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7,327 results for “Pathway”
Revisiting steroidogenic pathways in the human placenta and primary human trophoblast cells
<p>Supplementary Table (Table S1)</p>
Data from: Exposure to environmental radionuclides is associated with altered metabolic and immunity pathways in a wild rodent
Wildlife inhabiting environments contaminated by radionuclides face putative detrimental effects of exposure to ionizing radiation, with biomarkers such as an increase in DNA damage and/or oxidative stress commonly associated with radiation exposure. To examine the effects of exposure to radiation on gene expression in wildlife, we conducted a de novo RNA sequencing study of liver and spleen tissues from a rodent, the bank vole Myodes glareolus. Bank voles were collected from the Chernobyl Exclusion Zone (CEZ), where animals were exposed to elevated levels of radionuclides, and from uncontaminated areas near Kyiv, Ukraine. Counter to expectations, we did not observe a strong DNA damage response in animals exposed to radionuclides, although some signs of oxidative stress were identified. Rather, exposure to environmental radionuclides was associated with upregulation of genes involved in lipid metabolism and fatty acid oxidation in the livers – an apparent shift in energy metabolism. Moreover, using stable isotope analysis, we identified that fur from bank voles inhabiting the CEZ had enriched isotope values of nitrogen: such an increase is consistent with increased fatty acid metabolism, but also could arise from a difference in diet or habitat between the CEZ and elsewhere. In livers and spleens, voles inhabiting the CEZ were characterized by immunosuppression, such as impaired antigen processing, and activation of leukocytes involved in inflammatory responses. In conclusion, exposure to low dose environmental radiation impacts pathways associated with immunity and lipid metabolism, potentially as a stress-induced coping mechanism.
Data from: Non-invasive imaging of CSF-mediated brain clearance pathways via assessment of perivascular fluid movement with DTI MRI
The glymphatics system describes a CSF-mediated clearance pathway for the removal of potentially harmful molecules, such as amyloid beta, from the brain. As such, its components may represent new therapeutic targets to alleviate aberrant protein accumulation that defines the most prevalent neurodegenerative conditions. Currently, however, the absence of any non-invasive measurement technique prohibits detailed understanding of glymphatic function in the human brain and in turn, it's role in pathology. Here, we present the first non-invasive technique for the assessment of glymphatic inflow by using an ultra-long echo time, low b-value, multi-direction diffusion weighted MRI sequence to assess perivascular fluid movement (which represents a critical component of the glymphatic pathway) in the rat brain. This novel, quantitative and non-invasive approach may represent a valuable biomarker of CSF-mediated brain clearance, working towards the clinical need for reliable and early diagnostic indicators of neurodegenerative conditions such as Alzheimer's disease.
Data from: Pathways of cryptic invasion in a fish parasite traced using coalescent analysis and epidemiological survey
Introduced species have the potential to outperform natives via the introduction of new parasites to which the native ecosystem is vulnerable. Cryptic diversity within an invasive species can obscure invasion patterns and confound proper management measures. The aim of this study is to use coalescent theory based methodology to trace recent routes of invasion in populations of Ligula intestinalis, a globally distributed fish parasite possessing both native and recently introduced populations in North Africa. Molecular analyses of mitochondrial DNA discerned a pronounced genetic divergence between introduced and native populations. Distribution of mitochondrial haplotypes demonstrated common origin of European populations with North African parasites sampled from introduced fish species in Tunisia. To test the suggested pathway of introduction, microsatellite data were examined in a model-based coalescent analysis using the software MIGRATE, where Europe to Tunisia direction of migration was favoured over alternative hypotheses of gene flow. Specificity of Tunisian populations to different host species was assessed in an epidemiologic survey confirming prevailing host-based division between introduced and native parasites in North Africa. This approach combining advanced analysis of molecular markers with host-specificity data allows revealing the evolution of host-parasite interactions following biological invasion and provides basis for devising future management measurements.
