cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7853570.v1
title: Dataset for: Exercise during Abstinence Normalizes Ultrastructural Synaptic Plasticity Associated with Nicotine-Seeking following Extended Access Self-Administration

description: Nicotine-craving progressively increases, or incubates, over abstinence following extended access self-administration. While not yet examined for nicotine, the incubation of cocaine-seeking is accompanied by changes in synaptic plasticity in the nucleus accumbens. Here, we determined whether such changes also accompany enhanced nicotine-seeking following extended access self-administration and abstinence, and whether exercise, a potential intervention for nicotine addiction, may exert its efficacy by normalizing these changes. Given that in humans, tobacco/nicotine use begins during adolescence, we used an adolescent-onset model. Nicotine-seeking was assessed in male rats following extended access nicotine or saline self-administration (23-hr/day, 10 days) and 10 days of abstinence, conditions known to induce the incubation of nicotine-seeking, using a within-session extinction/cue-induced reinstatement procedure. A subset of rats had 2-hr/day access to a running wheel during abstinence. Ultrastructural alterations of synapses in the nucleus accumbens core and shell were examined using electron microscopy. Nicotine-seeking was elevated following extended access self-administration and abstinence (in sedentary group), and levels of seeking were associated with an increase in the density of asymmetric (excitatory) and symmetric (inhibitory) synapses onto dendrites in the core, as well as longer asymmetric synapses onto spines, a marker of synaptic potentiation, in both the core and shell. Exercise normalized each of these changes; however, in the shell, exercise and nicotine similarly increased synapse length. Together, these findings indicate an association between nicotine-seeking and synaptic plasticity in the nucleus accumbens, particularly the core, and indicate that the efficacy of exercise to reduce nicotine-seeking may be mediated by reversing these adaptations.
DOI: 10.6084/m9.figshare.7853555
title: CCDB_3563.jpg

description: Correlative microscopic characterization of dendritic spines in a transgenic mouse model of hyperdopaminergia: The dopamine transporter knockout mouse
DOI: 10.6084/m9.figshare.7853561
title: MultipleTaxaClustersFamiliyGenus

description: Clustering results with multiple families and genera of the metazoan mitochondrial gene sequences.
DOI: 10.6084/m9.figshare.7853471
title: Host Frequency

description: Hosts extracted from DOIs<br>
DOI: 10.6084/m9.figshare.7853462
title: 10,000 DOIs

description: Randomly sampled 10,000 DOIs from a broader dataset of crawled scholarly resources<br>
DOI: 10.6084/m9.figshare.7853471.v1
title: Host Frequency

description: Hosts extracted from DOIs<br>
DOI: 10.6084/m9.figshare.7853555.v1
title: CCDB_3563.jpg

description: Correlative microscopic characterization of dendritic spines in a transgenic mouse model of hyperdopaminergia: The dopamine transporter knockout mouse
DOI: 10.6084/m9.figshare.7853462.v1
title: 10,000 DOIs

description: Randomly sampled 10,000 DOIs from a broader dataset of crawled scholarly resources<br>
DOI: 10.6084/m9.figshare.7853405
title: t1.nii

description: T1W image of 60 yr old<br>
DOI: 10.6084/m9.figshare.7853399
title: A Method to Facilitate Cancer Detection and Type Classification from Gene Expression Data using a Deep Autoencoder and Neural Network

description: A Method to Facilitate Cancer Detection and Type Classification from Gene Expression Data using a Deep Autoencoder and Neural Network <br> With the increased affordability and availability of whole-genome sequencing, large-scale and high-throughput gene expression is widely used to characterize diseases, including cancers. However, establishing specificity in cancer diagnosis using gene expression data continues to pose challenges due to the high dimensionality and complexity of the data. Here we present models of deep learning (DL) and apply them to gene expression data for the diagnosis and categorization of cancer. In this study, we have developed two DL models using messenger ribonucleic acid (mRNA) datasets available from the Genomic Data Commons repository. Our models achieved 98% accuracy in cancer detection, with false negative and false positive rates below 1.7%. In our results, we demonstrated that 18 out of 32 cancer-typing classifications achieved more than 90% accuracy. Due to the limitation of a small sample size (less than 50 observations), certain cancers could not achieve a higher accuracy in typing classification, but still achieved high accuracy for the cancer detection task. To validate our models, we compared them with traditional statistical models. The main advantage of our models over traditional cancer detection is the ability to use data from various cancer types to automatically form features to enhance the detection and diagnosis of a specific cancer type.
DOI: 10.6084/m9.figshare.7853306
title: All data

