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226 results for “confidence”
Fig. 4. A in Assessing confidence intervals for stratigraphic ranges of higher taxa: The case of Lissamphibia
Fig. 4. A comparison of the origination (A–C) and diversification (B, C) times of Lissamphibia according to time−calibrated phylogenetic trees of (A) Stegocephali, (B) Lissamphibia based on the molecular analysis by Zhang et al. (2005), and (C) Lissamphibia based on the fossil record (Marjanović and Laurin 2007). In A, the stem of Lissamphibia is placed as high in the geological section as plausible under the various phylogenetic hypotheses: (I) as the sister−group of Doleserpeton; (II) within Branchiosauridae; (III) as the sister−group of the Doleserpeton + Amphibamus clade; (IV) as the sister−group of Lysorophia; (V) polyphyletic from within "lepospondyls" (caecilians, or caecilians and caudates) and "temnospondyls". Known stratigraphic ranges are shown as thick lines, ghost ranges as thin lines. In B, the 95% credibility intervals of molecular dates are represented by blank boxes; the best estimates and lower and upper boundaries of the credibility intervals are also indicated in parentheses. In C, the numbers given next to the nodes represent the age estimates (Ma) based on the assumptions used for the supertree by Marjanović and Laurin (2007: fig. 9b). In parentheses follow the ranges of minimum (rather than actual) divergence dates as obtained using various minimum branch length assumptions (Marjanović and Laurin 2007: appendix 4); these ranges, also represented as blank boxes, are not true confidence intervals. The colored boxes represent the confidence intervals on the lower bound of the stratigraphic range of Lissamphibia calculated in the present paper (1–6 correspond to the lower half of Table 4: CI 1–Cl 6), where the bottom of the rectangle shows the lower limit of the 75% confidence interval and the black bar in each colored box corresponds to the lower limit of the 50% confidence interval. Abbreviations: Arch, Archaeobatrachia; Cry, Cryptobranchoidea; Mississi., Mississippian; Sal, Salamandridae.
Fig. 3. A in Assessing confidence intervals for stratigraphic ranges of higher taxa: The case of Lissamphibia
Fig. 3. A histogram of the curves (C) representing the recovery potential functions showing each period's or epoch's fraction of the total recovery potential calculated under eleven different assumptions (Table 4: CI 1–CI 6, which assume six different rates across extinction events and two different ages of origin for each except CI 6 which is independent of the age of origin). A bar chart of these data would be more appropriate than a dot−andline graph, but much more difficult to read. The total recovery potential un− der each assumption (i.e., the area under each "curve") is 1. Note the wide divergence between CI 6, which is based only on the exposure area of sedimentary rocks (Table 1), and all others, which include an exponential model of diversification. The much lower recovery potential of CI 1–Cl 5 in the Paleozoic generates correspondingly wider CIs.
Fig. 2. Lissamphibian biodiversity through time. A in Assessing confidence intervals for stratigraphic ranges of higher taxa: The case of Lissamphibia
Fig. 2. Lissamphibian biodiversity through time. A. Number of species found in each geologic stage. B. Standardized species numbers, calculated to account for uneven stage durations. C. Number of lineages, obtained by adding the number of recorded species and the number of ghost lineages for each geologic stage. Major biological crises identified in other taxa are shown as continuous gray lines. Minor crises that may have affected lissamphibians are shown as dashed gray lines. Since most post−Miocene species are excluded, this figure ends with the terminal Miocene. Minimum (white) and maximum (black) values have been calculated under various assumptions about the age of several middle Miocene species and the status of specimens with questionable affinities. The geologic timescale follows Gradstein et al. (2004) in all figures. Abbreviations: J, Jurassic; K, Cretaceous; M, Miocene; O, Oligocene; P, Permian; Pg, Paleogene; Tr, Triassic.
