cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25392/leicester.data.14242085
title: INPHARED_DATABASE

description: inphared.pl (INfrastructure for a PHAge REference Database) is a perl script which downloads and filters phage genomes from Genbank to provide the most complete phage genome database possible.Useful information, including viral taxonomy and bacterial host data, is extracted from the Genbank files and provided in a summary table. Genes are called on the genomes using Prokka and this output is used to gather metrics which are summarised in the output files, as well as useful input files for vConTACT2. The data provided is all genomes up to Jan 2021. This can be downloaded so users do not have to repeat the process of consistent gene calling on existing genomes. The folder GenomesDB contains subfolders each containing a subfolder that is named on the accession number of each phage. Within each folder are re-called genes in the following format *.ffn*.faa The complete genome *fna and genbank file without any annotation *gbf See https://github.com/RyanCook94/<br><br><br><br><br><br>
DOI: 10.25392/leicester.data.14242085.v1
title: INPHARED_DATABASE

description: inphared.pl (INfrastructure for a PHAge REference Database) is a perl script which downloads and filters phage genomes from Genbank to provide the most complete phage genome database possible.Useful information, including viral taxonomy and bacterial host data, is extracted from the Genbank files and provided in a summary table. Genes are called on the genomes using Prokka and this output is used to gather metrics which are summarised in the output files, as well as useful input files for vConTACT2. The data provided is all genomes up to Jan 2021. This can be downloaded so users do not have to repeat the process of consistent gene calling on existing genomes. The folder GenomesDB contains subfolders each containing a subfolder that is named on the accession number of each phage. Within each folder are re-called genes in the following format *.ffn*.faa The complete genome *fna and genbank file without any annotation *gbf See https://github.com/RyanCook94/<br><br><br><br><br><br>
DOI: 10.5281/zenodo.4682077
title: Statistics Corona

description: In this dataset we can find information related to the population of all the countries listed in the website <em>Worldometers. </em>The dataset is composed, among others, with information like <strong>Country, Total Cases, New Cases or TotalDeaths.</strong><strong> </strong>The dataset was created with the idea to implement it in any project where this information could help to fight against Covid-19.
DOI: 10.5281/zenodo.4682076
title: Statistics Corona

description: In this dataset we can find information related to the population of all the countries listed in the website <em>Worldometers. </em>The dataset is composed, among others, with information like <strong>Country, Total Cases, New Cases or TotalDeaths.</strong><strong> </strong>The dataset was created with the idea to implement it in any project where this information could help to fight against Covid-19.
DOI: 10.34808/jv9h-p675
title: Long-term hindcast simulation of currents in the Baltic Sea

description: The dataset contains the results of numerical modelling of currents over a period of 50 years (1958-2007) in the Baltic Sea . A long-term hindcast simulation was performed using a three-dimensional hydrodynamic model PM3D (Kowalewski and Kowalewska-Kalkowska, 2017), a new version of the M3D model (Kowalewski, 1997).  The hydrodynamic model was coupled with a numerical dynamic-thermodynamic model of sea ice (Herman et al. 2011).
The model is based on the Princeton Ocean Model (POM) developed at Princeton University (Blumberg and Mellor, 1987). Like POM, the M3D/PM3D model uses the Mellor-Yamada turbulence scheme and sigma vertical coordinates. The simulation was carried out in a rectangular grid of 3' (latitude) and 6' (longitude) resolution. The spatial resolution was 3 nautical miles, i.e. about 5.5 km. An open boundary was located between the Skagerrak and the Kattegat along the parallel connecting Skagen and Göteborg, where the water exchange with the North Sea takes place. A radiation condition based on Somerfield’s concept for velocities  vertically averaged and normal to the boarder  plane was applied. Atmospheric forcing for the period 1958-2007 was performed using the regional at amospheric climate model REMO (REgional MOdel) which was based on the numerical weather prediction model EM (Europa-Model) of the German Weather Forecast Service (DWD).
The eastward and northward components of surface currents and at a depth of 5 m, 10 m, 15 m, 20 m, 30 m,  40 m, 50 m and 60 m m were recorded every three hours in the computational grid of the model in unproiected form: LatLong, WGS 84 (EPSG: 4326). Analysis of the Baltic Sea current data spanning five decades showed  a higher stability of subsurface current eddies relative to the stability of ephemeral surface currents (Jędrasik and Kowalewski, 2019).
Kowalewski M.;1997; A three-dimensional, hydrodynamic model of the Gulf of Gdańsk; Oceanol. Stud., 26 (4); 77–98
Kowalewski M., Kowalewska-Kalkowska H., 2017, Sensitivity of the Baltic Sea level prediction to spatial model resolution, Journal of Marine Systems 173, 101–113, http://dx.doi.org/10.1016/j.jmarsys.2017.05.001
Jędrasik J., Kowalewski M., 2019, Mean annual and seasonal circulation patterns and long-term variability of currents in the Baltic Sea, J. Mar. Syst., 193, 1-26, doi:10.1016/j.jmarsys.2018.12.011
Herman, A., Jedrasik, J., Kowalewski, M., 2011, Numerical modelling of thermodynamics and dynamics of sea ice in the Baltic Sea. Ocean Science, 7(2), 257-276. https://doi.org/10.5194/os-7-257-2011  Surface and 20 m deep currents in the Baltic Sea on the first and last day of the simulation
DOI: 10.5281/zenodo.4682776
title: Expanding the role of bitter taste receptor in extra oral tissues: TAS2R38 is expressed in human adipocytes

