cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.4152956
title: Replication Package for the Paper: "An Empirical Analysis of the Manual Detection of Code Smells via Code Review"

description: This repository contains the data and results from the paper "An Empirical Analysis of the Manual Detection of Code Smells via Code Review" submitted to SANER 2021. <strong>1. "data.zip" contains the following three folders: </strong> <strong>1). data folder</strong> The data folder contains the retrieved 1,174 reviews that discuss code smells. Each review includes four parts: Code Change URL, Code Smell, Code Smell Discussion, and Source Code URL. <strong>2). scripts folder</strong> The scripts folder contains the Python script that was used to search for code smell terms and the list of code smell terms. <em>keywords.txt</em> contains the keywords associated with code smells, such as "smell, duplication, and dead". <em>get_changes.py</em> is used for getting code changes from OpenStack. <em>get_comments.py</em> is used for getting review comments for each code change. <em>keywords_search.py</em> is used for searching review comments that contain at least one keyword. <em>keywords_improve.py</em> is used for improving the keyword-based mining approach. <em>tools.py</em> is used for supporting the process of keywords improving. <strong>3). project folder</strong> The project folder contains the MAXQDA project files. The files can be opened by MAXQDA 12 or higher versions, which are available at https://www.maxqda.com/ for download. You may also use the free 14-day trial version of MAXQDA 2018, which is available at https://www.maxqda.com/trial for download. <em>Data Labeling & Encoding for RQ2.mx12</em> is the results of data labeling and encoding for RQ2, which were analyzed by the MAXQDA tool. <em>Data Labeling & Encoding for RQ3.mx12</em> is the results of data labeling and encoding for RQ3, which were analyzed by the MAXQDA tool. <strong>2. Keywords associated with code smells.pdf</strong> This file contains the final set of keywords associated with code smells that we identified by following the systematic approach proposed by Bosu and his colleagues in their paper: Identifying the Characteristics of Vulnerable Code Changes: An Empirical Study, FSE 2014.
DOI: 10.5281/zenodo.4468026
title: hg38 Jannovar data files

description: Transcript files for Jannovar (PMID:24677618).
DOI: 10.5281/zenodo.4311512
title: hg38 Jannovar data files

description: Transcript files for Jannovar (PMID:24677618).
DOI: 10.6084/m9.figshare.13643216
title: Meso-Cenozoic Uplift-Exhumation history of the Qilian Shan，NE Tibetan Plateau: constrains from low-temperature thermochronological signals

description: The Xining Basin Caijiabao and Mojiazhuang sections AFT ages and CJB Paleocurrent directions data
DOI: 10.6084/m9.figshare.13643216.v1
title: Meso-Cenozoic Uplift-Exhumation history of the Qilian Shan，NE Tibetan Plateau: constrains from low-temperature thermochronological signals

description: The Xining Basin Caijiabao and Mojiazhuang sections AFT ages and CJB Paleocurrent directions data
DOI: 10.5281/zenodo.4447005
title: Raw Data related to Research Article: Scaling of metal-clad InP nanodisk lasers: optical performance and thermal effects, Optics Express, volume 29, issue 3, 2021

description: These are the plotted and raw data used to obtain figures shown in: P. Tiwari, P. Wen, D. Caimi, S. Mauthe, N. Vico Triviño, M. Sousa, and K. E. Moselund, Scaling of metal-clad InP nanodisk lasers: optical performance and thermal effects., Optics Express, volume 29, issue 3, 2021 Please comply with copyright rules of the Optical Society of America under the terms of the OSA Open Access Publishing Agreement.: https://www.osapublishing.org/library/license_v1.cfm#VOR-OA
DOI: 10.5281/zenodo.4447004
title: Raw Data related to Research Article: Scaling of metal-clad InP nanodisk lasers: optical performance and thermal effects, Optics Express, volume 29, issue 3, 2021

description: These are the plotted and raw data used to obtain figures shown in: P. Tiwari, P. Wen, D. Caimi, S. Mauthe, N. Vico Triviño, M. Sousa, and K. E. Moselund, Scaling of metal-clad InP nanodisk lasers: optical performance and thermal effects., Optics Express, volume 29, issue 3, 2021 Please comply with copyright rules of the Optical Society of America under the terms of the OSA Open Access Publishing Agreement.: https://www.osapublishing.org/library/license_v1.cfm#VOR-OA
DOI: 10.13145/bacdive147063.20191129.4.1
title: Robbsia andropogonis