Data from: Postglacial expansion pathways of red mangrove, Rhizophora mangle, in the Caribbean Basin and Florida
PREMISE OF THE STUDY: The Last Glacial Maximum (LGM) was a period of massive range contraction. Post-LGM, water-dispersed coastal species, including the red mangrove (Rhizophora mangle), expanded poleward as propagules were transported by ocean currents. We assessed postglacial marine expansion pathways for R. mangle within the Caribbean Basin and Florida. METHODS: Six microsatellite loci were used to genotype 237 individuals from nine R. mangle populations in the Caribbean, Florida, and Northwest Africa. We evaluated genetic variation, population structure, gene flow along alternative post-LGM expansion pathways to Florida, and potential long-distance dispersal (LDD) from West Africa to Caribbean islands. KEY RESULTS: These R. mangle populations had substantial genetic structure (FST = 0.37, P < 0.0001) with three discrete population clusters (Caribbean mainland, Caribbean islands, and Florida). Genetic connectivity along the mainland pathway (Caribbean mainland to Florida) vs. limited gene dispersal along the Antilles Island pathway (Caribbean islands to Florida) supported Florida recolonization from Caribbean mainland sources. Genetic similarity of Northwest Africa and two Caribbean islands provided evidence for trans-Atlantic LDD. We did not find a pattern of decreasing genetic diversity with latitude. CONCLUSIONS: We outline a complex expansion history for R. mangle, with discrete pathways of recolonization for Florida and Caribbean islands. Contrary to expectation, connectivity to putative Caribbean mainland refugial populations via ocean currents, and not latitude, appears to dictate genetic diversity within Caribbean island and Florida R. mangle. These findings provide a framework for further investigation of additional water-dispersed neotropical species, and insights for management initiatives.
Identifying and characterizing stress pathways of concern for consumer safety in next generation risk assessment
<p>Many substances for which consumer safety risk assessments need to be conducted are not associated with specific toxicity modes of action, but rather exhibit non-specific toxicity leading to cell stress. In this work, a cellular stress panel is described, consisting of 36 biomarkers representing mitochondrial toxicity, cell stress and cell health, measured predominantly using high content imaging. To evaluate the panel, data were generated for thirteen substances at exposures consistent with typical use-case scenarios. These included some that have been shown to cause adverse effects in a proportion of exposed humans and have a toxicological mode-of-action associated with cellular stress (e.g. doxorubicin, troglitazone, diclofenac), and some that are not associated with adverse effects due to cellular stress at human-relevant exposures (e.g. caffeine, niacinamide and phenoxyethanol). For each substance, concentration response data were generated for each biomarker at three timepoints. A Bayesian model was then developed to quantify the evidence for a biological response, and if present, a credibility range for the estimated point of departure (PoD) was determined. PoDs were compared with the plasma C<sub>max</sub> associated with the typical substance exposures, and indicated a clear differentiation between 'low' risk and 'high' risk chemical exposure scenarios. </p> <p>Developing robust methods to characterize the in vitro bioactivity of xenobiotics is an important part of non-animal safety assessment. The results presented show that the cellular stress panel can be used, together with other new approach methodologies, to identify chemical exposures that are protective of consumer health.</p>
Data from: Estimating contributions of pelagic and benthic pathways to consumer production in coupled marine food webs
1. Pelagic and benthic systems usually interact, but their dynamics and production rates differ. Such differences influence the distribution, reproductive cycles, growth rates, stability and productivity of the consumers they support. Consumer preferences for, and dependence on, pelagic or benthic production are governed by the availability of these sources of production and consumer life history, distribution, habitat, behavioural ecology, ontogenetic stage and morphology. 2. Diet studies may demonstrate the extent to which consumers feed on prey in pelagic or benthic environments. But they do not discriminate benthic production directly supported by phytoplankton from benthic production recycled through detrital pathways. The former will track the dynamics of phytoplankton production more closely than the latter. 3. We develop and apply a new analytical method that uses carbon (C) and sulfur (S) natural abundance stable isotope data to assess the relative contribution of pelagic and benthic pathways to fish consumer production. 4. For 13 species of fish that dominate community biomass in the northern North Sea (estimated >90% of total biomass), relative modal use of pelagic pathways ranged from <25% to >85%. Use of both C and S isotopes as opposed to just C reduced uncertainty in relative modal use estimates. Temporal comparisons of relative modal use of pelagic and benthic pathways revealed similar ranking of species dependency over four years, but annual variation in relative modal use within species was typically 10-40%. 5. For the total fish consumer biomass in the study region, the C and S method linked approximately 70% and 30% of biomass to pelagic and benthic pathways respectively. As well as providing a new method to define consumers' links to pelagic and benthic pathways our results demonstrate that a substantial proportion of fish biomass, and by inference production, in the northern North Sea is supported by production that has passed through transformations on the seabed.
