cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7726454
title: Data Carpentry Genomics Curriculum Example Data

description: p.p1 {margin: 0.0px 0.0px 0.0px 0.0px; font: 16.0px 'Andale Mono'; color: #29f914; background-color: #000000} span.s1 {font-variant-ligatures: no-common-ligatures} These files are intended for use with the Data Carpentry Genomics curriculum (https://datacarpentry.org/genomics-workshop/). Files will be useful for instructors teaching this curriculum in a workshop setting, as well as individuals working through these materials on their own. <br> This curriculum is normally taught using Amazon Web Services (AWS). Data Carpentry maintains an AWS image that includes all of the data files needed to use these lesson materials. For information on how to set up an AWS instance from that image, see https://datacarpentry.org/genomics-workshop/setup.html. Learners and instructors who would prefer to teach on a different remote computing system can access all required files from this FigShare dataset. <br> This curriculum uses data from a long term evolution experiment published in 2016: Tempo and mode of genome evolution in a 50,000-generation experiment (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4988878/) by Tenaillon O, Barrick JE, Ribeck N, Deatherage DE, Blanchard JL, Dasgupta A, Wu GC, Wielgoss S, Cruveiller S, Médigue C, Schneider D, and Lenski RE. (doi: 10.1038/nature18959). All sequencing data sets are available in the NCBI BioProject database under accession number PRJNA294072 (https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA294072). <br> backup.tar.gz: contains original fastq files, reference genome, and subsampled fastq files. Directions for obtaining these files from public databases are given during the lesson https://datacarpentry.org/wrangling-genomics/02-quality-control/index.html). On the AWS image, these files are stored in <code>~/.backup</code> directory. 1.3Gb in size. <br> Ecoli_metadata.xlsx: an example Excel file to be loaded during the R lesson. <br> shell_data.tar.gz: contains the files used as input to the Introduction to the Command Line for Genomics lesson (https://datacarpentry.org/shell-genomics/). <br> sub.tar.gz: contains subsampled fastq files that are used as input to the Data Wrangling and Processing for Genomics lesson (https://datacarpentry.org/wrangling-genomics/). 109Mb in size. <br> solutions: contains the output files of the Shell Genomics and Wrangling Genomics lessons, including <code>fastqc</code> output, sam, bam, bcf, and vcf files. <br> vcf_clean_script.R: converts vcf output in .solutions/wrangling_solutions/variant_calling_auto to single tidy data frame.<br> <br> combined_tidy_vcf.csv: output of vcf_clean_script.R <br>
DOI: 10.5281/zenodo.7707563
title: Master chart- Oral Squamous Cell Carcinoma cases

description: Details of OSCC patients demographic data , clinical and histopathological diagnosis
DOI: 10.5281/zenodo.7707562
title: Master chart- Oral Squamous Cell Carcinoma cases

description: Details of OSCC patients demographic data , clinical and histopathological diagnosis
DOI: 10.6084/m9.figshare.22231990
title: Challenges to Dialysis Treatment during the COVID-19 Pandemic: A Qualitative Study of Patients’ and Experts’ Perspectives.

description: Hereby I present the content analysis of interviews of this project and the natural language processing technique results. We used Atlas.ti version 8 for analysis and coding. We supported our content analysis of interviews with a natural language processing technique called Latent Dirichlet Allocation (LDA) to support the thematic analysis. LDA is an unsupervised, generative, probabilistic topic modelling technique that extracts meanings of a pre-defined number of topics/concepts. The number of concepts resulted from the clearest differentiation in the representation of heat maps and in examination of words (topic coherence). For this purpose, we first created a semantic space by stemming the words, removing stop words (such as 'and', 'the', 'a' and similar) and converting all text to lowercase. In addition, punctuation marks, names and personal words were removed from the text. LDA analyzes texts by considering word frequency in combination with the co-occurrence of words. LDA characterizes concepts based on word frequency and the words that best distinguish one concept from others. Separate analyses was conducted for physicians, nurses, HD patients and PD patients, assuming that these four groups had different experiences during the two COVID-19 waves. R software was used to conduct the LDA.
DOI: 10.6084/m9.figshare.22231990.v1
title: Challenges to Dialysis Treatment during the COVID-19 Pandemic: A Qualitative Study of Patients’ and Experts’ Perspectives.

