cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.19375325
title: Supplementary Material for: Identification of subclasses of decompensated cirrhotic patients with acute kidney injury with different responses to fluid input

description: Introduction: Acute kidney injury is a heterogeneous disease in decompensated cirrhotic patients. The aims of our study were to detect subphenotypes of cirrhotic patients with acute kidney injury and explore clinical traits in patients with different subclasses. Methods: All enrolled patients were identified from a clinical database. Clinical and laboratory variables were used to perform latent profile analysis (LPA). Clinical traits in each class were compared. A multivariable logistic regression model and a Cox model were used to explore the independent association of fluid input and mortality outcome. Results: A total of 439 AKI patients with decompensated cirrhosis were enrolled in our study, including 113 patients in profile 1 and 326 patients in profile 2, by the LPA model. Profile 1 had higher mortality (61.1%) than profile 2 (36.81%). Moreover, profile 1 had a higher MELD score (median 39, IQR 34 to 43) than profile 2(P&lt;0.001). Higher cumulative fluid input in the first 24 h for profile 1 was associated with an increased risk of hospital mortality (OR 1.33, 95% CI 1.02 to 1.75) and 90-day mortality(HR 1.39, 95%CI 1.08-1.78). Conclusions: In this study, two distinct subclasses of decompensated cirrhotic patients with acute kidney injury were identified, with different clinical outcomes and fluid input responses.
DOI: 10.6084/m9.figshare.19375325.v1
title: Supplementary Material for: Identification of subclasses of decompensated cirrhotic patients with acute kidney injury with different responses to fluid input

description: Introduction: Acute kidney injury is a heterogeneous disease in decompensated cirrhotic patients. The aims of our study were to detect subphenotypes of cirrhotic patients with acute kidney injury and explore clinical traits in patients with different subclasses. Methods: All enrolled patients were identified from a clinical database. Clinical and laboratory variables were used to perform latent profile analysis (LPA). Clinical traits in each class were compared. A multivariable logistic regression model and a Cox model were used to explore the independent association of fluid input and mortality outcome. Results: A total of 439 AKI patients with decompensated cirrhosis were enrolled in our study, including 113 patients in profile 1 and 326 patients in profile 2, by the LPA model. Profile 1 had higher mortality (61.1%) than profile 2 (36.81%). Moreover, profile 1 had a higher MELD score (median 39, IQR 34 to 43) than profile 2(P&lt;0.001). Higher cumulative fluid input in the first 24 h for profile 1 was associated with an increased risk of hospital mortality (OR 1.33, 95% CI 1.02 to 1.75) and 90-day mortality(HR 1.39, 95%CI 1.08-1.78). Conclusions: In this study, two distinct subclasses of decompensated cirrhotic patients with acute kidney injury were identified, with different clinical outcomes and fluid input responses.
DOI: 10.6084/m9.figshare.19518133
title: Tonnages, durations of ore formation, durations of magma cycles associated with mineralization, Sr/Y values of magmas and depths of formation of porphyry Cu-Au deposits

description: This table provides a summary of Cu and Au endowments of ~120 porphyry Cu-Au deposits, durations of ore formation, durations of magma cycles associated with mineralization, Sr/Y values of magmas and depths of formation of porphyry Cu-Au deposits<br>
DOI: 10.6084/m9.figshare.19518133.v3
title: Tonnages, durations of ore formation, durations of magma cycles associated with mineralization, Sr/Y values of magmas and depths of formation of porphyry Cu-Au deposits

description: This table provides a summary of Cu and Au endowments of ~120 porphyry Cu-Au deposits, durations of ore formation, durations of magma cycles associated with mineralization, Sr/Y values of magmas and depths of formation of porphyry Cu-Au deposits<br>
DOI: 10.34740/kaggle/dsv/3421457
title: Russian Invasion of Ukraine
DOI: 10.6084/m9.figshare.19534342
title: Geochemical compositions of zircons from eruptive centers and mineralized porphyry copper deposits

description: Geochemical compositions of zircons from eruptive centers from various geodynamic settings (rift: Bishop Tuff; subduction-related: Lassen Peak, Fish Canyon Tuff, FCT, Kneeling Nun Tuff) and mineralized porphyry copper deposits (data from various references)<br>
DOI: 10.6084/m9.figshare.19534342.v2
title: Geochemical compositions of zircons from eruptive centers and mineralized porphyry copper deposits

description: Geochemical compositions of zircons from eruptive centers from various geodynamic settings (rift: Bishop Tuff; subduction-related: Lassen Peak, Fish Canyon Tuff, FCT, Kneeling Nun Tuff) and mineralized porphyry copper deposits (data from various references)<br>
DOI: 10.6084/m9.figshare.19534342.v1
title: Geochemical compositions of zircons from eruptive centers and mineralized porphyry copper deposits

