cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.9770687.v2
title: Metadata record for: De novo transcriptome assembly and analysis of the freshwater araphid diatom Fragilaria radians, Lake Baikal

description: This dataset contains key characteristics about the data described in the Data Descriptor De novo transcriptome assembly and analysis of the freshwater araphid diatom Fragilaria radians, Lake Baikal. <br> Contents: <br> 1. human readable metadata summary table in CSV format 2. machine readable metadata file in JSON format 3. machine readable metadata file in ISA-Tab format (zipped folder)<br><br>Versioning Note:Version 2 was generated when the metadata format was updated from JSON to JSON-LD. This was an automatic process that changed only the format, not the contents, of the metadata.<br><br>
DOI: 10.6084/m9.figshare.9770687.v1
title: Metadata record for: De novo transcriptome assembly and analysis of the freshwater araphid diatom Fragilaria radians, Lake Baikal

description: This dataset contains key characteristics about the data described in the Data Descriptor De novo transcriptome assembly and analysis of the freshwater araphid diatom Fragilaria radians, Lake Baikal. <br> Contents: <br> 1. human readable metadata summary table in CSV format 2. machine readable metadata file in JSON format <br><br>
DOI: 10.6084/m9.figshare.9768116
title: Acute changes in cortical activation during active ankle movement after whole-body vibration for spasticity in hemiplegic legs of stroke patients: a functional near-infrared spectroscopy study

description: <b>Background</b>: A recent study revealed that whole-body vibration (WBV) tends to decrease spasticity in stroke-related hemiplegic legs. However, acute changes in cortical activation after WBV are unclear. <b>Objective</b>: To examine whether WBV induces acute changes in sensorimotor cortical activation in patients with stroke-related hemiplegic legs. <b>Methods</b>: Eleven stroke patients (mean age 52.6 [SD 15.4] years; median time after stroke 3 [25<sup>th</sup> and 75<sup>th</sup> percentiles; 3 and 10.5, respectively] months) participated in a comparative before-and-after intervention trial. Six healthy adults were also studied. WBV at 30 Hz was applied for 5 min to the hamstrings, gastrocnemius, and soleus muscles. Spasticity was assessed according to the modified Ashworth scale (MAS). Active and passive range of motion (A-ROM and <i>P</i>-ROM, respectively) were also measured. Change in Oxy-Hb concentration in bilateral sensorimotor cortex associated with voluntary ankle dorsiflexion of the affected limb was assessed via functional near-infrared spectroscopy (fNIRS) before and immediately after WBV. <b>Results</b>: MAS score, A-ROM, and <i>P</i>-ROM improved immediately after WBV. In the patients, while there was no significant interaction between effects of region (ipsilesional and contralesional sensorimotor cortex) and the WBV intervention (before and immediately after WBV) (<i>F</i><sub>1,10</sub> = 0.702, <i>p</i> = .422), there was a significant main effect of the WBV intervention (<i>F</i><sub>1,10</sub> = 6.971, <i>p</i> = .025). In the healthy participants, there was no association with the WBV intervention or region. <b>Conclusions</b>: In patients with stroke-related spastic-hemiplegic legs, WBV might result not only in clinical improvement but also in acute increase in sensorimotor cortical activation.
DOI: 10.6084/m9.figshare.9768116.v1
title: Acute changes in cortical activation during active ankle movement after whole-body vibration for spasticity in hemiplegic legs of stroke patients: a functional near-infrared spectroscopy study

