cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.3084202.v1
title: Code for producing the simulations in 'Nearly Neutral Evolution Across the Drosophila melanogaster Genome'

description: Files containing the SLiM input files and processing code used to run SLiM and produce figures 4 and 5 in the manuscript 'Nearly Neutral Evolution Across the Drosophila melanogaster Genome'. <br>The full SLiM manual, and the software, are available from: https://messerlab.org/slim/ <br><br>- - - - - - - - - - <br>Figure 4 notes:<br>Please see ‘figure4-SLiM_input_example.txt’ for reference. This is an example of an input file used for SLiM.<br>To produce the figure, the frequency of adaptive mutations (class ‘m1’), as a proportion of total mutations that occur, was altered by changing the initializeGenomicElementType() line. The frequencies used were as follows: 0.05%, 0.1%, 0.15%, 0.2%, 0.25%, 0.3%, 0.35%, 0.4%, 0.45% and 0.5%.<br>example line from script, such that m1 mutations occur as 0.05% of all mutations:initializeGenomicElementType("g1", c(m1, m2, m3, m4, m5, m6, m7, m8, m9, m10), c(0.0005, 0.11105555, 0.11105555, 0.11105555, 0.11105555, 0.11105555, 0.11105555, 0.11105555, 0.11105555, 0.11105555)).<br>Allowing for recombination:initializeRecombinationRate() line was changed: using parameters 0.00001 and 0.00005.<br>For figure 4, we calculated the nucleotide site diversity of each different class of mutation. The python code for performing the analysis is available- the code has been divided into three files, that are labelled in order in which they should be run.<br>- - - - - - - - - - <br>Figure 5 notes:<br>Please see ‘figure5-SLiM_input_example.txt’ for reference. This is an example of an input file used for SLiM.<br><br>Again, the frequency of adaptive mutations (class ‘m1’), as a proportion of total mutations that occur, was altered by changing the initializeGenomicElementType() line. The frequencies used were as follows: 0.05%, 0.1%, 0.2%, 0.3%, 0.4%, 0.5%, 0.8% and 1%.<br>Deleterious mutations and neutral mutations occur with equal frequency, with deleterious mutations having fitness effects draw from a gamma distribution.<br>The python code for performing the analysis is available, as above- the code is largely similar, however, in figure 5, rather than nucleotide site diversity, synonymous and nonsynonymous polymorphism counts are used.<br><br><br><br><br>
DOI: 10.6084/m9.figshare.5446489.v1
title: Transcriptome - Sphaerothecum destruens (rosette agent)

description: Reads are deposited in NCBI: https://www.ncbi.nlm.nih.gov/sra/SRX737879<br><br> Assembly in-home BGI to obtain Unigene (contigs)- ORF prediction using TransDecoder (Trinity plugin) and PfamScan to obtain coding sequences (CDS files) from transcripts (mRNA)- Protein translations are included (pep)<br>- clean.fasta: Assembly cleaned from cross-contamination of other species multiplexed (Corallochytrium limacisporum India, Ichthyophonus hoferi and Nutomonas longa) after applying CroCo V0.1.1 (Simion et al. in prep). It may contain bacterial contamination.<br><br><strong>Guifré Torruella, Alex de Mendoza, Xavier Grau-Bové, Meritxell Antó, </strong>Mark A. Chaplin<strong>, Javier del Campo, </strong>Laura Eme, Gregorio Pérez-Cordón, Christopher M. Whipps, Krista M. Nichols, Richard Paley, Andrew J. Roger, Ariadna Sitjà-Bobadilla, Stuart Donachie,<strong> and Iñaki Ruiz-Trillo. </strong>(2015)<br><em>Phylogenomics reveals convergent evolution of lifestyles in close relatives of animals and fungi.</em><br><strong><em>Current Biology </em></strong>25(18):2404-10.<br><br>www.multicellgenome.com
DOI: 10.17632/k4gn85drc9
title: Oxidative liquefaction - approach for complex plastic waste stream conversion

description: The oxidative liquefaction method was used to get the data shown here. This method has been used to break down the polymer matrix of wind turbine blades (WTB), municipal solid waste (MSW), personal protective equipment (PPE), and photovoltaic panels (PV) and measure the total polymer degradation. In this experiment, the effects of five different parameters, such as reaction temperature, residence time, pressure, waste-to-liquid ratio, and oxidant concentration, on resin degradation were studied in detail. Experiments were performed in the temperature range of 250°C to 350°C with a residence time of 30 to 90 minutes, at a pressure of 20 to 40 bar, a waste-to-liquid ratio of 5-25%, and oxidant concentrations of 15-45% by weight.
DOI: 10.17632/ktcsh7sykv
title: 3D point cloud measurements of the surface of HFMI treated and untreated linear butt welds