description: Geochemical compositions of zircons from eruptive centers from various geodynamic settings (rift: Bishop Tuff; subduction-related: Lassen Peak, Fish Canyon Tuff, FCT, Kneeling Nun Tuff) and mineralized porphyry copper deposits (data from various references)<br>
DOI: 10.5255/ukda-sn-855584
title: Ethiopian Orthodox Clergy Assessment of Workshop Series on Domestic Violence Delivered in Ethiopia, 2021

description: The current dataset includes assessment questionnaire responses by clergy participating in a workshop series on domestic violence that was designed by Project dldl/ድልድል and co-delivered with the support of the Ethiopian Orthodox Church Development and Inter-Church Aid Commission (EOC DICAC) in Amhara region, Ethiopia. The questionnaires were collected as part of the programme's evaluation approach, which comprised of a pre-workshop interest form that asked participants background information and a post-workshop assessment that asked them to assess different aspects of the workshops. A total of 155 assessment questionnaires were collected from clergy participants across 7 workshops. The participants were asked to respond to 7 assessment questions at the end of each workshop. Their responses were transcribed from the paper-based questionnaires in Amharic and were subsequently translated to English with the help of professional and native-speaking translators.
DOI: 10.6084/m9.figshare.19536004
title: Soil respiration dataset from a temperate forest (St Jones Reserve)

description: Dataset of automated measurements of soil CO<sub>2</sub> , CH<sub>4</sub> and N<sub>2</sub>O fluxes from a temperate forest. The study was conducted at the St Jones Reserve, Dover, Delaware. For more details see:<br> Petrakis, S., J. Barba, B. Bond-Lamberty, and R. Vargas. 2018. Using greenhouse gas fluxes to define soil functional types. Plant and soil 423:285–294.
DOI: 10.6084/m9.figshare.17912198
title: Genome Annotation of Arsenophonus from Apis mellifera

description: Annotation table for genome sequence of <i>Arsenophonus</i> derived from <i>Apis mellifera</i> honey bees (Genbank accessions CP084222 – CP084228). <br>Genome annotation was performed with the NCBI Prokaryotic Genome Annotation Pipeline.<br>Column A: locus identifier tagColumn B: Feature (CDS, rRNA, tRNA)Column C: attributes. Free text: pseudo= likely pseudogeneColumn D: sequence type (main chromosome vs plasmid)Column E: plasmid identified (if plasmid) - 1 to 6.Column F: Start point in genome (base #)Column G: End point in genome (base #)Column H: Strand (+/-)Column I: Product accession # (if protein coding)Column J: Gene nameColumn K: Gene symbolColumn L: gene length (bp)Column M: product length (aa)Column N: Kegg annotation identifier.Column O: Predicted biosynthesis function, as predicted by Anti-SMASH.Column P: pfam domains identified (by identifier)Column Q: pfam domains identified (by name)<br><br>
DOI: 10.6084/m9.figshare.17912198.v1
title: Genome Annotation of Arsenophonus from Apis mellifera

description: Annotation table for genome sequence of <i>Arsenophonus</i> derived from <i>Apis mellifera</i> honey bees (Genbank accessions CP084222 – CP084228). <br>Genome annotation was performed with the NCBI Prokaryotic Genome Annotation Pipeline.<br>Column A: locus identifier tagColumn B: Feature (CDS, rRNA, tRNA)Column C: attributes. Free text: pseudo= likely pseudogeneColumn D: sequence type (main chromosome vs plasmid)Column E: plasmid identified (if plasmid) - 1 to 6.Column F: Start point in genome (base #)Column G: End point in genome (base #)Column H: Strand (+/-)Column I: Product accession # (if protein coding)Column J: Gene nameColumn K: Gene symbolColumn L: gene length (bp)Column M: product length (aa)Column N: Kegg annotation identifier.Column O: Predicted biosynthesis function, as predicted by Anti-SMASH.Column P: pfam domains identified (by identifier)Column Q: pfam domains identified (by name)<br><br>
DOI: 10.6084/m9.figshare.12979826
title: Fecundity and fertility impacts of Rickettsia symbiont infection in the bed bug Cimex lectularius

