cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.6743339
title: Natural selection by pathogens increases genetic variation in susceptibility to infection

description: Datasets to measure genetic variation in viral load to natural and non-natural sigma viruses of four Drosophila species, along with MCMCglmm R script to analyse data.
DOI: 10.6084/m9.figshare.6743327
title: BSGC

description: Marine biofilm specific genes defined by comparison between 101 biofilm metagenomes and global seawater metagenomes. Nonredundant genes only present in marine biofilms are defined as biofilm specific gene cagalogue (BSGC).
DOI: 10.6084/m9.figshare.6743327.v1
title: BSGC

description: Marine biofilm specific genes defined by comparison between 101 biofilm metagenomes and global seawater metagenomes. Nonredundant genes only present in marine biofilms are defined as biofilm specific gene cagalogue (BSGC).
DOI: 10.6084/m9.figshare.6743309
title: Subject 3_csv

description: csv files of S3
DOI: 10.6084/m9.figshare.6743324
title: Biofilm Core Gene Catalogue

description: Biofilm core genes defined by 101 marine biofilm metagenomes
DOI: 10.6084/m9.figshare.6743324.v1
title: Biofilm Core Gene Catalogue

description: Biofilm core genes defined by 101 marine biofilm metagenomes
DOI: 10.6084/m9.figshare.6743309.v1
title: Subject 3_csv

description: csv files of S3
DOI: 10.6084/m9.figshare.6743276
title: Ribosome profiling in cyanobacteria

description: Supplemental material for "Ribosome profiling of <i>Synechocystis</i> reveals altered ribosome allocation at carbon starvation" by Karlsen <i>et al.</i>, 2018 (DOI: 10.1128/mSystems.00126-18).<br><i>Legends.pdf</i> contains the full legends, while short descriptions are shown below.<br><br><b>Table S1. Grubbs test for outliers in RPF RPKM data at HC and LC.<br><br>Table S2. RNA RPKM, RPF RPKM, and translational efficiencies at HC and LC.<br><br>Table S3. Intragenic PS pattern correlation between samples.<br><br>Figure S1. Puromycin incorporation reveals translation under C<sub>i</sub> starvation.<br><br>Figure S2. Comparison and Pearson correlation of RPF RPKM under the different conditions.<br><br>Figure S3. Transcription level (mRNA) and protein synthesis rate (RPF; ribosome protected footprints) of the slr0373-slr0374-slr0376 operon in HC* (-5 min sample) and LC (24 h sample) conditions.<br><br>Figure S4. Pause score (PS) distribution for every codon in each condition.<br><br>Figure S5. Detailed view of the 5’ UTR pause score (PS) profile in each condition.<br><br>Figure S6. Average ORF pause score (PS) at 5’ and 3’ ends with different filtering of ORFs.<br><br>Figure S7. Pause score (PS) plots for (A) ssl1911 (<i>gifA</i>), (B) slr1834 (<i>psaA</i>) and (C) ssr0390 (<i>psaK1</i>).<br><br>Figure S8. Correlation of 5' UTR, ORF, and 3' UTR RPF RPKM, for each condition, and correlation of 5' UTR, ORF, and 3' UTR fold change (FC) in RPF RPKM from HC* (-5 min) to LC (24 h).<br><br>Figure S9. ORF pause score (PS) patterns are highly correlated between two conditions if the RPF RPKM is high.<br><br>Figure S10. Sucrose density gradient profiles of MNase digested polysomes shows elevated levels of dimerized ribosomes (100S) at LC.</b><b><br></b><b>Figure S11. RPF read length distribution for each sample.</b><b><br></b><b>Figure S12. Total read count per nucleotide at gene 5’ and 3’ ends for each sample.<br></b><b><br>Text S1. Supplemental methods with details of ribosome profiling and RNAseq sample preparation.</b><br><br>
DOI: 10.6084/m9.figshare.6743267
title: Supplementary Material for: Tolerability and Efficacy of Neoadjuvant Chemotherapy with a Tri-Weekly Interval Methotrexate, Doxorubicin, Vinblastine, and Cisplatin Regimen for Patients with Locally Advanced Bladder Cancer

