cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5522/04/14216594
title: Experimental Assessment of Skull Aberration and Transmission Loss at 270 kHz for Focused Ultrasound Stimulation of the Primary Visual Cortex

description: This data was collected in order to assess acoustic field aberrations and transmission loss induced by human skulls in the context of focused ultrasound stimulation of the primary visual cortex (V1) region of the brain. A 2 element spherically focusing annular array ultrasound transducer (H115, driven at 270 kHz, Sonic Concepts) was used to generate an acoustic field. Measurements were performed with a 0.2 mm PVDF needle hydrophone (Precision Acoustics) with right angle connector to reduce its length so it could be accommodated within the skull cavity. The transducer was driven under quasi continuous wave conditions at low drive level to produce a linear field. The transducer was held in a fixed position, the skull was positioned to obtain the correct focal alignment and the hydrophone was held in a 3D printed mount with manual alignment in the axial direction and automated scanning in the lateral directions. Measurements were performed inside 3 human skulls which had previously had the superior section of the parietal and frontal bones removed. Measurements were made with the transducer positioned at two locations for each skull corresponding to the focal region intersecting with the positions of the left and right V1 regions of the brain, with a 1 cm separation between source and skull. For each position, the hydrophone was aligned with the focus inside the skull, then a planar scan was performed covering the largest possible area while avoiding collision of the hydrophone with the skull bone. The skull was then removed and a 2<sup>nd</sup> scan was performed in water as a reference, the axial position was determined from time of flight in free field during these reference water scans. The study consists of 6 datasets, each of which contains a planar scan made within the skull cavity, and a reference planar scan in water after the skull was removed, preserving the coordinates. File 1: skull 2120, left V1 File 2: skull 2120, right V1 File 3: skull 2150, left V1 File 4: skull 2150, right V1 File 5: skull 2125, left V1 File 6: skull 2125, right V1
DOI: 10.5522/04/14216594.v1
title: Experimental Assessment of Skull Aberration and Transmission Loss at 270 kHz for Focused Ultrasound Stimulation of the Primary Visual Cortex

description: This data was collected in order to assess acoustic field aberrations and transmission loss induced by human skulls in the context of focused ultrasound stimulation of the primary visual cortex (V1) region of the brain. A 2 element spherically focusing annular array ultrasound transducer (H115, driven at 270 kHz, Sonic Concepts) was used to generate an acoustic field. Measurements were performed with a 0.2 mm PVDF needle hydrophone (Precision Acoustics) with right angle connector to reduce its length so it could be accommodated within the skull cavity. The transducer was driven under quasi continuous wave conditions at low drive level to produce a linear field. The transducer was held in a fixed position, the skull was positioned to obtain the correct focal alignment and the hydrophone was held in a 3D printed mount with manual alignment in the axial direction and automated scanning in the lateral directions. Measurements were performed inside 3 human skulls which had previously had the superior section of the parietal and frontal bones removed. Measurements were made with the transducer positioned at two locations for each skull corresponding to the focal region intersecting with the positions of the left and right V1 regions of the brain, with a 1 cm separation between source and skull. For each position, the hydrophone was aligned with the focus inside the skull, then a planar scan was performed covering the largest possible area while avoiding collision of the hydrophone with the skull bone. The skull was then removed and a 2<sup>nd</sup> scan was performed in water as a reference, the axial position was determined from time of flight in free field during these reference water scans. The study consists of 6 datasets, each of which contains a planar scan made within the skull cavity, and a reference planar scan in water after the skull was removed, preserving the coordinates. File 1: skull 2120, left V1 File 2: skull 2120, right V1 File 3: skull 2150, left V1 File 4: skull 2150, right V1 File 5: skull 2125, left V1 File 6: skull 2125, right V1
DOI: 10.6084/m9.figshare.14220098
title: Morphological and functional measurements