description: <b>Background</b>: A recent study revealed that whole-body vibration (WBV) tends to decrease spasticity in stroke-related hemiplegic legs. However, acute changes in cortical activation after WBV are unclear. <b>Objective</b>: To examine whether WBV induces acute changes in sensorimotor cortical activation in patients with stroke-related hemiplegic legs. <b>Methods</b>: Eleven stroke patients (mean age 52.6 [SD 15.4] years; median time after stroke 3 [25<sup>th</sup> and 75<sup>th</sup> percentiles; 3 and 10.5, respectively] months) participated in a comparative before-and-after intervention trial. Six healthy adults were also studied. WBV at 30 Hz was applied for 5 min to the hamstrings, gastrocnemius, and soleus muscles. Spasticity was assessed according to the modified Ashworth scale (MAS). Active and passive range of motion (A-ROM and <i>P</i>-ROM, respectively) were also measured. Change in Oxy-Hb concentration in bilateral sensorimotor cortex associated with voluntary ankle dorsiflexion of the affected limb was assessed via functional near-infrared spectroscopy (fNIRS) before and immediately after WBV. <b>Results</b>: MAS score, A-ROM, and <i>P</i>-ROM improved immediately after WBV. In the patients, while there was no significant interaction between effects of region (ipsilesional and contralesional sensorimotor cortex) and the WBV intervention (before and immediately after WBV) (<i>F</i><sub>1,10</sub> = 0.702, <i>p</i> = .422), there was a significant main effect of the WBV intervention (<i>F</i><sub>1,10</sub> = 6.971, <i>p</i> = .025). In the healthy participants, there was no association with the WBV intervention or region. <b>Conclusions</b>: In patients with stroke-related spastic-hemiplegic legs, WBV might result not only in clinical improvement but also in acute increase in sensorimotor cortical activation.
DOI: 10.6084/m9.figshare.9768071
title: Training and test datasets used for building graph convolutional deep neural network model for prediction molecular electrostatic surfaces

description: The model build using these datasets can be found at https://github.com/AstexUK/ESP_DNN/tree/master/esp_dnn<br>The dataset themselves can be opened using xarray Python library (http://xarray.pydata.org/en/stable/#)
DOI: 10.6084/m9.figshare.9768101.v1
title: QMaker-datasets.zip

description: Pfam datasets for QMaker
DOI: 10.6084/m9.figshare.9768101.v2
title: QMaker-datasets.zip

description: Pfam datasets for QMaker
DOI: 10.6084/m9.figshare.9768026
title: Classification of GABAergic interneurons by leading neuroscientists

description: n 2013, we asked 48 leading neuroscientists to classify 320 interneurons by inspecting images of their morphology. That study was the first to quantify the degree of agreement among neuroscientists in morphology-based interneuron classification, showing high agreement for the chandelier and Martinotti types, yet low agreement for most of the remaining types considered. Here we present the dataset containing the classification choices by the neuroscientists according to interneuron type as well as to five prominent morphological features.
DOI: 10.6084/m9.figshare.9768020
title: Kopec_Rothberg_deGroot_MthK_Gating_Source_Data.zip

description: Raw data from MD simulations of MthK gating.<br>
DOI: 10.6084/m9.figshare.9768101.v3
title: Input datasets and output matrices of QMaker

description: QMaker-datasets.zip: Seven datasets which were used to test QMakermatrices-normalized.zip: Seven output matrices (corresponding to these above datasets) <br>
DOI: 10.6084/m9.figshare.9768026.v1
title: Classification of GABAergic interneurons by leading neuroscientists

description: n 2013, we asked 48 leading neuroscientists to classify 320 interneurons by inspecting images of their morphology. That study was the first to quantify the degree of agreement among neuroscientists in morphology-based interneuron classification, showing high agreement for the chandelier and Martinotti types, yet low agreement for most of the remaining types considered. Here we present the dataset containing the classification choices by the neuroscientists according to interneuron type as well as to five prominent morphological features.
DOI: 10.6084/m9.figshare.9767993
title: Supplementary Material for: Proopiomelanocortin Processing in the Hypothalamus Is Directly Regulated by Saturated Fat: Implications for the Development of Obesity