description: <b><i>Objective:</i></b> Compared with standard treatment, a modified tri-weekly MVAC (methotrexate, doxorubicin, vinblastine, and cisplatin) treatment regimen with a high cisplatin dose intensity shows good efficacy and lower toxicity. Thus, we retrospectively investigated the tolerability and efficacy of a modified tri-weekly MVAC neoadjuvant regimen. <b><i>Methods:</i></b> We analyzed 25 patients with locally advanced bladder cancer medicated by a modified tri-weekly MVAC neoadjuvant regimen that omits treatment on days 15 and 22. The efficacy and tolerability were assessed retrospectively. <b><i>Results:</i></b> The numbers of patients in clinical stages 2, 3, and 4 were 13 (52.0%), 1 (4.0%), and 11 (44.0%), respectively. Surgery could be performed on all patients. Five patients (20.0%) had no cancer remaining in their surgical specimens. Remaining non-muscle-invasive cancer without metastasis was observed in 7 patients (28.0%), and the total downstaging rate was 44.0%. The 5-year overall and relapse-free survival rates were 79.0 and 75.0%, respectively. The overall relative dose intensity was 0.90. Serious hematologic toxicities rated grade 3 or greater were leukopenia in 6 patients (24.0%) and anemia in 1 patient (4.0%). <b><i>Conclusions:</i></b> Sufficient efficacy and tolerability of a modified tri-weekly MVAC neoadjuvant regimen were suggested. Thus, tri-weekly modified MVAC may be an option for neoadjuvant chemotherapy of advanced bladder cancer.
DOI: 10.6084/m9.figshare.6743216
title: Subject 2_csv

description: csv files of S2
DOI: 10.6084/m9.figshare.6743216.v1
title: Subject 2_csv

description: csv files of S2
DOI: 10.6084/m9.figshare.6743204
title: Supplementary Material for: Characterization of Pattern Recognition Receptor Expression and Functionality in Liver Primary Cells and Derived Cell Lines

description: Different liver cell types are endowed with immunological properties, including cell-intrinsic innate immune functions that are important to initially control pathogen infections. However, a full landscape of expression and functionality of the innate immune signaling pathways in the major human liver cells is still missing. In order to comparatively characterize these pathways, we purified primary human hepatocytes, hepatic stellate cells, liver sinusoidal endothelial cells (LSEC), and Kupffer cells (KC) from human liver resections. We assessed mRNA and protein expression level of the major innate immune sensors, as well as checkpoint-inhibitor ligands in the purified cells, and found Toll-like receptors (TLR), RIG-I-like receptors, as well as several DNA cytosolic sensors to be expressed in the liver microenvironment. Amongst the cells tested, KC were shown to be most broadly active upon stimulation with PRR ligands emphasizing their predominant role in innate immune sensing the liver microenvironment. By KC immortalization, we generated a cell line that retained higher innate immune functionality as compared to THP1 cells, which are routinely used to study monocyte/macrophages functions. Our findings and the establishment of the KC line will help to understand immune mechanisms behind antiviral effects of TLR agonists or checkpoint inhibitors, which are in current preclinical or clinical development.
DOI: 10.6084/m9.figshare.6743207.v1
title: GBIF for CREST database

description: This database contains all the presence records of plants, beetles, chironomids, foraminifera and diatoms contained in the GBIF database in April 2018.<br>The coordinates of the presence records have been homogenised on a 0.25x0.25° grid, and corresponding bioclimatic values from the Worldclim2.0 database have been added.<br>These data are formatted and ready to use by the CREST software. Additional python scripts have been added to group plant species into pollen types.
DOI: 10.6084/m9.figshare.6743207.v2
title: GBIF for CREST database

description: This database contains all the presence records of plants, beetles, chironomids, foraminifera and diatoms contained in the GBIF database in April 2018.<br>The coordinates of the presence records have been homogenised on a 0.25x0.25° grid, and corresponding bioclimatic values from the Worldclim2.0 database have been added.<br>These data are formatted and ready to use by the CREST software. Additional python scripts have been added to group plant species into pollen types.
DOI: 10.6084/m9.figshare.6743207.v3
title: GBIF for CREST database

description: This database contains all the presence records of plants, beetles, chironomids, foraminifera and diatoms contained in the GBIF database in April 2018.<br>The coordinates of the presence records have been homogenised on a 0.25x0.25° grid, and corresponding bioclimatic values from the Worldclim2.0 database have been added.<br>These data are formatted and ready to use by the CREST software. Additional python scripts have been added to group plant species into pollen types.
DOI: 10.6084/m9.figshare.6743207.v4
title: GBIF for CREST database

