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6,467 results for “process”
Data from: Process-based species pools reveal the hidden signature of biotic interactions amid the influence of temperature filtering
A persistent challenge in ecology is to tease apart the influence of multiple processes acting simultaneously and interacting in complex ways to shape the structure of species assemblages. We implement a heuristic approach that relies on explicitly defining species pools and permits assessment of the relative influence of the main processes thought to shape assemblage structure: environmental filtering, dispersal limitations and biotic interactions. We illustrate our approach using data on the assemblage composition and geographic distribution of hummingbirds, a comprehensive phylogeny and morphological traits. The implementation of several process-based species pool definitions in null models suggests that temperature, but not precipitation or dispersal limitation, acts as the main regional filter of assemblage structure. Incorporating this environmental filter directly into the definition of assemblage-specific species pools revealed an otherwise hidden pattern of phylogenetic evenness, indicating that biotic interactions might further influence hummingbird assemblage structure. Such hidden patterns of assemblage structure call for a reexamination of a multitude of phylogenetic- and trait-based studies that did not explicitly consider potentially important processes in their definition of the species pool. Our heuristic approach provides a transparent way to explore patterns and refine interpretations of the underlying causes of assemblage structure.
Data from: Individual variation, population-specific behaviours, and stochastic processes shape marine migration phenologies
1. The phenology of long distance migrations can influence individual fitness, moderate population dynamics, and regulate the availability of ecosystem services to other trophic levels. Phenology varies within and among populations, and can be influenced by conditions individuals experience both prior to departure and encounter en route. 2. Assessing how intrinsic and extrinsic factors (e.g. individual physical condition vs. environmental conditions) interact to influence variation in migratory phenologies across ecological scales is often limited due to logistical constraints associated with tracking large numbers of individuals from multiple populations simultaneously. 3. We used two natural tags, DNA and otolith microstructure analysis, to estimate the relative influence of individual traits (life history strategy, body size at departure, and growth during migration), population-specific strategies, and interannual variability on the phenology of marine migrations in juvenile sockeye salmon Oncorhynchus nerka. 4. We show that the timing and duration of juvenile sockeye salmon migrations were correlated with both life history strategy and body size, while migration duration was also correlated with departure timing and growth rates during migration. Even after accounting for the effect of individual traits, several populations exhibited distinct migration phenologies. Finally, we observed substantial interannual and residual variation, suggesting stochastic environmental conditions moderate the influence of carry-over effects that develop prior to departure, as well as population-specific strategies. 5. Migratory phenologies are shaped by complex interactions between drivers acting at multiple ecological and temporal scales. Given evidence that intraspecific diversity can stabilize ecological systems, conservation efforts should seek to maintain migratory variation among populations and preserve locally adapted phenotypes; however, variation within populations, which may buffer systems from environmental stochasticity, should also be regularly assessed and preserved.
Data from: Investigating the timing of origin and evolutionary processes shaping regional species diversity: insights from simulated data and Neotropical butterfly diversification rates
Different diversification scenarios have been proposed to explain the origin of extant biodiversity. However, most existing meta-analyses of time-calibrated phylogenies rely on approaches that do not quantitatively test alternative diversification processes. Here, I highlight the shortcomings of using species divergence ranks, which is a method widely used in meta-analyses. Divergence ranks consist of categorizing cladogenetic events to certain periods of time, typically to either Pleistocene or to pre-Pleistocene ages. This approach has been claimed to shed light on the origin of most extant species and the timing and dynamics of diversification in any biogeographical region. However, interpretations drawn from such method often confound two fundamental questions in macroevolutionary studies, tempo (timing of evolutionary rate shifts) and mode ("how" and "why" of speciation). By using simulated phylogenies under four diversification scenarios, constant-rate, diversity-dependence, high extinction, and high speciation rates in the Pleistocene, I showed that interpretations based on species divergence ranks might have been seriously misleading. Future meta-analyses of dated phylogenies need to be aware of the impacts of incomplete taxonomic sampling, tree topology, and divergence time uncertainties, as well as they might be benefited by including quantitative tests of alternative diversification models that acknowledge extinction and diversity dependence.
