Find research datasets worth reusing

opencc-by-4.0Jun 2022View details →

Frequency dataset for "Profile-based measures of lexical variation. Four case studies on variation in word choice between Belgian and Netherlandic Dutch."

The dataset is structured according to: <ul> <li>the lexical field (CLOTHING, TRAFFIC, IT, and EMOTION);</li> <li>the part of speech (noun or adjective);</li> <li>the corpus;</li> <li>the concept;</li> <li>the term.</li> </ul> It first gives the absolute frequency as found in the corpus and also after it was disambiguated. The concept frequency and relative frequency is calculated based on the "disambiguated" absolute frequency. More information can be found in this dissertation: Daems, Jocelyne. 2022. Profile-based measures of lexical variation. Four case studies on variation in word choice between Belgian and Netherlandic Dutch. KU Leuven.

opencc-pddcJul 2022View details →

Dataset: The availability and completeness of open funder metadata - Case study for publications funded by the Dutch Research Council

Data and code belonging to the manuscript: The availability and completeness of open funder metadata - Case study for publications funded by the Dutch Research Council  Abstract: Research funders spend considerable efforts collecting information on outcomes of the research they fund. To help funders track publication output associated with their funding, Crossref initiated FundRef in 2013, enabling publishers to register funding information using persistent identifiers. However, it is hard to assess the coverage of funder metadata because it is unknown how many articles are the result of funded research and therefore should include funder metadata.  In this paper we looked at 5,004 publications reported by researchers to be the result of funding by a specific funding agency: the Dutch Research Council NWO. Only 67% of these articles contain funding information in Crossref, with a subset acknowledging NWO as funder name and/or Funder IDs linked to NWO (53% and 45%, respectively).  Web of Science (WoS), Scopus and Dimensions are all able to infer additional funding information from funding statements in the full text of the articles. Funding information in Lens largely corresponds to that in Crossref, with some additional funding information likely taken from PubMed.   We observe interesting differences between publishers in the coverage and completeness of funding metadata in Crossref compared to proprietary databases, highlighting potential to increase the quality of open metadata on funding.  This dataset contains the following files: <ul> <li>DOIs_unique_CR_Lens_Wos_Scopus_Dim.csv - Dataset of unique DOIs (n= 5,004) with collected information from Crossref and presence/absence of funder information in Lens, Web of Science, Scopus  and Dimensions </li> <li>NWO_funder_names_Crossref.txt - List of funder name variants for NWO found in Crossref</li> <li>Google_Apps_Script.js - Google Apps Script for retrieving information from Crossref and processing Dimensions results </li> <li>DOI_cleaning.R - R script for cleaning DOIs</li> </ul>

opencc-by-4.0Dec 2021View details →

MS2Query case study files

The raw data, consensus spectra and annotation by MS2Query for the case studies.

opencc-by-4.0Jul 2022View details →

An Empirical Evaluation of Competitive Programming AI: A Case Study of AlphaCode

Abstract AlphaCode, the code generation system by DeepMind, is an AI technology for assisting software developers in solving competitive programming problems using natural language problem descriptions. However, there is no existing work comparing AlphaCode-generated codes with human codes. In this paper, we conduct an empirical study to find code similarities and performance differences between AlphaCode-generated codes and human codes. We collect 44 generated codes in C++ and Python languages from AlphaCode official website that solve 22 problems on Codeforces. We then retrieve 31,736 human codes by using Codeforces API. The results show that (i) the generated code from AlphaCode and the human code is not similar (i.e., the similarity of 0.26 for both C++ and Python), however, the code fragments in the generated code are comprised of various human codes (i.e., uniqueness of 3.30\% and 8.94\% for C++ and Python respectively) and (ii) the generated code performs on par with or worse than the human code in terms of execution time and memory usage. Moreover, AlphaCode employs excessive nested loops and unnecessary variable declarations  (e.g., used \textit{long long} instead of \textit{int}), which causes a low performance regarding our manual investigation.

Trained models and code accompanying 'Downscaling using Deep Convolutional Autoencoders, a case study for South East Asia'

Trained models and code accompanying 'Downscaling using Deep Convolutional Autoencoders, a case study for South East Asia'.

opencc-by-4.0Jun 2022View details →

Datasets accompanying 'Downscaling using Deep Convolutional Autoencoders, a case study for South East Asia'

Datasets required to replicate the experiment described in the paper: 'Downscaling using Deep Convolutional Autoencoders, a case study for South East Asia' This includes NetCDF files used to generate training data and processed climate data for model training, trained models and outputs from model predictions. It also contains the datasets used for comparisons (CORDEX and CMIP6)

Species as conservation umbrellas: a case study with lesser prairie-chicken (Tympanuchus pallidicinctus) in the southern Great Plains of North America

Qualitative index of conservation benefit conferred by management for the lesser prairie chicken on non-target at-risk wildlife species.