description: In outbred mice, susceptibility or resistance to diet-induced obesity is associated with rapid changes in hypothalamic proopiomelanocortin (POMC) levels. Here, we evaluated 3 hypotheses that potentially explain the development of the different obesity phenotypes in outbred Swiss mice. First, rapid and differential changes in the gut microbiota in obesity-prone (OP) and obesity-resistant (OR) mice fed on a high-fat diet (HFD) might cause differential efficiencies in fatty acid harvesting leading to changes in systemic fatty acid concentrations that in turn affect POMC expression and processing. Second, independently of the gut microbiota, OP mice might have increased blood fatty acid levels after the introduction of a HFD, which could affect POMC expression and processing. Third, fatty acids might act directly in the hypothalamus to differentially regulate POMC expression and/or processing in OP and OR mice. We evaluated OP and OR male Swiss mice using 16S rRNA sequencing for the determination of gut microbiota; gas chromatography for blood lipid determination; and immunoblot and real-time polymerase chain reaction for protein and transcript determination and indirect calorimetry. Some experiments were performed with human pluripotent stem cells differentiated into hypothalamic neurons. We did not find evidence supporting the first 2 hypotheses. However, we found that in OP but not in OR mice, palmitate induces a rapid increase in hypothalamic <i>POMC</i>, which is followed by increased expression of proprotein convertase subtilisin/kexin type 1 <i>PC1/3</i>. Lentiviral inhibition of hypothalamic <i>PC1/3</i> increased caloric intake and body mass in both OP and OR mice. In human stem cell-derived hypothalamic cells, we found that palmitate potently suppressed the production of POMC-derived peptides. Palmitate directly regulates <i>PC1/3</i> in OP mice and likely has a functional impact on POMC processing.
DOI: 10.6084/m9.figshare.9767930
title: Impulsive acoustic noise in three different scenarios

description: We acquired the acoustic data in three different scenarios using a setup with four channels (microphones) without audio source (only noise):1. Indoor scenario: A silent environment inside an empty auditorium;<br>2. Hall scenario: A mixed indoor/outdoor environment at the same auditorium hall;<br>3. Outdoor scenario: Outside the auditorium.<br><br>The setup is a low-cost setup with a ReSpeaker Core v1 (MT7688) board using the Analog-to-Digital Converter (ADC) AC108 with four ADC delta-sigma, 48 kHz of sample rate, and 3.3 V voltage range, with four microphones connected to a Raspberry Pi 3 (model B) processor to collect and store the data.<br>If you used the datasets, please consider citing our paper: "Acoustic Impulsive Noise Based on Non-Gaussian Models: An Experimental Evaluation", https://doi.org/10.3390/s19122827<br>
DOI: 10.6084/m9.figshare.9767993.v1
title: Supplementary Material for: Proopiomelanocortin Processing in the Hypothalamus Is Directly Regulated by Saturated Fat: Implications for the Development of Obesity

description: In outbred mice, susceptibility or resistance to diet-induced obesity is associated with rapid changes in hypothalamic proopiomelanocortin (POMC) levels. Here, we evaluated 3 hypotheses that potentially explain the development of the different obesity phenotypes in outbred Swiss mice. First, rapid and differential changes in the gut microbiota in obesity-prone (OP) and obesity-resistant (OR) mice fed on a high-fat diet (HFD) might cause differential efficiencies in fatty acid harvesting leading to changes in systemic fatty acid concentrations that in turn affect POMC expression and processing. Second, independently of the gut microbiota, OP mice might have increased blood fatty acid levels after the introduction of a HFD, which could affect POMC expression and processing. Third, fatty acids might act directly in the hypothalamus to differentially regulate POMC expression and/or processing in OP and OR mice. We evaluated OP and OR male Swiss mice using 16S rRNA sequencing for the determination of gut microbiota; gas chromatography for blood lipid determination; and immunoblot and real-time polymerase chain reaction for protein and transcript determination and indirect calorimetry. Some experiments were performed with human pluripotent stem cells differentiated into hypothalamic neurons. We did not find evidence supporting the first 2 hypotheses. However, we found that in OP but not in OR mice, palmitate induces a rapid increase in hypothalamic <i>POMC</i>, which is followed by increased expression of proprotein convertase subtilisin/kexin type 1 <i>PC1/3</i>. Lentiviral inhibition of hypothalamic <i>PC1/3</i> increased caloric intake and body mass in both OP and OR mice. In human stem cell-derived hypothalamic cells, we found that palmitate potently suppressed the production of POMC-derived peptides. Palmitate directly regulates <i>PC1/3</i> in OP mice and likely has a functional impact on POMC processing.
DOI: 10.6084/m9.figshare.9768101.v4
title: Input datasets and output matrices of QMaker

description: QMaker-datasets.zip: Two Pfam datasets which were used with QMakerMatrices-normalized.zip: Seven output matrices for Pfam, Pfam-gb, Bird, Insect, Mammal, Plant, and Yeast datasets.<br>
DOI: 10.6084/m9.figshare.9767732
title: Five Minute Dungeon Timer Data

