cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.23506875.v1
title: Supplementary Material for: EZH2 Expression in Retinoblastoma: a Potential Therapeutic Target

description: Introduction: The enhancer of zeste homolog 2 (EZH2) is a member of the polycomb repressive complex 2 (PRC2) and is important in cell cycle regulation. Increased expression of EZH2 has been reported in retinoblastoma (RB). The aim of the study was to determine EZH2 expression and compare this with clinicopathological parameters in RB and to assess its relationship with tumor cell proliferation. Methods: Ninety-nine retrospective cases of enucleated RB were included in the present study. Expression of EZH2 and the marker of cell proliferation, Ki67, were investigated by immunohistochemistry. Results: Among the 99 cases of retinoblastoma in this study, EZH2 was found highly expressed (positive expression rate≥70%) in 92 cases. EZH2 was expressed in tumor cells but absent in normal retinal tissues. The expression of EZH2 was positively linked to Ki67 expression (r=0.65, P&lt;0.001). Discussion/Conclusion: Elevated EZH2 expression was found in most RB cases, indicating that EZH2 could be a potential therapeutic target for RB.
DOI: 10.6084/m9.figshare.5632222.v1
title: Forecasting ILI Twitter Data

description: This data can be used to replicate influenza-like illness (ILI) nowcasting and forecasting experiments from Twitter.<br>
DOI: 10.6084/m9.figshare.26562724.v1
title: Supplementary Material for: Balloon Pulmonary Angioplasty for Chronic Thromboembolic Pulmonary Disease: success rate and Complications among Different Patient Populations

description: Introduction: Balloon pulmonary angioplasty (BPA) is an effective intervention for patients with chronic thromboembolic pulmonary disease (CTEPD). We aim to identify the patient group with a low success rate or high complication rate of BPA, which is still unclear.
Methods: Both CTEPD patients with or without pulmonary hypertension (CTEPH and NoPH-CTEPD) were included. CTEPH patients were divided into groups with or without pulmonary endarterectomy (PEA-CTEPH and NoPEA-CTEPH). The efficacy and safety of BPA were compared among the groups.
Results: There were 450, 66, and 41 sessions in the NoPEA-CTEPH, PEA-CTEPH, and NoPH-CTEPD groups, respectively. The success rate (≥ 1 degree improvement in flow grade) in the PEA-CTEPH group was 94.5%, significantly lower than that in the NoPEA-CTEPH (97.1%) and NoPH-CTEPD (98.4%) groups (P=0.014). The percentage of complete flow recovery in treated vessels was also lower in PEA-CTEPH group. BPA-related complication rate in NoPEA-CTEPH, PEA-CTEPH, and NoPH-CTEPD patients was 6.1%, 6.0%, and 0.0%, respectively (P=0.309). One BPA-related death occurred (solely in NoPEA-CTEPH). Mean pulmonary artery pressure ≥ 41.5 mmHg was a predictor of BPA-related complications. NoPEA-CTEPH patients had more improvement in 6-minute-walk-distance (6MWD, 87±93 m -NoPEA-CTEPH vs 40±43 m -PEA-CTEPH vs 18±20 m -NoPH-CTEPD, P=0.012).
Conclusions: BPA was safe and effective for all CTEPD groups with less improvement for the PEA-CTEPH and NoPH-CTEPD groups. The success rate of BPA was lower in the PEA-CTEPH group and the complication rate was lower in the NoPH-CTEPD group. Pre-BPA treatment to lower pulmonary artery pressure should not be overlooked in CTEPD patients.
DOI: 10.6084/m9.figshare.7146464.v1
title: Matrices and network analyses based (mainly) on Wahl-O-Mat questionaires

description: This fileset includes a data-summarising spread-sheet (*.xlsx) file and an archive including the NEXUS-formatted scored Wahl-O-Mat questionaires for the German federal election 2017, and the state-elections in Lower Saxony 2017 and Bavaria 2013 and 2018.Also included the data used to illustrate (coarse) topical differences between Swedish parties competing in the 2018 election and which entered parliament.<br><br>The NEXUS-files included in the 7z-archive (*.nex) providing the scored questionaires have been generated with and are optimised for Mesquite and PAUP*, Splits-NEXUS-files (*.dist) include the computed pairwise "political" distances and the raw neighbour-net splits graphs used as basis for the infographic in the related posts (in English or German links below; computed using the software SplitsTree<br>See the links below and the first sheet in the xlsx-file for further information.<br>
DOI: 10.6084/m9.figshare.12610973.v8
title: test_tar_gz

