cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25400/lincolnuninz.19394312
title: A1M&5.6_Seed – Mixed inoculation results of Serratia strains A1MO2 and 5.6 when continually re-seeded in LB broth

description: CFU measurements collected with Serratia entomophila strains A1MO2 and 5.6 over a period of seven days when cultured together in LB broth and inoculated at varying ratios. The cultures were collected and seeded into new flasks each day to characterise the impact of continually replenished nutrients on competition outcomes. Data includes both the raw colony counts from LB agar plates using antibiotics, the final CFU counts, and log10 transformed CFU counts, which were used in subsequent analysis. The data explores the interactions between a pathogenic strain (A1MO2) and an isogenic non-pathogenic strain (5.6) in a nutrient-rich environment.
DOI: 10.25400/lincolnuninz.19394312.v1
title: A1M&5.6_Seed – Mixed inoculation results of Serratia strains A1MO2 and 5.6 when continually re-seeded in LB broth

description: CFU measurements collected with Serratia entomophila strains A1MO2 and 5.6 over a period of seven days when cultured together in LB broth and inoculated at varying ratios. The cultures were collected and seeded into new flasks each day to characterise the impact of continually replenished nutrients on competition outcomes. Data includes both the raw colony counts from LB agar plates using antibiotics, the final CFU counts, and log10 transformed CFU counts, which were used in subsequent analysis. The data explores the interactions between a pathogenic strain (A1MO2) and an isogenic non-pathogenic strain (5.6) in a nutrient-rich environment.
DOI: 10.25400/lincolnuninz.19394333
title: RNAseq_Data – Chromosomal genetic differences between Serratia strains A1MO2 and 5.6

description: A comparison between chromosomal gene expression between pathogenic Serratia entomophila strain A1MO2 (5.6+pADAP), and the isogenic non-pathogenic, plasmid-free strain of 5.6. The data helped to identify operons of interest which may confer increased competitive capabilities to 5.6 during mixed inoculation with A1MO2. The data is colour coded depending on strain, with lighter colours indicating increased expression in one strain, and darker colours indicating significantly increased expression. No colour indicates no difference between the strains. The predicted gene names and cluster of orthologous groups (COG) identifiers are included.
DOI: 10.25400/lincolnuninz.19394333.v1
title: RNAseq_Data – Chromosomal genetic differences between Serratia strains A1MO2 and 5.6

description: A comparison between chromosomal gene expression between pathogenic Serratia entomophila strain A1MO2 (5.6+pADAP), and the isogenic non-pathogenic, plasmid-free strain of 5.6. The data helped to identify operons of interest which may confer increased competitive capabilities to 5.6 during mixed inoculation with A1MO2. The data is colour coded depending on strain, with lighter colours indicating increased expression in one strain, and darker colours indicating significantly increased expression. No colour indicates no difference between the strains. The predicted gene names and cluster of orthologous groups (COG) identifiers are included.
DOI: 10.25400/lincolnuninz.19394324
title: LV_Comp_Data – Parameters obtained from fitting Lotka/Volterra-style competition models to in vitro competition data

description: A variety of parameters used to construct Lotka/Volterra-style competition models for mixed inoculation in vitro data of Serratia spp. The data includes both initial and optimised data obtained using the gauseR package for R, including the growth rates, self-limitation strength, and competition coefficients.
DOI: 10.25400/lincolnuninz.19394324.v1
title: LV_Comp_Data – Parameters obtained from fitting Lotka/Volterra-style competition models to in vitro competition data

description: A variety of parameters used to construct Lotka/Volterra-style competition models for mixed inoculation in vitro data of Serratia spp. The data includes both initial and optimised data obtained using the gauseR package for R, including the growth rates, self-limitation strength, and competition coefficients.
DOI: 10.25400/lincolnuninz.19394576
title: Larvae_Macerates – Mixed inoculation results of Serratia strains A1MO2 and 5.6 isolated from grass grub macerate samples