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive147064.20191129.4.1
title: Pseudomonas asplenii

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.6084/m9.figshare.19663862
title: Additional file 2 of The reporting and handling of missing data in longitudinal studies of older adults is suboptimal: a methodological survey of geriatric journals

description: Additional file 2.
DOI: 10.6084/m9.figshare.7081832
title: Additional file 10: of Comparative transcriptome analysis reveals that tricarboxylic acid cycle-related genes are associated with maize CMS-C fertility restoration

description: DEGs homologous to Arabidopsis male sterility (MS)/reproduction (MR) genes. (XLSX 35 kb)
DOI: 10.6084/m9.figshare.7081862.v1
title: Additional file 12: of Comparative transcriptome analysis reveals that tricarboxylic acid cycle-related genes are associated with maize CMS-C fertility restoration

description: Identification of PPR genes among DEGs. â Directionâ means relative to the expression level in NIL_Rf4. (XLSX 13 kb)
DOI: 10.21942/uva.23496923.v2
title: Dataset - Global geodiversity components are not equally represented in UNESCO Global Geoparks

description: This dataset contains: <br> <strong>geodiversity_metrics_geotifs.zip</strong> Geotiff layers of the geodiversity metrics (lithology diversity, soil diversity, slope range, slope standard deviation, lake area and river length). These layers were computed by Hannes Versteegh. <br> <strong>geodiversity_component_total_geodiversity_layers.zip</strong> Geotiff layers of the geodiversity components (lithological, soil, topographical and hydrological diversity) and total geodiversity. These layers were computed by Hannes Versteegh. <br> <strong>scripts_results_analysis_geodiversity_UGGs.zip</strong> 1) the scripts and data used to sample geodiversity metrics and total geodiversity in random polygons (e.g. creating the polygons, and the sampling of the metrics and total geodiversity layers). The random polygons used for the analysis are provided as well as feature classes in a geodatabase (.gdb). Scripts in python, with arcpy module from ESRI's ArcGIS. 2) the results yielded from the zonal statistics calculation for polygons and UGGs 3) the scripts used to import the zonal statistics results to python, and to analyse and visualise the data. The legend of the soil grids dataset is included as well, since this is necessary for the analysis of the soil types.
DOI: 10.6084/m9.figshare.25211147
title: Supplementary Material for: Chondromyxoid Fibroma of the Clavicle: A Case Report of a Rare Clinical Entity

description: <b><i>Introduction:</i></b> Chondromyxoid fibroma is a rare benign cartilaginous tumor that accounts for less than 1% of all bone tumors and involves long bones of the lower extremities more frequently. Therefore, the clavicle is a rare location of involvement for this entity. <b><i>Case Presentation:</i></b> The authors report a case of a diaphyseal chondromyxoid fibroma of the right clavicle in a 30-year-old male that was submitted to en bloc resection of the lesion and reconstruction with an autologous tricortical graft from the iliac crest. The post-operative period was uneventful, and the patient had regained excellent function of this right shoulder. At 2 years of follow-up, there was no evidence of a recurrence of the disease. <b><i>Conclusion:</i></b> Chondromyxoid fibroma of the clavicle should be included in the differential diagnosis of an indolent growing mass in this anatomic location.
DOI: 10.6084/m9.figshare.7138787.v1
title: Additional file 6: of Comparative analysis of Cd-responsive maize and rice transcriptomes highlights Cd co-modulated orthologs

description: Table S6. Eight hundred eighty plant orthologous groups composed of Cd-responsive orthologs in maize and rice. (XLSX 78Â kb)
DOI: 10.6084/m9.figshare.19663899
title: Luteolin impacts deoxyribonucleic acid repair by modulating the mitogen-activated protein kinase pathway in colorectal cancer

