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Set of extracted feature tracks for the year 2016.
<p>Dataframe composed of a set of trajectories identified and tracked from one yearlong of weather radar composites of the German Weather Service (DWD).</p>
Composer Attribution of Renaissance Motets (Iberian Polyphony around 1500): MIDIs and Extracted Features
<p><br> This distribution includes MIDI files used in the experiments described in the "Composer Attribution of Renaissance Motets: A Case Study Using Statistical Features and Machine Learning" chapter of the book The Anatomy of Iberian Polyphony around 1500. Multi-part motets have been separated out into separate MIDI files. We edited the files for consistency, which included adjusting elements that could interfere with encoding rhythm consistently (e.g. standardized rhythmic value rates, eliminating fermatas, etc.).</p> <p>The MIDI files in the nonIb_noMB group were taken from the Josquin Research Project (JRP), who have kindly granted us permission to re-publish them here with our modifications. These are redistributed with a "CC BY-SA 4.0" license: https://github.com/josquin-research-project/jrp-scores/blob/master/LICENSE.txt. The Iberian MIDI files were produced from editions created by The Anatomy of Late 15th- and Early 16th-Century Iberian Polyphonic Music project (https://iberianpolyphonicmusic.wordpress.com), and are included here after our modifications, with permission. We digitised the nonIb_MBonly MIDI files ourselves using Sibelius. All these files are distributed under a "CC BY-SA 4.0" license" license (https://creativecommons.org/licenses/by-sa/4.0/). The included "Catalogue.pdf" file outlines the contents of this corpus in its entirety.</p> <p>This distribution also includes the "Renaissance-safe" features extracted using jSymbolic 2.2 (http://jmir.sourceforge.net) from the MIDI encodings included here. Details on all the features extracted with the software are available in the jSymbolic manual (http://jmir.sourceforge.net/manuals/jSymbolic_manual/home.html). These are presented as follows:</p> <p>- FeatureDefinitions.xml: Descriptions of all extracted features, encoded in ACE XML 1.0, as output directly by jSymbolic. This file does not include any feature values (these are found in the FeatureValues.xml file).</p> <p>- FeatureValues.xml: Extracted feature values, encoded in ACE XML 1.0, as output directly by jSymbolic. The features are described in the FeatureDefinitions.xml file. Class values are implied by the folder containing each MIDI file.</p> <p>- FeatureValues_BasicCSV: Extracted feature values encoded in a CSV file, as output directly by jSymbolic (with complete file paths truncated). Class values are implied by the folder containing each MIDI file.</p> <p>- FeatureValues_HumanReadable.xlsx: Extracted features formatted into a human-readable Microsoft Excel file. Group averages and standard deviations have been added to the bottom, and the "Length_In_Breves" feature is added in a column at the right (it is included separately because it is not calculated directly by jSymbolic 2.2).</p> <p>- FeatureValues_WekaReady.csv: Extracted feature values encoded in a CSV file in a format readable by Weka (https://www.cs.waikato.ac.nz/ml/weka/). Class values have been added in a column on the right, and file paths have been removed, as required by Weka.</p>
Insights from quantum chemical calculations into inner and outer-sphere complexation of plutonium(IV) by monoamide and carbamide extractants - Dataset
<p>Supplementary information for "Insights from quantum chemical calculations into inner and outer-sphere complexation of plutonium(IV) by monoamide and carbamide extractants"<br> The attached 'Pu-inner-outer.zip' unpacks two directories that contains the optimized molecular structures in xyz format.<br> - Inner-sphere/ for the inner-sphere complexes<br> - Outer-sphere/ for the outer-sphere complexes in their geometries I and II<br> </p>
Characterization, functional properties and antioxidant activities of macromolecular extracts isolated from Porphyra yezoensis