description: Data from playing Five Minute Dungeon in two classes at YorkU.<br>MetadataRep is the replicate of playing the game.Date is calendar date.Boss is the monster to defeat.Outcome is won or lost defined as whether completed and beat the boss in less than 5 minutes using the timer app associated with the game.Time is in seconds and is the moment a given team called out that they beat that particular boss.Joy is how much fun it was to play based on that instance. These measure is a Likert Scale from 1 to 5 with 1 being not fun at all and 5 being awesome.<br><br>
DOI: 10.6084/m9.figshare.9768101.v5
title: Datasets and matrices of QMaker

description: QMaker-datasets.zip: Pfam datasets which were used with QMaker (training Pfam, testing Pfam, training Pfam-gb, and testing Pfam-gb).<br>Matrices-normalized.zip: Seven output matrices for Pfam, Pfam-gb, Bird, Insect, Mammal, Plant, and Yeast datasets.<br>
DOI: 10.6084/m9.figshare.9768101.v6
title: Datasets and matrices of QMaker

description: QMaker-datasets.zip: Pfam datasets which were used with QMaker (training Pfam, testing Pfam, training Pfam-gb, and testing Pfam-gb).<br>Matrices-normalized.zip: Seven output matrices for Pfam, Pfam-gb, Bird, Insect, Mammal, Plant, and Yeast datasets.<br>
DOI: 10.6084/m9.figshare.9767732.v1
title: Five Minute Dungeon Timer Data

description: Data from playing Five Minute Dungeon Timer in two classes at YorkU.<br>Rep is the replicate of playing the game.Date is calendar date.Boss is the monster to defeat.Outcome is won or lost defined as whether completed and beat the boss is less than 5 minutes using the timer app associated with the game.Time is in seconds and is the moment a given team called out that they beat that particular boss.Joy is how much fun it was to play based on that instance. These measure is a Likert Scale from 1 to 5 with 1 being not fun at all and 5 being awesome.<br><br>
DOI: 10.6084/m9.figshare.9768101.v7
title: Datasets, matrices and supplementary figure for QMaker

description: QMaker-datasets.zip: Pfam datasets which were used with QMaker (training Pfam, testing Pfam, training Pfam-gb, and testing Pfam-gb).<br>Matrices-normalized.zip: Eight output matrices for LG, Pfam, Pfam-gb, Bird, Insect, Mammal, Plant, and Yeast datasets.<br>Figure S1.pdf: The performance of five matrices, i.e., Q.pfam, Q.pfam.gb, JTT, LG, WAG on five clade-specific datasets, i.e., Bird, Plant, Insect, Yeast Mammal.<br>
DOI: 10.6084/m9.figshare.9767567
title: On the development of sleep states in the first weeks of life - REVISED

description: Related to https://www.biorxiv.org/content/10.1101/678144v1<br>data_scripts has three folders: data, results and scripts. For more details please see README <br>
DOI: 10.6084/m9.figshare.9767567.v1
title: On the development of sleep states in the first weeks of life - REVISED

description: Related to https://www.biorxiv.org/content/10.1101/678144v1<br>data_scripts has three folders: data, results and scripts. For more details please see README <br>
DOI: 10.6084/m9.figshare.9767513
title: Supplementary Material for: Direct Oral Anticoagulant Plasma Levels for the Management of Acute Ischemic Stroke