description: test_tar_gz
DOI: 10.6084/m9.figshare.14404883.v1
title: Supplementary Material for: Protective and Anti-Aging Effects of 5 Cosmeceutical Peptide Mixtures on Hydrogen Peroxide-Induced Premature Senescence in Human Skin Fibroblasts

description: Skin aging usually leads to the excessive deterioration of the dermal extracellular matrix, loss of antimicrobial function, loss of skin barrier function, and a series of inflammatory processes. Bioactive peptides have been widely used in cosmetics due to their protective effects on skin and efficient absorption. Combination of different peptides may lead to synergistic or antagonistic effects, so different formulas need to be designed and tested properly. In this study, 5 functional cosmeceutical peptides were tested on their individual and mixed activities to detect a suitable anti-aging and protective formula from our experiments. After the individual activity test, the optimal concentration is 200 μg/mL of carnosine for the superoxide dismutase (SOD) activity, 200 μg/mL of GHK peptide for the hydroxyproline (HYP) content activity, 100 μg/mL of acetyl tetrapeptide-5 for the angiotensin-converting enzyme 1 activity, 400 μg/mL of hexapeptide-11 for the HYP content activity, and 400 μg/mL of acetyl hexapeptide-3 for the catecholamine content activity. According to the optimal concentration of these 5 cosmeceutical peptides, 6 formulations of peptide mixtures were designed and tested for their anti-aging activities and protective effects against hydrogen peroxide-induced premature senescence in human skin fibroblasts. One of the cosmeceutical peptide mixtures (carnosine + acetyl tetrapeptide-5 + hexapeptide-11 + acetyl hexapeptide-3) significantly reduced the intracellular malondialdehyde and hydroxyl free radical contents and increased the HYP and human elastin contents as well as the enzymatic activities of SOD and glutathione peroxidase. Our study suggests that this formula of cosmeceutical peptide mixtures could be a promising agent for use in anti-aging and protective cosmetics.
DOI: 10.6084/m9.figshare.14815911.v2
title: Root hydraulic conductivity dataset in Arabidopsis thaliana wild-type and endodermal barrier mutants

description: Root hydraulic conductivity data in <i>Arabidopsis thaliana</i> Col-0 (WT) line and mutants <i>CDEF</i>, <i>esb1 CDEF</i>, and <i>sgn3 myb36</i>.<br>
DOI: 10.6084/m9.figshare.22568293.v1
title: Supplementary tables_ Murugathasan et. al

description: Excel sheets of Data as explained in manuscript
DOI: 10.6084/m9.figshare.7127726.v11
title: PPTC RNAseq and Genomic Alterations

description: Data deposited here have origins through the National Cancer Institute Pediatric Preclinical Testing Consortion (NCI PPTC) and Alex's Lemonade Stand.<br>The RNAseq data is an FPKM matrix of 250 samples measured across 51,968 genes.<br>The alterations matrix consist of deleterious DNA mutations, DNA copy number alterations, and fusions of varying functional confidence.<br>Gene expression classifiers are applied to the gene expression matrix and the results are interpreted in https://github.com/marislab/pdx-classification
DOI: 10.6084/m9.figshare.12316907.v1
title: multipolesDB.rar

description: database of small multipoles up to 19 vertices<br>
DOI: 10.17632/mbbvr44txv
title: Mobile origin-licensing factors confer resistance to conflicts with RNA polymerase. Scherr et al (Part 6)

description: Mobile origin-licensing factors confer resistance to conflicts with RNA polymerase