Data from: An integrated pathway for building regional phylogenies for ecological studies
Aims: Phylogenies are increasingly used in community ecology, biogeography and macroecology. However, sourcing a phylogeny comprising the entire species pool for a focal region can be difficult. Typically, a bespoke phylogeny must be created requiring considerable data manipulation and the use of many standalone software. Here we present a suite of methodological tools within the popular R environment that help to build molecular phylogenies appropriate for ecological studies with a regional focus. Innovation: Our R package regPhylo provides a pipeline to construct a Bayesian posterior distribution of time-calibrated trees suitable to address ecological questions. The novel contributions of regPhylo include options to: use prior phylogenetic knowledge through flexible topological constraints; include spatial metadata in sourcing DNA sequences; and include taxa without DNA sequences and then infer consequent phylogenetic uncertainty. Specifically, regPhylo helps researchers: retrieve DNA sequences; enhance available metadata; select DNA sequences based on their length or spatial proximity to the region of study; align sequences; and perform quality control. Output from the pipeline is a file ready to run in the Bayesian tree reconstruction software BEAST2, appropriate for estimating time-calibrated trees and including phylogenetic uncertainty for downstream analyses. Main conclusions: Overall, regPhylo improves the integration of popular standalone phylogenetic software into the flexible R environment. It provides a novel approach to include topological constraints based on prior knowledge, include taxa without DNA sequences, and select spatially appropriate DNA sequences. When coupled with a Bayesian tree-building process, our approach provides estimates of uncertainty in both topology and branch-lengths. We demonstrate the utility of the package by constructing a posterior distribution of time-calibrated phylogenies for the New Zealand marine ray-finned fishes (Actinopterygii) providing the unprecedented opportunity to include phylogenetic information in downstream ecological analyses for marine fishes in this region.
Data from: Creating new evolutionary pathways through bio-invasion: the population genetics of brushtail possums in New Zealand
Rapid increases in global trade and human movement have created novel mixtures of organisms bringing with them the potential to rapidly accelerate the evolution of new forms. The common brushtail possum (Trichosurus vulpecula), introduced into New Zealand from Australia in the 19th Century, is one such species having been sourced from multiple populations in its native range. Here, we combine microsatellite DNA and GIS-based spatial data to show that T.vulpecula originating from at least two different Australian locations exhibit a population structure that is commensurate with their introduction history and which cannot be explained by landscape features alone. Most importantly, we identify a hybrid zone between the two subspecies which appears to function as a barrier to dispersal. When combined with previous genetic, morphological and captive studies, our data suggest that assortative mating between the two subspecies may operate at a behavioural or species recognition level rather than through fertilization, genetic incompatibility, or developmental inhibition. Nevertheless, hybridization between the two subspecies of possum clearly occurs, creating the opportunity for novel genetic combinations that would not occur in their natural ranges and which is especially likely given that multiple contact zones occur in New Zealand. This discovery has implications for wildlife management in New Zealand because multiple contact zones are likely to influence the dispersal patterns of possums and because differential susceptibility to baiting with sodium fluoroacetate between possums of different origins, may promote novel genetic forms.
