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Flongle data for KnowYourCG: Facilitating base-level sparse methylome interpretation
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Ground, Object and Interpretant
<p><strong>Ground, Object and Interpretant</strong></p> <p> </p> <p>Logic, in its general sense, is, as I believe I have shown, only another name for <em><strong>semiotic</strong></em> ({sémeiötiké}), the quasi-necessary, or formal, doctrine of signs. By describing the doctrine as "quasi-necessary," or formal, I mean that we observe the characters of such signs as we know, and from such an observation, by a process which I will not object to naming Abstraction, we are led to statements, eminently fallible, and therefore in one sense by no means necessary, as to what <em><strong>must be</strong></em> the characters of all signs used by a "scientific" intelligence, that is to say, by an intelligence capable of learning by experience. As to that process of abstraction, it is itself a sort of observation. The faculty which I call abstractive observation is one which ordinary people perfectly recognize, but for which the theories of philosophers sometimes hardly leave room. It is a familiar experience to every human being to wish for something quite beyond his present means, and to follow that wish by the question, "Should I wish for that thing just the same, if I had ample means to gratify it?" To answer that question, he searches his heart, and in doing so makes what I term an abstractive observation. He makes in his imagination a sort of skeleton diagram, or outline sketch, of himself, considers what modifications the hypothetical state of things would require to be made in that picture, and then examines it, that is, <em><strong>observes</strong></em> what he has imagined, to see whether the same ardent desire is there to be discerned. By such a process, which is at bottom very much like mathematical reasoning, we can reach conclusions as to what <em><strong>would be</strong></em> true of signs in all cases, so long as the intelligence using them was scientific. The modes of thought of a God, who should possess an intuitive omniscience superseding reason, are put out of the question. Now the whole process of development among the community of students of those formulations by abstractive observation and reasoning of the truths which <em><strong>must</strong></em> hold good of all signs used by a scientific intelligence is an observational science, like any other positive science, notwithstanding its strong contrast to all the special sciences which arises from its aiming to find out what <em><strong>must be</strong></em> and not merely what <em><strong>is</strong></em> in the actual world. Charles Sanders Peirce, Collected Papers of Charles Sanders Peirce, ed. by Charles Hartshorne, Paul Weiss, and Arthur W. Burks, 8 vols. (Cambridge, MA: Harvard University Press, 1931-1958), 2.227.</p> <p> </p> <p>A sign, or <em><strong>representamen</strong></em>, is something which stands to somebody for something in some respect or capacity. It addresses somebody, that is, creates in the mind of that person an equivalent sign, or perhaps a more developed sign. That sign which it creates I call the <em><strong>interpretant</strong></em> of the first sign. The sign stands for something, its <em><strong>object</strong></em>. It stands for that object, not in all respects, but in reference to a sort of idea, which I have sometimes called the <em><strong>ground</strong></em> of the representamen. "Idea" is here to be understood in a sort of Platonic sense, very familiar in everyday talk; I mean in that sense in which we say that one man catches another man's idea, in which we say that when a man recalls what he was thinking of at some previous time, he recalls the same idea, and in which when a man continues to think anything, say for a tenth of a second, in so far as the thought continues to agree with itself during that time, that is to have a <em><strong>like</strong></em> content, it is the same idea, and is not at each instant of the interval a new idea. <em>Ibid, </em>2.228.</p> <p> </p> <p>In consequence of every representamen being thus connected with three things, the ground, the object, and the interpretant, the science of semiotic has three branches. The first is called by Duns Scotus <em><strong>grammatica speculativa</strong></em>. We may term it <em><strong>pure grammar</strong></em>. It has for its task to ascertain what must be true of the representamen used by every scientific intelligence in order that they may embody any <em><strong>meaning</strong></em>. The second is logic proper. It is the science of what is quasi-necessarily true of the representamina of any scientific intelligence in order that they may hold good of any <em><strong>object</strong></em>, that is, may be true. Or say, logic proper is the formal science of the conditions of the truth of representations. The third, in imitation of Kant's fashion of preserving old associations of words in finding nomenclature for new conceptions, I call <em><strong>pure rhetoric</strong></em>. Its task is to ascertain the laws by which in every scientific intelligence one sign gives birth to another, and especially one thought brings forth another. <em>Ibid, </em>2.229.</p> <p> </p> <p>Written c. 1897</p>
The zebra mussel (Dreissena polymorpha) as a model organism for ecotoxicological studies: a prior 1H NMR spectrum interpretation of a whole body extract for metabolism monitoring.
