cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5524/102275
title: A Virtual Library for Behavioral Performance in Standard Conditions – Experiment 04 Q28 Effect of an NMDA lesion of the OFC on the development of sensitization and compulsive checking

description: Beyond their specific experiment, video records of behavior have future value; for example, as inputs for new experiments or for yet unknown types of analysis of behaviorsimilar to tissue or blood sample banks in life sciences where clinically-derived or otherwise well-described experimental samples are stored to be available for some unknown potential future purpose. <br>Research using an animal model of obsessive-compulsive disorder employed a standardized paradigm where the behavior of rats in a large open field was video recorded for 55 min on each test. From 43 experiments, there are 19,976 such trials that amount to over 2 years of continuous recording. In addition to videos, there are two video-derived raw data objects: XY locomotion coordinates, and plots of animal trajectory. To motivate future use, the three raw data objects are annotated with a general schemaone that abstracts the data records from their particular experiment while providing, at the same time a detailed list of independent variables bearing on behavioral performance. The raw data objects are deposited as 43 datasets but constitute, functionally, a library containing one large dataset. <br>Size and annotation schema give the library high re-use potential: in applications using machine learning techniques, statistical evaluation of subtle factors, simulation of new experiments, or as educational resource. Ultimately, the library can serve both as the seed and the test bed to create a machine searchable virtual library of linked open datasets for behavioral performance in defined conditions.
DOI: 10.5524/102276
title: A Virtual Library for Behavioral Performance in Standard Conditions – Experiment 05 Q28 Effect of an NMDA lesion of the OFC on the expression of sensitization and compulsive checking

description: Beyond their specific experiment, video records of behavior have future value; for example, as inputs for new experiments or for yet unknown types of analysis of behaviorsimilar to tissue or blood sample banks in life sciences where clinically-derived or otherwise well-described experimental samples are stored to be available for some unknown potential future purpose. <br>Research using an animal model of obsessive-compulsive disorder employed a standardized paradigm where the behavior of rats in a large open field was video recorded for 55 min on each test. From 43 experiments, there are 19,976 such trials that amount to over 2 years of continuous recording. In addition to videos, there are two video-derived raw data objects: XY locomotion coordinates, and plots of animal trajectory. To motivate future use, the three raw data objects are annotated with a general schemaone that abstracts the data records from their particular experiment while providing, at the same time a detailed list of independent variables bearing on behavioral performance. The raw data objects are deposited as 43 datasets but constitute, functionally, a library containing one large dataset. <br>Size and annotation schema give the library high re-use potential: in applications using machine learning techniques, statistical evaluation of subtle factors, simulation of new experiments, or as educational resource. Ultimately, the library can serve both as the seed and the test bed to create a machine searchable virtual library of linked open datasets for behavioral performance in defined conditions.
DOI: 10.5524/102278
title: A Virtual Library for Behavioral Performance in Standard Conditions – Experiment 07 Q26 Effect of an NMDA lesion of the NAc on the development of sensitization and compulsive checking (batch 2)

description: Beyond their specific experiment, video records of behavior have future value; for example, as inputs for new experiments or for yet unknown types of analysis of behaviorsimilar to tissue or blood sample banks in life sciences where clinically-derived or otherwise well-described experimental samples are stored to be available for some unknown potential future purpose. <br>Research using an animal model of obsessive-compulsive disorder employed a standardized paradigm where the behavior of rats in a large open field was video recorded for 55 min on each test. From 43 experiments, there are 19,976 such trials that amount to over 2 years of continuous recording. In addition to videos, there are two video-derived raw data objects: XY locomotion coordinates, and plots of animal trajectory. To motivate future use, the three raw data objects are annotated with a general schemaone that abstracts the data records from their particular experiment while providing, at the same time a detailed list of independent variables bearing on behavioral performance. The raw data objects are deposited as 43 datasets but constitute, functionally, a library containing one large dataset. <br>Size and annotation schema give the library high re-use potential: in applications using machine learning techniques, statistical evaluation of subtle factors, simulation of new experiments, or as educational resource. Ultimately, the library can serve both as the seed and the test bed to create a machine searchable virtual library of linked open datasets for behavioral performance in defined conditions.
DOI: 10.5524/102281
title: A Virtual Library for Behavioral Performance in Standard Conditions – Experiment 10 Q29 Effect of CP809101 (5HT2C agonist) on the expression of sensitization and compulsive checking in an open field bordered by a low ledge

