cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.4452055
title: Measurement report: quantifying source contribution of fossil fuels and biomass-burning black carbon aerosol in the southeastern margin of the Tibetan Plateau

description: Anthropogenic emissions of Black carbon (BC) aerosol are transported from Southeast Asia to the southwestern Tibetan Plateau (TP) during the pre-monsoon; however, the quantities of BC from different anthropogenic sources and the transport mechanisms are still not well constrained because there have been no high-time-resolution BC source apportionments. Intensive measurements were taken in a transport channel for pollutants from Southeast Asia to the southeastern margin of TP during the pre-monsoon to investigate the influences of fossil fuels and biomass burning on BC. A receptor model coupled multi-wavelength absorption with aerosol species concentrations was used to retrieve site-specific Ångström exponents (AAE) and mass absorption cross-sections (MAC) for BC. An ‘aethalometer model’ that used those values showed that biomass burning had a larger contribution to BC mass than fossil fuels (BCbiomass = 57% versus BCfossil = 43%). The potential source contribution function indicated that BCbiomass was transported to the site from northeastern India and northern Burma, The Weather Research and Forecasting model coupled with chemistry (WRF-Chem) model indicated that 40% of BCbiomass originated from Southeast Asia, while the high BCfossil was transported from the southwest of sampling site. A radiative transfer model indicated that the average atmospheric direct radiative effects (DRE) of BC was +4.6 ± 2.4 W m<sup>-2</sup> with +2.5 ± 1.8 W m<sup>-2</sup> from BCbiomass and +2.1 ± 0.9 W m<sup>-2</sup> from BCfossil. The DRE of BCbiomass and BCfossil produced heating rates of 0.07 ± 0.05 and 0.06 ± 0.02 K day<sup>-1</sup>, respectively. This study provides insights into sources of BC over a transport channel to the southeastern TP and the influence of the cross-border transportation of biomass burning emissions from Southeast Asia during the pre-monsoon.
DOI: 10.6084/m9.figshare.13614200
title: Supplementary Material for: The Eya1 Phosphatase Mediates Shh-Driven Symmetric Cell Division of Cerebellar Granule Cell Precursors

description: During neural development, stem and precursor cells can divide either symmetrically or asymmetrically. The transition between symmetric and asymmetric cell divisions is a major determinant of precursor cell expansion and neural differentiation, but the underlying mechanisms that regulate this transition are not well understood. Here, we identify the Sonic hedgehog (Shh) pathway as a critical determinant regulating the mode of division of cerebellar granule cell precursors (GCPs). Using partial gain and loss of function mutations within the Shh pathway, we show that pathway activation determines spindle orientation of GCPs, and that mitotic spindle orientation correlates with the mode of division. Mechanistically, we show that the phosphatase Eya1 is essential for implementing Shh-dependent GCP spindle orientation. We identify atypical protein kinase C (aPKC) as a direct target of Eya1 activity and show that Eya1 dephosphorylates a critical threonine (T410) in the activation loop. Thus, Eya1 inactivates aPKC, resulting in reduced phosphorylation of Numb and other components that regulate the mode of division. This Eya1-dependent cascade is critical in linking spindle orientation, cell cycle exit and terminal differentiation. Together these findings demonstrate that a Shh-Eya1 regulatory axis selectively promotes symmetric cell divisions during cerebellar development by coordinating spindle orientation and cell fate determinants.
DOI: 10.6084/m9.figshare.13614200.v1
title: Supplementary Material for: The Eya1 Phosphatase Mediates Shh-Driven Symmetric Cell Division of Cerebellar Granule Cell Precursors

