cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7283546.v1
title: Non-invasive visualisation and identification of fluorescent Leishmania tarentolae in infected sand flies

description: A total of 2 x 10<sup>6 </sup>parasites were pelleted (1200xg, 10 min) and washed once with ice-cold PBS before resuspending in 1ml of blood meal (sheep blood mixed with heat-inactivated serum) and fed to the insects using a chick skin membrane with the Hemotek apparatus at 37 °C as described above. Groups of ~80 females were fed for one hour, after which 60 fully-engorged individuals were separated and kept under standard laboratory conditions until required for experimental work. Negative control groups were flies fed only on sheep blood and manipulated as stated above. Sand fly mortality was recorded daily and 14 insects were dissected 5 days post infection (DPI), when defecation had already taken place and parasites have likely established an infection. Parasite counts were performed by dissecting individual midguts in PBS and manually homogenizing them in 50 ul of PBS. Total parasites were counted under the microscope using a haemocytometer. Percentage of infected flies 5 DPI was recorded and sand fly survival was evaluated every day for the duration of the experiment. Three biological replicates were performed.
DOI: 10.7284/116976
title: GNSS (Global Navigation Satellite System) data collected during research cruise SAV-14-17 using a Furuno GP-90 instrument system onboard the platform RV Savannah

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7283519
title: Mapas TCC (Modelos de distribuição potencial)

description: MaxEnt modelling of tree ferns from Brazil
DOI: 10.7284/116977
title: GNSS (Global Navigation Satellite System) data collected during research cruise SAV-14-18 using a Furuno GP-90 instrument system onboard the platform RV Savannah

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7283546.v2
title: Non-invasive visualisation and identification of fluorescent Leishmania tarentolae in infected sand flies

description: A total of 2 x 10<sup>6 </sup>parasites were pelleted (1200xg, 10 min) and washed once with ice-cold PBS before resuspending in 1ml of blood meal (sheep blood mixed with heat-inactivated serum) and fed to the insects using a chick skin membrane with the Hemotek apparatus at 37 °C as described above. Groups of ~80 females were fed for one hour, after which 60 fully-engorged individuals were separated and kept under standard laboratory conditions until required for experimental work. Negative control groups were flies fed only on sheep blood and manipulated as stated above. Sand fly mortality was recorded daily and 14 insects were dissected 5 days post infection (DPI), when defecation had already taken place and parasites have likely established an infection. Parasite counts were performed by dissecting individual midguts in PBS and manually homogenizing them in 50 ul of PBS. Total parasites were counted under the microscope using a haemocytometer. Percentage of infected flies 5 DPI was recorded and sand fly survival was evaluated every day for the duration of the experiment. Three biological replicates were performed.
DOI: 10.6084/m9.figshare.7283519.v1
title: Mapas TCC (Modelos de distribuição potencial)

description: MaxEnt modelling of tree ferns from Brazil
DOI: 10.7284/120500
title: ADCP (Acoustic Doppler Current Profiler) data collected during research cruise SAV-14-19 using a RDI WM-300 instrument system onboard the platform RV Savannah

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7283510
title: ABM Cell Migration Data and Its Statistics

description: The folder contains two subfolders.<br><br>1. AgentBasedModel_SpatioTemporalResults<br><br>The data in this folder is simulation results of the agent-based model for inflammation in .mat format.<br><br>The data consists of array of 100x100 matrices. The size of the array is 10000, the number of simulation iterations.<br>Hence the data is 10000x100x100 array. Each with 10 repetitions/trials.<br><br>The data is arranged based on cases presented in the paper. The file is separated by simulation trials and four categories.<br>The file name denotes this as follows,<br><br>The appendix _tr denote trial number, e.g. _tr6 means trial 6<br><br>The file name begins with category, e.g. epth_ means epithelial agents<br><br>The categories are as follows,<br><br>&gt; files with epth prefix: epithelial cells matrix, 0= death, 1=alive<br>&gt; files with fbr prefix: fibroblast cells matrix, 0= empty (no fibroblast present), 11 or -2= a fibroblast present<br>&gt; files with mcr prefix: macrophage cells matrix, 0=empty (no macrophage present), 1 or 2= a macrophage present<br>&gt; files with mot prefix: matrix of both macrophage and fibroblast, 0=empty (no macrophage present) else= a motile cell (either fibroblast or macrophage) present <br><br><br><br>2. TransferEntropy<br>The data here are the calculated Transfer Entropy. <br><br>The files are stored in folder according to cases as described in the paper.<br><br>In each file, users can find ten 20x20 matrices. Each entry is transfer entropy value of macrophage and fibroblast.<br><br>The indexing is T(fibroblast, macrophage).<br><br>From these matrices, probability distribution can be created, and networks of Macrophage and Fibroblast can be generated. These are explained in the paper.
DOI: 10.6084/m9.figshare.7283546.v4
title: Non-invasive visualisation and identification of fluorescent Leishmania tarentolae in infected sand flies