description: dataset of gene expression of TAS2R38 in adipose tissues and adipocytes
DOI: 10.5281/zenodo.4682775
title: Expanding the role of bitter taste receptor in extra oral tissues: TAS2R38 is expressed in human adipocytes

description: dataset of gene expression of TAS2R38 in adipose tissues and adipocytes
DOI: 10.34808/vbdz-5209
title: Long-term hindcast simulation of water temperature and salinity in the Baltic Sea

description: The dataset contains the results of numerical modelling of water temperature and salinity over a period of 50 years (1958-2007) in the Baltic Sea. A long-term hindcast simulation was performed using a three-dimensional hydrodynamic model PM3D (Kowalewski and Kowalewska-Kalkowska, 2017), a new version of the M3D model (Kowalewski, 1997).  The hydrodynamic model was coupled with a numerical dynamic-thermodynamic model of sea ice (Herman et al. 2011).
The model is based on the Princeton Ocean Model (POM) developed at Princeton University (Blumberg and Mellor, 1987). Like POM, the M3D/PM3D model uses the Mellor-Yamada turbulence scheme and sigma vertical coordinates. The simulation was carried out in a rectangular grid of 3' (latitude) and 6' (longitude) resolution. The spatial resolution was 3 nautical miles, i.e. about 5.5 km. An open boundary was located between the Skagerrak and the Kattegat along the parallel connecting Skagen and Göteborg, where the water exchange with the North Sea takes place. A radiation condition based on Somerfield’s concept for velocities  vertically averaged and normal to the boarder  plane was applied. Atmospheric forcing for the period 1958-2007 was performed using the regional at atmospheric climate model REMO (REgional MOdel) which was based on the numerical weather prediction model EM (Europa-Model) of the German Weather Forecast Service (DWD).
The spatial distribution of water temperature and salinity was recorded twice a day, at a depth of 0 m, 5 m, 10 m, 15 m, 20 m, 30 m,  40 m, 50 m and 60 m in the model's computational grid in unproiected form (LatLong, WGS 84, EPSG: 4326). The validation of the modeling results for the period 1958-2007 showed a root mean square error (RMSE)  of the water temperature from 0.9 to 1.4 °C, and in the case of salinity RMSE was from 0.16 to 0.5 psu for various stations in the Baltic Sea (Jędrasik i Kowalewski, 2019).
 Kowalewski M.;1997; A three-dimensional, hydrodynamic model of the Gulf of Gdańsk; Oceanol. Stud., 26 (4); 77–98
Kowalewski M., Kowalewska-Kalkowska H., 2017, Sensitivity of the Baltic Sea level prediction to spatial model resolution, Journal of Marine Systems 173, 101–113, http://dx.doi.org/10.1016/j.jmarsys.2017.05.001
Jędrasik J., Kowalewski M., 2019, Mean annual and seasonal circulation patterns and long-term variability of currents in the Baltic Sea, J. Mar. Syst., 193, 1-26, doi:10.1016/j.jmarsys.2018.12.011
Herman, A., Jedrasik, J., Kowalewski, M., 2011, Numerical modelling of thermodynamics and dynamics of sea ice in the Baltic Sea. Ocean Science, 7(2), 257-276. https://doi.org/10.5194/os-7-257-2011  Surface salinity and temperature on the first and last days of stimulation
DOI: 10.34808/sp38-pj44
title: Long-term hindcast simulation of sea level in the Baltic Sea

