cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.6981764.v1
title: Polarization and Distribution of Tumor-Associated Macrophages and COX-2 Expression in Basal Cell Carcinoma of the Ocular Adnexae

description: <i>Purpose</i>: Basal cell carcinoma (BCC) is a locally invasive skin tumor which can be subdivided into a circumscribed nodular and an invasive fibrosing subtype. There is increasing evidence that macrophages play an important role in interacting between tumor cells and their microenvironment, thereby affecting not only the invasive potential but also the patients’ prognosis. Thus, we wanted to compare these two BCC variants with regard to tumor-related inflammation, COX-2 expression, distribution, and polarization of tumor-associated macrophages. <i>Material and Methods</i>: 30 BCCs (nodular: <i>n</i> = 15; fibrosing: <i>n</i> = 15) of the ocular adnexae were investigated by histopathology and immunohistochemistry. The grade of inflammation was evaluated on hematoxylin and eosin stains (score: 0–3). Immunohistochemical stains for CD68 (macrophages), Ki67 (proliferative activity), and COX-2 as well as immunofluorescence stains for CD68 and CD163 (to distinguish M1 and M2 macrophage subtypes) were performed. SPSS was used for statistical analysis. <i>Results</i>: Fibrosing BCCs were predominantly located on the lower lid, while nodular BCCs showed a broader distribution (<i>p</i> = 0.013). The fibrosing BCC subtype was associated with a higher degree of inflammation (<i>p</i> p = 0.012). COX-2-positive cells were predominantly located on the infiltrating edge of the tumor. Macrophage polarization was balanced regarding M1 and M2 macrophage subtypes. There was no difference in macrophage number (<i>p</i> = 0.389) or polarization (<i>p</i> = 0.161) between nodular and fibrosing BCC. <i>Conclusions</i>: The findings indicate that COX-2 represents a factor for invasion of BCC. Macrophage polarization did not play a major role for aggressive behavior. However, other inflammatory components than tumor-associated macrophages seem to be involved in tissue destruction and thereby an invading growth pattern since fibrosing BCC revealed a significantly more intense inflammatory reaction in the surrounding tissue.
DOI: 10.6084/m9.figshare.6981680.v1
title: “Study aimed at determining the status of the Family Planning and Contraception Program as a baseline for comparison with performance evaluations”

description: <b>Introducción: </b> la planificación familiar (PF) es uno de los servicios clave que brindan los sistemas de atención médica. Extendiéndose más allá de los asuntos de salud sexual y reproductiva, su área de influencia impacta directamente en el desarrollo de individuos y naciones. Después de 60 años de intensas actividades de PF en México, y a la luz de la reciente reestructuración del suministro y financiamiento de servicios de salud, los servicios deben evaluarse desde la perspectiva del usuario. <b>Objetivo:</b>Con base en un marco conceptual integral, este artículo evalúa la calidad de los servicios de PF provistos por el Ministerio de Salud de México (MS). El análisis considera no solo la accesibilidad y la disponibilidad, sino también las percepciones de los usuarios sobre el proceso de atención, particularmente en lo que respecta a las relaciones interpersonales que experimentan con el personal y el tipo de información que se les proporciona. <b>Material y métodos:</b> Este estudio utilizó un diseño descriptivo y cualitativo basado en el muestreo de variación máxima en seis estados mexicanos. Incluyó visitas a 12 clínicas en áreas urbanas y rurales. El análisis temático se realizó en 86 entrevistas semiestructuradas administradas a usuarios de servicios de PF. <b>Resultados:</b>Si bien el acceso fue descrito por los usuarios como "fácil", sus experiencias revelaron barreras normalizadas. Uno de nuestros principales hallazgos se refería a la disponibilidad inversa, lo que significa que los métodos anticonceptivos disponibles generalmente no eran los preferidos por los usuarios, por lo que su selección se vio afectada por la escasez de suministros. Los desafíos incluyeron la falta de respeto por la libre elección de los usuarios de PF y la violencia durante las consultas por anticoncepción después de un evento obstétrico . Finalmente, la información proporcionada a los usuarios dejó un margen de mejora considerable. <b>Conclusiones</b>Después de seis décadas de suministro de servicios de PF, los resultados indican una serie de problemas de calidad que pueden ser la base de la demanda no satisfecha informada en la literatura. Con base en un esquema conceptual integral, el presente estudio analiza la calidad de los servicios, destacando áreas de mejora que el Ministerio de Salud debería considerar en los esfuerzos futuros.
DOI: 10.6084/m9.figshare.6981620
title: 3D dataset.zip

