cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5524/102292
title: A Virtual Library for Behavioral Performance in Standard Conditions – Experiment 21 Q37 Effect of mCPP dose (0.625 and 1.25 mg/kg) co-injected with a fixed dose of QNP (0.125 mg/kg) on the development of sensitization and induction 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.
DOI: 10.5524/102294
title: A Virtual Library for Behavioral Performance in Standard Conditions – Experiment 23 Q39 Effect of mCPP dose (0.3125 0.625 or 1.25 mg/kg) on the expression of sensitization and compulsive checking induced by QNP (0.125 mg/kg)

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: 10.5524/102295
title: A Virtual Library for Behavioral Performance in Standard Conditions – Experiment 24 Q34 Effect of acute escitalopram on the acute response to 8OHDPAT

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: 10.5524/102299
title: A Virtual Library for Behavioral Performance in Standard Conditions – Experiment 28 Q44 Effect of ritanserin (5-HT2A/C receptors blocker) on the attenuation by mCPP of the expression of quinpirole-induced 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: 10.5524/102305
title: A Virtual Library for Behavioral Performance in Standard Conditions – Experiment 34 Q24 Effect of a circular arena on development of sensitization and compulsive checking induced by QNP (0.5 mg/kg)

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: 10.5524/102313
title: A Virtual Library for Behavioral Performance in Standard Conditions – Experiment 42 Q41 Effects of NAc lesion plus mCPP (0.625 mg/kg on injections 1-6) or 8OHDPAT (.0625 mg/kg on injections 7-10) in producing 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: 10.5524/102315
title: Interactive Data Visualisation

description: Interactive data visualisation unlocks data exploration by the reader. This collection of interactive data visualisation illustrates how researchers can create interactive data visualisation with little extra work with their current tools.
DOI: 10.5524/102318
title: Supporting data for "svaRetro and svaNUMT: modular packages for annotating retrotransposed transcripts and nuclear integration of mitochondrial DNA in genome sequencing data"

description: Nuclear integration of mitochondrial genomes and retro-copied transcript insertions are often-overlooked biologically important aspects of structural variant annotation. While tools for their detection exist, these typically rely on re-analysis of primary data using specialised detectors rather than leveraging calls from general-purpose structural variant callers. Such re-analysis potentially leads to additional computational expense and does not take advantage of advances in general-purpose structural variant calling.<br>Here, we present svaRetro and svaNUMT, R packages that provide functions for annotating novel genomic events such as non-reference retro-copied transcripts and nuclear integration of mitochondrial DNA. The packages were developed to work within the Bioconductor framework. We evaluate the performance of these packages to detect events using simulations and public benchmarking datasets and annotate processed transcripts in a public structural variant database.<br>svaRetro and svaNUMT provide modular, SV-caller agnostic tools for downstream annotation of structural variant calls.
DOI: 10.5524/102320
title: Supporting data for "learnMSA: Learning and Aligning Large Protein Families"

description: The alignment of large numbers of protein sequences is a challenging task and its importance grows rapidly along with the size of biological datasets. State-of-the-art algorithms have a tendency to produce less accurate alignments with an increasing number of sequences. This is a fundamental problem since many downstream tasks rely on accurate alignments. <br>We present learnMSA, a novel statistical learning approach of profile hidden Markov models (pHMMs) based on batch gradient descent. Fundamentally different from popular aligners, we fit a custom recurrent neural network architecture for (p)HMMs to potentially millions of sequences with respect to a maximum a posteriori objective and decode an alignment. We rely on automatic differentiation of the log-likelihood and thus, our approach is different from existing HMM training algorithms like BaumWelch. Our method does not involve progressive, regressive or divide-and-conquer heuristics. We use uniform batch sampling to adapt to large datasets in linear time without the requirement of a tree. When tested on ultra-large protein families with up to 3.5 million sequences, learnMSA is both more accurate and faster than state-of-the-art tools. On the established benchmarks HomFam and BaliFam with smaller sequence sets it matches state-of-the-art performance. All experiments where done on a standard workstation with a GPU. <br> Our results show that learnMSA does not share the counter-intuitive drawback of many popular heuristic aligners which can substantially lose accuracy when many additional homologs are input. LearnMSA is a future-proof framework for large alignments with many opportunities for further improvements.
DOI: 10.5524/102322
title: Supporting data for "Defining the characteristics of interferon-alpha-stimulated human genes: insight from expression data and machine-learning"