description: Crosses were undertaken between male and female bedbugs of differing Rickettsia infection status. The fecundity of the females (#fertile eggs laid) and their fertility rate (#fertile eggs/total) was then recorded until the female stopped laying fertile eggs.<br>Column A: replicate (cross)Column B: origin of female in the cross (F4 and S1 are different isoline; subline is after the underscore)Column C: origin of male in the cross (nomenclature as for column B).Column D: Rickettsia infection status of female parent: R+ is with Rickettsia, R- without.Column E: Rickettsia infection status of the male parent ((nomenclature as for column D).Column F: Isoline of individuals (two independent isolines, F4, S1)Column G: Date on which focal individuals emerged as adults.Column H: Date on which focal individuals were mated.Column I: Number of fertile eggs laid by female from the cross.Column J: Number of infertile eggs laid by female from the cross.Column K: Total eggs laid (Column I+ Column J)Column L: Proportion eggs that were fertile (Column I/Column K)Column M: period (days) over which the female laid eggs (fertile or infertile).
DOI: 10.6084/m9.figshare.12221069
title: Raw qPCR data for Spiroplasma (dnaA) and D. hydei (rp49) quantification

description: Roche LightCycler® 480 Instrument, 384-well output file, with 3 technical triplicates for each biological sample.<br>This file is an input for the script implementing Pfaffl Method to raw, quality checked Cp values (qPCR threshold cycles) from the Roche LightCycler® 480 Instrument, 384-well, with technical replicates for each sample.<br>Data includes two positive controls for QC (SpiroCTR & 25.1old).<br>Negative controls were removed manually at the melting curve analysis step (all showed no signs of amplification).<br>For details of output file format, see manufacturers instructions <br>http://icob.sinica.edu.tw/pubweb/bio-chem/Core Facilities/Data/R401-core/LightCycler480 II_Manual_V1.5.pdf<br><br><br>
DOI: 10.6084/m9.figshare.12979778
title: Impact of Rickettsia symbiont infection on the development rate and sex ratio of the common bed bug Cimex lectularius.

description: Females with and without Rickettsia were allowed to mate and produce progeny. The development time of their progeny and sex of progeny was recorded to ascertain if Rickettsia affected a) host development rate and b) host sex ratio.<br>Column A: Individual numberColumn B: Pot in which individual was housed (block effect)Column C: Source population: S1 and F4 are independent bedbug isolines.Column D: Rickettsia infection status: R+ = with symbiont R-= without symbiont.Column E: Sex of individual (male/female): ascertained as adult, following developmentColumn F: Development time (in days): period from first instar nymph to adulthood.<br>
DOI: 10.6084/m9.figshare.12979778.v1
title: Impact of Rickettsia symbiont infection on the development rate and sex ratio of the common bed bug Cimex lectularius.

description: Females with and without Rickettsia were allowed to mate and produce progeny. The development time of their progeny and sex of progeny was recorded to ascertain if Rickettsia affected a) host development rate and b) host sex ratio.<br>Column A: Individual numberColumn B: Pot in which individual was housed (block effect)Column C: Source population: S1 and F4 are independent bedbug isolines.Column D: Rickettsia infection status: R+ = with symbiont R-= without symbiont.Column E: Sex of individual (male/female): ascertained as adult, following developmentColumn F: Development time (in days): period from first instar nymph to adulthood.<br>
DOI: 10.6084/m9.figshare.12979826.v1
title: Fecundity and fertility impacts of Rickettsia symbiont infection in the bed bug Cimex lectularius

description: Crosses were undertaken between male and female bedbugs of differing Rickettsia infection status. The fecundity of the females (#fertile eggs laid) and their fertility rate (#fertile eggs/total) was then recorded until the female stopped laying fertile eggs.<br>Column A: replicate (cross)Column B: origin of female in the cross (F4 and S1 are different isoline; subline is after the underscore)Column C: origin of male in the cross (nomenclature as for column B).Column D: Rickettsia infection status of female parent: R+ is with Rickettsia, R- without.Column E: Rickettsia infection status of the male parent ((nomenclature as for column D).Column F: Isoline of individuals (two independent isolines, F4, S1)Column G: Date on which focal individuals emerged as adults.Column H: Date on which focal individuals were mated.Column I: Number of fertile eggs laid by female from the cross.Column J: Number of infertile eggs laid by female from the cross.Column K: Total eggs laid (Column I+ Column J)Column L: Proportion eggs that were fertile (Column I/Column K)Column M: period (days) over which the female laid eggs (fertile or infertile).
DOI: 10.6084/m9.figshare.12214070
title: Impact of thermal environment on Spiroplasma titre in D. hydei

