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published: 2019-07-26
Data used in paper published in the Journal of Applied Ecology titled " Bee diversity in tallgrass prairies affected by management and its effects on above- and below-ground resources" Bee Community file contains info on bees sampled in each site. The first column contain the Tallgrass Prairie Sites sampled all additional columns contain the bee species name in the first row and all individuals recorded. Plant Community file contains info on plants sampled in each site. The first column contain the Tallgrass Prairie Sites sampled all additional columns contain the plant species name in the first row and all individuals recorded. Soil PC1 file contains the soil PC1 values used in the analyses. The first column contain the Tallgrass Prairie Sites sampled, the second column contains the calculated soil PC1 values.
keywords: bee; community; tallgrass prairie; grazing
published: 2019-07-08
# Overview These datasets were created in conjunction with the dissertation "Predicting Controlled Vocabulary Based on Text and Citations: Case Studies in Medical Subject Headings in MEDLINE and Patents," by Adam Kehoe. The datasets consist of the following: * twin_not_abstract_matched_complete.tsv: a tab-delimited file consisting of pairs of MEDLINE articles with identical titles, authors and years of publication. This file contains the PMIDs of the duplicate publications, as well as their medical subject headings (MeSH) and three measures of their indexing consistency. * twin_abstract_matched_complete.tsv: the same as above, except that the MEDLINE articles also have matching abstracts. * mesh_training_data.csv: a comma-separated file containing the training data for the model discussed in the dissertation. * mesh_scores.tsv: a tab-delimited file containing a pairwise similarity score based on word embeddings, and MeSH hierarchy relationship. ## Duplicate MEDLINE Publications Both the twin_not_abstract_matched_complete.tsv and twin_abstract_matched_complete.tsv have the same structure. They have the following columns: 1. pmid_one: the PubMed unique identifier of the first paper 2. pmid_two: the PubMed unique identifier of the second paper 3. mesh_one: A list of medical subject headings (MeSH) from the first paper, delimited by the "|" character 4. mesh_two: a list of medical subject headings from the second paper, delimited by the "|" character 5. hoopers_consistency: The calculation of Hooper's consistency between the MeSH of the first and second paper 6. nonhierarchicalfree: a word embedding based consistency score described in the dissertation 7. hierarchicalfree: a word embedding based consistency score additionally limited by the MeSH hierarchy, described in the dissertation. ## MeSH Training Data The mesh_training_data.csv file contains the training data for the model discussed in the dissertation. It has the following columns: 1. pmid: the PubMed unique identifier of the paper 2. term: a candidate MeSH term 3. cit_count: the log of the frequency of the term in the citation candidate set 4. total_cit: the log of the total number the paper's citations 5. citr_count: the log of the frequency of the term in the citations of the paper's citations 6. total_citofcit: the log of the total number of the citations of the paper's citations 7. absim_count: the log of the frequency of the term in the AbSim candidate set 8. total_absim_count: the log of the total number of AbSim records for the paper 9. absimr_count: the log of the frequency of the term in the citations of the AbSim records 10. total_absimr_count: the log of the total number of citations of the AbSim record 11. log_medline_frequency: the log of the frequency of the candidate term in MEDLINE. 12. relevance: a binary indicator (True/False) if the candidate term was assigned to the target paper ## Cosine Similarity The mesh_scores.tsv file contains a pairwise list of all MeSH terms including their cosine similarity based on the word embedding described in the dissertation. Because the MeSH hierarchy is also used in many of the evaluation measures, the relationship of the term pair is also included. It has the following columns: 1. mesh_one: a string of the first MeSH heading. 2. mesh_two: a string of the second MeSH heading. 3. cosine_similarity: the cosine similarity between the terms 4. relationship_type: a string identifying the relationship type, consisting of none, parent/child, sibling, ancestor and direct (terms are identical, i.e. a direct hierarchy match). The mesh_model.bin file contains a binary word2vec C format file containing the MeSH term embeddings. It was generated using version 3.7.2 of the Python gensim library (https://radimrehurek.com/gensim/). For an example of how to load the model file, see https://radimrehurek.com/gensim/models/word2vec.html#usage-examples, specifically the directions for loading the "word2vec C format."