description: Gene expression data measured by in situ hybridization and cellular resolution 3D imaging.
DOI: 10.6084/m9.figshare.6981563
title: Dataset for "Similarity in fog and rainfall intermittency"

description: Final data used in the study "Similarity in fog and rainfall intermittency". <br>
DOI: 10.6084/m9.figshare.6981485
title: Emerging_hot_spots.shp

description: Emerging hot spot output shapefile. Each 8km x 8km cell is categorised as a type of hot / cold spot. The PATTERN variable is gives the category of each cell. View in ArcMap / QGIS. Input data from Hansen (2013) (see http://earthenginepartners.appspot.com/science-2013-global-forest)
DOI: 10.6084/m9.figshare.6981563.v1
title: Dataset for "Similarity in fog and rainfall intermittency"

description: Final data used in the study "Similarity in fog and rainfall intermittency". <br>
DOI: 10.6084/m9.figshare.6980180
title: Transcriptomes of cochlear hair cells

description: RNA-seq-based transcriptomes of cochlear inner and outer hair cells from adult mouse cochleae. Hair cell-specific transcriptomes obtained from microarray technique and neonatal hair cells are also included for comparison.
DOI: 10.7284/107001
title: Winch data collected during research cruise W1109C using a Markey DUSH-5 instrument system onboard the platform RV Wecoma
DOI: 10.6084/m9.figshare.6980018
title: DEM_016383_009592

description: HiRISE DEM produced from image pairs ESP_016383_1705 and PSP_009582_1705.
DOI: 10.6084/m9.figshare.6980054
title: Data and code from: Size-by-environment interactions: a neglected dimension of species' responses to environmental variation

description: <b>General Information</b>See the 'ReadMe.md' in the root directory of this fileset for information on running the codes. Email Andrew Tredennick (atredenn@gmail.com) if you encounter any issues. <br><br>Note that several of our IPM-based analyses take a while to run, so these codes are not presented as "source-and-get-results", but rather as guides through our analyses. They will, of course, run, but their implementation is not as seamless as the codes for fitting the models.<br>Any updates to these materials can be accessed on the Github page for this project: https://github.com/atredennick/size-environment.<br><b><br></b><b>Citation Information</b>This file set contains data and code to reproduce the results reported in:<br>Tredennick, A.T., B.J. Teller, Adler, P.B., Hooker, G., Ellner, S.P. (In press). Size-by-environment interactions: a neglected dimension of species' responses to environmental variation. <i>Ecology Letters</i>.<br>If you use the data or code deposited here, please cite the original paper (above) as well as this fileset:<br>Tredennick, A.T., B.J. Teller, Adler, P.B., Hooker, G., Ellner, S.P. (2018). Date and code from: Size-by-environment interactions: a neglected dimension of species' responses to environmental variation. <i>Figshare. </i>10.6084/m9.figshare.6980054.
DOI: 10.6084/m9.figshare.6980018.v1
title: DEM_016383_009592

description: HiRISE DEM produced from image pairs ESP_016383_1705 and PSP_009582_1705.
DOI: 10.6084/m9.figshare.6979985
title: Sequences of SynHbP2.docx

description: Synthetic sequence of DNA that can drive gene expression at the anterior of fly embryo at blastoderm stage.
DOI: 10.6084/m9.figshare.6979985.v1
title: Sequences of SynHbP2.docx