description: Beyond their specific experiment, video records of behavior have future value; for example, as inputs for new experiments or for yet unknown types of analysis of behaviorsimilar to tissue or blood sample banks in life sciences where clinically-derived or otherwise well-described experimental samples are stored to be available for some unknown potential future purpose. <br>Research using an animal model of obsessive-compulsive disorder employed a standardized paradigm where the behavior of rats in a large open field was video recorded for 55 min on each test. From 43 experiments, there are 19,976 such trials that amount to over 2 years of continuous recording. In addition to videos, there are two video-derived raw data objects: XY locomotion coordinates, and plots of animal trajectory. To motivate future use, the three raw data objects are annotated with a general schemaone that abstracts the data records from their particular experiment while providing, at the same time a detailed list of independent variables bearing on behavioral performance. The raw data objects are deposited as 43 datasets but constitute, functionally, a library containing one large dataset. <br>Size and annotation schema give the library high re-use potential: in applications using machine learning techniques, statistical evaluation of subtle factors, simulation of new experiments, or as educational resource. Ultimately, the library can serve both as the seed and the test bed to create a machine searchable virtual library of linked open datasets for behavioral performance in defined conditions.
DOI: 10.5524/102282
title: A Virtual Library for Behavioral Performance in Standard Conditions – Experiment 11 Q33 Effect of substitution of QNP with 8OHDPAT on the expression of sensitization and compulsive checking

description: Beyond their specific experiment, video records of behavior have future value; for example, as inputs for new experiments or for yet unknown types of analysis of behaviorsimilar to tissue or blood sample banks in life sciences where clinically-derived or otherwise well-described experimental samples are stored to be available for some unknown potential future purpose. <br>Research using an animal model of obsessive-compulsive disorder employed a standardized paradigm where the behavior of rats in a large open field was video recorded for 55 min on each test. From 43 experiments, there are 19,976 such trials that amount to over 2 years of continuous recording. In addition to videos, there are two video-derived raw data objects: XY locomotion coordinates, and plots of animal trajectory. To motivate future use, the three raw data objects are annotated with a general schemaone that abstracts the data records from their particular experiment while providing, at the same time a detailed list of independent variables bearing on behavioral performance. The raw data objects are deposited as 43 datasets but constitute, functionally, a library containing one large dataset. <br>Size and annotation schema give the library high re-use potential: in applications using machine learning techniques, statistical evaluation of subtle factors, simulation of new experiments, or as educational resource. Ultimately, the library can serve both as the seed and the test bed to create a machine searchable virtual library of linked open datasets for behavioral performance in defined conditions.
DOI: 10.5524/102284
title: A Virtual Library for Behavioral Performance in Standard Conditions – Experiment 13 Q34 Effect of QNP+8OHDPAT co-treatment on the expression of sensitization and compulsive checking

description: Beyond their specific experiment, video records of behavior have future value; for example, as inputs for new experiments or for yet unknown types of analysis of behaviorsimilar to tissue or blood sample banks in life sciences where clinically-derived or otherwise well-described experimental samples are stored to be available for some unknown potential future purpose. <br>Research using an animal model of obsessive-compulsive disorder employed a standardized paradigm where the behavior of rats in a large open field was video recorded for 55 min on each test. From 43 experiments, there are 19,976 such trials that amount to over 2 years of continuous recording. In addition to videos, there are two video-derived raw data objects: XY locomotion coordinates, and plots of animal trajectory. To motivate future use, the three raw data objects are annotated with a general schemaone that abstracts the data records from their particular experiment while providing, at the same time a detailed list of independent variables bearing on behavioral performance. The raw data objects are deposited as 43 datasets but constitute, functionally, a library containing one large dataset. <br>Size and annotation schema give the library high re-use potential: in applications using machine learning techniques, statistical evaluation of subtle factors, simulation of new experiments, or as educational resource. Ultimately, the library can serve both as the seed and the test bed to create a machine searchable virtual library of linked open datasets for behavioral performance in defined conditions.
DOI: 10.5524/102285
title: A Virtual Library for Behavioral Performance in Standard Conditions – Experiment 14 Q45 Effect of a low dose of 8OHDPAT (0.0625) co-injected with a threshold dose of QNP (0.0625 mg/kg) on the development of sensitization and compulsive checking

description: Beyond their specific experiment, video records of behavior have future value; for example, as inputs for new experiments or for yet unknown types of analysis of behaviorsimilar to tissue or blood sample banks in life sciences where clinically-derived or otherwise well-described experimental samples are stored to be available for some unknown potential future purpose. <br>Research using an animal model of obsessive-compulsive disorder employed a standardized paradigm where the behavior of rats in a large open field was video recorded for 55 min on each test. From 43 experiments, there are 19,976 such trials that amount to over 2 years of continuous recording. In addition to videos, there are two video-derived raw data objects: XY locomotion coordinates, and plots of animal trajectory. To motivate future use, the three raw data objects are annotated with a general schemaone that abstracts the data records from their particular experiment while providing, at the same time a detailed list of independent variables bearing on behavioral performance. The raw data objects are deposited as 43 datasets but constitute, functionally, a library containing one large dataset. <br>Size and annotation schema give the library high re-use potential: in applications using machine learning techniques, statistical evaluation of subtle factors, simulation of new experiments, or as educational resource. Ultimately, the library can serve both as the seed and the test bed to create a machine searchable virtual library of linked open datasets for behavioral performance in defined conditions.
DOI: 10.5524/102248
title: Supporting data for "Genome of a Giant (Trevally): <i>Caranx ignobilis</i>"