Part 6. Raw microscopy data contained in separate zip files. Each file contains tif images collected with MicroManager 1.4. 
Transcription_high-chromatin-licensed-DNA_ATP
Transcription_licensed-DNA_ATPgS_HS
Transcription_licensed-DNA_ATPgS_LS
Transcription_licensed-DNA_ATP_HS
Transcription_licensed-DNA_ATP_LS
Transcription_overlicensed-DNA_ATP_HS
DOI: 10.6084/m9.figshare.22273129.v5
title: 3D representative model

description: The 3D reconstruction model of the rock XCT data
DOI: 10.25452/figshare.plus.24486904.v2
title: Microconfined High-Pressure Transcritical Channel Flow Dataset

description: First comprehensive, open-source dataset carefully curated and structured for studying microconfined high-pressure transcritical fluid channel flows under various regimes. In particular, the dataset contains 18 direct numerical simulations of carbon dioxide at different bulk pressure and velocities confined between differentially-heated walls. For all cases, the thermodynamic conditions selected impose the fluid to undergo a transcritical trajectory across the pseudo-boiling region. The data collection comprises an array of physical quantities that enable comprehensive parametric analyses spanning laminar, transitional, and turbulent flow regimes. This data repository is poised to provide access to the detailed study and modeling of the complex physics observed in high-pressure transcritical fluid environments, especially those closely linked to improving microfluidics performance.The data is structured in a manner where individual cases are allocated in dedicated folders, facilitating in this way convenient access and data processing. Each case folder is structured in different FTT subfolders, which contain 10 snapshot files of the corresponding FTT uniformly spaced in time. Additionally, there is a README.txt file in each case folder that provides essential information about the individual case, such as (i) key independent parameters, (ii) dimensionless numbers, (iii) details on the calculation of the stretching factor in the y-direction, and (iv) the time advancement technique. The dataset files within the FTT subfolders are stored in the Hierarchical Data Format version 5 (h5), an open-source file format capable of handling complex and diverse data. There is also an associated xdmf file that contains data descriptions for these files, which can be visualized with, for example, the open-source software Paraview. Moreover, each case folder also includes a configuration file and a substances library file in YAML format. Likewise, there are C++ files in both .cpp and .hpp formats, allowing users to replicate the simulations for further investigation and/or verification. Finally, a post-processing script is supplied with the dataset, specifically designed to streamline the presentation of primary variables while concurrently computing derived quantities.
DOI: 10.6084/m9.figshare.25215236.v1
title: Valp1: a newly identified temperate phage facilitating coexistence of lysogenic and non-lysogenic populations of Vibrio anguillarum

description: Isolation and characterization of the Valp1 phage, a new temperate phage of V. anguillarum.
DOI: 10.17632/76kcwsgs94
title: Data for: Promoting Financial Literacy among the Elderly

description: Stata code and data for the manuscript titled "Promoting Financial Literacy among the Elderly: Consequences on Confidence". We conduct an impact evaluation of a two-hour lecture targeting the elderly population. We find that the intervention does not have a significant impact on knowledge but has a significant effect on confidence and (partly) on overconfidence.
DOI: 10.6084/m9.figshare.28558211.v1
title: Supplementary Material for: Machine learning-based model for predicting severe exacerbations in adult-onset type 2 inflammatory asthma

description: Introduction: Currently, scholars have applied machine learning to the clinical prediction of acute asthma exacerbations. However, given the heterogeneity of inflammatory phenotypes in asthma, it is imperative to develop machine learning models tailored to specific asthma inflammatory phenotypes.
Objective: To develop predictive models to identify risk factors for the severe exacerbations in adult-onset type 2 inflammatory asthma, which could help facilitate early diagnosis and intervention, potentially reducing healthcare costs.
Methods: Retrospective analysis of patients with acute exacerbations of type 2 inflammatory asthma at Shenzhen People's Hospital from May 2017 to September 2022. Patients were categorized into mild-to-moderate exacerbation (n=300) and severe exacerbation groups (n=209). We collected clinical data from all participants, including demographic characteristics, laboratory results, pulmonary function test results, comorbidities, and asthma medication use. We tested four models: decision trees, logistic regression, random forests, and LightGBM. For each model, 80% of the dataset was used for training and 20% was used to validate the models. The area under (AUC) the receiver operator characteristic (ROC) curve was calculated for each model.
Results: Multivariate Logistic regression revealed that low ACT scores, low FEV1/FVC ratio, a history of diabetes, high absolute neutrophil count, and a family history of asthma were independent risk factors for severe exacerbations of type 2 inflammatory asthma. LightGBM outperformed all other models, achieving the highest AUC of 0.9344, with sensitivity = 0.8293, specificity =0.9180, PPV = 0.8718, and NPV = 0.8889. The accuracy stood at 0.8824, with an F1 score of 0.8500. The top ten clinical variables impacting the prediction outcome in the LightGBM model were ACT score, FEV1/FVC ratio, age, lactate dehydrogenase, FEV1 % predicted, fasting blood glucose, angiotensin-converting enzyme, duration of disease, Neutrophil-to-lymphocyte ratio, platelet-to-lymphocyte ratio. Finally, through DCA, the clinical decision-support value of the LightGBM model was confirmed, demonstrating its maximum net benefit for type 2 asthma patients across a threshold probability range of 20% to 80%.
Conclusions: We have developed and established a prediction model for severe exacerbations of adult-onset type 2 inflammatory asthma using the LightGBM machine learning approach, which exhibits good predictive performance. This model can aid in the early prediction and prevention of severe exacerbations of adult-onset type 2 inflammatory asthma.
DOI: 10.6084/m9.figshare.13473207.v1
title: Global patterns of subgenome evolution in organelle-targeted genes of six allotetraploid angiosperms