<p>NMR data of the zebra mussel <em>Dreissena polymorpha</em> whole body polar extract metabolome</p> <p>- 1D <sup>1</sup>H annotated spectrum - 600 MHz</p> <p>- 2D <sup>1</sup>H-<sup>1</sup>H JRES spectrum - 600 MHz</p> <p>- 2D<sup>1</sup>H-<sup>1</sup>H COSY spectrum - 600 MHz</p> <p>- 2D<sup>1</sup>H-<sup>1</sup>H TOCSY spectrum - 600 MHz</p> <p>- 2D<sup>1</sup>H-<sup>13</sup>C HSQC spectrum - 600 MHz</p> <p>- 2D<sup>1</sup>H-<sup>13</sup>C HSQC spectrum - 800 MHz</p> <p>- 2D<sup>1</sup>H-<sup>31</sup>P HSQC spectrum - 800 MHz</p> <p>- <sup>1</sup>H annotated spectrum description tables (.xlsx)</p> <p>- Instructions for data visualization in Topspin</p>
Signals interpreted as archaic introgression are driven primarily by accelerated evolution in Africa
<p>Non-African humans appear to carry a few percent archaic DNA due to ancient inter-breeding. This modest legacy and its likely recent timing imply that most introgressed fragments will be rare and hence will occur mainly in the heterozygous state. I tested this prediction by calculating D statistics, a measure of legacy size, for pairs of humans where one of the pair was conditioned always to be either homozygous or heterozygous. Using coalescent simulations, I confirmed that conditioning the non-African to be heterozygous increased D while conditioning the non-African to be homozygous reduced D to zero. Repeating with real data reveals the exact opposite pattern. In African – non-African comparisons, D is near-zero if the African individual is held homozygous. Conditioning one of two Africans to be either homozygous or heterozygous invariably generates large values of D, even when both individuals are drawn from the same population. Invariably, the African with more heterozygous sites (conditioned heterozygous > unconditioned > conditioned homozygous) appears less related to the archaic. In contrast, the same analysis applied to pairs of non-Africans always yields near-zero D, showing that conditioning does not create large D without an underlying signal to expose. Large D values in humans are therefore driven almost entirely by heterozygous sites in Africans acting to increase divergence from related taxa such as Neanderthals. In comparison with heterozygous Africans, individuals that lack African heterozygous sites, whether non-African or conditioned homozygous African, always appear more similar to archaic outgroups, a signal previously interpreted as evidence for introgression. I hope these analyses will encourage others to consider increased divergence as well as increased similarity to archaics as mechanisms capable of driving asymmetrical base-sharing.</p>
Using ecological context to interpret spatiotemporal variation in natural selection
<p>Spatiotemporal variation in natural selection is expected, but difficult to estimate. Pollinator-mediated selection on floral traits provides a good system for understanding and linking variation in selection to differences in ecological context. We studied pollinator-mediated selection in five populations of <i>Dalechampia scandens</i> (Euphorbiaceae) in Costa Rica and Mexico. Using a nonlinear path-analytical approach, we assessed several functional components of selection, and linked variation in pollinator-mediated selection across time and space to variation in pollinator assemblages. After correcting for estimation error, we detected moderate variation in net selection on two of four blossom traits. Both the opportunity for selection and the mean strength of selection decreased with increasing reliability of cross-pollination. Selection for pollinator attraction was consistently positive and stronger on advertisement than reward traits. Selection on traits affecting pollen transfer from the pollinator to the stigmas was strong only when there was a mismatch between pollinator and blossom size under unreliable cross-pollination. These results illustrate how consideration of trait function and ecological context can facilitate both the detection and the causal understanding of spatiotemporal variation in natural selection.</p>
Quantifying tensions in cosmological parameters: Interpreting the DES evidence ratio (supplementary inference products)
<p>These are the nested sampling inference products and input files that were used to compute results for <a href="https://arxiv.org/abs/1902.04029">arXiv:1902.04029</a> and <a href="https://arxiv.org/abs/1903.06682">arXiv:1903.06682</a></p> <p>An example plotting script and plots from the papers are included to demonstrate usage.</p> <p>Filename conventions:</p> <p>runs_default: default prior widths</p> <p>runs_narrow: narrowest prior widths</p> <p>runs_medium: intermediate prior widths</p> <p>planck: Planck 2018 baseline likelihoods</p> <p>SH0ES: Riess et al 2018 Hubble likelihood</p> <p>BAO: BOSS DR12 baryonic acoustic oscillations + redshift space distortion likelihood</p> <p>DES: Dark Energy Survey Y1 baseline</p> <p>Software used:</p> <p>CosmoChord <a href="https://github.com/williamjameshandley/CosmoChord/tree/e2f7020bd9d4254230097037fb6ebaee95a3d558">https://github.com/williamjameshandley/CosmoChord/tree/e2f7020bd9d4254230097037fb6ebaee95a3d558</a></p>