description: These data are morphological measurements and adhesion data for <i>Correlophus ciliatus</i> toe pads and tail pads
DOI: 10.6084/m9.figshare.14220098.v1
title: Morphological and functional measurements

description: These data are morphological measurements and adhesion data for <i>Correlophus ciliatus</i> toe pads and tail pads
DOI: 10.5281/zenodo.4488797
title: VAFW cylinders 2020, S1, S2, S4, S8, DIC raw data

description: The files contain the raw data obtained with digital image correlation (DIC) of variable-angle filament-wound (VAFW) cylinders. The data is used as an input for the stitching algorithm described in the manuscript: Castro, S. G. P., Almeida, J. H. S., Jr., St-Pierre, L., & Wang, Z. (2021, March 5). Measuring geometric imperfections of variable-angle filament-wound cylinders with a simple digital image correlation setup. https://doi.org/10.31224/osf.io/kn6x5 In that manuscript, the naming convention translates as follows. Cylinder name in the dataset &lt;--&gt; cylinder name in the manuscript: S1 &lt;--&gt; MA S2 &lt;--&gt; CA S4 &lt;--&gt; VAFW4 S8 &lt;--&gt; VAFW8 All coordinates (x,y,z) and the imperfection amplitude (imp) are in millimeters. Each measurement, e.g. "S1-1-measurement-1" is organized in a separate folder, where: "S1-1-cal-XXX.tif" are the pictures used for calibrating the DIC system "S1-1-XXX.tif" are the pictures used to extract the cloud of points that represent the imperfect shell surface "S1-1-measurement-XXXdeg.csv" contains the extracted data of one out of the six angular positions "S1-1-XXX.out" and "S1-1*.z3d" are binary files saved by the Vic3D system
DOI: 10.5281/zenodo.4608163
title: REcoM2 code for MITgcm v62r with added parameterizations

description: This dataset contains the scripts necessary to run the REcoM2 package with MITgcm v62r for the West Antarctic Peninsula. It includes a parameterization to include non-linearities in PAR due to the influence of partial sea-ice coverage as in Long et al. (2015). Long, M.C., Lindsay, K., Holland, M.M. (2015). Modeling photosynthesis in sea ice covered waters, Journal of Advances in Modeling Earth Systems, 07. doi:10.1002/2015MS000436
DOI: 10.5281/zenodo.4608162
title: REcoM2 code for MITgcm v62r with added parameterizations

description: This dataset contains the scripts necessary to run the REcoM2 package with MITgcm v62r for the West Antarctic Peninsula. It includes a parameterization to include non-linearities in PAR due to the influence of partial sea-ice coverage as in Long et al. (2015). Long, M.C., Lindsay, K., Holland, M.M. (2015). Modeling photosynthesis in sea ice covered waters, Journal of Advances in Modeling Earth Systems, 07. doi:10.1002/2015MS000436
DOI: 10.6084/m9.figshare.12656165.v12
title: COVID-19 Case Reports in China

description: Chinese prefectural level governments started to report daily confirmed COVID-19 cases online, starting from January 2020. The disclosures may contain the mobility, potential exposure scenario, epidemiological characteristics, and other useful information of individual cases. We organized a group of content coders since early March 2020, kept monitoring the information updates, manually extracted useful information from the public disclosures, and compiled these datasets.We welcome any form of collaborations with us and non-commercial reuse of our dataset. We highly encourage interested parties to examine the data, report errors in our coding, and help us to keep the data updated.The detailed data description can be found on SSRN preprint server https://dx.doi.org/10.2139/ssrn.3705815.
DOI: 10.6084/m9.figshare.14223107.v1
title: 19505381.fastq.gz

description: WGS of canine stool microbiome
DOI: 10.6084/m9.figshare.14223107
title: 19505381.fastq.gz

description: WGS of canine stool microbiome
DOI: 10.6084/m9.figshare.14223086.v1
title: 19505374.fastq.gz