<p><em>Porphyra yezoensis</em> is one of the most economical seaweed species in China. Determining how to make full use of mature <em>P. yezoensis </em>and exploring new ways to increase the value of its resources are important subjects of research for the development of the laver breeding industry. In this study, we provide a simple method to comprehensively extract the bioactive substances from <em>P. yezoensis</em>. The characteristics, functional properties and antioxidant activities of two types of biopolymer extract from <em>P. yezoensis</em> were studied and analyzed relatively. Based on the characterization of water-soluble concentrate (WPC) and alkali-soluble concentrate (APC), obtained via chemical analysis, FT-IR, TGA and differential scanning calorimetry (DSC), they both had typical polysaccharide and protein characteristics and steady composition. APC showed higher nitrogen solubility, water holding capacity and foaming ability. APC could not only be used as a protein supplement; it also performs well in improving the properties of foods in terms of water-holding and fat-absorption. The emulsifying activity and oil-holding capacity of WPC were observed to be higher than those of APC; thus, WPC has the potential to be used as an emulsifier. Surprisingly, WPC and APC have radical scavenging capacity in vitro, which broadens the direction of their application.</p>
Towards Olfactory Information Extraction from Text: A Case Study on Detecting Smell Experiences in Novels
<p>Dataset accompanying "Ryan Brate, Paul Groth and Marieke van Erp (2020) Towards Olfactory Information Extraction from Text: A Case Study on Detecting Smell Experiences in Novels. LaTeCH-CLfL 2020. Barcelona, December 2020."</p> <p>Abstract:</p> <p>Environmental factors determine the smells we perceive, but societal factors factors shape the importance, sentiment and biases we give to them. Descriptions of smells in text, or as we call them `smell experiences', offer a window into these factors, but they must first be identified. To the best of our knowledge, no tool exists to extract references to smell experiences from text. In this paper, we present two variations on a semi-supervised approach to identify smell experiences in English literature. The combined set of patterns from both implementations offer significantly better performance than a keyword-based baseline.</p>
................................................................................................................................................. Fig. 3. SDSPAGE analysis of total bacterial protein extracts of the four roe deer isolates as well as other Bartonella species. Extracts of total bacterial protein were separated by SDSPAGE and stained with Coomassie brilliant blue. Lanes: M, molecular mass markers; 1, R1T; 2, R3; 3, R4; 4, R6; 5, Bartonella henselae; 6, Bartonella quintana; 7, Bartonella bacilliformis; 8, Bartonella elizabethae; 9, Bartonella clarridgeiae; 10, Bartonella alsatica; 11, Bartonella tribocorum; 12, Bartonella grahamii. in Bartonella schoenbuchii sp. nov., isolated from the blood of wild roe deer.
................................................................................................................................................. Fig. 3. SDSPAGE analysis of total bacterial protein extracts of the four roe deer isolates as well as other Bartonella species. Extracts of total bacterial protein were separated by SDSPAGE and stained with Coomassie brilliant blue. Lanes: M, molecular mass markers; 1, R1T; 2, R3; 3, R4; 4, R6; 5, Bartonella henselae; 6, Bartonella quintana; 7, Bartonella bacilliformis; 8, Bartonella elizabethae; 9, Bartonella clarridgeiae; 10, Bartonella alsatica; 11, Bartonella tribocorum; 12, Bartonella grahamii.
Nematodes carried by beetles and remaining in malt extract agar (MEA)
<p>To show the importance of vector switching of nematodes in the evolution of the <i>Bursaphelenchus xylophilus</i> group, we tested a hypothesis that "<i>Bursaphelenchus doui</i> (or its ancestor) was transferred by <i>Acalolepta fraudatrix</i>, <i>Acalolepta sejuncta</i>, and/or<i> Monochamus subfasciatus</i> (or their ancestral species) from broad-leaved trees to conifers, switched vectors from these cerambycid beetles to <i>Monochamus</i> beetles in conifers, and then evolved into the common ancestor of <i>Bursaphelenchus mucronatus</i> and <i>B. xylophilus</i>." We used a simple nematode-loading method to beetles and produced 20 binary combinations of five <i>B. xylophilus</i> group species and four cerambycid beetle species in the tribe Lamiini. The affinity of the nematodes for the beetles was examined based on phoretic stage formation of the nematodes. Phoretic stages of <i>B. doui</i> appeared in all beetle species examined, namely <i>A</i><i>calolepta luxuriosa</i>, <i>Psacothea hilaris</i>, <i>A. fraudatrix</i>, and <i>M</i><i>onochamus alternatus</i>, although the affinity of the nematode for <i>M. alternatus</i> was weak. This finding indicates that <i>B. doui</i> could switch vectors to conifer-using <i>Monochamus</i> beetles after transfer by <i>A. fraudatrix</i> from broad-leaved trees to conifers. We conclude that vector switching of nematodes could have potentially happened during the evolutionary history of the <i>B. xylophilus</i> group.</p>
