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774 results for “novelty”
Emotion-Antecedent Appraisal Checks: EEG and EMG datasets for Novelty and Pleasantness
<p>The Electroencaphalography (EEG) and facial Electromyography (EMG) signals included in this data set were collected in the context of a previous study conducted by van Peer, Grandjean and Scherer (2014). That study addressed three fundamental questions regarding the mechanisms underlying the appraisal process: Whether appraisal criteria are processed (a) in a fixed sequence, (b) independent of each other, and (c) by different neural structures or circuits. In that study, an oddball paradigm with affective pictures was used to experimentally manipulate novelty and intrinsic pleasantness appraisals. EEG was recorded during task performance, together with facial EMG, to measure, respectively, cognitive processing and efferent responses stemming from the appraisal manipulations. The data set made here publicly available contains the exact same data used by Coutinho, Gentsch, van Peer, Scherer and Schuller (to appear). The only difference in relation to the original data is that the some of the pre-processing steps (i.e., the processing of the raw data) were changed in order to improve the detection of artifacts. The full details of the original study, data collected, pre-processing steps and final data set are included in the paper distributed with the data (study1_dataset.pdf).</p> <p><strong>References</strong></p> <p>Coutinho E, Gentsch k, van Peer JM, Scherer KR & Schuller BW (to appear). Evidence of Emotion-Antecedent Appraisal Checks in Electroencephalography and Facial Electromyography. <em>PloS One</em>.</p> <p>van Peer JM, Grandjean D, Scherer KR (2014). Sequential unfolding of appraisals: EEG evidence for the interaction of novelty and pleasantness. <em>Emotion, </em>14(1), 51-63.</p>
Generation of transcriptional novelty by transposable element insertions in Arabidopsis, Genome Sequencing and eccDNA Data
<p><strong>Raw Illumina sequencing data from the Manuscript entitled "Generation of transcriptional novelty by transposable element insertions in Arabidopsis"</strong></p> <p><strong>A. Illumina genome sequencing reads of Arabidopsis control and hcLines that contain novel transposable element insertions.</strong></p> <p>To identify the genomic position of the new <em>ONSEN</em> insertions, the extracted DNA of the 11 selected lines (nine lines with new insertions and two control lines) was sent to BGI, Hong-Kong for Illumina paired-end 150 bp sequencing, aiming for a minimum of 20X sequencing coverage. Quality control of the raw reads was done using FastQC (Andrews S. (2010). FastQC: a quality control tool for high throughput sequence data. Available online at: <a href="http://www.bioinformatics.babraham.ac.uk/projects/fastqc">http://www.bioinformatics.babraham.ac.uk/projects/fastqc</a>) and trimming/clipping was done using Trimmomatic with parameters ILLUMINACLIP: TruSeq3:2:30:10 LEADING:20 TRAILING:20 SLIDINGWINDOW:4:20 and MINLEN:36. Quality of the reads was deemed excellent and no further actions were taken.</p> <p>Samples identifications: genome_hcLineX with "_1" indicating the forward and "_2" the reverse reads.</p> <p><strong>B. Illumina eccDNA sequencing of Arabidopsis control and hcLines following stress treatments</strong></p> <p>Extrachromosomal circular DNA was prepared and sequenced as follows: twenty plants from each petri dish were pooled separately and DNA was extracted using the CTAB method (<a href="https://dx.doi.org/10.17504/protocols.io.quidwue">dx.doi.org/10.17504/protocols.io.quidwue</a>). Following the mobilome-seq method described in (Lanciano et al., 2017), for all samples, we digested linear DNA from 2 µg of total DNA for 17 hours at 37<sup>o</sup>C using 10 U of PlasmidSafe (<em>LubioScience cat# E3101K</em>), followed by enzyme denaturation (30 mins at 70<sup>o</sup>C). Digested DNA was precipitated with isopropanol supplemented with 1 µg of GlycoBlue coprecipitant (<em>Fisher Scientific cat# 10391565</em>). Circular DNA was then amplified through rolling circle amplification (RCA) with the Illustra TempliPhi kit (<em>GE Healthcare cat# 25-6400-10</em>), following the manufacturer recommendation and leaving the reaction for 16h at 30<sup>o</sup>C. DNA was once again precipitated with isopropanol and sent for Illumina paired end 150 bp sequencing at BGI, Hong Kong. </p> <p>Samples identification: </p> <p>eccDNA_A.thaliana_ctrl: control reads</p> <p>eccDNA_A.thaliana_HS: heat stressed plants reads</p> <p>eccDNA_A.thaliana_AZ_HS: reads of alpha-amanitin, zebularine and heat-stressed plants</p> <p>"R1" indicates forward and "R2" reverse reads.</p> <p> </p>
Novelty and emergent patterns in sperm: morphological diversity and evolution of spermatozoa and sperm conjugation in ground beetles (Coleoptera: Carabidae)
