cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.6605753.v1
title: Trehalose reduces retinal degeneration, neuroinflammation and storage burden caused by a lysosomal hydrolase deficiency

description: The accumulation of undegraded molecular material leads to progressive neurodegeneration in a number of lysosomal storage disorders (LSDs) that are caused by functional deficiencies of lysosomal hydrolases. To determine whether inducing macroautophagy/autophagy via small-molecule therapy would be effective for neuropathic LSDs due to enzyme deficiency, we treated a mouse model of mucopolysaccharidosis IIIB (MPS IIIB), a storage disorder caused by deficiency of the enzyme NAGLU (alpha-N-acetylglucosaminidase [Sanfilippo disease IIIB]), with the autophagy-inducing compound trehalose. Treated <i>naglu</i><sup>–/–</sup> mice lived longer, displayed less hyperactivity and anxiety, retained their vision (and retinal photoreceptors), and showed reduced inflammation in the brain and retina. Treated mice also showed improved clearance of autophagic vacuoles in neuronal and glial cells, accompanied by activation of the TFEB transcriptional network that controls lysosomal biogenesis and autophagic flux. Therefore, small-molecule-induced autophagy enhancement can improve the neurological symptoms associated with a lysosomal enzyme deficiency and could provide a viable therapeutic approach to neuropathic LSDs.
DOI: 10.6084/m9.figshare.6605753.v2
title: Trehalose reduces retinal degeneration, neuroinflammation and storage burden caused by a lysosomal hydrolase deficiency

description: The accumulation of undegraded molecular material leads to progressive neurodegeneration in a number of lysosomal storage disorders (LSDs) that are caused by functional deficiencies of lysosomal hydrolases. To determine whether inducing macroautophagy/autophagy via small-molecule therapy would be effective for neuropathic LSDs due to enzyme deficiency, we treated a mouse model of mucopolysaccharidosis IIIB (MPS IIIB), a storage disorder caused by deficiency of the enzyme NAGLU (alpha-N-acetylglucosaminidase [Sanfilippo disease IIIB]), with the autophagy-inducing compound trehalose. Treated <i>naglu</i><sup>–/ –</sup> mice lived longer, displayed less hyperactivity and anxiety, retained their vision (and retinal photoreceptors), and showed reduced inflammation in the brain and retina. Treated mice also showed improved clearance of autophagic vacuoles in neuronal and glial cells, accompanied by activation of the TFEB transcriptional network that controls lysosomal biogenesis and autophagic flux. Therefore, small-molecule-induced autophagy enhancement can improve the neurological symptoms associated with a lysosomal enzyme deficiency and could provide a viable therapeutic approach to neuropathic LSDs. <b>Abbreviations</b>: ANOVA: analysis of variance; <i>Atg7</i>: autophagy related 7; AV: autophagic vacuoles; CD68: cd68 antigen; ERG: electroretinogram; ERT: enzyme replacement therapy; GAPDH: glyceraldehyde-3-phosphate dehydrogenase; GFAP: glial fibrillary acidic protein; GNAT2: guanine nucleotide binding protein, alpha transducing 2; HSCT: hematopoietic stem cell transplantation; INL: inner nuclear layer; LC3: microtubule-associated protein 1 light chain 3 alpha; MPS: mucopolysaccharidoses; NAGLU: alpha-N-acetylglucosaminidase (Sanfilippo disease IIIB); ONL: outer nuclear layer; PBS: phosphate-buffered saline; PRKCA/PKCα: protein kinase C, alpha; S1BF: somatosensory cortex; SQSTM1: sequestosome 1; TEM: transmission electron microscopy; TFEB: transcription factor EB; VMP/VPL: ventral posterior nuclei of the thalamus
DOI: 10.15131/shef.data.6605330
title: Oryx headings

description: Data of headings of Oryx (Oryx leucoryx) in degrees, gathered at 40Hz resolution. Six paths: each file contains a single column giving the headings over time. <br><br>Details are given in Potts JR, Börger L, Scantlebury M, Bennet NC, Alagaili A, Wilson RP (in press) Finding turning-points in ultra-high-resolution animal movement data. Methods Ecol Evol. DOI: 10.1111/2041-210X.13056
DOI: 10.15131/shef.data.6605330.v1
title: Oryx headings

description: Data of headings of Oryx (Oryx leucoryx) in degrees, gathered at 40Hz resolution. Six paths: each file contains a single column giving the headings over time. <br><br>Details are given in Potts JR, Börger L, Scantlebury M, Bennet NC, Alagaili A, Wilson RP (in press) Finding turning-points in ultra-high-resolution animal movement data. Methods Ecol Evol. DOI: 10.1111/2041-210X.13056
DOI: 10.6084/m9.figshare.6605237
title: SummaryComputationsFiles4Upload from Inflation versus filling-in: why we feel we see more than we actually do in peripheral vision

description: This folder contains the data & code for Experiment 2
DOI: 10.6084/m9.figshare.6605228
title: CrowdingFiles4UPload from Inflation versus filling-in: why we feel we see more than we actually do in peripheral vision

description: This folder contains the data & code for Experiment 1
DOI: 10.6084/m9.figshare.6605228.v1
title: CrowdingFiles4UPload from Inflation versus filling-in: why we feel we see more than we actually do in peripheral vision

description: This folder contains the data & code for Experiment 1
DOI: 10.6084/m9.figshare.6605111
title: Zenkevitchiidae fam. nov. (Crustacea: Gammaroidea), with description of new subterranean amphipods from extremely deep cave habitats