Ranomaly test dataset extracted from BioProject PRJNA421256
<p>Fastq file and sample-metadata.csv to test with rAnomaly package.</p>
MEDI: Macronutrient Extraction and Determination from Invertebrates, a rapid, cheap and streamlined protocol
<p>Macronutrients, comprising carbohydrates, proteins and lipids, underpin many ecological processes, but their quantification in ecological studies is often inaccurate and laborious, requiring large investments of time and bulk samples, which make individual-level studies impossible. This study presents MEDI (Macronutrient Extraction and Determination from Invertebrates), a protocol for the direct, rapid and relatively low-cost determination of macronutrient content from single small macroinvertebrates.</p> <p>Macronutrients were extracted by a sequential process of soaking in 1:12 chloroform:methanol solution to remove lipid and then solubilizing tissue in 0.1 M NaOH. Proteins, carbohydrates and lipids were determined by colorimetric assays from the same individual specimens.</p> <p>The limits of detection of MEDI with the equipment and conditions used were 0.067 mg ml-1, 0.065 mg ml-1 and 0.006 mg ml-1 for proteins, carbohydrates and lipids, respectively. Adjusting the volume of reagents used for extraction and determination can broaden the range of concentrations that can be detected. MEDI successfully identified taxonomic differences in macronutrient content between five insect species.</p> <p>MEDI can directly and rapidly determine macronutrient content in tiny (dry mass ~3 mg) and much larger individual invertebrates. Using MEDI, the total macronutrient content of over 50 macroinvertebrates can be determined within around three days of collection at a cost of ~$1.35 per sample.</p>
Aphicidal and antifeedant activity of Synandrospadix vermitoxicus extracts against Myzus persicae on potato plants
<p>Supplemental raw data and statistics of López-Isasmendi et al.</p>
Data from: Concordance in wetland physicochemical conditions, vegetation, and surrounding land cover is robust to data extraction approach
Concordance among wetland physicochemical conditions, vegetation, and surrounding land cover may result from the influence of land cover on the sources of plant propagules, on physicochemical conditions, and their subsequent determination of growing conditions. Alternatively, concordance may result if differences in climate, soils, and species pools are spatially confounded with differences in human population density and land conversion. Further, we expect that land cover within catchment boundaries will be more predictive than land cover in symmetrical buffers if runoff is a major pathway. We measured concordance between land cover, wetland vegetation and physicochemical conditions in 48 prairie pothole wetlands, controlling for inter-wetland distance. We contrasted land-cover data collected over a four-year period by multiple extraction approaches including topographically-delineated catchments and nested 30 m to 5,000 m radius buffers. After factoring out inter-wetland distance, physiochemical conditions were significantly concordant with land cover. Vegetation was not significantly concordant with land cover, though it was strongly and significantly concordant with physicochemical conditions. More, concordance was as strong when land cover was extracted from buffers <500 m in radius as from catchments, indicating the mechanism responsible is not topographically constrained. We conclude that local landscape structure does not directly influence wetland vegetation composition, but rather that vegetation depends on physicochemical conditions in the wetland (which are affected by surrounding land cover) and on regional factors such as the vegetation species pool and geographic gradients in climate, soil type, and land use.
FIGURE 1. Virtual extract from a water-colour painting from Brian H in On the identity, nomenclatural status and authorship of Coluber monticolus Cantor, 1839 (Reptilia: Serpentes)
FIGURE 1. Virtual extract from a water-colour painting from Brian H. Hodgson`s collection of drawings kept in the Zoological Library of the Natural History Museum, London, U.K. The depicted specimen from the "Hills at Nipal" was determined by Albert C. L. Günther as "? Simotes russelli", a taxon presently regarded as a synonym of Oligodon arnensis (Shaw, 1802). In fact, the drawing shows a specimen of the brown morphotype of the Many-banded cat snake, Boiga multifasciata (Blyth, 1860). Artist unknown. Source: Library and Archives, Natural History Museum, London.