description: CFU measurements for <i>Serratia entompohila</i> strains A1MO2 and 5.6 when isolated from grass grub macerate samples collected over a period of 14 days. The study investigated the impact of mixed inoculation between pathogen (A1MO2) and non-pathogen (5.6) on amber disease onset and growth within the larvae. Data includes both the raw colony counts from LB agar plates using antibiotics, the final CFU counts, and log<sub>10</sub> transformed CFU counts, which were used in subsequent analysis.
DOI: 10.25400/lincolnuninz.19394576.v1
title: Larvae_Macerates – Mixed inoculation results of Serratia strains A1MO2 and 5.6 isolated from grass grub macerate samples

description: CFU measurements for <i>Serratia entompohila</i> strains A1MO2 and 5.6 when isolated from grass grub macerate samples collected over a period of 14 days. The study investigated the impact of mixed inoculation between pathogen (A1MO2) and non-pathogen (5.6) on amber disease onset and growth within the larvae. Data includes both the raw colony counts from LB agar plates using antibiotics, the final CFU counts, and log<sub>10</sub> transformed CFU counts, which were used in subsequent analysis.
DOI: 10.25400/lincolnuninz.19394405
title: A1M&5.6_Malt – Mixed inoculation results of Serratia strains A1MO2 and 5.6 in maltose M9 medium

description: CFU measurements collected with Serratia entomophila strains A1MO2 and 5.6 over a period of seven days when cultured together in a 20 % maltose M9 medium, and inoculated at varying ratios. Data includes both the raw colony counts from LB agar plates using antibiotics, the final CFU counts, and log10 transformed CFU counts, which were used in subsequent analysis. This analysis was conducted following the observation of significantly increased expression of maltose-related operons in 5.6 during RNA sequencing, and explores how the increased expression of those operons influenced competition between the strains.
DOI: 10.25400/lincolnuninz.19394405.v1
title: A1M&5.6_Malt – Mixed inoculation results of Serratia strains A1MO2 and 5.6 in maltose M9 medium

description: CFU measurements collected with Serratia entomophila strains A1MO2 and 5.6 over a period of seven days when cultured together in a 20 % maltose M9 medium, and inoculated at varying ratios. Data includes both the raw colony counts from LB agar plates using antibiotics, the final CFU counts, and log10 transformed CFU counts, which were used in subsequent analysis. This analysis was conducted following the observation of significantly increased expression of maltose-related operons in 5.6 during RNA sequencing, and explores how the increased expression of those operons influenced competition between the strains.
DOI: 10.25400/lincolnuninz.19394525
title: Soil_Microcosm – Mixed inoculation results of Serratia strains A1MO2 and 5.6 in 20 g soil microcosms

description: CFU measurements collected with Serratia entomophila strains A1MO2 and 5.6 when inoculated at mixed ratios in 20 g soil microcosms and assessed over a period of eight weeks. The study was conducted to determine whether competition between the strains changed based on being grown in soil samples when compared to nutrient-rich liquid media. Data includes both the raw colony counts from LB agar plates using antibiotics, the final CFU counts, and log10 transformed CFU counts, which were used in subsequent analysis.
DOI: 10.25400/lincolnuninz.19394525.v1
title: Soil_Microcosm – Mixed inoculation results of Serratia strains A1MO2 and 5.6 in 20 g soil microcosms

description: CFU measurements collected with Serratia entomophila strains A1MO2 and 5.6 when inoculated at mixed ratios in 20 g soil microcosms and assessed over a period of eight weeks. The study was conducted to determine whether competition between the strains changed based on being grown in soil samples when compared to nutrient-rich liquid media. Data includes both the raw colony counts from LB agar plates using antibiotics, the final CFU counts, and log10 transformed CFU counts, which were used in subsequent analysis.
DOI: 10.5281/zenodo.6392198
title: Artifacts for Characterizing Human Aspects in Reviews of COVID-19 Apps