description: A total of 2 x 10<sup>6 </sup>parasites were pelleted (1200xg, 10 min) and washed once with ice-cold PBS before resuspending in 1ml of blood meal (sheep blood mixed with heat-inactivated serum) and fed to the insects using a chick skin membrane with the Hemotek apparatus at 37 °C as described above. Groups of ~80 females were fed for one hour, after which 60 fully-engorged individuals were separated and kept under standard laboratory conditions until required for experimental work. Negative control groups were flies fed only on sheep blood and manipulated as stated above. Sand fly mortality was recorded daily and 14 insects were dissected 5 days post infection (DPI), when defecation had already taken place and parasites have likely established an infection. Parasite counts were performed by dissecting individual midguts in PBS and manually homogenizing them in 50 ul of PBS. Total parasites were counted under the microscope using a haemocytometer. Percentage of infected flies 5 DPI was recorded and sand fly survival was evaluated every day for the duration of the experiment. Three biological replicates were performed.
DOI: 10.6084/m9.figshare.7283546.v3
title: Non-invasive visualisation and identification of fluorescent Leishmania tarentolae in infected sand flies

description: A total of 2 x 10<sup>6 </sup>parasites were pelleted (1200xg, 10 min) and washed once with ice-cold PBS before resuspending in 1ml of blood meal (sheep blood mixed with heat-inactivated serum) and fed to the insects using a chick skin membrane with the Hemotek apparatus at 37 °C as described above. Groups of ~80 females were fed for one hour, after which 60 fully-engorged individuals were separated and kept under standard laboratory conditions until required for experimental work. Negative control groups were flies fed only on sheep blood and manipulated as stated above. Sand fly mortality was recorded daily and 14 insects were dissected 5 days post infection (DPI), when defecation had already taken place and parasites have likely established an infection. Parasite counts were performed by dissecting individual midguts in PBS and manually homogenizing them in 50 ul of PBS. Total parasites were counted under the microscope using a haemocytometer. Percentage of infected flies 5 DPI was recorded and sand fly survival was evaluated every day for the duration of the experiment. Three biological replicates were performed.
DOI: 10.7284/120503
title: CTD (Conductivity, Temperature, Depth) data collected during research cruise SAV-14-19 using a Sea-Bird SBE-25 instrument system onboard the platform RV Savannah

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7283510.v2
title: ABM Cell Migration Data and Its Statistics

description: The folder contains two subfolders.<br><br>1. AgentBasedModel_SpatioTemporalResults<br><br>The data in this folder is simulation results of the agent-based model for inflammation in .mat format.<br><br>The data consists of array of 100x100 matrices. The size of the array is 10000, the number of simulation iterations.<br>Hence the data is 10000x100x100 array. Each with 10 repetitions/trials.<br><br>The data is arranged based on cases presented in the paper. The file is separated by simulation trials and four categories.<br>The file name denotes this as follows,<br><br>The appendix _tr denote trial number, e.g. _tr6 means trial 6<br><br>The file name begins with category, e.g. epth_ means epithelial agents<br><br>The categories are as follows,<br><br>&gt; files with epth prefix: epithelial cells matrix, 0= death, 1=alive<br>&gt; files with fbr prefix: fibroblast cells matrix, 0= empty (no fibroblast present), 11 or -2= a fibroblast present<br>&gt; files with mcr prefix: macrophage cells matrix, 0=empty (no macrophage present), 1 or 2= a macrophage present<br>&gt; files with mot prefix: matrix of both macrophage and fibroblast, 0=empty (no macrophage present) else= a motile cell (either fibroblast or macrophage) present <br><br><br><br>2. TransferEntropy<br>The data here are the calculated Transfer Entropy. <br><br>The files are stored in folder according to cases as described in the paper.<br><br>In each file, users can find ten 20x20 matrices. Each entry is transfer entropy value of macrophage and fibroblast.<br><br>The indexing is T(fibroblast, macrophage).<br><br>From these matrices, probability distribution can be created, and networks of Macrophage and Fibroblast can be generated. These are explained in the paper.
DOI: 10.7284/116978
title: GNSS (Global Navigation Satellite System) data collected during research cruise SAV-14-19 using a Furuno GP-90 instrument system onboard the platform RV Savannah