Data from: An alternative interpretation of the Paleogene turtle Cardichelyon rogerwoodi as a hinged kinosternoid
<p><i>Cardichelyon rogerwoodi</i> is an enigmatic fossil turtle from the late Paleocene to early Eocene of North America. Previous analyses suggested affiliation with Testudinoidea, in particular the big-headed turtle <i>Platysternon megacephalum</i>, based on the presence of multiple musk-duct foramina and a large head. We here highlight previously undocumented characteristics for this turtle, notably the presence of short costiform processes, a rib-like axillary process, and a posterior plastral hinge. Phylogenetic analysis places <i>Cardichelyon rogerwoodi</i> within Testudinoidea but the exclusion of testudinoids suggest an affiliation with Dermatemydidae. Using consilience with external data we favor placement within Kinosternoidea. <i>Cardichelyon rogerwoodi</i> is therefore an aberrant, hinged kinosternoid that developed in situ in North America during the Paleocene long before the arrival of testudinoids on this continent in the early Eocene.</p>
Interpretive Panel-Pointe du Hoc, France
Quick capture of one of the interpretive panels located near the Pointe du Hoc visitor's center in Normandy, France. This model was created from 118 images that were processed in RealityCapture. Source: Objaverse 1.0 / Sketchfab
Validity of two automatic artifact reduction software methods in ictal EEG interpretation. Dataset 1
<p>Unprocessed electroencephalogram recordings of seizures from deidentified study patients with epilepsy prior to and following processing using the AR2 (artifact reduction 2) software method. The files are stored in European Data Format (.EDF). "_out" files have been processed by AR2.</p>
DeepAnnotation: A novel interpretable deep learning-based genomic selection model that integrates comprehensive functional annotations
<p>1. Update package, example dataset, and demo code of DeepAnnotation</p> <p>2. Update the transformed genotype data, the phenotype data, the comprehensive functional annotation data for Duroc prepared by RNAfold, DeepSEA, easyMF models, and the four types of input data for training DeepAnnotation model</p> <p>3. Add the conserved functional annotation</p> <p> </p>
Dataset for paper "Interpreting the shifts in forest structure, plant community composition, diversity, and functional identity by using remote sensing-derived wildfire severity"
<p>Interpreting the shifts in forest structure, plant community composition, diversity, and functional identity by using remote sensing-derived wildfire severity . New collected data</p>
Fig. 8 in A New Interpretation of the Oldest Fossil Bee (Hymenoptera: Apidae)
Fig. 8. Exploratory phylogeny of tribe Meliponini (length 42, CI 0.52, RI 0.80).
Coordinate files from LipIDens: Simulation assisted interpretation of lipid densities in cryo-EM structures of membrane proteins.
<p>Coordinate files from the first and last frame of coarse-grained (CG) and atomistic (AT) molecular dynamics (MD) simulations used throughout the LipIDens pipeline.</p><p>CG simulations were run for HHAT, OTOP1, ELIC, MscS, TRPV6, ChRmine, Ste2, Connexin-50, NPC1 and the PAT complex. All CG simulations were run for 10 x 15 μs with the exception of NPC1 which was simulated for 10 x 30 μs.</p><p>AT simulations were run for HHAT (5 x 200 ns) and ELIC (3 x 200 ns) in apo configurations.</p><p><strong>File description:</strong></p><p>Directories for each protein are listed with the suffix CG or AT used to indicate the simulation resolution. </p><p>md_fit_firstframe_<i>X</i>.gro - GROMACS structure file for the first frame of replicate <i>X</i>. </p><p>md_fit_lastframe_<i>X</i>.gro - GROMACS structure file for the last frame of replicate <i>X</i>. </p>
"iDCNNPred: An interpretable deep learning model for virtual screening and identification of PI3Ka inhibitors against triple-negative breast cancer"
<p>In this study, we proposed a novel interpretable deep convolutional neural network prediction (iDCNNPred) system for classifying molecular bioactivity and identifying predictive potential inhibitors for the PI3Ka isoform protein. This system utilizes 2D molecular image representation as input features, instead of traditional molecular fingerprints or descriptors.</p> <p><strong>The datasets used for model construction, prediction and screening of chemical library are provided in this uploaded data in <a href="../api/records/10947610/draft/files/Molecular_image_Custom_DCNN_datasets.zip/content" target="_blank" rel="noopener noreferrer">Molecular_image_Custom_DCNN_datasets.zip</a> file for Custom-DCNN models and <a href="../api/records/10947610/draft/files/Molecular_image_pre_trained_datasets.zip/content" target="_blank" rel="noopener noreferrer">Molecular_image_pre_trained_datasets.zip</a> file for Pre-trained fine-tuned models. </strong><strong>The final run of models results given in file <a href="../api/records/10947610/draft/files/Custom_DCNN_Pre_trained_models.zip/content" target="_blank" rel="noopener noreferrer">Custom_DCNN_Pre_trained_models.zip</a></strong></p>
The impact of deep learning aid on the workload and interpretation accuracy of radiologists on chest computed tomography: a cross-over reader study.