description: This database contains all the presence records of plants, beetles, chironomids, foraminifera and diatoms contained in the GBIF database in April 2018.<br>The coordinates of the presence records have been homogenised on a 0.25x0.25° grid, and corresponding bioclimatic values from the Worldclim2.0 database have been added.<br>These data are formatted and ready to use by the CREST software. Additional python scripts have been added to group plant species into pollen types.<br><b>To download the latest version of the database, please follow this link: https://figshare.com/articles/GBIF_for_CREST_database/6743207/3</b>
DOI: 10.6084/m9.figshare.6743207.v5
title: GBIF for CREST database

description: This database contains all the presence records of plants, beetles, chironomids, foraminifera and diatoms contained in the GBIF database in April 2018.<br>The coordinates of the presence records have been homogenised on a 0.25x0.25° grid, and corresponding bioclimatic values from the Worldclim2.0 database have been added.<br>These data are formatted and ready to use by the CREST software. Additional python scripts have been added to group plant species into pollen types.<br><b>To download the latest version of the database, please follow this link: https://figshare.com/articles/GBIF_for_CREST_database/6743207</b>
DOI: 10.6084/m9.figshare.6743120
title: Subject 1_csv

description: CSV files of S1
DOI: 10.6084/m9.figshare.6743120.v1
title: Subject 1_csv

description: CSV files of S1
DOI: 10.6084/m9.figshare.6743075
title: Interaction between autophagic vesicles and the <i>Coxiella</i>-containing vacuole requires CLTC (clathrin heavy chain)

description: <i>Coxiella burnetii</i> is an intracellular bacterial pathogen which causes Q fever, a human infection with the ability to cause chronic disease with potentially life-threatening outcomes. In humans, <i>Coxiella</i> infects alveolar macrophages where it replicates to high numbers in a unique, pathogen-directed lysosome-derived vacuole. This compartment, termed the <i>Coxiella</i>-containing vacuole (CCV), has a low internal pH and contains markers both of lysosomes and autophagosomes. The CCV membrane is also enriched with CLTC (clathrin heavy chain) and this contributes to the success of the CCV. Here, we describe a role for CLTC, a scaffolding protein of clathrin-coated vesicles, in facilitating the fusion of autophagosomes with the CCV. During gene silencing of <i>CLTC</i>, CCVs are unable to fuse with each other, a phenotype also seen when silencing genes involved in macroautophagy/autophagy. MAP1LC3B/LC3B, which is normally observed inside the CCV, is excluded from CCVs in the absence of CLTC. Additionally, this study demonstrates that autophagosome fusion contributes to CCV size as cell starvation and subsequent autophagy induction leads to further CCV expansion. This is CLTC dependent, as the absence of CLTC renders autophagosomes no longer able to contribute to the expansion of the CCV. This investigation provides a functional link between CLTC and autophagy in the context of <i>Coxiella</i> infection and highlights the CCV as an important tool to explore the interactions between these vesicular trafficking pathways.
DOI: 10.6084/m9.figshare.6743051
title: Bat fly-associated Laboulbeniales log and trees files LSU

description: Output log and .trees files of the BEAST analysis of the LSU dataset, under a TPM2uf+G model of nucleotide substitution. Two independent runs were performed for 40 million generations.<br><br>--Haelewaters et al. 2018. Laboulbeniales hyperparasites (Fungi, Ascomycota) of bat flies: Independent origins and host associations. DOI:10.1002/ece3.4359<br>ABSTRACTThe aim of this study was to explore the diversity of ectoparasitic fungi (Ascomycota, Laboulbeniales) that use bat flies (Diptera, Hippoboscoidea) as hosts. Bat flies themselves live as ectoparasites on the fur and wing membranes of bats (Mammalia, Chiroptera); hence this is a tripartite parasite system. Here, we collected bats, bat flies, and Laboulbeniales, and conducted phylogenetic analyses of Laboulbeniales to contrast morphology with ribosomal sequence data. Parasitism of bat flies by Laboulbeniales arose three times independently, once in the Eastern Hemisphere (Arthrorhynchus) and twice in the Western Hemisphere (Gloeandromyces, Nycteromyces). We hypothesize that the genera Arthrorhynchus and Nycteromyces evolved independently from lineages of ectoparasites of true buge (Hemiptera). We assessed phylogenetic diversity of the genus Gloeandromyces by considering the LSU rDNA region. Phenotypic plasticity and position-induced morphological adaptations go hand in hand. Different morphotypes belong to the same phylogenetic species. Two species, G. pageanus and G. streblae, show divergence by host utilization. In our assessement of coevolution, we only observe congruence between the Old World clades of bat flies and Laboulbeniales. The other associations are the result of the roosting ecology of the bat hosts. This study has considerably increased our knowledge about bats and their associated ectoparasites and shown the necessity of including molecular data in Laboulbeniales taxonomy. <br>KEYWORDSAscomycota, ectoparasites, host specialization, phenotypic plasticity, ribosomal DNA, taxonomy
DOI: 10.6084/m9.figshare.6743057.v1
title: Genetic data-Dongxiang.xlsx