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7283510.v1
title: ABM Cell Migration Data and Its Stastics

description: Notes<br><br>The folder contains two subfolders.<br><br>1. AgentBasedModel_SpatioTemporalResults<br><br>The data in this folder is simulation results of the agent-based model for inflammation in .mat format.<br><br>The data consists of array of 100x100 matrices. The size of the array is 10000, the number of simulation iterations.<br>Hence the data is 10000x100x100 array. Each with 10 repetitions/trials.<br><br>The data is arranged based on cases presented in the paper. The file is separated by simulation trials and four categories.<br>The file name denotes this as follows,<br><br>The appendix _tr denote trial number, e.g. _tr6 means trial 6<br><br>The file name begins with category, e.g. epth_ means epithelial agents<br><br>The categories are as follows,<br><br>&gt; files with epth prefix: epithelial cells matrix, 0= death, 1=alive<br>&gt; files with fbr prefix: fibroblast cells matrix, 0= empty (no fibroblast present), 11 or -2= a fibroblast present<br>&gt; files with mcr prefix: macrophage cells matrix, 0=empty (no macrophage present), 1 or 2= a macrophage present<br>&gt; files with mot prefix: matrix of both macrophage and fibroblast, 0=empty (no macrophage present) else= a motile cell (either fibroblast or macrophage) present <br><br><br><br>2. TransferEntropy<br>The data here are the calculated Transfer Entropy. <br><br>The files are stored in folder according to cases as described in the paper.<br><br>In each file, users can find ten 20x20 matrices. Each entry is transfer entropy value of macrophage and fibroblast.<br><br>The indexing is T(fibroblast, macrophage).<br><br>From these matrices, probability distribution can be created, and networks of Macrophage and Fibrbolast can be generated. These are explained in the paper.<br><br>
DOI: 10.6084/m9.figshare.7283504
title: Mapas TCC (Unidades de Conservação)

description: MaxEnt modelling of tree ferns from Brazil
DOI: 10.26180/5bda27018b1f7
title: p1 day 2 attend condition

description: participant 2 day 2 attend condition raw EEG data
DOI: 10.7284/120504
title: Gyrocompass data collected during research cruise SAV-14-19 using a Yokogawa CMZ700B instrument system onboard the platform RV Savannah

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7283504.v1
title: Mapas TCC (Unidades de Conservação)

description: MaxEnt modelling of tree ferns from Brazil
DOI: 10.6084/m9.figshare.7283498
title: The effects of organic amendments and plastic mulch on soil bacterial and fungal communities over time in tomato cropping systems

description: Bacterial and fungal amplicons from 16S and ITS (Internal Transcribed Spacer) rRNA (ribosomal RNA) genes using Illumina sequencing technique. Bacterial and fungal libraries included each one a compressed fastq.gz files (R1 and R2) containing sequence and quality data. <br>
DOI: 10.7284/120502
title: Meteorological Station data collected during research cruise SAV-14-19 using a RM Young 26800 instrument system onboard the platform RV Savannah

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/120501
title: Singlebeam Echosounder data collected during research cruise SAV-14-19 using a Furuno FCV-582 instrument system onboard the platform RV Savannah

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7283498.v2
title: The effects of organic amendments and plastic mulch on soil bacterial and fungal communities over time in tomato cropping systems

description: Bacterial and fungal amplicons from 16S and ITS (Internal Transcribed Spacer) rRNA (ribosomal RNA) genes using Illumina sequencing technique. Bacterial and fungal libraries included each one a compressed fastq.gz files (R1 and R2) containing sequence and quality data. <br>
DOI: 10.7284/120505
title: TSG (Thermosalinograph) data collected during research cruise SAV-14-19 using a Sea-Bird SBE-21 instrument system onboard the platform RV Savannah

