cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.c.3618287_d10.v1
title: Additional file 11: of Transcriptome analysis and molecular marker discovery in Solanum incanum and S. aethiopicum, two close relatives of the common eggplant (Solanum melongena) with interest for breeding

description: SNP calling results. The file in VCF format provides the list of SNVs (SNPs and INDELs) identified in S. incanum, S. aethiopicum, S. melongena and S. torvum transcriptomes by mapping against S. melongena genome. For each SNV are indicated their position in eggplant genome scaffold, the allele of reference (eggplant genome allele) and the alternative allele (the transcriptomes allele), the quality of the SNV, the filters applied and detailed information about SNP calling process for each SNV and the different kind of transcriptome ID combinations in order to filter the intraspecific and interspecific polymorphisms. The different filter applied for in silico selection were: CS60 (the SNV is closer than 60 nucleotides to another SNV), HV0.05 (the region has more than 5.0 SVNs per 100 bases), CL60 (the SNV is closer than 60 nucleotides to the reference edge), CEF (SNV is not a CAP detectable by the enzyme: cheap_ones), VKF (it is not an SNP). (7Z 38609Â kb)
DOI: 10.17605/osf.io/a6mt4
title: Raw Data

description: Raw datasets collected from multiple sources.
DOI: 10.60893/figshare.jva.28883240.v1
title: Supplemental Material

description: Contains supplemental Figs. S1 and S2
DOI: 10.17632/hr2kxs47jy
title: Original data for fatty acid lability model

description: the original data of "Quantifying the origins of labile estuarine particulate organic matter of varying reactivity using a fatty acid isotope model based on a genetic algorithm"
DOI: 10.6084/m9.figshare.27987131.v2
title: Archimate Exchange Model file containing the ArchiMate views extracted by the EA mining from API process.

description: It is part of the paper titled "Mining Enterprise Architecture Artifacts using API Gateway Logs Reinforced with Ontologies" that publish the results of the research pursuing to automate the modeling of EA elements from API Gateway Logs. It contains the result of extraction, which can be imported into any compatible ArchiMate modelling tool.
DOI: 10.11583/dtu.24152910.v1
title: Reverse Logistics Support Tool Feature Model

description: The Feature Model of the RL support tool represents the raw data for the RL Support Tool. It represents the knowledge base in terms of the activities and considerations related to RL design in the form of a hierarchical relationship. Additionally, the constraints part integrates additional cross-hierarchical restrictions - together forming the basis for developing a configuration system.This data is part of the Collection- Reverse Logistics Support Tool (10.11583/DTU.c.6839169)
DOI: 10.6084/m9.figshare.14458665.v1
title: instagram_compressed_JPEG_1.zip

description: JPEG images are uploaded to instagram, and the original and the downloaded versions are provided. This dataset contains images that are uploaded as a single post.
DOI: 10.6084/m9.figshare.22902806.v1
title: Datasets MS

description: Data sets MS “Effects of micro-algae oil replacement on growth, omega-3 deposition and gut microbiome composition of Nile tilapia (Oreochromis niloticus)
DOI: 10.17632/pmtjyvmvn8
title: small molecule targeting α-synuclein mRNA

description: The protein α-synuclein is an important drug target for the treatment of Parkinson’s disease, but it is an intrinsically disordered protein lacking typical small molecule binding pockets. The mRNA encoding α-synuclein (SNCA), on the other hand, has regions of ordered structure in the 5’ untranslated region (UTR) near the start codon. Here, we present an integrated approach to identify small molecules that bind this structure and inhibit α-synuclein translation. A drug-like, RNA-focused compound collection was studied for binding to the 5’UTR of SNCA mRNA, affording Synucleozid-2.0, a drug-like small molecule that mechanistically inhibits ribosomes from assembling onto SNCA mRNA. We further converted it into a ribonuclease recruiting chimera (RIBOTAC) to degrade the SNCA mRNA in cells with improved potency. RNA-seq and proteomics studies demonstrated that Synucleozid-RIBOTAC (Syn-RIBOTAC) is selective in cells. Syn-RIBOTAC also improved ~50% of genes abnormally expressed in patient-derived iPSC-induced dopamine neurons. The RIBOTAC optimization strategy improved the bioactivity of lead compound by at least 5-fold. Broadly, one strategy to expand druggability of the proteome is to target the mRNAs that encode for “undruggable” proteins. 