description: The dataset contains the results of numerical modelling of sea level fluctuations over a period of 50 years (1958-2007) in the Baltic Sea. A long-term hindcast simulation was performed using a three-dimensional hydrodynamic model PM3D (Kowalewski and Kowalewska-Kalkowska, 2017), a new version of the M3D model (Kowalewski, 1997). The hydrodynamic model was coupled with a numerical dynamic-thermodynamic model of sea ice (Herman et al. 2011).
The model is based on the Princeton Ocean Model (POM) developed at Princeton University (Blumberg and Mellor, 1987). Like POM, the M3D/PM3D model uses the Mellor-Yamada turbulence scheme and sigma vertical coordinates. The simulation was carried out in a rectangular grid of 3' (latitude) and 6' (longitude) resolution. The spatial resolution was 3 nautical miles, i.e. about 5.5 km. An open boundary was located between the Skagerrak and the Kattegat along the parallel connecting Skagen and Göteborg, where the water exchange with the North Sea takes place. A radiation condition based on Somerfield’s concept for velocities  vertically averaged and normal to the boarder  plane was applied. Atmospheric forcing for the period 1958-2007 was performed using the regional at amospheric climate model REMO (REgional MOdel) which was based on the numerical weather prediction model EM (Europa-Model) of the German Weather Forecast Service (DWD).
The sea level spatial distributions were recorded in the model's computational grid in unprojected form (LatLong, WGS 84, EPSG: 4326) with an hourly time interval. Sea level values are expressed in metres relative to the mean level of the Baltic Sea in the PM3D model. The validation of the sea level modeling results for the period 2010-2015 showed (Kowalewski and Kowalewska-Kalkowska, 2017) a root mean square error (RMSE) of 8 to 13 cm for various stations in the Baltic Sea.
Kowalewski M.;1997; A three-dimensional, hydrodynamic model of the Gulf of Gdańsk; Oceanol. Stud., 26 (4); 77–98
Kowalewski M., Kowalewska-Kalkowska H., 2017, Sensitivity of the Baltic Sea level prediction to spatial model resolution, Journal of Marine Systems 173, 101–113, http://dx.doi.org/10.1016/j.jmarsys.2017.05.001
Jędrasik J., Kowalewski M., 2019, Mean annual and seasonal circulation patterns and long-term variability of currents in the Baltic Sea, J. Mar. Syst., 193, 1-26, doi:10.1016/j.jmarsys.2018.12.011
Herman, A., Jedrasik, J., Kowalewski, M. (2011). Numerical modelling of thermodynamics and dynamics of sea ice in the Baltic Sea. Ocean Science, 7(2), 257-276. https://doi.org/10.5194/os-7-257-2011
DOI: 10.6084/m9.figshare.14159756.v1
title: Insights and clinical potential of proteomics in understanding spermatogenesis

description: <b>Introduction</b>: With the worldwide decline on male fertility potential, the importance of the insight of the spermatogenic process has been increasing. In recent years, proteomic methodologies have been applied to seminal fluid of infertile men to search for infertility potential biomarkers. However, to understand the spermatogenic event and to search for treatment to spermatogenic impairment, comparative analysis of testicular proteomics is considered a powerful methodology. <b>Areas covered</b>: Herein, we present a critical overview of the studies addressing proteomic alterations in the development of spermatogenesis during puberty, as well as during the different phases of the spermatogenic event. The comparative studies of the proteomic testicular profile of men with and without spermatogenic impairment are also discussed and key proteins and pathways involved highlighted. <b>Expert opinion</b>: The usage of whole human testicular tissue with its heterogeneous cellular composition makes proteome data interpretation particularly challenging. This may be minimized by controlled experiments involving the collection of testicular tissue and sperm from the same individuals, integrated in a clinically characterized cohort of healthy and infertile men. The analysis of specific subcellular proteomes can add more information to the proteomic puzzle, opening new treatment possibilities for infertile/subfertile men.
DOI: 10.6084/m9.figshare.14159756
title: Insights and clinical potential of proteomics in understanding spermatogenesis

