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4,563 results for “correlations”
Supplementary information: Cell volume (3D) correlative microscopy facilitated by intracellular fluorescent nanodiamonds as multi-modal probes
<p><em>Supplementary video files for manuscript</em>:</p> <p><strong>Cell volume (3D) correlative microscopy facilitated by intracellular fluorescent nanodiamonds as multi-modal probes</strong></p> <p>Neeraj Prabhakar<sup>1,2*</sup>, Ilya Belevich<sup>3</sup>, Markus Peurla<sup>4,5,6</sup>, Xavier Heiligenstein<sup>7</sup>, Huan-Cheng Chang<sup>8</sup>, Cecilia Sahlgren<sup>2</sup>, Eija Jokitalo<sup>3</sup> and Jessica M. Rosenholm<sup>1</sup></p> <ol> <li>Pharmaceutical Sciences Laboratory, Faculty of Science and Engineering, Åbo Akademi University, Turku, 20520, Finland.</li> <li>Cell Biology, Faculty of Science and Engineering, Åbo Akademi University, Turku, 20520 Finland.</li> <li>Electron Microscopy Unit, Helsinki Institute of Life Science - Institute of Biotechnology, University of Helsinki, Helsinki, FI-00014, Finland</li> <li>Institute of Biomedicine, Faculty of Medicine, University of Turku, Turku, 20520, Finland.</li> <li>Cancer Research Laboratory FICAN West, Institute of Biomedicine, University of Turku, 20520 Turku, Finland</li> <li>Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520 Turku, Finland</li> <li>CryoCapCell, 155 Boulevard de l’Hopital, 75013 Paris, France.</li> <li>Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei, 10617, Taiwan.</li> </ol>
Data from: Correlates of rate heterogeneity in avian ecomorphological traits
Heterogeneity in rates of trait evolution is widespread, but it remains unclear which processes drive fast and slow character divergence across global radiations. Here, we test multiple hypotheses for explaining rate variation in an ecomorphological trait (beak shape) across a globally distributed group (birds). We find low support that variation in evolutionary rates of species is correlated with life history, environmental mutagenic factors, range size, number of competitors, or living on islands. Indeed, after controlling for the negative effect of species' age, 80% of variation in species‐specific evolutionary rates remains unexplained. At the clade level, high evolutionary rates are associated with unusual phenotypes or high species richness. Taken together, these results imply that macroevolutionary rates of ecomorphological traits are governed by both ecological opportunity in distinct adaptive zones and niche differentiation among closely related species.
Data from: Dairy products viscosity estimated by laser speckle correlation
Dairy products exhibit several physical properties that are crucial to define whether we like the food or not: firmness, creaminess, thickness, or lightness. Viscosity changes the flow properties of food and influences the appearance and the consistency of a product; this control variable is important in most production stages—manufacture, processing, and storage. Viscosity of heterogeneous products at a given temperature depends on its composition and physical state of its substances. Although rheology provides a method to access the product viscosity, it lacks non-contact full-field monitoring. We apply a simple correlation analysis of laser speckle images to evaluate viscosity properties of dairy products. Our approach ensures robust measurements with high degree of detectability.
Data from: Sexual selection and diversification: reexamining the correlation between dichromatism and speciation rate in birds
Theory predicts that sexual selection can serve as an important driver of speciation, but phylogenetic comparative analyses have failed to demonstrate a consistent effect of sexual selection on species richness at macroevolutionary scales. Sexual dichromatism in birds is an example of a phenotypic trait that is hypothesized to reflect the intensity of sexual selection, yet previous studies have reached ambiguous conclusions regarding its role in promoting species diversification. Here, we revisit this problem by pairing published spectrophotometer estimates of plumage dichromatism in the bird-visible range with a newly developed method for modeling speciation rates on phylogenetic trees that explicitly accounts for diversification rate variation through time and among clades. We find little evidence linking dichromatism to speciation across birds, using several measures of dichromatism and macroevolutionary diversification. These results suggest that sexual dichromatism plays a limited role in determining speciation rates at macroevolutionary scales in birds.
