via parent and teacher reports made an average of 2 years post-operatively. RESULTS: Parents viewed their children as having greater social difficulties than reported in standardisation samples. Although the overall level of difficulty fell below clinically significant cut-offs, the proportion of children who were rated as having clinically significant levels of difficulties approached significance. Teachers rated these children as displaying more symptoms of anxiety and depression, although the levels remained subclinical. DISCUSSION: These results are discussed in view of the complex interaction between neurological and environmental variables involved in social-emotional functioning following surgical treatment for epilepsy.

Adolescent↗

Proteomic profiling of bone for the estimation of post-mortem interval and post-mortem submersion interval: a systematic review.

Accurate estimation of the Post-Mortem Interval (PMI) and Post-Mortem Submersion Interval (PMSI) remains a persistent challenge in forensic science, especially when traditional morphological and entomological methods fail due to advanced decomposition or in aquatic environments. Proteomic profiling of bone tissues has recently emerged as a promising approach, leveraging the predictable degradation patterns of bone proteins to estimate time since death more reliably. This systematic review, conducted in accordance with PRISMA guidelines, analyzed 24 peer-reviewed studies focusing on the application of proteomic techniques to bone tissue for PMI and PMSI estimation. The included studies were evaluated based on sample type, analytical techniques used, identified biomarkers, environmental conditions assessed, and the overall reliability and reproducibility of the findings. The review found that specific bone proteins, particularly collagen, osteocalcin, fetuin-A, etc. exhibited consistent degradation patterns that correlated strongly with elapsed post-mortem time. Cortical bone was identified as a more stable and informative matrix compared to trabecular bone. Mass spectrometry, especially LC-MS/MS, emerged as the predominant analytical technique due to its high sensitivity and accuracy in detecting low-abundance proteins over extended PMIs and PMSIs. However, protein degradation rates were significantly influenced by environmental variables such as temperature, humidity, soil pH, and microbial activity. This review also emphasizes the transformative role of bone proteomics in advancing forensic science while identifying key gaps that must be addressed to achieve global standardization and practical implementation in diverse forensic contexts. The integration of proteomics with other emerging technologies, such as machine learning algorithms and computational modeling, may further enhance the precision of PMI and PMSI estimation in future applications.

Postmortem Changes↗

Cell death in development: shaping the embryo.

Cell death in animals is normally classified as type I (apoptotic), type II (autophagic) or necrotic. Of the biologically controlled types of death, in most embryos apoptosis is the most common, although in metamorphosis and in cells with massive cytoplasm type II is often seen, and intermediate forms are seen. For vertebrate embryos other than mammals, apoptosis is not seen prior to gastrulation but thereafter is used to sculpt the organs of the embryo, while overproduction of cells with subsequent death of excess cells is a common means of generating high specificity with low information cost. In zebrafish at least, the inability of embryos prior to the maternal-zygotic transition to undergo apoptosis appears to derive from the inability of the cells to resist lysis once apoptosis begins, rather than any inhibition of apoptosis. In mammalian embryos, apoptosis is seen during cavitation. Thereafter, as in other embryos, cell death plays a major role in shaping and sculpting the embryo. In those situations that have been carefully studied, cell death is under tight genetic control (including regulation of gene products whose function in cell death is not yet known, such as cdk5), with activation of apoptosis sometimes regulated by local environmental variables.

Animals↗

Amazonia and the modern carbon cycle: lessons learned.

In this paper, we review some critical issues regarding carbon cycling in Amazonia, as revealed by several studies conducted in the Large Scale Biosphere Atmosphere Experiment in Amazonia (LBA). We evaluate both the contribution of this magnificent biome for the global net primary productivity/net ecosystem exchange (NPP/NEE) and the feedbacks of climate change on the dynamics of Amazonia. In order to place Amazonia in a global perspective and make the carbon flux obtained through the LBA project comparable with global carbon budgets, we extrapolated NPP/NEE values found by LBA studies to the entire area of the Brazilian Amazon covered by rainforest. The carbon emissions due to land use changes for the tropical regions of the world produced values from 0.96 to 2.4 Pg C year(-1), while atmospheric CO2 inversion models have recently indicated that tropical lands in the Americas could be exchanging a net 0.62+/-1.15 Pg C year(-1) with the atmosphere. The difference calculated from these two methods would imply a local sink of approximately 1.6-1.7 Pg C year(-1), or a source of 0.85 ton C ha(-1) year(-1). Using our crude extrapolation of LBA values for the Amazon forests (5 million km2) we estimate a range for the C flux in the region of -3.0 to 0.75 Pg C year(-1). The exercise here does not account for environmental variability across the region, but it is an important driver for present and future studies linking local process (i.e. nutrient availability, photosynthetic capacity, and so forth) to global and regional dynamic approaches.

