cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.20456625
title: Data.xlsx

description: We determined SOC, its fraction content and soil aggregates with three vegetation restoration practices to determine the effects of vegetation restoration on SOC stability and driving mechanisms. The K2CrO7-H2SO4 oxidation and titration using FeSO4 was used for SOC analysis (Bao, 2000). The soil samples were sieved and digested using potassium dichromate and concentrated sulfuric acid. After digestion, carbon content was measured by titration. The acid hydrolysis used for ROC analysis (Rovira et al., 2002). The samples were digestd with hydrochloric acid and washed with distilled water until hydrochloric acid was free. After drying, the carbon content was measured by potassium dichromate oxidation and external heating method. Easily oxidizable carbon (EOC) was extracted with KMnO4 then measured using the method of oxidation (Loginow et al., 1987). Soil samples were oxidized with KMnO4 for 1 h and diluted with distilled water for colorimetry. Carbon content was calculated according to KMnO4 consumption. DOC was extracted from fresh soil with deionized water (Alburquerque et al., 2014). Samples were shaken in high pure water for 1 h, and then filtered by filtration membrane. The carbon content in the filtrate was determined by total organic carbon analyzer (Elementar, Germeany). MBC was extracted using the chloroform (CHCl3) fumigation-incubation method (Qiang et al., 2004). Fresh samples were fumigated with CHCl3 for 24h, and the fresh samples were taken as control. The fumigated and fresh samples were extracted with K2SO4, shaken for 1 h, and calculated from the difference in carbon content and conversion coefficient measured between fumigated and control samples. Soil aggregates was analysed by particle size analysis approach. Following Six et al (2002b), the sieves of a vibrating sieving instrument were placed in a bucket in the order of 0.25 and 0.053 mm from top to bottom. Air-dried soil was then placed on the top sieve layer after removing the plant residues and small stones. Then the laster particle size analyzer (Ke Jing BT-9300ST) was turned on for particle size analysis and aggregates were weighed and recorded. Soil aggregates were divided into macroaggregate (&gt; 0.25 mm), microaggregate (0.25 - 0.053 mm) and unaggregated silt + clay (&lt; 0.053 mm). SOC contents of the aggregate fractions soil were determined using the method of KMnO4 oxidation (Loginow et al., 1987). SOC component allocation ratio can reflect SOC conversion efficiency and indirectly characterize SOC stability. SOC component distribution proportion (ROC/SOC, EOC/SOC, DOC/SOC and MBC/SOC) was calculated as follows (Blair et al., 2000) ： (1) The proportion of aggregates associated SOC in total SOC is also known as the contribution rate of aggregates associated SOC to total SOC. The soil aggregates associated SOC contribution rate was calculated as follows (Li et al., 2014): (2) Where, aggregates associated SOC content of aggregates with different particle sizes.
DOI: 10.6084/m9.figshare.20456625.v1
title: Data.xlsx