description: <i>Caranx ignobilis,</i> commonly known as the giant kingfish or giant trevally, is a large, reef-associated apex predator. It is a prized sportfish, targeted heavily throughout its tropical and subtropical range in the Indian and Pacific Oceans, and it has drawn significant interest in aquaculture due to an unusual tolerance for freshwater. In this study, we present a draft assembly of the estimated 625.92Mbp nuclear genome of a <i>C. ignobilis</i> individual from Hawaiian waters, which have recently been shown to host a genetically distinct population. The 97.4% BUSCO complete assembly has a contig NG50 of 7.3Mbp and scaffold NG50 of 46.3Mbp. Twenty-five of the 203 scaffolds contain 90% of the genome. We also present the raw Pacific Biosciences continuous long reads from which the assembly was created. A Hi-C dataset (Dovetail Genomics Omni-C) and Illumina-based RNA-seq from eight tissues are also presented; the latter of which can be particularly useful for annotation and studies of freshwater tolerance. Overall, this genome assembly and supporting data is a valuable tool for ecological and comparative genomics studies of kingfish and other carangoid fishes.
DOI: 10.5524/102252
title: Supporting data for "Near-chromosomal <i>de novo</i> assembly of Bengal tiger genome reveals genetic hallmarks of apex-predation"

description: The tiger, a poster child for conservation, remains an endangered apex predator. Continued survival and recovery will require a comprehensive understanding of their genetic diversity and the use of such information for population management. A high-quality tiger genome assembly will be an important tool for conservation genetics, especially for the Indian tiger, the most abundant subspecies in the wild. Here, we present high-quality near-chromosomal genome assemblies of a female and a male wild Indian tiger (<i>Panthera tigris tigris</i>). Our assemblies had a scaffold N50 of &gt;140 Mb, with 19 scaffolds, corresponding to the 19 numbered chromosomes, containing 95% of the genome. Our assemblies also enabled detection of longer stretches of runs of homozygosity compared to previous assemblies which will improve estimates of genomic inbreeding. Comprehensive genome annotation identified 26,068 protein-coding genes, including several gene families involved in key morphological features such as the teeth, claws, vision, olfaction, taste, and body stripes. We also identified 301 microRNAs, 365 small nucleolar RNAs, 632 tRNAs and other noncoding RNA elements, several of which are predicted to regulate key biological pathways that likely contribute to tigers apex predatory traits. We identify signatures of positive selection in the tiger genome that are consistent with the <i>Panthera</i> lineage. Our high-quality genome will enable use of non-invasive samples for comprehensive assessment of genetic diversity, thus supporting effective conservation and management of wild tiger populations
DOI: 10.5524/102261
title: Supporting data for "A Virtual Library for Behavioral Performance in Standard Conditions – Rodent Spontaneous Activity in an Open Field during Repeated Testing and after Treatment with Drugs or Brain Lesions"

description: Beyond their specific experiment, video records of behavior have future value; for example, as inputs for new experiments or for yet unknown types of analysis of behaviorsimilar to tissue or blood sample banks in life sciences where clinically-derived or otherwise well-described experimental samples are stored to be available for some unknown potential future purpose. <br>Research using an animal model of obsessive-compulsive disorder employed a standardized paradigm where the behavior of rats in a large open field was video recorded for 55 min on each test. From 43 experiments, there are 19,976 such trials that amount to over 2 years of continuous recording. In addition to videos, there are two video-derived raw data objects: XY locomotion coordinates, and plots of animal trajectory. To motivate future use, the three raw data objects are annotated with a general schemaone that abstracts the data records from their particular experiment while providing, at the same time a detailed list of independent variables bearing on behavioral performance. The raw data objects are deposited as 43 datasets but constitute, functionally, a library containing one large dataset. <br>Size and annotation schema give the library high re-use potential: in applications using machine learning techniques, statistical evaluation of subtle factors, simulation of new experiments, or as educational resource. Ultimately, the library can serve both as the seed and the test bed to create a machine searchable virtual library of linked open datasets for behavioral performance in defined conditions.<br>This top-level dataset, which details the animals used in the complete set of videography experiments, links to 43 experiment-level datasets which contain download links to RAWDATA objects in the Federated Research Data Repository (FRDR) and the annotations (metadata) for those RAWDATA objects. The GigaDB "Sample" and "Files" tabs in these experiment-level datasets show annotations for metadata variables in GigaDB vocabulary. However, this vocabulary was insufficient to meet the objective of having a general schema, "one that abstracts the data records from their particular experiment while providing, at the same time a detailed list of independent variables bearing on behavioral performance." Such a general schema is described in the <i>GigaScience</i> publication linked to this dataset. The complete set of metadata annotations are contained in the "SampleTab_Expt" and "FilesTab_Expt" tabular data files for each experiment-level datasets. For each experiment-level dataset, by clicking on the "Files" Tab and then "FTP site" a researcher can swiftly access the "SampleTab_Expt" and "FilesTab_Expt" tabular data files that are archived in GigaDB.
DOI: 10.5524/102264
title: Supporting data for "annotate_my_genomes: an easy-to-use pipeline to improve genome annotation and uncover neglected genes by hybrid RNA sequencing."