description: The data consists of 3D point clouds of linear butt welds untreated or high-frequency mechanical impact (HFMI) treated. The scans have been acquired using a Wenglor MLWL131 profile sensor mounted onto a KUKA KR 60-3 industrial manipulator. The purpose of the data was to develop and validate an automated system for robotic weld toe treatment and quality assurance. A 3D surface representation of the weld allows for identifying the location of the weld toe, which can be used for automatically generating an adaptive robotic trajectory for treating the weld. Subsequently, the treated weld can be rescanned, and the quantitative quality measures (e.g., indentation depth and groove width) can automatically be determined for quality assurance. The welds have therefore been treated using three different approaches to compare the treatment quality: - Manual ("MAN"): The weld is treated manually by a human operator. - Robotic manual ("ROB_M"): The weld is treated using a robot that follows a manually programmed straight trajectory. - Robotic adaptive ("ROB_A"): The weld is treated using a robot that follows an automatically generated trajectory that is adapted to the inconsistency of the weld toe. The treatment is generated based on a point cloud of the weld. The data set consists of 36 scans, representing 50 mm sections of butt weld with two weld toes, all acquired using the same straight scanning trajectory and normal to the surface of the sample. 18 of these scans are of untreated weld, whereas the remaining 18 are HFMI treated welds. 6 scans of each treatment type: manual, robotic manual, and robotic adaptive. The data set is divided into three folders for each of the treatment types: manual, robotic manual, and robotic adaptive. Each file is structured as four columns (X, Y, Z, I), where I is the measured backscatter intensity from the laser, and named as 'treatment type-platenumber-sectionnumber-status.txt': - Treatment type (manual, robotic manual, robotic adaptive). - Plate number defining the sample number of the welded plate (1) - Section number defining the scanned section of the plate for each treatment type (1 – 6) - Status defines whether the weld is untreated or treated (before, after) Hence, the file 'ROB_M-1-1-before.txt" is the weld section that is to be treated with robotic manual, plate number 1, section 1 of the treatment type, before treatment.
DOI: 10.17632/yv85ckvvvb
title: Data for: Modelling and Statistical Analysis of YouTube's Educational Videos: A Channel Owner's Perspective

description: The data contains YouTube analytics of a channel owner. It is of the format of excel and has sheets corresponding to video, geography, date, subscription status, YouTube Product, translation use, Device etc. Each of these data is in the form of a sheet in the excel file. It contains columns like Video title, Video ID, Video length (minutes), Video created, Watch time (minutes), Views, YouTube Red watch time (minutes), YouTube Red views, Average view duration (minutes),Card clicks, Cards shown, Clicks per card shown, Ad impressions, YouTube Red watch time (hours), Annotation clicks, Likes, Likes added, Likes removed, Dislikes, Dislikes added, Dislikes removed, Shares Comments, Videos in playlists, Videos added to playlists Videos removed from playlists, Subscribers, Subscribers gained Subscribers lost Average percentage viewed, Watch time (hours). Value of the data This data could be used by the scientific community to get a lot of information about the YouTube Educational videos, their statistics and user preferences and behaviours. Acknowledgements saurabhschool: https://www.youtube.com/user/saurabhschool References https://www.youtube.com/user/saurabhschool
DOI: 10.6084/m9.figshare.28930613.v1
title: database_and_syntax

description: This study explores how the gender of a hypothetical person who masturbates alone (male: Emilio vs. female: Elena) influences perceptions of their sexual satisfaction and personal agency (achievement/status, reliability, charisma, leadership/social skills). It also examines whether adherence to the Sexual Double Standard (SDS) and Social Dominance Orientation (SDO) predicts these perceptions.
DOI: 10.6084/m9.figshare.7756544.v1
title: Protein quantification by Standard Test Tube protocol (Pierce BCA Protein Assay Kit)

description: Purified proteins were quantified using the Standard Test Tube Protocol (Pierce BCA Protein Assay Kit) following manufacturer specifications by producing a BSA colour response curve as standard curve. Protein samples were diluted when required in order to be within the assay sensitivity (0 - 2 mg/ml)
DOI: 10.6084/m9.figshare.20525310.v1
title: gangue dataset

description: this file contains dataset of gangue found with coal and is used in the classification of coal and gnague. <br>
DOI: 10.6084/m9.figshare.25126109.v1
title: Supplementary Material for: Outcomes of post-immunotherapy durable responders of advanced hepatocellular carcinoma - with emphasis on locoregional therapy for oligoprogression

description: Introduction
The progression patterns, dispositions, and outcomes of patients with advanced hepatocellular carcinoma (HCC) who achieved durable responses with immunotherapy remain poorly characterized. 