Data from: Effect of reaction solvent on hydroxyapatite synthesis in sol-gel process
Synthesis of hydroxyapatite (HA) through sol–gel process in different solvent systems is reported. Calcium nitrate tetrahydrate (CNTH) and diammonium hydrogen phosphate (DAHP) were used as calcium and phosphorus precursors, respectively. Three different synthesis reactions were carried out by changing the solvent media, while keeping all other process parameters constant. A measure of 0.5 M aqueous DAHP solution was used in all reactions while CNTH was dissolved in distilled water, tetrahydrofuran (THF) and N,N-dimethylformamide (DMF) at a concentration of 0.5 M. Ammonia solution (28–30%) was used to maintain the pH of the reaction mixtures in the 10–12 range. All reactions were carried out at 40 ± 2°C for 4 h. Upon completion of the reactions, products were filtered, washed and calcined at 500°C for 2 h. It was clearly demonstrated through various techniques that the dielectric constant and polarity of the solvent mixture strongly influence the chemical structure and morphological properties of calcium phosphate synthesized. Water-based reaction medium, with highest dielectric constant, mainly produced β-calcium pyrophosphate (β-CPF) with a minor amount of HA. DMF/water system yielded HA as the major phase with a very minor amount of β-CPF. THF/water solvent system with the lowest dielectric constant resulted in the formation of pure HA.
Data from: Limited by the roof of the world: mountain radiations of Apollo swallowtails controlled by diversity-dependence processes
Mountainous areas comprise a substantial part of the world species richness, but the evolutionary origins and diversification of this biodiversity remain elusive. Diversification may result from differences in clade age (longer time to diversify), net diversification rates (faster speciation rate), or carrying capacities (number of niches). The likelihood of these macroevolutionary scenarios was assessed for six clades of Apollo swallowtails (Parnassius) that diversified mainly in the Himalayan-Tibetan region. The analyses suggest that neither the clade age, nor the speciation rate could explain the mountain butterfly diversification. Instead diversity-dependence models were strongly supported for each group. Models further estimated clades' carrying capacities that approximate the current number of species, indicating that diversity equilibrium is reached (or close to be). The results suggest that diversification of mountain butterflies was controlled by ecological limits, which governed the number of niches, and provide macroevolutionary justification for regarding mountains as islands.
Data from: Ultrasonic-enhanced replacement of lead in lead hydrometallurgy process from lead leaching solution
In this paper, ultrasonic enhanced replacement of lead by zinc in lead leaching solution was studied. The effects of reaction time, rotational speed, temperature, concentration of leaching solution and the ratio of the surface area of the zinc plate immersed in the leaching solution to the volume of leaching solution (S:V) were studied under both conventional and ultrasonic conditions. The optimum ultrasonic assisted replacement conditions were as follows: the S:V of 0.04 (4cm2/100ml), reaction temperature of 30 °C, replacement time of 30 min, and the concentration of leaching solution is 5 g/L, leading to the replacement rate of lead is 94.84%. Compared with conventional replacement process, the reaction time of ultrasonic enhanced substitution could be reduced to one half, and the demand of reaction temperature, leaching solution concentration and other conditions was decreased accordingly. Introducing ultrasonic into the replacement reaction is promising to reduce the energy consumption in hydrometallurgical industry also caters to the demand of environment protection.