<p>The beetle family Carabidae, with about 40,000 species, exhibits enough diversity in sperm structure and behavior to be an excellent model system for studying patterns and processes of sperm evolution. We explore their potential, documenting<b> </b>sperm form in 177 species of ground beetles using light microscopy and collecting data on 1 qualitative and 7 quantitative sperm phenotypic traits. Our sampling captures 61% of the tribal-level diversity of ground beetles. These data highlight the notable morphological diversity of sperm in ground beetles and suggest that sperm in the group have dynamic evolutionary histories with much morphological innovation and convergence. Sperm vary among species in total length (48–3,400mm), head length (0.5–270mm), and head width (0.2–6.3mm). Most ground beetles make sperm with heads that are indistinct from the flagella at the gross morphological level. However, some or all <i>Omophron</i>,<i>Trachypachus</i>, and Dyschiriini make broad-headed sperm that show morphological differences between species. Most ground beetles package their sperm into groups of sperm, termed conjugates, and ground beetles show variation in conjugate form and in the number and arrangement of sperm in a conjugate. Most ground beetles make sperm conjugates by embedding their sperm in a hyaline rod or spermatostyle. The spermatostyle is remarkably variable among species and varies in length from 17–41,000mm. Several unrelated groups of ground beetles make only singleton sperm, including Nebriinae, Cicindelinae, many Trechinae, and the tribe Paussini. In order to study patterns in sperm evolution, we combine these data with a low-resolution phylogeny of ground beetles. Results from modern comparative analyses suggest the following: sperm differ from conjugates in some aspect of their underlying evolutionary process, sperm have influenced conjugate evolution and vice versa, and conjugation with a spermatostyle likely evolved early within the history of Carabidae and it has been lost independently at least three times.</p>
SQANTI-SIM: a simulator of controlled transcript novelty for lrRNA-seq benchmark
<p>In this repository, we present the PacBio and ONT simulated datasets used for benchmarking transcriptome reconstruction tools, as evaluated in the manuscript titled "<i>SQANTI-SIM: a simulator of controlled transcript novelty for lrRNA-seq benchmark</i>". The dataset includes simulated long reads, short reads, CAGE peaks, and a reduced reference annotation. Additionally, we have included reconstructed transcriptomes from each method, along with SQANTI3 output files. The SQANTI-SIM software can be accessed on GitHub at the following URL: <a href="https://github.com/ConesaLab/SQANTI-SIM">https://github.com/ConesaLab/SQANTI-SIM</a>.</p>
Evolutionary novelties underlie sound production in baleen whales
<p>Experimental and modelling data from the paper "Evolutionary novelties underlie sound production in baleen whales." </p>
FIGURE 5 in A new sexually dichromatic miniature Characidium (Characiformes: Crenuchidae) from the rio Guaporé, rio Madeira basin, Brazil, with remarkable morphological novelties to the genus
FIGURE 5 | Characidium fleurdelis, paratypes, INPA 59848, lateral view: A. Freshly preserved specimens, top male, 22.2 mm SL; bottom mature female with ovocytes seen by transparency on belly as a yellowish area, 24.1 mm SL; B. Live specimens, top male, 20.6 mm SL; bottom mature female, 24.0 mm SL. All from rio Guaporé sub basin, rio Madeira basin, Rondônia, Brazil.
FIGURE 4 in A new sexually dichromatic miniature Characidium (Characiformes: Crenuchidae) from the rio Guaporé, rio Madeira basin, Brazil, with remarkable morphological novelties to the genus
FIGURE 4 | Pseudotympanum of Characidium fleurdelis UFBA 9234, paratype, 20.6 mm SL, right side in lateral view. Overlying skin and adipose tissue removed. ls, lateralis superficialis; oi, obliquus inferioris; os, obliquus superioris. Asterisk indicates the rib of fifth vertebrae.
FIGURE 3 in A new sexually dichromatic miniature Characidium (Characiformes: Crenuchidae) from the rio Guaporé, rio Madeira basin, Brazil, with remarkable morphological novelties to the genus
FIGURE 3 | Osteological characteristics in cleared and stained specimens of Characidium fleurdelis, UFBA 9234, paratypes: A. Weberian apparatus and first ribs, black arrows indicate dorsal rounded processes on first ribs, female, 23.5 mm SL, dorsal view; B. Caudal-fin bony elements, black arrows indicate neural and haemal spines of the antepenultimate vertebra, posteriormost intermuscular bones removed, female, 23.5 mm SL, lateral view; C. Anal-fin radials and first haemal spines in male, 21.0 mm SL, asterisks indicate elongate and flattened haemal spines, black arrow indicates one radial with plate-like bony expansions, lateral view; D. Anal-fin radials and first haemal spines in female, asterisks indicate elongate haemal spines, black arrow indicates one radial without plate-like bony expansion, 23.5 mm SL, lateral view.