keywords: MEDLINE;MeSH;Medical Subject Headings;Indexing
published: 2019-07-08
Wikipedia category tree embeddings based on wikipedia SQL dump dated 2017-09-20 (<a href="https://archive.org/download/enwiki-20170920">https://archive.org/download/enwiki-20170920</a>) created using the following algorithms: * Node2vec * Poincare embedding * Elmo model on the category title The following files are present: * wiki_cat_elmo.txt.gz (15G) - Elmo embeddings. Format: category_name (space replaced with "_") <tab> 300 dim space separated embedding. * wiki_cat_elmo.txt.w2v.gz (15G) - Elmo embeddings. Format: word2vec format can be loaded using Gensin Word2VecKeyedVector.load_word2vec_format. * elmo_keyedvectors.tar.gz - Gensim Word2VecKeyedVector format of Elmo embeddings. Nodes are indexed using * node2vec.tar.gz (3.4G) - Gensim word2vec model which has node2vec embedding for each category identified using the position (starting from 0) in category.txt * poincare.tar.gz (1.8G) - Gensim poincare embedding model which has poincare embedding for each category identified using the position (starting from 0) in category.txt * wiki_category_random_walks.txt.gz (1.5G) - Random walks generated by node2vec algorithm (https://github.com/aditya-grover/node2vec/tree/master/node2vec_spark), each category identified using the position (starting from 0) in category.txt * categories.txt - One category name per line (with spaces). The line number (starting from 0) is used as category ID in many other files. * category_edges.txt - Category edges based on category names (with spaces). Format from_category <tab> to_category * category_edges_ids.txt - Category edges based on category ids, each category identified using the position (starting from 1) in category.txt * wiki_cats-G.json - NetworkX format of category graph, each category identified using the position (starting from 1) in category.txt Software used: * <a href="https://github.com/napsternxg/WikiUtils">https://github.com/napsternxg/WikiUtils</a> - Processing sql dumps * <a href="https://github.com/napsternxg/node2vec">https://github.com/napsternxg/node2vec</a> - Generate random walks for node2vec * <a href="https://github.com/RaRe-Technologies/gensim">https://github.com/RaRe-Technologies/gensim</a> (version 3.4.0) - generating node2vec embeddings from random walks generated usinde node2vec algorithm * <a href="https://github.com/allenai/allennlp">https://github.com/allenai/allennlp</a> (version 0.8.2) - Generate elmo embeddings for each category title Code used: * wiki_cat_node2vec_commands.sh - Commands used to * wiki_cat_generate_elmo_embeddings.py - generate elmo embeddings * wiki_cat_poincare_embedding.py - generate poincare embeddings
keywords: Wikipedia; Wikipedia Category Tree; Embeddings; Elmo; Node2Vec; Poincare;
published: 2019-07-11
We studied the effect of windstorm disturbance on forest invasive plants in southern Illinois. This data includes raw data on plant abundance at survey points, compiled data used in statistical analyses, and spatial data for surveyed plots and units. This file package also includes a readme.doc file that describes the data in detail, including attribute descriptions.
keywords: tornado, blowdowns, derecho, invasive plants, Shawnee National Forest, southern Illinois
published: 2019-06-22
keywords: conspecific attraction; fruit-eating bird; Hawaiian flora; playback experiment; seed dispersal; social information; Zosterops japonicas
published: 2019-07-08
These files contain the data presented in the manuscript entitles "Iron redox reactions can drive microtopographic variation in upland soil carbon dioxide and nitrous oxide emissions".
