cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.20071892
title: Supplementary Material for: Differential Gene Expression in Cord Blood of Infants Diagnosed with Cerebral Palsy: a Pilot Analysis of the BEAM Cohort

description: The Beneficial Effects of Antenatal Magnesium (BEAM) clinical trial was conducted between 1997-2007, and demonstrated a significant reduction in cerebral palsy (CP) in preterm infants who were exposed to peripartum magnesium sulfate (MgSO4). However, the mechanism by which MgSO4 confers neuroprotection remains incompletely understood. Cord blood samples from this study were interrogated during an era when next generation sequencing was not widely accessible and few gene expression differences or biomarkers were identified between treatment groups. Our goal was to use bulk RNA deep sequencing to identify differentially expressed genes comparing the following four groups: newborns who ultimately developed CP treated with MgSO4 or placebo, and controls (newborns who ultimately did not develop CP) treated with MgSO4 or placebo. Those who died after birth were excluded. We found that MgSO4 upregulated expression of SCN5A only in the control group, with no change in gene expression in cord blood of newborns who ultimately developed CP. Regardless of MgSO4 exposure, expression of NPBWR1 and FTO were upregulated in cord blood of newborns who ultimately developed CP compared with controls. These data support that MgSO4 may not exert its neuroprotective effect through changes in gene expression. Moreover, NPBWR1 and FTO may be useful as biomarkers, and may suggest new mechanistic pathways to pursue in understanding the pathogenesis of CP. The small number of cases ultimately available for this secondary analysis, with male predominance and mild CP phenotype, is a limitation of the study. In addition, differentially expressed genes were not validated by qRT-PCR.
DOI: 10.6084/m9.figshare.20160377
title: Supplementary Material for: S3 Guideline “Smoking and Tobacco Dependence: Screening, Diagnosis, and Treatment” – Short Version

description: <b><i>Introduction:</i></b> In addition to the prevention of tobacco consumption, the establishment and assurance of high-quality treatment for harmful use and dependence on tobacco products remains an important health-related task in Germany. Regular updating of the Association of the Scientific Medical Societies (AWMF) S3 guideline “Smoking and Tobacco Dependence: Screening, Diagnosis, and Treatment” (Tobacco Guideline) offers a sustainable and reputable source of knowledge on smoking cessation. <b><i>Methods:</i></b> Under the auspices of the German Society for Psychiatry, Psychotherapy, Psychosomatics, and Neurology (DGPPN) and the German Society for Addiction Research and Addiction Therapy (DG-Sucht), the Tobacco Guideline was revised in 2019–2020 by 63 experts, who were involved in the development process of the text, in 11 working groups. Undue influence of conflicts of interest on the guideline could be minimized through careful conflict of interest management. Delegates from 50 professional societies discussed the 80 guideline recommendations and voted online. <b><i>Results:</i></b> In addition to recommendations for screening and diagnostics, the Tobacco Guideline takes a positive stance towards the use of low-threshold counseling and support services. If, due to the severity of the tobacco-related disorder, brief counseling, telephone counseling, or internet- or smartphone-based methods are not sufficiently effective, individual or group behavioral therapy, possibly in combination with medication, is indicated. If nicotine replacement therapy is not effective, varenicline or bupropion should be offered. Alternative strategies with a lower level of recommendation are hypnotherapy, mindfulness-based treatments, or medication with cytisine. In adolescents and pregnant women, the use of medication should be limited to well-specified exceptions and nicotine replacement. The mean agreement with the recommendations reached a value of 98%. A general overview of the treatment recommendations of the Tobacco Guideline is provided by three clinical algorithms.
DOI: 10.7294/20213357
title: Experimental development and model implementation of a lake spray source function: dataset.

description: We develop a lake spray aerosol (LSA) emission parameterization using laboratory experiments and use the CMAQ model to implement it for Great Lakes surface emissions. See the abstract of the associated manuscript for more information about this research. <br>
DOI: 10.17632/6r7d2pg2zk.1
title: Early-life adversity programs long-term cytokine and microglia expression within the HPA axis in female Japanese quail

description: Q-PCR data from published manuscript: Walker, D. J., Zimmer, C., Larriva, M., Healy, S.D. & Spencer, K. A. (2019). Early-life adversity programs long-term cytokine and microglia expression within the HPA axis in female Japanese quail. Journal of Experimental Biology (in press).
DOI: 10.6084/m9.figshare.21079591
title: Supplementary Material for: Extended Pelvic Lymph Node Dissection Does Not Affect Functional Outcomes during Bilateral Nerve-Sparing Radical Prostatectomy

