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667 results for “Null”
Distinguishing mutations and null alleles from genotyping errors using mother progeny comparisons in Brazilian pine (Araucaria angustifolia)
the rate of null alleles, mutations and genotyping errors in microsatellite loci, using Araucaria angustifolia, a threatened species, as a case study. We estimated the rates of the different types of genotyping deviations using mother-progeny genotype comparison from 50 seed-trees and their respective progeny (seeds). A total of 2336 A. angustifolia samples were genotyped, and we found that the rate of null alleles was 0.045. From the 1972 mother-progeny comparisons, the overall genotype deviation rate was 1.58%, consisting of 145 inconsistences (mutations), 339 null alleles and 210 genotyping errors. In terms of seed numbers, 128 (6.5%) showed inconsistencies in at least one locus, 118 (6.0%) null alleles, and 321 (16.3%) genotyping errors. This is the first study to describe the inconsistences (mutations) between mother-progeny genotypes for A. angustifolia, and the outcome makes it clear that an understanding of these genotyping deviations must be considered in assessing the accuracy of inferences made based on population genetics analyses.
Data accompanying "In silico analysis of the profilaggrin sequence indicates alterations in the stability, degradation route, and intracellular protein fate in filaggrin null mutation carriers" article.
<p>This research was supported by the National Science Centre, Poland, grant PRELUDIUM number 2021/41/N/NZ1/03473 to NS, National Science Centre, Poland, grant SONATA BIS number 2019/34/E/NZ6/00354 to DG-O, as well as POIR.04.04.00-00-21FA/16–00 grant, carried out within the First TEAM programme of the Foundation for Polish Science co-financed by the European Union under the European Regional Development Fund (awarded to DG-O). WP was supported by the National Science Centre, Poland, grant SONATA-BIS number 2021/42/E/NZ1/00190. SB is supported by a Wellcome Trust Senior Research Fellowship (220875/Z/20/Z).</p>
TMC435HPC3001 - An Efficacy, Safety and Tolerability Study for TMC435 vs Telaprevir in Combination With PegINFα-2a and Ribavirin in Chronic Hepatitis C Patients Who Were Null or Partial Responders to
ClinicalTrials.gov study NCT01485991. IPD Sharing: Not stated. Countries: 24. Publications: 1.
Prevalence of Ethnic Neutropenia and Duffy Null Phenotype in Neonates
ClinicalTrials.gov study NCT06908616. IPD Sharing: NO. Countries: 1. Publications: 3.
A Study of TMC435 in Combination With PSI-7977 (GS7977) in Chronic Hepatitis C Genotype 1-Infected Prior Null Responders To Peginterferon/Ribavirin Therapy or HCV Treatment-Naive Patients
ClinicalTrials.gov study NCT01466790. IPD Sharing: Not stated. Countries: 2. Publications: 1.
Assessment of the stream invertebrate β-diversity along an elevation gradient using a bidimensional null model analysis
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Data from: A new null model approach to quantify performance and significance for ecological niche models of species distributions
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RNAseq analysis of heart samples collected from wild-type and ZNF768 null mice 8 hours post-irradiation
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Data from: An output-null signature of inertial load in motor cortex
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Discordant phylogeographic patterns in ecologically similar sympatric sister species: Revisiting the null hypothesis of comparative phylogeography
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The disruption index suffers from citation inflation and is confounded by shifts in scholarly citation practice: synthetic citation networks for bibliometric null models
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A graphical null model for scaling biodiversity-ecosystem functioning relationships
1. Global biodiversity is declining at rates faster than at any other point in human history. Experimental manipulations at small spatial scales have demonstrated that communities with fewer species consistently produce less biomass than higher diversity communities. Understanding how the global extinction crisis is likely to impact global ecosystem functioning requires applying these local experimental results at substantially larger spatial and temporal scales. 2. Here we propose a null model for scaling biodiversity-ecosystem functioning relationships using observed macroecological patterns. We use species-area and biomass-area curves to predict species richness – biomass relationships at multiple scales and validate these predictions with data from a Minnesota grassland and a Panamanian tropical dry forest. 3. Our null model accurately predicts species richness-biomass relationships across scales from these species-area and biomass-area relationships. However, we note two important caveats that will increase our ability to apply experimentally collected data to the global scale problem of species loss. First when ecosystem functioning is measured as per unit area (e.g., biomass m-2), as is common in biodiversity-ecosystem functioning experiments, the slope of the biodiversity ecosystem functioning relationship should decrease with increasing scale. Alternatively, when ecosystem functioning is not measured per unit area (e.g., summed total biomass), as is common in scaling studies, the slope of the biodiversity-ecosystem functioning relationship should increase with increasing spatial scale. Second, the underlying macroecological patterns of biodiversity experiments are predictably different from some naturally assembled systems. For example, in non-successional naturally assembled ecosystem, biomass is unlikely to change directionally through time. Biodiversity-ecosystem functioning experiments, however, often start from bare ground and biomass increases through time. From these underlying patterns, we would predict that the slope of the biodiversity-productivity relationship in a naturally assembled system not undergoing succession would decrease with increasing time. Alternatively, in an experiment we would predict an increase over time. 4. This paper provides a simple but novel null hypothesis for scaling any relationship between biodiversity and any ecosystem function in space and time. These predictions provide crucial insights into how and when we can extend results from small scale biodiversity experiments to naturally assembled regional and global ecosystems.
