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1,294 results for “reactions”
Proton-transfer-reaction time-of-flight mass spectrometry (PTR-TOF-MS) as a tool for studying animal volatile organic compound (VOC) emissions
<p>1. Chemical sensing in vertebrates is crucial in their lives, and efforts are undertaken towards deciphering their chemical language. Volatile organic compounds (VOCs) is a group of chemicals believed to play an essential role in a wide variety of animal interactions. Therefore, understanding what animals sense themselves and untangling the ecological role of their volatile cues can be accomplished by analysing VOC emissions. A Proton-Transfer Reaction Time-of-Flight Mass Spectrometer (PTR-TOF-MS) is an instrument that measures VOCs in real-time in an air sample. Since this technique acts as a hyper-sensitive 'nose' it has a similar potential in deciphering the chemical language of vertebrates.</p> <p>2. Here, we validate the use of PTR-TOF-MS as a tool to measure VOCs from vertebrates, which in turn will help resolve vertebrate interactions through VOCs. The instrument monitors and records the full spectrum of VOCs emitted by an individual with a high accuracy and low detection limit, including transient VOC emissions. We propose and test diverse measuring configurations that allow for measurement of VOC emissions from different vertebrates and their exudates: full body, specific parts of the body, urine and femoral pores. In addition, we test configurations for sudden and short-lasting processes as VOCs emitted during adder skin shedding as well as the emissions of skin secretions upon mechanical and physiological stimulation in amphibia. Our configurations work in tandem with Gas Chromatography Mass Spectrometry (GC-MS) to allow compound structure verification.</p> <p>3. We discuss the configurations and methodologies used and conclude with recommendations for further studies, such as the choice of chamber size and flow. We also report the results of the measurements on vertebrates —that are novel to science— and discuss their ecological meaning.</p> <p>4. We argue that PTR-TOF-MS has a high potential to resolve important unanswered questions in vertebrate chemical ecology with great adaptability to a wide range of experimental setups. If combined with a structure verification tool, such as GC-MS, the creative deployment of PTR-TOF-MS in various future study designs will lead to the identification of ecologically relevant VOCs.</p>
Molecular configuration data for the reactions between radicals of formamide and vinyl cyanide
<p>The files in the folder /datafile in SuppMater.zip contain optimized atomistic configurations of the reactant (RC), the intermediate (IM), the transition state (TS) and the product (PD) of the reactions between partially dehydrogenated radicals of formamide (H2NCHO) and vinyl cyanide (H2CCHCN) for producing 1H-pyrimidin-2-one (C4H4N2O). The data are obtained by using density functional theory calculations with the M06 functional with 6-31+G(d,p)/6-311++G(d,p) basis sets as implemented in Gaussian 16 B.01. The name of these file consists of two parts separated by "_" including the ID of the reaction (defined in the manuscript), and the molecular state name. For instance, "C4-TS2.data" stands for the 2nd transition state in the reaction C4. Each file may contain one or two molecules/radicals.</p> <p>The total number of the atoms in the first molecule will be read on the first line; the corresponding Gibbs free energy (G, in a.u., with thermal free energy correction at 100 K) on the second, and the atomic type and three atomic Cartesian coordinates on the following lines. The second molecule will be read after the first one in the same format, except for that G is already given with the first molecule for the entire state (of multiple molecules). The filenames started by "Cytosine", "Uracil" and "Thymine" correspond to the reactions between C4H4N2O and amino, methyl or hydroxyl to produce cytosine, thymine or uracil, respectively.</p> <p>The file "RateCoefficient.pdf" contains the rate coefficients as a function of the temperature for the most favourable pathways for the reactions between dehydrogenated formamide and vinyl cyanide.</p>
Data from: Genetic correlations and little genetic variance for reaction norms may limit potential for adaptation to pollution by ionic and nanoparticulate silver in a whitefish (Salmonidae)
For natural populations to adapt to anthropogenic threats, heritable variation must persist in tolerance traits. Silver nanoparticles, the most widely used engineered nanoparticles, are expected to increase in concentrations in freshwaters. Little is known about how these particles affect wild populations, and whether genetic variation persists in tolerance to permit rapid evolutionary responses. We sampled wild adult whitefish and crossed them in vitro full factorially. In total, 2896 singly raised embryos of 48 families were exposed to two concentrations (0.5 μg/L; 100 μg/L) of differently sized silver nanoparticles or ions (silver nitrate). These doses were not lethal; yet higher concentrations prompted embryos to hatch earlier and at a smaller size. The induced hatching did not vary with nanoparticle size and was stronger in the silver nitrate group. Additive genetic variation for hatching time was significant across all treatments, with no apparent environmental dependencies. No genetic variation was found for hatching plasticity. We found some treatment-dependent heritable variation for larval length and yolk volume, and one instance of additive genetic variation for the reaction norm on length at hatching. Our assessment suggests that the effects of silver exposure on additive genetic variation vary according to trait and silver source. While the long-term fitness consequences of low-level silver exposure on whitefish embryos must be further investigated to determine whether it is, in fact, detrimental, our results suggest that the evolutionary potential for adaptation to these types of pollutants may be low.
