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1,719 results for “Making”
Does natural root grafting make trees better competitors?
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WaveMAP analysis of extracellular waveforms from monkey premotor cortex during decision-making
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Supplementary datasets for: Polymorphic short tandem repeats make widespread contributions to blood and serum traits
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Data for paper: The making of a genetic cline: introgression of oceanic genes into coastal cod populations in the North East Atlantic
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Collective decision-making when quantity is more important than quality: Lessons from a kidnapping social parasite
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Figure 2 in The behaviour of Cotinis nitida Linnaeusı the green June beetle (Coleoptera: Scarabaeidae)ı on mowed lawns makes them especially vulnerable to bird predators
Figure 2. An American crow searching for prey while walking on the lawn in the manner of all avian predators of the green June beetle except the blue jays that scan for prey while perching in trees in and around the lawn in northern Virginia.
How to make a #theDress
<p>Supplementary material for article Witzel & Toscani (2020) <strong>How to make a #theDress</strong>, <em>Journal of the Optical Society of America A</em>, 37(4), doi: <a href="https://doi.org/10.1364/JOSAA.381311">https://doi.org/10.1364/JOSAA.381311</a>.</p> <p><strong>Additional sources</strong>: The code has also been uploaded to <a href="https://github.com/christophWit/dressmaker">GitHub</a> for future developments: <a href="https://github.com/christophWit/dressmaker">https://github.com/christophWit/dressmaker</a></p> <p> </p><p><em>Content:</em></p> <p></p> <p><strong>A. SURVEY</strong></p> <p>- survey.pdf: A pdf-print of the google form that implemented the online survey. Text is in German; for translation see article.</p> <p><strong>B. IMAGE PROCESSING AND STIMULUS PRODUCTION: </strong></p> <p>- dressmaker.m: Matlab function that maps the color distribution of new images onto the major hue dimension (principal component of chromaticities) of #theDress; according to the study, the resulting images yield individual differences similar to #theDress. Run without input to see the example from Figure 1 (for this, dressmaker.m needs to be in the same folder as image.mat).</p> <p>- image.mat: A Matlab data file that contains the original images and masks that distinguish the objects in the images from their background. The images and their mask are used as input to dressmaker.m to create the stimulus images used in the study.</p> <p>- example_dressmaking.m: Matlab script that illustrates how dressmaker.m can be used with the 5 new images used in the study and provided by images.mat. Of course, the function can be used with still other images...</p> <p><strong>C. DATA</strong></p> <p>- data.xlsx consists of seven data sheets. The first six provide data from the lab experiment, seperatly for #theDress, the tie, jacket, egg, fish, and peep hole. The last sheet contains the data from the online survey.</p> <p><strong>For details see readme.pdf.</strong></p>
Experimental Data for "What Makes a Top-Performing Precision Medicine Search Engine? Tracing Main System Features in a Systematic Way" at SIGIR2020
<p>This deposit contains data used for the experiments reported in the paper "<a href="https://doi.org/10.1145/3397271.3401048">What Makes a Top-Performing Precision Medicine Search Engine? Tracing Main System Features in a Systematic Way</a>", most notably the ElasticSearch 5.4 indices used for the reported experiments.</p> <p>To load the indices into an ElasticSearch cluster of your own, use the restore function described in the <a href="https://www.elastic.co/guide/en/elasticsearch/reference/5.4/modules-snapshots.html">ElasticSearch documentation</a>.</p> <p>The names of the index snapshots contained here are</p> <ul> <li>ct1718 for the indexed ClinicalTrials data used in the TREC-PM challenges in <a href="http://www.trec-cds.org/2017.html">2017</a> and <a href="http://www.trec-cds.org/2018.html">2018</a>.</li> <li>ct19 for the indexed ClinicalTrials data used in the TREC-PM challenge in <a href="http://www.trec-cds.org/2019.html">2019</a>.</li> <li>ba1718 for the indexed PubMed data used in the TREC-PM challenges in <a href="http://www.trec-cds.org/2017.html">2017</a> and <a href="http://www.trec-cds.org/2018.html">2018</a>.</li> <li>ba19 for the indexed PubMed data used in the TREC-PM challenge in <a href="http://www.trec-cds.org/2019.html">2019</a>.</li> </ul> <p>The other file contains the original output that <a href="https://www.automl.org/automated-algorithm-design/algorithm-configuration/smac/">SMAC</a> wrote to disc during the parameter optimization process. There are directories for the biomedical abstracts (BA) and clinical trials (ct) and for each respective 10 fold cross validation split. Those file contain the exact parameter configurations and their evalation score (the infNDCG metric was used) in live-runXX.json files.</p> <p>The code to these files is located in <a href="https://zenodo.org/record/3856403">this Zenodo deposit</a>.</p>
Consistent patterns of distractor effects during decision making
The value of a third potential option or distractor can alter the way in which decisions are made between two other options. Two hypotheses have received empirical support: that a high value distractor improves the accuracy with which decisions between two other options are made and that it impairs accuracy. Recently, however, it has been argued that neither observation is replicable. Inspired by neuroimaging data showing that high value distractors have different impacts on prefrontal and parietal regions, we designed a dual route decision-making model that mimics the neural signals of these regions. Here we show in the dual route model and empirical data that both enhancement and impairment effects are robust phenomena but predominate in different parts of the decision space defined by the options' and the distractor's values. However, beyond these constraints, both effects co-exist under similar conditions. Moreover, both effects are robust and observable in six experiments.