description: Synthetic sequence of DNA that can drive gene expression at the anterior of fly embryo at blastoderm stage.
DOI: 10.7284/104349
title: GNSS (Global Navigation Satellite System) data collected during research cruise WS1102 using a Raytheon 320 WAAS instrument system onboard the platform RV F.G. Walton Smith
DOI: 10.6084/m9.figshare.6979940
title: Data and analysis scripts accompanying Card et al. Novel ecological and climatic conditions drive rapid adaptation in invasive Florida Burmese pythons

description: Data processing and analysis scripts and intermediate and final datasets accompanying Card et al. Novel ecological and climatic conditions drive rapid adaptation in invasive Florida Burmese pythons. Molecular Ecology. See README.txt for a full manifest of the files.
DOI: 10.6084/m9.figshare.6979940.v1
title: Data and analysis scripts accompanying Card et al. Novel ecological and climatic conditions drive rapid adaptation in invasive Florida Burmese pythons

description: Data processing and analysis scripts and intermediate and final datasets accompanying Card et al. Novel ecological and climatic conditions drive rapid adaptation in invasive Florida Burmese pythons. Molecular Ecology. See README.txt for a full manifest of the files.
DOI: 10.6084/m9.figshare.6979883.v1
title: Amino acid alignment of spore killer resistance gene (rsk) in Neurospora.

description: The fungus <i>Neurospora</i> intermedia harbours two meiotic drive elements known as <i>Spore killer 2</i> (<i>Sk-2</i>) and <i>Spore killer 3</i> (<i>Sk-3</i>). Different alleles at the <i>rsk</i> locus confers resistance against these.<br>This dataset contains a trimmed amino acid alignment of the <i>rsk</i> gene from 98 strains of <i>Neurospora</i>.<br>This dataset was deposited as part of the paper Svedberg et al. (In press) "Convergent evolution of complex genomic rearrangements in two fungal meiotic drive elements". See paper for further details: https://www.nature.com/articles/s41467-018-06562-x (DOI:10.1038/s41467-018-06562-x)<br>For more details on <i>rsk</i>, see: Hammond et al. (2012). Molecular dissection of Neurospora Spore killer meiotic drive elements. Proc. Natl. Acad. Sci. U.S.A. <i>109</i>, 12093–12098.
DOI: 10.6084/m9.figshare.6979811
title: The Content Analysis for Technology-Mediated Sharing Literature Survey

description: This set of figures shows distinctive groups describing one aspect of sharing (e.g., "sharing for self-expression") with aggregated absolute and relative code counts for each group within both digital and physical sharing contexts. Absolute values describe how many codes of a given group we have encountered in our data corpus. Relative values were calculated as the sum of the absolute values of a category within a sharing sphere (i.e., digital or physical), over the number of groups in the category.
DOI: 10.6084/m9.figshare.6979844
title: PF Benchmark Problem 1

description: Phase Field Benchmark Results for Problem 1
DOI: 10.6084/m9.figshare.6979811.v1
title: The Content Analysis for Technology-Mediated Sharing Literature Survey

description: This set of figures shows distinctive groups describing one aspect of sharing (e.g., "sharing for self-expression") with aggregated absolute and relative code counts for each group within both digital and physical sharing contexts. Absolute values describe how many codes of a given group we have encountered in our data corpus. Relative values were calculated as the sum of the absolute values of a category within a sharing sphere (i.e., digital or physical), over the number of groups in the category.
DOI: 10.6084/m9.figshare.6979844.v1
title: PF Benchmark Problem 1

description: Phase Field Benchmark Results for Problem 1
DOI: 10.6084/m9.figshare.6979778
title: RAW DATA_OVA core shell.xlsx