Clinically relevant or statistically significant: effects, p-values and confidence intervals
<p><span>When evaluating and interpreting medical studies, a distinction must be made as to whether the result is clinically relevant and/or statistically significant. For this decision, it is best to calculate effects, p-values and confidence intervals. A decision can be made depending on the effects and the p-values or confidence intervals (e.g. 95% CI). </span></p> <p><span>The diagram illustrates the different scenarios of a clinically relevant and/or statistically significant result. </span></p>
Post-hypnotic suggestion improves confidence and speed of memory access with long-lasting effects
<p>The attempt to improve memory has a long tradition. Previous studies do not provide clear evidence concerning the longevity of memory-improving effects which is crucial for clinical applications. In our study, we use the post-hypnotic suggestion of easy remembering to establish long-lasting effects, as post-hypnotic suggestions can be activated with a cue after the hypnotic state. We tested 24 highly suggestible participants in an online study. Participants learned word lists and recalled them later in a recognition memory task where both learned and new words were presented and participants rated their recognition confidence. At the beginning of the study, participants were hypnotized and the post-hypnotic suggestion to remember easily was associated with a cue that participants used during the recognition memory task in the easy-remembering condition. In a control condition, the same participants used a neutral cue. One week later, participants repeated both conditions with new word lists, relying on the same post-hypnotic suggestion they received the week before.</p> <p>Participants were significantly faster and more confident in their recognition ratings in the easy-remembering condition compared to the control condition, and this effect persisted over one week. Crucially, the increased speed and confidence in the easy-remembering condition did not affect memory accuracy; numerically, participants were even slightly better at discriminating old from new words in the easy-remembering condition. These findings demonstrate that post-hypnotic suggestions of easy remembering improve recognition confidence and speed with long-lasting effects, which makes it a promising intervention for patients experiencing subjective memory impairments.</p> <p>All experimental files to run the study in Gorilla are accessible via this link: https://app.gorilla.sc/openmaterials/430668</p>
Free Energy Differences from Molecular Simulations: Exact Confidence Intervals from Transition Counts
<p>Supporting data for <strong>Free Energy Differences from Molecular Simulations: Exact Confidence Intervals from Transition Counts</strong></p> <p>Molecular simulations make it possible to predict equilibrium constants and corresponding free energy differences. For a system that exists in two states A and B, the equilibrium constant K can be predicted as K = t_B / t_A, where<br> t_B and t_A are times spent in states B and A, respectively. The free energy can be calculated as Delta G = -kT log(K). Here we propose a new method for calculation of confidence intervals for K and Delta G. The ratio of the true<br> value of K and estimated K follows the F-distribution with degrees of freedom df1 = number of B to A transitions and df2 = number of A to B transitions. This makes it possible to calculated the confidence interval of K solely from<br> the number of transitions.</p> <p>The code in the directory errors was used to calculate Table 1 of the article. The code in the directory type1error was used to generate 10000 first time passage times for a transition from A to B and B to A as random numbers with<br> exponential distribution. This was done for different combinations of number of transition and values of K. Number of confidence intervals not spanning the predefined value of K (type 1 errors) was expected to be 5 % for 95-% confidence intervals. This was in agreement with the result.</p> <p>The code in the directory type1errorodd was used to run similar experiment as type1error, but with number of A to B transitions higher than B to A by one. The code in the directory threestates was used to run similar experiment as<br> type1error and type1errorodd but for a system with three states A, B and C. The directory glycerol contains a trajectory, evolution of values of torsion angles and the code for analysis of the simulation of glycerol in water.</p> <p>The directory ffmp contains evolution of values of RMSD from the native structure, manual assignments of folded and unfolded states and the code for analysis of simulations of fast folding miniproteins (original data from Lindorf-Larsen et al. Science 2011, 334(6055) 517-520).</p> <p>The directory se contains the code for calculation of standard errors numerically and by the method presented in the article.</p> <p>The directory parallel presents the code for calculations supporting our method to calculate rate and equilibrium constants in parallel simulations.</p> <p>Codes written in R were executed using R version 3.4.4 by running:<br> <em>$ R –no-save < code.R > code.log</em></p> <p>File md5sums contains md5sum codes for all files.</p> <p> </p>