FIGURE 6 in A new sexually dichromatic miniature Characidium (Characiformes: Crenuchidae) from the rio Guaporé, rio Madeira basin, Brazil, with remarkable morphological novelties to the genus
FIGURE 6 | A. Map with part of the rio Madeira basin, Brazil, showing the type locality (black star) of Characidium fleurdelis; symbol may represent more than one locality or lot. B. Sampling locality of Characidium fleurdelis, Rondônia, Corumbiara town, Vitória da União district, stream tributary of rio Oimerê, tributary of rio Corumbiara, rio Guaporé sub basin, rio Madeira basin.
FIGURE 1 in A new sexually dichromatic miniature Characidium (Characiformes: Crenuchidae) from the rio Guaporé, rio Madeira basin, Brazil, with remarkable morphological novelties to the genus
FIGURE 1 | Characidium fleurdelis: A. Holotype, MZUSP126956, female, 21.6 mm standard length, lateral view; B. Paratype, UFBA 9234, female, 22.9 mm SL, lateral, dorsal and ventral views; C. Paratype, UFBA 9234, female, 23.8 mm SL, lateral view; D. Paratype, UFBA 9234, male, 20.6 mm SL, lateral view; E. Paratype, UFBA 9233, juvenile, 17.4 mm SL, lateral view. All from rio Guaporé sub basin, rio Madeira basin, Rondônia, Brazil.
Fig. 2 in Novelties from the Northern Mountains Complex of Madagascar IV: A new Rinorea Aubl. (Violaceae) of restricted range from the Galoko and Kalabinono massifs
Fig. 2. – Distribution map of Rinorea callmanderi Wahlert (stars) in Madagascar plotted on a map of forest cover in 2000 (grey)
Fig. 3 in Novelties from the Northern Mountains Complex of Madagascar V: A new threatened Pandanus (Pandanaceae) from the Kalobinono massif
Fig. 3. – Photograph of Pandanus kalobinonensis Callm., Razakamal. & Luino. [Luino & Razakamalala et al. 106] [Photo: I. Luino]
Fig. 2 in Novelties from the Northern Mountains Complex of Madagascar V: A new threatened Pandanus (Pandanaceae) from the Kalobinono massif
Fig. 2. – Pandanus kalobinonensis Callm., Razakamal. & Luino. A. Fruiting branch; B. Detail of the syncarp; C. Drupe; D. Cross section of a drupe; E. Basal section of a leaf; F. Mid section of a leaf; G. Apex section of a leaf. [A–D: Razakamalala et al. 7586, TAN; E–G: Luino & Razakamalala 106, TAN] [Drawing: R.L. Andriamiarisoa]
Fig. 3. – Peperomia robusta G. Mathieu. A in Endemic Peperomia (Piperaceae) novelties from eastern Madagascar
Fig. 3. – Peperomia robusta G. Mathieu. A. General habit; B. Apical part of flowering stem; C. Infrutescence.
Fig. 2. – Peperomia robusta G. Mathieu. A in Endemic Peperomia (Piperaceae) novelties from eastern Madagascar
Fig. 2. – Peperomia robusta G. Mathieu. A. General habit; B. Detail of node; C. Fruit (lateral view).
Fig. 2 in Novelties from the Northern Mountains Complex of Madagascar IV: A new Rinorea Aubl. (Violaceae) of restricted range from the Galoko and Kalabinono massifs
Fig. 2. – Distribution map of Rinorea callmanderi Wahlert (stars) in Madagascar plotted on a map of forest cover in 2000 (grey) following HARPER et al. (2007). Areas outlined in black are protected areas.
Fig. 1. – Rinorea callmanderi Wahlert. A in Novelties from the Northern Mountains Complex of Madagascar IV: A new Rinorea Aubl. (Violaceae) of restricted range from the Galoko and Kalabinono massifs
Fig. 1. – Rinorea callmanderi Wahlert. A. Inflorescence; B. Flowering branch; C. Flower; D. Leaf, abaxial surface. [Callmander 582, G] [Drawing: R. L. Andriamiarisoa
Fig. 4. – Peperomia variilimba G. Mathieu. A in Endemic Peperomia (Piperaceae) novelties from eastern Madagascar
Fig. 4. – Peperomia variilimba G. Mathieu. A. General habit; B. Detail of node; C. Fruit (lateral view). [Mathieu 447, BR] [Drawing: G. Mathieu]
Fig. 3. – Peperomia robusta G. Mathieu. A in Endemic Peperomia (Piperaceae) novelties from eastern Madagascar
Fig. 3. – Peperomia robusta G. Mathieu. A. General habit; B. Apical part of flowering stem; C. Infrutescence. [Nusbaumer 1639] [Photos: L. Nusbaumer]
Fig. 1. – Peperomia irrasa G. Mathieu. A in Endemic Peperomia (Piperaceae) novelties from eastern Madagascar
Fig. 1. – Peperomia irrasa G. Mathieu. A. General habit; B. Detail of node; C. Detail of leaf apex. [Humbert 24638, BR, P] [Drawing: G. Mathieu]
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.