description: <b><i>Introduction:</i></b> A possible association between extended pelvic lymph node dissection (ePLND) in radical prostatectomy (RPE) and functional outcomes such as erectile function (EF) and continence recovery has been previously considered. This association stems from the direct proximity of ePLND to the pelvic plexus. In this paper, we aimed to critically examine an association of ePLND with functional outcomes in patients who underwent bilateral nerve-sparing RPE. <b><i>Methods:</i></b> 272 out of 782 patients from a randomized, patient-blinded, multicenter trial were retrospectively classified into two groups based on the D’Amico criteria: 114 had no PLND and 158 had ePLND. Continence (no pad/safety pad) and EF (Index of Erectile Function-5 [IIEF-5] questionnaire ≥17; sufficient erection for sexual intercourse) were assessed at 3, 6, and 12 months as well as postsurgical complications (Clavien-Dindo Classification). <b><i>Results:</i></b> After 12 months of follow-up, no significant difference for potency could be found between men without and subjected to ePLND: IIEF-5 ≥17 (23.2% vs. 27.2%; <i>p</i> = 0.55) and sufficient erection for intercourse (44.1% vs. 45.6%; <i>p</i> = 0.84). A multiple linear regression analysis demonstrated that while preoperative EF (<i>p</i> &lt; 0.001), pathological tumor stage (<i>p</i> = 0.027), and robot-assisted bilateral nerve-sparing RPE (<i>p</i> &lt; 0.001) were independent predictors of EF recovery, the same did not apply to ePLND. No association was detected for continence recovery (94.2% vs. 89.7%; <i>p</i> = 0.22) and complications of any grade after surgery (11.4% vs. 16.5%; <i>p</i> = 0.24). <b><i>Conclusion:</i></b> ePLND is not associated with increased risk of erectile dysfunction, incontinence or complications after bilateral nerve-sparing RPE.
DOI: 10.6084/m9.figshare.21079744
title: Supplementary Material for: Hypotension at Hospital Presentation and Post-Contrast Acute Kidney Injury following Computed Tomography with Contrast Media

description: <b><i>Introduction:</i></b> Post-contrast acute kidney injury (PC-AKI) is a major complication of contrast media usage; risks for PC-AKI are generally evaluated before computed tomography (CT) with contrast at the emergency department (ED). Although persistent hypotension (systolic blood pressure [sBP] &lt;80 mm Hg for 1 h) is associated with increased PC-AKI incidence, it remains unclear whether transient hypotension that is haemodynamically stabilized before CT is a risk of PC-AKI. We hypothesized that hypotension on ED arrival would be associated with higher PC-AKI incidence even if CT with contrast was performed after patients are appropriately resuscitated. <b><i>Methods:</i></b> This multicentre retrospective observational study was conducted at three tertiary care centres during 2013–2014. We identified 280 patients who underwent CT with contrast at the ED. Patients were classified into two groups based on sBP on arrival (&lt;80 vs. ≥80 mm Hg); hypotension was considered as transient because CT with contrast has always been performed after patients were stabilized at participating hospitals. PC-AKI incidence was compared between the groups; inverse probability weighting (IPW) was conducted to adjust background characteristics. <b><i>Results:</i></b> Eighteen patients were excluded due to chronic haemodialysis, cardiac arrest on arrival, or death within 72 h; 262 were eligible for this study. PC-AKI incidence was higher in the transient hypotension group than the normotension group {7/27 (28.6%) vs. 24/235 (10.2%), odds ratio (OR) 3.08 (95% confidence interval [CI] 1.18–8.03), <i>p</i> = 0.026}, which was confirmed by IPW (OR 3.25 [95% CI 1.99–5.29], <i>p</i> &lt; 0.001). <b><i>Conclusion:</i></b> Transient hypotension at the ED was associated with PC-AKI development.
DOI: 10.6084/m9.figshare.7665632
title: The role of genetic diversity in the evolution and maintenance of environmentally-cued, male alternative reproductive tactics: datasets.