description: This study aimed to investigate the effects of luteolin on colorectal cancer (CRC) and explore its underlying mechanism. HCT-116 and HT-29 cells were treated with luteolin, cisplatin, or selumetinib. The cell survival, cell proliferation, apoptosis and cell cycle distribution, and DNA damage were detected using Cell Counting Kit-8, colony formation, flow cytometry, and immunofluorescence staining analysis, respectively. Western blotting was used to detect the expression of apoptosis-related, cycle-related, DNA-damage-related, and mitogen-activated protein kinase (MAPK) pathway-related proteins. Luteolin showed inhibitory effects on cellular growth by reducing cell survival and proliferation, inducing apoptosis and DNA damage, and arresting the cell cycle in a concentration-dependent manner in HCT-116 and HT-29 cells. Meanwhile, luteolin increased the expression of pro-apoptotic proteins, p-CHK1 (central to the induction of cell cycle arrest), and DNA excision repair protein and decreased anti-apoptotic proteins, G2-M phase-related proteins, and DNA repair proteins. The combination of cisplatin and luteolin significantly decreased cell survival and increased the apoptosis rate of HCT-116 and HT-29 cells compared with cisplatin alone. Bioinformatic analysis using the Comparative Toxicogenomics Database and STITCH and MalaCards databases showed that the MAPK pathway is involved in the pharmacology of luteolin. Furthermore, western blotting demonstrated that luteolin plays an inhibitory role by suppressing the MAPK signaling pathway in CRC, which is enhanced when combined with selumetinib. Luteolin can also prevent tumourigenesis in CRC in vivo. In conclusion, luteolin suppressed cell proliferation, blocked the cell cycle, and induced DNA damage and apoptosis progression in CRC cells by mediating the MAPK pathway
DOI: 10.6084/m9.figshare.25003082
title: Supplementary Material for: Protein kinase N1 level predicts acute kidney injury in patients undergoing cardiac surgery：A prospective cohort study

description: Introduction: The objective of this study is to examine the utility of protein kinase N1 (PKN1) as a biomarker of cardiac surgery-associated AKI (CSA-AKI).
Methods: A prospective cohort study of 110 adults undergoing on–pump cardiac surgery was conducted. The associations between post-operative PKN1 and CSA-AKI, AKI severity, need for renal replacement therapy (RRT), duration of AKI, length of ICU stay and post-operative hospital stay were evaluated. 
Results: Patients were categorized into three groups according to PKN1 tertiles. The incidence of CSA-AKI in the third tertile was 3.4-fold higher than that in the first. PKN1 was an independent risk factor for CSA-AKI. The discrimination of PKN1 to CSA-AKI assessed by ROC curve indicated that the AUC was 0.70, and the best cutoff was 5.025ng/mL. This group (&gt;5.025ng/mL) was more likely to develop CSA-AKI (P&lt;0.001). The combined AUC of EuroSCORE, aortic cross-clamp time and PKN1 was 0.82 (P&lt;0.001). A higher level of PKN1 related to increased need for RRT, longer duration of AKI, and length of ICU and post-operative hospital stays.
Conclusions: PKN1 could be a potential biomarker for the prediction of CSA-AKI. The combination of PKN1, EuroSCORE and aortic cross-clamp time were likely to predict the occurrence of CSA-AKI.
DOI: 10.6084/m9.figshare.19663899.v1
title: Luteolin impacts deoxyribonucleic acid repair by modulating the mitogen-activated protein kinase pathway in colorectal cancer

description: This study aimed to investigate the effects of luteolin on colorectal cancer (CRC) and explore its underlying mechanism. HCT-116 and HT-29 cells were treated with luteolin, cisplatin, or selumetinib. The cell survival, cell proliferation, apoptosis and cell cycle distribution, and DNA damage were detected using Cell Counting Kit-8, colony formation, flow cytometry, and immunofluorescence staining analysis, respectively. Western blotting was used to detect the expression of apoptosis-related, cycle-related, DNA-damage-related, and mitogen-activated protein kinase (MAPK) pathway-related proteins. Luteolin showed inhibitory effects on cellular growth by reducing cell survival and proliferation, inducing apoptosis and DNA damage, and arresting the cell cycle in a concentration-dependent manner in HCT-116 and HT-29 cells. Meanwhile, luteolin increased the expression of pro-apoptotic proteins, p-CHK1 (central to the induction of cell cycle arrest), and DNA excision repair protein and decreased anti-apoptotic proteins, G2-M phase-related proteins, and DNA repair proteins. The combination of cisplatin and luteolin significantly decreased cell survival and increased the apoptosis rate of HCT-116 and HT-29 cells compared with cisplatin alone. Bioinformatic analysis using the Comparative Toxicogenomics Database and STITCH and MalaCards databases showed that the MAPK pathway is involved in the pharmacology of luteolin. Furthermore, western blotting demonstrated that luteolin plays an inhibitory role by suppressing the MAPK signaling pathway in CRC, which is enhanced when combined with selumetinib. Luteolin can also prevent tumourigenesis in CRC in vivo. In conclusion, luteolin suppressed cell proliferation, blocked the cell cycle, and induced DNA damage and apoptosis progression in CRC cells by mediating the MAPK pathway
DOI: 10.6084/m9.figshare.12848175
title: Myeloproliferative neoplasms treated with hydroxyurea, pegylated interferon alpha-2A or ruxolitinib: clinicohematologic responses, quality-of-life changes and safety in the real-world setting

