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opencc-zeroDec 2022View details →

Supporting information for: The correct name for an Aquilegia (Ranunculaceae) hybrid of the parentage Aquilegia flavescens × A. formosa

Aquilegia x miniana (J.F.Macbr. & Payson) Cronk, hybr. & stat. nov. is the correct name for the hybrid Aquilegia flavescens S.Watson x A. formosa Fisch. ex DC. var. formosa. In 1916, Payson and Macbride, while exploring the mountains of Idaho, found populations of Aquilegia that were pink in flower colour and appeared intermediate between the yellow-flowered A. flavescens and red-flowered A. formosa. They named these plants A. flavescens var. miniana J.F.Macbr. & Payson. There has been uncertainty over whether their type collections (in GH, RM, MO, US, E, CM, CAS, NY) do indeed represent hybrids or pink-flowered morphs of A. flavescens. Using a Wells diagram, the holotype (in the Gray Herbarium of Harvard University) is shown to be intermediate, allowing its identification as a clear hybrid. However, some of the isotype material is indistinguishable from A. flavescens. The holotype matches material from British Columbia that has been determined as being of hybrid origin using molecular and morphological data. A. flavescens var. miniana J.F.Macbr. & Payson is, therefore, an available name for the hybrid, which is here raised to the status of hybrid binomial.

opencc-by-4.0Feb 2023View details →

Information integration for decision-making in desert locusts

Locust swarms can extend over hundred kilometers, and starvation compels this ancient pest to devour everything in its path. Theory suggests that gregarious behavior benefits foraging efficiency, yet the role of social cohesion remains elusive. To this end, we collected high-resolution trajectories of individual and grouped gregarious desert locusts in a 2-choice assay with patches of either similar or different quality. Carefully maintaining animals' identities allowed us to monitor each individual's experience and estimate the leaky accumulation process of personally-acquired and socially-derived evidence. We fitted data to a Bayesian model to gain insight into the decision-making system for patch selection. By disentangling the relative contribution of each information class, our study suggests that locusts balance incongruent evidence but reinforce congruent ones. We provide insight into the collective foraging decisions of social (but non-eusocial) insects and present locusts as a powerful empirical system to study individual choices and consequent collective dynamics.

opencc-by-4.0May 2022View details →

Field margins as substitute habitat for the conservation of birds in agricultural wetlands; Supplementary information

Supplementary material, dataset and script links to the research paper submit for recommendation by PCI Ecology.

opencc-zeroMar 2023View details →

Supporting Information: Measuring Functional Redundancy Using Generalized Hill Numbers

A number of metrics for quantifying the amount of functional redundancy in a community have been proposed over the years. Two of the most popular metrics are based on comparing a taxonomic diversity measure with a generalized form of the same measure that accounts for functional dissimilarities between taxa. These two metrics express redundancy as either an absolute or relative difference between the taxonomic diversity measure and its generalized form. Because they express the amount of redundancy in a community in terms of raw diversity values, both redundancy metrics are susceptible to the same issues that complicate the interpretation of most commonly used diversity indices. It is possible to overcome these issues by restating these two indices using a Hill numbers framework. As a growing number of authors have noted, these modified metrics provide a more intuitive quantitative definition of functional redundancy when used to rank communities. Beyond this intuitive definition, measuring redundancy in terms of Hill numbers allows researchers to control the influence of rare taxa on the output value, enabling ecologists to better predict how a community is expected to respond when exposed to an external perturbation that selectively eliminates rare or common taxa. Here I show that, of the two possible Hill number-based redundancy metrics, the form based on a popular absolute redundancy metric is extremely sensitive to differences in taxonomic diversity and can provide a misleading picture of how much redundancy is present in a community. For this reason, I argue that Hill number-based functional redundancy should be quantified using a relative metric that explicitly accounts for differences in effective taxonomic diversity. The proposed Hill number-based relative redundancy measure is shown to provide a much more complete picture of the distribution of redundant taxa within a community, highlighting subtle patterns that are completely missed by the Hill number-based absolute redundancy metric.

Supporting information for "Kinetics of CN(v=1) reactions with butadiene isomers at low temperature by cw-Cavity Ringdown in a pulsed Laval flow with theoretical modelling of rates and entrance channel branching

This file contains the master equation inputs for all the reactions studied, as well as all the details on stationary points and VRC-TST fluxes necessary to reproduce the simulations.

Supporting data for: Immersive information seeking - a scoping review of information seeking in virtual reality environments

Dataset that contains of all reviewed research items obtained for the Scoping Literature Review Immersive information seeking - a scoping review of information seeking in virtual reality environments.