description: Hereby I present the content analysis of interviews of this project and the natural language processing technique results. We used Atlas.ti version 8 for analysis and coding. We supported our content analysis of interviews with a natural language processing technique called Latent Dirichlet Allocation (LDA) to support the thematic analysis. LDA is an unsupervised, generative, probabilistic topic modelling technique that extracts meanings of a pre-defined number of topics/concepts. The number of concepts resulted from the clearest differentiation in the representation of heat maps and in examination of words (topic coherence). For this purpose, we first created a semantic space by stemming the words, removing stop words (such as 'and', 'the', 'a' and similar) and converting all text to lowercase. In addition, punctuation marks, names and personal words were removed from the text. LDA analyzes texts by considering word frequency in combination with the co-occurrence of words. LDA characterizes concepts based on word frequency and the words that best distinguish one concept from others. Separate analyses was conducted for physicians, nurses, HD patients and PD patients, assuming that these four groups had different experiences during the two COVID-19 waves. R software was used to conduct the LDA.
DOI: 10.5281/zenodo.7609546
title: WorldCereal open global harmonized reference data repository (CC-BY-SA licensed data sets)

description: Within the<strong> ESA funded</strong> WorldCereal project we have built an open harmonized reference data repository at global extent for model training or product validation in support of land cover and crop type mapping. Data from 2017 onwards were collected from many different sources and then harmonized, annotated and evaluated. These steps are explained in the harmonization protocol (10.5281/zenodo.7584463). This protocol also clarifies the naming convention of the shape files and the WorldCereal attributes (LC, CT, IRR, valtime and sampleID) that were added to the original data sets. This publication includes those harmonized data sets of which the original data set was published under the CC-BY-SA license or a license similar to CC-BY-SA. See document "_In-situ-data-World-Cereal - license - CC-BY-SA.pdf" for an overview of the original data sets.
DOI: 10.5281/zenodo.7609545
title: WorldCereal open global harmonized reference data repository (CC-BY-SA licensed data sets)

description: Within the<strong> ESA funded</strong> WorldCereal project we have built an open harmonized reference data repository at global extent for model training or product validation in support of land cover and crop type mapping. Data from 2017 onwards were collected from many different sources and then harmonized, annotated and evaluated. These steps are explained in the harmonization protocol (10.5281/zenodo.7584463). This protocol also clarifies the naming convention of the shape files and the WorldCereal attributes (LC, CT, IRR, valtime and sampleID) that were added to the original data sets. This publication includes those harmonized data sets of which the original data set was published under the CC-BY-SA license or a license similar to CC-BY-SA. See document "_In-situ-data-World-Cereal - license - CC-BY-SA.pdf" for an overview of the original data sets.
DOI: 10.5281/zenodo.5788583
title: Experimental Comparison of LiteStrat vs iStar

description: Data from an experimental comparison of LiteStrat and iStar modelling methods. Data was collected from a quasi-experiment with 28 undergraduate subjects with a between-subjects design, considering two independent variables: the treatment (LiteStrat and i*) and a blocking variable (the problem). We assessed the accuracy and completeness of the produced models as well as the efficiency and satisfaction with the method of the subjects.
DOI: 10.5281/zenodo.5792994
title: Experimental Comparison of LiteStrat vs iStar

description: Data from an experimental comparison of LiteStrat and iStar modelling methods. Data was collected from a quasi-experiment with 28 undergraduate subjects with a between-subjects design, considering two independent variables: the treatment (LiteStrat and i*) and a blocking variable (the problem). We assessed the accuracy and completeness of the produced models as well as the efficiency and satisfaction with the method of the subjects.
DOI: 10.5281/zenodo.5795487
title: Experimental Comparison of LiteStrat vs iStar