description: IV relationships from NMDA receptor and AMPA/kainate currents from hippocampal Schaffer-CA1 synapses from sham and sound stimulated animals.-Data from AMPA/kainate EPSCs recorded at -80 mV from Schaffer-CA1 synapses in hippocampal pyramidal neurons from rats sham and sound stimulated animals.-Data from NMDA EPSCs recorded at 70 mV from Schaffer-CA1 synapses in hippocampal pyramidal neurons from rats sham and sound stimulated animals. All glutamatergic currents were recorded in the presence of picrotixi.-Data from GABAergic spontaneous IPSCs (in the presence of DNQX) and miniature IPSCs recorded at --80 mV. mIPSCs were recorded in the presence of TTX.<br>The sound stimulation protocol was described in Cunha <i>et al., </i><i>Neuroscience</i>. 310:114-27. 2015.
DOI: 10.6084/m9.figshare.7853399.v1
title: A Method to Facilitate Cancer Detection and Type Classification from Gene Expression Data using a Deep Autoencoder and Neural Network

description: A Method to Facilitate Cancer Detection and Type Classification from Gene Expression Data using a Deep Autoencoder and Neural Network <br> With the increased affordability and availability of whole-genome sequencing, large-scale and high-throughput gene expression is widely used to characterize diseases, including cancers. However, establishing specificity in cancer diagnosis using gene expression data continues to pose challenges due to the high dimensionality and complexity of the data. Here we present models of deep learning (DL) and apply them to gene expression data for the diagnosis and categorization of cancer. In this study, we have developed two DL models using messenger ribonucleic acid (mRNA) datasets available from the Genomic Data Commons repository. Our models achieved 98% accuracy in cancer detection, with false negative and false positive rates below 1.7%. In our results, we demonstrated that 18 out of 32 cancer-typing classifications achieved more than 90% accuracy. Due to the limitation of a small sample size (less than 50 observations), certain cancers could not achieve a higher accuracy in typing classification, but still achieved high accuracy for the cancer detection task. To validate our models, we compared them with traditional statistical models. The main advantage of our models over traditional cancer detection is the ability to use data from various cancer types to automatically form features to enhance the detection and diagnosis of a specific cancer type.
DOI: 10.6084/m9.figshare.7853186
title: Drosophila melanogaster CasX sites

description: This is an annotated list of potential CasX (Cas12e) editing sites based on Ensembl Release 95 for <i>Drosophila melanogaster</i>. The sites are annotated with location contig, start, end, target sequence, PAM sequence, uniqueness among editing sites, and overlaps with known exons.
DOI: 10.6084/m9.figshare.7853219
title: Danio rerio CasX sites

description: This is an annotated list of potential CasX (Cas12e) editing sites based on Ensembl Release 95 for <i>Danio rerio</i>. The sites are annotated with location contig, start, end, target sequence, PAM sequence, uniqueness among editing sites, and overlaps with known exons.
DOI: 10.6084/m9.figshare.7853186.v1
title: Drosophila melanogaster CasX sites

description: This is an annotated list of potential CasX (Cas12e) editing sites based on Ensembl Release 95 for <i>Drosophila melanogaster</i>. The sites are annotated with location contig, start, end, target sequence, PAM sequence, uniqueness among editing sites, and overlaps with known exons.
DOI: 10.6084/m9.figshare.7853219.v1
title: Danio rerio CasX sites

description: This is an annotated list of potential CasX (Cas12e) editing sites based on Ensembl Release 95 for <i>Danio rerio</i>. The sites are annotated with location contig, start, end, target sequence, PAM sequence, uniqueness among editing sites, and overlaps with known exons.
DOI: 10.6084/m9.figshare.7851899
title: Saccharomyces cerevisiae CasX sites

description: This is an annotated list of potential CasX (Cas12e) editing sites based on Ensembl Release 95 for <i>Saccharomyces cerevisiae</i>. The sites are annotated with location contig, start, end, target sequence, PAM sequence, uniqueness among editing sites, and overlaps with known exons.
DOI: 10.6084/m9.figshare.7852172
title: Global Flow