Data from: Neural correlates of successful and unsuccessful strategical mechanisms involved in uncertain decision-making
The ability to develop successful long-term strategies in uncertain situations relies on complex neural mechanisms. Although lesion studies have shown some of the mechanisms involved, it is still unknown why some healthy subjects are able to make the right decision whereas others are not. The aim of our study was to investigate neurophysiological differences underlying this ability to develop a successful strategy in a group of healthy subjects playing a monetary card game called the Iowa Gambling Task (IGT). In this task, subjects have to win and earn money by choosing between four decks of cards, two were advantageous in the long term and two disadvantageous. Twenty healthy right-handed subjects performed the IGT while their cerebral activity was recorded by electroencephalography. Based on their behavioral performances, two groups of subjects could clearly be distinguished: one who selected the good decks and thus succeeded in developing a Favorable strategy (9 subjects) and one who remained Undecided (11 subjects). No neural difference was found between each group before the selection of a deck, but in both groups a greater negativity was found emerging from the right superior frontal gyrus 600 ms before a disadvantageous selection. During the processing of the feedback, an attenuation of the P200 and P300 waveforms was found for the Undecided group, and a P300 originating from the medial frontal gyrus was found in response to a loss only in the Favorable group. Our results suggest that undecided subjects are hyposensitive to the valence of the cards during gambling, which affects the feedback processing.
Data from: Optogenetically induced low-frequency correlations impair perception
Deployment of covert attention to a spatial location can cause large decreases in low-frequency correlated variability among neurons in macaque area V4 whose receptive-fields lie at the attended location. It has been estimated that this reduction accounts for a substantial fraction of the attention-mediated improvement in sensory processing. These estimates depend on assumptions about how population signals are decoded and the conclusion that correlated variability impairs perception, is purely hypothetical. Here we test this proposal directly by optogenetically inducing low-frequency fluctuations, to see if this interferes with performance in an attention-demanding task. We find that low-frequency optical stimulation of neurons in V4 elevates correlations among pairs of neurons and impairs the animal's ability to make fine sensory discriminations. Stimulation at higher frequencies does not impair performance, despite comparable modulation of neuronal responses. These results support the hypothesis that attention-dependent reductions in correlated variability contribute to improved perception of attended stimuli.
Data from: ConfeitoGUI: a toolkit for size-sensitive community detection from a correlation network
Analysis of the large amounts of data accumulated in public databanks can facilitate a more comprehensive understanding of molecular biological processes. Community detection from molecular biological data is paramount in characterizing evolutionary and functional traits of organisms based on gene homology and co-expression, respectively. Although there are common tools to detect local communities from a large network, no toolkit exists for detecting communities that include an element of interest based on size sensitivity, i.e., functionality to obtain local communities with preferred sizes. Herein, we present the ConfeitoGUI toolkit for detecting local communities from a correlation network involving size sensitivity. We compared the toolkit with other common tools for detection in reconstructing communities of microarray experiments of mice. In the results, ConfeitoGUI was observed to be preferable for detecting communities whose sizes are similar to those of original communities compared to other common tools. By changing simple parameters representing sizes for the toolkit, a user can obtain local communities with preferred sizes, which is beneficial for further analysis of members belonging to the communities.
