cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1483473.v2
title: Small RNA deep sequencing discriminates subsets of extracellular vesicles released by melanoma cells – Evidence of unique microRNA cargos

description: Melanoma cells release different types of extracellular vesicles (EVs) into the extracellular milieu that are involved with communication and signaling in the tumor microenvironment. Subsets of EVs include exosomes, microvesicles, and apoptotic bodies that carry protein and genetic (RNA) cargos. To define the contribution of the RNA cargo of melanoma cell derived EVs we performed small RNA sequencing to identify different small RNAs in the EV subsets. Using validated centrifugation protocols, we separated these EV subsets released by the melanoma cell line MML-1, and performed RNA sequencing with the Ion Torrent platform. Various, but different, non-coding RNAs were detected in the EV subsets, including microRNA, mitochondrial associated tRNA, small nucleolar RNA, small nuclear RNA, Ro associated Y-RNA, vault RNA and Y-RNA. We identified in total 1041 miRNAs in cells and EV subsets. Hierarchical clustering showed enrichment of specific miRNAs in exosomes, including hsa-miR-214-3p, hsa-miR-199a-3p and hsa-miR-155-5p, all being associated with melanoma progression. Comparison of exosomal miRNAs with miRNAs in clinical melanoma samples indicate that multiple miRNAs in exosomes also are expressed specifically in melanoma tissues, but not in benign naevi. This study shows for the first time the presence of distinct small RNAs in subsets of EVs released by melanoma cells, with significant similarities to clinical melanoma tissue, and provides unique insights into the contribution of EV associated extracellular RNA in cancer.
DOI: 10.6084/m9.figshare.1483475.v3
title: A bacterial homolog YciH of eukaryotic translation initiation factor eIF1 regulates stress-related gene expression and is unlikely to be involved in translation initiation fidelity

description: YciH is a bacterial protein, homologous to eukaryotic translation initiation factor eIF1. Preceding evidence obtained with the aid of <i>in vitro</i> translation initiation system suggested that it may play a role of a translation initiation factor, ensuring selection against suboptimal initiation complexes. Here we studied the effect of <i>Escherichia coli yciH</i> gene inactivation on translation of model mRNAs. Neither the translation efficiency of leaderless mRNAs, nor mRNAs with non AUG start codons, was found to be affected by YciH <i>in vivo</i>. Comparative proteome analysis revealed that <i>yciH</i> gene knockout leads to a more than fold2- increase in expression of 66 genes and a more than fold2- decrease in the expression of 20 genes. Analysis of these gene sets allowed us to suggest a role of YciH as an inhibitor of translation in a stress response rather than the role of a translation initiation factor.
DOI: 10.6084/m9.figshare.1483448
title: Two-frame tilt-shift error estimation and phase demodulation algorithm

description: Codes and instructions of figures reproduction for the paper: M. Wielgus, Z. Sunderland, K. Patorski, "Two-frame tilt-shift error estimation and phase demodulation algorithm", Optics Letters 2015 (in press)
DOI: 10.6084/m9.figshare.1483473.v3
title: Small RNA deep sequencing discriminates subsets of extracellular vesicles released by melanoma cells – Evidence of unique microRNA cargos

description: Melanoma cells release different types of extracellular vesicles (EVs) into the extracellular milieu that are involved with communication and signaling in the tumor microenvironment. Subsets of EVs include exosomes, microvesicles, and apoptotic bodies that carry protein and genetic (RNA) cargos. To define the contribution of the RNA cargo of melanoma cell derived EVs we performed small RNA sequencing to identify different small RNAs in the EV subsets. Using validated centrifugation protocols, we separated these EV subsets released by the melanoma cell line MML-1, and performed RNA sequencing with the Ion Torrent platform. Various, but different, non-coding RNAs were detected in the EV subsets, including microRNA, mitochondrial associated tRNA, small nucleolar RNA, small nuclear RNA, Ro associated Y-RNA, vault RNA and Y-RNA. We identified in total 1041 miRNAs in cells and EV subsets. Hierarchical clustering showed enrichment of specific miRNAs in exosomes, including hsa-miR-214-3p, hsa-miR-199a-3p and hsa-miR-155-5p, all being associated with melanoma progression. Comparison of exosomal miRNAs with miRNAs in clinical melanoma samples indicate that multiple miRNAs in exosomes also are expressed specifically in melanoma tissues, but not in benign naevi. This study shows for the first time the presence of distinct small RNAs in subsets of EVs released by melanoma cells, with significant similarities to clinical melanoma tissue, and provides unique insights into the contribution of EV associated extracellular RNA in cancer.
DOI: 10.6084/m9.figshare.1483473.v5
title: Small RNA deep sequencing discriminates subsets of extracellular vesicles released by melanoma cells – Evidence of unique microRNA cargos