keywords: Iron; redox; carbon dioxide; nitrous oxide; chemodenitrification; Feammox; dissimilatory iron reduction; upland soils; flooding; global change
published: 2019-06-12
The data set contains Supplemental data sets for the Manuscript entitled "Where are they hiding? Testing the body snatchers hypothesis in pyrophilous fungi." Environmental sampling: Amplification of nuclear DNA regions (ITS1 and ITS2) were completed using the Fluidigm Access Array and the resulting amplicons were sequenced on an Illumina MiSeq v2 platform runs using rapid 2 × 250 nt paired-end reads. Illumina sequencing run amplicons that were size selected into <500nt and >500nt sub-pools, then remixed together <500nt: >500nt by nM concentration in a 1x:3x proportion. All amplification and sequencing steps were performed at the Roy J. Carver Biotechnology Center at the University of Illinois Urbana-Champaign. ITS1 region primers consisted of ITS1F (5'-CTTGGTCATTTAGAGGAAGTAA-'3) and ITS2 (5'-GCTGCGTTCTTCATCGATGC-'3). ITS2 region primers consisted of fITS7 (5'-GTGARTCATCGAATCTTTG-'3) and ITS4 (5'-TCCTCCGCTTATTGATATGC-'3). Supplemental files 1 through 5 contain the raw data files. Supplemental 1 is the ITS1 Illumina MiSeq forward reads and Supplemental 2 is the corresponding index files. Supplemental 3 is the ITS2 Illumina MiSeq forward reads and Supplemental 4 is the corresponding index files. Supplemental 5 is the map file needed to process the forward reads and index files in QIIME. Supplemental 6 and 7 contain the resulting QIIME 1.9.1. OTU tables along with UNITE, NCBI, and CONSTAX taxonomic assignments in addition to the representative OTU sequence. Numeric samples within the OTU tables correspond to the following: 1 Brachythecium sp. 2 Usnea cornuta 3 Dicranum sp. 4 Leucodon julaceus 5 Lobaria quercizans 6 Rhizomnium sp. 7 Dicranum sp. 8 Thuidium delicatulum 9 Myelochroa aurulenta 10 Atrichum angustatum 11 Dicranum sp. 12 Hypnum sp. 13 Atrichum angustatum 14 Hypnum sp. 15 Thuidium delicatulum 16 Leucobryum sp. 17 Polytrichum commune 18 Atrichum angustatum 19 Atrichum angustatum 20 Atrichum crispulum 21 Bryaceae 22 Leucobryum sp. 23 Conocephalum conicum 24 Climacium americanum 25 Atrichum angustatum 26 Huperzia serrata 27 Polytrichum commune 28 Diphasiastrum sp. 29 Anomodon attenuatus 30 Bryoandersonia sp. 31 Polytrichum commune 32 Thuidium delicatulum 33 Brachythecium sp. 34 Leucobryum glaucum 35 Bryoandersonia sp. 36 Anomodon attenuatus 37 Pohlia sp. 38 Cinclidium sp. 39 Hylocomium splendens 40 Polytrichum commune 41 negative control 42 Soil 43 Soil 44 Soil 45 Soil 46 Soil 47 Soil If a sample number is not present within the OTU table; either no sequences were obtained or no sequences passed the quality filtering step in QIIME. Supplemental 8 contains the Summary of unique species per location.
published: 2019-06-13
This lexicon is the expanded/enhanced version of the Moral Foundation Dictionary created by Graham and colleagues (Graham et al., 2013). Our Enhanced Morality Lexicon (EML) contains a list of 4,636 morality related words. This lexicon was used in the following paper - please cite this paper if you use this resource in your work. Rezapour, R., Shah, S., & Diesner, J. (2019). Enhancing the measurement of social effects by capturing morality. Proceedings of the 10th Workshop on Computational Approaches to Subjectivity, Sentiment and Social Media Analysis (WASSA). Annual Conference of the North American Chapter of the Association for Computational Linguistics (NAACL), Minneapolis, MN. In addition, please consider citing the original MFD paper: <a href="https://doi.org/10.1016/B978-0-12-407236-7.00002-4">Graham, J., Haidt, J., Koleva, S., Motyl, M., Iyer, R., Wojcik, S. P., & Ditto, P. H. (2013). Moral foundations theory: The pragmatic validity of moral pluralism. In Advances in experimental social psychology (Vol. 47, pp. 55-130)</a>.
keywords: lexicon; morality
published: 2018-06-05
A complete building coverage area dataset (i.e. area occupied by building structures, excluding other built surfaces such as roads, parking lots, and public parks) at the level of census block groups for the contiguous United States (CONUS). The dataset was assembled based on an ensemble prediction of nonlinear hierarchical models to account for spatial heterogeneities in the distribution of built surfaces across different urban communities. Percentage of impervious land and housing density were used as predictors of the estimated area of buildings and cross-validation results showed that the product estimated area represented by buildings with a mean error of 0.049 %.