spindle cell variant diffuse large B-cell lymphoma (NGS annotation file; high confidence calls) hematolrep-2136295
<p>Diffuse large B-cell lymphoma with spindle cell morphology is a rare variant. We present the case of a 74-year-old male who initially presented with a right supraclavicular (lymph) node enlargement. Histological analysis showed a proliferation of spindle-shaped cells with narrow cytoplasms. An immunohistochemical panel was used to exclude other tumors, such as melanoma, carcinoma, and sarcoma. The lymphoma was characterized by a cell-of-origin subtype of germinal center B-cell-like (GCB) based on Hans’ classifier (CD10-negative, BCL6-positive, and MUM1-negative); EBER negativity, and the absence of BCL2, BCL6, and MYC rearrangements. Mutational profiling using a custom panel of 168 genes associated with aggressive B-cell lymphomas confirmed mutations in ACTB, ARID1B, DUSP2, DTX1, HLA-B, PTEN, and TNFRSF14. Based on the LymphGen 1.0 classification tool, this case had an ST2 subtype prediction. The immune microenvironment was characterized by moderate infiltration of M2-like tumor-associated macrophages (TMAs) with positivity of CD163, CSF1R, CD85A (LILRB3), and PD-L1; moderate PD-1 positive T cells, and low FOXP3 regulatory T lymphocytes (Tregs). Immunohistochemical expression of PTX3 and TNFRSF14 was absent. Interestingly, the lymphoma cells were positive for HLA-DP-DR, IL-10, and RGS1, which are markers associated with poor prognosis in DLBCL. The patient was treated with R-CHOP therapy, and achieved a metabolically complete response.</p> <p>Carreras J, Kikuti YY, Miyaoka M, Hiraiwa S, Tomita S, Ikoma H, Kondo Y, Ito A, Nagase S, Miura H, Roncador G, Colomo L, Hamoudi R, Campo E, Nakamura N. Mutational Profile and Pathological Features of a Case of Interleukin-10 and RGS1-Positive Spindle Cell Variant Diffuse Large B-Cell Lymphoma. <em>Hematology Reports</em>. 2023; 15(1):188-200. https://doi.org/10.3390/hematolrep15010020</p>
Serial Dependence improves performance and biases confidence-based decisions
<p>We uploaded all the sessions in one file for each participant.<br> Each file contains a single matrix called “RESP1”.<br> The columns contain the following information:</p> <ul> <li>1<sup>st</sup>: Orientation of top stimulus.</li> <li>2<sup>nd</sup>: Orientation of bottom stimulus.</li> <li>3<sup>rd</sup>: 1 whether current top orientation was equal of previous top orientation; 2 whether current bottom orientation was equal of previous bottom orientation.</li> <li>4<sup>th</sup>: 0 whether top orientation was as right orientation. 1 whether top orientation was as left orientation.</li> <li>5<sup>th</sup>: orientation of left stimulus.</li> <li>6<sup>th</sup>: Stimulus chosen to judge (1 top; 2 bottom).</li> <li>7<sup>th</sup>: 1 whether chosen stimulus had same orientation of previous in the same position, otherwise 0.</li> <li>8<sup>th</sup>: Orientation response (1 left; 2 right).</li> <li>9<sup>th</sup>: 1 response correct, 0 response wrong.</li> <li>10<sup>th</sup>: Timestamp of start presentation of the stimulus.</li> <li>11<sup>th</sup>: Timestamp of end presentation of the stimulus.</li> <li>12<sup>th</sup>: Timestamp of chosen stimulus.</li> <li>13<sup>th</sup>: Timestamp of orientation judgment.</li> <li>14<sup>th</sup>: 1 whether variable stimulus was up or down (2).</li> <li>15<sup>th</sup>: Noise level of top stimulus.</li> <li>16<sup>th</sup>: Noise level of bottom stimulus.</li> <li>17<sup>th</sup>: 1 whether participant chosen the variable stimulus, otherwise 0.</li> <li>18<sup>th</sup>: 1 whether variable stimulus was a continuous stimulus, otherwise 0.</li> </ul>
Dataset supporting the paper "Expanding the coverage of regulons from high-confidence prior knowledge for accurate estimation of transcription factor activities"
<p>Datasets involved in the construction and benchmarking of the CollecTRI-derived regulons as presented in the paper "Expanding the coverage of regulons from high-confidence prior knowledge for accurate estimation of transcription factor activities".</p>
CONFIDENCE-AI Financial Education for Caregivers (CONFIDENCE-AI)
ClinicalTrials.gov study NCT06134180. IPD Sharing: YES. Countries: 1. Publications: 3.
Data and code for: Combining eddy covariance towers, field measurements, and the MEMS 2 ecosystem model improves confidence in the climate impacts of bioenergy with carbon capture and storage
Open the record for dataset details and reuse information.