Evolutionary pathways to communal and cooperative breeding in Carnivores
<p>In animal societies, individuals can cooperate in a variety of tasks, including rearing young. Such cooperation is observed in complex social systems, including communal and cooperative breeding. In mammals, both these social systems are characterized by delayed dispersal and alloparenting, whereas only cooperative breeding involves reproductive suppression. While the evolution of communal breeding has been linked to direct fitness benefits of alloparenting, the direct fitness cost of reproductive suppression has led to the hypothesis that the evolution of cooperative breeding is driven by indirect fitness benefits accrued through raising the offspring of related individuals. To decipher between the evolutionary scenarios leading to communal and cooperative breeding in carnivores, we investigated the coevolution among delayed dispersal, reproductive suppression, and alloparenting. We reconstructed ancestral states and transition rates between these traits. We found that cooperative breeding and communal breeding evolved along separate pathways, with delayed dispersal as the first step for both of them. The three traits coevolved, enhancing and stabilizing each other, which resulted in cooperative social systems being stable as opposed to intermediate configurations. These findings promote the key role of coevolution among traits to stabilize cooperative social systems, and highlight the specificities of evolutionary patterns of sociality in carnivores.</p>
Data from: Thermal plasticity of growth and development varies adaptively among alternative developmental pathways
Polyphenism, the expression of discrete alternative phenotypes, is often a consequence of a developmental switch. Physiological changes induced by a developmental switch potentially affect reaction norms, but the evolution and existence of alternative reaction norms remains poorly understood. Here, we demonstrate that, in the butterfly Pieris napi (Lepidoptera: Pieridae), thermal reaction norms of several life history traits vary adaptively among switch-induced alternative developmental pathways of diapause and direct development. The switch was affected both by photoperiod and temperature, ambient temperature during late development having the potential to override earlier photoperiodic cues. Directly developing larvae had higher development and growth rates than diapausing ones across the studied thermal gradient. Reaction norm shapes also differed between the alternative developmental pathways, indicating pathway-specific selection on thermal sensitivity. Relative mass increments decreased linearly with increasing temperature and were higher under direct development than diapause. Contrary to predictions, population phenology did not explain trait variation or thermal sensitivity, but our experimental design probably lacks power for finding subtle phenology effects. We demonstrate adaptive differentiation in thermal reaction norms among alternative phenotypes, and suggest that the consequences of an environmentally dependent developmental switch primarily drive the evolution of alternative thermal reaction norms in P. napi.
Data from: Recurrent and recent selective sweeps in the piRNA pathway
Uncontrolled transposable element (TE) insertions and excisions can cause chromosome breaks and mutations with dramatic deleterious effects. The PIWI interacting RNA (piRNA) pathway functions as an adaptive TE silencing system during germline development. Several essential piRNA pathway proteins appear to be rapidly evolving, suggesting that TEs and the silencing machinery may be engaged in a classical "evolutionary arms race." Using a variety of molecular evolutionary and population genetic approaches, we find that the piRNA pathway genes rhino, krimper, and aubergine show patterns suggestive of extensive recurrent positive selection across Drosophila species. We speculate that selection on these proteins reflects crucial roles in silencing unfamiliar elements during vertical and horizontal transmission of TEs into naïve populations and species, respectively.
Data from: Sex-specific pathways of parental age effects on offspring lifetime reproductive success in a long-lived seabird
The conditions under which individuals are reared vary and sensitivity of offspring to such variation is often sex-dependent. Parental age is one important natal condition with consequences for aspects of offspring fitness, but reports are mostly limited to short-term fitness consequences and do not take into account offspring sex. Here we used individual-based data from a large colony of a long-lived seabird, the common tern Sterna hirundo, to investigate longitudinal long-term fitness consequences of parental age in relation to both offspring and parental sex. We found that recruited daughters from older mothers suffered from reduced annual reproductive success. Recruited sons from older fathers were found to suffer from reduced lifespan. Both effects translated to reductions in offspring lifetime reproductive success. Besides revealing novel sex-specific pathways of trans-generational parental age effects on offspring fitness, which inspire studies of potential underlying mechanisms, our analyses show that reproductive senescence is only observed in the common tern when including trans-generational age effects. In general, our study shows that estimates of selective pressures underlying the evolution of senescence, as well as processes such as age-dependent mate choice and sex allocation, will depend on whether causal trans-generational effects exist and are taken into account.