Methods
Patients with advanced HCC who received immune checkpoint inhibitor (ICI)-based immunotherapy and achieved durable responses were retrospectively included. A durable response was defined as partial response (PR) or stable disease (SD) per RECIST 1.1 for more than 8 months after initiation of immunotherapy. Oligoprogression and polyprogression were defined as progression at ≤ 3 and &gt; 3 lesions, respectively. 

Results
A total of 91 durable responders (63 PR and 28 SD) were identified. The majority had chronic viral hepatitis (n=69, 75.8%). Forty-seven (51.6%) and 44 (48.4%) patients received the index immunotherapy as first-line and second or beyond-line therapy, respectively. Fifty-four (59.3%) patients subsequently developed progression, with a predominant pattern of oligoprogression (66.7%). The median overall survival (OS) was 46.2 months (95% CI: 34.1–58.3). For patients with subsequent progression, employment of locoregional therapy (LRT) for progression was associated with prolonged OS (univariate analysis: hazard ratio [HR] 0.397, p=0.009; multivariate analysis: HR 0.363, p=0.050). Patients with oligoprogression who received LRT showed longer median OS than those who did not (48.4 vs. 20.5 months, p&lt;0.001). In contrast, the median OS of patients with polyprogression who received LRT was not different from those without LRT (27.7 vs. 25.5 months, p=0.794).

Conclusion
Approximately 60% of the post-immunotherapy durable responders of HCC subsequently develop progression. Proactive LRT may further rescue patients who develop subsequent oligoprogression. Prospective studies are mandatory to clarify the proper management of durable responders with subsequent progression.
DOI: 10.17632/n8z7hzyn7k
title: Capillary Heterogeneity Linked to Methane Lateral Migration in Shallow Unconfined Aquifers

description: Simulations were performed using CMG-GEM. Sample input file for one of the scenarios is given here.
DOI: 10.17632/rpd23t5w42
title: Data for: Improved integrated water resource modelling by combining DPSIR and system dynamics conceptual modelling techniques

description: This document contains the main codes and equations Of Integrated water resources model of Gorganroud-Gharesu.
DOI: 10.6084/m9.figshare.11791698.v2
title: DepMap 20Q1 Public

description: This dataset contains the results of Avana library CRISPR-Cas9 genome-scale knockout (prefixed with Achilles) as well as mutation, copy number and gene expression data (prefixed with CCLE) for cancer cell lines as part of the Broad Institute’s Cancer Dependency Map project. We have repackaged our fileset to include all quarterly-updating datasets produced by DepMap.<br>The Avana CRISPR-Cas9 genome-scale knockout data has expanded to include 739 cell lines, the RNAseq data includes 1270 cell lines, and the copy number data includes 1713 cell lines. Please see the README files for details regarding data processing pipeline procedures updates.<br>As our screening efforts continue, we will be releasing additional cancer dependency data on a quarterly basis for unrestricted use. For the latest datasets available, further analyses, and to subscribe to our mailing list visit https://depmap.org.<br>Descriptions of the experimental methods and the CERES algorithm are published in http://dx.doi.org/10.1038/ng.3984. Some cell lines were process using copy number data based on the Sanger Institute whole exome sequencing data (COSMIC: http://cancer.sanger.ac.uk.cell_lines, EGA accession number: EGAD00001001039) reprocessed using CCLE pipelines. A detailed description of the pipelines and tool versions for CCLE expression can be found here: https://github.com/broadinstitute/gtex-pipeline/blob/v9/TOPMed_RNAseq_pipeline.md.<br>v2 changes: The sample_info.csv file in version 1 was missing lineage information for some cell lines. Version 2 corrects this.<br>
DOI: 10.6084/m9.figshare.1200153.v1
title: Stainton Sandstone