description: <b>Introduction:</b> Real-world data of responses, quality-of-life (QOL) changes and adverse events in patients with myeloproliferative neoplasms (MPN) on conventional therapy (hydroxyurea ± anagrelide), pegylated interferon alpha-2A (PEG-IFNα-2A) or ruxolitinib are limited. <b>Methods:</b> We prospectively studied MPN patients receiving conventional therapy, PEG-IFNα-2A or ruxolitinib. Next-generation sequencing of 69 myeloid-related genes was performed. Clinicohematologic responses, adverse events, and QOL (determined by the Myeloproliferative Neoplasm Symptom Assessment Form Total Symptom Score, MPN-SAF TSS) were evaluated. <b>Results:</b> Seventy men and fifty-five women with polycythemia vera (PV) (<i>N</i> = 23), essential thrombocythemia (ET) (<i>N</i> = 56) and myelofibrosis (MF) (<i>N</i> = 46) were studied for a median of 36 (range: 19–42) months. In PV, responses were comparable for different modalities. <i>CREBBP</i> mutations were associated with inferior responses. In ET, PEG-IFNα-2A resulted in superior clinicohematologic complete responses (CHCR) (<i>P </i>= 0.045). In MF, superior overall response rates (ORR) were associated with ruxolintib (<i>P </i>= 0.018) and <i>JAK2</i>V617F mutation (<i>P </i>= 0.04). For the whole cohort, ruxolitinib led to rapid and sustained reduction in spleen size within the first 6 months, and significant improvement of QOL as reflected by reduction in MPN-SAF TSS (<i>P</i> &lt; 0.001). Adverse events of grades 1–2 were observed in 44%, 62% and 20% of patients receiving conventional therapy, PEG-IFNα-2A and ruxolitinib respectively; and of grade 3–4 in 7% and 9% of patients receiving PEG-IFNα-2A and ruxolitinib. <b>Conclusions:</b> Conventional therapy, PEG-IFNα-2A and ruxolitinib induced responses in all MPN subtypes. PEG-IFNα-2A led to superior CHCR in ET; whereas ruxolitinib resulted in superior ORR in MF, and significant reduction in spleen size and improvement in QOL.
DOI: 10.6084/m9.figshare.12848175.v1
title: Myeloproliferative neoplasms treated with hydroxyurea, pegylated interferon alpha-2A or ruxolitinib: clinicohematologic responses, quality-of-life changes and safety in the real-world setting

description: <b>Introduction:</b> Real-world data of responses, quality-of-life (QOL) changes and adverse events in patients with myeloproliferative neoplasms (MPN) on conventional therapy (hydroxyurea ± anagrelide), pegylated interferon alpha-2A (PEG-IFNα-2A) or ruxolitinib are limited. <b>Methods:</b> We prospectively studied MPN patients receiving conventional therapy, PEG-IFNα-2A or ruxolitinib. Next-generation sequencing of 69 myeloid-related genes was performed. Clinicohematologic responses, adverse events, and QOL (determined by the Myeloproliferative Neoplasm Symptom Assessment Form Total Symptom Score, MPN-SAF TSS) were evaluated. <b>Results:</b> Seventy men and fifty-five women with polycythemia vera (PV) (<i>N</i> = 23), essential thrombocythemia (ET) (<i>N</i> = 56) and myelofibrosis (MF) (<i>N</i> = 46) were studied for a median of 36 (range: 19–42) months. In PV, responses were comparable for different modalities. <i>CREBBP</i> mutations were associated with inferior responses. In ET, PEG-IFNα-2A resulted in superior clinicohematologic complete responses (CHCR) (<i>P </i>= 0.045). In MF, superior overall response rates (ORR) were associated with ruxolintib (<i>P </i>= 0.018) and <i>JAK2</i>V617F mutation (<i>P </i>= 0.04). For the whole cohort, ruxolitinib led to rapid and sustained reduction in spleen size within the first 6 months, and significant improvement of QOL as reflected by reduction in MPN-SAF TSS (<i>P</i> &lt; 0.001). Adverse events of grades 1–2 were observed in 44%, 62% and 20% of patients receiving conventional therapy, PEG-IFNα-2A and ruxolitinib respectively; and of grade 3–4 in 7% and 9% of patients receiving PEG-IFNα-2A and ruxolitinib. <b>Conclusions:</b> Conventional therapy, PEG-IFNα-2A and ruxolitinib induced responses in all MPN subtypes. PEG-IFNα-2A led to superior CHCR in ET; whereas ruxolitinib resulted in superior ORR in MF, and significant reduction in spleen size and improvement in QOL.
DOI: 10.5281/zenodo.10297799
title: Data from the Untethered Balloon Launch of a Holographic Imager Into Cloud Near Adelaide, South Australia in August 2020