description: This archive contains the artifacts associated with our study titled "Characterizing Human Aspects in Reviews of COVID-19 Apps". Specifically, the archive contains:<br> * The dataset of reviews we downloaded from the App Store and the Google Play store (`Reviews.zip`)<br> * The keywords we used to filter the reviews (`Keywords.json`)<br> * The filtered dataset of reviews (`Filtered_Reviews.zip`)<br> * The codebook to characterize human aspects (`Human_Aspects_Codebook.pdf`)<br> * The codebook to characterize review types (`Review_Types_Codebook.pdf`)<br> * The labeled App Store reviews (`Labeled_Reviews-Apple_Store.csv`)<br> * The labeled Google Play store reviews (`Labeled_Reviews-Apple_Store.csv`)
DOI: 10.5281/zenodo.6392197
title: Artifacts for Characterizing Human Aspects in Reviews of COVID-19 Apps

description: This archive contains the artifacts associated with our study titled "Characterizing Human Aspects in Reviews of COVID-19 Apps". Specifically, the archive contains:<br> * The dataset of reviews we downloaded from the App Store and the Google Play store (`Reviews.zip`)<br> * The keywords we used to filter the reviews (`Keywords.json`)<br> * The filtered dataset of reviews (`Filtered_Reviews.zip`)<br> * The codebook to characterize human aspects (`Human_Aspects_Codebook.pdf`)<br> * The codebook to characterize review types (`Review_Types_Codebook.pdf`)<br> * The labeled App Store reviews (`Labeled_Reviews-Apple_Store.csv`)<br> * The labeled Google Play store reviews (`Labeled_Reviews-Apple_Store.csv`)
DOI: 10.6084/m9.figshare.16528455.v1
title: Fungal Field Mesocosm Data

description: Data set of 10 fungal isolates in litterbags at Loma Ridge National Landmark in Southern California into drought and ambient plots, which were dispatched November 8, 2017 and collected April 30, 2018 and November 7, 2018. Data correspond to results from each litterbag: mass loss, growth yield, percent moisture, fungal hyphal length, Cohen's D effect size (between drought and ambient plots), and extracellular enzyme activities (cellobiohydrolase, b-glucosidase, b-xylosidase, and N-acetyl-b-D-glucosaminidase).
DOI: 10.6084/m9.figshare.16528455
title: Fungal Field Mesocosm Data

description: Data set of 10 fungal isolates in litterbags at Loma Ridge National Landmark in Southern California into drought and ambient plots, which were dispatched November 8, 2017 and collected April 30, 2018 and November 7, 2018. Data correspond to results from each litterbag: mass loss, growth yield, percent moisture, fungal hyphal length, Cohen's D effect size (between drought and ambient plots), and extracellular enzyme activities (cellobiohydrolase, b-glucosidase, b-xylosidase, and N-acetyl-b-D-glucosaminidase).
DOI: 10.5281/zenodo.6392171
title: Vignettes: Removing unwanted variation from TCGA RNA-Seq data.

description: This repository contains all datasets that are required for the vignettes of R.Molania et.al bioRxiv paper (https://www.biorxiv.org/content/10.1101/2021.11.01.466731v1).
DOI: 10.5281/zenodo.6392170
title: Vignettes: Removing unwanted variation from TCGA RNA-Seq data.

description: This repository contains all datasets that are required for the vignettes of R.Molania et.al bioRxiv paper (https://www.biorxiv.org/content/10.1101/2021.11.01.466731v1).
DOI: 10.6084/m9.figshare.19442654
title: Carotenoid binding in Gloeobacteria Rhodopsin provides insights into divergent evolution of xanthorhodopsin types

