cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5738790.v1
title: Additional file 6: Figure S5. of Under control: how a dietary additive can restore the gut microbiome and proteomic profile, and improve disease resilience in a marine teleostean fish fed vegetable diets

description: Krona analysis of the relative abundance of intestinal bacterial OTUs identified in fish fed D4. (HTML 250 kb)
DOI: 10.6084/m9.figshare.5738766
title: Additional file 5: Figure S4. of Under control: how a dietary additive can restore the gut microbiome and proteomic profile, and improve disease resilience in a marine teleostean fish fed vegetable diets

description: Krona analysis of the relative abundance of intestinal bacterial OTUs identified in fish fed D3. (HTML 246 kb)
DOI: 10.6084/m9.figshare.5738766.v1
title: Additional file 5: Figure S4. of Under control: how a dietary additive can restore the gut microbiome and proteomic profile, and improve disease resilience in a marine teleostean fish fed vegetable diets

description: Krona analysis of the relative abundance of intestinal bacterial OTUs identified in fish fed D3. (HTML 246 kb)
DOI: 10.6084/m9.figshare.5738757
title: Additional file 4: Figure S3. of Under control: how a dietary additive can restore the gut microbiome and proteomic profile, and improve disease resilience in a marine teleostean fish fed vegetable diets

description: Krona analysis of the relative abundance of intestinal bacterial OTUs identified in fish fed D2. (HTML 243 kb)
DOI: 10.6084/m9.figshare.5738757.v1
title: Additional file 4: Figure S3. of Under control: how a dietary additive can restore the gut microbiome and proteomic profile, and improve disease resilience in a marine teleostean fish fed vegetable diets

description: Krona analysis of the relative abundance of intestinal bacterial OTUs identified in fish fed D2. (HTML 243 kb)
DOI: 10.6084/m9.figshare.5738742
title: Additional file 3: Figure S2. of Under control: how a dietary additive can restore the gut microbiome and proteomic profile, and improve disease resilience in a marine teleostean fish fed vegetable diets

description: Krona visualisation of the relative abundance of intestinal bacterial OTUs identified in fish fed D1. (HTML 238 kb)
DOI: 10.6084/m9.figshare.5738742.v1
title: Additional file 3: Figure S2. of Under control: how a dietary additive can restore the gut microbiome and proteomic profile, and improve disease resilience in a marine teleostean fish fed vegetable diets

description: Krona visualisation of the relative abundance of intestinal bacterial OTUs identified in fish fed D1. (HTML 238 kb)
DOI: 10.6084/m9.figshare.5738736
title: Additional file 4: Table S3. of Deep convolutional neural networks for pan-specific peptide-MHC class I binding prediction

description: Detailed results for 5-fold cross-validation. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.5738736.v1
title: Additional file 4: Table S3. of Deep convolutional neural networks for pan-specific peptide-MHC class I binding prediction

description: Detailed results for 5-fold cross-validation. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.5738724
title: Additional file 2: of Reporting quality of randomized controlled trials in patients with HIV on antiretroviral therapy: a systematic review

description: Included studies and the information extracted from them. (XLSX 29 kb)
DOI: 10.6084/m9.figshare.5738724.v1
title: Additional file 2: of Reporting quality of randomized controlled trials in patients with HIV on antiretroviral therapy: a systematic review

description: Included studies and the information extracted from them. (XLSX 29 kb)
DOI: 10.6084/m9.figshare.5738715
title: Additional file 2: Table S1. of Under control: how a dietary additive can restore the gut microbiome and proteomic profile, and improve disease resilience in a marine teleostean fish fed vegetable diets

description: Percentage of the different bacterial OTUs identified in intestinal mucus of fish fed different diets. The results can be sorted by Phylum, Family, Genus and Species (OTUs). Numbers represent the mean percentage of four replicate pools. (XLSX 63 kb)
DOI: 10.6084/m9.figshare.5738715.v1
title: Additional file 2: Table S1. of Under control: how a dietary additive can restore the gut microbiome and proteomic profile, and improve disease resilience in a marine teleostean fish fed vegetable diets

description: Percentage of the different bacterial OTUs identified in intestinal mucus of fish fed different diets. The results can be sorted by Phylum, Family, Genus and Species (OTUs). Numbers represent the mean percentage of four replicate pools. (XLSX 63 kb)
DOI: 10.6084/m9.figshare.5738712
title: Additional file 3: Table S2. of Deep convolutional neural networks for pan-specific peptide-MHC class I binding prediction