description: The advancement of hybrid sequencing technologies is increasingly expanding genome assemblies that are often annotated using hybrid sequencing transcriptomics, leading to improved genome characterization and the identification of novel genes and isoforms in a wide variety of organisms.<br>We developed an easy-to-use genome-guided transcriptome annotation pipeline that uses assembled transcripts from hybrid sequencing data as input and distinguishes between coding and long non-coding RNAs by integration of several bioinformatic approaches, including gene reconciliation with previous annotations in GTF format. We demonstrated the efficiency of this approach by correctly assembling and annotating all exons from the chicken SCO-spondin gene (containing more than 105 exons), including the identification of missing genes in the chicken reference annotations by homology assignments.<br>Our method helps to improve the current transcriptome annotation of the chicken brain. Our pipeline, implemented on Anaconda/Nextflow and Docker is an easy-to-use package that can be applied to a broad range of species, tissues, and research areas helping to improve and reconcile current annotations. The code and datasets are publicly available in GitHub.
DOI: 10.5524/102265
title: Supporting data for "Accurate gene consensus at low nanopore coverage"

description: Nanopore technologies allow high throughput sequencing of long strands of DNA at the cost of a relatively large error rate. This limits its use in the reading of amplicon libraries in which there are only a few mutations per variant and therefore they are easily confused with the sequencing noise. Consensus calling strategies reduce the error but sacrifice part of the throughput on reading typically 30 to 100 times each member of the library. <br>In this work, we develop SINGLe (SNPs In Nanopore reads of Gene Libraries), an error correction method to reduce the noise in nanopore reads of amplicons containing point variations. SINGLe exploits that in an amplicon library, all reads are very similar to a wild type sequence, from which it is possible to experimentally characterize the position-specific systematic sequencing error pattern. Then, it uses this information to reweight the confidence given to nucleotides that do not match the wild type in individual variant reads, and incorporates it on the consensus calculation. <br>We tested SINGLe in a mutagenic library of the KlenTaq polymerase gene, where the true mutation rate was below the sequencing noise. We observed that contrary to other methods, SINGLe compensates for the systematic errors made by the basecallers. Consequently, SINGLe converges to the true sequence using as little as 5 reads per variant, fewer than other available methods.
DOI: 10.5524/102272
title: A Virtual Library for Behavioral Performance in Standard Conditions – Experiment 01 Q22 Effect of an NMDA lesion of the infralimbic ctx on expression of compulsive checking

description: Beyond their specific experiment, video records of behavior have future value; for example, as inputs for new experiments or for yet unknown types of analysis of behaviorsimilar to tissue or blood sample banks in life sciences where clinically-derived or otherwise well-described experimental samples are stored to be available for some unknown potential future purpose. <br>Research using an animal model of obsessive-compulsive disorder employed a standardized paradigm where the behavior of rats in a large open field was video recorded for 55 min on each test. From 43 experiments, there are 19,976 such trials that amount to over 2 years of continuous recording. In addition to videos, there are two video-derived raw data objects: XY locomotion coordinates, and plots of animal trajectory. To motivate future use, the three raw data objects are annotated with a general schemaone that abstracts the data records from their particular experiment while providing, at the same time a detailed list of independent variables bearing on behavioral performance. The raw data objects are deposited as 43 datasets but constitute, functionally, a library containing one large dataset. <br>Size and annotation schema give the library high re-use potential: in applications using machine learning techniques, statistical evaluation of subtle factors, simulation of new experiments, or as educational resource. Ultimately, the library can serve both as the seed and the test bed to create a machine searchable virtual library of linked open datasets for behavioral performance in defined conditions.