cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.17632/954dxdncrv
title: NADH-driven polyhydroxybutyrate accumulation in E. coli dataset 2

description: Generation of polyhydroxybutyrate (PHB) as a fermentation product enables the coupling of growth and product generation. Moreover, the reduction of oxygen supply should reduce operative cost and increase product yield. Generation of PHB as a fermentation product depends on the in vivo activity of an NADH-preferring acetoacetyl-CoA reductase. Proof of this concept requires the characterization of an NADH-preferring acetoacetyl-CoA reductase and PHB accumulation in a species naturally incapable of doing so, for example, Escherichia coli. This dataset contains three folders. The Enzyme Kinetics data folder contains: (1) Enzyme stability assays (Selwyn tests). (2) Initial rates versus acetoacetyl-CoA concentration and progress curves from reactions catalyzed by the acetoacetyl-CoA reductase from Candidatus Accumulibacter phosphatis (AARCAp) and another enzyme (AARChimera), who is a modification of the acetoacetyl-CoA reductase from Cupriavidus necator where the original residues N37-S38-P39-R40-R41 were replaced by the residues E37-F38-D39-K40-P41 from AARCAp; (3) Scripts to analyze these kinetic data with the software DYNAFIT and files resulting from the analysis with DYNAFIT, (4) a MATLAB script to calculate the relative consumption of NADH and NADPH (5) a MATLAB script to calculate the metabolic flux capacity of the reaction catalyzed by an acetoacetyl-CoA reductase at different NADH/NAD ratios. The "Fermentations" folder contains: (1) An Excel file with the biomass composition of an engineered E. coli strain: ((F– λ– ilvG– rfb-50 rph-1 (DE3) ΔadhE ΔadhP ΔldhA Δpta ΔmhpF)) transformed with the plasmid pCOLA-phaCACnecatorphaBCAp-cscABK. phaCA genes encodes for the polyhydroxybutyrate synthase and the acetyl-coenzyme A acetyltransferase from C. necator respectively; phaBCAp gene encodes for the enzyme AARCAp; cscABK genes encodes for the sucrose hydrolase, the sucrose:proton symporter and fructose kinase from E. coli W, respectively. (2) The MATLAB file “ecolicore.mat” which contains an E. coli wild type in silico model. (3) A MATLAB script to generate an in silico model of the engineered strain, considering plasmid and protein burdens. (4) An in silico metabolic model of the engineered E. coli strain. (5) A MATLAB script to calculate the reconciled specific rates during the continuous growth of such strain. Two steady-states, characterized by different levels of oxygen limitation, were studied. Sucrose was employed as the sole carbon source and the dilution rate was D=0.1 1/h. (6) An Excel file with the observed unbalanced and reconciled specific rates of the engineered strain during the growth in the continuous culture. (7) A MATLAB script to calculate the reconciled rates and the metabolic fluxes distributions. (8) Metabolic fluxes distributions in an Excel table and over a Metabolic fluxes distribution map. The "Plasmids DNA sequence maps" folder contains the DNA sequence maps of different plasmids employed in this research.
DOI: 10.6084/m9.figshare.20000507.v2
title: Dong et al., Subduction initiation without volcanic arc magmas, insight from two young subduction zones in the West Pacific

description: The input files necessary for the numerical subduction models contained within Dong et al.(submitted to GRL). The version of ASPECT and plugin refer to Holt and Condit ,2021, G-cubed. （https://doi.org/10.5281/zenodo.4543413）
DOI: 10.6084/m9.figshare.23632395.v11
title: Data from Xiao et al.xlsx

description: Data from Xiao et al. submitted to JGR-Biogeosciences
DOI: 10.6084/m9.figshare.25898476.v1
title: Dataset: AbraLlama: Predicting Abraham Model Solute Descriptors and Modified Solvent Parameters Using Llama

description: This dataset is the modeling dataset for the paper "AbraLlama: Predicting Abraham Model Solute Descriptors and Modified Solvent Parameters Using Llama." It includes current Abraham model solvent parameter values along with their predicted modified values. The model is accessible as an app on Hugging Face at https://huggingface.co/spaces/ttmn/AbraLlama.
DOI: 10.17632/g4bfvxf2bt
title: Supplementary - Tocilizumab for polyarteritis nodosa

description: Supplementary - Tocilizumab for polyarteritis nodosa
DOI: 10.17632/tv98zysmt4
title: GENERAL POPULATION AWARENESS ON BASIC LIFE SUPPORT IN HARYANA: A SURVEY STUDY