description: <b><i>Introduction:</i></b> The management of acute ischemic stroke in patients on direct oral anticoagulants (DOACs) is challenging. However, the substance-specific plasma level could guide treatment decisions on recanalization therapies. We present a plasma-level-based protocol for emergency treatment of stroke patients on oral anticoagulants. Bleeding complications and clinical outcome for patients on DOACs are reported and compared to patients on vitamin K antagonists (VKAs). <b><i>Methods:</i></b> In patients with acute ischemic stroke and suspected use of DOACs within 48 h prior to hospital admission, plasma levels were measured using the calibrated Xa-activity (apixaban, edoxaban, rivaroxaban) or the Hemoclot®-assay (dabigatran). Levels &lt;50 ng/mL were supportive for thrombolysis, while high values &gt;100 ng/mL excluded patients from recombinant tissue plasminogen activator use. For patients on VKAs, the cutoff was set at international normalized ratio of 1.7. Endovascular thrombectomy of a large vessel occlusion was performed independently from coagulation testing. Consecutive patients were included in an observational registry. <b><i>Results:</i></b> Five hundred and twenty-two patients (261 on VKAs and 261 on DOACs) were included. Thirty patients (11.5%) on VKAs and 24 (9.2%) on DOACs received thrombolysis, followed by mechanical thrombectomy in 10 and 14 patients, respectively. Seventeen patients in each group received thrombectomy only. Symptomatic intracranial hemorrhage associated with thrombolysis occurred in 1 patient on VKA (3.3%) and 1 on DOAC (4.2%; <i>p</i> = 0.872). The turnaround time of specific assays did not show a significant delay in comparison to standard coagulation parameters. <b><i>Conclusion:</i></b> DOAC plasma levels could support decisions on emergency treatment of ischemic stroke. Systemic thrombolysis below suggested thresholds appears preliminary feasible and safe without an excess in bleeding complications.
DOI: 10.6084/m9.figshare.9767564
title: Borup Fiord Pass - Metagenome Assembled Genomes (MAGs) and Sample Metagenomes

description: These are the Metagenome Assembled Genomes and individual sample metagenomes generated and presented for a publication in preparation to mSystems.<br><br>These data were generated from samples collected at Borup Fiord Pass between 2014 and 2017.
DOI: 10.6084/m9.figshare.9767732.v2
title: Five Minute Dungeon Timer Data

description: Data from playing Five Minute Dungeon Timer in two classes at YorkU.<br>Rep is the replicate of playing the game.Date is calendar date.Boss is the monster to defeat.Outcome is won or lost defined as whether completed and beat the boss is less than 5 minutes using the timer app associated with the game.Time is in seconds and is the moment a given team called out that they beat that particular boss.Joy is how much fun it was to play based on that instance. These measure is a Likert Scale from 1 to 5 with 1 being not fun at all and 5 being awesome.<br><br>
DOI: 10.6084/m9.figshare.9767564.v2
title: Borup Fiord Pass - Metagenome Assembled Genomes (MAGs) and Sample Metagenomes

description: These are the Metagenome Assembled Genomes and individual sample metagenomes generated and presented for a publication in preparation to mSystems.<br><br>These data were generated from samples collected at Borup Fiord Pass between 2014 and 2017.
DOI: 10.6084/m9.figshare.9767495
title: Supplementary Material for: Poor Perceived Health is Associated with Current use of Electronic Cigarette among Current and Former Smokers: Findings from the CONSTANCES Cohort

description: <b><i>Background:</i></b> Electronic cigarettes (e-cigarettes) have become increasingly popular, yet beyond social or technical features, the specific health-related reasons adults use e-cigarettes remain poorly understood. <b><i>Objective:</i></b> To explore the cross-sectional associations between perceived health and current e-cigarette use in a large population-based cohort. <b><i>Methods:</i></b> From the participants included in the French CONSTANCES cohort (a large general-purpose national population-based cohort) from 2015 to 2017, we included 18,300 ever tobacco smokers with data on their e-cigarette use. We used logistic regressions to estimate the associations between e-cigarette use and perceived health (global and respiratory), stratifying on participants’ smoking status and adjusting for sociodemographic characteristics. To examine the role of objective health features (reported diagnoses and measured parameters during a health examination), we adjusted for prior history of respiratory and cardiovascular diseases, diabetes, cancer, spirometry, and blood pressure. Finally, we examined the effect of additionally adjusting for several health-related behaviors. <b><i>Results:</i></b> Participants with poor perceived health (global and respiratory) were at greater risk of e-cigarette use. These associations remained unchanged after adjustment for objective health features and health-related behaviors (e.g., in current smokers, for global perceived health, an odds ratio of 1.10 [95% CI 1.03–1.16] per increase on an 8-point scale from very good to very poor). <b><i>Conclusions:</i></b> Our findings suggest that the more current and former smokers felt unhealthy, the more they tended to currently use e-cigarettes. People who regularly use e-cigarettes should obtain medical supervision that takes into account not only objective diagnoses and measurements but also perceived health. Counseling practices could include assessing perceived health status to reinforce motivation to quit smoking.