Biomass↗

Dimensional approaches to designing better experimental ecosystems: a practitioners guide with examples.

Enclosed, experimental ecosystems ("mesocosms") are now widely used research tools in ecology. However, the small size, short duration and often simplified biological and physical complexity of mesocosm experiments raises questions about extrapolating results from these miniaturized ecosystems to nature. Dimensional analysis, a technique widely used in engineering to create scale models, employs "compensatory distortion" as a means of maintaining functional similarity in properties and relationships of interest. An earlier paper outlined a general approach to applying dimensional analysis to the construction and interpretation of mesocosm experiments (Petersen and Hastings in Am Nat 157:324, 2001). In this paper we use examples, largely drawn from the aquatic literature, to illustrate how dimensional approaches might be used to maintain key ecological properties. Such key properties include effective habitat size, environmental variability, vertical and horizontal gradients, and interactions among habitats. We distinguish both continuous and discrete approaches that can be used to achieve functional similarity through compensatory distortion. In addition to its potential as a tool for improving the realism of experimental ecosystems, the dimensional approach points towards new options for developing, testing and advancing our understanding of scaling relationships in nature.

Body Size↗

Effects of range position, inter-annual variation and density on demographic transition rates of Hornungia petraea populations.

The central-marginal model assumes unfavourable and more variable environmental conditions at the periphery of a species' distribution range to negatively affect demographic transition rates, finally resulting in reduced population sizes and densities. Previous studies on density-dependence as a crucial factor regulating plant population growth have mainly focussed on fecundity and survival. Our objective is to analyse density-dependence in combination with the effect of inter-annual variation and range position on all life stages of an annual plant species, Hornungia petraea, including germination and seed incorporation into the seed bank. As previous studies on H. petraea had revealed a pattern opposite to existing theory with lower population densities at the distribution centre in Italy than at the periphery in Germany, we hypothesised that (1) demographic transition rates are lower, (2) the inter-annual variation in demographic transition rates is higher and (3) the intensity of density-dependence is weaker in Italy than in Germany. To analyse demographic transition rates, we used an autoregressive covariance strategy for repeated measures including density and inter-annual variation. All the three hypotheses were confirmed, but the impact of range position, density-dependence and inter-annual variation differed among the transition steps. All transition rates except fecundity were higher in the German populations than in the Italian populations. Germination rate and incorporation rate into the seed bank were strongly density-dependent. Central populations showed a larger inter-annual variation in fecundity and winter survival rate. Winter survival rate was the only transition step with a stronger density-dependence in peripheral populations. In most cases, these differences between distribution centre and periphery would not have emerged without taking density-dependence and inter-annual variation into account. We conclude that including range position, inter-annual variation and density-dependence in one single statistical model is an important tool for the interpretation of demographic patterns regarding the central-marginal model.

Analysis of Variance↗

Flood-deposited wood debris and its contribution to heterogeneity and regeneration in a semi-arid riparian landscape.

We investigated whether large woody debris (LWD) piles create nodes of environmental resources that contribute to the recovery of riparian vegetation and that also augment the heterogeneity and resilience of the riverine system. River and riparian systems are typified by a large degree of heterogeneity and complex interactions between abiotic and biotic elements. Disturbance such as floods re-distribute the resources, such as LWD, and thereby add greater complexity to the system. We examined this issue on a semi-arid savanna river where approximately a 100-year return interval flood in 2000 uprooted vegetation and deposited substantial LWD. We investigated the micro-environment within the newly established LWD piles and compared this with conditions at adjacent reference sites containing no LWD. We found soil nutrient concentrations to be significantly higher in LWD piles compared with the reference plots (total N +19%, available P +51%, and total C +36%). Environmental variables within LWD piles and reference sites varied with landscape position in the river-riparian landscape and with LWD pile characteristics. Observed differences were generally between piles located in the terrestrial and riparian areas as compared to piles located on the macro-channel floor. After 3 years the number and cover of woody species were significantly higher when associated with LWD piles, regardless of landscape position or pile type. We conclude that LWD piles formed after large floods act as resource nodes by accumulating fine sediments and by retaining soil nutrients and soil moisture. The subsequent influence of LWD deposition on riparian heterogeneity is discerned at several spatial scales including within and between LWD piles, across landscape positions and between channel types. LWD piles substantially influence the initial developmental of riparian vegetation as the system regenerates following large destructive floods.

