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3,937 results for “number”
Species interactions and diversity: a unified framework using Hill numbers
<p>Biodiversity describes the variety of organisms on planet earth. Ecologists have long hoped for a synthesis between analyses of biodiversity and analyses of biotic interactions among species, such as predation, competition, and mutualism. However, it is often unclear how to connect details of these interactions with complex modern analyses of biodiversity. To resolve this gap, we propose a unification of models of biotic interactions and measurements of diversity. We show that analyses of biodiversity obscure details about biotic interactions. For example, identical changes in biodiversity can arise from predation, competition or mutualism. Our approach indicates that traditional models of community assembly miss key facets of diversity change. Instead, we suggest that analyses of diversity change should focus on partitions, which measure mechanisms that directly shape changes in diversity, notably species level selection and immigration, rather than traditional analyses of biotic interactions.</p>
The Role of Spatial Information in an Approximate Cross-Modal Number Matching Task
<p>Data for article:</p> <p>The Role of Spatial Information in an Approximate Cross-Modal Number Matching Task</p>
Genbank and BOLD accession numbers of sequences from "New insights into the diversity of cryptobenthic Cirripectes blennies in the Mascarene Archipelago sampled using Autonomous Reef Monitoring Structures (ARMS)"
<p><strong>Abstract:</strong></p> <p>Autonomous Reef Monitoring Structures (ARMS) are artificial mini-reefs designed for standardised sampling of sessile and small motile cryptobenthic organisms. ARMS are also effective for collecting small cryptobenthic fishes, such as the combtooth blennies of the genus <em>Cirripectes</em>. Recent studies discovered several <em>Cirripectes</em> species endemic to islands or archipelagos, in spite of the generally broad distributions of tropical and subtropical blennies. Thus, in order to evaluate the diversity and distribution of <em>Cirripectes</em> species in the Mascarene Archipelago, a little studied region but an important biodiversity hotspot, complete mitochondrial genomes and nuclear rhodopsin genes were sequenced for 39 specimens collected with ARMS deployed on outer reef slopes at Reunion and Rodrigues islands. Mitochondrial COI sequences were analysed to integrate these specimens within the largest dataset of publicly available sequences. Three species were found in the Mascarene Archipelago, <em>Cirripectes castaneus, C. randalli, </em>and <em>C. stigmaticus</em>. <em>C. castaneus</em> and <em>C. stigmaticus</em> both have an Indo-Pacific distribution with several haplotypes shared among distant localities. In agreement with the literature, <em>C. randalli </em>shows a small-range endemism restricted to the Mascarenes. We confirmed the presence of <em>C. castaneus, C. randalli </em>and <em>C. stigmaticus </em>in Rodrigues, and the presence of <em>C. stigmaticus</em> in Reunion. This study contributes to fill the gaps in taxonomic and molecular knowledge of the reef cryptobiome in the South-West Indian Ocean, and provides the first complete mitogenomes for the genus, a crucial step for future molecular-based inventories (e.g. eDNA).</p> <p><strong>Content of this repository:</strong></p> <p>Genbank and BOLD accession numbers of sequences from "New insights into the diversity of cryptobenthic <em>Cirripectes</em> blennies in the Mascarene Archipelago sampled using Autonomous Reef Monitoring Structures (ARMS)" published in<em> Ecology and Evolution</em> (2023)</p>
Data for: Neural basis of social influence of observing other's perception in dot-number estimation
<p>This functional magnetic resonance imaging study reports the neural basis of the social influence of observing others' perceptions in dot-number estimation. We found that the medial prefrontal cortex (MPFC) was associated with the detection of the self-other discrepancy. The posterior part of MPFC was especially functionally connected with the right superior parietal lobule (SPL), which is sensitive to numerical perception. The SPL activation was modulated after observing others' perceptions in the dot-number estimation task. Furthermore, the multivariate pattern analysis showed that the spatial activity patterns altered after the observation. These suggest that the MPFC detects the self-other discrepancy of numerical perception and communicates with the number-sensitive SPL, and triggers the modulation of the activation in the SPL.</p>
Data from: Effective population size in a partially clonal plant is not predicted by the number of genetic individuals