Data from: Environmental DNA from seawater samples correlate with trawl catches of subarctic, deepwater fishes
Remote polar and deepwater fish faunas are under pressure from ongoing climate change and increasing fishing effort. However, these fish communities are difficult to monitor for logistic and financial reasons. Currently, monitoring of marine fishes largely relies on invasive techniques such as bottom trawling, and on official reporting of global catches, which can be unreliable. Thus, there is need for alternative and non-invasive techniques for qualitative and quantitative oceanic fish surveys. Here we report environmental DNA (eDNA) metabarcoding of seawater samples from continental slope depths in Southwest Greenland. We collected seawater samples at depths of 188–918 m and compared seawater eDNA to catch data from trawling. We used Illumina sequencing of PCR products to demonstrate that eDNA reads show equivalence to fishing catch data obtained from trawling. Twenty-six families were found with both trawling and eDNA, while three families were found only with eDNA and two families were found only with trawling. Key commercial fish species for Greenland were the most abundant species in both eDNA reads and biomass catch, and interpolation of eDNA abundances between sampling sites showed good correspondence with catch sizes. Environmental DNA sequence reads from the fish assemblages correlated with biomass and abundance data obtained from trawling. Interestingly, the Greenland shark (Somniosus microcephalus) showed high abundance of eDNA reads despite only a single specimen being caught, demonstrating the relevance of the eDNA approach for large species that can probably avoid bottom trawls in most cases. Quantitative detection of marine fish using eDNA remains to be tested further to ascertain whether this technique is able to yield credible results for routine application in fisheries. Nevertheless, our study demonstrates that eDNA reads can be used as a qualitative and quantitative proxy for marine fish assemblages in deepwater oceanic habitats. This relates directly to applied fisheries as well as to monitoring effects of ongoing climate change on marine biodiversity—especially in polar ecosystems.
Data from: Heterozygosity–fitness correlations in a wild mammal population: accounting for parental and environmental effects
HFCs (heterozygosity–fitness correlations) measure the direct relationship between an individual's genetic diversity and fitness. The effects of parental heterozygosity and the environment on HFCs are currently under-researched. We investigated these in a high-density U.K. population of European badgers (Meles meles), using a multimodel capture–mark–recapture framework and 35 microsatellite loci. We detected interannual variation in first-year, but not adult, survival probability. Adult females had higher annual survival probabilities than adult males. Cubs with more heterozygous fathers had higher first-year survival, but only in wetter summers; there was no relationship with individual or maternal heterozygosity. Moist soil conditions enhance badger food supply (earthworms), improving survival. In dryer years, higher indiscriminate mortality rates appear to mask differential heterozygosity-related survival effects. This paternal interaction was significant in the most supported model; however, the model-averaged estimate had a relative importance of 0.50 and overlapped zero slightly. First-year survival probabilities were not correlated with the inbreeding coefficient (f); however, small sample sizes limited the power to detect inbreeding depression. Correlations between individual heterozygosity and inbreeding were weak, in line with published meta-analyses showing that HFCs tend to be weak. We found support for general rather than local heterozygosity effects on first-year survival probability, and g2 indicated that our markers had power to detect inbreeding. We emphasize the importance of assessing how environmental stressors can influence the magnitude and direction of HFCs and of considering how parental genetic diversity can affect fitness-related traits, which could play an important role in the evolution of mate choice.
Replication package for the study "Broken Windows: Correlating historical and new code quality"
<p>Is the quality of existing code correlated with the quality of subsequent changes? According to the (controversial) broken windows theory, which inspired this study, disorder sets descriptive norms and signals behavior that further increases it. From a large code corpus, we examine whether code history does indeed affect the evolution of code quality. We examine C code quality metrics and Java code smells in specific files, and see whether subsequent commits by developers continue on that path. We check whether developers tailor the quality of their commits based on the quality of the file they commit to. Our results show that history matters, that developers behave differently depending on some aspects of the code quality they encounter, and that programming style inconsistency is not necessarily related to structural qualities. These findings have implications for both software practice and research.</p><p>This replication package contains the data and source code used in the study.</p>