description: BACKGROUND AND PURPOSE: Basic Life Support (BLS) is essential because it preserves the life and maintains the viability of patients with life-threatening diseases or injuries until a group of paramedics or hospital professionals can offer specialist treatment. Serious injuries and respiratory problems can arise from a variety of situations. The population's confidence to respond promptly when necessary and degree of reluctance are considerably increased and decreased by BLS awareness among those who have relatives with heart conditions.This study was conducted to investigated the awareness of BLS among general population.
DOI: 10.6084/m9.figshare.106620.v4
title: Lab Notebook, 2012

description: Permanent archive of Carl Boettiger's open lab notebook entries for the year 2012 (http://www.carlboettiger.info/archives.html). Entries are archived in plain text UTF-8. Written in pandoc-flavored Markdown. Meets the goals of the Data Management Plan: http://www.carlboettiger.info/2012/10/09/data-management-plan.html
DOI: 10.6084/m9.figshare.1367441.v1
title: DISEASES v1 (human, experiments, filtered)

description: This file constitutes the filtered experiments channel on human proteins for the last version of the DISEASES database to use STRING v9 protein identifiers.
DOI: 10.6084/m9.figshare.28464731.v1
title: Global vegetation cover disturbance change dataset in 2000-2020 (part 1:0-90)

description: This dataset describes the types of changes in different vegetation, mainly involving four vegetation types: forest, shrub, grassland, and cropland. Nine main types of vegetation disturbance were identified for the four vegetation types: farmland expansion or occupation (Type 1), afforestation/conversion of farmland to forests/secondary forests, etc. (Type 2), forest degradation/fallow/newly shrubs/artificial shrubs (Type 3), deforestation/shrub degradation/fallow (Type 4), built-up expansion or occupation (Type 5), vegetation degradation to bare land/fire (Type 6), water flooding into wetlands (Type 7), water flooding/artificial water bodies (Type 8), and vegetation expansion (Type 10). The Spatial resolution of this dataset is 30m (due to factors such as cloud and image quality, some area's spatial resolution is resampled to 40m).To verify the production accuracy of the global vegetation cover disturbance change dataset, we randomly selected 2425 sample points worldwide. These sample points cover different vegetation types: cropland (615), forest (617), shrub (762), grassland (431). Meanwhile, these sample points also cover 9 main types of vegetation disturbance: Type 1（189）、Type 2（197）、Type 3（195）、Type 4（212）、Type 5（279）Type 6（282）、Type 7（319）、Type 8（308）、Type 10（444）。The overall accuracy of the dataset is as high as 85%. The accuracy of most types of disturbances is close to or exceeds 80%. Among them, the accuracy such as cropland, shrubs, grasslands, built-up area, bare land, wetlands, and water bodies were 84%, 83%, 77%, 83%, 85%, 87%, and 87%, respectively. In contrast, the accuracy of vegetation expansion type disturbance is as high as 92%.
DOI: 10.6084/m9.figshare.29145449.v1
title: serum P4 data

description: This dataset supports a sub-analysis of a prospective randomized controlled trial investigating the predictive value of serum progesterone levels on the day of pregnancy testing in HRT-FET cycles.<br>ROC curve analysis was performed by formulation, using serum P4 and its change (ΔP4).<br>The data correspond to the figures and results presented in the submitted manuscript.
DOI: 10.6084/m9.figshare.8159180.v1
title: Microtubules stained fixed HeLa cell

description: A fixed HeLa cell with alpha-tubulin stained, using Star488 secondary antibodies (Abberior, Germany). Sample was imaged with a Nikon A1 confocal microscope, with excitation wavelength 488nm, 60x/1.4 oil immersion objective, 0.4 AU pinhole and GaAsP detector.
DOI: 10.17632/2jdyyyd8hx
title: Cell type specific binocular interactions

description: Projections from each eye are segregated in separate domains within the dorsal lateral geniculate nucleus (dLGN). Yet, in vivo studies indicate that the activity of single dLGN neurons can be influenced by visual stimuli presented to either eye. In this study we explored whether intrinsic circuits mediate binocular interactions in the mouse dLGN. We employed dual color optogenetics in vitro to selectively activate input from each eye and recorded synaptic responses in thalamocortical (relay) cells as well as inhibitory interneurons, which have extensive dendritic arbors that are not confined to eye specific domains. While most relay cells received monocular retinal input, most interneurons received binocular retinal input and most relay cells received binocular retinogeniculate-evoked inhibition. In recordings from closely-spaced pairs of relay cells and interneurons, the most common relationship observed was retinogeniculate excitation of interneurons paired with inhibition of relay cells via activation of inputs from the same eye(s). Moreover, relay cells that received binocular inhibition were located in and around the ipsilateral patch of retinogeniculate terminals, suggesting that interneuron output is spatially related to retinal input. Finally, we found that dLGN interneurons are interconnected, displaying both monocular and binocular inhibition in response to retinal activation. In sum, our results indicate that geniculate interneurons provide one of the first locations where signals from the two eyes can be compared, integrated, and adjusted before being transmitted to cortex, shedding new light on the role of the thalamus in binocular vision.
DOI: 10.6084/m9.figshare.21440484.v3
title: Rehearsal_031322.mat