description: In Stewart et al., 2019,"The role of genetic diversity in the evolution and maintenance of environmentally-cued, male alternative reproductive tactics", BMC Evolutionary Biology, we tested 16 nuclear simple sequence repeats (nSSRs) primer pairs designed for Rhizoglyphus robini, optimizing the primer pairs and concomitant PCR protocol for our own populations using Dreamtaq polymerase (Thermo Fisher Scientific). After protocol optimization, we found only 9 of the 16 nSSRs amplified well for our populations, of which 3 loci revealed fixation, and 6 demonstrating both clean/readable peaks and polymorphism across individuals. These 6 nSSRs were chosen for the genotyping of all remaining individuals. Here, the datasets generated and analysed in our study are presented.<br>
DOI: 10.5281/zenodo.5226389
title: Assessment of the data assimilation framework for the prototype Rapid Refresh Forecast System and impacts on forecasts of convective storms

description: The compressed file contains the data and scripts necessary for the numerical experiments conducted in this research and the processing and visualization of the results. It includes the namelist files used for the model when using cold and warm start, the analyses in each experiment, and the grid, topography and surface climatology along with the model configuration file, the file used in the analyses to read the horizontal and vertical scales from an external file, all scripts used to execute every task of the workflow, all scripts used to process model outputs with MET, as well as all scripts and data used to create all figures of the paper.
DOI: 10.5285/0a6d85d7-fc9c-4d68-a58d-e792f68ae9f4
title: High resolution vector polygons of the Antarctic coastline

description: Coastline for Antarctica created from various mapping and remote sensing sources, provided as polygons with 'land', 'ice shelf', 'ice tongue' or 'rumple' attribute. Covering all land and ice shelves south of 60S. Suitable for topographic mapping and analysis. Data compiled, managed and distributed by the Mapping and Geographic Information Centre and the UK Polar Data Centre, British Antarctic Survey on behalf of the Scientific Committee on Antarctic Research.
description: Dataset compiled from a variety of Antarctic map and satellite image sources. The dataset was created using ArcGIS and QGIS GIS software programmes and has been checked for basic topography and geometry checks, but does not contain strict topology. Quality varies across the dataset and certain areas where high resolution source data were available are suitable for large scale maps whereas other areas are only suitable for smaller scales. Each polygon contains a 'surface' attribute with either 'land', 'ice shelf', 'ice tongue' or 'rumple'. Details of when and how each line was created can be found in the attributes of the high resolution polyline coastline dataset. Data sources range in time from 1990s-2020 - individual lines contain exact source dates.
DOI: 10.17632/8k92jssr5r.1
title: Convective Storms and Lightning Characteristics over the Western Ghats of India

description: These are the data (in mat format) of radar derived storm properties, lightning and reanalysis illustrated in the figures of Utsav et al (2021) manuscript "Relationship between Convective Storm Properties and Lightning Over the Western Ghats" submitted to JGR Atmospheres.
DOI: 10.5281/zenodo.7058171
title: Emergent tracer dynamics in constrained quantum systems

description: This repository contains the dataset, the code files to create the dataset, and a python file to plot the data for the corresponding publication.
DOI: 10.21258/1049140
title: Schweizerisches Landesforstinventar - Ergebnistabelle Nr. 200804
DOI: 10.5281/zenodo.2390875
title: Carrillo-Briceño et al. 2018 (raw isotopic data) - Neogene Caribbean elasmobranchs: diversity, paleoecology and paleoenvironmental significance of the Cocinetas Basin assemblage (Guajira Peninsula, Colombia)

description: The file contains the raw isotopic data for the article entitled '<strong>Neogene Caribbean elasmobranchs: diversity, paleoecology and paleoenvironmental significance of the Cocinetas Basin assemblage (Guajira Peninsula, Colombia)</strong>'. It includes the correction for the values first produced by our mass spectrometer and how the corrections were proceeded. Several runs were performed and these are detailed with comments and remarks. Any doubt or question about these corrections are welcomed by me, László Kocsis and Torsten Vennemann for discussion or further considerations.
DOI: 10.5281/zenodo.545818
title: Ground Deformation Maps Of The Visso And Norcia 2016 Earthquakes Captured From Sentinel-1 Sar

description: The dataset contains the Line Of Sight (LOS) deformation maps obtained by applying Differential SAR Interferometry (DinSAR) to Sentinel-1 Interferometric Wide-swath (or TOPSAR) imagery.

Two maps are provided: the first maps is the LOS deformation estimated from ascending data, the second map is the LOS deformation from descending images.

Maps are expressed in metres and are provided in raster geotiff format.