The impact of learning opportunities on the development of learning and decision making: an experiment with passerine birds
<p>Learning abilities have been shown to be influenced by the developmental context, namely through experiments that imposed severe nutritional and/or environmental constraints (i.e. lack of enrichment). In contrast, we know little on the impact of opportunities for learning on the development of cognition in animals, despite that such opportunities are known to influence human cognitive development. We exposed young zebra finches (<i>Taenopygia guttata</i>) (n=26) to one of three experimental conditions, i.e. an environment where (i) the presence of food was predicted by one colour cue (associative learning), (ii) a combination of two-colour cues (conditional learning), or (iii) colour cues were non-informative (control). After conducting two different discrimination tasks, our results show that experience with predictive cues can cause increased choice accuracy and decision-making speed. Our first learning task showed that<span> individuals in the associative treatment outperformed the control treatment, while task 2 showed that individuals in the conditional treatment shad shorter latencies when making choices compared to the control treatment.</span> We found no support for a speed-accuracy trade-off. This dataset provides a rare longitudinal and experimental examination of the effect of predictive vs non-predictive cues during development on the cognition of adult animals.</p>
Evidence for two main domestication trajectories in Saccharomyces cerevisiae linked to distinct bread-making processes
<p>Data and code supporting the manuscript "Evidence for two main domestication trajectories in <em>Saccharomyces cerevisiae</em> linked to distinct bread-making processes" by Bigey et al. (2020)</p>
Traces of Gradle and Make builds
<p>This is the benchmark accompanied the OOPSlA'20 paper "A Model for Detecting Faults in Build Specification".</p>
Data from: Great spotted cuckoo eggshell microstructure characteristics can make eggs stronger
Obligate avian brood parasites lay stronger eggs than their hosts or non-parasitic relatives because they are rounder and have a thicker eggshell. Additionally, some other characteristics of the brood parasitic eggshells related to their microstructure such as size and orientation of calcite crystal units could also contribute to generating even stronger shells. An eggshell microstructure formed by small randomly oriented calcite crystal units can increase the robustness of the eggshells of birds. Here, the eggshell microstructure of avian brood parasites as well as their hosts have been characterized in detail, using X-ray diffraction analyses to estimate the size and degree of orientation of calcite crystal units making the eggshell. Specifically, the brood parasitic great spotted cuckoo (Clamator glandarius) and two hosts (jackdaws, Corvus monedula and magpie, Pica pica) and one non-host species (the pigeon, Columba livia domestica) were considered. Calcite crystal of the eggshell of the brood parasitic species was smaller and more randomly oriented than those of the eggshells of non-parasitic species, which suggest that eggshell microstructure would contribute to explain why parasitic eggs are more resistant to breakage than those of their hosts.
A courtship behavior that makes monandrous females polyandrous
Females of many animal species mate several times with different males (polyandry), whereas females of some species mate with a single male (monandry) only once. Little is known about the mechanisms by which these different mating systems evolve. Females of <i>Drosophila prolongata</i> mate serially, unlike <i>D. melanogaster</i> females that refuse to remate for several days after their first mating (remating suppression, RS). Nevertheless, interestingly, non-virgin <i>D. prolongata</i> females refuse to remate with males that are prohibited from performing their species-specific courtship behavior, leg vibration (LV), suggesting that LV overrides RS making it cryptic in <i>D. prolongata</i>. In this study, we examined how long this cryptic RS persists. Surprisingly, it was sustained for at least two weeks, showing that RS is substantially augmented in <i>D. prolongata</i> compared to that of <i>D. melanogaster</i>. The two most closely related species to <i>D. prolongata</i>, <i>D. rhopaloa</i> and <i>D. carrolli</i>, do not perform LV and showed augmented RS, supporting the idea that augmented RS could have evolved before LV was acquired. These results suggested that <i>D. prolongata</i> females are intrinsically monandrous, whereas the newly evolved courtship behavior makes them polyandrous. This is a rare case in which a proximate mechanism of polyandry evolution from monandry is demonstrated.