description: Micro-Computed Tomography (micro-CT) segmented image of Stainton Sandstone. The micro-CT image is segmented according to the variation of grey values between grains (bright- 255 grey value) and pores (dark- 0 grey value) using the watershed segmentation algorithm in the Avizo software. Details of the images (voxel resolution and image size) is present as a text file. The image can be visualized in visualization software such as Fiji ((http://fiji.sc/Fiji) or Avizo. If you utilise this in a scientific publication then please mention in the acknowledgements that this data is courtesy of Qatar Carbonates and Carbon Storage Research Centre, Imperial College London. For more information, please contact Saurabh M Shah at saurabh.shah10@imperial.ac.uk or Edo S Boek at e.boek@imperial.ac.uk
DOI: 10.6084/m9.figshare.13370117.v2
title: Raw data of sample methylation in Genome-wide DNA methylation analysis.csv

description: We screened for potential warfarin dose-associated CpGs by comparison of genome-wide DNA methylation between the case groups(low dose group and high dose group) and control groups(medium dose group).We isolated DNA from peripheral blood cell samples by using the QIAamp DNA Blood Mini Kit (Cat.#51306; Qiagen, German). DNA bisulfite conversion was done in a bisulfite batch with the Zymo EZ DNA MethylationTM Kit (Cat.#D5001, Zymo, USA). Genome-wide DNA methylation was measured by Illumina Infinium HumanMethylation 450 K BeadChip (Cat.#WG-314-1001, Illumina, USA).Data from genome-wide methylation were analyzed using the GenomeStudio Software (version V2011.1, Illumina, San Diego, CA, USA).
DOI: 10.6084/m9.figshare.21089560.v4
title: A Global Typical Meteorological Year Database on ERA5 Dataset - DeST format

description: A global typical meteorological year (TMY) database covers 38,947 stations worldwide. Each typical meteorological year data file includes dry-bulb temperature (°C) and absolute humidity (g/kg air), dew point (°C), direct normal irradiance (W/m2), diffuse horizontal irradiance (W/m2), global horizontal irradiance (W/m2), pressure (Mbar), wind direction, wind speed (m/s), etc. at 1-hour intervals. The data is created with Chinese Standard Weather Database method to reflect the average level of historical weather based on the fifth-generation atmospheric reanalysis product released by the European Center (ERA5). The dataset is saved in a 55 GB database of compressed CSV files and uploaded to a website where users can obtain the required TMY data for certain cities according to the longitude and latitude information. This TMY-ERA5 dataset is fundamental and essential in building system designs of international construction projects, building performance simulation, etc. especially for some countries lacking ground meteorological stations or missing meteorological year data in the building profession. It can be used as references for other meteorological climate studies.
DOI: 10.6084/m9.figshare.26026711.v1
title: Passive source reverse time migration based on the spectral element method

description: This data includes the main functions used for passive source RTM bashed on the SEM method
DOI: 10.6084/m9.figshare.4038414.v2
title: Expression and prognostic significance of the autoimmune regulator gene in breast cancer cells

description: The autoimmune regulator gene (AIRE) plays a fundamental role in tolerance by promoting the expression of tissue-specific antigens in medullary thymic epithelial cells (mTECs). Recently, AIRE expression was detected also in human keratinocytes and in tumors originating in stratified epithelia. Here, we tested whether AIRE is expressed in cancer cells. We analyzed AIRE expression in cancer cases from The Cancer Genome Atlas (TCGA) RNA-seq dataset and we found association with better outcome. AIRE protein expression was verified by immunohistochemistry in a cohort of 39 human breast cancer specimens and its prognostic relevance was confirmed in microarray-based gene expression data set NKI-295 and KM-Plotter. Both in the RNA-seq and gene expression datasets analyzed, AIRE expression was an independent strong prognostic factor for relapse-free survival (RFS), particularly in estrogen receptor-positive tumors. Enrichment of translation-related pathways was observed in AIRE-expressing tumors by Ingenuity Pathway Analysis and a significant increase of cells in G1 phase and activation of caspase cascades was induced by AIRE transfection in breast cancer luminal cell lines, suggesting that AIRE-induced over-translation of proteins lead to cycle arrest and apoptosis. These data are the first to identify AIRE expression in breast cancer and an association with prognosis.
DOI: 10.6084/m9.figshare.670620.v3
title: Photosynthesis data

description: Photosynthetic traits of the dominant tree species as well as the environmental factors at Daxiagu Tianlongshan were measured in the summer seasons of 2007, 2008 and 2009.
DOI: 10.6084/m9.figshare.7227470.v1
title: Flexible planning, executive function and language in young children

description: Flexible planning, executive function and language in young children
DOI: 10.6084/m9.figshare.24512299.v1
title: Shipment Checklist