Data from: Quantitative genetic divergence and standing genetic (co)variance in thermal reaction norms along latitude
Although the potential to adapt to warmer climate is constrained by genetic trade-offs, our understanding of how selection and mutation shape genetic (co)variances in thermal reaction norms is poor. Using 71 isofemale lines of the fly Sepsis punctum, originating from northern, central and southern European climates, we tested for divergence in juvenile development rate across latitude at five experimental temperatures. To investigate effects of evolutionary history in different climates on standing genetic variation in reaction norms, we further compared genetic (co)variances between regions. Flies were reared on either high or low food resources to explore the role of energy-acquisition in determining genetic trade-offs between different temperatures. Although the latter had only weak effects on the strength and sign of genetic correlations, genetic architecture differed significantly between climatic regions, implying that evolution of reaction norms proceeds via different trajectories at high versus low latitude in this system. Accordingly, regional genetic architecture was correlated to region-specific differentiation. Moreover, hot development temperatures were associated with low genetic variance and stronger genetic correlations compared to cooler temperatures. We discuss the evolutionary potential of thermal reaction norms in light of their underlying genetic architectures, evolutionary histories and the materialization of trade-offs in natural environments.
Data from: Individual variation in parental care reaction norms: integration of personality and plasticity
Personality (consistent differences between individuals in behavior) and plasticity (changes within individuals in behavior) are often viewed as separate and opposing phenomena. We tested this idea by analyzing parental care reaction norms in a bird that exhibits biparental care. Personality in provisioning behavior existed (r ic=0.11) and persisted despite being reduced after accounting for individual differences in environment. Plasticity was also evident and differed between the sexes. Male visit rate was associated with changes in brood size and time of day, but female visit rate was associated with changes in nestling age and date. In both sexes changes in visit rate were positively correlated with changes in their partner's visit rate. Both sexes also exhibited multidimensional reaction norms; interaction terms revealed that within-individual visit rates increased more steeply with brood size when nestlings were older, and the effect of the partner's visit rate was sensitive to variation in date, precipitation, and the focal bird's age. Individuals also varied in how they responded (reaction norm slope) to changes in nestling age and partner visits. Moreover, parental personality was interdependent with individual plasticity in several ways. Individuals of both sexes with a high visit rate also responded more positively to changes in nestling age, and males also showed this pattern with changes in partner visit rate. Explicit use of the behavioral reaction norm integrated personality and plasticity, revealed that these are not opposing concepts, and stimulated new hypotheses about sexual conflict over care and provisioning as a life-history trait.
Data from: Posttraumatic stress reactions in parents of children esophageal atresia.
Objective – The aim of this study was to investigate psychological stress in parents of children with esophageal atresia and to explore factors associated with the development of Posttraumatic Stress disorder (PTSD). Design - Self-report questionnaires were administered to parents of children with EA. Domains included: (1) sociodemographic data, current personal difficulties, assessment scales for the quality of life and for the global health status of the child (2) French-validated versions of the Perinatal Posttraumatic Stress disorder Questionnaire and of the State-Trait Anxiety Inventory. Associations between PTSD and severity of the neonatal course, presence of severe sequelae at 2 years of age, and quality of life and global health status of children according to their parents' perception were studied. Setting – a Tertiary care University Hospital Results - Among 64 eligible families, 54 parents of 38 children (59%) participated to the study. PTSD was present in 32 (59%) parents; mothers were more frequently affected than fathers (69 vs 46%, p=0.03). Four mothers (8%) had severe anxiety. PTSD was neither associated with neonatal severity nor with severe sequelae at 2 years. Parents with PTSD rated their child's quality of life and global health status significantly lower (7.5 vs 8.6; p=0.01 and 7.4 vs 8.3; p=0.02 respectively). Conclusions - PTSD is frequent in parents of children with esophageal atresia, independently of neonatal severity and presence of severe sequelae at 2 years of age. Our results highlight the need for a long-term psychological support of families.