description: In comparison with the most preferred genetic marker utilized in forensic science (STR), insertion/deletion analysis possesses further benefits, like absence of stutter peak, low mutation rate and enabling mixed stain analysis. At present, a total of 169 unrelated healthy Dongxiang individuals dwelling in Dongxiang Autonomous county of Gansu province were recruited in our study to appraise the forensic usefulness of the panel including 30 autosomal diallelic genetic markers. The insertion allele frequencies were in the range of 0.1598 at HLD 111 to 0.8850 at HLD 118. The cumulative match of probability and the combined probability of exclusion were estimated based on independence of pairwise loci, with the values of 3.96×10<sup>-11</sup> and 0.9886, respectively, which showed tremendous potential of this panel to be qualified for forensic personal identification in Chinese Dongxiang group. And it could also be used as a complementary tool for forensic parentage testing when combined with standard STR genetic markers. Furthermore, calculation of the <i>D<sub>A</sub></i> distance and <i>F<sub>st</sub></i> values of pairwise populations, phylogenetic reconstruction, multidimensional scaling analysis, structure clustering analysis were also conducted to probe the genetic relationships between Dongxiang group and the other 30 reference populations. Results demonstrated that Dongxiang ethnic group might be genetically closer related with most Chinese populations involved in our study, especially Tibet groups, Xibe group and several Han populations.
DOI: 10.6084/m9.figshare.6743075.v3
title: Interaction between autophagic vesicles and the <i>Coxiella</i>-containing vacuole requires CLTC (clathrin heavy chain)

description: <i>Coxiella burnetii</i> is an intracellular bacterial pathogen which causes Q fever, a human infection with the ability to cause chronic disease with potentially life-threatening outcomes. In humans, <i>Coxiella</i> infects alveolar macrophages where it replicates to high numbers in a unique, pathogen-directed lysosome-derived vacuole. This compartment, termed the <i>Coxiella</i>-containing vacuole (CCV), has a low internal pH and contains markers both of lysosomes and autophagosomes. The CCV membrane is also enriched with CLTC (clathrin heavy chain) and this contributes to the success of the CCV. Here, we describe a role for CLTC, a scaffolding protein of clathrin-coated vesicles, in facilitating the fusion of autophagosomes with the CCV. During gene silencing of <i>CLTC</i>, CCVs are unable to fuse with each other, a phenotype also seen when silencing genes involved in macroautophagy/autophagy. MAP1LC3B/LC3B, which is normally observed inside the CCV, is excluded from CCVs in the absence of CLTC. Additionally, this study demonstrates that autophagosome fusion contributes to CCV size as cell starvation and subsequent autophagy induction leads to further CCV expansion. This is CLTC dependent, as the absence of CLTC renders autophagosomes no longer able to contribute to the expansion of the CCV. This investigation provides a functional link between CLTC and autophagy in the context of <i>Coxiella</i> infection and highlights the CCV as an important tool to explore the interactions between these vesicular trafficking pathways.
DOI: 10.6084/m9.figshare.6743051.v1
title: Bat fly-associated Laboulbeniales log and trees files LSU