Data from: The same picture through different lenses: quantifying the effects of two preservation pathways on Green River Formation insects
Insects in the fossil record are generally preserved in lacustrine shales or in amber. For those in lacustrine shales, preservation is usually via keroginization or mineralization. Given the extended period of microbial decay required to generate ions for mineralization, there is a predicted inherent bias toward lower preservation quality for this pathway by most taphonomic indices compared with keroginization. This study tests this hypothesis by comparing multiple measures of preservation quality between sites with similar sedimentology in the Eocene Green River Formation of Colorado. Here, insects are either mineralized in iron oxides (likely after pyrite) at the Paleoburn site or keroginized at the Anvil Points site. Generally, the prediction that keroginization preserves soft-bodied fossils with higher preservational quality than mineralization is affirmed, but with some caveats. Beetles, known for their robust cuticles, are proportionately more abundant at the Paleoburn site, but eight of the nine orders recorded are shared between sites. As predicted, insects show lower preservation fidelity at the Paleoburn site, but they also show higher degrees of disarticulation. This second bias should be acquired primarily during the biostratinomy stage, and not early diagenesis. Nonetheless, higher-energy biostratinomic conditions may be compatible with taphonomic conditions that promote mineralization over keroginization. Comparing the inherent taphonomic bias of different preservation pathways is often difficult, since fossil deposits may be preserved millions of years or thousands of kilometers apart. By studying two different preservation pathways of insects within the same formation, we can affirm that keroginization does indeed preserve recalcitrant organic matter with higher quality than pyritization or iron-oxide mineralization. Additionally, some guidelines can be proposed concerning the body parts and taxa that can be compared, and for what purpose, when contrasting mineralized and keroginized soft-bodied deposits.
Data from: Birth date predicts alternative life-history pathways in a fish with sequential reproductive tactics
In species with plastic expression of alternative reproductive tactics (ARTs), individuals of the same sex, usually males, can adopt different reproductive tactics depending on factors such as body size. The 'birth date hypothesis' proposes that condition-dependent expression of ARTs may ultimately depend on birth date, because individuals born at different times of the year may achieve different sizes and express different reproductive tactics accordingly. However, this has rarely been tested. Here, we tested this hypothesis in a fish with ARTs, the peacock blenny (Salaria pavo). A long-term (6 years) mark–recapture study demonstrated that ARTs in the peacock blenny were sequential and that males may follow at least two alternative life-history pathways: a nest-holder pathway, in which males express the nest-holder tactic from their first breeding season onwards, and a parasitic pathway, where males reproduce on their first breeding season as sneaker males and subsequently as nest-holders. We have found evidence of a birth date effect on the expression of ARTs in the peacock blenny. Males following the nest-holder pathway are born earlier and are larger at the first breeding season than males following the parasitic pathway, but they have similar growth curves. The mechanisms underlying a birth date effect are far from clear and might be diverse. We have not found support for a mechanism of body size threshold triggering sexual maturation and subsequent ARTs. A mechanism of tactic determination that is strictly based on timing of first maturation is also unlikely. A proxy of lifetime reproductive success shows crossing (body size associated) fitness curves for the two main life-history pathways.