<p>Data used to perform statistical analysis in "The impact of deep learning aid on the workload and interpretation accuracy of radiologists on chest computed tomography: a cross-over reader study.". </p>
Three-dimensional Unfolding and Unfaulting Dataset for Structural Interpretation Using Self-Supervised Learning
<p>This dataset accompanies the study "Three-dimensional unfolding and unfaulting for structural interpretation using self-supervised learning." It provides synthetic data used to develop and validate a novel 3-D lightweight neural network framework for restoring deformed geological structures to their flattened state. The data include highly deformed examples with complex faulting and folding, designed to test the model's ability to compute precise shifts that realign stratigraphic layers. </p>
Supplementary files from: Improving inference and avoiding over-interpretation of hidden-state diversification models: Specialized plant breeding has no effect on diversification in frogs
<p>The hidden-state speciation and extinction (HiSSE) model helps avoid spurious results when testing whether a character affects diversification rates. However, care must be taken to optimally analyze models and interpret results. Recently, Tonini et al. (2020; TEA hereafter) studied anuran (frog and toad) diversification with HiSSE methods. They concluded that their focal state, breeding in phytotelmata, increases net diversification rates. Yet this conclusion is counterintuitive, because the state that purportedly increases net diversification rates is 14 times rarer among species than the alternative. Herein I revisit TEA's analyses and demonstrate problems with inferring model likelihoods, conducting post-hoc tests, and interpreting results. I also re-evaluate their top models and find that diverse strategies are necessary to reach the parameter values that maximize each model's likelihood. In contrast to TEA, I find no support for an effect of phytotelm breeding on net diversification rates in Neotropical anurans. In particular, even though the most highly supported models include the focal character, averaging parameter estimates over hidden states shows that the focal character does not influence diversification rates. Finally, I suggest ways to better analyze and interpret complex diversification models – both state-dependent and beyond – for future studies in other organisms.</p>
Interpreting past trophic ecology of a threatened species, kea (Nestor notabilis), from museum specimens
<p>When ecosystems are under severe pressure or environments change, trophic position and intraspecific niche width may decrease or narrow, signalling that conservation action is required. In New Zealand, alpine and sub-alpine ecosystems have been extensively modified through farming since 19th century European settlement, with consequences for indigenous species such as the kea (Nestor notabilis). We investigated feather stable isotope values in the kea and predicted a lower trophic position in modern kea populations, to reflect reduced lowland habitat and a mixed diet with more plant material. We predicted that size and sex would influence trophic values in this sexually dimorphic species, with larger birds more likely to have a high protein diet. We examined potential dietary changes in 68 museum collected kea from 1880s to 2000s, first recording accession details including provenance and sex, and measuring culmen length. We used bulk carbon and nitrogen stable isotopes analyses (BSIA) of feathers and a further feather subset using compound-specific stable isotopes analyses of amino acids (CSIA-AA) to obtain isotopic values and estimate trophic position. BSIA showed δ15N values in kea feathers declined through time, and could indicate that early century kea were highly omnivorous, with δ15N values on average higher than in modern kea. Variance in δ15N values was greater after 1950, driven by a few individuals. Few differences between males and females were evident, although females in the south region had lower δ15N values. There was a tendency for large male birds to have higher trophic values, perhaps reflecting dominant male bird behaviour noted in historical records. Nonetheless, CSIA-AA performed on a subset of the data suggested that variation in BSIA is likely due to baseline changes rather than relative trophic position which may be more homogenous than these data indicate. Although there was more variability in modern kea, we suggest caution in interpretation. Stable isotope data, particularly CSIA-AA, from museum specimens can reveal potential change in ecological networks, as well as sexually dimorphic feeding patterns within species. The data can reveal temporal and regional variation in species trophic position and changes in ecosystem integrity to inform conservation decision-making.</p>
FIG. 8 in Gaming and divination pieces, markers of ownership, or all three? Zooarchaeology and the interpretation of knuckle bones found in tombs of the Iberian necropolis of El Poblado (Coimbra del Barranco Ancho, Murcia, Spain)
FIG. 8. — Knuckle bones found in Tomb 116. Scale bar: 2 cm. Photo credit: J. Gómez Carrasco.
FIG. 7 in Gaming and divination pieces, markers of ownership, or all three? Zooarchaeology and the interpretation of knuckle bones found in tombs of the Iberian necropolis of El Poblado (Coimbra del Barranco Ancho, Murcia, Spain)
FIG. 7. — Knuckle bones found in Tomb 70. Scale bar: 2 cm. Photo credit: J. Gómez Carrasco.
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.