Fluorescence image time series for pair correlation function analysis
<p>Data files for the tutorial "<a href="https://github.com/cgohlke/ipcf.ipynb">Pair Correlation Function Analysis of Fluorescence Fluctuations in Big Image Time Series using Python</a>", presented at the Big Data Image Processing & Analysis BigDIPA workshops 2016, 2017, and 2018.<br><br>The <strong>Simulation_Channel.bin</strong> file contains the result of a simulation of fluorescent particles diffusing on a 64x64 grid. The grid contains a diagonal, 300 nm wide channel, which restricts free diffusion. The file was produced using the Globals for Images, SimFCS software. The array shape is (32000, 64, 64), the data type is uint16.<br><br>The <strong>Simulation_Channel.ipcf.bin</strong> file contains the expected results of an ipCF analysis with 32 points at radius 6, and 32 bins. The array shape is (52, 52, 32, 30), the data type is float32.<br><br>The <strong>nih3t3-egfp_2.zip</strong> dataset contains a time series of SPIM images of a biological cell. It consists 35,000 TIFF files of 1024x512 16-bit grayscale samples each, 34.5 GB total.</p>
Microscopic simulations of the dynamics of excitonic many-body correlations coupled to quantum light
<p>Dataset of the publication "Microscopic simulations of the dynamics of excitonic many-body correlations coupled to quantum light" H. Rose, P. R. Sharapova, and T. Meier, Proc. SPIE 12884, Ultrafast Phenomena and Nanophotonics XXVIII, 1288403 (2024). ( https://doi.org/10.1117/12.2690245 ). The zip file includes the data on which the plots shown in figures 1 and 2 are based.</p>
Determination of fluoroquinolones concentration among biofilm-forming and non-forming uropathogenic Acinetobacter Calcoaceticus-Baumannii complex and their correlation to fluoroquinolone-resistant genes
<p><em>Acinetobacter </em>spp., the predominant cause of urinary tract infection (UTI), is increasingly resistant to fluoroquinolones. Resistance to fluoroquinolones poses a serious health problem in the treatment of urinary tract infections, which are mostly associated with chromosomal mutations encoded by topoisomerase IV. The objective of the study was to detect the <em>blaOXA-23</em>, <em>qnrB,</em> and <em>acc(6l)-lb-cr</em> genes in fluoroquinolone-resistant biofilm-producing ACB complex<em> </em>isolated from UTI-suspected patients.</p> <p>A hospital-based cross-sectional study was carried out at the Nepal Police Hospital, Kathmandu, from April 2019 to January 2021. A total of 598 urine specimens were processed, and 78 <em>ACB</em> complex were isolated from a total of 366 positive cultures, which were identified based on colony morphology, Gram's staining reaction, and various biochemical tests. The antimicrobial susceptibility pattern was determined by the modified Kirby-Bauer disk diffusion method, and the result was interpreted according to CLSI guidelines. The minimum inhibitory concentration (MIC) values of levofloxacin and ciprofloxacin for fluoroquinolone-resistant <em>ACB </em>were determined by the broth dilution method. The fluoroquinolone-resistant <em>ACB </em>was selected for <em>blaOXA-23</em>, <em>qnrB, </em>and <em>acc(6l)-lb-cr</em> gene detection by polymerase chain reaction.</p> <p>ACB complex was isolated more in females 26 (55.31%); outpatients 42 (53.84); and in the age group of 21–40 years 27 (34.61%). The majority of ACB<em> complex </em>isolates were sensitive to Ciprofloxacin 5 (6.41%) and Levofloxacin 10 (12.82%). However, most of them were resistant to Ciprofloxacin 64 (82.05%) and Levofloxacin 60 (76.92%). A total of 78 (21.31%) ACB complex isolates were found to be multidrug resistant. The MICs of Ciprofloxacin and Levofloxacin ranged from 4 to 256 μl/ml. Among 78 (82.05%) fluoroquinolone-resistant ACB<em> isolates, the</em> <em>blaOXA-23</em> gene was found on 32 (41.02%) isolates, the <em>acc(6l)-Ib-cr</em> gene on 3 (3.84%) isolates, and the <em>qnrB</em> gene on 1 (1.28%) isolates.</p> <p>The presence of <em>blaOXA-23</em>, <em>acc(6l)-Ib-cr</em>, and <em>qnrB</em> genes and biofilm formation lead to the emergence of fluoroquinolone-resistant strains of the ACB<em> complex</em>. So, the identification of responsible genes is required for AMR surveillance and guidelines for empirical therapy, which aid in preventing the emergence of antibiotic-resistant isolates.</p>
Pupillometry correlates of visual priming, and their dependency on autistic traits