description: Novogene shipment checklist v1.2
DOI: 10.6084/m9.figshare.25340806.v2
title: Output of centroAnno and reference methods on simulated datasets

description: All experiment results of centroAnno and reference methods on simulated datasets.
DOI: 10.17632/ytg69cxxsx
title: AI in Special Education: Providing Customized Learning Solutions for Diverse Learners

description: This research explores the potential of Artificial Intelligence (AI) to transform special education by providing tailored learning experiences for students with diverse needs. Special education often requires highly individualized instruction, which can be challenging for teachers to deliver at scale. AI technologies, including adaptive learning platforms, natural language processing, and emotion recognition, offer promising solutions by personalizing educational content to match each learner’s unique cognitive and emotional profile.

The study examines various AI-driven tools designed to assist students with learning disabilities, autism, speech impairments, and other challenges. These tools adapt in real-time to each student’s pace, preferences, and responses, offering customized feedback, exercises, and reinforcement. By analyzing student interactions, AI systems can identify specific areas where a learner struggles, recommend targeted interventions, and monitor progress over time.

This research also addresses the ethical considerations and practical challenges in deploying AI for special education. Topics include data privacy, the need for unbiased algorithms, and the role of teachers in guiding AI interactions. Ultimately, this study aims to provide insights into how AI can bridge learning gaps, foster independence, and improve educational outcomes for diverse learners in inclusive environments.
DOI: 10.6084/m9.figshare.20130794.v6
title: Dataset: An IoT-Enriched Event Log for Process Mining in Smart Factories

description: Modern technologies such as the Internet of Things (IoT) are becoming increasingly important in various domains, including Business Process Management (BPM) research. One main research area in BPM is process mining, which can be used to analyze event logs, e.g., for checking the conformance of running processes. However, there are only a few IoT-based event logs available for research purposes. Some of them are artificially generated and the problem occurs that they do not always completely reflect the actual physical properties of smart environments. In this paper, we present an IoT-enriched XES event log that is generated by a physical smart factory. For this purpose, we create the DataStream/SensorStream XES extension for representing IoT-data in event logs. Finally, we present some preliminary analysis and properties of the log.
DOI: 10.6084/m9.figshare.7037498.v1
title: Tomato HsfA1a plays a critical role in plant drought tolerance by activating <i>ATG</i> genes and inducing autophagy

description: Autophagy plays critical roles in plant responses to stress. In contrast to the wealth of information concerning the core process of plant autophagosome assembly, our understanding of the regulation of autophagy is limited. In this study, we demonstrated that transcription factor HsfA1a played a critical role in tomato tolerance to drought stress, in part through its positive role in induction of autophagy under drought stress. <i>HsfA1a</i> expression was induced by drought stress. Virus-induced <i>HsfA1a</i> gene silencing reduced while its overexpression increased plant drought tolerance based on both symptoms and membrane integrity. <i>HsfA1a</i>-silenced plants were more sensitive to endogenous ABA-mediated stomatal closure, while its overexpression lines were resistant under drought stress, indicating that phytohormone ABA did not play a major role in <i>HsfA1a</i>-induced drought tolerance. On the other hand, <i>HsfA1a</i>-silenced plants increased while its overexpression decreased the levels of insoluble proteins which were highly ubiquitinated under drought stress. Furthermore, drought stress induced numerous <i>ATGs</i> expression and autophagosome formation in wild-type plants. The expression of <i>ATG10</i> and <i>ATG18f</i>, and the formation of autophagosomes were compromised in <i>HsfA1a</i>-silenced plants but were enhanced in <i>HsfA1a</i>-overexpressing plants. Both electrophoretic mobility shift assay and chromatin immunoprecipitation coupled with qPCR analysis revealed that HsfA1a bound to <i>ATG10</i> and <i>ATG18f</i> gene promoters. Silencing of <i>ATG10</i> and <i>ATG18f</i> reduced HsfA1a-induced drought tolerance and autophagosome formation in plants overexpressing <i>HsfA1a</i>. These results demonstrate that HsfA1a induces drought tolerance by activating <i>ATG</i> genes and inducing autophagy, which may promote plant survival by degrading ubiquitinated protein aggregates under drought stress.
DOI: 10.6084/m9.figshare.11918292.v1
title: Statistical Analysis for realtime PCR.pzf

description: Realtime PCR graphs-Alexidine treatment
DOI: 10.6084/m9.figshare.14681430.v1
title: DATA TRIAL

description: SHARING TRIAL DATA