description: The position of carotenoid in xanthorhodopsin has been elucidated. However, a challenging expression of this opsin and a complex biosynthesis carotenoid in the laboratory hold back the insightful study of this rhodopsin. Here, we demonstrated co-expression of the xanthorhodopsin type isolated from <i>Gloeobacter violaceus</i> PCC 7421-Gloeobacter rhodopsin (GR) with a biosynthesized keto-carotenoid (canthaxanthin) targeting the carotenoid binding site. Direct mutation-induced changes in carotenoid-rhodopsin interaction revealed three crucial features: (1) carotenoid locked motif (CLM), (2) carotenoid aligned motif (CAM), and color tuning serines (CTS). Our single mutation results at 178 position (G178W) confirmed inhibition of carotenoid binding; however, the mutants showed better stability and proton pumping, which was also observed in the case of carotenoid binding characteristics. These effects demonstrated an adaptation of microbial rhodopsin that diverges from carotenoid harboring, along with expression in the dinoflagellate <i>Pyrocystis lunula</i> rhodopsin and the evolutionary substitution model. The study highlights a critical position of the carotenoid binding site, which significantly allows another protein engineering approach in the microbial rhodopsin family
DOI: 10.6084/m9.figshare.19367138
title: Figure 2, 3, 4 data

description: <b>Figure 2: </b>Structural-based alteration of targeting mutants and the interaction of the retinal and carotenoid chromophores. (a) Maximum absorption shifted of targeted mutants. (b) The local view of mutation position shows in the red sphere Ser 221 for the strongest red-shifted and the blue sphere for Ser 181 for the strongest blue-shifted. (c) UV-vis spectra of wild type, S181G, and S221G. (d) Purified samples in 0.02% DDM. (e) Comparison of proton pumping with and without carotenoid, helix E mutants showed a reduction of proton pumping enhancement as a response to lower binding ration; however, helix F mutants with higher carotenoid binding ratio disrupted the benefit of carotenoid in proton pumping, suggesting the challenge of energy transfer and light absorption.
DOI: 10.6084/m9.figshare.19367138.v2
title: Figure 2, 3, 4 data

description: <b>Figure 2: </b>Structural-based alteration of targeting mutants and the interaction of the retinal and carotenoid chromophores. (a) Maximum absorption shifted of targeted mutants. (b) The local view of mutation position shows in the red sphere Ser 221 for the strongest red-shifted and the blue sphere for Ser 181 for the strongest blue-shifted. (c) UV-vis spectra of wild type, S181G, and S221G. (d) Purified samples in 0.02% DDM. (e) Comparison of proton pumping with and without carotenoid, helix E mutants showed a reduction of proton pumping enhancement as a response to lower binding ration; however, helix F mutants with higher carotenoid binding ratio disrupted the benefit of carotenoid in proton pumping, suggesting the challenge of energy transfer and light absorption.
DOI: 10.6084/m9.figshare.19367138.v1
title: Figure 2, 3, 4 data

description: <b>Figure 2: </b>Structural-based alteration of targeting mutants and the interaction of the retinal and carotenoid chromophores. (a) Maximum absorption shifted of targeted mutants. (b) The local view of mutation position shows in the red sphere Ser 221 for the strongest red-shifted and the blue sphere for Ser 181 for the strongest blue-shifted. (c) UV-vis spectra of wild type, S181G, and S221G. (d) Purified samples in 0.02% DDM. (e) Comparison of proton pumping with and without carotenoid, helix E mutants showed a reduction of proton pumping enhancement as a response to lower binding ration; however, helix F mutants with higher carotenoid binding ratio disrupted the benefit of carotenoid in proton pumping, suggesting the challenge of energy transfer and light absorption.
DOI: 10.6084/m9.figshare.19367129
title: Figure 1 data

description: <b>Figure 1: </b>Co-expression of GR wild-type and mutants with canthaxanthin. (a) GR wild-type with only retinal (blue line), GR-expressed with both retinal and carotenoid (black line), single mutation G178W expressed with both retinal and carotenoid (green line). Complete chromophore extraction from purified samples showed blue, black, and green (dot line), respectively. (b) Absorption spectra of the mutant on helix E near glycine 178, carotenoid locked motif. (c) Absorption spectra of mutant on helix F, carotenoid aligned motif. (d) Local view of targeting mutation site, a structure alignment of GR (pdb:6nwd) and XR (pdb:3ddl), and the purified GR variants co-expressed with retinal/carotenoid
DOI: 10.6084/m9.figshare.19367129.v2
title: Figure 1 data