<p>Estimating effective population size (<em>N</em><sub>e</sub>) is important for theoretical and practical applications in evolutionary biology and conservation. Nevertheless, estimates of <em>N</em><sub>e</sub> in organisms with complex life-history traits remain scarce because of the challenges associated with estimation methods. Partially clonal plants capable of both vegetative (clonal) growth and sexual reproduction are a common group of organisms for which the discrepancy between the apparent number of individuals (ramets) and the number of genetic individuals (genets) can be striking, and it is unclear how this discrepancy relates to <em>N</em><sub>e</sub>.</p> <p>In this study, we analysed two populations of the orchid <em>Cypripedium calceolus</em> to understand how the rate of clonal vs. sexual reproduction affected <em>N</em><sub>e</sub>. We genotyped >1,000 ramets at microsatellite and SNP loci, and estimated contemporary <em>N</em><sub>e</sub> with the linkage disequilibrium method, starting from the theoretical expectation that variance in reproductive success among individuals caused by clonal reproduction and by constraints on sexual reproduction would lower <em>N</em><sub>e</sub>. We considered factors potentially affecting our estimates, including different marker types and sampling strategies, and the influence of pseudoreplication in genomic datasets on <em>N</em><sub>e</sub> confidence intervals. The magnitude of <em>N</em><sub>e</sub>/<em>N</em><sub>ramets </sub>and <em>N</em><sub>e</sub>/<em>N</em><sub>genets</sub> ratios we provide may be used as reference points for other species with similar life-history traits. Our findings demonstrate that <em>N</em><sub>e</sub> in partially clonal plants cannot be predicted based on the number of genets generated by sexual reproduction, because demographic changes over time can strongly influence <em>N</em><sub>e</sub>. This is especially relevant in species of conservation concern, in which population declines may not be detected by only ascertaining the number of genets.</p>
Supporting Information: Measuring Functional Redundancy Using Generalized Hill Numbers
<p>A number of metrics for quantifying the amount of functional redundancy in a community have been proposed over the years. Two of the most popular metrics are based on comparing a taxonomic diversity measure with a generalized form of the same measure that accounts for functional dissimilarities between taxa. These two metrics express redundancy as either an absolute or relative difference between the taxonomic diversity measure and its generalized form. Because they express the amount of redundancy in a community in terms of raw diversity values, both redundancy metrics are susceptible to the same issues that complicate the interpretation of most commonly used diversity indices.</p> <p>It is possible to overcome these issues by restating these two indices using a Hill numbers framework. As a growing number of authors have noted, these modified metrics provide a more intuitive quantitative definition of functional redundancy when used to rank communities. Beyond this intuitive definition, measuring redundancy in terms of Hill numbers allows researchers to control the influence of rare taxa on the output value, enabling ecologists to better predict how a community is expected to respond when exposed to an external perturbation that selectively eliminates rare or common taxa.</p> <p>Here I show that, of the two possible Hill number-based redundancy metrics, the form based on a popular absolute redundancy metric is extremely sensitive to differences in taxonomic diversity and can provide a misleading picture of how much redundancy is present in a community. For this reason, I argue that Hill number-based functional redundancy should be quantified using a relative metric that explicitly accounts for differences in effective taxonomic diversity. The proposed Hill number-based relative redundancy measure is shown to provide a much more complete picture of the distribution of redundant taxa within a community, highlighting subtle patterns that are completely missed by the Hill number-based absolute redundancy metric.</p>
Simulation dataset of "Wave activities throughout a low-Mach number quasi-parallel shock: 2-D hybrid simulations"
<p>Simulation dataset of "Wave activities throughout a low-Mach number quasi-parallel shock: 2-D hybrid simulations", including magnetic fields, number density and average velocities of particles.</p>
Correlation of viral loads in disease transmission could affect early estimates of the reproduction number
<p>This dataset accompanies the an article titled, 'Correlation of viral loads in disease transmission could affect early estimates of the reproduction number', by T. Harris et al. which can be found at https://arxiv.org/abs/2211.08673.</p> <p>Abstract:</p> <p>Early estimates of the transmission properties of a newly emerged pathogen are critical to an effective public health response, and are often based on limited outbreak data. Here, we use simulations to investigate how correlations between the viral load of cases in transmission chains can affect estimates of these fundamental transmission properties. Our computational model simulates a disease transmission mechanism in which the viral load of the infector at the time of transmission influences the infectiousness of the infectee. These correlations in transmission pairs produce a population-level convergence process during which the distributions of initial viral loads in each subsequent generation converge to a steady state. We find that outbreaks arising from index cases with low initial viral loads give rise to early estimates of transmission properties that could be misleading. These findings demonstrate the potential for transmission mechanisms to affect estimates of the transmission properties of newly emerged viruses in ways that could be operationally significant to a public health response.</p> <p> </p> <p>Contents of this dataset include: </p> <ul> <li>Model code - including experiments (python3)</li> <li>Estimation code (R)</li> <li>Code used for figure production (python3 & R)</li> <li>Raw data produced from Experiments 1-3 and presented in the text (.csv & .Rdata)</li> </ul> <p>See 'README.md' in main upload folder for more information</p>