Analysis of Variance↗

Intrinsic effects of species on leaf litter and root decomposition: a comparison of temperate grasses from North and South America.

Plant species affect natural ecosystems through interactions between environmental and genetic factors. The importance of plant species in controlling decomposition is now well-established through its influence on litter quality, which affects mass loss and nutrient release. At the same time, direct species effects are often confounded with indirect site effects due to the ecophysiological responses of plants to environmental variability. We evaluated the intrinsic effects of species on litter quality and decomposition, comparing 14 native perennial grass species from three different grassland ecosystems in North and South America. Plants were grown under controlled greenhouse conditions to eliminate any indirect effects of climate on litter quality, and senescent material of leaf litter and roots were collected. The initial litter nutrient quality and the carbon quality were assessed, and decomposition was determined over a period of one year by placing litterbags in a common grassland site. In spite of constant growth conditions, species' litter showed broad and significant differences in N, P and lignin concentration, as well as C:N ratio, with the greatest differences occurring between C(3) and C(4) species and leaf litter and root material. In addition, decomposition was significantly different among species and between leaf litter and roots within species, with constants (k) ranging from 1.50 to 3.65 year(-1) for leaf litter, and 0.51-1.82 year(-1) for roots. These results highlight the fact that, independent of climate or edaphic changes due to human activity, changes in plant species or in allocation patterns among plant organs in grassland ecosystems could have a large effect on carbon turnover. At the same time, the way in which intrinsic species characteristics affect decomposition demonstrates a large degree of functional convergence among species from grasslands of North and South America.

Carbon↗

[Multidisciplinary treatment program on chronic low back pain, part 3. Psychosocial aspects].

PROBLEM: The majority of authors agree today that psychosocial factors have more influence on a successful treatment of chronic back pain than other variables, in particular medical findings. Therefore treatments aim to integrate psychotherapeutic intervention in order to lessen emotional impairment, to change behavioral patterns (which advocate rest and the avoidance of physical activity), and to change cognitive attitudes and fears concerning exercise and work ability. Nevertheless, the interplay of cognitive measures and disability in treatment programs still remains an unclear issue. METHODS: Ninety disabled patients with chronic low back pain were admitted to an 8-week outpatient program of functional restoration and behavioral support. The program consisted of a pre-program (education, stretching and calisthenic exercises) and an intensive treatment period (physical exercises, back school education, cognitive behavioral group therapy, relaxation training, occupational therapy, vocational counseling), which took place for 5 weeks, 7 h a day, as an outpatient program. The targets of the psychological interventions were (a) to change maladaptive behavior (inactivity, social withdrawal) and increase the patient's activity level at home, (b) to alter maladaptive cognitions (somatization, catastrophizing, passive expectations concerning treatment) and to improve their own positive coping skills, (c) to identify and stop operant conditioned behavior, and (d) to prevent depressive symptoms and strengthen the level of emotional control. The program's philosophy encouraged the patients' active efforts to improve their functional status within a therapeutic environment that reinforced positive behavior traits conductive to getting well. The main therapeutic target was to facilitate a return to work. Apart from a medical examination and a personal interview, the patients' physical impairment, pain descriptions, and psychological distress (according to different criteria for evaluation) were also measured. This included variables such as depression, psychovegetative complaints, quality of life and workplace satisfaction, disability, and coping with disease. Measurements were repeated at the end of the 8-week program, and following 6- and 12-month intervals. RESULTS: In comparison with the initial values, a statistically significant improvement became evident in reducing pain, disability, depression, and psychovegetative signs (P < 0.001). Nearly all results remained stable at the 6- and 12-months examinations. Apart from these results, coping measurements demonstrated little improvement in the three factorial coping dimensions. By use of regression analyses, a differentiated description of psychosocial connections became apparent in three different ways of coping (catastrophizing, searching for information, cognitive control) and parameters of disability. Disability levels corresponded poorly with pain descriptions, physical impairment and coping dimensions. This result indicates that disability should be viewed as a separate component in assessing the patients' description of low back pain. CONCLUSION: An analysis of coping dimensions demonstrated that current cognitive measures might be too general to explain low back disability adequately. In addition, the results indicate that the use of the 'catastrophizing' factor as a separate variable is questionable, since it may simply be a symptom of depression. The relevance of coping as a sensitive parameter for change is also addressed. It is suggested that an alteration in coping strategies may be an important treatment effect, but is subject to individual prerequisites to maximize treatment response. Thus, future research must focus on the complex interactions between personality variables, environmental factors, and the coping demands posed by the specific nature of pain problems. A more lengthy evaluation of so-called 'fear-avoidance beliefs' in combination with 'disability' and coping dimensions could possibly lead to further treatment on the development of chronicity in chronic low back pain patients.