description: Data from the reherarsal done on 03/13/22.
DOI: 10.6084/m9.figshare.4262921.v11
title: Resources for communicating Drosophila research in schools and on science fairs

description: This online repository contains resources generated by the Manchester Fly Facility for the science communication of <i>Drosophila</i> research both on science fairs and in schools. The materials comprise posters, PowerPoint presentations, movies, sticker and T-shirt designs, experimental instructions, logistics documents etc. An overview of all documents is provided in the Contents.pdf file. Further explanations about the rationale and strategy of our outreach activities can be taken from our recent article:<br><br>Patel, S., Prokop, A. (2017). The Manchester Fly Facility: Implementing an objective-driven long-term science communication initiative. Semin Cell Dev Biol 70, 38-48 -- http://www.sciencedirect.com/science/article/pii/S1084952117303312<br><br>
DOI: 10.25416/ntr.25746423.v1
title: #RSVPNursing Gamification in Nursing education-Game based pedagogy-Innovation in Nursing & Allied health education .pptx

description: <strong>#RSVPNursing </strong>
<strong>Gamification in learning through Virtual escape room and interactive quiz</strong> .
Gamebased pedagogy in Nursing 
An new innovative and enagiging approach for educators and learners.
DOI: 10.6084/m9.figshare.14571513.v1
title: Supplementary Material for: Cyclosporine A Treatment of Proteinuria in a New Case of MAFB-Associated Glomerulopathy without Extrarenal Involvement: A Case Report

description: The <i>MAFB</i> gene encodes an important basic leucine zipper transcription factor that functions in glomerular podocytes, macrophages, and osteoclasts. Recently, <i>MAFB</i> was identified as the gene that was responsible for causing nephropathy with focal segmental glomerulosclerosis (FSGS) with multicentric carpotarsal osteolysis (MCTO) or Duane retraction syndrome (DRS). Here, we describe a patient with nephropathy associated with FSGS who exhibited a novel stop-gain variant in the <i>MAFB</i> gene (NM_005461:c.590C&gt;A (p.Ser197Ter)). The patient’s father exhibited proteinuria with FSGS with possible DRS, whereas the patient exhibited nephropathy with FSGS and nearly normal eye movement and hearing function, as well as intact bone structure in the extremities. Conventional oral steroids or immunosuppressive drugs have not demonstrated effectiveness for patients with nephropathy who exhibit pathogenic variants in <i>MAFB</i>, except for a patient with nephropathy with FSGS and MCTO who experienced attenuated proteinuria within the subnephrotic range in response to cyclosporine A (CyA) treatment for at least 4 years. Thus, we attempted administration of CyA in our patient. Unexpectedly, the patient demonstrated good and rapid responses to CyA, including a partial reduction in proteinuria from approximately 2.0 g/g Cr to proteinuria within the subnephrotic range (0.27 g/g Cr) after 13 months of observation. Our findings suggest that CyA may be a suitable treatment option for patients with nephropathy with FSGS who exhibit pathogenic <i>MAFB</i> variants.
DOI: 10.6084/m9.figshare.22574299.v1
title: wc2.1_30s_bio_12.tif

description: Bioclim environmental variables 30 arcsec
DOI: 10.6084/m9.figshare.11778900.v2
title: Metadata record for: A dataset of radar-recorded heart sounds and vital signs including synchronised reference sensor signal

description: This dataset contains key characteristics about the data described in the Data Descriptor A dataset of radar-recorded heart sounds and vital signs including synchronised reference sensor signal. <br> Contents: <br> 1. human readable metadata summary table in CSV format 2. machine readable metadata file in JSON format <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.27926826.v1
title: The raw EEG recordings used for detecting driver fatigue.