description: Raw data Fig 2, Fig 3A-F, Fig 4A-H from the manuscript: "Ovalbumin-containing core-shell implants suitable to obtain a delayed IgG1 antibody response in support of a biphasic pulsatile release profile in mice"
DOI: 10.6084/m9.figshare.6979805
title: Bacteria_16S_rRNA_sequences.fa

description: Bacterial 16S rRNA sequences used for phylogeny
DOI: 10.6084/m9.figshare.6979778.v1
title: RAW DATA_OVA core shell.xlsx

description: Raw data Fig 2, Fig 3A-F, Fig 4A-H from the manuscript: "Ovalbumin-containing core-shell implants suitable to obtain a delayed IgG1 antibody response in support of a biphasic pulsatile release profile in mice"
DOI: 10.6084/m9.figshare.6979805.v1
title: Bacteria_16S_rRNA_sequences.fa

description: Bacterial 16S rRNA sequences used for phylogeny
DOI: 10.6084/m9.figshare.6979772
title: DEM_018018_026866

description: HiRISE DEM produced from image pair ESP_018018_1705 and ESP_026866_1705.
DOI: 10.6084/m9.figshare.6979772.v1
title: DEM_018018_026866

description: HiRISE DEM produced from image pair ESP_018018_1705 and ESP_026866_1705.
DOI: 10.6084/m9.figshare.6979739
title: Supplementary Material for: A Minimal lncRNA-mRNA Signature Predicts Sensitivity to Neoadjuvant Chemotherapy in Triple-Negative Breast Cancer

description: <b><i>Background/Aims:</i></b> Triple-negative breast cancer (TNBC) is a highly aggressive malignancy that responds in a diverse manner to neoadjuvant chemotherapy (NAC). This study was aimed to uncover an RNA signature in TNBC patients which predicts pathological complete responses (pCR) to NAC by analyzing long noncoding RNA (lncRNA) and coding gene expression. <b><i>Methods:</i></b> Microarray datasets from 26 TNBC patients receiving NAC including ten patients showing pCR were obtained from the Gene Expression Omnibus database. <b><i>Results:</i></b> A total of 172 coding genes and 84 lncRNAs were differentially expressed between patients achieving pCR and those who did not. Filtering based on the predictive efficacy of response to NAC using receiver operator characteristic curve (ROC) and area under the curve (AUC) shortlisted 23 lncRNAs and 15 coding genes from consideration. Finally, a response score consisting of 1 lncRNA and 2 coding genes was developed: response score = 2.595*BPESC1 – 1.09*WDR72 –1.428*GADD45A – 0.731. The response score had good predictive performance (AUC=0.931, <i>p</i>&lt; 0.01) and at the cut-off of 0.545, the response score had sensitivity and specificity of 0.8 and 0.9, respectively. <b><i>Conclusion:</i></b> We propose a simple gene expression signature of only three RNA species could be employed clinically to predict pCR in TNBC patients receiving NAC.
DOI: 10.6084/m9.figshare.6979745
title: Supplementary Material for: miR-122-5p Inhibits the Proliferation, Invasion and Growth of Bile Duct Carcinoma Cells by Targeting ALDOA