description: This archive contains estimates of runoff to all river outlets globally, excluding Greenland and Antarctica, based on routing through the simulated topological network at 30-minute spatial resolution (STN-30p, version 6.01;<br>2004–07) flow network [Vörösmarty et al. 2000; downloaded from Water Systems Analysis Group (2007)] at 1/2-degree latitude-by-longitude resolution using the Lohmann et al. (1996, 1998) routing model. The data set is a hybrid of simulated and observed streamflow for 4 model-method combinations, as described in<br>Clark, E.A., J. Sheffield, M.T.H. van Vliet, B. Nijssen, and D.P. Lettenmaier, 2015, Continental runoff into the oceans (1950-2008), J. Hydrometeor., http://dx.doi.org/10.1175/JHM-D-14-0183.1.
DOI: 10.6084/m9.figshare.7852493
title: Caenorhabditis elegans CasX sites

description: This is an annotated list of potential CasX (Cas12e) editing sites based on Ensembl Release 95 for <i>Caenorhabditis elegans</i>. The sites are annotated with location contig, start, end, target sequence, PAM sequence, uniqueness among editing sites, and overlaps with known exons.
DOI: 10.6084/m9.figshare.7853033
title: Genetic and antigenic heterogeneity of infectious bronchitis virus in South America: implications for control programmes

description: Infectious bronchitis virus (IBV) is a persistent sanitary problem for the South American poultry industry despite extensive vaccination. The IBV single-stranded RNA genome has high rates of mutation and recombination that generate a notorious virus variability. Since most IBV vaccines are type-specific, there is a need for constant surveillance of the circulating lineages and knowledge about their genetic and antigenic properties. Here we present an integrative analysis that provides the pattern of genetic variation of the South American IBV strains and information about their antigenic characteristics. The genetic analysis was performed using the S1 complete coding sequences of all available South American strains, including newly obtained Argentine and Uruguayan field samples. Our phylogenetic and phylodynamic analyses evidence that three main lineages (GI-1, GI-11 and GI-16) are extensively circulating in South American flocks. Strains of the GI-1 lineage (Massachusetts-type) were detected in Argentina, Brazil, Chile and Colombia. The GI-11 lineage is an exclusively South American lineage that emerged in the 1950s, and is the predominant lineage in Brazil and Uruguay at present. The GI-16 lineage emerged around 1979, and is currently circulating in most South American territories (Argentina, Chile, Uruguay, Colombia and Peru). The virus cross-neutralization test performed here reveals very low antigenic relatedness between GI-11 and GI-16 lineages (i.e. they are different serotypes). The results of this study extend our knowledge about the present and past IBV variability in South America and provide relevant elements to improve the control programmes by considering the genetic and antigenic attributes of IBV.
DOI: 10.6084/m9.figshare.7851899.v1
title: Saccharomyces cerevisiae CasX sites

description: This is an annotated list of potential CasX (Cas12e) editing sites based on Ensembl Release 95 for <i>Saccharomyces cerevisiae</i>. The sites are annotated with location contig, start, end, target sequence, PAM sequence, uniqueness among editing sites, and overlaps with known exons.
DOI: 10.6084/m9.figshare.7852493.v1
title: Caenorhabditis elegans CasX sites

description: This is an annotated list of potential CasX (Cas12e) editing sites based on Ensembl Release 95 for <i>Caenorhabditis elegans</i>. The sites are annotated with location contig, start, end, target sequence, PAM sequence, uniqueness among editing sites, and overlaps with known exons.
DOI: 10.6084/m9.figshare.7851764
title: Self_as_Doer and Physical Activity_Share.sav

description: Data from a study which explores how barrier self-efficacy mediates the relationship between self-as-doer identity and physical activity behaviors.
DOI: 10.6084/m9.figshare.7851767
title: Codes and data - Lebreton et al. PLoSCb 2019

description: This folder contains all codes and data necessary to reproduce the analyses and results reported in 'Contextual influence on confidence judgments in human reinforcement learning’.<br><br>Please note that the codes needs Matlab R2014b or a more resent version, with the Statistics and Machine Learning toolbox<br>
DOI: 10.6084/m9.figshare.7853033.v1
title: Genetic and antigenic heterogeneity of infectious bronchitis virus in South America: implications for control programmes