description: Detailed results for leave-one-out cross-validation. (XLSX 16 kb)
DOI: 10.6084/m9.figshare.5738712.v1
title: Additional file 3: Table S2. of Deep convolutional neural networks for pan-specific peptide-MHC class I binding prediction

description: Detailed results for leave-one-out cross-validation. (XLSX 16 kb)
DOI: 10.6084/m9.figshare.5738694
title: Additional file 2: Table S4. of Deep convolutional neural networks for pan-specific peptide-MHC class I binding prediction

description: Detailed prediction results for the IEDB HLA-I benchmark datasets. (XLSX 18 kb)
DOI: 10.6084/m9.figshare.5738694.v1
title: Additional file 2: Table S4. of Deep convolutional neural networks for pan-specific peptide-MHC class I binding prediction

description: Detailed prediction results for the IEDB HLA-I benchmark datasets. (XLSX 18 kb)
DOI: 10.6084/m9.figshare.5738679
title: Additional file 1: Table S1. of Deep convolutional neural networks for pan-specific peptide-MHC class I binding prediction

description: Detailed description of the training dataset. (XLSX 16 kb)
DOI: 10.6084/m9.figshare.5738679.v1
title: Additional file 1: Table S1. of Deep convolutional neural networks for pan-specific peptide-MHC class I binding prediction

description: Detailed description of the training dataset. (XLSX 16 kb)
DOI: 10.6084/m9.figshare.5738637
title: Additional file 3: Table S2. of Invasive micropapillary carcinoma of the breast overexpresses MUC4 and is associated with poor outcome to adjuvant trastuzumab in HER2-positive breast cancer

description: Histological subtypes of the cohort (n = 113). (XLSX 9 kb)
DOI: 10.6084/m9.figshare.5738637.v1
title: Additional file 3: Table S2. of Invasive micropapillary carcinoma of the breast overexpresses MUC4 and is associated with poor outcome to adjuvant trastuzumab in HER2-positive breast cancer

description: Histological subtypes of the cohort (n = 113). (XLSX 9 kb)
DOI: 10.6084/m9.figshare.5738622
title: Additional file 2: Table S1. of Invasive micropapillary carcinoma of the breast overexpresses MUC4 and is associated with poor outcome to adjuvant trastuzumab in HER2-positive breast cancer

description: Clincopathological characteristics of the cohort. (XLS 30 kb)
DOI: 10.6084/m9.figshare.5738622.v1
title: Additional file 2: Table S1. of Invasive micropapillary carcinoma of the breast overexpresses MUC4 and is associated with poor outcome to adjuvant trastuzumab in HER2-positive breast cancer

description: Clincopathological characteristics of the cohort. (XLS 30 kb)
DOI: 10.6084/m9.figshare.5738619
title: Additional file 1: Figure S1. of Photoperiodic responses of Sahelian malaria mosquitoes Anopheles coluzzii and An. arabiensis

description: Cage design of Experiment 2, with plastic “shelter” in one corner of the cage. Figure S2. The relative lipid content of female An. arabiensis (white circles) and An. coluzzii (black squares) under three photoperiod treatments (Experiment 1; panel a) and four photoperiod-temperature treatment combinations (Experiment 2; panel b). Least square means ± 95% CI are given for each trait and significantly different values within each species are designated with letters. The grey dotted line denotes the critical comparison between wet-season and dry-season An. coluzzii in each experiment. (ZIP 3439 kb)
DOI: 10.6084/m9.figshare.5738619.v1
title: Additional file 1: Figure S1. of Photoperiodic responses of Sahelian malaria mosquitoes Anopheles coluzzii and An. arabiensis

description: Cage design of Experiment 2, with plastic “shelter” in one corner of the cage. Figure S2. The relative lipid content of female An. arabiensis (white circles) and An. coluzzii (black squares) under three photoperiod treatments (Experiment 1; panel a) and four photoperiod-temperature treatment combinations (Experiment 2; panel b). Least square means ± 95% CI are given for each trait and significantly different values within each species are designated with letters. The grey dotted line denotes the critical comparison between wet-season and dry-season An. coluzzii in each experiment. (ZIP 3439 kb)
DOI: 10.6084/m9.figshare.5738580
title: Raw data PONE-D-17-36203.zip

description: Raw data of PONE-D-17-36203
DOI: 10.6084/m9.figshare.5738577
title: Integration of microRNA-mRNA profiles and pathway analysis of plant isoquinoline alkaloid berberine in SGC-7901 gastric cancers cells