Assessing confidence in root placement on phylogenies: an empirical study using non-reversible models for Mammals
<p>Using time-reversible Markov models is a very common practice in phylogenetic analysis, because although we expect many of their assumptions to be violated by empirical data, they provide high computational efficiency. However, these models lack the ability to infer the root placement of the estimated phylogeny. In order to compensate for the inability of these models to root the tree, many researchers use external information such as using outgroup taxa or additional assumptions such as molecular-clocks. In this study, we investigate the utility of non-reversible models to root empirical phylogenies and introduce a new bootstrap measure, the <i>rootstrap</i>, which provides information on the statistical support for any given root position.</p> <p>Availability and implementation: rootstrap support is implemented in IQ-TREE 2 and a tutorial is available at the iqtree webpage <a href="http://www.iqtree.org/doc/Rootstrap">http://www.iqtree.org/doc/Rootstrap</a>. In addition, a python script is available at <a href="https://github.com/suhanaser/Rootstrap">https://github.com/suhanaser/Rootstrap</a></p>
Adaptation to hand-tapping affects sensory processing of numerosity directly: evidence from reaction times and confidence
<p>Each file contains a matrix called “MatriceRisultati”. Each row of the matrix “MatriceRisultati” is a trial. </p> <p>The columns contain the following information:</p> <ul> <li>1<sup>st</sup>: Number of trial</li> <li>2<sup>nd</sup>: Test numerosity</li> <li>3<sup>rd</sup>: Subject response on numerosity </li> <li>4<sup>th</sup>: Subject response on their confidence level</li> <li>5<sup>th</sup>: Response time</li> <li>6<sup>th</sup>: 0 if the test numerosity< 16; 1 if the test numerosity> 16</li> </ul>
Bioinformatic pipeline from: Increasing confidence for discerning species and population compositions from metabarcoding assays of environmental samples: case studies of fishes in the Laurentian Great Lakes and Wabash River
<p>Community composition data are essential for conservation management, facilitating identification of rare native and invasive species, along with abundant ones. However, traditional capture-based morphological surveys require considerable taxonomic expertise, are time consuming and expensive, can kill rare taxa and damage habitats, and often are prone to false negatives. Alternatively, metabarcode assays can be used to assess the genetic identity and compositions of entire communities from environmental samples, comprising a more sensitive, less damaging, and relatively time- and cost-efficient approach. However, there is a trade-off between the stringency of bioinformatic filtering needed to remove false positives and the potential for false negatives. The present investigation thus evaluated use of four mitochondrial (mt) DNA metabarcode assays and a customized bioinformatic pipeline to increase confidence in species identifications by removing false positives, while achieving high detection probability. Positive controls were used to calculate sequencing error, and results that fell below those cutoff values were removed, unless found with multiple assays. The performance of this approach was tested to discern and identify North American freshwater fishes using lab experiments (mock communities and aquarium experiments) and processing of a bulk ichthyoplankton sample. The method then was applied to field environmental (e)DNA water samples taken concomitant with electrofishing surveys and morphological identifications. This protocol detected 100% of species present in concomitant electrofishing surveys in the Wabash River and an additional 21 that were absent from traditional sampling. Using single 1 L water samples collected from just four locations, the metabarcoding assays discerned 73% of the total fish species that were discerned in comparison to four months of an extensive electrofishing river survey in the Maumee River, along with an additional nine species. In both rivers, total fish species diversity was best resolved when all four metabarcode assays were used together, which identified 35 additional species missed by electrofishing. Ecological distinction and diversity levels among the fish communities also were better resolved with the metabarcode assays than with morphological sampling and identifications, especially with the combined assays. At the population-level, metabarcode analyses targeting the invasive round goby <i>Neogobius melanostomus</i> and the silver carp <i>Hypophthalmichthys molitrix</i> identified all population haplotype variants found using Sanger sequencing of morphologically sampled fish, along with additional intra-specific diversity, meriting further investigation. Overall findings demonstrated that the use of multiple metabarcode assays and custom bioinformatics that filter potential error from true positive detections improves confidence in evaluating biodiversity.</p>
Confidant Chairs (Las Sillas Confidentes)