description: <b>Figure 1: </b>Co-expression of GR wild-type and mutants with canthaxanthin. (a) GR wild-type with only retinal (blue line), GR-expressed with both retinal and carotenoid (black line), single mutation G178W expressed with both retinal and carotenoid (green line). Complete chromophore extraction from purified samples showed blue, black, and green (dot line), respectively. (b) Absorption spectra of the mutant on helix E near glycine 178, carotenoid locked motif. (c) Absorption spectra of mutant on helix F, carotenoid aligned motif. (d) Local view of targeting mutation site, a structure alignment of GR (pdb:6nwd) and XR (pdb:3ddl), and the purified GR variants co-expressed with retinal/carotenoid
DOI: 10.6084/m9.figshare.19367129.v1
title: Figure 1 data

description: <b>Figure 1: </b>Co-expression of GR wild-type and mutants with canthaxanthin. (a) GR wild-type with only retinal (blue line), GR-expressed with both retinal and carotenoid (black line), single mutation G178W expressed with both retinal and carotenoid (green line). Complete chromophore extraction from purified samples showed blue, black, and green (dot line), respectively. (b) Absorption spectra of the mutant on helix E near glycine 178, carotenoid locked motif. (c) Absorption spectra of mutant on helix F, carotenoid aligned motif. (d) Local view of targeting mutation site, a structure alignment of GR (pdb:6nwd) and XR (pdb:3ddl), and the purified GR variants co-expressed with retinal/carotenoid
DOI: 10.6084/m9.figshare.19442933
title: Dataset on bitcoin carbon footprint and energy consumption

description: The daily frequency data on minimum, maximum, and optimal bitcoin annualized energy consumption from July 7, 2010 to December 4, 2021.
DOI: 10.6084/m9.figshare.18848765
title: How heated is it? Understanding GitHub locked issues

description: Replication package <br>Paper:Isabella Ferreira, Bram Adams, and Jinghui Cheng. 2022. <i>How heated is it? Understanding GitHub locked issues. </i>In 19th International Conference on Mining Software Repositories (MSR ’22), May 23–24, 2022, Pittsburgh, PA, USA.<br>
DOI: 10.6084/m9.figshare.18848765.v1
title: How heated is it? Understanding GitHub locked issues

description: Replication package <br>Paper:Isabella Ferreira, Bram Adams, and Jinghui Cheng. 2022. <i>How heated is it? Understanding GitHub locked issues. </i>In 19th International Conference on Mining Software Repositories (MSR ’22), May 23–24, 2022, Pittsburgh, PA, USA.<br>
DOI: 10.5517/ccdc.csd.cc294gjg
title: CCDC 2119455: Experimental Crystal Structure Determination

description: Related Article: Ben He, Sikun Zhang, Yueyan Zhang, Guoping Li, Bingjie Zhang, Wenqiang Ma, Bin Rao, Ruitong Song, Lei Zhang, Yanfeng Zhang, Gang He|2022|J.Am.Chem.Soc.|144|4422|doi:10.1021/jacs.1c11577
DOI: 10.5517/ccdc.csd.cc28ksg3
title: CCDC 2102465: Experimental Crystal Structure Determination

description: Related Article: Wei Liu, Zexin Wang, Renfu Li, Liwei Chen, Xiang Lin, Shitao Sun, Zhenli Li, Jinle Hao, Bin Lin, Xinli Wang, Lijun Xie|2022|J.Mol.Struct.|1260|132728|doi:10.1016/j.molstruc.2022.132728
DOI: 10.5517/ccdc.csd.cc2bcftz
title: CCDC 2155951: Experimental Crystal Structure Determination