keywords: Building Coverage Area; Urban Geography; Regional; Sustainability; US Census Block Groups; CONUS Data
published: 2018-12-31
Sixty undergraduate STEM lecture classes were observed across 14 departments at the University of Illinois Urbana-Champaign in 2015 and 2016. We selected the classes to observe using purposive sampling techniques with the objectives of (1) collecting classroom observations that were representative of the STEM courses offered; (2) conducting observations on non-test, typical class days; and (3) comparing these classroom observations using the Class Observation Protocol for Undergraduate STEM (COPUS) to record the presence and frequency of active learning practices utilized by Community of Practice (CoP) and non-CoP instructors. Decimal values are the result of combined observations. All COPUS codes listed are from Smith (2013) "The Classroom Observation Protocol for Undergraduate STEM (COPUS): A New Instrument to Characterize STEM Classroom Practices" paper. For more information on the data collection process, see "Evidence that communities of practice are associated with active learning in large STEM lectures" by Tomkin et. al. (2019) in the International Journal of STEM Education.
keywords: COPUS, Community of Practice
published: 2019-06-03
This dataset contains raw data associated with the red fox Y-chromosome assembly (see https://doi.org/10.3390/genes10060409). It includes a fasta file of the 171 scaffolds from the red fox reference genome assembly identified as likely to contain Y-chromosome sequence, the raw BLAST results, and the ABySS assemblies described in the manuscript.
keywords: Y-chromosome; carnivore; Vulpes vulpes; sex chromosomes; MSY; Y-chromosome genes; copy-number variation; BCORY2; UBE1Y; next-generation sequencing
published: 2019-05-31
The data are provided to illustrate methods in evaluating systematic transactional data reuse in machine learning. A library account-based recommender system was developed using machine learning processing over transactional data of 383,828 transactions (or check-outs) sourced from a large multi-unit research library. The machine learning process utilized the FP-growth algorithm over the subject metadata associated with physical items that were checked-out together in the library. The purpose of this research is to evaluate the results of systematic transactional data reuse in machine learning. The analysis herein contains a large-scale network visualization of 180,441 subject association rules and corresponding node metrics.
keywords: evaluating machine learning; network science; FP-growth; WEKA; Gephi; personalization; recommender systems
published: 2019-05-31
This dataset includes all data presented in the manuscript entitled: "Dynamic controls on field-scale soil nitrous oxide hot spots and hot moments across a microtopographic gradient"
keywords: denitrification; depressions; microtopography; nitrous oxide; soil oxygen; soil temperature
published: 2019-05-07
Data set of trophic cascade in mesocosms experiments for zooplankton (biomass and body size) and phytoplankton (chlorophyll a concentration) caused by Bluegill as well as zooplankton production in those same treatment groups. Zooplankton were collected by tube sampler and phytoplankton were collected through grab samples.
keywords: Trophic cascades; size-selective predation; compensatory mechanisms; biomanipulation; invasive fish; Daphnia; Moina
published: 2019-05-10
Data necessary for production of figures presented in "Efficient enzyme coupling algorithms identify functional pathways in genome-scale metabolic models" by Pradhan et al.
keywords: Efficient enzyme coupling algorithms identify functional pathways in genome-scale metabolic models;
published: 2019-05-16
The associated data sets include information on stable isotopes from organic matter sources in high elevation lakes, the percentage of production assimilated from the different sources of organic matter, and the relationship between different metrics for trophic position and environmental variables.
keywords: Stable isotopes; macroinvertebrate production; trophic position
published: 2018-11-20
A dataset of acoustic impulse responses for microphones worn on the body. Microphones were placed at 80 positions on the body of a human subject and a plastic mannequin. The impulse responses can be used to study the acoustic effects of the body and can be convolved with sound sources to simulate wearable audio devices and microphone arrays. The dataset also includes measurements with different articles of clothing covering some of the microphones and with microphones placed on different hats and accessories. The measurements were performed from 24 angles of arrival in an acoustically treated laboratory. Related Paper: Ryan M. Corey, Naoki Tsuda, and Andrew C. Singer. "Acoustic Impulse Responses for Wearable Audio Devices," IEEE International Conference on Acoustics, Speech, and Signal Processing (ICASSP), Brighton, UK, May 2019. All impulse responses are sampled at 48 kHz and truncated to 500 ms. The impulse response data is provided in WAVE audio and MATLAB data file formats. The microphone locations are provided in tab-separated-value files for each experiment and are also depicted graphically in the documentation. The file wearable_mic_dataset_full.zip contains both WAVE- and MATLAB-format impulse responses. The file wearable_mic_dataset_matlab.zip contains only MATLAB-format impulse responses. The file wearable_mic_dataset_wave.zip contains only WAVE-format impulse responses.