Data have been processed with GAMMA Interferometric processor.

Ascending data details:

SAR pairs are dated 2016/10/27 and 2016/11/02, acquired on relative orbit number 44, by Sentinel-1B and Sentinel-1A, respectively.

The DEM used for removing the topographic phase is the SRTM 1 arc second. The interferogram has been generated by applying a 1x5 multi-look factor in azimuth and range, respectively.

Final product has been geocoded in UTM WGS84 33 Nord projection, with a posting of 20 m.

Descending data details:

SAR pairs are dated 2016/10/26 and 2016/11/01, acquired on relative orbit number 22, by Sentinel-1B and Sentinel-1A, respectively.

The DEM used for removing the topographic phase is the SRTM 1 arc second. The interferogram has been generated by applying a 2x10 multi-look factor in azimuth and range, respectively.

Final product has been geocoded in UTM WGS84 33 Nord projection, with a posting of 40 m.
DOI: 10.5281/zenodo.6659531
title: Dynamic FRET example videos related to "Mars, a molecule archive suite for reproducible analysis and reporting of single-molecule properties from bioimages"

description: Videos of dynamic switching between iso-I and iso-II conformations of a holiday junction at 50 mM Magnesium resulting in high and low FRET from Cy3 and Alexa647 labels positioned on the arms. Holiday junctions are surface immobilized through a biotin attachment and imaged using TIRF microscopy. The camera sensor is split using a dual view so that the acceptor emission is on the top and the donor emission is on the bottom. Videos from each position are provided as compressed zip files containing a sequence of tif files and associated metadata text file. Image sequences were collected using Micro-Manager 2.0 using ALEX or alternating laser excitation with alternating 637 and 532 pulses separated as two different channels. Beam profile images are provided for 637 and 532 excitation allowing for correction of the non-uniform beam profiles. The following 2D affine transformation matrix can be used to transform from the top acceptor emission region to the bottom donor emission region during processing. Affine 2D transformation from top to bottom: (m00, m01, m02, m10, m11, m12), (1.00276, 0.000208, 1.01236, 0.000267, 1.00312, 507.21025) A detailed image processing workflow for this dataset using Mars can be found under the example section at https://duderstadt-lab.github.io/mars-docs/ or directly at https://duderstadt-lab.github.io/mars-docs/examples/FRET_dynamic/
DOI: 10.6084/m9.figshare.20046839
title: Supplementary Material for: Spontaneous Resolution of Macular Edema with Abnormal Vessel Crossing near the Central Macula by Congenital Retinal Macrovessel

description: We present a case of a congenital retinal macrovessel (CRM) with spontaneous resolution of cystoid macular edema. A 39-year-old woman with sudden decreased vision in her right eye was referred to our clinic and found to have a CRM with macular edema. Her visual acuity was 20/25. A week later, the macular edema disappeared without any treatment, and her visual acuity was 20/15. We performed optical coherence tomography angiography and fluorescein angiography (FA), which revealed no obstruction of retinal flow but a slight disturbance of retinal flow near the central fovea on FA. We encountered a case of spontaneous resolution of macular edema with abnormal vessel crossing near the central macula by a CRM, and multimodal imaging was useful for investigating the pathology of the disease.
DOI: 10.6084/m9.figshare.20522397.v1
title: Falik et al Interplant communication of drought cues, JEcol 2022-469, data.xlsx

description: Raw data for Falik et al. Interplant communication of drought cues, JEcol 2022-469
DOI: 10.6084/m9.figshare.21080674
title: Supplementary Material for: The Effect of Auditory Cues on Static Postural Control: A Systematic Review and Meta-Analysis

description: <b><i>Introduction:</i></b> The purpose of this systematic review and meta-analysis was to summarize the results related to the effects of auditory cues on static postural control. <b><i>Methods:</i></b> MEDLINE/PubMed, EMBASE, SCOPUS, LILACS, CINAHL, CENTRAL, Web of Science, PEDro, and Google Scholar were searched from inception until September 2020. Risk of bias was evaluated by both reviewers using Newcastle-Ottawa Quality Assessment Scale (NOS). <b><i>Results:</i></b> Twelve studies with 403 participants were included in the review and 9 studies with 305 participants in the meta-analysis. Results show that auditory cues have significant effects on postural sway in the anterior-posterior direction (<i>p</i> = 0.001), postural sway in the medial-lateral direction (<i>p</i> = 0.001), and static balance (<i>p</i> = 0.001). A low to high heterogeneity was observed across all comparisons. <b><i>Conclusions:</i></b> Results of this meta-analysis revealed that auditory cues decrease postural sway in the anterior-posterior and medial-lateral direction; it also improves static balance. Thus, it can be concluded that auditory cues improve static postural control. Our results suggest that the auditory system can be a determinant of static postural control along with other sensory systems including visual, vestibular, and proprioception systems. Also, this study implies that auditory cues can be a significant therapeutic approach to improve static postural control.
DOI: 10.6084/m9.figshare.7583846
title: qPCR calculations and statistical analysis from "Transcriptomics illuminates the invasive lifestyle of the salmon gut pathogen Spironucleus salmonicida"