description: During neural development, stem and precursor cells can divide either symmetrically or asymmetrically. The transition between symmetric and asymmetric cell divisions is a major determinant of precursor cell expansion and neural differentiation, but the underlying mechanisms that regulate this transition are not well understood. Here, we identify the Sonic hedgehog (Shh) pathway as a critical determinant regulating the mode of division of cerebellar granule cell precursors (GCPs). Using partial gain and loss of function mutations within the Shh pathway, we show that pathway activation determines spindle orientation of GCPs, and that mitotic spindle orientation correlates with the mode of division. Mechanistically, we show that the phosphatase Eya1 is essential for implementing Shh-dependent GCP spindle orientation. We identify atypical protein kinase C (aPKC) as a direct target of Eya1 activity and show that Eya1 dephosphorylates a critical threonine (T410) in the activation loop. Thus, Eya1 inactivates aPKC, resulting in reduced phosphorylation of Numb and other components that regulate the mode of division. This Eya1-dependent cascade is critical in linking spindle orientation, cell cycle exit and terminal differentiation. Together these findings demonstrate that a Shh-Eya1 regulatory axis selectively promotes symmetric cell divisions during cerebellar development by coordinating spindle orientation and cell fate determinants.
DOI: 10.6084/m9.figshare.13614263
title: Supplementary Material for: Observed and Modeled Positive Predictive Values Using Cell-free DNA Testing for Fetal Trisomy in a Clinical Laboratory Population

description: <b><i>Introduction:</i></b> The objective of this study was to explore different approaches to communicating the positive predictive value (PPV) of cell-free DNA screening for fetal trisomy. <b><i>Methods:</i></b> PPV was established for 4 maternal age-groups (&lt;30, 30–34, 35–39, and &gt;39 years) from clinical laboratory data and compared to the modeled PPV from an online calculator. In women under 35, PPV was compared between 2 subsets, high risk and low risk, classified based on the diagnosis codes that were provided to the laboratory. <b><i>Results:</i></b> In 503 high-probability trisomy 21 results, the observed PPVs in the 4 age-groups were 97.0% (&lt;30), 98.9% (30–34), 99.5% (35–39), and 96.3% (&gt;39), all higher than those from the calculator, which ranged from 53 to 95%. Likewise, PPVs were 77.4–97.0% observed versus 16–78% modeled in 131 trisomy 18 cases and 30.4–80.0% observed versus 6–61% modeled in 80 trisomy 13 cases. In women under 35, PPV for the trisomies combined was 90.4% in the higher-risk group compared to 79.7% in the lower-risk group. <b><i>Conclusion:</i></b> Modeling PPV based on maternal age will provide an underestimate in a clinical population. Although the PPV is higher for the samples with higher-risk diagnosis codes, the information that accompanies clinical samples is too general to model PPV for a specific patient.
DOI: 10.6084/m9.figshare.13614377
title: Ovarian data used in CHETAH paper

description: This is the ovarian data set used in the CHETAH paper:<br> Kanter, Jurrian K. de, Philip Lijnzaad, Tito Candelli, Thanasis Margaritis, and Frank C. P. Holstege. “CHETAH: A Selective, Hierarchical Cell Type Identification Method for Single-Cell RNA Sequencing.” <i>Nucleic Acids Research</i>. Accessed July 1, 2019. https://doi.org/10.1093/nar/gkz543 <br>it was described in Schelker, Max, Sonia Feau, Jinyan Du, Nav Ranu, Edda Klipp, Gavin MacBeath, Birgit Schoeberl, and Andreas Raue. “Estimation of Immune Cell Content in Tumour Tissue Using Single-Cell RNA-Seq Data.” <i>Nature Communications</i> 8, no. 1 (December 11, 2017): 2032. https://doi.org/10.1038/s41467-017-02289-3<br>(but no longer available in figshare). <br>The Seurat 3 SingleCellExperiment format, consisting of <br> 25462 genes x 3114 cells of types with meta.data 'celltypes' distributed as<br> Unknown 125 CD4 T cell 323 CD8 T cell 31 reg. T cell 1 B cell 18 Macrophage 2057 Dendritic 114 NK 109 CAF 36 Tumor 300<br>For the other data in the CHETAH paper see https://figshare.com/s/aaf026376912366f81b6<br><br>
DOI: 10.6084/m9.figshare.13614377.v1
title: Ovarian data used in CHETAH paper