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/120508
title: CTD (Conductivity, Temperature, Depth) data collected during research cruise SAV-14-20 using a Sea-Bird SBE-25 instrument system onboard the platform RV Savannah

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.26180/5bda25c939b05
title: p1 day 1 non-attend EEG data

description: p1 day 1 non-attend EEG data
DOI: 10.6084/m9.figshare.7283480
title: Induced stress data files

description: Data used to generate figures of for the paper "Effects of Induced Stress on Seismic Waves: validation based on Ab Initio Calculations". Calculations performed for two crystals: NaCl (prefix=NaCl) and MgO (prefix=MgO). Brief description of the files:<br>prefix_calculated_data.dat<br>Energy, pressure, volume, and elastic coefficients for a cubic crystal<br>prefix_Xi.datData used to generate figure 1. (Elastic coefficients)<br>prefix_Xip.datData used to generate figure 2 (Elastic coefficients derivatives)<br>prefix_induced_pressure.datData used to generate figure3<br>prefix_induced_uniaxial_stretch.datData used to generate figure 4<br>prefix_induced_uniaxial_stretch_dev_stress.datData used to generate figure 5<br>prefix_induced_uniaxial_stretch_ind_press.datData used to generate figure 6<br><br><br>
DOI: 10.6084/m9.figshare.7283471
title: Elucidating the survival and response of carbapenem resistant <i>Klebsiella pneumoniae</i> after exposure to imipenem at sub-lethal concentrations

description: The increasing prevalence of antibiotic resistant pathogens poses a serious threat to global health. However, less emphasis has been placed to co-relate the gene expression and metabolism of antibiotic resistant pathogens. This study aims to elucidate gene expression and variations in metabolism of multidrug resistant <i>Klebsiella pneumoniae</i> after exposure to antibiotics. Phenotypic responses of three genotypically distinct carbapenem resistant <i>Klebsiella pneumoniae</i> (CRKP) strains untreated and treated with sub-lethal concentrations of imipenem were investigated via phenotype microarrays (PM). The gene expression and metabolism of the strain harboring <i>bla</i><sub>NDM-1</sub> before and after exposure to sub-lethal concentration of imipenem were further investigated by RNA-sequencing (RNA-Seq) and <sup>1</sup>H NMR spectroscopy respectively. Most genes related to cell division, central carbon metabolism and nucleotide metabolism were downregulated after imipenem treatment. Similarly, <sup>1</sup>H NMR spectra obtained from treated CRKP showed decrease in levels of bacterial end products (acetate, pyruvate, succinate, formate) and metabolites involved in nucleotide metabolism (uracil, xanthine, hypoxanthine) but elevated levels of glycerophosphocholine. The presence of anserine was also observed for the treated CRKP while FAPγ-adenine and methyladenine were only present in untreated bacterial cells. As a conclusion, the studied CRKP strain exhibited decrease in central carbon metabolism, cell division and nucleotide metabolism after exposure to sub-lethal concentrations of imipenem. The understanding of the complex biological system of this multidrug resistant bacterium may help in the development of novel strategies and potential targets for the management of the infections.
DOI: 10.7284/116979
title: GNSS (Global Navigation Satellite System) data collected during research cruise SAV-14-20 using a Furuno GP-90 instrument system onboard the platform RV Savannah

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7283471.v1
title: Elucidating the survival and response of carbapenem resistant <i>Klebsiella pneumoniae</i> after exposure to imipenem at sub-lethal concentrations