Data from: Long-term sound and movement recording tags to study natural behaviour and reaction to ship noise of seals
The impact of anthropogenic noise on marine fauna is of increasing conservation concern with vessel noise being one of the major contributors. Animals that rely on shallow coastal habitats may be especially vulnerable to this form of pollution. Very limited information is available on how much noise from ship traffic individual animals experience, and how they may react to it due to a lack of suitable methods. To address this, we developed long‐duration audio and 3D‐movement tags (DTAGs) and deployed them on three harbor seals and two gray seals in the North Sea during 2015–2016. These tags recorded sound, accelerometry, magnetometry, and pressure continuously for up to 21 days. GPS positions were also sampled for one seal continuously throughout the recording period. A separate tag, combining a camera and an accelerometer logger, was deployed on two harbor seals to visualize specific behaviors that helped interpret accelerometer signals in the DTAG data. Combining data from depth, accelerometer, and audio sensors, we found that animals spent 6.6%–42.3% of the time hauled out (either on land or partly submerged), and 5.3%–12.4% of their at‐sea time resting at the sea bottom, while the remaining time was used for traveling, resting at surface, and foraging. Animals were exposed to audible vessel noise 2.2%–20.5% of their time when in water, and we demonstrate that interruption of functional behaviors (e.g., resting) in some cases coincides with high‐level vessel noise. Two‐thirds of the ship noise events were traceable by the AIS vessel tracking system, while one‐third comprised vessels without AIS. This preliminary study demonstrates how concomitant long‐term continuous broadband on‐animal sound and movement recordings may be an important tool in future quantification of disturbance effects of anthropogenic activities at sea and assessment of long‐term population impacts on pinnipeds.
Data from: Latitudinal variation in thermal reaction norms of post-winter pupal development in two butterflies differing in phenological specialization
Latitudinal clines in thermal reaction norms of development are a common phenomenon in temperate insects. Populations from higher latitudes often develop faster throughout the range of relevant temperatures (i.e countergradient variation) because they must be able to complete their life cycle within a shorter seasonal time window compared to populations at lower latitudes. In the present study, we experimentally demonstrate that two species of butterflies Anthocharis cardamines (L.) and Pieris napi (L.) instead show a cogradient variation in thermal reaction norms of post-winter pupal development so that lower latitude populations develop faster than higher latitude populations. The two species share host plants but differ in the degree of phenological specialization, as well as in the patterns of voltinism. We suggest that the pattern in A. cardamines, a univoltine phenological specialist feeding exclusively on flowers and seedpods, is the result of selection for matching to the phenological pattern of its local host plants. The other species, P. napi, is a phenological generalist feeding on the leaves of the hosts and it shows a latitudinal cline in voltinism. Because the latitudinal pattern in P. napi was an effect of slow development in a fraction of the pupae from the most northern population, we hypothesize that this population may include both bivoltine and univoltine genotypes. Consequently, although the two species both showed cogradient patterns in thermal reaction norms, it appears likely that this was for different reasons.
Data from: Shared decision-making as a cost-containment strategy: US physician reactions from a cross-sectional survey
Objective: To assess US physicians' attitudes towards using shared decision-making (SDM) to achieve cost containment. Design: Cross-sectional mailed survey. Setting: US medical practice. Participants: 3897 physicians were randomly selected from the AMA Physician Masterfile. Of these, 2556 completed the survey. Main outcome measures: Level of enthusiasm for "Promoting better conversations with patients as a means of lowering healthcare costs"; degree of agreement with "Decision support tools that show costs would be helpful in my practice" and agreement with "should promoting SDM be legislated to control overall healthcare costs". Results: Of 2556 respondents (response rate (RR) 65%), two-thirds (67%) were 'very enthusiastic' about promoting SDM as a means of reducing healthcare costs. Most (70%) agreed decision support tools that show costs would be helpful in their practice, but only 24% agreed with legislating SDM to control costs. Compared with physicians with billing-only compensation, respondents with salary compensation were more likely to strongly agree that decision support tools showing costs would be helpful (OR 1.4; 95% CI 1.1 to 1.7). Primary care physicians (vs surgeons, OR 1.4; 95% CI 1.0 to 1.6) expressed more enthusiasm for SDM being legislated as a means to address healthcare costs. Conclusions: Most US physicians express enthusiasm about using SDM to help contain costs. They believe decision support tools that show costs would be useful. Few agree that SDM should be legislated as a means to control healthcare costs.