This is the supplemental dataset for our manuscript currently published at PNAS (doi: 10.1073/pnas.2306682120)
DOI: 10.17632/svz439j8hb
title: Training dataset for acoustic emission analysis

description: Training dataset containing acoustic emission features of various damage mechanisms of composite materials. Collected acoustic emission features: maximum amplitude in dB (A), rise time in µs (R), total duration in µs (D), number of threshold counts (CNTS), total energy in eu (E) and average frequency in MHz (F).
DOI: 10.6084/m9.figshare.16922569.v1
title: Supplementary Material for: Supplemental scleral buckle for the management of rhegmatogenous retinal detachment by pars plana vitrectomy: A meta-analysis of randomized controlled trials

description: Objectives: The present review aims to synthesize evidence from randomized controlled trials (RCTs) that compared outcomes of pars plana vitrectomy (PPV) with and without a supplementary scleral buckle (SB) for management of rhegmatogenous retinal detachment (RRD). Methods: The authors searched MEDLINE, EMBASE, and CENTRAL to identify RCTs in English that compared PPV with and without supplemental SB. Risk of bias was assessed according to Cochrane Risk of Bias 2 tool. We present risk ratios (RRs), mean differences (MDs), and 95% confidence intervals (CIs) estimated using random effects meta-analyses. Results: We identified six RCTs involving 705 eyes. Primary reattachment (6 studies, 345 eyes PPV, 324 eyes PPV+SB; RR 0.99, 95% CI 0.93-1.06, I2 = 0%, p = 0.78) and final anatomic success rates (4 studies, 272 eyes PPV, 267 eyes PPV+SB; RR 1.00, 95% CI 0.98-1.02, I2 = 0%, p = 0.89) were similar between the two groups. Postoperative visual acuity improvement (5 studies, 244 eyes PPV, 222 eyes PPV+SB; MD 6.09 letters, 95% CI -0.47-12.64, I2 = 69%, p = 0.07) and frequency of adverse events (6 studies, 1294 observations PPV, 1221 observations PPV+SB; RR 0.76, 95% CI 0.57-1.01, I2 = 25%, p = 0.06) likewise did not differ significantly between the treatment groups. Conclusion: Low-certainty evidence from RCTs did not demonstrate a benefit in placement of a supplemental scleral buckle during vitrectomy for management of RRD in the current analysis. Additional high-quality trials are needed to provide more precise estimates of effect.
DOI: 10.6084/m9.figshare.25661574.v1
title: <b>Genotype imputation, integration for </b><b>genome-wide association studies and genomic prediction of blackleg resistance in Canola</b>

description: Background:Integrating germplasm populations genotyped by different genotyping platforms via genotype imputation is a way to utilize accumulated genetic resources. In this study, we used 278 canola samples genotyped via whole-genome sequencing (WGS) at 10X coverage to evaluate the imputation accuracy of three imputation approaches. The optimal imputation methods were used to impute and integrate two Canola genotype datasets: a diverse canola collection genotyped by genotyping-by-sequencing via transcriptome (GBS-t) and a double haploid (DH) line collection genotyped with low-coverage WGS (skim-WGS). The genomic prediction accuracy (GP) and detection power of marker‒trait association (GWAS) of the combined population for blackleg resistance were evaluated.Results:The empirical imputation accuracy (r2) measured as the squared correlation between observed and imputed genotypes was moderate for Minimac3 when imputing from the GBS-t density to the WGS. The accuracy dramatically improved from 0.64 to 0.82 by removing SNPs with poor Minimac3-reported R2 (R2 &lt; 0.2) quality statistics. The r2 for GLIMPSE was higher than that for Beagle when imputing from different low-coverage to full-coverage WGS. We imputed and integrated the diverse canola collection and the DH lines, and the combined population showed similar or slightly greater prediction accuracy (PA) for blackleg resistance traits than did each of the single populations with ~921K SNPs. Higher marker-trait association (MTA) detection powers were indicated with the combined population; however, similar numbers of MTAs were discovered when each single population was combined in a meta-GWAS.Conclusion:It is feasible to impute and integrate germplasms from different sequencing platforms for downstream analyses. However, genetic heterogeneity across populations could add complexity to the analyses. Increasing the sample size by combining datasets showed slightly greater prediction accuracy and greater detection power in GWASs in the present study.<br>
DOI: 10.6084/m9.figshare.27636240.v1
title: Supplementary Material for: Assisted reproductive technology, pregnancy and recurrent disease in melanoma patients: a 30-year single institution experience.

description: Objectives
The aim of this study is to assess differences in melanoma recurrence between patients conceiving spontaneously versus those undergoing assisted reproductive technology (ART), to determine use of ART in post-melanoma patients and to examine the impact of counseling of this specific patient group.