Environmental Reconstructions Based on Aquatic and Terrestrial Snails Originating from the Early Bronze Age and the Late Islamic Period– A Stable Isotope Case Study from the Al-Khashbah Archaeological Site, Sultanate of Oman

Supplementary data for the article: "Environmental Reconstructions Based on Aquatic and Terrestrial Snails Originating from the Early Bronze Age and the Late Islamic Period– A Stable Isotope Case Study from the Al-Khashbah Archaeological Site, Sultanate of Oman"

opencc-by-4.0Nov 2022View details →

Anticipated versus Actual Effects of Platform Design Change: A Case Study of Twitter's Character Limit

The design of online platforms is both critically important and challenging, as any changes may lead to unintended consequences, and it can be hard to predict how users will react. Here we conduct a case study of a particularly important real-world platform design change: Twitter's decision to double the character limit from 140 to 280 characters to soothe users' need to "cram'' or  "squeeze'' their tweets, informed by modeling of historical user behavior. In our analysis, we contrast Twitter's anticipated pre-intervention predictions about user behavior with actual post-intervention user behavior: Did the platform design change lead to the intended user behavior shifts, or did a gap between anticipated and actual behavior emerge? Did different user groups react differently? We find that even though users do not "cram'' as much under 280 characters as they used to under 140 characters, emergent "cramming'' at the new limit seems to not have been taken into account when designing the platform change. Furthermore, investigating textual features, we find that, although post-intervention ``crammed'' tweets are longer, their syntactic and semantic characteristics remain similar and indicative of "squeezing''. Applying the same approach as Twitter policy-makers, we create updated counterfactual estimates and find that the character limit would need to be increased further to reduce cramming that re-emerged at the new limit. We contribute to the rich literature studying online user behavior with an empirical study that reveals a dynamic interaction between platform design and user behavior, with immediate policy and practical implications for the design of socio-technical systems.

Headache in workers. A matched case-control study

Data utilized for the study to be published

Data for 'Vast ecosystem disturbance in a warming climate may jeopardize our climate goal of reducing CO2: a case study for the megafires in Australian 'Black Summer''

These data support the manuscript 'Vast ecosystem disturbance in a warming climate may jeopardize our climate goal of reducing CO2 a case study for the megafires in Australian ‘Black Summer'', including megafire CO2 emissions  in Australian 'Black Summer' estimated by BBM model and a top-down method. The  delta RF simulations by GEOS-Chem RRTMG are also contained. In each separate folder there is a README.txt file as a user's guide. The methodology for deriving the datasets and more information can be found in the manuscript and SI.

Supplementary materials of the paper entitled: "Metamorphic Testing Meets Regression Testing: A Case Study of Scientific Software Maintenance"

Supplementary materials of the paper entitled: “Metamorphic Testing Meets Regression Testing: A Case Study of Scientific Software Maintenance” file01 - source code for detecting and comparing output relations of a given metamorphic relation file02 - interview transcripts and qualitative coding results file03 - system script for compiling SWMM, creating sSWMM simulation outputs, and logging execution time file04 - source code for SWMM 5.1.014 file05 - source code for SWMM 5.1.015 file06 - a suite of 40 regression tests (40 .inp files) file07 - result table for 760 cases (19 MRs × 40 .inp files) file08 - 491 automatically generated follow-up .inp files via reuse file09 - result table for mutation analysis file10 - output files for mutation analysis with metamorphic testing:         a. Original source output         b. Original follow-up output         c. Mutant source output         d. Mutant follow-up output

Integrative species delimitation reveals fine-scale allopatric speciation in a good-flying insect: A case study on Cylindera pseudocylindriformis complex (Coleoptera, Cicindelidae)

Alpha taxonomy is fundamental for many biological fields. Delineation of species boundary, however, can be challenging in a species complex, where different species share a similar morphology and diagnostic characters may not be available. In this context, integrative approaches that incorporate molecular and morphological data sets and account for speciation history can be helpful to alpha taxonomy. Different approaches to species delimitation based on different assumptions are complementary, and by integrating the results from multiple approaches we can generate a more reliable and objective taxonomic decision. In this study, we applied three molecular approaches to species delimitation and inferred the demographic history based on an isolation with migration model to test a morphologically based taxonomic hypothesis for the Cylindera pseudocylindriformis complex. We discuss the association between genetic divergence and microhabitat specialization, and we further corroborated that C. subtilis sp. nov. is a valid new species by integrating the results from model-based species delimitation and the genealogical divergence index. We argue that genetic endemism can form at a small geographic scale, even in a winged insect-like tiger beetle. Our results also indicated that there may still be undocumented species diversity of Taiwanese Cylindera remaining to be discovered.