Data from: Intraspecific variability and reaction norms of forest understory plant species traits
1.Trait-based models of ecological communities typically assume intraspecific variation in functional traits is not important, though such variation can change species trait rankings along gradients in resources and environmental conditions, and thus influence community structure and function. 2. We examined the degree of intraspecific relative to interspecific variation, and reaction norms of 11 functional traits for 57 forest understory plant species, including: intrinsic water-use efficiency (iWUE), Δ15N, 5 leaf traits, 2 stem traits and 2 root traits along gradients in light, nitrogen, moisture and understory cover. 3. Our results indicate that interspecific trait variation exceeded intraspecific variation by at least 50% for most, but not all traits. Intraspecific variation in Δ15N, iWUE, leaf nitrogen content and root traits was high (47-70%) compared with most leaf traits and stem traits (13-38%). 4. Δ15N varied primarily along gradients in abiotic conditions, while light and understory cover were relatively less important. iWUE was related primarily to light transmission, reflecting increases in photosynthesis relative to stomatal conductance. Leaf traits varied mainly as a function of light availability, with some reaction norms depending on understory cover. Plant height increased with understory cover, while stem specific density was related primarily to light. Resources, environmental conditions and understory cover did not contribute strongly to the observed variation in root traits. 5. Gradients in resources, environmental conditions and competition all appear to control intraspecific variability in most traits to some extent. However, our results suggest that species cross-over (i.e., trait rank reversals) along the gradients measured here are generally not a concern. 6. Intraspecific variability in understory plant species traits can be considerable. However, trait data collected under a narrow range of environmental conditions appears sufficient to establish species rankings and scale between community and ecosystem levels using trait-based models. Investigators may therefore focus on obtaining a sufficient sample size within a single set of conditions rather than characterizing trait variation across entire gradients in order to optimize sampling efforts.
Data from: Looking into the past – the reaction of three grouse species to climate change over the last million years using whole genome sequences
Tracking past population fluctuations can give insight into current levels of genetic variation present within species. Analysing population dynamics over larger time scales can be aligned to known climatic changes to determine the response of species to varying environments. Here, we applied the Pairwise Sequentially Markovian Coalescent (PSMC) model to infer past population dynamics of three widespread grouse species; black grouse, willow grouse and rock ptarmigan. This allowed the tracking of the effective population size (Ne) of all three species beyond 1 Mya, revealing that i) early Pleistocene cooling (~2.5 Mya) caused an increase in the willow grouse and rock ptarmigan populations, ii) the mid-Brunhes event (~430 kya) and following climatic oscillations decreased the Ne of willow grouse and rock ptarmigan, but increased the Ne of black grouse and iii) all three species reacted differently to the last glacial maximum (LGM) – black grouse increased prior to it, rock ptarmigan experienced a severe bottleneck and willow grouse was maintained at large population size. We postulate that the varying PSMC signal throughout the LGM depicts only the local history of the species. Nevertheless, the large population fluctuations in willow grouse and rock ptarmigan indicate that both species are opportunistic breeders while black grouse tracks the climatic changes more slowly and is maintained at lower Ne. Our results highlight the usefulness of the PSMC approach in investigating species' reaction to climate change in the deep past, but also that caution should be taken in drawing general conclusions about the recent past.
Repeatability and heritability of social reaction norms in a wild agamid lizard
In the evolutionary transition from solitary to group living, it should be adaptive for animals to respond to the environment and choose when to socialise to reduce conflict and maximise access to resources. Due to the associated proximate mechanisms (e.g. neural network, endocrine system), it is likely that this behaviour varies between individuals according to genetic and non-genetic factors. We used long-term behavioural and genetic data from a population of eastern water dragons (Intellagama lesueurii) to explore variation in plasticity of social behaviour, in response to sex ratio and density. To do so, we modelled individual variation in social reaction norms, which describe individuals' mean behaviour and behavioural responses to changes in their environment, and partitioned variance into genetic and non-genetic components. We found that reaction norms were repeatable over multiple years, suggesting that individuals consistently differed in their behavioural responses to changes in the social environment. Despite high repeatability of reaction norm components, trait heritability was below our limit of detection based on power analyses (h2 < 0.12), leading to very little power to detect heritability of plasticity. This was in contrast to a relatively greater amount of variance associated with environmental effects. This could suggest that mechanisms such as social learning and frequency-dependence may shape variance in reaction norms, which will be testable as the dataset grows. --