description: WGS of canine stool microbiome
DOI: 10.6084/m9.figshare.14223086
title: 19505374.fastq.gz

description: WGS of canine stool microbiome
DOI: 10.6084/m9.figshare.13158479
title: Reference-grade genome sequence and annotation of Gossypium rotundifolium (K2)

description: The reference-grade cotton genome assemblies and annotation of <i>Gossypium rotundifolium</i> (K<sub>2</sub>) using Oxford Nanopore sequencing technology.
DOI: 10.6084/m9.figshare.13158476
title: Reference-grade genome sequence and annotation of Gossypium raimondii (D5)

description: The reference-grade cotton genome assemblies and annotations of <i>Gossypium </i><i>raimondii</i> (D<sub>5</sub>) using Oxford Nanopore sequencing technology.
DOI: 10.6084/m9.figshare.13158476.v3
title: Reference-grade genome sequence and annotation of Gossypium raimondii (D5)

description: The reference-grade cotton genome assemblies and annotations of <i>Gossypium </i><i>raimondii</i> (D<sub>5</sub>) using Oxford Nanopore sequencing technology.
DOI: 10.6084/m9.figshare.13158467
title: Reference-grade genome sequence and annotation of Gossypium arboreum (A2)

description: The reference-grade cotton genome assemblies and annotation of <i>Gossypium </i><i>arboreum</i> (A<sub>2</sub>) using Oxford Nanopore sequencing technology.
DOI: 10.6084/m9.figshare.13158467.v4
title: Reference-grade genome sequence and annotation of Gossypium arboreum (A2)

description: The reference-grade cotton genome assemblies and annotation of <i>Gossypium </i><i>arboreum</i> (A<sub>2</sub>) using Oxford Nanopore sequencing technology.
DOI: 10.21227/yb2m-w662
title: Day-Ahead Forecasting using LSTM with Rolling windows

description: The project involves day-ahead forecasting which takes a model fit into historical data and predicts future demand of electricity. Time series forecasting methods are used as the dataset contains an explicit order dependence between observations, i.e. a time dimension which makes the problem difficult to handle but makes the prediction more accurate. Various machine learning and deep learning algorithms were used to accomplish this work. Results obtained by autoregressive integrated moving average(ARIMA), autoregressive moving average with explanatory variable(ARIMAX), seasonal autoregressive moving average(SARIMA), seasonal autoregressive moving average(SARIMAX) and long short term memory(LSTM) recurrent neural networks with rolling windows were compared and the one with least error, i.e. LSTM with rolling windows was used for time series prediction.
DOI: 10.5281/zenodo.4608313
title: Namelists required to run REcoM2 biogeochemistry with sea ice and physics configuration of MITgcm for the West Antarctic Peninsula

description: This dataset contains the namelists that describe the initial conditions, forcing files and specific package configurations used to run the REcoM2 (Regulated Ecosystem Model version 2) biogeochemical model with sea ice and ocean physics configuration of the MITgcm (general circulation model) for the West Antarctic Peninsula (WAP).
DOI: 10.5281/zenodo.4608312
title: Namelists required to run REcoM2 biogeochemistry with sea ice and physics configuration of MITgcm for the West Antarctic Peninsula

description: This dataset contains the namelists that describe the initial conditions, forcing files and specific package configurations used to run the REcoM2 (Regulated Ecosystem Model version 2) biogeochemical model with sea ice and ocean physics configuration of the MITgcm (general circulation model) for the West Antarctic Peninsula (WAP).
DOI: 10.6084/m9.figshare.14219129
title: Rapid evolution and host immunity drive the rise and fall of carbapenem resistance during an acute Pseudomonas aeruginosa infection

description: Data from publication "Rapid evolution and host immunity drive the rise and fall of carbapenem resistance during an acute <i>Pseudomonas aeruginosa</i> infection". <br>
DOI: 10.6084/m9.figshare.14219129.v1
title: Rapid evolution and host immunity drive the rise and fall of carbapenem resistance during an acute Pseudomonas aeruginosa infection