description: We determined SOC, its fraction content and soil aggregates with three vegetation restoration practices to determine the effects of vegetation restoration on SOC stability and driving mechanisms. The K2CrO7-H2SO4 oxidation and titration using FeSO4 was used for SOC analysis (Bao, 2000). The soil samples were sieved and digested using potassium dichromate and concentrated sulfuric acid. After digestion, carbon content was measured by titration. The acid hydrolysis used for ROC analysis (Rovira et al., 2002). The samples were digestd with hydrochloric acid and washed with distilled water until hydrochloric acid was free. After drying, the carbon content was measured by potassium dichromate oxidation and external heating method. Easily oxidizable carbon (EOC) was extracted with KMnO4 then measured using the method of oxidation (Loginow et al., 1987). Soil samples were oxidized with KMnO4 for 1 h and diluted with distilled water for colorimetry. Carbon content was calculated according to KMnO4 consumption. DOC was extracted from fresh soil with deionized water (Alburquerque et al., 2014). Samples were shaken in high pure water for 1 h, and then filtered by filtration membrane. The carbon content in the filtrate was determined by total organic carbon analyzer (Elementar, Germeany). MBC was extracted using the chloroform (CHCl3) fumigation-incubation method (Qiang et al., 2004). Fresh samples were fumigated with CHCl3 for 24h, and the fresh samples were taken as control. The fumigated and fresh samples were extracted with K2SO4, shaken for 1 h, and calculated from the difference in carbon content and conversion coefficient measured between fumigated and control samples. Soil aggregates was analysed by particle size analysis approach. Following Six et al (2002b), the sieves of a vibrating sieving instrument were placed in a bucket in the order of 0.25 and 0.053 mm from top to bottom. Air-dried soil was then placed on the top sieve layer after removing the plant residues and small stones. Then the laster particle size analyzer (Ke Jing BT-9300ST) was turned on for particle size analysis and aggregates were weighed and recorded. Soil aggregates were divided into macroaggregate (&gt; 0.25 mm), microaggregate (0.25 - 0.053 mm) and unaggregated silt + clay (&lt; 0.053 mm). SOC contents of the aggregate fractions soil were determined using the method of KMnO4 oxidation (Loginow et al., 1987). SOC component allocation ratio can reflect SOC conversion efficiency and indirectly characterize SOC stability. SOC component distribution proportion (ROC/SOC, EOC/SOC, DOC/SOC and MBC/SOC) was calculated as follows (Blair et al., 2000) ： (1) The proportion of aggregates associated SOC in total SOC is also known as the contribution rate of aggregates associated SOC to total SOC. The soil aggregates associated SOC contribution rate was calculated as follows (Li et al., 2014): (2) Where, aggregates associated SOC content of aggregates with different particle sizes.
DOI: 10.34848/ot5aad/yatxkt
title: Nube de palabras.PNG

description: Palabras clave del autor más recurrentes en los documentos
DOI: 10.34848/ot5aad/1t0g3l
title: Relación entre paises.png

description: Relaciones entre países de los estudios descritos
DOI: 10.34848/ot5aad/3xbdgp
title: Tags sin países.png

description: Tags o etiquetas agregadas a cada documento, determinadas desde el proyecto
DOI: 10.34848/ot5aad/ytue96
title: Relación entre paises x tiempo.png

description: Mapa de evolución de términos por año y relación entre ellos
DOI: 10.34848/ot5aad/gvcs5d
title: Nube de palabras Nvivo.png

description: Palabras clave del autor más recurrentes en los documentos
DOI: 10.34848/ot5aad/rngfn7
title: Concurrencias palabras.png

description: Relación entre palabras claves de los documentos
DOI: 10.5281/zenodo.6976950
title: datasets for USEARCH SINTAX classifier used in dix-seq

description: <strong>1. datasets</strong> The datasets include : rdp_16s_v18_sp, PR2_4.14 and unite_10.05.2021 <strong>2. USERACH formatdb</strong> ../binaries/usearch -makeudb_usearch rdp_16s_v18_sp.fasta -output rdp_16s_v18_sp.udb<br> ../binaries/usearch -makeudb_usearch PR2_4.14.fasta -output PR2_4.14.udb<br> ../binaries/usearch -makeudb_usearch unite_10.05.2021.fasta -output unite_10.05.2021.udb<br> <strong>3. Preprint</strong> Dix-seq: An integrated pipeline for fast amplicon data analysis Yongjun wei, Tianqi Ren, Lei Zhang bioRxiv 2020.05.11.089748; doi: https://doi.org/10.1101/2020.05.11.089748
DOI: 10.5281/zenodo.6976949
title: datasets for USEARCH SINTAX classifier used in dix-seq