description: <b><i>Background/Aims:</i></b> Bile duct cancer, although not among the most common tumors, still accounts for more and more worldwide deaths each year. By attempting to verify an overexpression of ALDOA in cholangiocarcinoma tissues and cells and explore the underlying molecular mechanism regulated by miR-122-5p, this study was designed to provide a potential molecular target in bile duct cancer treatment. <b><i>Methods:</i></b> Western blot and immunohistochemistry were performed to detect the ALDOA protein level in duct carcinoma tissues. The transfection efficiency was confirmed by western blot and/or RT-qPCR assay. The proliferation of bile duct carcinoma cells was determined by MTT and colony formation assay. The invasion ability of bile duct carcinoma cells was evaluated with Transwell invasion assay. Flow cytometry detected cell apoptosis of bile duct carcinoma cells. The miRNAs which modulate <i>ALDOA</i> were filtrated from bioinformatics software and clinical specimens. The target relationship was confirmed by dual luciferase reporter assay. Furthermore, a xenograft model was completed to verify the impact of miRNA on inhibition growth of bile duct carcinoma cells. <b><i>Results:</i></b> ALDOA was found up-regulated in bile duct carcinoma tissues and cells. Knockdown of <i>ALDOA</i> promoted the apoptosis of cells and inhibited the proliferation and invasion of bile duct carcinoma cells. Bioinformatics and clinical specimens indicated the negative correlation and targeted regulation between miR-122-5p and <i>ALDOA</i>. By down-regulating ALDOA, overexpression of miR-122-5p appeared to promote cell apoptosis and significantly inhibit cell proliferation, invasion <i>in vitro</i> and suppress the tumor growth <i>in vivo</i>. <b><i>Conclusion:</i></b> miR-122-5p inhibited proliferation and invasion of bile duct carcinoma cells and promoted cell apoptosis by targeting <i>ALDOA</i> expression.
DOI: 10.6084/m9.figshare.6979739.v1
title: Supplementary Material for: A Minimal lncRNA-mRNA Signature Predicts Sensitivity to Neoadjuvant Chemotherapy in Triple-Negative Breast Cancer

description: <b><i>Background/Aims:</i></b> Triple-negative breast cancer (TNBC) is a highly aggressive malignancy that responds in a diverse manner to neoadjuvant chemotherapy (NAC). This study was aimed to uncover an RNA signature in TNBC patients which predicts pathological complete responses (pCR) to NAC by analyzing long noncoding RNA (lncRNA) and coding gene expression. <b><i>Methods:</i></b> Microarray datasets from 26 TNBC patients receiving NAC including ten patients showing pCR were obtained from the Gene Expression Omnibus database. <b><i>Results:</i></b> A total of 172 coding genes and 84 lncRNAs were differentially expressed between patients achieving pCR and those who did not. Filtering based on the predictive efficacy of response to NAC using receiver operator characteristic curve (ROC) and area under the curve (AUC) shortlisted 23 lncRNAs and 15 coding genes from consideration. Finally, a response score consisting of 1 lncRNA and 2 coding genes was developed: response score = 2.595*BPESC1 – 1.09*WDR72 –1.428*GADD45A – 0.731. The response score had good predictive performance (AUC=0.931, <i>p</i>&lt; 0.01) and at the cut-off of 0.545, the response score had sensitivity and specificity of 0.8 and 0.9, respectively. <b><i>Conclusion:</i></b> We propose a simple gene expression signature of only three RNA species could be employed clinically to predict pCR in TNBC patients receiving NAC.
DOI: 10.6084/m9.figshare.6979745.v1
title: Supplementary Material for: miR-122-5p Inhibits the Proliferation, Invasion and Growth of Bile Duct Carcinoma Cells by Targeting ALDOA

description: <b><i>Background/Aims:</i></b> Bile duct cancer, although not among the most common tumors, still accounts for more and more worldwide deaths each year. By attempting to verify an overexpression of ALDOA in cholangiocarcinoma tissues and cells and explore the underlying molecular mechanism regulated by miR-122-5p, this study was designed to provide a potential molecular target in bile duct cancer treatment. <b><i>Methods:</i></b> Western blot and immunohistochemistry were performed to detect the ALDOA protein level in duct carcinoma tissues. The transfection efficiency was confirmed by western blot and/or RT-qPCR assay. The proliferation of bile duct carcinoma cells was determined by MTT and colony formation assay. The invasion ability of bile duct carcinoma cells was evaluated with Transwell invasion assay. Flow cytometry detected cell apoptosis of bile duct carcinoma cells. The miRNAs which modulate <i>ALDOA</i> were filtrated from bioinformatics software and clinical specimens. The target relationship was confirmed by dual luciferase reporter assay. Furthermore, a xenograft model was completed to verify the impact of miRNA on inhibition growth of bile duct carcinoma cells. <b><i>Results:</i></b> ALDOA was found up-regulated in bile duct carcinoma tissues and cells. Knockdown of <i>ALDOA</i> promoted the apoptosis of cells and inhibited the proliferation and invasion of bile duct carcinoma cells. Bioinformatics and clinical specimens indicated the negative correlation and targeted regulation between miR-122-5p and <i>ALDOA</i>. By down-regulating ALDOA, overexpression of miR-122-5p appeared to promote cell apoptosis and significantly inhibit cell proliferation, invasion <i>in vitro</i> and suppress the tumor growth <i>in vivo</i>. <b><i>Conclusion:</i></b> miR-122-5p inhibited proliferation and invasion of bile duct carcinoma cells and promoted cell apoptosis by targeting <i>ALDOA</i> expression.
DOI: 10.6084/m9.figshare.6979727
title: SAOM model parameters and meta-analysis from Social interactions shape individual and collective personality in social spiders