description: This is the ovarian data set used in the CHETAH paper:<br> Kanter, Jurrian K. de, Philip Lijnzaad, Tito Candelli, Thanasis Margaritis, and Frank C. P. Holstege. “CHETAH: A Selective, Hierarchical Cell Type Identification Method for Single-Cell RNA Sequencing.” <i>Nucleic Acids Research</i>. Accessed July 1, 2019. https://doi.org/10.1093/nar/gkz543 <br>it was described in Schelker, Max, Sonia Feau, Jinyan Du, Nav Ranu, Edda Klipp, Gavin MacBeath, Birgit Schoeberl, and Andreas Raue. “Estimation of Immune Cell Content in Tumour Tissue Using Single-Cell RNA-Seq Data.” <i>Nature Communications</i> 8, no. 1 (December 11, 2017): 2032. https://doi.org/10.1038/s41467-017-02289-3<br>(but no longer available in figshare). <br>The Seurat 3 SingleCellExperiment format, consisting of <br> 25462 genes x 3114 cells of types with meta.data 'celltypes' distributed as<br> Unknown 125 CD4 T cell 323 CD8 T cell 31 reg. T cell 1 B cell 18 Macrophage 2057 Dendritic 114 NK 109 CAF 36 Tumor 300<br>For the other data in the CHETAH paper see https://figshare.com/s/aaf026376912366f81b6<br><br>
DOI: 10.5281/zenodo.4452124
title: Supplementary Material and Code of Evidence for immunity to SARS-CoV-2 from epidemiological data series

description: This Supplementary Material file, Code and Data correspond to the manuscript: Evidence for immunity to SARS-CoV-2 from epidemiological data series<br> Pablo Yubero, Alvar A. Lavin, Juan F Poyatos<br> medRxiv 2020.07.22.20160028; doi: https://doi.org/10.1101/2020.07.22.20160028
DOI: 10.5281/zenodo.4452123
title: Supplementary Material and Code of Evidence for immunity to SARS-CoV-2 from epidemiological data series

description: This Supplementary Material file, Code and Data correspond to the manuscript: Evidence for immunity to SARS-CoV-2 from epidemiological data series<br> Pablo Yubero, Alvar A. Lavin, Juan F Poyatos<br> medRxiv 2020.07.22.20160028; doi: https://doi.org/10.1101/2020.07.22.20160028
DOI: 10.17632/jzfknp7sjv.1
title: Data for: The development of stationary battery storage systems in Germany – Status 2020

description: The Forschungszentrum Jülich (FZJ IEK-3) has been collecting the data of large-scale battery storage systems (LSS) in Germany since 2012. It contains location, installed capacity, installed power, investment, battery technology, commissioning date, operational status, area of application, and further information on the different LSS projects. We conducted our research through the evaluation of many press releases, prequalification results for ancillary services and bilateral contact to project planners and owners. The database is constantly updated. It contains both realized and planned BSS. The database is not exhaustive, as not all realized projects have publicly available information that can be included in it. Furthermore, storage systems outside of Germany, which are operating at least partly on the German market, are not included in the database. The project-specific sources are also included in the database to make the extended search for any information easier. The database was published together with our paper "The Development of Stationary Battery Storage Systems in Germany – Status 2020". The database provides an update to the database (http://dx.doi.org/10.17632/2rjg6v32d8.1) which was published together with our paper "The Development of Stationary Battery Storage Systems in Germany – A Market Review".
DOI: 10.6084/m9.figshare.13614512.v1
title: Ten-m::YFP_YFP670smFISH_γ5β′2aMBONsomata

description: Ten-m::YFP YFP smFISH in γ5β′2a MBON somata
DOI: 10.6084/m9.figshare.13614512
title: Ten-m::YFP_YFP670smFISH_γ5β′2aMBONsomata