description: The human gastric cancer cell line SGC-7901 was treated by berberine at 20uM for 24h, and the control group was not treated with berberine. Total RNA was extracted, and sequenced. The mRNA and miRNA expression profiles were established based on the RNA-sequencing and miRNA-sequencing. Some novel miRNAs were also found.<br>
DOI: 10.6084/m9.figshare.5738568
title: CESM1 precip

description: Precip data for NCAR-CESM1 model
DOI: 10.6084/m9.figshare.5738565
title: GISS data

description: GISS-E2 data
DOI: 10.6084/m9.figshare.5738565.v1
title: GISS data

description: GISS-E2 data
DOI: 10.6084/m9.figshare.5738562
title: GFDL precip data

description: GFDL data
DOI: 10.6084/m9.figshare.5738439.v4
title: Tattooed Human Mummies, List Version 3.0

description: The following presents a global data set identifying tattooed human mummies from the archaeological record. The initial version of this list (Version 1.0) was compiled in 2016 for inclusion as Table 1 in the journal article “The World’s Oldest Tattoos” (Deter-Wolf et al. 2016). Benoît Robitaille, Lars Krutak, and Sébastien Galliot all contributed to that initial effort. Changes between versions are detailed below. Entries in the data table are organized broadly by date, and rely on direct dating wherever possible. Where radiocarbon data is available, dates represent calibrated ranges. Each entry also includes documentation wherever possible as to the associated archaeological culture, site, and significant source material. At the present time, unpublished and/or unprovenienced specimens from museums and private collections are not generally included in the data set. Changes from Version 2.0 to 3.0: · Sources Added. · Improved citations and corrected date ranges as necessary <br> · New entries for additional Andean specimens Changes from Version 1.0 to 2.0: · Deleted “Loulan Beauty” from Gumugou, Qäwrighul, China, who is not tattooed. · Updated Egyptian data per Friedman (2017:Table 1) · Improved citations and corrected date ranges as necessary · New entries for Timbac Rockshelter and Andean specimens<br><br><br>
DOI: 10.6084/m9.figshare.5738436
title: Nucleotide sequence for Rbp and chaperone of Pja

description: Nucleotide sequence of the R-type syringacin tail fiber and chaperone protein used to swap R-type syringacin killing activity in associated manuscript.
DOI: 10.6084/m9.figshare.5738436.v1
title: Nucleotide sequence for Rbp and chaperone of Pja

description: Nucleotide sequence of the R-type syringacin tail fiber and chaperone protein used to swap R-type syringacin killing activity in associated manuscript.
DOI: 10.6084/m9.figshare.5738427
title: R scripts for hierarchical clustering

description: To be used with .csv files from associated manuscript to hierarchically cluster data. Two scripts within this one .txt file, one for killing matrix and one for sensitivity matrix.
DOI: 10.6084/m9.figshare.5738427.v2
title: R scripts for hierarchical clustering

description: To be used with .csv files from associated manuscript to hierarchically cluster data. Two scripts within this one .txt file, one for killing matrix and one for sensitivity matrix.
DOI: 10.6084/m9.figshare.5738352
title: Greater Colo­Rectal Activation Phenotype (CRAP) in Exercised Dystrophic Mice.csv

description: Fecal output data for exercised and resting dystrophic and normal mice.
DOI: 10.6084/m9.figshare.5738352.v1
title: Greater Colo­Rectal Activation Phenotype (CRAP) in Exercised Dystrophic Mice.csv

description: Fecal output data for exercised and resting dystrophic and normal mice.
DOI: 10.6084/m9.figshare.5735274
title: Effect of Microtubule Disruption on Dynamics of Acidic Organelles in the Axons of Primary Cultured Retinal Ganglion Cells