A streamlined approach for fluorescence labelling of low copy-number plasmids for determination of conjugation frequency by flow cytometry
<p><span>Bacterial conjugation plays a major role in the dissemination of antibiotic resistance and virulence traits through horizontal transfer of plasmids. </span>Robust <span>measurement</span> of<span> the conjugation frequency of plasmids between bacterial strains and species </span>is therefore important <span>to understand the transfer dynamics </span>and epidemiology <span>of conjugative plasmids. In this study, we present a streamlined experimental approach for fluorescence labelling of low copy-number conjugative plasmids that allows plasmid transfer frequency during filter mating to be measured by flow cytometry. A blue fluorescence gene is inserted into a conjugative plasmid of interest using a simple homologous recombineering procedure. </span><span>A small non-conjugative plasmid, which carries a red fluorescence gene with a toxin-antitoxin system that functions as a plasmid stability module, is used to label the recipient bacterial strain. This offers the dual advantage of circumventing chromosomal modifications of recipient strains and ensuring that the red fluorescence gene-bearing plasmid can be stably maintained in recipient cells in an antibiotic-free environment during conjugation. A strong constitutive promoter allows the two fluorescence genes to be strongly and constitutively expressed from the plasmids, thus allowing flow cytometers to clearly distinguish between donor, recipient and transconjugant populations in a conjugation mix for monitoring conjugation frequencies more precisely over time. </span></p>
The number of glyphosate resistant seeds produced by each of three bee species as they visit alfalfa flowers in sequence during a foraging bout
<p>Since the release of genetically engineered (GE) crops, there has been increased concern about the introduction of GE genes into non-GE fields of a crop and their spread to feral or wild cross-compatible relatives. More recently, attention has been given to the differential impact of distinct pollinators on gene flow, with the goal of developing isolation distances associated with specific managed pollinators. To examine the differential impact of bee species on gene movement, we <span>quantified the relationship between the probability of getting a GE seed in a pod, and the order in which a flower was visited, or the cumulative distance traveled by a bee in a foraging bout. We refer to these relationships as 'seed curves' and compare these seeds curves among three bee species. </span>The experiments used <em><span>Medicago sativa</span></em><span> L. plants carrying three copies of the glyphosate resistance (GR) allele as pollen donors (<em>M. sativa</em> is a tetraploid), such that each pollen grain carried the GR allele, and conventional plants as pollen recipients. </span><span>Different foraging metrics, including the number of GR seeds produced over a foraging bout, were also quantified and contrasted among bee species. The lowest number of GR seeds set per foraging bout, and the GR seeds set at the shortest distances, were produced following leafcutting bee visits. In contrast, GR seeds were found at the longest distances following bumble bee visits. Values for honey bees were intermediate. The ranking of bee species based on seed curves correlated well with field-based gene flow estimates. Thus, differential seed curves of bee species, which describe patterns of seed production within foraging bouts, translated into distinct abilities of bee species to move genes at a landscape level. Bee behavior at a local scale (foraging bout) helps predict gene flow and </span><span>the spread of GE genes at the landscape scale. </span></p>
Nemo2 (Numbers, fEatures, MOdels, version 2) Testing Files
<p>The publications and research associated with this software is currently under review in the "<em>Journal</em> of <em>Systems</em> and <em>Software</em>".</p> <p>You can find the official Github repository of this dataset in: <a href="https://github.com/danieljmg/Nemo2_models">https://github.com/danieljmg/Nemo2_models</a></p>
FIG. 12 in Analysis of lichen secondary chemistry doubled the number of Cetrelia W.L. Culb. & C.F. Culb. species (Parmeliaceae, lichenised Ascomycota) in Hungary
FIG. 12. — Altitudinal distribution of Cetrelia W.L.Culb.& C.F.Culb.species in Hungary.