description: Data from an experimental comparison of LiteStrat and iStar modelling methods. Data was collected from a quasi-experiment with 28 undergraduate subjects with a between-subjects design, considering two independent variables: the treatment (LiteStrat and i*) and a blocking variable (the problem). We assessed the accuracy and completeness of the produced models as well as the efficiency and satisfaction with the method of the subjects.
DOI: 10.5281/zenodo.5796614
title: Experimental Comparison of LiteStrat vs iStar

description: Data and materials from an experimental comparison of LiteStrat and iStar modelling methods. Data was collected from a quasi-experiment with 28 undergraduate subjects with a between-subjects design, considering two independent variables: the treatment (LiteStrat and i*) and a blocking variable (the problem). We assessed the accuracy and completeness of the produced models as well as the efficiency and satisfaction with the method of the subjects.
DOI: 10.5281/zenodo.7408976
title: Experimental Comparison of LiteStrat vs iStar

description: Data and materials from an experimental comparison of LiteStrat and iStar modelling methods. Data was collected from a quasi-experiment with 28 undergraduate subjects with a between-subjects design, considering two independent variables: the treatment (LiteStrat and i*) and a blocking variable (the problem). We assessed the accuracy and completeness of the produced models as well as the efficiency and satisfaction with the method of the subjects.
DOI: 10.5281/zenodo.7622995
title: Experimental Comparison of LiteStrat vs iStar

description: Data and materials from an experimental comparison of LiteStrat and iStar modelling methods. Data was collected from a quasi-experiment with 28 undergraduate subjects with a between-subjects design, considering two independent variables: the treatment (LiteStrat and i*) and a blocking variable (the problem). We assessed the accuracy and completeness of the produced models as well as the efficiency and satisfaction with the method of the subjects.
DOI: 10.5281/zenodo.5788582
title: Experimental Comparison of LiteStrat vs iStar

description: Data and materials from an experimental comparison of LiteStrat and iStar modelling methods. Data was collected from a quasi-experiment with 28 undergraduate subjects with a between-subjects design, considering two independent variables: the treatment (LiteStrat and i*) and a blocking variable (the problem). We assessed the accuracy and completeness of the produced models as well as the efficiency and satisfaction with the method of the subjects.
DOI: 10.5281/zenodo.7494413
title: Multiplex imaging of breast cancer lymph node metastases identifies prognostic single-cell populations independent of clinical classifiers

description: This repository contains the raw IMC data of ZTMA 21 and 25 of the matched primary breast cancer and lymph node metastasis study presented in Fischer and Jackson et al., 2023. The code that was used to process and analyze this data can be found at https://github.com/BodenmillerGroup/BC_LN_metastses. The zip files starting with ZTMA contain the raw IMC measurements (mcd and txt) of the respective parts of the TMA. The TMA measurements are split up into parts in order to avoid huge files.
DOI: 10.5281/zenodo.7494412
title: Multiplex imaging of breast cancer lymph node metastases identifies prognostic single-cell populations independent of clinical classifiers

description: This repository contains the raw IMC data of ZTMA 21 and 25 of the matched primary breast cancer and lymph node metastasis study presented in Fischer and Jackson et al., 2023. The code that was used to process and analyze this data can be found at https://github.com/BodenmillerGroup/BC_LN_metastses. The zip files starting with ZTMA contain the raw IMC measurements (mcd and txt) of the respective parts of the TMA. The TMA measurements are split up into parts in order to avoid huge files.
DOI: 10.5281/zenodo.7494727
title: Multiplex imaging of breast cancer lymph node metastases identifies prognostic single-cell populations independent of clinical classifiers

description: This repository contains the continuation of dataset 10.5281/zenodo.7494413 and 10.5281/zenodo.7494509. The file tiff_stacks_masks.zip contains the IMC image stacks and single-cell masks as tiff files. The IHC_TMAs.zip contains the scans of the IHC stains of ZTMA25 and the QuPATH projects used to extract the single-cell data (incl. the single-cell measurements as csv files).
DOI: 10.5281/zenodo.7494726
title: Multiplex imaging of breast cancer lymph node metastases identifies prognostic single-cell populations independent of clinical classifiers