Data from: Membrane-assisted extraction of monoterpenes: from in-silico solvent screening towards biotechnological process application
This work focuses on the process development of membrane-assisted solvent extraction of hydrophobic compounds such as monoterpenes. Beginning with the choice of suitable solvents, quantum chemical calculations with the simulation tool COSMO-RS were carried out to predict the partition coefficient (logP) of (S)-(+)-carvone and terpinen-4-ol in various solvent-water systems and validated afterwards with experimental data. COSMO-RS results show good prediction accuracy for nonpolar solvents like n-hexane, ethyl acetate and n-heptane even in the presence of salts and glycerol in aqueous medium. Based on the high logP value, n-heptane was chosen for the extraction of (S)-(+)-carvone in a lab-scale hollow-fiber membrane contactor. Two operation modes are investigated where experimental and theoretical mass transfer values, based on their related partition coefficients were compared. In addition, the process is evaluated in terms of extraction efficiency and overall product recovery, and its biotechnological application potential discussed. Our work demonstrates that the combination of in-silico prediction by COSMO-RS with membrane-assisted extraction is a promising approach for the recovery of hydrophobic compounds from aqueous solutions.
Data from: Multiple processes drive genetic structure of humpback whale (Megaptera novaeangliae) populations across spatial scales
Elucidating patterns of population structure for species with complex life histories, and disentangling the processes driving such patterns, remains a significant analytical challenge. Humpback whale (Megaptera novaeangliae) populations display complex genetic structures that have not been fully resolved at all spatial scales. We generated a data set of nuclear markers for 3,575 samples spanning the seven breeding stocks and substocks found in the South Atlantic and western and northern Indian Oceans. For the total sample, and males and females separately, we assessed genetic diversity, tested for genetic differentiation between putative populations and isolation by distance, estimated the number of genetic clusters without a priori population information, and estimated rates of gene flow using maximum likelihood and Bayesian approaches. At the ocean basin scale, structure is governed by geographic distance (IBD p<0.05) and female fidelity to breeding areas, in line with current understanding of the drivers of broad-scale population structure. Consistent with previous studies, the Arabian Sea breeding stock was highly genetically differentiated (FST 0.034-0.161; p<0.01 for all comparisons). However, the breeding stock boundary between west South Africa and east Africa was more porous than expected based on genetic differentiation, cluster, and gene flow analyses. Instances of male-fidelity to breeding areas and relatively high rates of dispersal for females were also observed between the three substocks in the western Indian Ocean. This mismatch between demographic units and current management boundaries may have ramifications for assessments of the status and continued protections of populations still in recovery from commercial whaling.
Data from: Digging through model complexity: using hierarchical models to uncover evolutionary processes in the wild
The growing interest for studying questions in the wild requires acknowledging that eco-evolutionary processes are complex, hierarchically structured and often partially observed or with measurement error. These issues have long been ignored in evolutionary biology, which might have led to flawed inference when addressing evolutionary questions. Hierarchical modelling (HM) has been proposed as a generic statistical framework to deal with complexity in ecological data and account for uncertainty. However, to date, HM has seldom been used to investigate evolutionary mechanisms possibly underlying observed patterns. Here, we contend the HM approach offers a relevant approach for the study of eco-evolutionary processes in the wild by confronting formal theories to empirical data through proper statistical inference. Studying eco-evolutionary processes requires considering the complete and often complex life histories of organisms. We show how this can be achieved by combining sequentially all life histories components and all available sources of information through HM. We demonstrate how eco-evolutionary processes may be poorly inferred or even missed without using the full potential of HM. As a case study, we use the Atlantic salmon and data on wild marked juveniles. We assess a reaction norm for migration and two potential trade-offs for survival. Overall, HM has a great potential to address evolutionary questions and investigate important processes that could not previously be assessed in laboratory or short time-scale studies.