description: Results of qPCR analysis of relative titre of Spiroplasma in D. hydei. Brief methods: D. hydei carrying Spiroplasma were reared at 18 C or 25 C. These were allowed to breed, and progeny reared at the focal temperature before being culled within 24h of entry to pupation. DNA from Individual pupae was purified using the phenol-chloroform methods. Real-time qPCR reactions were then carried out for the <i>dnaA</i> gene (<i>Spiroplasma</i>) and the <i>rp49</i> gene (<i>D. hydei</i> reference), using the LightCycler 480 (Roche). <br>Column A: Replicate (A or B)Column B: Temperature treatment (18 or 25 C)Column C: Biological replicateColumn D: dnaA/rp49 ratio across three technical replicatesColumn E: Median dnaA/rp49 ratio for 18 C block A, used as standardColumn F:dnaA/rp49 ratio standardised against median dnaA/rp49 for 18C block AColumn G: Median ratio for each treatment/blockColumn H: Median fold change in Spiroplasma titre for 25 vs 18 for each block.
DOI: 10.6084/m9.figshare.12213758
title: Spiroplasma prevalence in D. hydei following passage under four different thermal regimes

description: The data represents screening results of F3 flies of <i>D. hydei</i> for <i>Spiroplasma</i> following two generations of passage at different temperatures. Column A: Origin of fly/<i>Spiroplasma</i> isoline. Two levels: Mexico or Cambridge isolines. Column B: Temperature. Temperature during passage over previous two generations. Four levels: 25 °C, 18°C, 18/15°C (diurnal variation), 15 °C. Column C: N of flies tested for <i>Spiroplasma</i>, which had passed QC for DNA template amplifiability using COI prmers. Column D: N of flies scoring as infected on <i>Spiroplasma</i> PCR assay. Column E: Prevalence. Point estimate of proportion flies infected (Column D/Column C) Column F: Upper confidence interval for <i>Spiroplasma</i> prevalence, calculated through binomial sampling. Column G: Lower confidence interval for <i>Spiroplasma</i> prevalence, calculated through binomial sampling.
DOI: 10.6084/m9.figshare.12214070.v1
title: Impact of thermal environment on Spiroplasma titre in D. hydei

description: Results of qPCR analysis of relative titre of Spiroplasma in D. hydei. Brief methods: D. hydei carrying Spiroplasma were reared at 18 C or 25 C. These were allowed to breed, and progeny reared at the focal temperature before being culled within 24h of entry to pupation. DNA from Individual pupae was purified using the phenol-chloroform methods. Real-time qPCR reactions were then carried out for the <i>dnaA</i> gene (<i>Spiroplasma</i>) and the <i>rp49</i> gene (<i>D. hydei</i> reference), using the LightCycler 480 (Roche). <br>Column A: Replicate (A or B)Column B: Temperature treatment (18 or 25 C)Column C: Biological replicateColumn D: dnaA/rp49 ratio across three technical replicatesColumn E: Median dnaA/rp49 ratio for 18 C block A, used as standardColumn F:dnaA/rp49 ratio standardised against median dnaA/rp49 for 18C block AColumn G: Median ratio for each treatment/blockColumn H: Median fold change in Spiroplasma titre for 25 vs 18 for each block.
DOI: 10.6084/m9.figshare.11857893
title: The most prophage dense complete bacterial genomes, with details on the methods used for sequencing and assembly

description: Prophage-dense existing completed genomes.<br>Column A: Genome Assembly IDColumn B: # main chrososome contigsColumn C: Genome size (bp)Column D: Genome %GCColumn E-H: # Regions predicted to have phage origins: E: Complete, F, Questionable G, Incomplete, H total. <br>Column I: Density of regions with phage origin (#/Mb)<br>Column J: Notes on any plasmids present, and their predicted phage content.<br>Column K, L: First Generation sequencing, Library prep, sequencing method.<br>Column M: Second generation sequencing effort<br>Column N: Third generation sequencing effort (nanopore, PacBio)<br>Column O: Targetted Gap closure approach<br>Column P: Backbone used for assembly, if any<br>Column Q: Year of publication/completion<br>Column R: Reference <br>
DOI: 10.6084/m9.figshare.12213758.v1
title: Spiroplasma prevalence in D. hydei following passage under four different thermal regimes

description: The data represents screening results of F3 flies of <i>D. hydei</i> for <i>Spiroplasma</i> following two generations of passage at different temperatures. Column A: Origin of fly/<i>Spiroplasma</i> isoline. Two levels: Mexico or Cambridge isolines. Column B: Temperature. Temperature during passage over previous two generations. Four levels: 25 °C, 18°C, 18/15°C (diurnal variation), 15 °C. Column C: N of flies tested for <i>Spiroplasma</i>, which had passed QC for DNA template amplifiability using COI prmers. Column D: N of flies scoring as infected on <i>Spiroplasma</i> PCR assay. Column E: Prevalence. Point estimate of proportion flies infected (Column D/Column C) Column F: Upper confidence interval for <i>Spiroplasma</i> prevalence, calculated through binomial sampling. Column G: Lower confidence interval for <i>Spiroplasma</i> prevalence, calculated through binomial sampling.
DOI: 10.6084/m9.figshare.12213875
title: Impact of thermal environment on the D. hydei/Spiroplasma protective symbiosis