description: <strong>1. datasets</strong> The datasets include : rdp_16s_v18_sp, PR2_4.14 and unite_10.05.2021 <strong>2. USERACH formatdb</strong> ../binaries/usearch -makeudb_usearch rdp_16s_v18_sp.fasta -output rdp_16s_v18_sp.udb<br> ../binaries/usearch -makeudb_usearch PR2_4.14.fasta -output PR2_4.14.udb<br> ../binaries/usearch -makeudb_usearch unite_10.05.2021.fasta -output unite_10.05.2021.udb<br> <strong>3. Preprint</strong> Dix-seq: An integrated pipeline for fast amplicon data analysis Yongjun wei, Tianqi Ren, Lei Zhang bioRxiv 2020.05.11.089748; doi: https://doi.org/10.1101/2020.05.11.089748
DOI: 10.25678/0006y0
title: Data for: Interaction-dependent effects of surface structure on microbial spatial self-organization

description: Surface-attached microbial communities consist of different cell types that, at least to some degree, organize themselves non-randomly across space (referred to as spatial self-organization). While spatial self-organization can have important effects on the functioning, ecology and evolution of communities, the underlying determinants of spatial self-organization remain unclear. Here, we hypothesize that the presence of physical objects across a surface can have important effects on spatial self-organization. Using pairs of isogenic strains of Pseudomonas stutzeri, we performed range expansion experiments in the absence or presence of physical objects and quantified the effects on spatial self-organization. We demonstrate that physical objects create local deformities along the expansion frontier, and these deformities increase in magnitude during range expansion. The deformities affect the densities of interspecific boundaries and diversity along the expansion frontier, and thus affect spatial self-organization, but the effects are interaction-dependent. For competitive interactions that promote sectorized patterns of spatial self-organization, physical objects increase the density of interspecific boundaries and diversity. By contrast, for cross-feeding interactions that promote dendritic patterns, they decrease the density of interspecific boundaries and diversity. These qualitatively different outcomes are probably caused by fundamental differences in the orientations of the interspecific boundaries. Thus, in order to predict the effects of physical objects on spatial self-organization, information is needed regarding the interactions present within a community and the general geometric shapes of spatial self-organization that emerge from those interactions. This article is part of the theme issue 'Conceptual challenges in microbial community ecology'.
DOI: 10.5281/zenodo.6976470
title: ObjectJ files for Quantification of ejaculate transfer and removal

description: Dataset accompanying manuscript "Evolution and co-evolution of the suck behaviour, a postcopulatory female resistance trait that manipulates received ejaculate" . These are the ObjectJ files that were used for quantification of ejaculate transfer and removal in <em>Macrostomum hamatum</em>, described in the manuscript.
DOI: 10.5281/zenodo.6976469
title: ObjectJ files for Quantification of ejaculate transfer and removal

description: Dataset accompanying manuscript "Evolution and co-evolution of the suck behaviour, a postcopulatory female resistance trait that manipulates received ejaculate" . These are the ObjectJ files that were used for quantification of ejaculate transfer and removal in <em>Macrostomum hamatum</em>, described in the manuscript.
DOI: 10.5517/ccdc.csd.cc29y1p0
title: CCDC 2143082: Experimental Crystal Structure Determination

description: Related Article: Murat Çınarlı|2022|J.Mol.Struct.|1269|133779|doi:10.1016/j.molstruc.2022.133779
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2byvv0
title: CCDC 2173653: Experimental Crystal Structure Determination

description: Related Article: Shariq Yousuf, Farukh Arjmand, Claudio Pettinari, Sartaj Tabassum|2022|Inorg.Chim.Acta|542|121105|doi:10.1016/j.ica.2022.121105
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2c06tf
title: CCDC 2174954: Experimental Crystal Structure Determination

description: Related Article: Hua-Rui Wang, Xu-Ke Tian, Ji-Rui Zhang, Meng-Yao Wen, Xiao-Gang Yang|2022|Dalton Trans.|51|11231|doi:10.1039/D2DT01649D
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2c2spy
title: CCDC 2177430: Experimental Crystal Structure Determination

description: Related Article: S.K. Mohamed, J.T. Mague, M. Akkurt, A.M. Alfayomy, S.M.A. Seri, S.A.A. Abdel-Raheem, M.A.A. Ul-Malik|2022|Acta Crystallogr.,Sect.E:Cryst.Commun.|78|846|doi:10.1107/S205698902200603X
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2cjwph
title: CCDC 2190977: Experimental Crystal Structure Determination