Data from: State-dependent judgement bias in Drosophila: evidence for evolutionarily primitive affective processes
Affective states influence decision-making under ambiguity in humans and other animals. Individuals in a negative state tend to interpret ambiguous cues more negatively than individuals in a positive state. We demonstrate that the fruit fly, Drosophila melanogaster, also exhibits state-dependent changes in cue interpretation. Drosophila were trained on a Go/Go task to approach a positive (P) odour associated with a sugar reward and actively avoid a negative (N) odour associated with shock. Trained flies were then either shaken to induce a purported negative state or left undisturbed (control), and given a choice between: air or P; air or N; air or ambiguous odour (1:1 blend of P:N). Shaken flies were significantly less likely to approach the ambiguous odour than control flies. This 'judgement bias' may be mediated by changes in neural activity that reflect evolutionarily primitive affective states. We cannot say whether such states are consciously experienced, but utilisation of this model organism's versatile experimental tool kit may facilitate elucidation of their neural and genetic basis.
Data from: Rapid diversification of sperm precedence traits and processes among three sibling Drosophila species
Postcopulatory sexual selection is credited with driving rapid evolutionary diversification of reproductive traits and the formation of reproductive isolating barriers between species. This judgment, however, has largely been inferred rather than demonstrated due to general lack of knowledge about processes and traits underlying variation in competitive fertilization success. Here, we resolved processes determining sperm fate in twice-mated females, using transgenic Drosophila simulans and D. mauritiana populations with fluorescently-labeled sperm heads. Comparisons among these two species and D. melanogaster revealed a shared motif in the mechanisms of sperm precedence, with postcopulatory sexual selection potentially occurring during any of the three discrete stages: (1) insemination, (2) sperm storage, and (3) sperm use for fertilization, and involving four distinct phenomena: (1) sperm transfer, (2) sperm displacement, (3) sperm ejection, and (4) sperm selection for fertilizations. Yet, underlying the qualitative similarities were significant quantitative differences in nearly every relevant character and process. We evaluate these species differences in light of concurrent investigations of within-population variation in competitive fertilization success and postmating/prezygotic reproductive isolation in hybrid matings between species to forge an understanding of the relationship between microevolutionary processes and macroevolutionary patterns as pertains to postcopulatory sexual selection in this group.
Data from: Resource composition mediates the effects of intraspecific variability in nutrient recycling on ecosystem processes
Despite the growing evidence for individual variation in trophic niche within populations, its potential indirect effects on ecosystem processes remains poorly understood. In particular, few studies have investigated how intraspecific trophic variability can modulate the effects of consumers on ecosystems through potential changes in nutrient excretion rates. Here, we first quantified the level of intraspecific trophic variability in 11 wild populations of the omnivorous fish Lepomis gibbosus. Outputs from stomach content and stable isotope analyses revealed that the degree of trophic specialization and trophic positions were highly variable between and within these wild populations. There was intrapopulation variation in trophic position of more than one trophic level, suggesting that individuals consumed a range of plant and animal resources. We then experimentally manipulated intraspecific trophic variability to assess how it can modulate consumer-mediated nutrient effects on relevant processes of ecosystem functioning. Specifically, three food sources varying in nutrient quality (e.g. plant material, macro-invertebrate and fish meat) were used individually or in combination to simulate seven diet treatment. Results indicated that intraspecific variability in growth and nitrogen excretion rates were more related to the composition of the diet rather than the degree of specialization, and increased with the trophic position of the diet consumed. We subsequently used microcosms and showed that critical ecosystem functions, such as primary production and community respiration, were affected by the variability in excretory products, and this effect was biomass-dependent. These results highlight the importance of considering variation within species to better assess the effects of individuals on ecosystems and, more specifically, the effects of consumer-mediated nutrient recycling because the body size and the trophic ecology of individuals are affected by a large spectrum of natural and human-induced environmental changes.