description: Ten-m::YFP YFP smFISH in γ5β′2a MBON somata
DOI: 10.6084/m9.figshare.13614515.v1
title: PKA-R2::YFP_YFP670smFISH_γ5β′2aMBONsomata

description: PKA-R2::YFP smFISH in γ5β′2a MBON somata
DOI: 10.6084/m9.figshare.13614515
title: PKA-R2::YFP_YFP670smFISH_γ5β′2aMBONsomata

description: PKA-R2::YFP smFISH in γ5β′2a MBON somata
DOI: 10.6084/m9.figshare.13614449
title: Table S1 - SDCBP paper.xlsx

description: Clinical and pathological characteristics of the 382 HNSCC patients analyzed by IHC.
DOI: 10.6084/m9.figshare.13614449.v1
title: Table S1 - SDCBP paper.xlsx

description: Clinical and pathological characteristics of the 382 HNSCC patients analyzed by IHC.
DOI: 10.15468/m9yk8e
title: A new species of Sarcophaga Meigen subgenus Hoa Rohdendorf (Diptera Sarcophagidae)

description: This dataset contains the digitized treatments in Plazi based on the original journal article Wang, Chao, Xue, Wan-Qi, Zhang, Dong, Pape, Thomas (2020): A new species of Sarcophaga Meigen subgenus Hoa Rohdendorf (Diptera Sarcophagidae). Zootaxa 4821 (3): 585-593, DOI: https://doi.org/10.11646/zootaxa.4821.3.9
DOI: 10.6084/m9.figshare.13072211
title: Forest.csv

description: Forest data in natural areas worldwide
DOI: 10.6084/m9.figshare.13614560.v1
title: PKA-R2::YFP_YFP670smFISH_γ1-pedcMBONsomata

description: PKA-R2::YFP smFISH in γ1-pedc MBON somata
DOI: 10.6084/m9.figshare.13614560
title: PKA-R2::YFP_YFP670smFISH_γ1-pedcMBONsomata

description: PKA-R2::YFP smFISH in γ1-pedc MBON somata
DOI: 10.17037/data.00000080
title: Identification and characterisation of bacterial TIR domains, with particular focus on yersinia pestis: Study Data

description: The TolllIL-l Receptor (TIR) domain is an essential signalling module in eukaryotic innate immune signalling pathways. Homotypic interaction between TIR domains allows the formation of a signalling platform in which molecules are able to interact and activate each other to initiate an immune signalling cascade. Proteins containing TIR domains have also been discovered in bacteria. Studies have subsequently shown that these proteins are able to modulate mammalian immune signalling pathways dependent on TIR interactions and that this forms an evasion strategy for bacterial pathogens. In this study a bioinformatic search for proteins containing TIR domains was carried out across unicellular organisms, including bacteria. TIR domain proteins (Tdps) from highly pathogenic bacteria were down-selected for investigation. After an initial screen of their activity, a Tdp from Yersinia pestis, the causative agent of plague, was down-selected for further investigation. The bioinformatic analysis found a high representation of Tdps in bacteria generally classified as non-pathogens, and that TIR domains are promiscuous in their co-occurrence with other domains. This analysis also showed that they are not necessarily conserved between strains and species. These findings question the universal role of Tdps in the pathogenic evasion of a host immune response and suggest they may have other functions. Initial screening of down-selected Tdps showed that they were able to modulate immune signalling pathways in vitro, but studies with a Tdp-deficient mutant of Y. pestis did not demonstrate a role for this protein in the virulence of Y. pestis in a mouse model. However, this Tdp-deficient mutant did display two characteristics in vitro: an increased autoaggregation phenotype when compared to wild-type Y. pestis and an inability to survive as well as wild-type bacteria in conditions of high salinity. These fmdings indicate that TIR domain proteins may have other roles in bacterial physiology unrelated to immune evasion.
DOI: 10.15468/qsw6tc
title: Syllidae (Annelida) from East Timor and the Philippines (Pacific Ocean), with the description of three new species of Syllis Savigny in Lamarck, 1818

