cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.6794006
title: Main serials that support the quality of research in optoelectronics and optical systems and their characteristics

description: A comprehensive citation analysis-based methodology for selecting the world scientific serials to be included in information environment for researchers in a specific natural or technical science is featured. The case study was fulfilled for serials to be included in information environment for researchers in optoelectronics and optical systems (OOS) with the use of Journal Citation Reports (JCR) data. The indices taken for serials assessment were: total citedness of a serial in the selected journals specialized in OOS; the “discipline impact factor” (Hirst 1978) i.e. the impact factor which numerator is the level of a serial citedness not by all the JCR-indexed journals, but by the specialized ones (in OOS), the denominator being the number of papers in a cited serial; the level of total citedness of the specialized journals in a serial under assessment; the “discipline susceptibility factor” of a serial (Lazarev and Skalaban 2016; Lazarev et al. 2017), i.e. the number of citations to the mentioned specialized journals made in a serial being assessed divided by the number of papers in a citing serial. The citation window is one year, the publication window is “5+1” years (i.e. 5 previous years plus the year of citing). With the application of the outlined methodology, the selection of serials believed to be necessary to implement research in OOS has been accomplished, and after application of threshold values, merging and elimination some of the data, the list of 538 periodicals has been determined. The second pair of indices reflects the susceptibility of the serials being determined to the research field represented by cited specialized journals.
DOI: 10.6084/m9.figshare.6793919
title: Raman spectra of shortite Na<sub>2</sub>Ca<sub>2</sub>(CO<sub>3</sub>)<sub>3</sub> compressed up to 8 GPa

description: A rare mineral shortite, Na<sub>2</sub>Ca<sub>2</sub>(CO<sub>3</sub>)<sub>3</sub>, occurs among groundmass minerals in unaltered kimberlites, which suggests its participation in the evolution of kimberlite system. This work presents a high pressure Raman spectroscopic study of natural shortite (Udachnaya east kimberlites) compressed in KBr up to 8 GPa in a diamond anvil cell. At ambient pressure the spectrum contains two strong bands related to symmetric C-O stretching vibrations, four in-plane bending modes, and several low-frequency modes of lattice vibrations. Upon the pressure increase up to 8 GPa, almost all the bands exhibit positive shift with the rate of 1–4 cm<sup>−1</sup>/GPa for the lattice modes and 3.6 and 3.9 cm<sup>−1</sup>/GPa for the C-O stretching modes. The shifts of Raman modes are rather regular, which implies the absence of reconstructive phase transitions within the studied pressure range, similarly to the behavior of nyerereite, a related carbonate mineral. However, minor anomalies in the ν/<i>P</i> and FWHM/<i>P</i> dependences, observed at about 2 GPa, suggest some rearrangement and disordering of carbonate groups. The obtained data can be used for the estimation of residual pressure in shortite-bearing inclusions in deep-seated minerals.
DOI: 10.6084/m9.figshare.6794006.v1
title: Main serials that support the quality of research in optoelectronics and optical systems and their characteristics

description: A comprehensive citation analysis-based methodology for selecting the world scientific serials to be included in information environment for researchers in a specific natural or technical science is featured. The case study was fulfilled for serials to be included in information environment for researchers in optoelectronics and optical systems (OOS) with the use of Journal Citation Reports (JCR) data. The indices taken for serials assessment were: total citedness of a serial in the selected journals specialized in OOS; the “discipline impact factor” (Hirst 1978) i.e. the impact factor which numerator is the level of a serial citedness not by all the JCR-indexed journals, but by the specialized ones (in OOS), the denominator being the number of papers in a cited serial; the level of total citedness of the specialized journals in a serial under assessment; the “discipline susceptibility factor” of a serial (Lazarev and Skalaban 2016; Lazarev et al. 2017), i.e. the number of citations to the mentioned specialized journals made in a serial being assessed divided by the number of papers in a citing serial. The citation window is one year, the publication window is “5+1” years (i.e. 5 previous years plus the year of citing). With the application of the outlined methodology, the selection of serials believed to be necessary to implement research in OOS has been accomplished, and after application of threshold values, merging and elimination some of the data, the list of 538 periodicals has been determined. The second pair of indices reflects the susceptibility of the serials being determined to the research field represented by cited specialized journals.
DOI: 10.6084/m9.figshare.6793919.v1
title: Raman spectra of shortite Na<sub>2</sub>Ca<sub>2</sub>(CO<sub>3</sub>)<sub>3</sub> compressed up to 8 GPa