description: Infectious bronchitis virus (IBV) is a persistent sanitary problem for the South American poultry industry despite extensive vaccination. The IBV single-stranded RNA genome has high rates of mutation and recombination that generate a notorious virus variability. Since most IBV vaccines are type-specific, there is a need for constant surveillance of the circulating lineages and knowledge about their genetic and antigenic properties. Here we present an integrative analysis that provides the pattern of genetic variation of the South American IBV strains and information about their antigenic characteristics. The genetic analysis was performed using the S1 complete coding sequences of all available South American strains, including newly obtained Argentine and Uruguayan field samples. Our phylogenetic and phylodynamic analyses evidence that three main lineages (GI-1, GI-11 and GI-16) are extensively circulating in South American flocks. Strains of the GI-1 lineage (Massachusetts-type) were detected in Argentina, Brazil, Chile and Colombia. The GI-11 lineage is an exclusively South American lineage that emerged in the 1950s, and is the predominant lineage in Brazil and Uruguay at present. The GI-16 lineage emerged around 1979, and is currently circulating in most South American territories (Argentina, Chile, Uruguay, Colombia and Peru). The virus cross-neutralization test performed here reveals very low antigenic relatedness between GI-11 and GI-16 lineages (i.e. they are different serotypes). The results of this study extend our knowledge about the present and past IBV variability in South America and provide relevant elements to improve the control programmes by considering the genetic and antigenic attributes of IBV.
DOI: 10.6084/m9.figshare.7853210.v1
title: Randomly generated article

description: article.pdf
DOI: 10.6084/m9.figshare.7851689
title: who_regimen_counts.tsv

description: WHO regimen counts for each tool and dataset.
DOI: 10.6084/m9.figshare.7851764.v1
title: Self_as_Doer and Physical Activity_Share.sav

description: Data from a study which explores how barrier self-efficacy mediates the relationship between self-as-doer identity and physical activity behaviors.
DOI: 10.6084/m9.figshare.7853210.v2
title: Randomly generated article with images

description: article.pdf
DOI: 10.6084/m9.figshare.7851674
title: EmojiGrid affective odor responses

description: . Observers (N=56, 24 males, mean age=24.3±4.6) sniffed 40 randomly presented odors (27 food and 13 non-food smells) with a wide range of perceived hedonic valences, ranging from unpleasant and arousing (e.g., feces, fish), via pleasant and calming (e.g., clove, cinnamon) to pleasant and stimulating (e.g., peach, caramel). After sniffing, the participants reported their affective appraisal of each odor using the EmojiGrid. This Excels sheet lists the resulting mean valence and arousal ratings (with their SD values), together with corresponding mean ratings that were obtained with alternative rating tools in previous studies in the literature.
DOI: 10.6084/m9.figshare.7851674.v1
title: EmojiGrid affective odor responses

description: . Observers (N=56, 24 males, mean age=24.3±4.6) sniffed 40 randomly presented odors (27 food and 13 non-food smells) with a wide range of perceived hedonic valences, ranging from unpleasant and arousing (e.g., feces, fish), via pleasant and calming (e.g., clove, cinnamon) to pleasant and stimulating (e.g., peach, caramel). After sniffing, the participants reported their affective appraisal of each odor using the EmojiGrid. This Excels sheet lists the resulting mean valence and arousal ratings (with their SD values), together with corresponding mean ratings that were obtained with alternative rating tools in previous studies in the literature.
DOI: 10.6084/m9.figshare.7851767.v1
title: Codes and data

description: This folder contains all codes and data necessary to reproduce the analyses and results reported in 'Contextual influence on confidence judgments in human reinforcement learning’.<br><br>Please note that the codes needs Matlab R2014b or a more resent version, with the Statistics and Machine Learning toolbox<br>
DOI: 10.6084/m9.figshare.7851632
title: Analysis and Design of Clinical Trials Using Additive Hazards Survival Endpoints

description: <b><i>Abstract–</i>The additive hazards model provides benefits in interpretation and theoretical properties over the proportional hazards model, particularly in noninferiority trials. We describe techniques for designing and analyzing trials with a score-type test using the additive hazards model, with a focus on noninferiority trials. Accordingly, the techniques are illustrated using two noninferiority trials, the SPORTIF III trial of anti-coagulants for patients with atrial fibrillation, and the CPORT-E trial evaluating percutaneous coronary intervention in different clinical setting. We also derive a powerful test, which can be conducted using standard statistical software to distinguish between the additive and proportional hazards models. This test is shown to be effective in simulated data and applied to data from a study of melanoma as well as a study of colon cancer.</b>
DOI: 10.6084/m9.figshare.7851608
title: SUPPLEMENTARY MATERIAL.docx