opencc-by-4.0Sep 2022View details →

Supporting dataset: Towards the Optimal Representation of Sub-Grid Heterogeneity in Land Surface Models - Upper Colorado River Basin study case

Supporting files for the manuscript "Towards the Optimal Representation of Sub-Grid Heterogeneity in Land Surface Models - Upper Colorado River Basin study case." The dataset contains the ESCF derived from the original 800 HydroBlocks simulations used to train/test the random forest models (RFM) to compute the annual mean ESCFs for soil moisture content, sensible heat, latent heat, and runoff, as well as the obtained RFM to compute the resulting number of tiles for a given configuration over the study domain. Besides, the dataset includes the ESCFs for the quasi-fully distributed simulation (QFD) and the input data layers required to run HydroBlocks simulations over the study domain.

Data for: Social-ecological vulnerability of fishing communities to climate change: a U.S. West Coast case study

Climate change is already impacting coastal communities, and ongoing and future shifts in fisheries species productivity from climate change have implications for the livelihoods and cultures of coastal communities. Harvested marine species in the California Current Large Marine Ecosystem support U.S. West Coast communities economically, socially, and culturally. Ecological vulnerability assessments exist for individual species in the California Current but ecological and human vulnerability are linked and vulnerability is expected to vary by community. Here, we present automatable, reproducible methods for assessing the vulnerability of U.S. West Coast fishing-dependent communities to climate change within a social-ecological vulnerability framework. We first assessed the ecological risk of marine resources, on which fishing communities rely, to 50 years of climate change projections. We then combined this with the adaptive capacity of fishing communities, based on social indicators, to assess the potential ability of communities to cope with future changes. Specific communities (particularly in Washington state) were determined to be at risk to climate change mainly due to economic reliance on at risk marine fisheries species, like salmon, hake, or sea urchins. But, due to higher social adaptive capacity, these communities were often not found to be the most vulnerable overall. Conversely, certain communities that were not the most at risk, ecologically and economically, ranked in the category of highly vulnerable communities due to low adaptive capacity based on social indicators (particularly in Southern California). Certain communities were both ecologically at risk due to catch composition and socially vulnerable (low adaptive capacity) leading to the highest tier of vulnerability. The integration of climatic, ecological, economic, and societal data reveals that factors underlying vulnerability are variable across fishing communities on the U.S West Coast, and suggests the need to develop a variety of well-aligned strategies to adapt to the ecological impacts of climate change.

Effectiveness of seasonal malaria chemoprevention administered in a mass campaign in the Kedougou region of Senegal in 2016: a Case-control study

Context Seasonal malaria chemoprevention (SMC) with Sulfadoxine-Pyrimethamine plus Amodiaquine (SPAQ) is a malaria prevention strategy recommended since 2012 by the World Health Organization (WHO) for children under 5 years of age. In Senegal, the scaling up of the SMC has started since 2013 in the south-eastern regions of the country with an extension of the target to 10 years old children. The scaling up of SMC requires a regular evaluation of the strategy as recommended by the WHO. This study was conducted to evaluate the effectiveness of SMC. Methodology A case-control study was conducted in some villages of the health districts of Saraya and Kedougou in the Kedougou region from July to December 2016. A "case" was a sick child, aged 3 months to 10 years, seen in consultation and with a positive RDT. The "control" was a child of the same age group with a negative RDT and living in the same compound as the case or in a neighbouring compound. Each case was matched with two controls. Exposure to SMC was assessed by interviewing the mothers/caretakers and by checking the SMC administration card. Results A total of 492 children, including 164 cases and 328 controls, were recruited for our study. Their mean ages were 5.32 (+/- 2.15) and 4.44 (+/-2.25) years for the cases and the controls respectively. Male children predominated in both cases (55.49%) and controls (51.22%) (p=0.18). Net ownership was 85.80% among cases and 90.85% among controls (p=0.053). The proportion of controls who received SMC was higher than that of cases (98.17% vs 85.98%; (p=1.10-7)). The protective effectiveness of SMC was 89% (IC 95% = 84–93%) (OR=0.11). Conclusion SMC is therefore an effective strategy in the control of malaria in children. Case-control studies are a good approach for monitoring the efficacy of drugs administered during SMC.

opencc-zeroSep 2022View details →

Modeling the demography of species providing extended parental care: A capture-recapture approach with a case study on Polar Bears (Ursus maritimus)