description: A rare mineral shortite, Na<sub>2</sub>Ca<sub>2</sub>(CO<sub>3</sub>)<sub>3</sub>, occurs among groundmass minerals in unaltered kimberlites, which suggests its participation in the evolution of kimberlite system. This work presents a high pressure Raman spectroscopic study of natural shortite (Udachnaya east kimberlites) compressed in KBr up to 8 GPa in a diamond anvil cell. At ambient pressure the spectrum contains two strong bands related to symmetric C-O stretching vibrations, four in-plane bending modes, and several low-frequency modes of lattice vibrations. Upon the pressure increase up to 8 GPa, almost all the bands exhibit positive shift with the rate of 1–4 cm<sup>−1</sup>/GPa for the lattice modes and 3.6 and 3.9 cm<sup>−1</sup>/GPa for the C-O stretching modes. The shifts of Raman modes are rather regular, which implies the absence of reconstructive phase transitions within the studied pressure range, similarly to the behavior of nyerereite, a related carbonate mineral. However, minor anomalies in the ν/<i>P</i> and FWHM/<i>P</i> dependences, observed at about 2 GPa, suggest some rearrangement and disordering of carbonate groups. The obtained data can be used for the estimation of residual pressure in shortite-bearing inclusions in deep-seated minerals.
DOI: 10.6084/m9.figshare.6793916
title: Comparison of phytotoxic effects of bio-synthesised copper oxide nanoparticle and ionic copper on <i>Elodea canadensis</i>

description: This study aims to investigate the phytotoxic effects of both <i>Punica granatum</i> peel extract directed copper oxide nanoparticles (CuONPs) and copper nitrate on <i>Elodea canadensis.</i> The CuONPs were characterised by UV–visible spectroscopy (UV-Vis), Dynamic Light Scattering (DLS), X-ray Diffraction (XRD), Scanning Electron Microscope (SEM), and Fourier Transform Infrared (FT-IR) Spectroscopy. The ratio of photosynthetic pigments, total soluble protein, malondialdehyde (MDA), catalase (CAT), ascorbate peroxidase (APX), and copper accumulation in the <i>E. canadensis</i> was determined to evaluate the phytotoxicity of the CuONPs and copper nitrate on <i>E. canadensis</i>. The significant improvements were observed in the growth rate of <i>E. canadensis</i>, chlorophyll a and b, carotenoid contents, and total soluble protein in the <i>E. canadensis</i> when it was exposed to the CuONPs. Additionally, CAT and APX activities and MDA contents were enhanced by accumulation of the CuONPs into the <i>E. canadensis</i>. These results suggested that oxidative stress was alleviated, owing to the result of an increase in the antioxidants such as CAT and APX, with an increase in the concentration of the CuONPs. Finally, the findings of this study show that copper nitrate has many negative effects on <i>E. canadensis</i> compared bio-synthesised CuONPs.
DOI: 10.6084/m9.figshare.6793916.v1
title: Comparison of phytotoxic effects of bio-synthesised copper oxide nanoparticle and ionic copper on <i>Elodea canadensis</i>

description: This study aims to investigate the phytotoxic effects of both <i>Punica granatum</i> peel extract directed copper oxide nanoparticles (CuONPs) and copper nitrate on <i>Elodea canadensis.</i> The CuONPs were characterised by UV–visible spectroscopy (UV-Vis), Dynamic Light Scattering (DLS), X-ray Diffraction (XRD), Scanning Electron Microscope (SEM), and Fourier Transform Infrared (FT-IR) Spectroscopy. The ratio of photosynthetic pigments, total soluble protein, malondialdehyde (MDA), catalase (CAT), ascorbate peroxidase (APX), and copper accumulation in the <i>E. canadensis</i> was determined to evaluate the phytotoxicity of the CuONPs and copper nitrate on <i>E. canadensis</i>. The significant improvements were observed in the growth rate of <i>E. canadensis</i>, chlorophyll a and b, carotenoid contents, and total soluble protein in the <i>E. canadensis</i> when it was exposed to the CuONPs. Additionally, CAT and APX activities and MDA contents were enhanced by accumulation of the CuONPs into the <i>E. canadensis</i>. These results suggested that oxidative stress was alleviated, owing to the result of an increase in the antioxidants such as CAT and APX, with an increase in the concentration of the CuONPs. Finally, the findings of this study show that copper nitrate has many negative effects on <i>E. canadensis</i> compared bio-synthesised CuONPs.
DOI: 10.6084/m9.figshare.6793784
title: Simple Measures of Individual Cluster-Membership Certainty for Hard Partitional Clustering