Design
This study is a 30-year analysis including data from a single center questionnaire and a retrospective cohort study. 

Participants/Materials
Women of childbearing age with a history of melanoma were requested to participate in our study. We selected patients who underwent either primary melanoma treatment or treatment of local / distant recurrence at our institute between 1994 and 2021. Each participant received a questionnaire and informed consent form. The questions concerned general health, primary tumor characteristics, utilization of ART, subsequent pregnancies and development of recurrent melanoma. Additional information was collected from the medical files. 

Setting
The research was conducted in a dedicated oncology center and tertiary referral center for melanoma in The Netherlands. 

Methods
Participants received the questionnaires by mail. Six weeks later a reminder was sent to non-responders. Analysis was performed using descriptive statistics. For comparisons between groups Chi-square tests were used. P-value was considered significant when below 0.05. A clinically relevant difference in recurrence rate was defined as a 10% difference.

Results
A total of 498 questionnaires were available for analyses, 449 from living patients and 49 from relatives of diseased patients. One hundred and seventy-nine patients (36%) with a history of melanoma became pregnant following their diagnosis. In this group, 28 patients (16%) attempted to conceive using ART, and eight of them experienced disease recurrence. There was no difference in the recurrence rate between patients who became pregnant after the diagnosis of melanoma and those who never subsequently conceived (37% vs 35%, p=0.609).

Limitations
The main limitations of the study are its size, observational design and questionnaire methodology. 

Conclusions
Pregnancy did not increase the risk of recurrent melanoma. The group of patients conceiving after ART was small and therefore it is difficult to confidently conclude that the recurrence risk is comparable to the other groups. Prospective international registration of these patients, their oncologic follow-up and possible use of assisted reproduction, will provide valuable information to determine any potential association between ART and risk of recurrent melanoma. This would enable health professionals to develop surveillance strategies and pre-conception counselling of patients wishing to conceive.
DOI: 10.6084/m9.figshare.28254443.v1
title: File S2_Summary of 265 high risk species

description: File S2
DOI: 10.6084/m9.figshare.28837001.v1
title: single cell data.zip

description: Single-cell, TCR and BCR raw data
DOI: 10.6084/m9.figshare.3569361.v2
title: Neotropical region: a shapefile of Morrone’s (2014) biogeographical regionalisation

description: This is a shapefile of the geographic limits proposed by Morrone (2014) based on occurrence data of endemic animals and plants of Latin America and the Caribbean.
DOI: 10.6084/m9.figshare.8262779.v2
title: The phylogenetic range of bacterial and viral pathogens of vertebrates: dataset and supplementary material

description: [N.B. This is an archived version of the code and data repository available at https://github.com/liampshaw/Pathogen-host-range.]<br><b>Associated preprint</b>: The phylogenetic range of bacterial and viral pathogens of vertebrates<br><b>doi</b>: https://doi.org/10.1101/670315<br><b>Authors</b>: Liam P. Shaw*, Alethea Wang*, David Dylus, Magda Meier, Grega Pogacnik, Christophe Dessimoz, Francois Balloux (* co-first authors)<br>This repository contains code to reproduce all figures and analyses in the associated paper analysing the host range of pathogen species. This is bundled together in the Rmarkdown notebook (Supplementary Text 1 of the manuscript). It also contains several data files. The image above is a schematic for the manual literature review used to construct the database of host-pathogen associations. For more information on the dataset collection methods and analysis, please see the preprint.<br>The main dataset contains a human-curated database of 12,212 host-pathogen associations: 2,595 bacterial and viral pathogens infecting 2,656 vertebrate host species across 90 host orders. It also contains a mitochondrial genome phylogeny for the host species.<br><br>Code can be altered to change any of the figures. Some explanatory text is provided, but not much. Any questions can be addressed via email (liam.philip.shaw at gmail dot com).<br>Unless otherwise stated, data related to viruses is plotted in red and bacteria in black. The code should take &lt;10 minutes to run on a standard laptop.<br><b>Note</b>: At several points code is adapted/reused from the supplementary code repository made available by Olival et. al. (2017):<br>- Olival et al. (2017) paper: Host and viral traits predict zoonotic spillover from mammals https://doi.org/10.1038/nature22975- Code repository: https://github.com/ecohealthalliance/HP3- MIT License: https://opensource.org/licenses/MIT<br>This mainly applies to several scripts in the `scripts' directory relating to the fitting and plotting of generalized additive models (GAMs) - more information is included where appropriate. All code here is also made available under the MIT License.
DOI: 10.17632/4sfhgj2z9g
title: E-Commerce Success Through Customer Experience: Insights from Shopee’s User Dynamics