description: Melanoma cells release different types of extracellular vesicles (EVs) into the extracellular milieu that are involved with communication and signaling in the tumor microenvironment. Subsets of EVs include exosomes, microvesicles, and apoptotic bodies that carry protein and genetic (RNA) cargos. To define the contribution of the RNA cargo of melanoma cell derived EVs we performed small RNA sequencing to identify different small RNAs in the EV subsets. Using validated centrifugation protocols, we separated these EV subsets released by the melanoma cell line MML-1, and performed RNA sequencing with the Ion Torrent platform. Various, but different, non-coding RNAs were detected in the EV subsets, including microRNA, mitochondrial associated tRNA, small nucleolar RNA, small nuclear RNA, Ro associated Y-RNA, vault RNA and Y-RNA. We identified in total 1041 miRNAs in cells and EV subsets. Hierarchical clustering showed enrichment of specific miRNAs in exosomes, including hsa-miR-214-3p, hsa-miR-199a-3p and hsa-miR-155-5p, all being associated with melanoma progression. Comparison of exosomal miRNAs with miRNAs in clinical melanoma samples indicate that multiple miRNAs in exosomes also are expressed specifically in melanoma tissues, but not in benign naevi. This study shows for the first time the presence of distinct small RNAs in subsets of EVs released by melanoma cells, with significant similarities to clinical melanoma tissue, and provides unique insights into the contribution of EV associated extracellular RNA in cancer.
DOI: 10.6084/m9.figshare.1483448.v1
title: Two-frame tilt-shift error estimation and phase demodulation algorithm

description: Codes and instructions of figures reproduction for the paper: M. Wielgus, Z. Sunderland, K. Patorski, "Two-frame tilt-shift error estimation and phase demodulation algorithm", Optics Letters 2015 (in press)
DOI: 10.6084/m9.figshare.1483439
title: Network Analysis

description: Network work at Cambridge
DOI: 10.6084/m9.figshare.1483473.v4
title: Small RNA deep sequencing discriminates subsets of extracellular vesicles released by melanoma cells – Evidence of unique microRNA cargos

description: Melanoma cells release different types of extracellular vesicles (EVs) into the extracellular milieu that are involved with communication and signaling in the tumor microenvironment. Subsets of EVs include exosomes, microvesicles, and apoptotic bodies that carry protein and genetic (RNA) cargos. To define the contribution of the RNA cargo of melanoma cell derived EVs we performed small RNA sequencing to identify different small RNAs in the EV subsets. Using validated centrifugation protocols, we separated these EV subsets released by the melanoma cell line MML-1, and performed RNA sequencing with the Ion Torrent platform. Various, but different, non-coding RNAs were detected in the EV subsets, including microRNA, mitochondrial associated tRNA, small nucleolar RNA, small nuclear RNA, Ro associated Y-RNA, vault RNA and Y-RNA. We identified in total 1041 miRNAs in cells and EV subsets. Hierarchical clustering showed enrichment of specific miRNAs in exosomes, including hsa-miR-214-3p, hsa-miR-199a-3p and hsa-miR-155-5p, all being associated with melanoma progression. Comparison of exosomal miRNAs with miRNAs in clinical melanoma samples indicate that multiple miRNAs in exosomes also are expressed specifically in melanoma tissues, but not in benign naevi. This study shows for the first time the presence of distinct small RNAs in subsets of EVs released by melanoma cells, with significant similarities to clinical melanoma tissue, and provides unique insights into the contribution of EV associated extracellular RNA in cancer.
DOI: 10.6084/m9.figshare.1483439.v1
title: Network Analysis

description: Network work at Cambridge
DOI: 10.6084/m9.figshare.1483372
title: Data for "Enhanced marine sulphur emissions offset global warming and impact rainfall"