description: This repository contains the continuation of dataset 10.5281/zenodo.7494413 and 10.5281/zenodo.7494509. The file tiff_stacks_masks.zip contains the IMC image stacks and single-cell masks as tiff files. The IHC_TMAs.zip contains the scans of the IHC stains of ZTMA25 and the QuPATH projects used to extract the single-cell data (incl. the single-cell measurements as csv files).
DOI: 10.5281/zenodo.7494509
title: Multiplex imaging of breast cancer lymph node metastases identifies prognostic single-cell populations independent of clinical classifiers

description: This repository contains the raw IMC data of ZTMA 26 as continuation of dataset <strong>10.5281/zenodo.7494413.</strong> The zip files starting with ZTMA contain the raw IMC measurements (mcd and txt) of those parts of the TMA. The TMA measurements are split up into parts in order to avoid huge files. Additionally, this repository contains the metadata of the patients analyzed in this study, the panel information and the single-cell data that was extracted from the multiplexed images together with the associated metadata in SingleCellExperiment format for analysis in R. The analysis.zip folder contains files that were written out during the analysis according to the scripts in https://github.com/BodenmillerGroup/BC_LN_metastses. The single-cell and other data outputs from CellProfiler can be found in the cpout.zip file. The IF_whole_sections.zip file contains the IF images of the primary breast cancer sections (czi files) and the extracted single-cell data.
DOI: 10.5281/zenodo.7494508
title: Multiplex imaging of breast cancer lymph node metastases identifies prognostic single-cell populations independent of clinical classifiers

description: This repository contains the raw IMC data of ZTMA 26 as continuation of dataset <strong>10.5281/zenodo.7494413.</strong> The zip files starting with ZTMA contain the raw IMC measurements (mcd and txt) of those parts of the TMA. The TMA measurements are split up into parts in order to avoid huge files. Additionally, this repository contains the metadata of the patients analyzed in this study, the panel information and the single-cell data that was extracted from the multiplexed images together with the associated metadata in SingleCellExperiment format for analysis in R. The analysis.zip folder contains files that were written out during the analysis according to the scripts in https://github.com/BodenmillerGroup/BC_LN_metastses. The single-cell and other data outputs from CellProfiler can be found in the cpout.zip file. The IF_whole_sections.zip file contains the IF images of the primary breast cancer sections (czi files) and the extracted single-cell data.
DOI: 10.6084/m9.figshare.22179500.v1
title: Broodstock development, induced spawning and larva rearing of the bilih, Mystacoleucus padangensis (Bleeker, 1852), a vulnerable species, and its domestication potential for new candidate aquaculture.

description: <em>Mystacoleucus padangensis</em> living in Lake Singkarak, Indonesia, has high potential market demand but is threatened by overfishing and has not been successfully cultured. This study describes the first broodstock development, induced breeding, and larval rearing of <em>M. padangensis</em>.
DOI: 10.6084/m9.figshare.20079194.v1
title: Figure 2

description: It comprises of raw data and analysis file of Figure 2 obtained by determining the mechanism behind tumor secretome induced neuritogenesis in PC12 cells. MRMT-1 conditioned medium exposed PC12 cells were treated with signaling pathway inhibitors (PI3Ki, ERKi and ACi) and neurite assay was performed. <br>
DOI: 10.6084/m9.figshare.22232029.v1
title: Supplementary Material for: Renal Lipoma-Like Angiomyolipoma of Tumour Thrombus Extending to the Confluence of Inferior Vena Cava with Right Atrium: A Rare Case Report and Literature Review