description: <b>Introduction</b>: With the worldwide decline on male fertility potential, the importance of the insight of the spermatogenic process has been increasing. In recent years, proteomic methodologies have been applied to seminal fluid of infertile men to search for infertility potential biomarkers. However, to understand the spermatogenic event and to search for treatment to spermatogenic impairment, comparative analysis of testicular proteomics is considered a powerful methodology. <b>Areas covered</b>: Herein, we present a critical overview of the studies addressing proteomic alterations in the development of spermatogenesis during puberty, as well as during the different phases of the spermatogenic event. The comparative studies of the proteomic testicular profile of men with and without spermatogenic impairment are also discussed and key proteins and pathways involved highlighted. <b>Expert opinion</b>: The usage of whole human testicular tissue with its heterogeneous cellular composition makes proteome data interpretation particularly challenging. This may be minimized by controlled experiments involving the collection of testicular tissue and sperm from the same individuals, integrated in a clinically characterized cohort of healthy and infertile men. The analysis of specific subcellular proteomes can add more information to the proteomic puzzle, opening new treatment possibilities for infertile/subfertile men.
DOI: 10.6084/m9.figshare.13633790
title: HDBR_BBR2_Cocktail_CBTprofiles

description: Core body temperature recorded for 32 h during the third and the eight week of two head-down tilt bed rest studies (BBR2-2: n = 5 participants, Cocktail: n = 8 participants).
DOI: 10.5519/qd.j1iplj8i
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (366482 records)
DOI: 10.6084/m9.figshare.14405351
title: Supplementary Material for: Mechanical and Ablative Minimally Invasive Techniques for Male LUTS due to Benign Prostatic Obstruction: A Systematic Review according to BPH-6 Evaluation

description: The treatment of male lower urinary tract symptoms (LUTS) due to benign prostatic obstruction represents one of the major interesting aspects in urological clinical practice. Although transurethral resection of the prostate is still considered the surgical gold standard for treatment of benign prostatic hyperplasia with prostate volume &lt;80 mL, various minimally invasive surgical treatments (MITs) have been developed to overcome the limitations of the “conventional” surgery. To date, there are no validated tools to evaluate the surgical outcomes of MITs; however, in the past, BPH-6 has been used for this purpose. In this systematic review, we evaluated the efficacy and safety of MITs according to BPH-6 score system. We focused our attention on MITs based on mechanical devices (prostatic urethral lift and the temporary implantable nitinol device) and techniques for prostate ablation (image guided robotic waterjet ablation and convective water vapor energy ablation). Evidence shows that MITs are capable of leading to an improvement in LUTS without having an overwhelming impact on complications and are a valid alternative to other treatments in patients who wish to preserve their sexual function or in case of inapplicability of conventional surgery. However, comparative studies between these techniques are still missing.
DOI: 10.6084/m9.figshare.14405384
title: Supplementary Material for: Preliminary Investigation about the Expression of G Protein-Coupled Receptors in Platelets from Patients with Chronic Immune Thrombocytopenic Purpura