description: <strong>Introduction:</strong>These data accompany the manuscript titled <em>"Enhanced marine sulphur emissions offset global warming and impact rainfall"</em> by B.S. Grandey and C. Wang (Scientific Reports, 2015). Please refer to the manuscript for details: http://www.nature.com/articles/srep13055. <strong>File size warning:</strong> These files are relatively large. <strong>Contents:</strong> 1x emissions file: -<em> p2012b_maxperlat_aerocom_mam3_dms_surf_1849-2100_c111017.nc</em> contains the modified DMS emissions for the EnDMS simulation. 6x transient simulation output data files: - <em>p2012b_R45_*</em> correspond to the three RCP4.5 simulations. - <em>p2012b_EnD_*</em> correspond to the three EnDMS simulations. - <em>f1</em>, <em>h1</em>, and <em>h2</em> refer to three sets of initial conditions. 5x presribed-SST simulation output data files: - <em>p2012b_F_*</em> contain the output data from the prescribed-SST simulations. Year-2000 climatological SST and greenhouse concentrations were prescribed. - <em>1850</em>, <em>2000</em>, and <em>2080</em> refer the year of the aerosol emissions. - <em>R45</em> and <em>EnD</em> refer to the RCP4.5 and EnDMS scenarios respectively. - Inside these precribed-SST simulation data files, the subscript "_d1" refers to clean-sky fluxes. "cDRE", "cCRE", and "cFNTOA" refer to the direct radiative effect, net cloud RFP, and net total RFP respectively. <strong>NetCDF file format:</strong> .nc is the extension for NetCDF format, a binary data format commonly used for climate model output data. These NetCDF files contain metadata which aid interpretation of the data. The metadata and data can be explored using the free Panoply software tool (http://www.giss.nasa.gov/tools/panoply/ [28-Aug-2015]). <strong>Contributions:</strong> Benjamin S. Grandey and Chien Wang designed the experiment. B.S.G. configured the model simulations and analysed the data. B.S.G. wrote the paper, with contributions from C.W.. <strong>Acknowledgments:</strong> This research was funded by the Singapore National Research Foundation (NRF) through the Singapore-MIT Alliance for Research and Technology (SMART) Center for Environmental Sensing and Modeling (CENSAM). This research was also supported by the U.S. National Science Foundation (AGS-0944121), U.S. DOE (DE-FG02-94ER61937), U.S. EPA (XA- 83600001-1), and the A*STAR Computational Resource Centre of Singapore (http://www.acrc.a-star.edu.sg) through the use of its high performance computing facilities. Phil Rasch, Balwinder Singh, and Jin-Ho Yoon provided initial conditions data and provided advice on the RCP4.5 model configuration.
DOI: 10.6084/m9.figshare.1483401
title: High Resolution Figures 1 and 2

description: Hi-res versions of the figures 1 and 2 from the report. Originally compiled by Claire Austin of Research Data Canada
DOI: 10.6084/m9.figshare.1483358
title: SchoolCalendar2015Cantabria

description: Perpetual calendar which gives the GMT times of lunar phases, equinoxes, solstices, and some other calendaric curiosities of any year.
DOI: 10.6084/m9.figshare.1483401.v1
title: High Resolution Figures 1 and 2

description: Hi-res versions of the figures 1 and 2 from the report. Originally compiled by Claire Austin of Research Data Canada
DOI: 10.6084/m9.figshare.1483341
title: SchoolCalendar2015Cantabria0

description: Perpetual calendar which adjusts automatically to any entered year and gives the (GMT) times of lunar phases, equinoxes, solstices, and some other calendaric curiosities.
DOI: 10.6084/m9.figshare.1483372.v8
title: Data for "Enhanced marine sulphur emissions offset global warming and impact rainfall"

description: <strong>Introduction:</strong>These data accompany the manuscript titled <em>"Enhanced marine sulphur emissions offset global warming and impact rainfall"</em> by B.S. Grandey and C. Wang (Scientific Reports, 2015). Please refer to the manuscript for details: http://www.nature.com/articles/srep13055. <strong>File size warning:</strong> These files are relatively large. <strong>Contents:</strong> 1x emissions file: -<em> p2012b_maxperlat_aerocom_mam3_dms_surf_1849-2100_c111017.nc</em> contains the modified DMS emissions for the EnDMS simulation. 6x transient simulation output data files: - <em>p2012b_R45_*</em> correspond to the three RCP4.5 simulations. - <em>p2012b_EnD_*</em> correspond to the three EnDMS simulations. - <em>f1</em>, <em>h1</em>, and <em>h2</em> refer to three sets of initial conditions. 5x presribed-SST simulation output data files: - <em>p2012b_F_*</em> contain the output data from the prescribed-SST simulations. Year-2000 climatological SST and greenhouse concentrations were prescribed. - <em>1850</em>, <em>2000</em>, and <em>2080</em> refer the year of the aerosol emissions. - <em>R45</em> and <em>EnD</em> refer to the RCP4.5 and EnDMS scenarios respectively. - Inside these precribed-SST simulation data files, the subscript "_d1" refers to clean-sky fluxes. "cDRE", "cCRE", and "cFNTOA" refer to the direct radiative effect, net cloud RFP, and net total RFP respectively. <strong>NetCDF file format:</strong> .nc is the extension for NetCDF format, a binary data format commonly used for climate model output data. These NetCDF files contain metadata which aid interpretation of the data. The metadata and data can be explored using the free Panoply software tool (http://www.giss.nasa.gov/tools/panoply/ [28-Aug-2015]). <strong>Contributions:</strong> Benjamin S. Grandey and Chien Wang designed the experiment. B.S.G. configured the model simulations and analysed the data. B.S.G. wrote the paper, with contributions from C.W.. <strong>Acknowledgments:</strong> This research was funded by the Singapore National Research Foundation (NRF) through the Singapore-MIT Alliance for Research and Technology (SMART) Center for Environmental Sensing and Modeling (CENSAM). This research was also supported by the U.S. National Science Foundation (AGS-0944121), U.S. DOE (DE-FG02-94ER61937), U.S. EPA (XA- 83600001-1), and the A*STAR Computational Resource Centre of Singapore (http://www.acrc.a-star.edu.sg) through the use of its high performance computing facilities. Phil Rasch, Balwinder Singh, and Jin-Ho Yoon provided initial conditions data and provided advice on the RCP4.5 model configuration.
DOI: 10.6084/m9.figshare.1483340
title: SchoolCalendar2015