description: Related Article: F.N. Naghiyev, V.N. Khrustalev, N.U. Venskovsky, T.A. Tereshina, A.N. Khalilov, M. Akkurt, A. Bhattarai, İ.G. Mamedov|2022|Acta Crystallogr.,Sect.E:Cryst.Commun.|78|833|doi:10.1107/S2056989022007356
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2cjwqj
title: CCDC 2190978: Experimental Crystal Structure Determination

description: Related Article: F.N. Naghiyev, V.N. Khrustalev, N.U. Venskovsky, T.A. Tereshina, A.N. Khalilov, M. Akkurt, A. Bhattarai, İ.G. Mamedov|2022|Acta Crystallogr.,Sect.E:Cryst.Commun.|78|833|doi:10.1107/S2056989022007356
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2ck5gl
title: CCDC 2191249: Experimental Crystal Structure Determination

description: Related Article: M. Stapf, U. Schmidt, W. Seichter, M. Mazik|2022|Acta Crystallogr.,Sect.E:Cryst.Commun.|78|825|doi:10.1107/S2056989022007411
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2ckmp8
title: CCDC 2191690: Experimental Crystal Structure Determination

description: Related Article: H.J. Shankara Prasad, Devaraju, Vinaya, H.S. Yathirajan, S.R. Parkin, C. Glidewell|2022|Acta Crystallogr.,Sect.E:Cryst.Commun.|78|840|doi:10.1107/S2056989022007472
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2ckmq9
title: CCDC 2191691: Experimental Crystal Structure Determination

description: Related Article: H.J. Shankara Prasad, Devaraju, Vinaya, H.S. Yathirajan, S.R. Parkin, C. Glidewell|2022|Acta Crystallogr.,Sect.E:Cryst.Commun.|78|840|doi:10.1107/S2056989022007472
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.6084/m9.figshare.20456727
title: Alpha-fetoprotein is involved in cellular stress response: evidence from short linear motifs

description: This item contains original files of local sequence alignment and gene ontology functional enrichment analysis
DOI: 10.6084/m9.figshare.20456727.v1
title: Alpha-fetoprotein is involved in cellular stress response: evidence from short linear motifs

description: This item contains original files of local sequence alignment and gene ontology functional enrichment analysis
DOI: 10.6084/m9.figshare.20456831.v1
title: Clinical and genomic characterisation of a fatal Puumala orthohantavirus case with low levels of neutralising antibodies

description: Orthohantaviruses are rodent-borne emerging viruses that cause haemorrhagic fever with renal syndrome (HFRS) in Eurasia and hantavirus pulmonary syndrome in America. Transmission between humans have been reported and the case-fatality rate ranges from 0.4% to 40% depending on virus strain. There is no specific and efficient treatment for patients with severe HFRS. Here, we characterised a fatal case of HFRS and sequenced the causing Puumala orthohantavirus (PUUV). PUUV RNA and virus specific neutralising antibodies were quantified in plasma samples from the fatal case and other patients with non-fatal PUUV infection. To investigate if the causing PUUV strain was different from previously known strains, Sanger sequencing was performed directly from the patient’s plasma. Biopsies obtained from autopsy were stained for immunohistochemistry. The patient had approximately tenfold lower levels of PUUV neutralising antibodies and twice higher viral load than was normally seen for patients with less severe PUUV infection. We could demonstrate unique mutations in the S and M segments of the virus that could have had an impact on the severity of infection. Due to the severe course of infection, the patient was treated with the bradykinin receptor inhibitor icatibant to reduce bradykinin-mediated vessel permeability and maintain vascular circulation. Our data suggest that bradykinin receptor inhibitor may not be highly efficient to treat patients that are at an advanced stage of HFRS. Low neutralising antibodies and high viral load at admission to the hospital were associated with the fatal outcome and may be useful for future predictions of disease outcome.
DOI: 10.6084/m9.figshare.20456831
title: Clinical and genomic characterisation of a fatal Puumala orthohantavirus case with low levels of neutralising antibodies