FIG. 9 in Analysis of lichen secondary chemistry doubled the number of Cetrelia W.L. Culb. & C.F. Culb. species (Parmeliaceae, lichenised Ascomycota) in Hungary
FIG. 9. — Distribution of Cetrelia monachorum (Zahlbr.) W.L. Culb. & C.F. Culb. in Hungary.
FIG. 8 in Analysis of lichen secondary chemistry doubled the number of Cetrelia W.L. Culb. & C.F. Culb. species (Parmeliaceae, lichenised Ascomycota) in Hungary
FIG. 8. — Distribution of Cetrelia chicitae (W.L.Culb.) W.L. Culb.& C.F. Culb.in Hungary.
Identifying Chern numbers of superconductors from local measurements
<p>This repository contains the following:</p> <p>1. Data for Fig.1b</p> <ul> <li>phase_diagram_gap_and_kf_in_0.1_12_e0_in_-0.8_0.8.txt</li> </ul> <p>2. Data for Fig.6a</p> <ul> <li>Chern_marker_scaling_vs_N_x_abs_C.1_kf_3.67900_e0_0.35400_gap0_0.30374_bandwidth_1.70100.txt</li> <li>Chern_marker_scaling_vs_N_x_abs_C.2_kf_2.87600_e0_0.28800_gap0_0.13449_bandwidth_1.56362.txt</li> <li>Chern_marker_scaling_vs_N_x_abs_C.3_kf_3.48700_e0_0.16200_gap0_0.15893_bandwidth_1.34522.txt</li> </ul> <p>3. Data for Fig.6b</p> <ul> <li>Chern_marker_scaling_vs_V_0_abs_C.1_gap_balanced_aver.0.2192_kf_3.67900_e0_0.35400_gap0_0.30374_bandwidth_1.70100.txt</li> <li>Chern_marker_scaling_vs_V_0_abs_C.2_gap_balanced_aver.0.2192_kf_2.87600_e0_0.28800_gap0_0.13449_bandwidth_1.56362.txt</li> <li>Chern_marker_scaling_vs_V_0_abs_C.3_gap_balanced_aver.0.2192_kf_3.48700_e0_0.16200_gap0_0.15893_bandwidth_1.34522.txt</li> </ul> <p>4. Shiba model test dataset</p> <ul> <li>Shiba_lattice_dataset.json</li> </ul>
Total estimated number of informal waste pickers or recyclers in Kathmandu Valley, as of December 2022
<p>Using key informants representing different parts of the informal waste management value chain, the RIPL project has produced an updated estimated total number of informal recyclers for Kathmandu Valley, in December 2022. The overview includes methods of calculation and names of key informants. </p>
Mbit/s-range alkali vapour spin noise quantum random number generators - DATASETS
<p>Two example datasets. Each dataset consists of 2 files; one, where spin noise is present in the spectrum (noise_on.npy) and one, where spin noise is absent (noise_off.npy). The former is used generate random numbers, while the latter is used to 1. find a baseline threshold \Sigma, as described in the paper, and 2. to find the spin noise spectrum. </p> <p>The spin noise spectrum can be found by subtracting the spectra of the first and second file, as it is only present in the first file. Every dataset should be filtered around the Larmor frequency prior to any bit generation. The width of the band-pass filter should be such that the entirety of the spin noise spectrum is contained.</p> <p>Bit generation is to be done by protocols described in the paper "Mbit/s-range alkali vapour spin noise quantum random number generators". All bitrates are calculated at \Sigma = 5 \sigma, where \sigma is the standard deviation of noise_off.npy for the given experiment.</p> <p>Cs12: Sample rate 50 MHz. Measured at a temperature of approximately 140 degrees C. The Larmor frequency is approximately 670 kHz. There is a large induced gradient present in the system, so the spin noise spectrum is not a Lorentzian shape, but is spread with a full-width half max of 500 kHz . Protocol 1 raw bitrates are approximately 40 kb/s, whereas protocol 2 raw bitrates are approximately 2.40 Mb/s.</p> <p>Cs14: Sample rate 100 MHz. Spin noise measurement (noise_on.npy) has 1G samples (16 bit signed). Background measurement (noise_off.npy) has 10M samples (16 bit signed). Measured at a temperature of approximately 140 degrees C. The Larmor frequency is approximately 440kHz ,T2 is approximately 2e-6 s. This is the dataset presented in the paper. Protocol 1 raw bitrates are approximately 40 kb/s, protocol 2 raw bitrates are approximately 1.97 Mb/s.</p>