description: This dataset was obtained from an untethered balloon launch into cloud near Adelaide, South Australia in August 2020. The balloon payload train consisted of a holographic imager, polarsonde, webcam, and meteorological sensors.

Data is organised as follows:



A netcdf file consisting of;



Raw RS41 radiosonde and data logger temperature and relative humidity profiles

Mean number density (30-second averaged) from the holographic imager  

Mean equivalent diameter (30-second averaged) from the holographic imager  

Raw polarsonde co and cross polarisation signals



A selection of focussed particle images 

A selection of webcam images

A figure summarising the results of HYSPLIT back trajectory modelling for the launch (FigS1)

A figure showing the HIMAWARI Cloud Type classification for the region surrounding the launch site (FigS2)


This dataset can be used to reproduce the key figures of the following paper submitted to Atmospheric Measurement Techniques (under review 2023):   

'A Light-Weight Holographic Imager for Cloud Microphysical Studies from an Untethered Balloon'.

Additional details about the instruments and measurements can be found in that publication.
DOI: 10.5281/zenodo.8140410
title: Dataset for the Amyloid-beta precursor protein antibody screening study

description: This project contains the following underlying data included in a study aiming at characterizing antibodies for the Amyloid-beta precursor protein. The study is available on Zenodo (https://doi.org/10.5281/zenodo.7971926).
DOI: 10.26207/304a-5f30
title: Lava flow and vent shapefiles for: The 2021 eruption of Pacaya Volcano, Guatemala – geophysical analysis through satellite geodesy and seismic noise correlations
DOI: 10.6084/m9.figshare.9178415
title: MOESM3 of Comparative transcriptome analysis reveals the genetic basis underlying the biosynthesis of polysaccharides in Hericium erinaceus

description: Additional file 3: Dataset 2. H. erinaceus-FPKM top10 transcript.
DOI: 10.6084/m9.figshare.8129660
title: Additional file 4: of A random walk-based method to identify driver genes by integrating the subcellular localization and variation frequency into bipartite graph

description: The results of GO and KEGG enrichment analysis in prostate cancer. (XLSX 112 kb)
DOI: 10.6084/m9.figshare.7080968
title: Convex Bidirectional Large Margin Classifiers

description: Classification problems are commonly seen in practice. In this article, we aim to develop classifiers that can enjoy great interpretability as linear classifiers, and at the same time have model flexibility as nonlinear classifiers. We propose convex bidirectional large margin classifiers to fill the gap between linear and general nonlinear classifiers for high-dimensional data. Our method provides a new data visualization tool for classification of high-dimensional data. The obtained bilinear projection structure makes the proposed classifier very interpretable. Additional shrinkage to approximate variable selection is also considered. Through analysis of simulated and real data in high-dimensional settings, our method is shown to have superior prediction performance and interpretability when there are potential subpopulations in the data. The computer code of the proposed method is available as supplemental materials.
DOI: 10.6084/m9.figshare.8129546
title: Additional file 5: of Biological and RNA regulatory function of MOV10 in mammalian germ cells

description: Table S6. Mass spectrometry analysis of subcellular MOV10 IP in mice testes. (XLSX 41 kb)
DOI: 10.6084/m9.figshare.9178409.v1
title: MOESM2 of Comparative transcriptome analysis reveals the genetic basis underlying the biosynthesis of polysaccharides in Hericium erinaceus

description: Additional file 2: Dataset 1. The specificÂ primers of 10 genes selected to qRT-PCR experiment.