Data from: Patterns and processes in complex landscapes: testing alternative biogeographic hypotheses through integrated analysis of phylogeography and community ecology in Hawai'i
The Island of Hawai'i is a dynamic assemblage of five volcanoes with wet forest habitat currently existing in four distinct natural regions that vary in area, age, and geographic isolation. In this complex landscape, alternative assumptions of the relative importance of specific habitat characteristics on evolutionary and ecological processes predict strikingly different general patterns of local diversity and regional similarity. In this study we compare alternative a priori hypotheses against observed patterns within two distinct biological systems and scales: community composition of wet forest vascular plant species and mitochondrial and nuclear genes of Drosophila sproati, a wet forest restricted endemic. All observed patterns display strong and similar regional structuring, with the greatest local diversity found in Kohala and the windward side of Mauna Loa, the least in Ka'ū and Kona, and a distinctive pattern of regional similarity that likely reflects the historical development of this habitat on the island. These observations largely corroborate a biogeographic model that integrates multiple lines of evidence, including climatic reconstruction, over those relying on single measures, such as current habitat configuration or substrate age. This method of testing alternative hypotheses across biological systems and scales is an innovative approach for understanding complex landscapes and should prove valuable in diverse biogeographic systems.
Data from: Neutral genetic processes influence MHC evolution in threatened gopher tortoises (Gopherus polyphemus)
Levels of adaptive genetic variation influence how species deal with environmental and ecological change, but these levels are frequently inferred using neutral genetic markers. Major histocompatibility complex (MHC) genes play a key role in the adaptive branch of the immune system and have been used extensively to estimate levels of adaptive genetic variation. Parts of the peptide binding region, sites where MHC molecules directly interact with pathogen and self-proteins, were sequenced from a MHC class I (95/441 tortoises) and class II (245/441 tortoises) gene in threatened and non-threatened populations of gopher tortoises (Gopherus polyphemus), and adaptive genetic variation at MHC genes was compared to neutral genetic variation derived from 10 microsatellite loci (441 tortoises). Genetic diversity at the MHC class II locus and microsatellites was greater in populations in the non-threatened portion of the gopher tortoise's range (MHC class II difference in mean A = 8.11, AR = 0.79, HO = 0.51, and HE = 0.16; microsatellite difference in mean A = 1.05 and AR = 0.47). Only MHC class II sequences showed evidence of positive selection (dN/dS > 1, Z = 1.81, P = 0.04). Historical gene flow as estimated with Migrate-N was greater than recent migration estimated with BayesAss, suggesting that populations were better connected in the past when habitat was less fragmented. MHC genetic differentiation was correlated with microsatellite differentiation (Mantel r = 0.431, P = 0.001) suggesting neutral genetic processes are influencing MHC evolution, and advantageous MHC alleles could be lost due to genetic drift.
Data from: Differential neural processing during motor imagery of daily activities in chronic low back pain patients
Chronic low back pain (chronic LBP) is both debilitating for patients but also a major burden on the health care system. Previous studies reported various maladaptive structural and functional changes among chronic LBP patients on spine- and supraspinal levels including behavioral alterations. However, evidence for cortical reorganization in the sensorimotor system of chronic LBP patients is scarce. Motor Imagery (MI) is suitable for investigating the cortical sensorimotor network as it serves as a proxy for motor execution. Our aim was to investigate differential MI-driven cortical processing in chronic LBP compared to healthy controls (HC) by means of functional magnetic resonance imaging (fMRI). Twenty-nine subjects (15 chronic LBP patients, 14 HC) were included in the current study. MI stimuli consisted of randomly presented video clips showing every-day activities involving different whole-body movements as well as walking on even ground and walking downstairs and upstairs. Guided by the video clips, subjects had to perform MI of these activities, subsequently rating the vividness of their MI performance. Brain activity analysis revealed that chronic LBP patients exhibited significantly reduced activity compared to HC subjects in MI-related brain regions, namely the left supplementary motor area and right superior temporal sulcus. Furthermore, psycho-physiological-interaction analysis yielded significantly enhanced functional connectivity (FC) between various MI-associated brain regions in chronic LBP patients indicating diffuse and non-specific changes in FC. Current results demonstrate initial findings about differences in MI-driven cortical processing in chronic LBP pointing towards reorganization processes in the sensorimotor network.