CA Jobs Dataset: Comprehensive Job Count Information by Company - February, 2023

<a href="https://tarta.ai/open-data/datasets/number-of-jobs-by-company-in-CA-0223">This dataset</a> provides a comprehensive view of the job market, highlighting the companies and cities that have the highest number of job opportunities. The <a href="https://tarta.ai/open-data/datasets">Tarta.ai dataset</a> is a valuable resource for anyone interested in the job market and provides a comprehensive view of the employment landscape across different industries and regions. This dataset was created by Tarta.ai and contains information on the number of jobs by company and city in California, with features such as: • Company name • City • State • Number of active jobs

opencc-zeroMar 2023View details →

Information transfer in mammalian glycan-based communication

Glycan-binding proteins, so-called lectins, are exposed on mammalian cell surfaces and decipher the information encoded within glycans translating it into biochemical signal transduction pathways in the cell. These glycan-lectin communication pathways are complex and difficult to analyze. However, quantitative data with single -cell resolution provide means to disentangle the associated signaling cascades. We chose C-type lectin receptors (CTLs) expressed on immune cells as a model system to study their capacity to transmit information encoded in glycans of incoming particles. In particular, we used NF-κBnuclear factor kappa-B-reporter cell lines expressing DC-specific ICAM-3–grabbing nonintegrin (DC-SIGN)DC-SIGN, macrophage C-type lectin (MCL), dectin-1, dectin-2, and minclemacrophage-inducible C-type lectin (MINCLE), as well as TNFαR and TLR-1&2 in monocytic cell lines and compared their transmission of glycan-encoded information. All receptors did transmit information with similar signaling capacity, except dectin-2. This lectin was identified to be less efficient in information transmission compared to the other CTLs, and even while en the sensitivity of the dectin-2 pathway was enhanced by overexpression of its co-receptor FcRγ, its transmitted information was not. Next, we expanded our investigation towards the integration of multiple signal transduction pathways including synergistic lectins, which is crucial during pathogen recognition. We show how the signaling capacity of lectin receptors using a similar signal transduction pathway (dectin-1 and dectin-2) areis being integrated by compromising between the lectins. In contrast, co-expression of MCL synergistically enhanced the dectin-2 signaling capacity, particularly at low -glycan stimulant concentration. By using dectin-2 and other lectins as examples, we demonstrate how signaling capacity of dectin-2 is modulated in the presence of other lectins, and therefore, the findings provide insight into how immune cells translate glycan information using

Supporting information for "Incoming Neutron Flux Corrections for Cosmic-ray Soil and Snow Sensors Using the Global Neutron Monitor Network"

This dataset includes 2 files that represent supporting information for McJannet, D and Desilets, D (Submitted 2023)"Incoming Neutron Flux Corrections for Cosmic-ray Soil and Snow Sensors Using the Global Neutron Monitor Network" Water Resources Research. File 1 - Supporting Information 1 - Example calculation: Excel sheet showing demonstration calaculations using the neutron intensity correction described in the paper File 2 - Supporting information 2 - List of neutron moniotr stations used in the paper and acknowledgment of their contribtuion

opencc-by-4.0Feb 2023View details →

Probe Ranking Information - Supplementary Table 2

List of the 1096 genomic loci (ordered by the lowest corrected q-values) investigated in the study "Validation of differentially methylated DNA regions in precancerous colorectal lesions". Genome coordinates are based on the GRCh37/hg19 genome assembly.

Supplementary Online Content to "Alterity marking and enhancing accessibility in lexical borrowing: Meta-information techniques in the use of incipient anglicisms in French and Italian"

<ul> <li>Overview of newspaper articles analysed in Sections 4 and 5</li> <li>Sources of the newspaper articles</li> <li>Sample analyses of the use of meta-information techniques in F2 and I3</li> </ul>

Supporting material for PyESDv1.0.1 An open-source Python framework for empirical-statistical downscaling of climate information

The nature and severity of climate change impacts varies significantly from region to region. Consequently, high-resolution climate information is needed for meaningful impact assessments and the design of mitigation strategies. This demand has led to an increase in the coupling of Empirical Statistical Downscaling (ESD) models to General Circulation Model (GCM) simulations of future climate. Here, we present a new open-source Python package (pyESD; github.com/Dan-Boat/PyESD) that implements several Perfect Prognosis ESD (PP-ESD) methods and the whole downscaling cycle. The latter includes routines for data preparation, predictor selection and construction, model selection and training, evaluation, utility tools for relevant statistical tests, visualization, and more. The package includes a collection of well-established Machine Learning algorithms and allows the user to choose a variety of estimators, cross-validation schemes, objective function measures, hyperparameter optimization, etc., in relatively few lines of code. The package is highly modular and flexible and allows quick and reproducible downscaling of any climate information, such as precipitation, temperature, wind speed, or even glacial retreat. The dataset presented here serves as supporting material for the package description and evaluation manuscript