description: Table S2
DOI: 10.6084/m9.figshare.6979727.v1
title: SAOM model parameters and meta-analysis from Social interactions shape individual and collective personality in social spiders

description: Table S2
DOI: 10.6084/m9.figshare.6979703
title: DEM_013651_013983

description: HiRISE DEM produced from image pair ESP_013983_1705 and ESP_013561_1705.
DOI: 10.6084/m9.figshare.6979703.v1
title: DEM_013651_013983

description: HiRISE DEM produced from image pair ESP_013983_1705 and ESP_013561_1705.
DOI: 10.6084/m9.figshare.6979694
title: DEM_002828_002551

description: HiRISE DEM produced from image pair PSP_028828_1700 and PSP_002551_1700.
DOI: 10.6084/m9.figshare.6979694.v1
title: DEM_002828_002551

description: HiRISE DEM produced from image pair PSP_028828_1700 and PSP_002551_1700.
DOI: 10.6084/m9.figshare.6979649
title: Supplementary Material for: Isolation and Quantification of Mimivirus-Like and Marseillevirus-Like Viruses from Soil Samples in An Aboriginal <b><i>(</i></b>Orang asli<b><i>)</i></b> Village in Peninsular Malaysia

description: <b><i>Background:</i></b> The giant amoebal viruses of Mimivirus and Marseillevirus are large DNA viruses and have been documented in water, soil, and sewage samples. The trend of discovering these giant amoebal viruses has been increasing throughout Asia with Japan, India, and Saudi Arabia being the latest countries to document the presence of these viruses. To date, there have been no reports of large amoebal viruses being isolated in South East Asia. <b><i>Objective:</i></b> In this study, we aim to discover these viruses from soil samples in an aboriginal village (Serendah village) in Peninsular ­Malaysia. <b><i>Method and Results:</i></b> We successfully detected and isolated both Mimivirus-like and Marseillevirus-like viruses using <i>Acanthamoeba castellanii.</i> Phylogeny analysis identified them as Mimivirus and Marseillevirus, respectively. <b><i>Conclusion:</i></b> The ubiquitous nature of both Mimivirus and Marseillevirus is further confirmed in our study as they are detected in higher quantity in soil that is near to water vicinities in an aboriginal village in Peninsular Malaysia. However, this study is limited by our inability to investigate the impact of Mimivirus and Marseillevirus on the aboriginal villagers. More studies on the potential impact of these viruses on human health, especially on the aborigines, are warranted.
DOI: 10.6084/m9.figshare.6979652
title: DEM_028488_024888

description: HiRISE DEM produced from image pair ESP_028488_1705 and ESP_024888_1705.
DOI: 10.7284/104402
title: GNSS (Global Navigation Satellite System) data collected during research cruise WS1107 using a Raytheon 320 WAAS instrument system onboard the platform RV F.G. Walton Smith
DOI: 10.6084/m9.figshare.6979634
title: DEM_034514_034092

description: HiRISE DEM from image pair ESP_034514_1700 and ESP_034092_1700.