description: Data from publication "Rapid evolution and host immunity drive the rise and fall of carbapenem resistance during an acute <i>Pseudomonas aeruginosa</i> infection". <br>
DOI: 10.6084/m9.figshare.14220134
title: µCT Data for Correlophus ciliatus tail 114324

description: µCT data for <i>Correlophus ciliatus</i> tails.
DOI: 10.6084/m9.figshare.14216526
title: The MIDI Linked Data Cloud

description: The study of music is highly interdisciplinary, and thus requires the combination of datasets from multiple musical domains, such as catalog metadata (authors, song titles, dates), industrial records (labels, producers, sales), and music notation (scores). While today an abundance of music metadata exists on the Linked Open Data cloud, datasets containing interoperable symbolic descriptions of music itself, i.e. music notation with note and instrument level information, are scarce. This is the MIDI Linked Data Cloud, a dataset that represents multiple collections of digital music in the MIDI standard format as Linked Data. At the time of writing, the dataset comprises 10,215,557,355 triples of 308,443 interconnected MIDI scores, and provides Web-compatible descriptions of their MIDI events.
DOI: 10.6084/m9.figshare.14222834
title: µCT data for Correlophus ciliatus tail 143739

description: Raw µCT data.
DOI: 10.6084/m9.figshare.14222993
title: µCT data for Correlophus ciliatus tail 153904

description: Raw µCT data.
DOI: 10.6084/m9.figshare.14222993.v1
title: µCT data for Correlophus ciliatus tail 153904

description: Raw µCT data.
DOI: 10.6084/m9.figshare.13158479.v5
title: Reference-grade genome sequences and annotations of Gossypium rotundifolium (K2)

description: The reference-grade cotton genome assemblies and annotation of <i>Gossypium rotundifolium</i> (K<sub>2</sub>) using Oxford Nanopore sequencing technology.
DOI: 10.6084/m9.figshare.14223971
title: Schmalstig Jainandan 2021 AJB duckweed Figs 1-4.xls

description: <b>Data for Figures 1-4 and Figures 5-9, Table 1 from article in American Journal of Botany 2021</b><b>Green light attenuates blue-light induced chloroplast avoidance movement</b> <b> in <i>Arabidopsis</i> and duckweed</b> Judy G. Schmalstig<sup>*</sup> and<sup> </sup>Kenneth Jainandan<sup></sup> Department of Biology, 1000 Holt Ave, Rollins College, Winter Park, FL 32789 <sup>*</sup>Correspondence: jschmalstig@rollins.edu <b>ABSTRACT</b> <b>PREMISE:</b> Chloroplast movement to the anticlinal walls in excess light, referred to as chloroplast avoidance movement, is one strategy to prevent high light damage. Chloroplast avoidance movement is mediated by the blue light photoreceptor phototropin. Since some blue light effects are reversed by green light, we investigated the effect of green wavelengths on chloroplast avoidance. <b>METHODS:</b> Chloroplast position was visualized via microscopy and by transmission of red light through the leaves of <i>Arabidopsis thaliana</i> L. and duckweed (<i>Landoltia punctata </i>(G. Mey.) Les & D.J. Crawford). <b>RESULTS:</b> Green light reduced blue-light induced chloroplast avoidance movement but only when green light was presented simultaneously with blue light. Green light alone had no effect on chloroplast position. An action spectrum for green light attenuation of chloroplast avoidance in duckweed revealed peaks at 510, 550, and 590 nm. Blue-light induced chloroplast avoidance movement in three <i>Arabidopsis </i>mutants with reduced nonphotochemical quenching, <i>npq1, npq4 and npq7</i> was not affected by green light. <b>CONCLUSIONS:</b> The action spectrum does not conform to any known photoreceptor. The lack of a green light response in the <i>npq</i> mutants of <i>Arabidopsis</i> suggest a possible role for the xanthophyll cycle or a signal from the chloroplast in control of chloroplast avoidance movement. <br>
DOI: 10.6084/m9.figshare.14223971.v1
title: Schmalstig Jainandan 2021 AJB duckweed Figs 1-4.xls