description: Excel table with Pfaffl calculations (qPCR_calc.xlsx)Prism file with statistical analysis (qPCRcalc.pzfx)Excel table of statistical analysis (qPCR_tests.xlsx; if reader does not have access to prism)
DOI: 10.17632/zrhfw4r6hb.1
title: Pseudo-Direct Numerical Simulation (P-DNS) databases

description: The databases contain the inertial stress tensors for the equilibrium state of DNS simulations of an RVE for given Id1 (and Id2). For more details see (paper in revision). Larreteguy, Gimenez, Nigro, Idelsohn. Improving the pseudo-direct numerical simulation method (P-DNS) for solving turbulent flows. 2021 Universidad Argentina de la Empresa (UADE), Lima 775, C1073AAO, Buenos Aires, Argentina Centre Internacional de Metodes Numerics en Enginyeria (CIMNE), Edifici C1 Campus Nord UPC C/ Gran Capità, S/N 08034, Barcelona, Spain Centro de Investigación de Métodos Computacionales (CIMEC), Col. RN 168, Km 0, Paraje El Pozo, 3000, Santa Fe, Argentina
DOI: 10.5281/zenodo.1249497
title: Datasets For "Precision And Accuracy Of Single-Molecule Fret Measurements – A Multi-Laboratory Benchmark Study"

description: Supplementary material (raw data) for Fig. 2 in "<strong>Precision and accuracy of single-molecule FRET measurements – a multi-laboratory benchmark study</strong>" to be published with Nature Methods

The confocal data is given in ht3 and hdf5 format.

For the TIRF data the original TIFF-stacks are uploaded including the calibration files.
DOI: 10.18739/a24q7qp6v
title: Detecting Glacier Calving Events from Ocean Waves and Underwater Acoustics, Saqardleq fjord, West Greenland 2013
DOI: 10.5281/zenodo.3479124
title: Fast Pixelated Detectors in Scanning Transmission Electron Microscopy. Part I: Data Acquisition, Live Processing and Storage

description: Scanning transmission electron microscopy data related to paper "Fast Pixelated Detectors in Scanning Transmission Electron Microscopy. Part I: Data Acquisition, Live Processing, and Storage": https://doi.org/10.1017/S1431927620001713
DOI: 10.6084/m9.figshare.21080914
title: Supplementary Material for: Awareness of Antimicrobial Resistance: Surveillance among Visitors of a Tertiary Care Center, Riyadh, Saudi Arabia

description: <b><i>Introduction:</i></b> Antimicrobial resistance (AMR) is a worldwide issue that was declared by the World Health Organization as a high-priority issue. However, there is a lack of awareness about AMR noticed in our community. Therefore, this study aims to assess the knowledge of the community regarding AMR. <b><i>Methodology:</i></b> A validated 24-item questionnaire was administered to the visitors of the outpatient clinic pharmacy waiting area to investigate their awareness of antibiotic resistance. <b><i>Results:</i></b> 397 questionnaires were received and analyzed. The questionnaire included questions asking what antibiotic resistance is, how to use antibiotics properly, and for which infections antibiotics are used. The findings showed that 161 (40.55%) of the respondents were classified as having sufficient knowledge of AMR. Moreover, the results revealed that there was a significant association between gender and the level of knowledge where females showed a better knowledge of AMR than males. Age was also an influencing factor since respondents aged between 18 and 45 (31.49%) years proved to have higher knowledge. <b><i>Conclusion:</i></b> Our findings showed that awareness of AMR and the proper usage of antibiotics seems to be lacking among the general population. Educating the general population through the health care system and public campaigns could change the community’s perception of antimicrobial usage and, consequently, increase awareness of AMR.