description: This dataset contains the digitized treatments in Plazi based on the original journal article Martínez, María José, Martín, Guillermo San (2020): Syllidae (Annelida) from East Timor and the Philippines (Pacific Ocean), with the description of three new species of Syllis Savigny in Lamarck, 1818. Zootaxa 4834 (2): 231-263, DOI: https://doi.org/10.11646/zootaxa.4834.2.5
DOI: 10.1285/i15910725v42p3
title: First substantiated record of Cotton Mouth jack Uraspis secunda (Carangidae) from the coast of Senegal (E-Atlantic)

description: A specimen of Cottonmouth jack Uraspis secunda (Poey, 1860) was recorded for the first time from the coast of Senegal. The specimen was immature measuring 118 mm for total length and 19.2 g for total body weight. In this note, the authors present a short description of one specimen and its main morphometric measurements and meristic characters. The distribution of U. secunda in its new area of capture is commented and discussed, together with its close relative species U. helvola (Forster, 1801).
DOI: 10.6084/m9.figshare.13599608.v1
title: BANG_GENOME.fasta

description: genome of aus rice
DOI: 10.6084/m9.figshare.13599608
title: BANG_GENOME.fasta

description: genome of aus rice
DOI: 10.6084/m9.figshare.13599935
title: repeat.zip

description: repeat annotation of banglami genome
DOI: 10.6084/m9.figshare.13599887.v1
title: banglami_gene_ annotation.zip

description: gene annotation of banglami genome
DOI: 10.6084/m9.figshare.13599935.v1
title: repeat.zip

description: repeat annotation of banglami genome
DOI: 10.6084/m9.figshare.13599887
title: banglami_gene_ annotation.zip

description: gene annotation of banglami genome
DOI: 10.15468/et2jkh
title: Description of two new Australian species of Abantiades Herrich-Schäffer (Lepidoptera: Hepialidae) and females of two further species with notes on their biogeography

description: This dataset contains the digitized treatments in Plazi based on the original journal article Moore, Michael D., Beaver, Ethan P., Velasco-Castrillón, Alejandro, Stevens, Mark I. (2020): Description of two new Australian species of Abantiades Herrich-Schäffer (Lepidoptera: Hepialidae) and females of two further species with notes on their biogeography. Zootaxa 4822 (1): 71-93, DOI: https://doi.org/10.11646/zootaxa.4822.1.3
DOI: 10.1285/i15910725v42p41
title: An unusually patterned Italian tree frog Hyla intermedia from Salento Peninsula, southern Italy (Amphibia: Hylidae)

description: Hyla intermedia is an endemic Italian tree frog species, distributed from the southern edge of the Alpine massif to the tip of Calabria and into Sicily. Previously referred as the widespread Hyla arborea, it has only recently been recognized as a distinct species. It shows a bright, uniformly green dorsal coloration. We report a previously unknown colour variant, displayed by an individual collected in Salento Peninsula. It differs from the typical form by its dark olive-brown background color with a contrasting marbled pattern on its dorsal and lateral surfaces. Similarly to typical individuals, this specimen was able to lighten its background color under the effect of stress, but its unusual marbled pattern was permanent. Marbled patterns are also known in other Hyla species, but were not so far recorded in H. intermedia.
DOI: 10.6084/m9.figshare.13614572
title: Table S1. Fluid flow and syntectonic veining in an Ediacaran foreland fold-thrust zone, western margin of the São Francisco Craton, Brazil

description: Table S1: Table showing the analyzed samples and their respective tectonic unit and analysis performed
DOI: 10.6084/m9.figshare.13614572.v1
title: Table S1. Fluid flow and syntectonic veining in an Ediacaran foreland fold-thrust zone, western margin of the São Francisco Craton, Brazil

description: Table S1: Table showing the analyzed samples and their respective tectonic unit and analysis performed
DOI: 10.6084/m9.figshare.13614569
title: Table S3. Fluid flow and syntectonic veining in an Ediacaran foreland fold-thrust zone, western margin of the São Francisco Craton, Brazil