keywords: Acoustic impulse responses; microphone arrays; wearables; hearing aids; audio source separation
published: 2019-05-22
This is the experimental data of isolated nanomagnet islands with or without the presence of large nanomagnet islands. The small islands are made of Permalloy materials with size of 170 nm by 470 nm by 2.5 nm. The systems are measured at a temperature where the small islands are fluctuating around room temperature. The data is recorded as photoemission electron microscopy intensity. More details about the data can be found in the note.txt and Spe_2016.xlsx file. Note: The raw data folders are stored in five volumes during the compression. All five volumes are needed in order to recover the original folder.
keywords: artificial spin ice; magnetism
published: 2019-05-20
This is the experimental data of tetris artificial spin ice. The islands are made of Permalloy materials with size of 170 nm by 470 nm by 2.5 nm. The systems are measured at a temperature where the islands are fluctuating around room temperature. The data is recorded as photoemission electron microscopy intensity. More details about the dataset can be found in the file Note.txt and Tetris_data_list.xlsx Note: 2 files name bl11_teris600_033 and bl11_tetris600_2_135 are not recorded in the excel sheet because they are corrupted during the measurement. Any data that is not recorded in the excel sheet is either corrupted or of low quality. From files *_028 to *_049, tetris is spelled with “t” while in the raw data folder without “t”. This is a typo. Throughout the dataset, tetris and teris are supposed to have the same meaning.
keywords: artificial spin ice
published: 2019-05-16
This repository includes scripts and datasets for the paper, "Statistically consistent divide-and-conquer pipelines for phylogeny estimation using NJMerge." All data files in this repository are for analyses using the logdet distance matrix computed on the concatenated alignment. Data files for analyses using the average gene-tree internode distance matrix can be downloaded from the Illinois Data Bank (https://doi.org/10.13012/B2IDB-1424746_V1). The latest version of NJMerge can be downloaded from Github (https://github.com/ekmolloy/njmerge).<br /> <strong>List of Changes:</strong> &bull; Updated timings for NJMerge pipelines to include the time required to estimate distance matrices; this impacted files in the following folder: <strong>data.zip</strong> &bull; Replaced "Robinson-Foulds" distance with "Symmetric Difference"; this impacted files in the following folders: <strong> tools.zip; data.zip; scripts.zip</strong> &bull; Added some additional information about the java command used to run ASTRAL-III; this impacted files in the following folders: <strong>data.zip; astral64-trees.tar.gz (new)</strong>
keywords: divide-and-conquer; statistical consistency; species trees; incomplete lineage sorting; phylogenomics
published: 2019-05-01
This dataset contains scripts and data developed as a part of the research manuscript titled “Spatial and Temporal Allocation of Ammonia Emissions from Fertilizer Application Important for Air Quality Predictions in U.S. Corn Belt”. This includes (1) Spatial and temporal factors for ammonia emissions from agricultural fertilizer usage developed using the hybrid ISS-DNDC method for the Midwest U.S., (2) CAMx job scripts and outputs of predictions of ambient ammonia and total and speciated PM2.5, (3) Observation data used to statistically evaluate CAMx predictions, and (4) MATLAB programs developed to pair CAMx predictions with ground-based observation data in space and time.
keywords: Air quality; Ammonia; Emissions; PM2.5; CAMx; DNDC; spatial resolution; Midwest U.S.