These chairs were installed in the "Plaza de la Independencia" or " Plaza Grande" of Mérida when it was remodeled in 1915. The then governor of Yucatán, General Salvador Alvarado, placed a central octagonal platform in the plaza along with other new designs, including a few pairs of these chairs. It is thought that their form and design are inspired by the "butacas confidentes" (confidant armchairs) from the French Renaissance period; a sense of abundance dominated everything and royalty used the most exquisite objects of design. These armchairs were a type of interior furniture designed for intimate conversation; they are very similar to the "sillas tú y yo". Today you can find these chairs all over the parks of the historic Centro of Mérida. On your next visit to our city, don't forget to enjoy them in the parks and on Paseo de Montejo, to rest and to take a few "selfies" while chatting with a friend or your partner; they are an ideal way to be transported to a romantic and personal space. Source: Objaverse 1.0 / Sketchfab
Sets of ChEMBL compounds with high or low confidence activity data
<p>Two sets of compounds assembled from ChEMBL release 20 that were annotated with high or low confidence activity data were provided in separate files. For each compound in a file, the unique compound identifier (i.e., molregno), the number of targets in individual years (from 1976 to 2014) and the list of target annotations (if any) was given.</p>
Confidence Matrices of Automatically Recognized Charters of the Monastery of Einsiedeln
<p>The data set consists of data gained through automatic text recognition with HTR+ models.<br>The model is usable within the Transkribus environment: <a href="https://readcoop.eu/model/charter-scripts-german-latin-french/">readcoop.eu/model/charter-scripts-german-latin-french/</a>.</p><p>Each folder is a group of documents, depending on the call-number in the archives (<a href="https://www.klosterarchiv.ch/">https://www.klosterarchiv.ch/</a>). Each sub-folder is a document and each CSV is a line of recognized text in the form of a Confidence Matrix.</p>
Calling structural variants with confidence from short-read data in wild bird populations
<p>Comprehensive characterisation of structural variation in natural populations has only become feasible in the last decade. To investigate the population genomic nature of structural variation (SV), reproducible and high-confidence SV callsets are first required. We created a population-scale reference of the genome-wide landscape of structural variation across 33 Nordic house sparrows (<em>Passer domesticus</em>) individuals. To produce a consensus callset across all samples using short-read data, we compare heuristic-based quality filtering and visual curation (Samplot/PlotCritic and Samplot-ML) approaches. We demonstrate that curation of SVs is important for reducing putative false positives and that the time invested in this step outweighs the potential costs of analysing short-read discovered SV datasets that include many potential false positives. We find that even a lenient manual curation strategy (e.g. applied by a single curator) can reduce the proportion of putative false positives by up to 80%, thus enriching the proportion of high-confidence variants. Crucially, in applying a lenient manual curation strategy with a single curator, nearly all (>99%) variants rejected as putative false positives were also classified as such by a more stringent curation strategy using three additional curators. Furthermore, variants rejected by manual curation failed to reflect the expected population structure from SNPs, whereas variants passing curation did. Combining heuristic-based quality-filtering with rapid manual curation of structural variants in short-read data can therefore become a time- and cost-effective first step for functional and population genomic studies requiring high-confidence SV callsets.</p>
Dataset from 'Klever, L., Mamassian, P., & Billino, J. (2022). Age-related differences in visual confidence are driven by individual differences in cognitive control capacities. Scientific Reports, 12, 1-13. doi: 10.1038/s41598-022-09939-7
<p>We provide two files; one data file contains data on which analyses are based, the other one gives the column labels for the data file.</p> <p>___________________________________________<br> For further questions, please contact:<br> lena.klever[at]psychol.uni-giessen.de</p>
RDF Dataset for article: A confidence predictor for logD using conformal regression and a support-vector machine
<p>RDF dataset described in article: "A confidence predictor for logD using conformal regression and a support-vector machine" (Manuscript in preparation).</p> <p>The dataset contains conformal logD values at 90% confidence level, computed for 91M compounds from PubChem, in RDF format.</p> <p>The .hdt.gz version contains the dataset in RDF HDT format (http://www.rdfhdt.org/), compressed with tar and gzip. The archive contains both the .hdt file, and an index file, generated by the hdtSearch C++ tool.</p> <p>The .ttl.gz file is a gzipped file in RDF Turtle format (https://www.w3.org/TR/turtle/).</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.