Controlling Business Object States in Business Process Models to Support Compliance
<p>Business process model</p>
Synchronization processes of new breeders in a bird colony
<p>Data set for the Ms Synchronization processes of new breeders in a bird colony.</p>
The relation between crawling and non-crawling 9-month-old infants' visual prediction abilities in spatial object processing.
<p>The data set Kubicek et al._JECP_DataSet.sav containts the data of the paper from Kubicek, C., Jovanovic, B., & Schwarzer, G. (2017). The relation between crawling and non-crawling 9-month-old infants' visual prediction abilities in spatial object processing. Journal of Experimental Child Psychology, 158, 64–76.</p> <p> </p>
Quasi-periodic Gaussian process rotation period posterior samples for 1132 Kepler objects of interest.
<p>1132 .h5 files containing light curves, hyperparameter priors, period priors and posterior samples for the QP-GP rotation period model in Angus, Morton, Aigrain, Foreman-Mackey & Rajpaul (2017).</p> <p>1132 .png light curve images.</p> <p>To load the samples in python:</p> <p>>>> df = pd.read_hdf("KOI-1.h5", key="samples")</p> <p>>>> ln_period_samples = df.ln_period</p> <p>>>> ln_A_samples = df.ln_A</p> <p>>>> ln_l_samples = df.ln_l</p> <p>>>> ln_G_samples = df.ln_G</p> <p>>>> ln_sigma_samples = df.ln_sigma</p> <p> </p>
Pre-processed B-cell receptor amplicon sequencing data from SRR1842411
<p>An example dataset containing B-cell receptor (BCR) gene sequences. This dataset is intended to be used for testing software tools developed to annotate (i.e. map Variable, Diversity and Joining segments) and perform clonal analysis of BCR sequencing data.</p> <p><strong>Sequencing:</strong></p> <p>Libraries prepared using 5'RACE from PBMCs of a healthy donor. Input molecules were tagged with unique molecular identifiers (UMIs). Sequencing was ran on MiSeq , 300+300bp reads.</p> <p><strong>Contents:</strong></p> <p>The dataset contains both raw sequencing reads and high-quality consensus sequences assembled using unique molecular tagging (UMI) approach. Consensus assembly corrects for sequencing errors and eliminates sequencing artifacts.</p> <ul> <li>age_ig_s7_R1.fastq.gz and age_ig_s7_R2.fastq.gz contain raw reads</li> <li>age_ig_s7_R1.t10.cf.fastq.gz and age_ig_s7_R2.t10.cf.fastq.gz contain consensus sequences</li> </ul> <p>All files contain an UMI tag sequence in their header, in form UMI:NNNN:QQQQ where N is the base character and Q is the quality character (for assembled consensuses the total number of reads is given instead of Q string).</p> <p>Note that consensus sequences were assembled using only raw sequences that correspond to UMI tags supported by at least 10 sequencing reads. That means that consensus sequence files contain a subset of all UMI tags found in raw sequences. Thus, if one wants to assess software performance on raw sequencing reads using assembled consensus sequences as a high-quality data standard, raw sequencing reads should be filtered to contain only those UMI tags that are present in consensus sequence file.</p> <p><strong>Citations:</strong></p> <p>The whole dataset was used to benchmark MiXCR software and was originally referenced in Bolotin DA, et al. MiXCR: software for comprehensive adaptive immunity profiling Nature methods 12(5):380-381, 2015.</p> <p>Data pre-processing was carried out using MIGEC software, Shugay M et al. Towards error-free profiling of immune repertoires. Nature Methods 11(6):653-655, 2014.</p> <p><strong>Contributors:</strong></p> <p>The dataset was generated in Prof. Chudakov lab (Adaptive Immunity Group in Masaryk University, Brno and Genomics of Adaptive Immunity Lab in Institute of Bioorganic Chemistry, Moscow). Sample preparation and sequencing was performed by Dr. Olga Britanova and Dr. Maria Turchaninova. Raw sequencing reads were pre-processed and uploaded by Dr. Mikhail Shugay.</p>
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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.