description: Output log and .trees files of the BEAST analysis of the LSU dataset, under a TPM2uf+G model of nucleotide substitution. Two independent runs were performed for 40 million generations.<br><br>--Haelewaters et al. 2018. Laboulbeniales hyperparasites (Fungi, Ascomycota) of bat flies: Independent origins and host associations. DOI:10.1002/ece3.4359<br>ABSTRACTThe aim of this study was to explore the diversity of ectoparasitic fungi (Ascomycota, Laboulbeniales) that use bat flies (Diptera, Hippoboscoidea) as hosts. Bat flies themselves live as ectoparasites on the fur and wing membranes of bats (Mammalia, Chiroptera); hence this is a tripartite parasite system. Here, we collected bats, bat flies, and Laboulbeniales, and conducted phylogenetic analyses of Laboulbeniales to contrast morphology with ribosomal sequence data. Parasitism of bat flies by Laboulbeniales arose three times independently, once in the Eastern Hemisphere (Arthrorhynchus) and twice in the Western Hemisphere (Gloeandromyces, Nycteromyces). We hypothesize that the genera Arthrorhynchus and Nycteromyces evolved independently from lineages of ectoparasites of true buge (Hemiptera). We assessed phylogenetic diversity of the genus Gloeandromyces by considering the LSU rDNA region. Phenotypic plasticity and position-induced morphological adaptations go hand in hand. Different morphotypes belong to the same phylogenetic species. Two species, G. pageanus and G. streblae, show divergence by host utilization. In our assessement of coevolution, we only observe congruence between the Old World clades of bat flies and Laboulbeniales. The other associations are the result of the roosting ecology of the bat hosts. This study has considerably increased our knowledge about bats and their associated ectoparasites and shown the necessity of including molecular data in Laboulbeniales taxonomy. <br>KEYWORDSAscomycota, ectoparasites, host specialization, phenotypic plasticity, ribosomal DNA, taxonomy
DOI: 10.6084/m9.figshare.6743075.v2
title: Interaction between autophagic vesicles and the <i>Coxiella</i>-containing vacuole requires CLTC (clathrin heavy chain)

description: <i>Coxiella burnetii</i> is an intracellular bacterial pathogen which causes Q fever, a human infection with the ability to cause chronic disease with potentially life-threatening outcomes. In humans, <i>Coxiella</i> infects alveolar macrophages where it replicates to high numbers in a unique, pathogen-directed lysosome-derived vacuole. This compartment, termed the <i>Coxiella</i>-containing vacuole (CCV), has a low internal pH and contains markers both of lysosomes and autophagosomes. The CCV membrane is also enriched with CLTC (clathrin heavy chain) and this contributes to the success of the CCV. Here, we describe a role for CLTC, a scaffolding protein of clathrin-coated vesicles, in facilitating the fusion of autophagosomes with the CCV. During gene silencing of <i>CLTC</i>, CCVs are unable to fuse with each other, a phenotype also seen when silencing genes involved in macroautophagy/autophagy. MAP1LC3B/LC3B, which is normally observed inside the CCV, is excluded from CCVs in the absence of CLTC. Additionally, this study demonstrates that autophagosome fusion contributes to CCV size as cell starvation and subsequent autophagy induction leads to further CCV expansion. This is CLTC dependent, as the absence of CLTC renders autophagosomes no longer able to contribute to the expansion of the CCV. This investigation provides a functional link between CLTC and autophagy in the context of <i>Coxiella</i> infection and highlights the CCV as an important tool to explore the interactions between these vesicular trafficking pathways.
DOI: 10.6084/m9.figshare.6743036
title: Bat fly-associated Laboulbeniales LSU dataset

description: This is the aligned LSU dataset, which was used as input for the assessment of the phylogenetic diversity in the bat fly-associated genus Gloeandromyces.<br><br>--Haelewaters et al. 2018. Laboulbeniales hyperparasites (Fungi, Ascomycota) of bat flies: Independent origins and host associations. DOI:10.1002/ece3.4359<br>ABSTRACTThe aim of this study was to explore the diversity of ectoparasitic fungi (Ascomycota, Laboulbeniales) that use bat flies (Diptera, Hippoboscoidea) as hosts. Bat flies themselves live as ectoparasites on the fur and wing membranes of bats (Mammalia, Chiroptera); hence this is a tripartite parasite system. Here, we collected bats, bat flies, and Laboulbeniales, and conducted phylogenetic analyses of Laboulbeniales to contrast morphology with ribosomal sequence data. Parasitism of bat flies by Laboulbeniales arose three times independently, once in the Eastern Hemisphere (Arthrorhynchus) and twice in the Western Hemisphere (Gloeandromyces, Nycteromyces). We hypothesize that the genera Arthrorhynchus and Nycteromyces evolved independently from lineages of ectoparasites of true buge (Hemiptera). We assessed phylogenetic diversity of the genus Gloeandromyces by considering the LSU rDNA region. Phenotypic plasticity and position-induced morphological adaptations go hand in hand. Different morphotypes belong to the same phylogenetic species. Two species, G. pageanus and G. streblae, show divergence by host utilization. In our assessement of coevolution, we only observe congruence between the Old World clades of bat flies and Laboulbeniales. The other associations are the result of the roosting ecology of the bat hosts. This study has considerably increased our knowledge about bats and their associated ectoparasites and shown the necessity of including molecular data in Laboulbeniales taxonomy. <br>KEYWORDSAscomycota, ectoparasites, host specialization, phenotypic plasticity, ribosomal DNA, taxonomy