description: <b><i>Objective:</i></b> The objective of this study was to determine the expression of G protein-coupled receptors (GPCRs) in platelets from adult patients with chronic immune thrombocytopenic purpura (ITP). <b><i>Methods:</i></b> Peripheral blood samples were collected from 40 patients with chronic ITP in the Second Affiliated Hospital of Shantou University Medical College, and 40 peripheral blood samples from healthy volunteers were collected; expressions of the adenosine diphosphate receptors (P2Y1 and P2Y12), alpha-2A adrenergic receptor (α2A-AR), and thromboxane A<sub>2</sub> receptor (TP) in platelets were detected by flow cytometry. Gα protein, protease-activated receptor 1 (PAR1), and protease-activated receptor 4 (PAR4) were analyzed by Western blot and analyzed statistically. <b><i>Results:</i></b> Flow cytometry measurements of mean fluorescence intensities showed platelets from patients with chronic ITP, compared to healthy individuals, had significantly higher levels of P2Y1 (31.4 ± 2.2 vs. 7.8 ± 0.8), P2Y12 (29.6 ± 2.1 vs. 7.2 ± 1.3), α2A-AR (25.8 ± 2.9 vs. 9.8 ± 0.9), and TP (39.8 ± 3.1 vs. 4.7 ± 0.6) (all <i>p</i> &lt; 0.01). Similarly, integrated optical density analysis of Western blots showed that platelets from patients with chronic ITP had significantly higher levels of Gα (1046.3 ± 159.96 vs. 254.49 ± 39.51), PAR1 (832.98 ± 98.81 vs. 203.92 ± 27.47), and PAR4 (1518.80 ± 272.45 vs. 431.27 ± 41.86) (all <i>p</i> &lt; 0.01). <b><i>Conclusion:</i></b> Expression of GPCRs is increased in platelets from patients with chronic ITP, suggesting that platelets of chronic ITP may participate in the complicated biological process by means of GPCR-mediated signaling pathways.
DOI: 10.11588/data/gyldh5/wcevxo
title: Optical and geochemical analyses of Piñas de Yucatán sample.pdf

description: Results and methods of optical and geochemical analyses conducted at the Piñas de Yucatán sample from cenote Xkolac.
DOI: 10.11588/data/gyldh5/kikq33
title: Methods to dataset.pdf

description: Detailed description of the methods used for sampling and analyses.
DOI: 10.11588/data/gyldh5/hg2x3c
title: Hydrogeochemical results of Mexico campaign 2020.xlsx

description: Table compiling the dataset of the hydrogeochemical results of Mexico campaign 2020.
DOI: 10.11588/data/gyldh5/gta4uw
title: Map of studied cenotes.png

description: Map of the Yucatán Peninsula showing the locations of the studied cenotes.
DOI: 10.6084/m9.figshare.14405372
title: Supplementary Material for: Swimming Exercise Ameliorates Hypertension-Induced Kidney Dysfunction via Alleviating Renal Interstitial Fibrosis and Apoptosis

description: <b><i>Background:</i></b> Hypertensive nephropathy is one of the major causes of ESRD. Exercise has been considered a nonpathological therapy for hypertension and its complications, yet mechanisms remain unclear. We sought to investigate whether periodic swimming could ameliorate hypertension-induced kidney dysfunction and its underlying mechanisms. <b><i>Methods:</i></b> Four-week male spontaneously hypertensive rats (SHRs) were randomly divided into the hypertension group (SHR, <i>n</i> = 8) and exercise group (SE, <i>n</i> = 8, 60 min swimming/day, 6 days per week, for 8 weeks). Wistar-Kyoto rats (WKY, <i>n</i> = 8) were served as a sedentary normotensive group. Bodyweight and blood pressure (BP) were recorded weekly. After 8-week sedentary or swimming exercise, lipids profile, BUN, and Cr were measured. The renal interstitial fibrosis was examined by the histopathological analysis using Masson’s trichrome staining and hematoxylin and eosin staining. The kidney cell apoptosis was tested by TUNEL staining. The expressions of critical proteins responsible for the TGF-β1/Smad signaling of fibrosis, that is, TGF-β1, Smad2/3, and Smad7, as well as apoptosis related proteins, Bax and Bcl-2 in kidney cortex tissues were measured. <b><i>Results:</i></b> The 8-week swimming exercise reduced BP and bodyweight, lowered concentrations of BUN, and serum Cr, compared with SHR. Exercise remarkably inhibited hypertension-induced tubular degeneration, cellular cluster, and tubular cell swelling as well as glomerular degeneration in the kidney cortical tissues, attenuated renal interstitial fibrosis, and renal cell apoptosis. Moreover, expressions of TGF-β1, Smad2/3, and Bax were higher in the SHR than the WKY, which were significantly suppressed by the exercise. In contrast, hypertension-reduced expressions of Smad7 and Bcl-2 were enhanced by the swimming exercise. Strong correlations were found between kidney function indices, blood lipids, and key protein expressions. <b><i>Conclusion:</i></b> Our results demonstrate beneficial effects of the periodic swimming on ameliorating hypertension-induced kidney dysfunction highlighting the potential of swimming exercise as a nonpathological therapy for early prevention of hypertension-caused kidney diseases.