English Abstract↗

Analysis of the growth of rimu (Dacrydium cupressinum) in South Westland, New Zealand, using process-based simulation models.

Two process-based models were used to identify the environmental variables limiting productivity in a pristine, mature forest dominated by rimu (Dacrydium cupressinum Sol. ex Lamb.) trees in South Westland, New Zealand. A model of canopy net carbon uptake, incorporating routines for radiation interception, photosynthesis and water balance was used to determine a value for quantum efficiency when climate variables were not limiting. The annual net carbon uptake by the canopy was estimated to be 1.1 kg C m(-2) and the quantum efficiency 22.6 mmol mol quanta(-1). This value of quantum efficiency, combined with other parameters obtainable from the literature, was then used in a model of forest productivity (3-PG), to simulate changes in net productivity and the allocation of carbon to tree components. The model was adjusted to match a measured stem increment of 10.6 Mg ha(-1) over a period of 13 years. To achieve this while maintaining a low, but stable value for leaf area index, it was necessary to set the site fertility rating very low and select high values for the parameters describing the proportional allocation of total carbon to roots. This approach highlighted nutrient availability as the principal constraint on productivity for the ecosystem and identified critical measurements that will be necessary for using the model to predict the effects of climate change on carbon sequestration. The low rates of carbon uptake and productivity are consistent with the low nutrient supply available from the highly leached, acid soils, most likely attributable to frequent saturation and a very shallow aerobic zone.

Carbon↗

Stomatal conductance in a tropical xerophilous shrubland at a lava substratum.

Diurnal variation in leaf stomatal conductance (gs) of three xerophilous species (Buddleia cordata, Senecio praecox and Dodonaea viscosa) was measured over a 10-month period during the dry and wet seasons in a shrubland that is developing in a lava substratum in Mexico. Averaged stomatal conductances were 147 and 60.2 (B. cordata), 145 and 24.8 (D. viscosa) and 142.8 and 14.1 mmol m(-2) s(-1) (S. praecox) during the wet and dry season respectively. Leaf water potential (Psi) varied in a range of -0.6 to -1.2 (S. praecox), -0.6 to -1.8 (B. cordata) and -0.9 to -3.4 MPa (D. viscosa) during the same measurement periods. Stomata were more sensitive to changes in irradiance, air temperature and leaf-air vapour pressure difference in the rainy season than the dry season. Although stomatal responses to Psi were difficult to distinguish in any season (dry or rainy), data for the entire period of measurement showed a positive correlation, stomata tending to open as Psi increased, but there is strong evidence of isohydric behaviour in S. praecox and B. cordata. A multiplicative model relating gs to environmental variables and to Psi accounted for 79%-83% of the variation of gs in three sites (pooled data); however, the performance of the model was poorer (60%-76%) for individual species from other sites not included in the pooled data.

Adaptation, Physiological↗

Morphological plasticity of Primula nutans to hummock-and-hollow microsites in an alpine wetland.

Hummock-and-hollow microtopography is common in wetlands of the Qinghai-Tibetan Plateau. The physical environment of hummocks contrasts strongly with that of hollows. To address how Primula nutans Georgi, a herbaceous species broadly distributed on the plateau, can inhabit both hummocks and hollows, we investigated the plasticity of its morphology and biomass growth in relation to the environmental variables during the growing season. The results are as follows: (1) total daily photosynthetic photon flux density, maximum soil temperature, and diurnal soil temperature range were significantly larger on the hummocks than in the hollows; (2) individual ramets had smaller leaves, higher leaf mass per unit area, and shorter petiole and peduncle length on the hummocks, but leaf and root dry weights per ramet differed little between microsites; (3) P. nutans allocated most of its dry mass to peduncles and flowers and the proportion of reproductive mass was significantly higher for plants in the hollows than on the hummocks; (4) the coefficients of variation of most morphological and biometric parameters was higher on hummocks than in hollows. The results suggest that P. nutans favors hummocks but can tolerate hollows through morphological adjustments in that the mass investment to peduncles and flowers is much larger in plants in the hollows than hummocks.

Ecosystem↗