Data from: Comparative analysis of DNA extraction methods to study the body surface microbiota of insects: a case study with ant cuticular bacteria
High-throughput sequencing of the 16S rRNA gene has considerably helped revealing the essential role of bacteria living on insect cuticles in the ecophysiology and behavior of their hosts. However, our understanding of host-cuticular microbiota feedbacks remains hampered by the difficulties to working with low bacterial DNA quantities as in individual insect cuticle samples, which are more prone to molecular biases and contaminations. Herein, we conducted a methodological benchmark on the cuticular bacterial loads retrieved from two Neotropical ant species of different body size and ecology: Atta cephalotes (~15 mm) and Pseudomyrmex penetrator (~5 mm). We evaluated the richness and composition of the cuticular microbiota, as well as the amount of biases and contamination produced by four DNA extraction protocols. We also addressed how bacterial communities' characteristics would be affected by the number of individuals or individual body size used for DNA extraction. Most extraction methods yielded similar results in term of bacterial diversity and composition for A. cephalotes (~15 mm). In contrast, greater amounts of artifactual sequences and contaminations, as well as noticeable differences in bacterial communities' characteristics were observed between the extraction methods for P. penetrator (~5 mm). We also found that large (~15 mm) and small (~5 mm) A. cephalotes individuals harbor different bacterial communities. Our benchmark hence suggests that cuticular microbiota of single insect individuals can be reliably retrieved provided that blank controls, appropriate data cleaning, and standardization of individual body size are considered in the experiment.
Data from: Can differential nutrient extraction explain property variations in a predatory trap?
Predators exhibit flexible foraging to facilitate taking prey that offer important nutrients. Because trap-building predators have limited control over the prey they encounter, differential nutrient extraction and trap architectural flexibility may be used as a means of prey selection. Here, we tested whether differential nutrient extraction induces flexibility in architecture and stickiness of a spider's web by feeding Nephila pilipes live crickets (CC), live flies (FF), dead crickets with the web stimulated by flies (CD) or dead flies with the web stimulated by crickets (FD). Spiders in the CD group consumed less protein per mass of lipid or carbohydrate, and spiders in the FF group consumed less carbohydrates per mass of protein. Spiders from the CD group built stickier webs that used less silk, whereas spiders in the FF group built webs with more radii, greater catching areas and more silk, compared with other treatments. Our results suggest that differential nutrient extraction is a likely explanation for prey-induced spider web architecture and stickiness variations.
Data from: High-throughput sequencing of nematode communities from total soil DNA extractions
Background: Nematodes are extremely diverse and numbers of species are predicted to be more than a million. Studies on nematode diversity are difficult and laborious using standard methods such as identification based on morphology and therefore high-throughput sequencing is an attractive alternative. Generally, primers that have been used for generating amplicons for sequencing are not nematode specific and also amplify other groups such as fungi and plantae. Thus a nematode enrichment step must be included that may introduce biases. Results: An amplification strategy, including a new primer, which selectively amplifies nematodes and other metazoans was developed. When this strategy was tested on DNA templates from a set of 22 agricultural soils, we obtained 64.4 % sequences of nematode origin in total, whereas the remaining sequences were almost entirely metazoan. The nematode sequences were derived from a broad taxonomic range and most sequences were from nematode taxa that have previously been found to be abundant in soil such as Tylenchida, Rhabditida, Dorylaimida, Triplonchida and Araeolaimida. Conclusions: This amplification and sequencing strategy for assessing nematode diversity was demonstrated to be able to collect a broad taxonomy of nematodes without prior enrichment and thus the method will be highly valuable in ecological studies of nematodes. Keywords: nematode, community, next-generation sequencing, SSU, diversity, 18S, rDNA
Data from: Decentralizing cell-free RNA sensing with the use of low-cost cell extracts
<p>Data and DNA sequences for the publication "Decentralizing cell-free RNA sensing with the use of low-cost cell extracts" (https://www.biorxiv.org/content/10.1101/2021.05.29.446205v1)</p>
Dataset for "Extracting Traceability Links between Javadoc Sentences and JUnit Test Code Lines"
<p>Dataset for "Extracting Traceability Links between Javadoc Sentences and JUnit Test Code Lines"</p>
Data from: Extracting DNA from 'jaws': high yield and quality from archived tiger shark (Galeocerdo cuvier) skeletal material