opencc-by-4.0Jul 2011View details →

Knowledge organization systems and their consequences for information retrieval

Traditionally, research on knowledge organization systems (KOS) and information retrieval discussed the relative advantages or disadvantages of using controlled vocabularies versus free-text or intellectual indexing versus automatic indexing methods for indexing and search. Experiments and case studies variously showed the superiority of either approach without reaching a final conclusion on this seemingly basic question. As full-text indexing has become more possible and now prevalent, the discussion of the relative merits of KOS – not only as substitute but in combination with full-text – was not settled but continued with new challenges. With the advent of the Semantic Web, KOS (now appearing as ontologies) became important tools in new information retrieval applications and were pushed once again to the research forefront. With different disciplines working in the field, the terminology around KOS has become more and more ambiguous up to the point that tracing research in the literature is difficult – ironically something that traditional KOS have always tried to mitigate. This paper summarizes recent discussions of the impact of KOS on information retrieval and attempts to show and unify different research strands from library science research on subject indexing, information retrieval and the Semantic Web. Whereas earlier impact studies on retrieval resulted in clearly measurable outcomes (for example changes in precision/recall), recent use of KOS in Semantic Web applications or other information systems has switched from pure search scenarios to exploration (browse) and contextualization, for which clear (and calculable) evaluation or quality standards and

opencc-by-4.0Apr 2023View details →

Supplementary material for 'The MAP metric in Information Retrieval Fault Localization'

<pre># map_bench4bl This is the supplementary material, data, and evaluation source code for the paper "The MAP metric in Information Retrieval Fault Localization" by Thomas Hirsch and Birgit Hofer. ## Preliminaries ### Python environment - Python 3.8 - pandas - numpy - matplotlib ## Datasets The [Bench4BL](https://github.com/exatoa/Bench4BL) dataset has been used in this evaluation, with the addition of intermediate files taken from the [SABL](http://dx.doi.org/10.5281/zenodo.4681242) experiment performed on this Bench4BL dataset. All data used in our evaluation is included in this repository. However, if the data is to be re-imported directly from these benchmark and datasets they have to be downloaded first and their local paths have to be set in [paths.py](paths.py). ### Bench4BL The Bench4BL dataset was published with the paper "Bench4BL: Reproducibility study on the performance of IR-based bug localization" by Lee, J., Kim, D., Bissyandé, T.F., Jung, W. and Le Traon, Y.. The dataset can be obtained [here](https://github.com/exatoa/Bench4BL). Follow the steps described in the corresponding [README](https://github.com/exatoa/Bench4BL/blob/master/README.md) to set up the dataset. The Bench4BL dataset contains the _old subjects_ subdataset, containing 558 bugs from AspectJ, JDT, PDE, SWT, and ZXing that have been widely used in older IRFL studies. This _old subjects_ subdataset was used in answering our RQ1, as discussed below, the corresponding scripts use _old subjects_ in their name to highlight this. #### SABL The SABL dataset is the online appendix of the paper "An Extensive Study of Smell-Aware Bug Localization" by TTakahashi, A., Sae-Lim, N., Hayashi, S. and Saeki, M.. The dataset can be downloaded [here](http://dx.doi.org/10.5281/zenodo.4681242). The experiments in this dataset build on top of Bench4BL and intermediate files are provided in the datapackage. #### Rankings Rankings for BLIA, BRTracer, and BugLocator were produced by running these tools on Bench4BL locally. Rankings for AmaLgam and BLUiR were taken from the SABL experiment dataset. ## Structure ### Folders Bench4BL ground truths: - bench4bl_old_subjects_summary - bench4bl_summary Localization results of the included tools in Bench4BL: - bench4bl_localization_results - bench4bl_localization_results_sabl Target projects size metrics: - cloc_results - cloc_results_old_subjects Utility functions: - utils Output folders containing results, generated figures and tables: - results - results_old_subjects ### Scripts Scripts for re-importing data from Bench4BL and SABL datasets: - data_preparation_step_1_cloc_bench4bl.py - data_preparation_step_1_cloc_old_subjects_bench4bl.py - data_preparation_step_2_import_ground_truth_from_bench4bl.py - data_preparation_step_2_import_ground_truth_from_old_subjects_bench4bl.py - data_preparation_step_3_import_bench4bl_ranking_results.py - data_preparation_step_3_import_sabl_ranking_results.py Utilities: - paths.py - utils/bench4bl_utils.py - utils/Logger.py ### Evaluation scripts for the corresponding research questions: **Dataset analysis:** - rq_0_dataset_analysis_bench4bl_issues.py **RQ1: How big is the average ground truth in Bench4BL datasets, and what proportion of bugs have a ground truth containing multiple files?** - rq_1_bench4bl_ground_truth_size.py - rq_1_old_subjects_bench4bl_ground_truth_size.py RQ2: Do the IRFL tools included in Bench4BL truncate their results? - rq_2_ranking_lengths.py **RQ3: How strong is $AP_{asrd}$ overestimating $AP_{mb}$ for truncated BugLocator retrieval results on the Bench4BL dataset? RQ3a: How strong is $AP_{asrd}$ overestimating $AP_{mb}$ for truncated BugLocator retrieval results when considering the bloated ground truth issue found in Bench4BL?** - rq_3_truncating_BugLocator_rankings_bench4bl.py **RQ3b: How strong is $AP_{asrd}$ overestimating $AP_{mb}$ for truncated BugLocator retrieval results when undefined $AP$ values are simply ignored?** - rq_3b_undefined_ap_BugLocator_rankings_bench4bl.py ## Licence All code and results are licensed under [CCA v4](https://creativecommons.org/licenses/by/4.0/), according to LICENSE file. Other licences may apply for some tools and datasets contained in this repo: [cloc-1.92.pl](https://github.com/AlDanial/cloc) under GPL v2, [Bench4BL](https://github.com/exatoa/Bench4BL) and [SABL](http://dx.doi.org/10.5281/zenodo.4681242) under CCA 4.0.</pre>