description: We propose two probability-like measures of individual cluster-membership certainty which can be applied to a hard partition of the sample such as that obtained from the Partitioning Around Medoids (PAM) algorithm, hierarchical clustering or k-means clustering. One measure extends the individual silhouette widths and the other is obtained directly from the pairwise dissimilarities in the sample. Unlike the classic silhouette, however, the measures behave like probabilities and can be used to investigate an individual's tendency to belong to a cluster. We also suggest two possible ways to evaluate the hard partition using these measures. We evaluate the performance of both measures in individuals with ambiguous cluster membership, using simulated binary datasets that have been partitioned by the PAM algorithm or continuous datasets that have been partitioned by hierarchical clustering and k-means clustering. For comparison, we also present results from soft-clustering algorithms such as soft analysis clustering (FANNY) and two model-based clustering methods. Our proposed measures perform comparably to the posterior-probability estimators from either FANNY or the model-based clustering methods. We also illustrate the proposed measures by applying them to Fisher's classic data set on irises.
DOI: 10.6084/m9.figshare.6793772
title: Novel miRNAs expressed in kidney

description: Novel miRNAs were sorted in accordance to total counts.
DOI: 10.6084/m9.figshare.6793772.v1
title: Novel miRNAs expressed in kidney

description: Novel miRNAs were sorted in accordance to total counts.
DOI: 10.6084/m9.figshare.6793769
title: miRNAs expressed in kidney

description: miRNAs were ranked in accordance to miRDeep2 average counts in nephron progenitors.
DOI: 10.6084/m9.figshare.6793769.v1
title: miRNAs expressed in kidney

description: miRNAs were ranked in accordance to miRDeep2 average counts in nephron progenitors.
DOI: 10.6084/m9.figshare.6793739
title: Prioritizing spatially aggregated cost-effective sites in natural reserves to mitigate human-induced threats

description: In this study, we illustrate a spatially explicit prioritization framework that integrates cost effectiveness analysis (CEA) and spatial clustering statistics to help stakeholders identify threat mitigation actions that are both spatially aggregated and cost-effective. This framework estimates expected biodiversity benefits in alternative sites, and evaluates associated costs using non-monetized proxy. We compared local autocorrelation-based clustering statistics, including local Moran’s <i>I</i>, Getis-Ord Gi*, and AMOEBA, to quantify the spatial aggregation of identified sites under given budgets. It is our finding that the CEA method produced more cost-effective threat mitigation sites, but these sites may be dispersed in space. Spatial clustering methods could identify spatially contiguous management sites with only minor loss in cost effectiveness. These spatially contiguous sites substantially contribute to reducing actual costs related to given biodiversity benefits. Integrating CEA with spatial clustering statistics provides stakeholders with solid support for prioritizing threat management actions that are both cost-effective and aggregated in space.
DOI: 10.6084/m9.figshare.6793739.v1
title: Prioritizing spatially aggregated cost-effective sites in natural reserves to mitigate human-induced threats

description: In this study, we illustrate a spatially explicit prioritization framework that integrates cost effectiveness analysis (CEA) and spatial clustering statistics to help stakeholders identify threat mitigation actions that are both spatially aggregated and cost-effective. This framework estimates expected biodiversity benefits in alternative sites, and evaluates associated costs using non-monetized proxy. We compared local autocorrelation-based clustering statistics, including local Moran’s <i>I</i>, Getis-Ord Gi*, and AMOEBA, to quantify the spatial aggregation of identified sites under given budgets. It is our finding that the CEA method produced more cost-effective threat mitigation sites, but these sites may be dispersed in space. Spatial clustering methods could identify spatially contiguous management sites with only minor loss in cost effectiveness. These spatially contiguous sites substantially contribute to reducing actual costs related to given biodiversity benefits. Integrating CEA with spatial clustering statistics provides stakeholders with solid support for prioritizing threat management actions that are both cost-effective and aggregated in space.
DOI: 10.6084/m9.figshare.6792347
title: Supplementary data set and R-code for "Using FishSim Animation Toolchain to investigate fish behavior: A case study on mate-choice copying in sailfin mollies" by Gierszewski, S., Baker, D., Müller, K., Hütwohl, J-M., Kuhnert, K-D., Witte, K. (2018)