Data from: Do convergent ecomorphs evolve through convergent morphological pathways? Cranial shape evolution in fossil hyaenids and borophagine canids (Carnivora, Mammalia)
Cases of convergent evolution, particularly within ecomorphological contexts, are instructive in identifying universally adaptive morphological features across clades. Tracing of evolutionary pathways by which ecomorphological convergence takes place can further reveal mechanisms of adaptation, which may be strongly influenced by phylogeny. Ecomorphologies of carnivorous mammals represent some of the most outstanding cases of convergent evolution in the Cenozoic radiation of mammals. This study examined patterns of cranial shape change in the dog (Canidae) and hyena (Hyaenidae) families, in order to compare the evolutionary pathways that led to the independent specialization of bone-cracking hypercarnivores within each clade. Geometric morphometrics analyses of cranial shape in fossil hyaenids and borophagine canids provided evidence for deep-time convergence in morphological pathways toward the independent evolution of derived bone-crackers. Both clades contained stem members with plesiomorphic generalist/omnivore cranial shapes, which evolved into doglike species along parallel pathways of shape change. The evolution of specialized bone-crackers from these doglike forms, however, continued under the constraint of a full cheek dentition and restriction on rostrum length reduction in canids, but not hyaenids. Functionally, phylogenetic constraint may have limited borophagine canids to crack bones principally with their carnassial instead of the third premolar as in hyaenids, but other cranial shape changes associated with durophagy nevertheless evolved in parallel in the two lineages. Size allometry was not a major factor in cranial shape evolution in either lineage, supporting the interpretation of functional demands as drivers for the observed convergence. The comparison between borophagines and hyaenids showed that differential effects of alternative functional "solutions" that arise during morphological evolution may be multiplied with processes of the "macroevolutionary ratchet" already in place to further limit the evolutionary pathways available to specialized lineages.
Data from: Life history traits and functional processes generate multiple pathways to ecological stability
Stability contributes to the persistence of ecological communities, yet the interactions among different stabilizing forces are poorly understood. We assembled mesocosms with an algal resource and 1-8 different clones of the consumer Daphnia ambigua and tracked algal and Daphnia abundances through time. We then fitted coupled ordinary differential equations (ODEs) to the consumer-resource time series. We show that variation in different components of stability (local stability and the magnitude of population fluctuations) across mesocosms arises through variation in life history traits and the functional processes represented by ODE model parameters. Local stability was enhanced by increased algal growth rate and Daphnia mortality and foraging rate. Population fluctuations were dampened by high Daphnia conversion efficiency and lower interaction strengths, low algal growth rate, high Daphnia death rate, and low Daphnia foraging. These results indicate that 1) stability in consumer-resource systems may arise through the net effect of multiple related stabilizing pathways, and 2) different aspects of stability can vary independently and may respond in opposite directions to the same forces.
Data from: Small RNAs from a big genome: the piRNA pathway and transposable elements in the salamander species Desmognathus fuscus
Most of the largest vertebrate genomes are found in salamanders, a clade of amphibians that includes 686 species. Salamander genomes range in size from 14 to 120 Gb, reflecting the accumulation of large numbers of transposable element (TE) sequences from all three TE classes. Although DNA loss rates are slow in salamanders relative to other vertebrates, high levels of TE insertion are also likely required to explain such high TE loads. Across the Tree of Life, novel TE insertions are suppressed by several pathways involving small RNA molecules. In most known animals, TE activity in the germline is primarily regulated by the Piwi-interacting RNA (piRNA) pathway. In this study, we test the hypothesis that salamanders' unusually high TE loads reflect the loss of the ancestral piRNA-mediated TE-silencing machinery. We characterized the small RNA pool in the female and male adult gonads, testing for the presence of small RNA molecules that bear the characteristics of TE-targeting piRNAs. We also analyzed the amino acid sequences of piRNA pathway proteins from salamanders and other vertebrates, testing whether the overall patterns of sequence divergence are consistent with conserved pathway function across the vertebrate clade. Our results do not support the hypothesis of piRNA pathway loss; instead, they suggest that the piRNA pathway is expressed in salamanders. Given these results, we propose hypotheses to explain how the extraordinary TE loads in salamander genomes could have accumulated, despite the expression of TE-silencing machinery.