Archived specimens are highly valuable sources of DNA for retrospective genetic/genomic analysis. However, often limited effort has been made to evaluate and optimize extraction methods, which may be crucial for downstream applications. Here, we assessed and optimized the usefulness of abundant archived skeletal material from sharks as a source of DNA for temporal genomic studies. Six different methods for DNA extraction, encompassing two different commercial kits and three different protocols, were applied to material, so-called bio-swarf, from contemporary and archived jaws and vertebrae of tiger sharks (Galeocerdo cuvier). Protocols were compared for DNA yield and quality using a qPCR approach. For jaw swarf, all methods provided relatively high DNA yield and quality, while large differences in yield between protocols were observed for vertebrae. Similar results were obtained from samples of white shark (Carcharodon carcharias). Application of the optimized methods to 38 museum and private angler trophy specimens dating back to 1912 yielded sufficient DNA for downstream genomic analysis for 68% of the samples. No clear relationships between age of samples, DNA quality and quantity were observed, likely reflecting different preparation and storage methods for the trophies. Trial sequencing of DNA capture genomic libraries using 20 000 baits revealed that a significant proportion of captured sequences were derived from tiger sharks. This study demonstrates that archived shark jaws and vertebrae are potential high-yield sources of DNA for genomic-scale analysis. It also highlights that even for similar tissue types, a careful evaluation of extraction protocols can vastly improve DNA yield.
Data from: A proteomic method to extract, concentrate, digest, and enrich peptides from fossils with colored (humic) substances for mass spectrometry analyses
Humic substances are break-down products of decaying organic matter that co-extract with proteins from fossils. These substances are difficult to separate from proteins in solution, and interfere with analyses of fossil proteomes. We introduce a method combining multiple recent advances in extraction protocols to both concentrate proteins from fossil specimens with high humic content, and remove humics, producing clean samples easily analyzed by mass spectrometry (MS). This method includes: 1) a non-demineralizing extraction buffer that eliminates protein loss during the demineralization step in routine methods; 2) filter-aided sample preparation (FASP) of peptides, which concentrates and digests extracts in one filter, allowing the separation of large humics after digestion; 3) centrifugal stage-tipping, which further clarifies and concentrates samples in a uniform process performed simultaneously on multiple samples. We apply this method to a moa fossil (~800¬–1000 yr) dark with humic content, generating colorless samples and enabling the detection of more proteins with greater sequence coverage than previous MS analyses on this same specimen. This workflow allows analyses of low-abundance proteins in fossils containing humics, and thus may widen the range of extinct organisms and regions of their proteomes we can explore with MS.
Data from: Improving PCR detection of prey in molecular diet studies: importance of group-specific primer set selection and extraction protocol performances
While morphological identification of prey remains in feces of predators is the method most commonly used to study trophic interactions, many studies indicate that this method does not detect all consumed prey. Polymerase Chain Reaction based methods are increasingly used to detect prey DNA in the predator food bolus and have proved themselves efficient, with high accuracy. When studying complex diet samples, the extraction of total DNA is a critical step, as PCR inhibitors may be co-extracted. Another critical step consist in carefully select suitable group-specific primer sets that should only amplify prey DNA from the targeted taxon. In this study, the food boluses of five Rattus rattus and seven Rattus exulans were analyzed using both morphological and molecular methods. We tested a panel of 30 PCR specific primer sets targeting Bird, Invertebrate and Plant sequences and four were finally selected to be use as group-specific primer pairs in PCR protocols. The performances of four DNA extraction protocols (QIAamp DNA stool mini kit, DNeasy mericon food kit and two CTAB-based methods) were compared using four variables: DNA concentration, A260/A280 absorbance ratio, food compartment analyzed (stomach or fecal contents), total number of prey specific PCR amplification per sample. Our results clearly indicate that the A260/A280 absorbance ratio, which varies between extraction protocols, is positively correlated to the number of PCR amplifications of each prey taxon. We recommend using the DNeasy mericon food kit (Qiagen), which yielded results very similar to those achieved with the morphological approach.
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.