description: Whole-genome duplications (WGDs), in which the number of nuclear genome copies is elevated as a result of autopolyploidy or allopolyploidy, are a prominent process of diversification in eukaryotes. The genetic and evolutionary forces that WGD imposes upon cytoplasmic genomes are not well understood, despite the central role that cytonuclear interactions play in eukaryotic function and fitness. Cellular respiration and photosynthesis depend upon successful interaction between the 3000+ nuclear-encoded proteins destined for the mitochondria or plastids and the gene products of cytoplasmic genomes in multi-subunit complexes such as OXPHOS, organellar ribosomes, Photosystems I and II, and Rubisco. Allopolyploids are thus faced with the critical task of coordinating interactions between nuclear and cytoplasmic genes that were inherited from different species. Because cytoplasmic genomes share a more recent history of common descent with the maternal nuclear subgenome than the paternal subgenome, evolutionary “mismatches” in allopolyploids might lead to accelerated rates of evolution in paternal homoeologs of organelle-targeted genes. We tested this hypothesis in maternal vs. paternal copies of organelle-targeted genes in six allotetraploids: Brachypodium hybridum (Poaceae), Chenopodium quinoa (Amaranthaceae), Coffea arabica (Rubiaceae), Gossypium hirsutum (Malvaceae), Nicotiana tabacum (Solanaceae), and Triticum dicoccoides (Poaceae). We report evidence that allopolyploid subgenomes exhibit highly biased rates of protein-sequence evolution genome-wide, but we did not observe global effects of cytonuclear incompatibilities on paternal homoeologs of organelle-targeted genes. We did, however, find taxon- and complex-specific evidence of cytonuclear incompatibilities in the mitochondrial enzyme complexes of allotetraploid wheat. There was mixed evidence for whether organelle-targeted genes re-diploidize more rapidly than non-organelle-targeted genes, indicating that additional work is needed to understand the evolution of cytonuclear stoichiometry. These global analyses provide insights into the complex evolutionary dynamics of allopolyploid genomes, showing that despite sharing the same nucleus, generation time, and ecological context, allopolyploid subgenomes have separate evolutionary trajectories.
DOI: 10.17632/dtwpybx6d9
title: BARRIER code: Calculation of fission barriers

description: Abstract Average values of various nuclear properties are only explained on average by the liquid drop model ( where the average might be taken over particle number or, alternatively, over deformation). To reproduce other aspects of nuclear structure, such as ground state spins and energy spectra, it was found elsewhere that a different description is necessary. In this regard, we calculated single particle energies as function of the deformation parameters of an axially deformed Woods-Saxon potential... Title of program: BARRIER Catalogue Id: ADKF_v1_0 Nature of problem Average values of various nuclear properties are only explained on the average by liquid drop model (where the average might be taken over particle number or, alternatively, over deformation). To reproduce other aspects of nuclear structure, such as ground state spins and energy spectra, it was found elsewhere that a different description was necessary. In this regard, we calculated single particle energies as functions of the deformation parameters of an axially deformed Woods Saxon potential, ... Versions of this program held in the CPC repository in Mendeley Data ADKF_v1_0; BARRIER; 10.1016/S0010-4655(99)00199-X This program has been imported from the CPC Program Library held at Queen's University Belfast (1969-2018)
DOI: 10.23641/asha.19529053.v1
title: Place-based versus default maps for CI and EAS (Dillon et al., 2022)