Data from: Photosynthetic pathways in Bromeliaceae: phylogenetic and ecological significance of CAM and C3 based on carbon isotope ratios for 1893 species
A comprehensive analysis of photosynthetic pathways in relation to phylogeny and elevational distribution was conducted in Bromeliaceae, an ecologically diverse Neotropical family containing large numbers of both terrestrial and epiphytic species. Tissue carbon isotope ratio (δ13C) was used to determine the occurrence of crassulacean acid metabolism (CAM) and C3 photosynthesis in 1893 species, representing 57% of species and all 56 genera in the family. The frequency of δ13C values showed a strongly bimodal distribution: 1074 species (57%) had values more negative than −20‰ (mode = −26.7‰), typical of predominantly daytime carbon fixation via the C3 pathway, whereas 819 species (43%) possessed values less negative than −20‰ (mode = −13.3‰), indicative of predominantly nocturnal fixation of carbon via the CAM pathway. Amongst the six almost exclusively terrestrial subfamilies in Bromeliaceae, Brocchinioideae, Lindmanioideae and Navioideae consisted entirely of C3 species, with CAM species being restricted to Hechtioideae (all species of Hechtia tested), Pitcairnioideae (all species belonging to a xeric clade comprising Deuterocohnia, Dyckia and Encholirium) and Puyoideae (21% of Puya spp.). Of the other two subfamilies, in the overwhelmingly epiphytic (plus lithophytic) Tillandsioideae, 28% of species possessed CAM photosynthesis, all restricted to the derived genus Tillandsia and tending towards the more extreme epiphytic 'atmospheric' life-form. In Bromelioideae, with comparable numbers of terrestrial and epiphytic species, 90% of taxa showed CAM; included in these are the first records of CAM photosynthesis in Androlepis, Canistropsis, Deinacanthon, Disteganthus, Edmundoa, Eduandrea, Hohenbergiopsis, Lymania, Pseudananas, Ronnbergia and Ursulaea. With respect to elevational gradients, the greatest number of C3 bromeliad species were found at mid-elevations between 500 and 1500 m, whereas the frequency of CAM species declined monotonically with increasing elevation. However, in Puya, at least ten CAM species have been recorded at elevations > 3000 m, showing that CAM photosynthesis is not necessarily incompatible with low temperatures. This survey identifies five major origins of CAM photosynthesis at a higher taxonomic level in Bromeliaceae, but future phylogenetic work is likely to reveal a more fine-scale pattern of gains and losses of this trait, especially in ecologically diverse and widely distributed genera such as Tillandsia and Puya
Data from: Geo-clustered chronic affinity: pathways from socio-economic disadvantages to health disparities
Objective: Our objective was to develop and test a new concept (affinity) analogous to multimorbidity of chronic conditions for individuals at census tract level in Memphis, TN. The use of affinity will improve the surveillance of multiple chronic conditions and facilitate the design of effective interventions. Methods: We used publicly available chronic condition data (Center for Disease Control and Prevention (CDC) 500 Cities project), socio-demographic data (U.S. Census Bureau) and demographics data (Environmental Systems Research Institute; ESRI). We examined the geographic pattern of the affinity of chronic conditions using global Moran's I and Getis-Ord Gi statistics and its association with socio-economic disadvantage (poverty, unemployment, and crime) using robust regression models. We also used the most common behavioral factor, smoking, and other demographic factors (percent of the male population, percent of the population 67 years and over and total population size) as control variables in the model. Results: A geo-distinctive pattern of clustered chronic affinity associated with socio-economic deprivation was observed. Statistical results confirmed that neighborhoods with higher rates of crime, poverty, and unemployment were associated with an increased likelihood of having a higher affinity among major chronic conditions. With the inclusion of smoking in the model, however, only the crime prevalence was statistically significantly associated with the chronic affinity. Conclusion: Chronic affinity disadvantages were disproportionately accumulated in socially disadvantaged areas. We showed links between commonly co-observed chronic diseases at the population level and systematically explored the complexity of affinity and socio-economic disparities. Our affinity score, based on publicly available datasets, served as a surrogate for multimorbidity at the population level, which may assist policymakers and public health planners to identify urgent hot spots for chronic disease and allocate clinical, medical and healthcare resources efficiently.
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.