description: These are the raw EEG recordings from twenty-six participants collected for driver fatigue detection. To protect personal privacy, each participant is identified by a unique numerical code. The .cnt files, generated using a 40-channel Neuroscan amplifier, contain EEG data recorded under two different states during the driving process.
DOI: 10.17632/ndm5f5bffn
title: Immunohistochemical staining - H&E

description: Figure 6h
DOI: 10.6084/m9.figshare.14179076.v1
title: Supplementary Material for: Kisspeptin-54 Accurately Identifies Hypothalamic Gonadotropin-Releasing Hormone Neuronal Dysfunction in Men with Congenital Hypogonadotropic Hypogonadism

description: <b><i>Background:</i></b> Hypogonadotropic hypogonadism (HH) is hypogonadism due to either hypothalamic or pituitary dysfunction. While gonadotropin-releasing hormone (GnRH) can directly test pituitary function, no specific test of hypothalamic function exists. Kisspeptin-54 (KP54) is a neuropeptide that directly stimulates hypothalamic GnRH release and thus could be used to specifically interrogate hypothalamic function. Congenital HH (CHH) is typically due to variants in genes that control hypothalamic GnRH neuronal migration or function. Thus, we investigated whether KP54 could accurately identify hypothalamic dysfunction in men with CHH. <b><i>Methods:</i></b> Men with CHH (<i>n</i> = 21) and healthy eugonadal men (<i>n</i> = 21) received an intravenous bolus of either GnRH (100 μg) or KP54 (6.4 nmol/kg), on 2 occasions, and were monitored for 6 h after administration of each neuropeptide. <b><i>Results:</i></b> Maximal luteinizing hormone (LH) rise after KP54 was significantly greater in healthy men (12.5 iU/L) than in men with CHH (0.4 iU/L; <i>p</i> &lt; 0.0001). KP54 more accurately differentiated CHH men from healthy men than GnRH (area under receiver operating characteristic curve KP54: 1.0, 95% CI 1.0–1.0; GnRH: 0.88, 95% CI 0.76–0.99). Indeed, all CHH men had an LH rise &lt;2.0 iU/L following KP54, whereas all healthy men had an LH rise &gt;4.0 iU/L. Anosmic men with CHH (i.e., Kallmann syndrome) had even lower LH rises after KP54 than did normosmic men with CHH (<i>p</i> = 0.017). Likewise, men identified to have pathogenic/likely pathogenic variants in CHH genes had even lower LH rises after KP54 than other men with CHH (<i>p</i> = 0.035). <b><i>Conclusion:</i></b> KP54 fully discriminated men with CHH from healthy men. Thus, KP54 could be used to specifically interrogate hypothalamic GnRH neuronal function in patients with CHH.
DOI: 10.6084/m9.figshare.3530531.v1
title: Appendix D. Results of models of species’ seedling survival rates as a function of shade-tolerance guild (light-demanding, intermediate, or shade tolerant) and species abundance in the BCI 50-ha plot, Panama.

description: Results of models of species’ seedling survival rates as a function of shade-tolerance guild (light-demanding, intermediate, or shade tolerant) and species abundance in the BCI 50-ha plot, Panama.
DOI: 10.6084/m9.figshare.22107611.v1
title: Evaluating Imbrication of Gravels_Qin

description: The 'Gen_Imb_Run.m' and 'Gen_Imb.m' are used to generate artificial gravel surfaces; The 'IncIndex2D' is used to calculate the inclination index; The 'IncIndex2D_RunNanxi' and 'IncIndex2D_RunSmart' used the 'IncIndex2D' code to calculate the orientation of gravel surfaces with data attached. The 'Lineardetr.m' is used to detrend a gravel surface; The 'MyRead' and 'ReadData' are used to read the data file; The 'Smart_wai_a,' 'Smart_wai_b,' and 'P06DEM_1cm-unit1cm' are gravel surfaces data.
DOI: 10.6084/m9.figshare.24042363.v1
title: Supplementary Material for: Association of aspirin with dementia or mild cognitive impairment: A systematic review and meta-analysis of randomized trials