description: Perpetual calendar which gives the GMT times of lunar phases, equinoxes, solstices, and some other calendaric curiosities of any year.
DOI: 10.6084/m9.figshare.1483358.v1
title: SchoolCalendar2015Cantabria

description: Perpetual calendar which gives the GMT times of lunar phases, equinoxes, solstices, and some other calendaric curiosities of any year.
DOI: 10.6084/m9.figshare.1483297
title: Giving Researchers Credit for their Data: Jisc RDS July 15 v3

description: Corrected: Report summarising Phase 1 of Jisc Research Data Spring project entitled: Giving Researchers Credit for their Data. Conducted between March-July 2015. Evidence of need from publishers and repositories for a Helper App that will enable researchers to publish their data using an automated tool.
DOI: 10.6084/m9.figshare.1483372.v7
title: Data for "Enhanced sulphur emissions offset global warming and impact rainfall"

description: <strong>Introduction</strong> These data accompany the manuscript entitled <em>"Enhanced sulphur emissions offset global warming and impact rainfall"</em> (details to follow later). Please refer to the manuscript for details. <strong>Contents</strong> 1x emissions file: -<em> p2012b_maxperlat_aerocom_mam3_dms_surf_1849-2100_c111017.nc</em> contains the modified DMS emissions for the EnDMS simulation. 6x transient simulation output data files: - <em>p2012b_R45_*</em> correspond to the three RCP4.5 simulations. - <em>p2012b_EnD_*</em> correspond to the three EnDMS simulations. - <em>f1</em>, <em>h1</em>, and <em>h2</em> refer to three sets of initial conditions. 5x presribed-SST simulation output data files: - <em>p2012b_F_*</em> contain the output data from the prescribed-SST simulations. Year-2000 climatological SST and greenhouse concentrations were prescribed. - <em>1850</em>, <em>2000</em>, and <em>2080</em> refer the year of the aerosol emissions. - <em>R45</em> and <em>EnD</em> refer to the RCP4.5 and EnDMS scenarios respectively. - Inside these precribed-SST simulation data files, the subscript "_d1" refers to clean-sky fluxes. "cDRE", "cCRE", and "cFNTOA" refer to the direct radiative effect, net cloud RFP, and net total RFP respectively. <strong>Contributions:</strong> Benjamin S. Grandey and Chien Wang designed the experiment. B.S.G. configured the model simulations and analysed the data. B.S.G. wrote the paper, with contributions from C.W.. <strong>Acknowledgments:</strong> This research was funded by the Singapore National Research Foundation (NRF) through the Singapore-MIT Alliance for Research and Technology (SMART) Center for Environmental Sensing and Modeling (CENSAM). This research was also supported by the U.S. National Science Foundation (AGS-0944121), US DOE (DE-FG02-94ER61937), US EPA (XA- 83600001-1), and the A*STAR Computational Resource Centre of Singapore (http://www.acrc.a-star.edu.sg) through the use of its high performance computing facilities. Phil Rasch, Balwinder Singh, and Jin-Ho Yoon provided initial conditions data and provided advice on the RCP4.5 model configuration.
DOI: 10.6084/m9.figshare.1483280
title: Time to Recruitment for a Single Grade Manpower System with Two Thresholds, Different Epochs for Inter-Decisions as an Order Statistics and Exits