description: The increasing prevalence of antibiotic resistant pathogens poses a serious threat to global health. However, less emphasis has been placed to co-relate the gene expression and metabolism of antibiotic resistant pathogens. This study aims to elucidate gene expression and variations in metabolism of multidrug resistant <i>Klebsiella pneumoniae</i> after exposure to antibiotics. Phenotypic responses of three genotypically distinct carbapenem resistant <i>Klebsiella pneumoniae</i> (CRKP) strains untreated and treated with sub-lethal concentrations of imipenem were investigated via phenotype microarrays (PM). The gene expression and metabolism of the strain harboring <i>bla</i><sub>NDM-1</sub> before and after exposure to sub-lethal concentration of imipenem were further investigated by RNA-sequencing (RNA-Seq) and <sup>1</sup>H NMR spectroscopy respectively. Most genes related to cell division, central carbon metabolism and nucleotide metabolism were downregulated after imipenem treatment. Similarly, <sup>1</sup>H NMR spectra obtained from treated CRKP showed decrease in levels of bacterial end products (acetate, pyruvate, succinate, formate) and metabolites involved in nucleotide metabolism (uracil, xanthine, hypoxanthine) but elevated levels of glycerophosphocholine. The presence of anserine was also observed for the treated CRKP while FAPγ-adenine and methyladenine were only present in untreated bacterial cells. As a conclusion, the studied CRKP strain exhibited decrease in central carbon metabolism, cell division and nucleotide metabolism after exposure to sub-lethal concentrations of imipenem. The understanding of the complex biological system of this multidrug resistant bacterium may help in the development of novel strategies and potential targets for the management of the infections.
DOI: 10.6084/m9.figshare.7283480.v1
title: Induced stress data files

description: Data used to generate figures of for the paper "Effects of Induced Stress on Seismic Waves: validation based on Ab Initio Calculations". Calculations performed for two crystals: NaCl (prefix=NaCl) and MgO (prefix=MgO). Brief description of the files:<br>prefix_calculated_data.dat<br>Energy, pressure, volume, and elastic coefficients for a cubic crystal<br>prefix_Xi.datData used to generate figure 1. (Elastic coefficients)<br>prefix_Xip.datData used to generate figure 2 (Elastic coefficients derivatives)<br>prefix_induced_pressure.datData used to generate figure3<br>prefix_induced_uniaxial_stretch.datData used to generate figure 4<br>prefix_induced_uniaxial_stretch_dev_stress.datData used to generate figure 5<br>prefix_induced_uniaxial_stretch_ind_press.datData used to generate figure 6<br><br><br>
DOI: 10.23641/asha.7283459
title: Sensitivity to morphosyntactic information (Deevy & Leonard, 2018)

description: <b>Purpose: </b>This study tested children’s sensitivity to tense/agreement information in fronted auxiliaries during online comprehension of questions (e.g., <i>Are the nice little dogs running?</i>). Data from children with developmental language disorder (DLD) were compared to previously published data from typically developing (TD) children matched according to sentence comprehension test scores.<b>Method: </b>Fifteen 5-year-old children with DLD and fifteen 3-year-old TD children participated in a looking-while-listening task. Children viewed pairs of pictures, 1 with a single agent and 1 with multiple agents, accompanied by a sentence with a fronted auxiliary (<i>is</i> + single agent or <i>are</i> + two agents) or a control sentence. Proportion looking to the target was measured.<b>Results: </b>Children with DLD did not show anticipatory looking based on the number information contained in the auxiliary (<i>is</i> or <i>are</i>) as the younger TD children had. Both groups showed significant increases in looking to the target upon hearing the subject noun (e.g., <i>dogs</i>).<b>Conclusions:</b> Despite the groups’ similar sentence comprehension abilities and ability to accurately respond to the information provided by the subject noun, children with DLD did not show sensitivity to number information on the fronted auxiliary. This insensitivity is considered in light of these children’s weaker command of tense/agreement forms in their speech. Specifically, we consider the possibility that failure to grasp the relation between the subject–verb sequence (e.g., <i>dogs running</i>) and preceding information (e.g., <i>are</i>) in questions in the input contributes to the protracted inconsistency in producing auxiliary forms in obligatory contexts by children with DLD.<b><br></b><b>Supplemental Material S1.</b> Example illustration paired with target sentences.<br><b>Supplemental Material S2.</b> Sentences used in the experimental task.<br>Deevy, P., & Leonard, L. B. (2018). Sensitivity to morphosyntactic information in preschool children with and without developmental language disorder: A follow-up study. <i>Journal of Speech, Language, and Hearing Research. </i>Advance online publication. https://doi.org/10.1044/2018_JSLHR-L-18-0038<br>