description: Orthohantaviruses are rodent-borne emerging viruses that cause haemorrhagic fever with renal syndrome (HFRS) in Eurasia and hantavirus pulmonary syndrome in America. Transmission between humans have been reported and the case-fatality rate ranges from 0.4% to 40% depending on virus strain. There is no specific and efficient treatment for patients with severe HFRS. Here, we characterised a fatal case of HFRS and sequenced the causing Puumala orthohantavirus (PUUV). PUUV RNA and virus specific neutralising antibodies were quantified in plasma samples from the fatal case and other patients with non-fatal PUUV infection. To investigate if the causing PUUV strain was different from previously known strains, Sanger sequencing was performed directly from the patient’s plasma. Biopsies obtained from autopsy were stained for immunohistochemistry. The patient had approximately tenfold lower levels of PUUV neutralising antibodies and twice higher viral load than was normally seen for patients with less severe PUUV infection. We could demonstrate unique mutations in the S and M segments of the virus that could have had an impact on the severity of infection. Due to the severe course of infection, the patient was treated with the bradykinin receptor inhibitor icatibant to reduce bradykinin-mediated vessel permeability and maintain vascular circulation. Our data suggest that bradykinin receptor inhibitor may not be highly efficient to treat patients that are at an advanced stage of HFRS. Low neutralising antibodies and high viral load at admission to the hospital were associated with the fatal outcome and may be useful for future predictions of disease outcome.
DOI: 10.6084/m9.figshare.20180440
title: Documenting occupant models for building performance simulation: a state-of-the-art

description: The number of occupancy and occupant behaviour models developed for building performance simulation (BPS) has steadily increased for the past four decades. However, their use is still limited in practice. This is partly due to the difficulty in understanding their utility and to the challenges related to their implementation into BPS. Both problems can be attributed to the lack of a framework for their description and communication. In this paper, we fill this gap by introducing a framework to document occupant models, that represents the state-of-the-art of available information on the topic. The framework consists of four blocks (description, development, evaluation, and implementation) and can also be regarded as a guideline to help researchers communicate their models transparently. Based on a systematic review, we verify to which degree existing academic papers on occupant models meet the framework, thus providing a self-critical assessment of the state-of-the-art of occupant models’ documentation.
DOI: 10.5281/zenodo.6954826
title: Data associated with PNAS Delworth et al 2022

description: Data accompanying journal publication.
DOI: 10.34740/kaggle/dsv/4048744
title: COVID Vaccination in World (updated daily)
DOI: 10.6084/m9.figshare.20456838
title: RaMP Database MySQL Dump v2.1.0 20220808

description: RaMP Relational Database of Metabolic Pathways Update. 20220808.
DOI: 10.6084/m9.figshare.20456838.v1
title: RaMP Database MySQL Dump v2.1.0 20220808

description: RaMP Relational Database of Metabolic Pathways Update. 20220808.
DOI: 10.17638/datacat.liverpool.ac.uk/1776
title: Stratifying clinical risk in patients with atrial fibrillation and chronic kidney disease by studying how abnormalities in clot structure/function and lipoproteins contribute to thrombosis and bleeding

description: Study dataset
DOI: 10.26208/q0q6-mg90
title: Supplementary data, code, and information for ‘Testing the Fidelity of Methods Used in Proxy-based Reconstructions of Past Climate’ (Journal of Climate, Mann et al. 2005)

description: Two widely used statistical approaches to reconstructing past climate histories from climate “proxy” data such as tree rings, corals, and ice cores are investigated using synthetic “pseudoproxy” data derived from a simulation of forced climate changes over the past 1200 yr. These experiments suggest that both statistical approaches should yield reliable reconstructions of the true climate history within estimated uncertainties, given estimates of the signal and noise attributes of actual proxy data networks.