description: E-Commerce Success Through Customer Experience: Insights from Shopee’s User Dynamics

This research object focus on the following construct:
1. Customer Experience Quality
2. Customer Satisfaction
3. Customer Loyalty
4. Word-of-mouth Behaviour

The purpose of this research is to investigate how customer experience on Shopee, a major e-commerce platform, influences customer satisfaction, loyalty intentions, and word-of-mouth behavior in a highly competitive digital marketplace. Using Partial Least Square Structural Equation Modeling (PLS-SEM) with second-order constructs, this study analyzes responses from 490 Shopee users gathered through a structured questionnaire, using seven-point Likert Scale These results underscore the crucial role of customer experience in shaping satisfaction and loyalty, essential for retaining a competitive edge in e-commerce. Thus, the industry depends on a seamless and personalized customer experience to enhance satisfaction, boost loyalty intentions, and generate valuable word-of-mouth advocacy.

from 490 respondent, we pruning dataset to 441 respondent to remove unnecessary data and Removes irrelevant or redundant data
DOI: 10.6084/m9.figshare.24794091.v1
title: Multiple microplastics soil-plant experiment

description: In this study, we investigated the effect of ten single microplastic and their combination to plant-soil system in three different soils.
DOI: 10.6084/m9.figshare.14551098.v1
title: Supplementary material - Oil interactions in world biomes.rar

description: We compiled 169 studies on the interactions between oil-offering flowers and floral visitors in world biomes, published until January 2021, and built a binary interaction matrix with 1460 links. The compiled database has 214 oil-offering flowers, distributed in 12 plant families, ten families recognized as oil flowers and two additional families (Gesneriaceae and Melastomataceae). Regarding floral visitors, 377 species were surveyed, bees were the most representative group (mainly oil-collecting bees).
DOI: 10.6084/m9.figshare.19188122.v3
title: Metacommunity dataset

description: The study covers a large area of natural forests in Northeastern China. The latitudinal and longitudinal ranges of the study region extend from 39–54°N (across 15 degree range) and 119–134°E (15 degree range), respectively. The climate varies from a middle temperate zone to a cool temperate zone. All these zones are characterized by strong seasonality with four distinctly different seasons. The main precipitation period is between July and September, and there is a harsh dry spring season.In the summer of 2017 and 2018, a total of 455 0.1-ha circlular (radius=17.84 m) forest plots were established in the region. All trees with a diameter at breast height (dbh) greater than 5 cm were identified, measured and mapped in each plot. To minimize the potentially bias resulting from uneven sampling coverage, we sampled a subset of plots to ensure even sampling coverage, leading to 300 plots.We used each of the forest plots and its nearest n neighbouring plots to define a particular regional community as a basis for calculating a species pool. In this study, all data are calculated in each regional community consisting of five to ten local plots (n=4, to 9, plus the focal plot in each case), respectively. Therefore, n+1 (i.e., 5 to 10) indicates the size of a regional community, and defines the spatial extent of each community (there are six extents: 5, 6, 7, 8, 9, 10 plots).
DOI: 10.6084/m9.figshare.25838296.v1
title: Data file 2. Raw data (Illumina and MinION) details

description: Total NGS data generated for this study related information
DOI: 10.6084/m9.figshare.27952326.v1
title: Supplementary Material for: Ectopic atrial beats may cause a ZigZag pattern at intrapartum recording of the fetal heart rate using fetal scalp electrode