description: Supplementary data set and R-code accompanying the article "Using <i>FishSim</i> Animation Toolchain to investigate fish behavior: A case study on mate-choice copying in sailfin mollies" by Gierszewski, S., Baker, D., Müller, K., Hütwohl, J-M., Kuhnert, K-D., Witte, K. (2018) in Journal of Visualized Experiments. e58435<br><br><br>
DOI: 10.6084/m9.figshare.6792191
title: Emerging patents in the therapeutic areas of glioma and glioblastoma

description: <b>Introduction</b>: Glioblastoma multiforme (GBM) is the most common and aggressive malignant glioma, with patients having a median survival of just over one year. Current chemotherapies, with surgery and radiotherapy, provide only minor patient benefit. There is a great need to discover and develop novel therapies for this devastating disease. <b>Areas covered</b>: The patent literature reveals novel therapies, providing insights into emerging GBM therapeutics. We have used the Google and USPTO patent databases to generate a detailed landscape of patents and patent applications from companies active in the areas of glioma and/or GBM. Specific patents have been grouped into six areas: novel compounds; treatments and therapeutic targets; combination therapies; immunotherapies; delivery methods; and biomarkers for diagnosis and prognosis. <b>Expert opinion</b>: There has been a steady increase in the number of patents on GBM over the last five years. Despite many new compounds being developed and patented for a broad range of cancers, only a small percentage of these are specifically targeted to GBM. Notable trends in the patent literature include both the development of combination therapies to combat the heterogeneous nature of GBM, and the use of immunotherapies building on the promise of cancer vaccines and CAR T-cell therapy.
DOI: 10.6084/m9.figshare.6792191.v1
title: Emerging patents in the therapeutic areas of glioma and glioblastoma

description: <b>Introduction</b>: Glioblastoma multiforme (GBM) is the most common and aggressive malignant glioma, with patients having a median survival of just over one year. Current chemotherapies, with surgery and radiotherapy, provide only minor patient benefit. There is a great need to discover and develop novel therapies for this devastating disease. <b>Areas covered</b>: The patent literature reveals novel therapies, providing insights into emerging GBM therapeutics. We have used the Google and USPTO patent databases to generate a detailed landscape of patents and patent applications from companies active in the areas of glioma and/or GBM. Specific patents have been grouped into six areas: novel compounds; treatments and therapeutic targets; combination therapies; immunotherapies; delivery methods; and biomarkers for diagnosis and prognosis. <b>Expert opinion</b>: There has been a steady increase in the number of patents on GBM over the last five years. Despite many new compounds being developed and patented for a broad range of cancers, only a small percentage of these are specifically targeted to GBM. Notable trends in the patent literature include both the development of combination therapies to combat the heterogeneous nature of GBM, and the use of immunotherapies building on the promise of cancer vaccines and CAR T-cell therapy.
DOI: 10.6084/m9.figshare.6792206.v1
title: Zipped data

description: The zipped data necessary to begin the workflow of "Predicting property damage from tornadoes with deep learning" by Jeremy Diaz and Maxwell Joseph (both at Earth Lab, Cooperative Institute for Research in Environmental Sciences, University of Colorado Boulder)
DOI: 10.6084/m9.figshare.6792206.v2
title: Tornado-predictive-modelling-data

description: The zipped data necessary to begin the workflow of "Predicting property damage from tornadoes with deep learning" by Jeremy Diaz and Maxwell Joseph (both at Earth Lab, Cooperative Institute for Research in Environmental Sciences, University of Colorado Boulder)
DOI: 10.6084/m9.figshare.6792206.v3
title: Data for "Predicting property damage from tornadoes with deep learning"

description: The zipped data necessary to begin the workflow of "Predicting property damage from tornadoes with deep learning" by Jeremy Diaz and Maxwell Joseph (both at Earth Lab, Cooperative Institute for Research in Environmental Sciences, University of Colorado Boulder)
DOI: 10.6084/m9.figshare.6792206
title: Data for "Predicting property damage from tornadoes with zero-inflated neural networks"

description: The zipped data necessary to replicate "Predicting property damage from tornadoes with zero-inflated neural networks" by Jeremy Diaz and Maxwell Joseph (both at Earth Lab, Cooperative Institute for Research in Environmental Sciences, University of Colorado Boulder). Contains our working versions of US Census Bureau, National Land Cover Database, and Storm Events Database data.
DOI: 10.6084/m9.figshare.6792098
title: Comparison of three-dimensional surface scanning techniques for capturing the external ear