description: The tables included show cross-tabulated results of mixed model analyses of data obtained on plasma concentrations of Peptide Y Y hormone and ad libitum food intake in volutnteers ingesting macronutrient containing microcapsules designed to release their contents in the stomach or distal small intestine.
DOI: 10.6084/m9.figshare.7851632.v1
title: Analysis and Design of Clinical Trials Using Additive Hazards Survival Endpoints

description: <b><i>Abstract–</i>The additive hazards model provides benefits in interpretation and theoretical properties over the proportional hazards model, particularly in noninferiority trials. We describe techniques for designing and analyzing trials with a score-type test using the additive hazards model, with a focus on noninferiority trials. Accordingly, the techniques are illustrated using two noninferiority trials, the SPORTIF III trial of anti-coagulants for patients with atrial fibrillation, and the CPORT-E trial evaluating percutaneous coronary intervention in different clinical setting. We also derive a powerful test, which can be conducted using standard statistical software to distinguish between the additive and proportional hazards models. This test is shown to be effective in simulated data and applied to data from a study of melanoma as well as a study of colon cancer.</b>
DOI: 10.6084/m9.figshare.7851536
title: ArCo Dataset

description: Linked Open Dataset of the ArCo project.
DOI: 10.6084/m9.figshare.7851578
title: Effort needed measure VAR index

description: Data used for analyses<br>
DOI: 10.6084/m9.figshare.7851584
title: Local Traditional FOODS with no missing values

description: This is the data set of a dietary survey on 178 adult women on reproductive age in Guasaganda (rural andes), with imputation of missing values using MICE (R package).<br>
DOI: 10.6084/m9.figshare.7851521
title: Combination of novel transcripts from de novo assembly and genes from reference annotations for 11 species

description: Details about the creation of these assemblies can be found at doi.org/10.1101/575837
DOI: 10.6084/m9.figshare.7851578.v1
title: Effort needed measure VAR index

description: Data used for analyses<br>
DOI: 10.6084/m9.figshare.7851584.v1
title: Local Traditional FOODS with no missing values

description: This is the data set of a dietary survey on 178 adult women on reproductive age in Guasaganda (rural andes), with imputation of missing values using MICE (R package).<br>
DOI: 10.1184/r1/7851515
title: Reorganized language network connectivity after left arcuate fasciculus resection: A case study

description: Dataset supporting a paper of the same title: Reorganized language network connectivity after left arcuate fasciculus resection: A case study<br><br>This dataset contains raw MRI data for the patient (DTI, fMRI, Anatomy) and 52 healthy control subjects (DTI, Anatomy). It also contains scripts used to produce the results of the paper including a BASH script to run tractography, and R scripts to run ANOVA on the functional connectivity data. Lastly, it includes summary level data in CSV files that were used as inputs to the scripts to produce the results.<br>ABSTRACT:Understanding the neural mechanisms that support spontaneous recovery of cognitive abilities can place important constraints on mechanistic theories of brain organization and function, and holds potential to inform clinical interventions. Connectivity-based MRI measures have emerged as a way to study how recovery from brain injury is modulated by changes in intra- and interhemispheric connectivity. Here we report a detailed and multi-modal case study of a 26 year-old male who presented with a left inferior parietal glioma infiltrating the left arcuate fasciculus. The patient underwent pre- and post-operative functional MRI and Diffusion Tensor Imaging, as well as behavioral assessments of language, motor, vision and praxis. The surgery for removal of the tumor was carried out with the patient awake, and direct electrical stimulation mapping was used to evaluate cortical language centers. The patient developed a specific difficulty with repeating sentences toward the end of the surgery, after resection of the tumor and partial transection of the arcuate fasciculus. The patient recovered from the sentence repetition impairments over several months after the operation. Coincident with the patient’s cognitive recovery, we document a pattern whereby intra-hemispheric functional connectivity was reduced in the left hemisphere, while inter-hemispheric connectivity increased between classic left hemisphere language regions and their right hemisphere homologues. These findings suggest that increased synchrony between the two hemispheres, in the setting of focal transection of the left arcuate fasciculus, may facilitate functional recovery.<br>