description: <b>Purpose: </b>Cochlear implant (CI) recipients demonstrate variable speech recognition when listening with a CI-alone or electric-acoustic stimulation (EAS) device, which may be due in part to electric frequency-to-place mismatches created by the default mapping procedures. Performance may be improved if the filter frequencies are aligned with the cochlear place frequencies, known as place-based mapping. Performance with default maps versus an experimental place-based map was compared for participants with normal hearing when listening to CI-alone or EAS simulations to observe potential outcomes prior to initiating an investigation with CI recipients.<b>Method:</b> A noise vocoder simulated CI-alone and EAS devices, mapped with default or place-based procedures. The simulations were based on an actual 24-mm electrode array recipient, whose insertion angles for each electrode contact were used to estimate the respective cochlear place frequency. The default maps used the filter frequencies assigned by the clinical software. The filter frequencies for the place-based maps aligned with the cochlear place frequencies for individual contacts in the low- to mid-frequency cochlear region. For the EAS simulations, low-frequency acoustic information was filtered to simulate aided low-frequency audibility. Performance was evaluated for the AzBio sentences presented in a 10-talker masker at +5 dB signal-to-noise ratio (SNR), +10 dB SNR, and asymptote.<b>Results: </b>Performance was better with the place-based maps as compared with the default maps for both CI-alone and EAS simulations. For instance, median performance at +10 dB SNR for the CI-alone simulation was 57% correct for the place-based map and 20% for the default map. For the EAS simulation, those values were 59% and 37% correct. Adding acoustic low-frequency information resulted in a similar benefit for both maps.<b>Conclusions:</b> Reducing frequency-to-place mismatches, such as with the experimental place-based mapping procedure, produces a greater benefit in speech recognition than maximizing bandwidth for CI-alone and EAS simulations. Ongoing work is evaluating the initial and long-term performance benefits in CI-alone and EAS users.<br><b>Supplemental Material S1.</b> Regression coefficients for the linear mixed model that compared performance between default and place-based maps that would be used clinically. <br><b>Supplemental Material S2. </b>Regression coefficients for the linear mixed model that assessed the benefit of adding acoustic low-frequency information to default maps with spectrally shifted information and place-based maps. <br>Dillon, M. T., O'Connell, B. P., Canfarotta, M. W., Buss, E., & Hopfinger, J. (2022). Effect of placed-based versus default mapping procedures on masked speech recognition: Simulations of cochlear implant alone and electric-acoustic stimulation. <i>American Journal of Audiology</i>. Advance online publication. https://doi.org/10.1044/2022_AJA-21-00123
DOI: 10.6084/m9.figshare.27917127.v1
title: Supplementary Material for: Perineural invasion for risk stratification in cutaneous squamous cell carcinoma: a scoping review

description: Introduction: Microscopic perineural invasion (mPNI) is a histopathological characteristic that can be found in cutaneous squamous cell carcinoma (cSCC). In the eight edition of the American Joint Committee on Cancer (AJCC), mPNI defined as the involvement of nerves ≥0.1mm and nerves deeper than the dermis is included in risk stratification of cSCC. The question remains whether other mPNI features are important for optimal cSCC staging. We aim to summarize the evidence from published studies on the independent association between various mPNI features and the risk of recurrence, metastasis and disease-specific death in patients with cSCC. 
Methods: Embase, PubMed, and Web of Science were searched from January 2023 to February 2024 to identify studies that reported the prognostic impact of mPNI features in patients ≥18 years with histopathologically verified cSCC. Data on study and tumour characteristics were extracted. 
Results: Nineteen studies met the inclusion criteria and evaluated one or more mPNI features in cSCC including nerve diameter, the extent of mPNI, the number of affected nerves, and depth of mPNI. Two studies provided evidence that ‘mPNI ≥0.1mm’ and ‘mPNI deeper than the dermis’ are significantly and independently associated with poor prognosis after correction for other mPNI features and high-risk factors. One of these studies additionally identified ‘involvement of ≥3 nerves’ as an independent and significant predictor of higher risk of local recurrence (HR, 2.17; 95% CI, 1.03-4.56; p=0.04). 
Conclusion: Besides ‘nerve diameter of ≥0.1mm’ and ‘depth of mPNI involvement’, ‘involvement of multiple nerves’ was found to be an independent risk factor for poor prognosis and should also be considered for appropriate risk stratification.