description: Congenital facial anomalies, such as microtia (malformation of the external ear), lead to significant psychosocial effects starting from early childhood. Three-dimensional (3D) scanning and advanced manufacturing are being investigated as a cheaper and more personalised method of fabricating reconstructive treatments for patients compared to traditional approaches. To date, most case studies have used expensive 3D scanners, yet, there is potential for low-cost devices to provide comparable results. This study aimed to investigate these different approaches. Both ears of 16 adult participants were scanned with three devices: Artec Spider (Artec Group), Intel<sup>®</sup> RealSense™ (Intel), and the Apple iPhone<sup>®</sup> 7 (Apple Inc.) combined with photogrammetry using 90, 60 and 30 photographs. The scanning time, processing time, accuracy, completeness, resolution and repeatability of each technique were assessed using the Artec Spider as a reference scanner. Our results show that the iPhone had the longest processing time however, this decreased nine-fold when reducing the number of photos from 90 to 30. There was no significant difference in the accuracy, completeness or repeatability of the iPhone scans with 90 photographs (1.4 ± 0.6 mm, 79.9%, 1.0 ± 0.1 mm), 60 photographs (1.2 ± 0.2, 79.3%, 0.9 ± 0.2 mm) or 30 photographs (1.2 ± 0.3 mm, 74.3%, 1.0 ± 0.2 mm). The Intel RealSesne performed significantly worse in each parameter (1.8 ± 03 mm; 46.6%, 1.4 ± 0.5). Additionally, the RealSense had significantly lower resolution with not enough detail captured for the application. These results demonstrate that the ear can be accurately 3D scanned using iPhone photographs. We would recommend capturing between 30 and 60 photographs of the ear to create a scan that is accurate but without the downfall of long processing time. Using these methods we aim to provide a more comfortable setting for the patient and a lower-cost and more personalised ear prosthesis.
DOI: 10.6084/m9.figshare.6792098.v1
title: Comparison of three-dimensional surface scanning techniques for capturing the external ear

description: Congenital facial anomalies, such as microtia (malformation of the external ear), lead to significant psychosocial effects starting from early childhood. Three-dimensional (3D) scanning and advanced manufacturing are being investigated as a cheaper and more personalised method of fabricating reconstructive treatments for patients compared to traditional approaches. To date, most case studies have used expensive 3D scanners, yet, there is potential for low-cost devices to provide comparable results. This study aimed to investigate these different approaches. Both ears of 16 adult participants were scanned with three devices: Artec Spider (Artec Group), Intel<sup>®</sup> RealSense™ (Intel), and the Apple iPhone<sup>®</sup> 7 (Apple Inc.) combined with photogrammetry using 90, 60 and 30 photographs. The scanning time, processing time, accuracy, completeness, resolution and repeatability of each technique were assessed using the Artec Spider as a reference scanner. Our results show that the iPhone had the longest processing time however, this decreased nine-fold when reducing the number of photos from 90 to 30. There was no significant difference in the accuracy, completeness or repeatability of the iPhone scans with 90 photographs (1.4 ± 0.6 mm, 79.9%, 1.0 ± 0.1 mm), 60 photographs (1.2 ± 0.2, 79.3%, 0.9 ± 0.2 mm) or 30 photographs (1.2 ± 0.3 mm, 74.3%, 1.0 ± 0.2 mm). The Intel RealSesne performed significantly worse in each parameter (1.8 ± 03 mm; 46.6%, 1.4 ± 0.5). Additionally, the RealSense had significantly lower resolution with not enough detail captured for the application. These results demonstrate that the ear can be accurately 3D scanned using iPhone photographs. We would recommend capturing between 30 and 60 photographs of the ear to create a scan that is accurate but without the downfall of long processing time. Using these methods we aim to provide a more comfortable setting for the patient and a lower-cost and more personalised ear prosthesis.
DOI: 10.6084/m9.figshare.6792044
title: Supplementary Tables

description: Supplementary Tables<br> Supplementary Table 1 all sequence data produced <br> Supplementary Table 2 Protein coding gene data <br> Supplementary Table 3 AnGeLi results for the 620 genes whose knockouts are viable, but have mean HMM state = 1 <br> Supplementary Table 4 linkers and primers design <br> Supplementary Table 5. European Nucleotide Archive (ENA) Acessions The study accession number is: PRJEB27324 <br>