description: A virus-infected cell triggers a signalling cascade resulting in the secretion of interferons (IFNs), which in turn induces the up-regulation of the IFN stimulated genes (ISGs) that play a role in anti-pathogen host defence. Here, we conducted analyses on large-scale data relating to evolutionary, gene expression, sequence composition, and network properties to elucidate factors associated with the stimulation of human genes in response to IFN-. <br>We find that ISGs are less evolutionary conserved than genes that are not significantly stimulated in IFN experiments (non-ISGs). ISGs show obvious depletion of GC-content in the coding region. This influences the representation of some compositions following the translation process. IFN repressed human genes (IRGs), down-regulated genes in IFN experiments, can have similar properties to the ISGs. Additionally, we design a machine-learning framework integrating the support vector machine and novel feature selection algorithm that achieves an area under the receiver operating characteristic curve (AUC) of 0.7455 for ISG prediction. Its application in other IFN-systems suggests the similarity between the ISGs triggered by type I and III IFNs. <br> ISGs have some unique properties that make them different from the non-ISGs. The representation of some properties have strong correlations with genes expression following IFN- stimulation, which can be used as predictive features in machine learning. Our model predicts several genes as putative ISGs that so far have shown no significant differential expression when stimulated with IFN- in the cell/tissue types in the available databases. A webserver implementing our method is accessible at http://isgpre.cvr.gla.ac.uk/. The docker image at https://hub.docker.com/r/hchai01/isgpre can be downloaded to reproduce the prediction.
DOI: 10.5524/102289
title: A Virtual Library for Behavioral Performance in Standard Conditions – Experiment 18 Q30 Effect of QNP dose (0 0.0312 0.0625 0.125 0.25 and 0.5 mg/kg) 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: 10.5524/102301
title: A Virtual Library for Behavioral Performance in Standard Conditions – Experiment 30 Q18 Effects of hypophysectomy on compulsive checking and cortical dendrites

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: 10.5524/102269
title: Genome assembly of a triploid <i>Pocillopora acuta</i>

description: This study details the genome assembly of the Hawaiian coral species <i>Pocillopora acuta</i>. Members of this genus are distributed worldwide and therefore of broad scientific and ecological importance. For <i>Poc. acuta</i>, a high-quality assembly was generated using short-read Illumina and long-read PacBio data. The <i>Poc. acuta</i> assembly is from a triploid individual, making it the first reference genome of a non-diploid coral animal. This genome assembly is a significant improvement over available data and provides an invaluable resource for supporting multi-omics studies into coral biology, not just in Hawaii, but also in other regions, where related species exist. The <i>Poc. acuta</i> assembly gives us, for the first time, a platform for studying polyploidy in corals, and its role in genome evolution and stress adaptation in these organisms.
DOI: 10.5524/102270
title: Genome assembly of <i>Pocillopora meandrina</i>

description: This study details the genome assembly of the Hawaiian coral species <i>Pocillopora meandrina</i>. Members of this genus are distributed worldwide and therefore of broad scientific and ecological importance. For <i>Poc. meandrina</i>, a high-quality assembly was generated using short-read Illumina and long-read PacBio data. This genome assembly is a significant improvement over available data and provides an invaluable resource for supporting multi-omics studies into coral biology, not just in Hawaii, but also in other regions, where related species exist.
DOI: 10.5524/102274
title: A Virtual Library for Behavioral Performance in Standard Conditions – Experiment 03 Q25 Effect of an NMDA lesion of the BLA 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.