description: Background: At present, the effect of aspirin in preventing dementia or mild cognitive impairment (MCI) is controversial. Clarifying their association is of interest for subsequent relevant clinical trials. Methods: Four databases (PubMed, Embase, Web of science, and the Cochrane library) were searched from inception to May 12, 2023 for randomized controlled trials (RCTs) that explored the effects between aspirin and dementia or MCI. Two reviewers independently extracted and analyzed data using Stata software. Discrepancy was resolved by a third reviewer. The primary outcomes were dementia and MCI. The secondary outcomes were cognitive decline and changes in cognitive scores. Results: Five RCTs with 46804 participants at randomization were included. For the primary outcomes, low certainty evidence showed that aspirin was not associated with dementia (OR=0.93, 95%CI (0.85, 1.03), P＞0.05, I2=0%) or MCI (OR=1.00, 95%CI (0.88, 1.14), P＞0.05, I2=3.3%). For the secondary outcomes, moderate certainty evidence showed that aspirin was not associated with cognitive decline (OR=1.02, 95%CI (0.93, 1.11), P＞0.05, I2=0%) and a change in global cognitive score (SMD=-0.01, 95%CI (-0.03, 0.02), P＞0.05, I2=0%). Low certainty evidence showed that aspirin was not associated with a change in verbal learning memory score (SMD=-0.04, 95%CI (-0.09, 0.01), P＞0.05; I2=72.5%). Conclusions: Low and moderate certainty evidence showed that aspirin was not associated with dementia, MCI, cognitive decline, or better cognitive scores. Future research may need to focus more on subtypes of dementia, mainly vascular dementia or other vascular neurocognitive diseases, and assess whether aspirin has long-term clinical benefits in a large sample of patients with dementia or MCI.
DOI: 10.6084/m9.figshare.25399294.v1
title: S1_Area approximation

description: This is the supplementary dataset S1 to the paper "How to quantify heavy mineral fertility from point-counting data". The data shows how the area of detrital grains was calculated by (1) using the measured longest and shortest grain diameter (a and b-axis) and approximating the area as circles, ellipses, squares and rectangles, and (2) by measuring the true area with the wand tool in ImageJ. The best-fit area approximation was identified by the least square method.
DOI: 10.6084/m9.figshare.25043753.v1
title: Supplementary files associated with the DRiDO microbiome manuscript

description: The Dietary Restriction in Diversity Outbred mice (DRiDO) study assessed how caloric restriction and fasting affect lifespan and health in a large population of genetically diverse mice. The DRiDO microbiome manuscript specifically focused on the microbiome data generated as part of this study. The microbiome dataset consists of 2997 metagenomic profiles from 913 Diversity Outbred mice. Here, we provide large supplementary files required for reproducing analyses performed in the manuscript.<br>Main DRiDO manuscript: https://www.biorxiv.org/content/10.1101/2023.11.28.568901Microbiome DRiDO manuscript: https://www.biorxiv.org/content/10.1101/2023.11.28.568137
DOI: 10.6084/m9.figshare.6994946.v2
title: Relative Power EEG and Bayley Scales Infant data

description: Spreadsheet with resting state relative power electroencephalography data and Bayley Scales of Infant Development Scales (version 3) scores for each infant participant at each assessment. Source data for manuscript "Relationships between variance in electroencephalography relative power and developmental status in infants with typical development and at risk for developmental disability: An observational study" by the same authors. Please note, a version 2 spreadsheet was uploaded on February 23, 2020. This fixed a transposed data error for electrode values at visit 1 in the original spreadsheet. This error occurred when we compiled variables to create a single spreadsheet for figshare, it did not affect our analyses. We would also like to note that for prediction of Bayley Raw Fine Motor scores at visit 3 with SD RP from visit 1 analyses included only infants with EEG data at both visits 1 and 3, N=22.
DOI: 10.17632/s43wm92cjb
title: Data for: Geochemistry and Zircon U-Pb Geochronology of the Oxidaban intrusive complex：Implication for Paleozoic Tectonic Evolution of the South Tianshan Orogenic Belt, China

description: This data set includes zircon U–Pb ages, major and trace elements geochemistry and Sr–Nd isotopic compositions of the intrusive rocks in Oxidaban, South Tianshan region, China.
DOI: 10.6084/m9.figshare.27311760.v1
title: Soil legacies of genotypic diversity enhance population resistance to water stress

description: While thepositive relationship between plant diversity and ecosystem functioning is frequently observed and often attributed to direct plant-plant interactions, it remains unclear whether and how the effects of plant diversity endure through soil legacy effects, particularly at thelevel of genotypic diversity.We manipulated the genotypic diversity of <i>Scirpus mariqueter</i>and tested its soil legacy effects on aconspecific phytometer under low- and high-water availabilityconditions. We found that genotypic diversity enhancedphytometer productivity through soil legacies, with stronger effects under low-water availability conditions, improving itsresistanceto water stress. Moreover, this effect was attributed to the association of asexual and sexual reproductive strategies by increasingramet number to ensure plant survival under low-water availabilityand promotingsexual reproduction to escape stress.The observed diversity effects were primarily associated with increased levels of microbial biomass in soils trained by populations with diverse genotypes. Our findings highlight the importance of plant genotypic diversity in modulating ecosystem functioning through soil legacies, and call for management measures that promote genetic diversity to make ecosystems sustainable in the face of climate change.