description: Angiomyolipoma (AML) complicated with tumour thrombus extending to the confluence of inferior vena cava (IVC) with right atrium is rarely observed. We report a female AML patient admitted to our centre on January 21, 2020, with complication of tumour thrombus extending to the confluence of IVC with right atrium and had no sign of difficult breathing. She underwent whole-abdominal enhanced CT for abdominal pain and was diagnosed with a possible renal AML with tumour thrombus. Open radical nephrectomy and thrombectomy of vena cava were performed. Intraoperative transoesophageal echocardiography indicated that the tumour thrombus has reached the confluence of IVC with right atrium. The operation took 255 min with an intraoperative haemorrhage of 800mL. The patient was discharged 7 days after surgery. Pathology revealed lipoma-like AML. Immunohistochemistry showed vimentin (+), EMA (−), HMB45 (+), S-100 (−), SMA (+), TFE-3 (−), melan A (+). After 2 years of follow-up, we found that the patient showed full recovery and had no recurrence. Therefore, lipoma-like AML should also be followed closely for recurrence and metastasis. When AML involves IVC tumour thrombus, open thrombectomy and radical nephrectomy are safe and effective methods.
DOI: 10.6084/m9.figshare.20079188.v4
title: Figure 3

description: It comprises of raw data and analysis file of Figure 3 obtained by determining the effect of tumor conditioned medium on peripheral sensory neuron differentiation. Dissociated sensory neurons were treated with control, 50% MRMT-1 derived conditioned medium and neurite assay was performed. <br>
DOI: 10.6084/m9.figshare.20079185.v3
title: Figure 4

description: It comprises of raw data and analysis file of Figure 4 obtained by determining the effect of tumorigenic dorsal root ganglion cell conditioned medium on cancer cell migration. Conditioned media obtained from culturing DRG cells were harvested from naive and tumor rats. Cell migration assay was performed to assess the number of MRMT-1 cells migrated from scratch. <br>
DOI: 10.6084/m9.figshare.20079182.v1
title: Supplementary Figure 1

description: It comprises of raw data and analysis file of Supplementary Figure 1 obtained by determining the effect of L929 conditioned medium on PC12 cell differentiation. PC12 cells were treated with naive medium, 10% and 50% L929 derived conditioned media for 72 hours and neurite assay was performed.
DOI: 10.6084/m9.figshare.22179500.v2
title: Broodstock development, induced spawning and larva rearing of the bilih, Mystacoleucus padangensis (Bleeker, 1852), a vulnerable species, and its domestication potential for new candidate aquaculture.

description: <em>Mystacoleucus padangensis</em> living in Lake Singkarak, Indonesia, has high potential market demand but is threatened by overfishing and has not been successfully cultured. This study describes the first broodstock development, induced breeding, and larval rearing of <em>M. padangensis</em>.
DOI: 10.6084/m9.figshare.21947222
title: Supplementary Material for: OXIS contacts and approximal caries in preschool children- A prospective cohort study

description: The present prospective cohort study was conducted to evaluate the susceptibility of OXIS contact areas namely O (open type), X (point type), I (straight type) and S (curved type) in the development of approximal caries. We conducted this study among 953 school children with 3812 contacts in Puducherry, India. At baseline, the contacts were assessed in accordance with OXIS criteria. At the end of 12 months, two calibrated dentists measured dental caries following the International Caries Detection and Assessment (ICDAS) criteria. Information about feeding practices, diet, and oral hygiene was collected by means of a structured questionnaire from each child’s parent. Data were analyzed by unadjusted and adjusted Poisson regression analysis with a multilevel approach. The two levels of analysis were tooth and child. Of 3,812 contacts observed during the follow-up, 127 (3.3%) were observed as carious. Poisson regression analysis revealed a significant association between type of contact and caries prevalence (p &lt; 0.05). The risk ratios for the development of approximal caries in X contacts were 2.4 (0.3-17.2), p value 0.38; in I contacts - 4.9 (1.2-19.9), p value 0.027; and in S contacts 8.2 (1.9-34.2), p value 0.004, when compared with the O contacts. Among the child variables, male gender (RR=2.1; 95%CI-1.3,3.5), parental supervision while toothbrushing (RR=1.6; 95%CI-1.1,2.4) and the use of toothpaste (RR=1.9; 95%CI-1.3,3.1) were found to be associated with approximal caries after adjustment for the other variables. Among the OXIS contacts, the S type was most susceptible to approximal caries due to its complex morphology, followed by I, X, and O.