description: ABSTRACT: In this paper, the problem of time to recruitment is studied using a univariate policy of recruitment involving two thresholds for a single grade manpower system with attrition generated by its policy decisions. Assuming that the policy decisions and exits occur at different epochs, a stochastic model is constructed and the variance of the time to recruitment is obtained when the inter-policy decision times and inter- exit times form an order statistics and an ordinary renewal process respectively. The analytical results are numerically illustrated with relevant findings by assuming specific distributions. Keywords: Single grade manpower system; decision and exit epochs; order statistics; ordinary renewal process; univariate policy of recruitment with two thresholds and variance of the time to recruitment.
DOI: 10.6084/m9.figshare.1483340.v1
title: SchoolCalendar2015

description: Perpetual calendar which gives the GMT times of lunar phases, equinoxes, solstices, and some other calendaric curiosities of any year.
DOI: 10.6084/m9.figshare.1483279
title: The factors importance to economization produced cheese mozzarella from cow’s milk

description: SUMMARY: Milk used for cheese making is normally standardized and heat treated. In some case, milk is homogenized. An acid – producing starter culture is then added. The standardization of milk has become necessary to ensure that the milk obtained from several producers or dairies is of a “standard” composition and condition throughout the year. This is critical in cheese making because the legal standards of various cheeses specify certain fat-to-protein rations. Though there are numerous cheese varieties, the manufacturing processes of most of them share several common steps. Variations at one or more steps during manufacture produce cheese of different textures and flavors. This study is done to research the examinations for production of mozzarella cheese, after research and analyses of physical-chemical peculiar feature of milk. We have followed the processes from drying of cheese until preparing it for market, physical-chemical peculiar feature. We carried out three experiments for each milk-kind. For every experiment, we took three patterns and analyzed. Production of this sort of cheese, the application of producing technology and the supply of Kosova’s trade market with mozzarella cheese produced from cow’s milk is the objective of this presentation work research. KEYWORDS: Cow, milk, coagulum, cheese, whey, mozzarella
DOI: 10.6084/m9.figshare.1483280.v1
title: Time to Recruitment for a Single Grade Manpower System with Two Thresholds, Different Epochs for Inter-Decisions as an Order Statistics and Exits

description: ABSTRACT: In this paper, the problem of time to recruitment is studied using a univariate policy of recruitment involving two thresholds for a single grade manpower system with attrition generated by its policy decisions. Assuming that the policy decisions and exits occur at different epochs, a stochastic model is constructed and the variance of the time to recruitment is obtained when the inter-policy decision times and inter- exit times form an order statistics and an ordinary renewal process respectively. The analytical results are numerically illustrated with relevant findings by assuming specific distributions. Keywords: Single grade manpower system; decision and exit epochs; order statistics; ordinary renewal process; univariate policy of recruitment with two thresholds and variance of the time to recruitment.
DOI: 10.6084/m9.figshare.1483297.v1
title: Giving Researchers Credit for their Data: Jisc RDS July 15

description: Report summarising Phase 1 of Jisc Research Data Spring project entitled: Giving Researchers Credit for their Data. Conducted between March-July 2015. Evidence of need from publishers and repositories for a Helper App that will enable researchers to publish their data using an automated tool.
DOI: 10.6084/m9.figshare.1483341.v1
title: SchoolCalendar

description: Perpetual calendar which adjusts automatically to any entered year and gives the (GMT) times of lunar phases, equinoxes, solstices, and some other calendaric curiosities.
DOI: 10.6084/m9.figshare.1483278
title: Design of CPW-fed Capacitive Coupled Patch Antenna for WiGig Applications

description: — The area of microstrip antennas has seen some inventive work in recent years and is one of the most dynamic fields of antenna theory. The ever increasing need for mobile communication and the emergence of newer technologies require an efficient design of antenna of smaller size for wider frequency range applications such as WiGig. The design, simulation, and characterization of a CPW-fed microstrip antenna capable of covering the entire IEEE 802.11ad (WiGig) frequency band (57–66 GHz) has been presented in this paper. A conductor-backed (CB) coplanar waveguide (CPW)-fed loop slot couples the energy to the patch antenna, resulting in a broad bandwidth. The substrate used here is quartz substrate (r=3.9, tan δ=0.0002 at 60 GHz), on top of which an SU-8-based three-dimensional (3-D) structure with air cavities has been placed. The patch metallization is deposited on top of this 3-D structure. Simulation of the proposed antenna has been carried out for different geometries and impedance tuning coupling mechanisms. Parametric study was included to determine the effect of design towards the antenna performance. The design was optimized to meet the best possible result. The proposed antenna has also found to be promising to be embedded with devices employing WiGig applications.