description: Related Article: Wei Liu, Zexin Wang, Renfu Li, Liwei Chen, Xiang Lin, Shitao Sun, Zhenli Li, Jinle Hao, Bin Lin, Xinli Wang, Lijun Xie|2022|J.Mol.Struct.|1260|132728|doi:10.1016/j.molstruc.2022.132728
DOI: 10.6084/m9.figshare.19443404.v1
title: Annotations of all species

description: Annotation used for the study.
DOI: 10.6084/m9.figshare.19443404
title: Annotations of all species

description: Annotation used for the study.
DOI: 10.6084/m9.figshare.19443503
title: Sample data (five types of features of one participant)

description: Sample data (five types of features of one participant)
DOI: 10.5281/zenodo.5902100
title: Reproducing nonlinear seismic response from in-situ soil dynamic parameters: application to the Delaney Park Downhole Array, Alaska

description: The zip file named 'seismic data at DPDA.zip' contains all the seismic data used in our study. The DEEPSOIL file named 'ground response analysis at DPDA.dp' contains the numerical models used in our study.
DOI: 10.5281/zenodo.5902099
title: Reproducing nonlinear seismic response from in-situ soil dynamic parameters: application to the Delaney Park Downhole Array, Alaska

description: The zip file named 'seismic data at DPDA.zip' contains all the seismic data used in our study. The DEEPSOIL file named 'ground response analysis at DPDA.dp' contains the numerical models used in our study.
DOI: 10.5281/zenodo.6392332
title: Urban Ventilation Planning and Its Associated Benefits based on Numerical Experiments : A case study in Beijing, China

description: dataset for Figures 1-7
DOI: 10.5281/zenodo.6392331
title: Urban Ventilation Planning and Its Associated Benefits based on Numerical Experiments : A case study in Beijing, China

description: dataset for Figures 1-7
DOI: 10.34740/kaggle/dsv/3374172
title: Our World in Data - COVID-19
DOI: 10.34820/fk2/v7dxil/in2f5b
title: Productivity TFPCH.pdf

description: :unav
DOI: 10.34820/fk2/v7dxil
title: Productivity TFPCH

description: Productivity Index TFPCH
DOI: 10.6084/m9.figshare.19444343
title: Factors associated with education continuation.docx

description: This table describes associate factors that affect parents decision on whether will allow their vulnerable children continue their education or not.
DOI: 10.6084/m9.figshare.19444343.v1
title: Factors associated with education continuation.docx

description: This table describes associate factors that affect parents decision on whether will allow their vulnerable children continue their education or not.
DOI: 10.6084/m9.figshare.14246327.v4
title: Historical world mapping and current distribution in Peru of Cinchona spp.: Contribution to restoration and conservation strategies

description: Peru is megadiverse in neotropical flora, and it hosts an important cinchona tree (Cinchona spp.) that is currently in danger of extinction. This research generated georeferenced global historical maps of Cinchona spp. and then determined climate-appropriate sites according to a prediction model to establish priority areas for their conservation and restoration. Four maps were obtained, one for each centenary, from 1737 to the present, with 10,860 occurrences of Cinchona. In the modeling with MaxEnt, 5.56% (71,482 km2) and 17.67% (227,261 km2) of Peru’s land area had high (&gt;0.6) and moderate probabilities (0.4-0.6), respectively, of supporting Cinchona. Only 27.44% (37,363.51 km2) and 11.99% (16,325.23 km2) of the areas with moderate and high potential for distribution, respectively, were covered by protected natural areas. Likewise, 64.95% (51149.00 km2) and 35.04% (27596.00 km2) of the moderate- and high-probability lands, respectively, correspond to degraded areas and are therefore considered a priority for restoration using Cinchona spp. The findings can spur a rethinking of the decision-making of the National Plan of Action for Reforestation with Species of the Genus Cinchona and other plans/tools for cinchona conservation.
DOI: 10.6084/m9.figshare.14246327
title: Dataset: Historical world mapping and current distribution in Peru of Cinchona spp.

description: This research generated georeferenced global historical maps of Cinchona spp. and then determined climate-appropriate sites according to a prediction model to establish priority areas for their conservation and restoration in Peru.