Evaluation Data for the Annotation of German and English New Testament Texts with Strong's Numbers
<p>This repository provides a gold standard for parallel Bible texts and offers annotation of 20 New Testament verses with Strong's numbers referring to Greek words.<br> <br> We considered three German texts (Luther 2017, Schlachter, and Hoffnung für alle) and two English texts (New Revised Standard Version and World English Bible),</p> <p>See <a href="https://github.com/jd-s/gold-standard-parallel-bible">https://github.com/jd-s/gold-standard-parallel-bible</a> for more information.</p>
Data from: Heteroaggregation of virions with microplastics reduces the number of active bacteriophages in aqueous environments
<p>The objective of this study is to explore the effects of microplastics on the viability of the bacteriophages in an aqueous environment. Bacteriophages (phages), i.e., viruses of bacteria, are essential in homeostasis. It is estimated that phages cause up to 40% of the death of all bacteria daily. Any factor affecting phage activity is vital for the whole food chain and the ecology of numerous niches. We hypothesize that the number of active phages decreases due to the virions' adsorption on microplastic particles or by the released leachables from additives used in the production of plastic, e.g., stabilizers, plasticizers, colorants, and reinforcements. We exposed three diverse phages, namely T4 (tailed), MS2 (icosahedral), and M13 (filamentous), to 1 mg/mL suspension of twelve industrial-grade plastics [acrylonitrile butadiene styrene (ABS), high-impact polystyrene (HIPS), poly-ε-caproamide (PA6), polycarbonate (PC), polyethylene (PE), polyethylene terephthalate (PET), poly(methyl methacrylate) (PMMA), polypropylene (PP), polystyrene (PS), polytetrafluoroethylene (PTFE), polyurethane (PUR), polyvinyl chloride (PVC)] shredded to obtain microparticles of radius ranging from 2 to 50 µm. The effect of leachables was measured upon exposure of phages not to particles themselves but to the buffer pre-incubated with microplastics. A double-overlay plaque counting method was used to assess phage titers. We employed a classical linear regression model to verify which physicochemical parameters (65 variables were tested) govern the decrease of phage titers. The key finding is that adsorption mechanisms result in up to complete scavenging of virions, whereas leachables deactivate up to 50% of phages. This study reveals microplastic pollution's plausible and unforeseen ecotoxicological effect causing phage deactivation. Also, phage transmission through adsorption can alter the balance of the food chain in the new environment. The effect depends mainly on the zeta potentials of the polymers and the phage type.</p>
Data from: Keep numbers in view: Red-eared sliders (Trachemys scripta elegans) learn to discriminate relative quantities
<p><span>The ability to discriminate relative quantities, one of the numerical competences, is considered as an adaptive trait in uncertain environments. Besides humans, previous studies have reported this capacity in several non-human primates and birds.</span><span> Here, we test whether red-eared sliders (<em>Trachemys scripta elegans</em>) can </span><span>discriminate different relative quantities</span><span>. Subjects were first trained to distinguish different stimuli with food reward. Then, they were tested with novel stimuli pairs to demonstrate how they distinguished the stimuli. The r</span><span>esults show that most subjects can complete the initial training and use relative quantity rather than absolute quantity to make choices during testing phase. This study provides behavioural evidence of relative quantity</span> <span>discrimination in a reptile species, and suggests that such capacity may be widespread among vertebrates.</span></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.