description: This spreadsheet is the data arising from Protection assays, with a 2x2x2 factorial design over two blocks. Factors = symbiont presence/absence, presence/absence of wasp attack, temperature alongside block effect. Response = Adult flies emerged, wasps emerged.<br>Brief method: D. hydei with and without Spiroplasma symbionts were reared at one of two focal temperatures (18, 25 C). They were then allowed to produce progeny, that were then exposed to attack by L. heterotoma wasps (control - no wasps). The data provide the outcome of these attacks in terms of the number of individuals surviving attack and emerging as flies, and the emergence of wasps. Note: the number of flies emerging and wasps emerging do not sum to the sample size, as death of both fly and wasp is a common outcome of parasitism. Column A: Temperature treatment (18 or 25 C) (Factor, Fixed effect) Column B: Vial code (Block/vial) Column C: Block: Block code [Factor, Random effect] Column D: Spiro_infected. 1 = with Spiroplasma sHy1, 0 = uninfected [Factor, Fixed effect] Column E: Wasp_Attack. 1 = attacked by <i>L. heterotoma</i> wasps, 0 = unattacked. [Factor, Fixed effect for fly survival models] Column F: Fly larvae Expose. # Fly larvae placed in vial. Column G: Adult flies emerged. # Adult flies emerging from vial Column H: Wasps emerged. # wasps emerging from vial (note will be 0 by default where wasp attack is 0)
DOI: 10.6084/m9.figshare.12213875.v1
title: Impact of thermal environment on the D. hydei/Spiroplasma protective symbiosis

description: This spreadsheet is the data arising from Protection assays, with a 2x2x2 factorial design over two blocks. Factors = symbiont presence/absence, presence/absence of wasp attack, temperature alongside block effect. Response = Adult flies emerged, wasps emerged.<br>Brief method: D. hydei with and without Spiroplasma symbionts were reared at one of two focal temperatures (18, 25 C). They were then allowed to produce progeny, that were then exposed to attack by L. heterotoma wasps (control - no wasps). The data provide the outcome of these attacks in terms of the number of individuals surviving attack and emerging as flies, and the emergence of wasps. Note: the number of flies emerging and wasps emerging do not sum to the sample size, as death of both fly and wasp is a common outcome of parasitism. Column A: Temperature treatment (18 or 25 C) (Factor, Fixed effect) Column B: Vial code (Block/vial) Column C: Block: Block code [Factor, Random effect] Column D: Spiro_infected. 1 = with Spiroplasma sHy1, 0 = uninfected [Factor, Fixed effect] Column E: Wasp_Attack. 1 = attacked by <i>L. heterotoma</i> wasps, 0 = unattacked. [Factor, Fixed effect for fly survival models] Column F: Fly larvae Expose. # Fly larvae placed in vial. Column G: Adult flies emerged. # Adult flies emerging from vial Column H: Wasps emerged. # wasps emerging from vial (note will be 0 by default where wasp attack is 0)
DOI: 10.6084/m9.figshare.11857836
title: Accessory gene content of a) Phage derived regions of the main A. nasoniae chromosome b) Extrachromosomal elements

description: Accessory gene content of a) Phage derived regions of the main A. nasoniae chromosome b) Extrachromosomal elements<br>a) Phage derived regions of main chromosome. ORFs identified as accessory (i.e. not core to phage function) through either identity on BLAST search, or presence of pfam domains.Column A: phage derived region identifierColumn B: CDS or tRNAColumn C: ORF start positionColumn D: ORF end positionColumn E: ORF length in nucleotidesColumn F: Coding strandColumn G: Locus tag IDColumn H: Gene product, by BLAST matchColumn I: pfam domain IDsColumn J: Notes on functional groupsColumn K: pfam domain function<br>b) Extrachromosomal elements. ORFs identified as accessory (i.e. not core to plasmid function) through either identity on BLAST search, or presence of pFam domains.<br>Column A: plasmid identifierColumn B: CDS or tRNAColumn C: ORF start positionColumn D: ORF end positionColumn E: ORF length in nucleotidesColumn F: Coding strandColumn G: Locus tag IDColumn H: Gene product, by BLAST matchColumn I: pfam domain IDsColumn J: Notes on functional groupsColumn K: pfam domain function