opencc-by-4.0Jul 2011View details →

How doctors apply semantic components to specify search in work-related information retrieval

Workplace searching is often context-specific and targets a ‘right answer’ within some domain-specific aspect of the search topic. We have developed the semantic component (SC) model that allows searchers to specify a search within context-specific aspects of the main topic of documents. The goal of our study was to gain insight into how family practice physicians at sundhed.dk, a national healthcare portal in Denmark, applied the SC model to formulate queries to solve work-related search tasks. The results showed that doctors used the model purposively when choosing search facets and search concepts. They were relatively consistent in their use. The findings provide promising evidence of the model’s potential usefulness.

opencc-by-4.0Apr 2023View details →

Bibliographic Information on PNAS Direct and Contributed Submissions

This dataset contains observations of 46,391 articles published as "Direct" or "Contributed" submissions in PNAS. Only includes publications in the Biological, Physical and Social Sciences sections. Variables: <ul> <li>extract_id: incremental ID</li> <li>topic: main section</li> <li>sub_label: labelled submission type</li> <li>pub_year: publication year</li> <li>review_time: number of days from the manuscript was received until it was accepted for publication</li> <li>ncs_full: The field normalised citation score, full counting</li> </ul> -

opencc-by-4.0Dec 2022View details →

Darbellay et al. Col2a1EGFP sensor supporting information

This upload is made in support of the Darbellay et al. Col2a1EGFP sensor manuscript. It contains the following files: Customized genome and index, based on GRCm39/mm39 <ul> <li>mm39_eGFP_SV40pA.fa</li> <li>mm39_eGFP_SV40pA.fa.fai</li> </ul> Customized references file used for gene expression quantification, based on GRCm39.104 <ul> <li>mergeOverlapGenesOfFilteredTranscriptsOfMus_musculus.GRCm39.104_ExonsOnly_UCSC.gtf</li> </ul> See Darbellay et al. Material & Methods for detailed explanations. Scripts used to generate the customized gtf file are available <a href="https://github.com/lldelisle/toolBoxForMutantAndWTGenomes/tree/5368aecec9b406d8e29f22331a3d7e51b6c4e5c8/scripts">here</a>.

opencc-zeroApr 2023View details →

Data for: Uncertainty about old information results in differential predator memory in tadpoles

As information ages, it may become less accurate, resulting in increased uncertainty for decision-makers. For example, chemical alarm cues are a source of public information about a nearby predator attack, and these cues can become spatially inaccurate through time. These cues can also degrade quickly under natural conditions, and cue receivers are sensitive to such degradation. Although numerous studies have documented predator-recognition learning from fresh alarm cues, no studies have explored learning from aged alarm cues and whether the uncertainty associated with this older information contributes to shortening the retention of learned responses (i.e., the 'memory window'). Here, we found that wood frog tadpoles, Lithobates sylvaticus, learned to recognize a novel odour as a predator when paired with alarm cues aged under natural conditions for up to one hour. However, only tadpoles conditioned with fresh alarm cues were found to retain this learned response when tested 9 days after conditioning. These results support the hypothesis that the memory window is shortened by the uncertainty associated with older information, preventing the long-term costs of a learned association that was based on potentially outdated information.

opencc-by-4.0Apr 2023View details →

Supplementary materials for Education and Information Technologies

Anonymized supplementary materials for publication 'Using Data Clustering to Reveal Trainees’ Behavior \\in Cybersecurity Education' in the journal Education and Information Technologies