description: Table S3: Result of fluid inclusion analysis
DOI: 10.6084/m9.figshare.13614569.v1
title: Table S3. Fluid flow and syntectonic veining in an Ediacaran foreland fold-thrust zone, western margin of the São Francisco Craton, Brazil

description: Table S3: Result of fluid inclusion analysis
DOI: 10.6084/m9.figshare.13614575
title: Table S2. Fluid flow and syntectonic veining in an Ediacaran foreland fold-thrust zone, western margin of the São Francisco Craton, Brazil

description: Table S2: Major elements of the samples analyzed by X-ray Fluorescence. Values in percentage
DOI: 10.6084/m9.figshare.13614575.v1
title: Table S2. Fluid flow and syntectonic veining in an Ediacaran foreland fold-thrust zone, western margin of the São Francisco Craton, Brazil

description: Table S2: Major elements of the samples analyzed by X-ray Fluorescence. Values in percentage
DOI: 10.1285/i15910725v42p59
title: Cases of anomalies in the goldfish Carassius auratus collected from the southern marshes of Iraq

description: Six morphological deformities were observed and examined in 6 specimens of the goldfish Carassius auratus collected from the southern marshes of Iraq, Basrah. These anomalies include: eye abnormalities (exophthalmos and enophthalmos), mouth deformity (dextral twisted mouth), ankylosis (fusion of vertebrae), lordosis (ventral curvature), pudgheadness (deformation of the front head bones) and scoliosis (lateral curvature). All cases were not fatal as they occurred in adult individuals. The paper discusses the possible causes for such deformities as well as the suitability of this kind of study for environmental monitoring.
DOI: 10.1285/i15910725v42p75
title: Fixation, preservation and freezing effects on morphometrics of two fish species collected from Lake Ganvié, Benin, West Africa

description: The goal of this study was to evaluate the impacts of various preservation methods on disparities in morphometric parameters while also providing correction factors to re-calculate the original body dimensions when sampled fish are measured at a future date. In this study, adult samples of O. niloticus and C. gariepinus collected from the waters of the Republic of Benin, West Africa was measured directly after capture, then either frozen, preserved in 70% ethanol, or in 10% formalin. Ethanol and formalin solutions were prepared using tap and distilled waters. They were again measured after one week of the initial measurement and thereafter on a weekly basis for 20 weeks. Formalin and ethanol solutions showed to cause a decrease in the three morphometric characters, total, standard and head lengths. In contrast, frozen O. niloticus and C. gariepinus showed less shrinkage. Of the three preservation procedures, freezing obviously produced the least distortions. Therefore, freezing is recommended as the most desirable preservation method, particularly in multi-disciplinary studies on fish ecology. Equations to correct the effect of fixation, preservation and freezing on fish size are provided so they will assist in the future ecological and physiological studies to pool field and laboratory data.
DOI: 10.1285/i15910725v42p83
title: Two new fish with maximum size records from the Eastern coasts of Saudi Arabia

description: During the study of the health of the fish species in the vicinity of Jubail City, Saudi Arabia, 3 specimens of Diplodus cervinus omanensis and 3 specimens of Acanthopagrus catenula were collected by fishermen using 30 x 10 m drifting gill nets of 25 mm mesh size and handed over to Ministry of Agriculture officials through their twice a week visits to fish landing areas and fish markets in Jubail. Diplodus cervinus omanensis (Oman porgy) and Acanthopagrus catenula (bridled seabream) represent new records for the Eastern coasts of the Arabian Peninsula and Saudi Arabian waters. Specimens of A. catenula were previously reported from the Iraqi marine waters, therefore, this is the 2nd appearance for this species in this part of the world. This study verifies parts of the diversity of the coastal fish communities of the eastern coasts of the Saudi Arabian waters, but also highlights that a large proportion of this area (the norther Arabian coast) has not been explored.