description: <i>Purpose</i>: Axonal transport is fundamental to autophagy in neuronal cells. To understand its biological significance in various conditions, it is necessary to monitor the process of autophagy. However, monitoring methods are often limited to static analyses, such as protein expression and histological observations. Autophagy has multistep process and is highly dynamic; therefore, additional techniques are necessary to study autophagy. In this study, we quantified the dynamics of autophagy-related organelle transport under conditions of dynamic instability and catastrophic disruption of microtubules using <i>in vitro</i> live imaging. <i>Materials and methods</i>: Retinal ganglion cells (RGCs) were isolated from postnatal day 3 Sprague–Dawley rats by immunopanning. After 7 days of culture, acidic organelles were stained by LysoTracker. Dynamics of acidic organelles was quantified using kymographs. Colchicine was used to induce microtubule disruption. Movement of acidic organelles was observed at five time points: before, and at 6, 24, 72, and 120 h after colchicine stimulation. Ethidium homodimer-1 (EthD-1) was used to determine cell viability. <i>Results</i>: The status of axonal transport of acidic organelles (<i>n</i> = 363) from 27 RGCs was classified into four categories: anterograde (1.4%), retrograde (90%), stationary (8.0%), and fluttering (0.28%). Six hours after the induction of microtubule disruption in 14 of 27 RGCs, almost all acidic organelles (<i>n</i> = 236) were stationary. All acidic components had completely stopped moving 24 h later. At 72 h after stimulation, axonal fragmentation, and shrinking and disappearance of soma were observed in 71% of RGCs. Finally, the remaining RGCs became positive for EthD-1. In the control (13 of 27 RGCs), axonal transport was maintained for 120 h and EthD-1-positive RGCs were not observed. <i>Conclusion</i>: Almost all acidic organelles were transported retrogradely along the axon, which was inhibited by colchicine. Understanding the dynamics of acidic organelles may provide useful parameters for characterizing autophagy of neuronal cells in pathophysiological conditions.
DOI: 10.6084/m9.figshare.5735274.v1
title: Effect of Microtubule Disruption on Dynamics of Acidic Organelles in the Axons of Primary Cultured Retinal Ganglion Cells

description: <i>Purpose</i>: Axonal transport is fundamental to autophagy in neuronal cells. To understand its biological significance in various conditions, it is necessary to monitor the process of autophagy. However, monitoring methods are often limited to static analyses, such as protein expression and histological observations. Autophagy has multistep process and is highly dynamic; therefore, additional techniques are necessary to study autophagy. In this study, we quantified the dynamics of autophagy-related organelle transport under conditions of dynamic instability and catastrophic disruption of microtubules using <i>in vitro</i> live imaging. <i>Materials and methods</i>: Retinal ganglion cells (RGCs) were isolated from postnatal day 3 Sprague–Dawley rats by immunopanning. After 7 days of culture, acidic organelles were stained by LysoTracker. Dynamics of acidic organelles was quantified using kymographs. Colchicine was used to induce microtubule disruption. Movement of acidic organelles was observed at five time points: before, and at 6, 24, 72, and 120 h after colchicine stimulation. Ethidium homodimer-1 (EthD-1) was used to determine cell viability. <i>Results</i>: The status of axonal transport of acidic organelles (<i>n</i> = 363) from 27 RGCs was classified into four categories: anterograde (1.4%), retrograde (90%), stationary (8.0%), and fluttering (0.28%). Six hours after the induction of microtubule disruption in 14 of 27 RGCs, almost all acidic organelles (<i>n</i> = 236) were stationary. All acidic components had completely stopped moving 24 h later. At 72 h after stimulation, axonal fragmentation, and shrinking and disappearance of soma were observed in 71% of RGCs. Finally, the remaining RGCs became positive for EthD-1. In the control (13 of 27 RGCs), axonal transport was maintained for 120 h and EthD-1-positive RGCs were not observed. <i>Conclusion</i>: Almost all acidic organelles were transported retrogradely along the axon, which was inhibited by colchicine. Understanding the dynamics of acidic organelles may provide useful parameters for characterizing autophagy of neuronal cells in pathophysiological conditions.
DOI: 10.6084/m9.figshare.5735154
title: Example dataset for OCTA processing

description: This is a dataset which can be processed by the MATLAB scripts given within this archive. There are also two .csv files which are used for undistorting the images and are essential for running the scripts.
DOI: 10.6084/m9.figshare.5735151
title: Design files for UC Davis FDML OCTA system

description: These are some descriptive files for helping a designer replicate our OCTA system.
DOI: 10.6084/m9.figshare.5735142
title: MATLAB script for OCTA processing

description: These are the MATLAB scripts (with a ReadMe.txt) that will allow the user to point to a data file (.I16), and set up the processing script to analyze it and generate image stacks.
DOI: 10.6084/m9.figshare.5735142.v1
title: MATLAB script for OCTA processing

description: These are the MATLAB scripts (with a ReadMe.txt) that will allow the user to point to a data file (.I16), and set up the processing script to analyze it and generate image stacks.
DOI: 10.17045/sthlmuni.5734887
title: Inside the production function: the effect of financial contracts on growing firms' technology use. Evidence from a field experiment in Uganda