<p>Data set for generating the figures with a file pf explanation accompanying </p>
Data from: Correlation between either Cupriavidus or Porphyromonas and primary pulmonary tuberculosis found by analysing the microbiota in patients' bronchoalveolar lavage fluid
Pulmonary tuberculosis (TB) has gained attention in recent decades because of its rising incidence trend; simultaneously, increasing numbers of studies have identified the relationship between microbiota and chronic infectious diseases. In our work, we enrolled 32 patients with primary TB characterised by unilateral TB lesion formation diagnosed by chest radiographic exam. Bronchoalveolar lavage fluid was taken from both lungs. Twenty-four healthy people were chosen as controls. Pyrosequencing was performed on the V3 hypervariable region of 16S rDNA in all bacterial samples and used as a culture-independent method to describe the phylogenetic composition of the microbiota. Through pyrosequencing, 271,764 amplicons were detected in samples and analysed using tools in the Ribosomal Database Project (RDP) and bioinformatics. These analyses revealed significant differences in the microbiota in the lower respiratory tract (LRT) of TB patients compared with healthy controls; in contrast, the microbiota of intra/extra-TB lesions were similar. These results showed that the dominant bacterial genus in the LRT of TB patients was Cupriavidus and not Streptococcus, which resulted in a significant change in the microbiota in TB patients. The abundance of Mycobacteria and Porphyromonas significantly increased inside TB lesions when compared with non-lesion-containing contralateral lungs. From these data, it can be concluded that Cupriavidus plays an important role in TB's secondary infection and that in addition to Mycobacteria, Porphyromonas may also be a co-factor in lesion formation. The mechanisms underlying this connection warrant further research.
Dataset from: Phonon downconversion to suppress correlated errors in superconducting qubits
<p>Quantum error correction can preserve quantum information in the presence of local errors, but correlated errors are fatal. For superconducting qubits, high-energy particle impacts from background radioactivity produce energetic phonons that travel throughout the substrate and create excitations above the superconducting ground state, known as quasiparticles, which can poison all qubits on the chip. We use normal metal reservoirs on the chip back side to downconvert phonons to low energies where they can no longer poison qubits. We introduce a pump-probe scheme involving controlled injection of pair-breaking phonons into the qubit chips. We examine quasiparticle poisoning on chips with and without back-side metallization and demonstrate a reduction in the flux of pair-breaking phonons by over a factor of 20. We use a Ramsey interferometer scheme to simultaneously monitor quasiparticle parity on three qubits for each chip and observe a two-order of magnitude reduction in correlated poisoning due to background radiation.</p> <p>Article has been accepted for publication in Nature Communications.</p>
DATASET_Corticosterone and glucose are correlated and show similar response patterns to temperature and stress in a free-living bird
<p>Dataset linked to the article "Corticosterone and glucose are correlated and show similar response patterns to temperature and stress in a free-living bird", published on Journal of Experimental Biology.</p>
Seismic scattering regimes from multiscale entropy and frequency correlations dataset
<p>Dataset accompanying manuscript published in Geophysical Journal International entitled</p> <p><a href="doi.org/10.1093/gji/ggae098"><em>Seismic scattering regimes from multiscale entropy and frequency correlations</em></a></p> <p> </p>
Geometries for "Reduced Scaling Correlated Natural Transition Orbitals for Multilevel Coupled Cluster Calculations"
<p>Formaldehyde, formaldehyde-in-water, and azobenzene dye geometries used in "Reduced Scaling Correlated Natural Transition Orbitals for Multilevel Coupled Cluster Calculations" in xyz-format.</p>
Correlation figure of metagenomics and metatranscriptomics sample
<p>Visualization codes from the 2nd "speeding up science workshop". This repository contains codes to plot and calculate correlation (linear regression) between metagenomic and metatranscriptomic sequencing results acquired from the same sample.</p> <p>There is an example of visualizing gene abundances (DNA) compared to their expression levels (RNA) included in the binder. The data are from one Mediterranean site from the TARA Oceans project (https://science.sciencemag.org/content/348/6237/1261359.long). The metagenomics come from sample accession SAMEA2619782, and the metatransciptomics come from SAMEA2619784.</p>
ScienceDex guides
Understand access before you commit
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.