description: <b>Data for Figures 1-4 and Figures 5-9, Table 1 from article in American Journal of Botany 2021</b><b>Green light attenuates blue-light induced chloroplast avoidance movement</b> <b> in <i>Arabidopsis</i> and duckweed</b> Judy G. Schmalstig<sup>*</sup> and<sup> </sup>Kenneth Jainandan<sup></sup> Department of Biology, 1000 Holt Ave, Rollins College, Winter Park, FL 32789 <sup>*</sup>Correspondence: jschmalstig@rollins.edu <b>ABSTRACT</b> <b>PREMISE:</b> Chloroplast movement to the anticlinal walls in excess light, referred to as chloroplast avoidance movement, is one strategy to prevent high light damage. Chloroplast avoidance movement is mediated by the blue light photoreceptor phototropin. Since some blue light effects are reversed by green light, we investigated the effect of green wavelengths on chloroplast avoidance. <b>METHODS:</b> Chloroplast position was visualized via microscopy and by transmission of red light through the leaves of <i>Arabidopsis thaliana</i> L. and duckweed (<i>Landoltia punctata </i>(G. Mey.) Les & D.J. Crawford). <b>RESULTS:</b> Green light reduced blue-light induced chloroplast avoidance movement but only when green light was presented simultaneously with blue light. Green light alone had no effect on chloroplast position. An action spectrum for green light attenuation of chloroplast avoidance in duckweed revealed peaks at 510, 550, and 590 nm. Blue-light induced chloroplast avoidance movement in three <i>Arabidopsis </i>mutants with reduced nonphotochemical quenching, <i>npq1, npq4 and npq7</i> was not affected by green light. <b>CONCLUSIONS:</b> The action spectrum does not conform to any known photoreceptor. The lack of a green light response in the <i>npq</i> mutants of <i>Arabidopsis</i> suggest a possible role for the xanthophyll cycle or a signal from the chloroplast in control of chloroplast avoidance movement. <br>
DOI: 10.6084/m9.figshare.14223992.v1
title: saturation

description: AA_saturationPCGs_saturation
DOI: 10.6084/m9.figshare.14223992
title: saturation

description: AA_saturationPCGs_saturation
DOI: 10.17903/fk2/znob7t
title: Το Διαδικτύο στην Κύπρο 2016 (Ελληνοκυπριακή και Τουρκοκυπριακή κοινότητα)

description: Το World Internet Project για την Κύπρο, υλοποιείται από το Τμήμα Επικοινωνίας και Σπουδών Διαδικτύου και χρηματοδοτείται από το Τεχνολογικό Πανεπιστήμιο Κύπρου. Αποτελεί μέρος του World Internet Project, ενός διεθνούς ερευνητικού προγράμματος που ξεκίνησε το 1999 και διοικείται από το Annenberg School Center for the Digital Future στο University of Southern California. Το πρώτο κύμα της έρευνας στην Κύπρο πραγματοποιήθηκε στα τέλη του 2008 και το δεύτερο την άνοιξη του 2010. Το τρίτο κύμα διεξήχθη το φθινόπωρο του 2012 τόσο στην Ελληνοκυπριακή όσο και στην Τουρκοκυπριακή κοινότητα. Μια παρόμοια διακοινοτική μέτρηση επαναλήφθηκε το φθινόπωρο του 2014 (τέταρτο κύμα) και το φθινόπωρο του 2016 (πέμπτο κύμα).
DOI: 10.5517/ccdc.csd.cc200bn1
title: CCDC 1847372: Experimental Crystal Structure Determination