description: Novel Insights
Continuous intrapartum fetal heart rate assessment by fetal scalp electrode may record arrythmias like recurrent atrial ectopic beats and depict an increased fetal heart rate variability mimicking a ZigZag pattern.
Introduction
Fetal scalp electrode (FSE) is considered the gold standard for the intrapartum monitoring of the fetal heart rate (FHR) being associated with the lowest rate of signal loss and artifacts including the recording of the maternal heart rate. FSE acquires a fetal electrocardiogram and evaluates the time intervals between successive R waves. As such, it allows the recording of the beat-to-beat fluctuation of the FHR. However, due to the precise estimation of the inter-beat interval, FSE may also demonstrate recurrent atrial ectopic beats and register a highly oscillatory FHR pattern mimicking a saltatory or ZigZag appearance. 
Case Presentation
We herein describe a case of intrapartum supraventricular ectopic beats leading to the recording of a saltatory appearance of the FHR that could be demonstrated using FSE only and precluded a reliable assessment of intrapartum fetal oxygenation. Transabdominal gray-scale and M-mode ultrasound assessment of the fetal heart documented supraventricular ectopic beats recurring in 1 out of 10-12 beats, thus supporting the hypothesis that the abnormal FHR pattern on the CTG trace was secondary to fetal arrhythmia and not to rapidly evolving fetal hypoxia.
Conclusion
In supraventricular fetal arrhythmia the use of FSE for continuous intrapartum FHR monitoring differently from external ultrasound transducer may capture a highly variable CTG pattern which is caused by the registration of the ectopic atrial beats and not by a rapidly evolving hypoxia.
DOI: 10.6084/m9.figshare.3527624.v1
title: Appendix A. Articles and data used in the meta-analysis.

description: Articles and data used in the meta-analysis.
DOI: 10.6084/m9.figshare.20193966.v1
title: Additional file 3 of Deep oncopanel sequencing reveals within block position-dependent quality degradation in FFPE processed samples

description: Additional file 3. List of known variants for four participating oncology panels.
DOI: 10.6084/m9.figshare.22109381.v1
title: Flavobacterium pangenome analysis: KEGG and phage

description: KEGG and prophage additional dataset for <em>Flavobacterium </em>spp
DOI: 10.6084/m9.figshare.27153984.v1
title: <b>Identification and validation of the transcription factor RFX1 as a biomarker for prognosis and inflammatory infiltration in colon cancer</b>

description: <b>Purpose:</b> The difficulty in targeting colon cancer may be attributed to the plastic regulation of transcription factors. The transcription factor RFX1 exhibits a high degree of plasticity in inducing cancer cells with environment-dependent properties such as drug resistance, immunosuppression, or metastasis. However, the exploration of the relevance of RFX1 in the tumor microenvironment of colon cancer is still in its infancy.<b>Methods:</b> We have gradually focused our attention from pan-cancer to the molecular characterisation of RFX1 in colon cancer. We classified colon cancers into subgroups with high and low RFX1 expression and characterised their immune profiles, mutational profiles, cancer immunotherapy and drug sensitivity. Combining RFX1 expression and persistent tumor mutation burden, we innovatively propose a novel nomogram clinical prediction model and validate its function, and the correlation between high expression and poorer prognosis.<b>Results:</b> Compared to TMB, pTMB is an independent predictor of prognosis in colon cancer patients. Innovatively, the predictive efficacy of the combination of RFX1 and pTMB expression was more robust and sensitive compared to the effect of RFX1 combined with TMB. Among them, patients in the RFX1<sup>high</sup>/pTMB<sup>high</sup> subgroup had the worst quality of survival and prognosis, whereas patients in the RFX1<sup>low</sup>/pTMB<sup>low</sup> subgroup had a relatively better prognosis. Clinical tumor samples and immunohistochemical microarray results strongly validate the robust predictive potential of nomogram clinical models dependent on RFX1 and pTMB expression.<b>Conclusion:</b> A nomogram model based on the transcription factor RFX1 combined with pTMB provides an alternative approach to the diagnosis and treatment of colon cancer.
DOI: 10.6084/m9.figshare.5926477.v1
title: tuberculosis drug resistant db.xls

description: Database includiing genotiping information from drug and multidrug resistant isolates from tuberculosis circulating in the state of Veracruz, Mexico.<br>
DOI: 10.17632/35t5yv3c63
title: Dairy calcium promotes the prebiotics effects

description: This dataset includes all raw data on bacterial diversity and composition analysis, and bacterial metabolic activity from an in vitro fermentation study.
DOI: 10.17632/3yt8y8rc2v
title: Offloading in fog computing using deep reinforcement learning

description: This project proposes a Deep Reinforcement Learning (DRL) method for offloading modeling. In designing modes, we consider all three critical components of memory consumption, the number of CPU cycles, and network mode.