1. In species providing extended parental care, one or both parents care for altricial young over a period including more than one breeding season. We expect large parental investment and long-term dependency within family units to cause high variability in life trajectories among individuals with complex consequences at the population level. So far, models for estimating demographic parameters in free-ranging animal populations mostly ignore extended parental care, thereby limiting our understanding of its consequences on parents and offspring life histories. 2. We designed a capture-recapture multi-event model for studying the demography of species providing extended parental care. It handles statistical multiple-year dependency among individual demographic parameters grouped within family units, variable litter size, and uncertainty on the timing at offspring independence. It allows for the evaluation of trade-offs among demographic parameters, the influence of past reproductive history on the caring parent's survival status, breeding probability and litter size probability, while accounting for imperfect detection of family units. We assess the model performance using simulated data, and illustrate its use with a long-term dataset collected on the Svalbard polar bears (Ursus maritimus). 3. Our model performed well in terms of bias and mean square error and in estimating demographic parameters in all simulated scenarios, both when offspring departure probability from the family unit occurred at a constant rate or varied during the field season depending on the date of capture. For the polar bear case study, we provide estimates of adult and dependent offspring survival rates, breeding probability and litter size probability. Results showed that the outcome of the previous reproduction influenced breeding probability. 4. Overall, our results show the importance of accounting for i) the multiple-year statistical dependency within family units, ii) uncertainty on the timing at offspring independence, and iii) past reproductive history of the caring parent. If ignored, estimates obtained for breeding probability, litter size, and survival can be biased. This is of interest in terms of conservation because species providing extended parental care are often long-living mammals vulnerable or threatened with extinction.

opencc-zeroSep 2022View details →

Data from: Exploring conflicts in whole genome phylogenetics: A case study within Manakins (Aves: Pipridae)

Some phylogenetic problems remain unresolved even when large amounts of sequence data are analyzed and methods that accommodate processes such as incomplete lineage sorting are employed. In addition to investigating biological sources of phylogenetic incongruence, it is also important to reduce noise in the phylogenomic dataset by using an appropriate filtering approach that addresses gene tree estimation errors. We present the results of a case study in manakins, focusing on the very difficult clade comprising the genera Antilophia and Chiroxiphia. Previous studies suggest that Antilophia is nested within Chiroxiphia, though relationships among Antilophia+Chiroxiphia species have been highly unstable. We extracted more than 11,000 loci (ultra-conserved elements and introns) from whole genomes and conducted analyses using concatenation and multi-species coalescent methods. Topologies resulting from analyses using all loci differed depending on the data type and analytical method, with two clades (Antilophia+Chiroxiphia and Manacus+Pipra+Machaeopterus) in the manakin tree showing incongruent results. We hypothesized that gene trees that conflicted with a long coalescent branch (e.g., the branch uniting Antilophia+Chiroxiphia) might be enriched for cases of gene tree estimation error, so we conducted analyses that either constrained those gene trees to include monophyly of Antilophia+Chiroxiphia or excluded these loci. While constraining trees reduced some incongruence, excluding the trees led to completely congruent species trees, regardless of the data type or model of sequence evolution used. We found that a suite of gene metrics (most importantly the number of informative sites and likelihood of intralocus recombination) collectively explained the loci that resulted in non-monophyly of Antilophia+Chiroxiphia. We also found evidence for introgression that may have contributed to the discordant topologies we observe in Antilophia+Chiroxiphia and led to deviations from expectations given the multi-species coalescent model. Our study highlights the importance of identifying factors that can obscure phylogenetic signal when dealing with recalcitrant phylogenetic problems, such as gene tree estimation error, incomplete lineage sorting and reticulation events.

opencc-by-4.0Sep 2022View details →

Data : Planktic-benthic foraminifera ratio (%P) as a tool for the reconstruction of paleobathymetry and geohazard: A case study from Taiwan

Details of the core sites used in this study, gear used for recovery, sediment horizon analyzed, coordinates,  water depth and foraminiferal data for the size fractions of >125 µm and >63 µm (only a subset of all the sites). Study sites are divided into East Taiwan that comprises the Southern Okinawa Trough (1), Nanao-Hoping-Hateruma Basins (2), and Taitung-Hualien (3). The area of West Taiwan is consisted of the Gaoping (4), Changchun sand Ridge (5), and Henghun Ridge (6) sectors. Gear for recovery are Box core (BC); Gravity core (GC) and Grab (G). Italic numbers in TOC column (in red) are average values, italic numbers in the Laboratory column show the laboratory where the TOC and C/N were analysed, namely Geosciences-NTU (1) , Institute of Oceanography-NTU (2) and National Sun-yat sen University (3). NaN= no available data.