Assessing the genetic diversity in Argopecten nucleus (Bivalvia: Pectinidae), a functional hermaphrodite species with extremely low population density and self-fertilization: effect of null alleles
<p>Argopecten nucleus is a functional hermaphroditic pectinid species that exhibits self-fertilization, whose natural populations have usually very low densities. In the present study, the genetic diversity of a wild population from Neguanje Bay, Santa Marta (Colombia), was estimated using microsatellite markers, and the effect of the presence of null alleles on this estimation was assessed. A total of 8 microsatellite markers were developed, the first described for this species, and their amplification conditions were standardized. They were used to determine the genotype of 48 wild individuals from Naguanje Bay, and 1010 individuals derived from the offspring of 38 directed crosses. For each locus, the frequencies of the identified alleles, including null alleles, were estimated using the statistical package Micro-Checker, and the parental genotypes were confirmed using segregation analysis. Three to 8 alleles per locus with frequencies from 0.001 to 0.632 were detected. The frequencies of null alleles ranged from 0.10 to 0.45, with Ho from 0.0 to 0.79 and He from 0.53 to 0.80. All loci were in H-W disequilibrium. The null alleles frequencies values were high, with lower estimations using segregation analysis than estimated using Micro-Checker. The present results show high levels of population genetic diversity, and indicate that null alleles were not the only cause of deviation from HW equilibrium in all loci, suggesting that the wild population under study presents signs of inbreeding and Wahlun effect.</p>
Data from: Reliability assessment of null allele detection: inconsistencies between and within different methods
Microsatellite loci are widely used in population genetic studies, but the presence of null alleles may lead to biased results. Here, we assessed five methods that indirectly detect null alleles and found large inconsistencies among them. Our analysis was based on 20 microsatellite loci genotyped in a natural population of Microtus oeconomus sampled during 8 years, together with 1200 simulated populations without null alleles, but experiencing bottlenecks of varying duration and intensity, and 120 simulated populations with known null alleles. In the natural population, 29% of positive results were consistent between the methods in pairwise comparisons, and in the simulated data set, this proportion was 14%. The positive results were also inconsistent between different years in the natural population. In the null-allele-free simulated data set, the number of false positives increased with increased bottleneck intensity and duration. We also found a low concordance in null allele detection between the original simulated populations and their 20% random subsets. In the populations simulated to include null alleles, between 22% and 42% of true null alleles remained undetected, which highlighted that detection errors are not restricted to false positives. None of the evaluated methods clearly outperformed the others when both false-positive and false-negative rates were considered. Accepting only the positive results consistent between at least two methods should considerably reduce the false-positive rate, but this approach may increase the false-negative rate. Our study demonstrates the need for novel null allele detection methods that could be reliably applied to natural populations.
Data from: Rate heterogeneity across Squamata, misleading ancestral state reconstruction and the importance of proper null model specification
The binary-state speciation and extinction (BiSSE) model has been used in many instances to identify state-dependent diversification and reconstruct ancestral states. However, recent studies have shown that the standard procedure of comparing the fit of the BiSSE model to constant-rate birth–death models often inappropriately favours the BiSSE model when diversification rates vary in a state-independent fashion. The newly developed HiSSE model enables researchers to identify state-dependent diversification rates while accounting for state-independent diversification at the same time. The HiSSE model also allows researchers to test state-dependent models against appropriate state-independent null models that have the same number of parameters as the state-dependent models being tested. We reanalyse two data sets that originally used BiSSE to reconstruct ancestral states within squamate reptiles and reached surprising conclusions regarding the evolution of toepads within Gekkota and viviparity across Squamata. We used this new method to demonstrate that there are many shifts in diversification rates across squamates. We then fit various HiSSE submodels and null models to the state and phylogenetic data and reconstructed states under these models. We found that there is no single, consistent signal for state-dependent diversification associated with toepads in gekkotans or viviparity across all squamates. Our reconstructions show limited support for the recently proposed hypotheses that toepads evolved multiple times independently in Gekkota and that transitions from viviparity to oviparity are common in Squamata. Our results highlight the importance of considering an adequate pool of models and null models when estimating diversification rate parameters and reconstructing ancestral states.
Data from: Null alleles are ubiquitous at microsatellite loci in the Wedge Clam (Donax trunculus)
Recent studies have reported an unusually high frequency of nonamplifying alleles at microsatellite loci in bivalves. Null alleles have been associated with heterozygous deficits in many studies. While several studies have tested for its presence using different analytical tools, few have empirically tested for its consequences in estimating population structure and differentiation. We characterised 16 newly developed microsatellite loci and show that null alleles are ubiquitous in the wedge clam, Donax trunculus. We carried out several tests to demonstrate that the large heterozygous deficits observed in the newly characterised loci were most likely due to null alleles. We tested the robustness of microsatellite genotyping for population assignment by showing that well-recognised biogeographic regions of the south Atlantic and south Mediterranean coast of Spain harbour genetically different populations.
NULL
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Data from: Fauxcurrence: simulating multi-species occurrences for null models in species distribution modelling and biogeography
<p>This dataset contains GPS coordinates of occurrences from 22 species from Sulawesi, Indonesia. It was used in the manuscript "Fauxcurrence: simulating multi-species occurrences for null models in species distribution modelling and biogeography" to demonstrate the utility of the fauxcurrence R package (<a href="https://github.com/ogosborne/fauxcurrence">https://github.com/ogosborne/fauxcurrence)</a>.</p>
PATTERNS OF RICHNESS OF FRESHWATER MOLLUSCS FROM CHILE: PREDICTIONS OF ITS DISTRIBUTION BASED ON NULL MODELS
<p>Script and data for GLM analysis and co-occurrence analysis. </p>
Device-independent null test of dimension of qubit at low operational cost
<p>The data and scripts for the test on IBM Quantum</p>
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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)
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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.