MD simulation trajectory and related files for DPPC bilayer in full hydration (Poger GROMOS 53A6_L, Gromacs 4.0.7, Reaction Field, traj 1)
<p>Equilibrated DPPC lipid bilayer simulation ran with Gromacs 4.0.7 using Reaction Field for computing electrostatics, Poger GROMOS 53A6_L force field in full hydration (dx.doi.org/10.1002/jcc.21396), 100ns, T=323K, 128 DPPC molecules, 5841 water molecules. This data is ran for the nmrlipids.blospot.fi project. More details from nmrlipids.blospot.fi and https://github.com/NMRLipids/nmrlipids.blogspot.fi. If data is used, please cite nmrlipids.blogspot.fi project and the original publication of the parameters (dx.doi.org/10.1002/jcc.21396).</p>
MD simulation trajectory and related files for DPPC bilayer in full hydration (Poger GROMOS 53A6_L, Gromacs 4.0.7, Reaction Field, traj 2)
<p>Equilibrated DPPC lipid bilayer simulation ran with Gromacs 4.0.7 using Reaction Field for computing electrostatics, Poger GROMOS 53A6_L force field in full hydration (dx.doi.org/10.1002/jcc.21396), 100ns, T=323K, 128 DPPC molecules, 5841 water molecules. This data is ran for the nmrlipids.blospot.fi project. More details from nmrlipids.blospot.fi and https://github.com/NMRLipids/nmrlipids.blogspot.fi. If data is used, please cite nmrlipids.blogspot.fi project and the original publication of the parameters (dx.doi.org/10.1002/jcc.21396).</p> <p> </p>
Data file for paper "The intriguing poison tolerance of non-precious metal oxygen reduction reaction (ORR) catalysts" DOI: 10.1039/C5TA05794A
<p>Data file containing data for figures and supplemental information for the paper</p> <p>The intriguing poison tolerance of non-precious metal oxygen reduction reaction (ORR) catalysts</p> <p>D. Malko, T. Lopes, E. Symianakis and A. R. Kucernak</p> <p>published in Journal of Materials Chemistry A, 2015</p> <p>DOI: 10.1039/C5TA05794A</p>
Data file for the paper "General Models for the Electrochemical Hydrogen Oxidation and Hydrogen Evolution Reactions – Theoretical Derivation and Experimental Results Under Near Mass-Transport Free Conditions", J. Phys Chem. C., 2016, DOI:10.1021/acs.jpcc.6b00011
<p>The data in this folder is supplementary information for the paper:<br /> Anthony Kucernak and Christopher Zalitis, "General Models for the Electrochemical Hydrogen Oxidation and Hydrogen Evolution Reactions – Theoretical Derivation and Experimental Results Under Near Mass-Transport Free Conditions", J. Phys Chem. C., 2016, DOI:10.1021/acs.jpcc.6b00011</p> <p>The information is © Anthony Kucernak</p> <p>A description of the models used in these files is provided in that paper. Below is a description of the files</p> <p>Experimental Data.xlsx - This file contains the experimental data used to produce figures 6 and 7 in the aforementioned paper<br /> Model.xlsx - This file contains verified versions of the Heyrovsky-Volmer, Tafel-Volmer and Heyrovsky-Tafel-Volmer mechanisms developed in the paper mentioned above. These excel spreadsheets may be used to fit experimental data user the Solver function in Excel.</p> <p>Heyrovsky-Tafel.cdf, Heyrovsky-Tafel-Volmer.cdf, Tafel-Volmer.cdf, Heyrovsky-Volmer.cdf - These are "computable document format" files produced using Wolfram Mathematica. They allow easy and quick modification of model parameters to allow real-time exploration of the effect of the parameters on current density (as linear and Tafel plots), hydrogen coverage, Effective Tafel slope, and derived parameters. The CDF viewer is availble to download from the Wolfram site - www.wolfram.com</p>
Snow-Induced Perturbations in Nitrous Acid (HONO) Levels: Insights into Heterogeneous Reactions During Wintertime in Mid-Latitude Regions
<ol> <li>Variations in HONO, PM2.5, NO2, and HONO/NO2 concentrations data</li> <li>Time series data of pollutants</li> </ol>
Exploring the Global Reaction Coordinate for Retinal Photoisomerization: A Graph Theory-Based Machine Learning Approach
<p>This repository contains i. optimized geometry of the cis and trans retinal, ii. figure labelling the internal coordinates of retinal. </p>
Data for Observational Evidence for Criegee Intermediate Oligomerization Reactions Relevant to Aerosol Formation in the Troposphere
Open the record for dataset details and reuse information.
Data of "Grazing intensity and horn status influence activity on pasture, physiological pre-slaughter reactions and meat quality in beef heifers"
<p>Raw data of the article of "Grazing intensity and horn status influence activity on pasture, physiological pre-slaughter reactions and meat quality in beef heifers". Dataset of 64 crossbred beef heifers. Both experimental independent variables (animal id, horn status, grazing intensity, replicate) and dependent variables (related to physical activity on pasture, behaviour tests, stress physiology and meat quality) are presented.</p>
ScienceDex guides
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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.