published: 2019-04-05
File Name: Inclusion_Criteria_Annotation.csv Data Preparation: Xiaoru Dong Date of Preparation: 2019-04-04 Data Contributions: Jingyi Xie, Xiaoru Dong, Linh Hoang Data Source: Cochrane systematic reviews published up to January 3, 2018 by 52 different Cochrane groups in 8 Cochrane group networks. Associated Manuscript authors: Xiaoru Dong, Jingyi Xie, Linh Hoang, and Jodi Schneider. Associated Manuscript, Working title: Machine classification of inclusion criteria from Cochrane systematic reviews. Description: The file contains lists of inclusion criteria of Cochrane Systematic Reviews and the manual annotation results. 5420 inclusion criteria were annotated, out of 7158 inclusion criteria available. Annotations are either "Only RCTs" or "Others". There are 2 columns in the file: - "Inclusion Criteria": Content of inclusion criteria of Cochrane Systematic Reviews. - "Only RCTs": Manual Annotation results. In which, "x" means the inclusion criteria is classified as "Only RCTs". Blank means that the inclusion criteria is classified as "Others". Notes: 1. "RCT" stands for Randomized Controlled Trial, which, in definition, is "a work that reports on a clinical trial that involves at least one test treatment and one control treatment, concurrent enrollment and follow-up of the test- and control-treated groups, and in which the treatments to be administered are selected by a random process, such as the use of a random-numbers table." [Randomized Controlled Trial publication type definition from https://www.nlm.nih.gov/mesh/pubtypes.html]. 2. In order to reproduce the relevant data to this, please get the code of the project published on GitHub at: https://github.com/XiaoruDong/InclusionCriteria and run the code following the instruction provided. 3. This datafile (V2) is a updated version of the datafile published at https://doi.org/10.13012/B2IDB-5958960_V1 with some minor spelling mistakes in the data fixed.
keywords: Inclusion criteri; Randomized controlled trials; Machine learning; Systematic reviews
published: 2018-07-29
This repository includes scripts, datasets, and supplementary materials for the study, "NJMerge: A generic technique for scaling phylogeny estimation methods and its application to species trees", presented at RECOMB-CG 2018. The supplementary figures and tables referenced in the main paper can be found in njmerge-supplementary-materials.pdf. The latest version of NJMerge can be downloaded from Github: https://github.com/ekmolloy/njmerge. ***When downloading datasets, please note that the following errors.*** In README.txt, lines 37 and 38 should read: + fasttree-exon.tre contains lines 1-25, 1-100, or 1-1000 of fasttree-total.tre + fasttree-intron.tre contains lines 26-50, 101-200, or 1001-2000 of fasttree-total.tre Note that the file names (fasttree-exon.tre and fasttree-intron.tre) are swapped. In tools.zip, the compare_trees.py and the compare_tree_lists.py scripts incorrectly refer to the "symmetric difference error rate" as the "Robinson-Foulds error rate". Because the normalized symmetric difference and the normalized Robinson-Foulds distance are equal for binary trees, this does not impact the species tree error rates reported in the study. This could impact the gene tree error rates reported in the study (see data-gene-trees.csv in data.zip), as FastTree-2 returns trees with polytomies whenever 3 or more sequences in the input alignment are identical. Note that the normalized symmetric difference is always greater than or equal to the normalized Robinson-Foulds distance, so the gene tree error rates reported in the study are more conservative. In njmerge-supplementary-materials.pdf, the alpha parameter shown in Supplementary Table S2 is actually the divisor D, which is used to compute alpha for each gene as follows. 1. For each gene, a random value X between 0 and 1 is drawn from a uniform distribution. 2. Alpha is computed as -log(X) / D, where D is 4.2 for exons, 1.0 for UCEs, and 0.4 for introns (as stated in Table S2). Note that because the mean of the uniform distribution (between 0 and 1) is 0.5, the mean alpha value is -log(0.5) / 4.2 = 0.16 for exons, -log(0.5) / 1.0 = 0.69 for UCEs, and -log(0.5) / 0.4 = 1.73 for introns.
keywords: phylogenomics; species trees; incomplete lineage sorting; divide-and-conquer
published: 2018-09-06
The XSEDE program manages the database of allocation awards for the portfolio of advanced research computing resources funded by the National Science Foundation (NSF). The database holds data for allocation awards dating to the start of the TeraGrid program in 2004 to present, with awards continuing through the end of the second XSEDE award in 2021. The project data include lead researcher and affiliation, title and abstract, field of science, and the start and end dates. Along with the project information, the data set includes resource allocation and usage data for each award associated with the project. The data show the transition of resources over a fifteen year span along with the evolution of researchers, fields of science, and institutional representation.
keywords: allocations; cyberinfrastructure; XSEDE