description: The data files contain data from interviews with Ugandan small business owners that are part of the project <i>Inside the production function: the effect of financial contracts on growing firms' technology use</i> evaluating the effect of loan contract structure on business performance See the readme_data file for more details on the data files. [<b>From readme data file</b>: "The codebooks and questionnaires are kept at UK Data Service Reshare, https://reshare.ukdataservice.ac.uk ... with the Data Collection name ... <i>Inside the Production Function: The Effect of Financial Contracts on Growing Firms</i>' <i>Technology Use. Evidence from a field experiment in Uganda."</i>
DOI: 10.17045/sthlmuni.5734887.v1
title: Inside the production function: the effect of financial contracts on growing firms' technology use. Evidence from a field experiment in Uganda

description: The data files contain data from interviews with Ugandan small business owners that are part of the project <i>Inside the production function: the effect of financial contracts on growing firms' technology use</i> evaluating the effect of loan contract structure on business performance See the readme_data file for more details on the data files. [<b>From readme data file</b>: "The codebooks and questionnaires are kept at UK Data Service Reshare, https://reshare.ukdataservice.ac.uk ... with the Data Collection name ... <i>Inside the Production Function: The Effect of Financial Contracts on Growing Firms</i>' <i>Technology Use. Evidence from a field experiment in Uganda."</i>
DOI: 10.6084/m9.figshare.5734857
title: Aflibercept for AMD with Good VA

description: We report 2-year outcomes of intravitreal aflibercept for exudative age-related macular degeneration with good visual acuity and examine baseline factors associated with good visual outcome.
DOI: 10.6084/m9.figshare.5734857.v1
title: Aflibercept for AMD with Good VA

description: We report 2-year outcomes of intravitreal aflibercept for exudative age-related macular degeneration with good visual acuity and examine baseline factors associated with good visual outcome.
DOI: 10.6084/m9.figshare.5734845
title: The first record of anguine lizards (Anguimorpha, Anguidae) from the early Miocene locality Ulm – Westtangente in Germany

description: The first fossil anguine material from the lower Miocene (MN 2) locality Ulm – Westtangente in Germany is described. The parietal and compound bone of the lower jaw can be attributed to <i>Ophisaurus holeci</i>, previously known only from younger age (MN 3–MN 7). Moreover, the parietal represents the largest parietal of this species. In other disarticulated material, such as frontal, maxilla, dentary and osteoderms, alpha taxonomy is not possible and these elements cannot be allocated at the species level. Despite a limited data source, a phylogenetic analysis was done (16 taxa, 36 characters) producing four equally parsimonious trees. The analysis shows a close relationship of <i>O. holeci</i> and the Eocene <i>Ophisauriscus quadrupes</i>. These two taxa form a monophyletic clade, a sister-clade to <i>Ophisaurus</i> + <i>Anguis</i>. However, more complete skeletal material of <i>O. holeci</i> is needed to support such a statement. We used our phylogenetic analysis to analyze trace character history for one frontal and three parietal characters. The palaeoenvironmental conditions of the locality Ulm – Westtangente bring further support of the previous hypothesis that <i>O. holeci</i> was adapted to environments with high ground water levels – environments around lakes or rivers.
DOI: 10.6084/m9.figshare.5734845.v1
title: The first record of anguine lizards (Anguimorpha, Anguidae) from the early Miocene locality Ulm – Westtangente in Germany

description: The first fossil anguine material from the lower Miocene (MN 2) locality Ulm – Westtangente in Germany is described. The parietal and compound bone of the lower jaw can be attributed to <i>Ophisaurus holeci</i>, previously known only from younger age (MN 3–MN 7). Moreover, the parietal represents the largest parietal of this species. In other disarticulated material, such as frontal, maxilla, dentary and osteoderms, alpha taxonomy is not possible and these elements cannot be allocated at the species level. Despite a limited data source, a phylogenetic analysis was done (16 taxa, 36 characters) producing four equally parsimonious trees. The analysis shows a close relationship of <i>O. holeci</i> and the Eocene <i>Ophisauriscus quadrupes</i>. These two taxa form a monophyletic clade, a sister-clade to <i>Ophisaurus</i> + <i>Anguis</i>. However, more complete skeletal material of <i>O. holeci</i> is needed to support such a statement. We used our phylogenetic analysis to analyze trace character history for one frontal and three parietal characters. The palaeoenvironmental conditions of the locality Ulm – Westtangente bring further support of the previous hypothesis that <i>O. holeci</i> was adapted to environments with high ground water levels – environments around lakes or rivers.
DOI: 10.6084/m9.figshare.5734833
title: Scripts and annotation of Exo70 gene families of the Poaceae

description: Analysis of the Exo70 gene family and NLR-Exo70
DOI: 10.6084/m9.figshare.5734833.v1
title: Scripts and annotation of Exo70 gene families of the Poaceae

description: Analysis of the Exo70 gene family and NLR-Exo70