description: Related Article: Eduardo C. Escudero-Adán, Antonio Bauzá, Claude Lecomte, Antonio Frontera, Pablo Ballester|2018|Phys.Chem.Chem.Phys.(PCCP)|20|24192|doi:10.1039/C8CP04401E
DOI: 10.6084/m9.figshare.14224064
title: 19505497.fastq.gz

description: WGS of canine stool microbiome
DOI: 10.6084/m9.figshare.14224064.v1
title: 19505497.fastq.gz

description: WGS of canine stool microbiome
DOI: 10.5281/zenodo.4608203
title: Collection of databaes for reproducible metaviromis analyses

description: Inphared Kraken2/minikraken Phigaro PhiX Vibrant Virsorter
DOI: 10.5281/zenodo.4573676
title: Conservation of aging and cancer epigenetic signatures across human and mouse

description: Aging and cancer are two interrelated biological processes, with aging being one of the most important risk factors for the development of cancer. Parallel epigenetic alterations have been described for both, although differences, especially within the DNA hypomethylation scenario, have also been identified in recent literature. While many of these observations arise from the use of mouse models, there is a lack of systematic and single-base resolution comparisons of human and mouse epigenetic patterns in the context of disease. However, such comparisons are especially significant with respect to the DNA methylation alterations found independently in the two species as they allow to establish the extent to which some of the observed similarities or differences arise from pre-existing species-specific epigenetic traits. Here, we have used reduced representation bisulfite sequencing to profile the brain methylomes of young and old, tumoral and non-tumoral brain samples from human and mouse. We first characterized the baseline epigenomic patterns of the species and subsequently focused on the DNA methylation alterations associated with cancer and aging. Next, we described the functional genomic and epigenomic context associated with the alterations, and finally we integrated our data in order to study interspecies DNA methylation levels at specific CpG sites. Globally, we found robust evidence for the conservation of cancer and aging-associated epigenomic patterns in both species, and our observations point towards the preservation of the functional consequences of these alterations at multiple levels of genomic regulation. This dataset contains information related to dataframes, databases, scripts and supplementary material mentioned in the original manuscript.
DOI: 10.5281/zenodo.4573675
title: Conservation of aging and cancer epigenetic signatures across human and mouse

description: Aging and cancer are two interrelated biological processes, with aging being one of the most important risk factors for the development of cancer. Parallel epigenetic alterations have been described for both, although differences, especially within the DNA hypomethylation scenario, have also been identified in recent literature. While many of these observations arise from the use of mouse models, there is a lack of systematic and single-base resolution comparisons of human and mouse epigenetic patterns in the context of disease. However, such comparisons are especially significant with respect to the DNA methylation alterations found independently in the two species as they allow to establish the extent to which some of the observed similarities or differences arise from pre-existing species-specific epigenetic traits. Here, we have used reduced representation bisulfite sequencing to profile the brain methylomes of young and old, tumoral and non-tumoral brain samples from human and mouse. We first characterized the baseline epigenomic patterns of the species and subsequently focused on the DNA methylation alterations associated with cancer and aging. Next, we described the functional genomic and epigenomic context associated with the alterations, and finally we integrated our data in order to study interspecies DNA methylation levels at specific CpG sites. Globally, we found robust evidence for the conservation of cancer and aging-associated epigenomic patterns in both species, and our observations point towards the preservation of the functional consequences of these alterations at multiple levels of genomic regulation. This dataset contains information related to dataframes, databases, scripts and supplementary material mentioned in the original manuscript.
DOI: 10.6084/m9.figshare.14224172.v1
title: Bankit

description: TblSRA table<br>
DOI: 10.6084/m9.figshare.14224172
title: Bankit

description: TblSRA table<br>
DOI: 10.6084/m9.figshare.14224085
title: 19505510.fastq.gz

description: WGS of canine stool microbiome
DOI: 10.6084/m9.figshare.14224085.v1
title: 19505510.fastq.gz

description: WGS of canine stool microbiome