Data from: A circuit mechanism for decision making biases and NMDA receptor hypofunction
<table> <tbody> <tr> <td>Decision-making biases can be features of normal behaviour, or deficits underlying neuropsychiatric symptoms. We used behavioural psychophysics, spiking-circuit modelling and pharmacological manipulations to explore decision-making biases during evidence integration. Monkeys showed a pro-variance bias (PVB): a preference to choose options with more variable evidence. The PVB was also present in a spiking circuit model, revealing a potential neural mechanism for this behaviour. To model possible effects of NMDA receptor (NMDA-R) antagonism on this behaviour, we simulated the effects of NMDA-R hypofunction onto either excitatory or inhibitory neurons in the model. These were then tested experimentally using the NMDA-R antagonist ketamine, a pharmacological model of schizophrenia. Ketamine yielded an increase in subjects' PVB consistent with lowered cortical excitation/inhibition balance from NMDA-R hypofunction predominantly onto excitatory neurons. These results provide a circuit-level mechanism that bridges across explanatory scales, from the synaptic to the behavioural, in neuropsychiatric disorders where decision-making biases are prominent.</td> </tr> <tr> </tr> </tbody> </table>
Raw fitness data (offspring number and weight), main dataset for manuscript: Female-specific resource limitation does not make the opportunity for selection more female biased
<p>The present dataset contains the entirety of the raw empirical data used in the manuscript entitled: "Female-specific resource limitation does not make the opportunity for selection more female biased". This data is composed of offspring count and weight, which represent proxys of fitness. Fitness was assessed for males and females independently, and across three different experimental treatments. These fitness measures are used to calculate the opportunity for selection, as the variance in realtive fitness. Detailed methods regarding data collection can be found in the main manuscript.</p>
Lee and Daunizeau choice data from: Trading mental effort for confidence in the metacognitive control of value-based decision-making
<p>Why do we carefully ponder some decisions, but not others? In this work, we derive a computational model of the metacognitive control of decisions or MCD. In brief, we assume that fast and automatic processes first provide an initial (and largely uncertain) representation of options' values, yielding prior estimates of decision difficulty. This uncertain value representation is then refined by deploying cognitive (e.g., attentional, mnesic) resources, the allocation of which is controlled by an effort-confidence tradeoff. Importantly, the anticipated benefit of allocating resources varies in a decision-by-decision manner according to the prior estimate of decision difficulty. The ensuing MCD model predicts choices, response time, subjective feeling of effort, choice confidence, and choice-induced preference change. We test these predictions in a systematic manner, using a dedicated behavioral paradigm. Our results provide a quantitative link between mental effort, choice confidence, and preference reversals, which could inform interpretations of related neuroimaging findings.</p>
Dataset of Correlation of clinical decision-making with probability of disease: A web-based study among general practitioners
<p>In databases we find the following information:</p> <p>- the true probability of the disease in the clinical vignette<br> - the probability of the disease estimated by the general practitioner (GP) in the clinical vignette<br> - the clinical decision of the general practitioner<br> - the baseline characteristics of the participants</p>
Making plasma science more open, collaborative, and reproducible
<p>The reproducibility crisis of modern science is the inability of scientists to reproduce roughly half of the results published in scientific journals. This crisis has affected a broad range of fields, such as psychology, chemistry, and oncology. While physicists tend to have high confidence that physics research is reproducible, no comprehensive studies have been performed to support or refute this claim. Nevertheless, the scientific, cultural, and institutional practices that contribute to the reproducibility crisis in other fields are also present in plasma science. This tutorial will describe how to implement best practices for scientific reproducibility into plasma research. The talk will begin by outlining sources of irreproducibility, such as cognitive biases, improper use of statistics, publication bias, closed access policies for data and software, and the reward system for modern academia. The talk will then describe remedies for these problems such as open access data policies; open metadata standards; open source software; training on proper use of statistics; pre-registration of research methodologies; independent methodological and statistical support; and valuing the reproducibility of research in tenure, hiring, and funding decisions.</p>
The choices we make and the impacts they have: Machine learning and species delimitation in North American box turtles (Terrapene spp.)
<p>Model-based approaches that attempt to delimit species are hampered by computational limitations as well as the unfortunate tendency by users to disregard algorithmic assumptions. Alternatives are clearly needed, and machine-learning (M-L) is attractive in this regard as it functions without the need to explicitly define a species concept. Unfortunately, its performance will vary according to which (of several) bioinformatic parameters are invoked. Herein, we gauge the effectiveness of M-L-based species-delimitation algorithms by parsing 64 variably-filtered versions of a ddRAD-derived SNP dataset involving North American box turtles (<i>Terrapene</i> spp.). Our filtering strategies included: (A) minor allele frequencies (MAF) of 5%, 3%, 1%, and 0% (=none), and (B) maximum missing data per-individual/per-population at 25%, 50%, 75%, and 100% (=none). We found that species-delimitation via unsupervised M-L impacted the signal-to-noise ratio in our data, as well as the discordance among resolved clades. The latter may also reflect biogeographic history, gene flow, incomplete lineage sorting, or combinations thereof (as corroborated from previously observed patterns of differential introgression). Our results substantiate M-L as a viable species-delimitation method, but also demonstrate how commonly observed patterns of phylogenetic discord can seriously impact M-L-classification.</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.