description: Previous phylogenetic analysis based on combined mitochondrial and nuclear gene sequences detected paraphyly of the Typhlogammaridae. To test this hypothesis a portion of large subunit (LSU-rDNA) gene sequences were obtained for typhlogammarid species from Caucasus. The Bayesian approach to LSU-rDNA sequences provided evidence for an independent origin of the Dinaric and Caucasus ‘typhlogammarid’ clades. A new family, Zenkevitchiidae fam. nov., is proposed to reconcile the observed phylogeny with the concept of monophyly. Using light microscopy, two mouthpart morphotypes of the Zenkevitchiidae fam. nov. species with quite different setae are identified. Taking into account these two morphotypes, a new classification is proposed – <i>Adaugammarus revazi</i> comb. nov., and <i>Adaugammarus sandroruffoi</i> comb. nov. Additionally, two new stygobiont zenkevitchiid amphipod species – <i>Adaugammarus kasiani</i> sp. nov. and <i>Kruberia relicta</i> sp. nov. – are described from Krubera Cave in Abkhazia. A distribution map and an identification key for the Zenkevitchiidae fam. nov. species of Transcaucasia are provided. http://zoobank.org/urn:lsid:zoobank.org:pub:90177B0C-BED0-4601-8CFC-3F774B22065C
DOI: 10.6084/m9.figshare.6605111.v1
title: Zenkevitchiidae fam. nov. (Crustacea: Gammaroidea), with description of new subterranean amphipods from extremely deep cave habitats

description: Previous phylogenetic analysis based on combined mitochondrial and nuclear gene sequences detected paraphyly of the Typhlogammaridae. To test this hypothesis a portion of large subunit (LSU-rDNA) gene sequences were obtained for typhlogammarid species from Caucasus. The Bayesian approach to LSU-rDNA sequences provided evidence for an independent origin of the Dinaric and Caucasus ‘typhlogammarid’ clades. A new family, Zenkevitchiidae fam. nov., is proposed to reconcile the observed phylogeny with the concept of monophyly. Using light microscopy, two mouthpart morphotypes of the Zenkevitchiidae fam. nov. species with quite different setae are identified. Taking into account these two morphotypes, a new classification is proposed – <i>Adaugammarus revazi</i> comb. nov., and <i>Adaugammarus sandroruffoi</i> comb. nov. Additionally, two new stygobiont zenkevitchiid amphipod species – <i>Adaugammarus kasiani</i> sp. nov. and <i>Kruberia relicta</i> sp. nov. – are described from Krubera Cave in Abkhazia. A distribution map and an identification key for the Zenkevitchiidae fam. nov. species of Transcaucasia are provided. http://zoobank.org/urn:lsid:zoobank.org:pub:90177B0C-BED0-4601-8CFC-3F774B22065C
DOI: 10.6084/m9.figshare.6605030
title: Supplementary Material for: Distinct Gene Expression Patterns between Nasal Mucosal Cells and Blood Collected from Allergic Rhinitis Sufferers

description: <b><i>Background:</i></b> Investigations of gene expression in allergic rhinitis (AR) typically rely on invasive nasal biopsies (site of inflammation) or blood samples (systemic immunity) to obtain sufficient genetic material for analysis. New methodologies to circumvent the need for invasive sample collection offer promise to further the understanding of local immune mechanisms relevant in AR. <b><i>Methods:</i></b> A within-subject design was employed to compare immune gene expression profiles obtained from nasal washing/brushing and whole blood samples collected during peak pollen season. Twelve adults (age: 46.3 ± 12.3 years) with more than a 2-year history of AR and a confirmed grass pollen allergy participated in the study. Gene expression analysis was performed using a panel of 760 immune genes with the NanoString nCounter platform on nasal lavage/brushing cell lysates and compared to RNA extracted from blood. <b><i>Results:</i></b> A total of 355 genes were significantly differentially expressed between sample types (9.87 to –9.71 log<sub>2</sub> fold change). The top 3 genes significantly upregulated in nasal lysate samples were Mucin 1 (<i>MUC1</i>), Tight Junction Protein 1 (<i>TJP1</i>), and Lipocalin-2 (<i>LCN2</i>). The top 3 genes significantly upregulated in blood samples were cluster of differentiation 3e (<i>CD3E</i>), FYN Proto-Oncogene Src Family Tyrosine Kinase (<i>FYN</i>) and cluster of differentiation 3d (<i>CD3D</i>). <b><i>Conclusions:</i></b> Overall, the blood and nasal lavage samples showed vastly distinct gene expression profiles and functional gene pathways which reflect their anatomical and functional origins. Evaluating immune gene expression of the nasal mucosa in addition to blood samples may be beneficial in understanding AR pathophysiology and response to allergen challenge.
DOI: 10.6084/m9.figshare.6604799
title: Supplementary Material for: Short-Form Bomanins Mediate Humoral Immunity in <b><i>Drosophila</i></b>

description: The Bomanins (Boms) are a family of a dozen secreted peptides that mediate the innate immune response governed by the <i>Drosophila</i> Toll receptor. We recently showed that deleting a cluster of 10 <i>Bom</i> genes blocks Toll-mediated defenses against a range of fungi and gram-positive bacteria. Here, we characterize the activity of individual Bom family members. We provide evidence that the Boms overlap in function and that a single <i>Bom</i> gene encoding a mature peptide of just 16 amino acids can act largely or entirely independent of other family members to provide phenotypic rescue in vivo. We further demonstrate that the <i>Boms</i> function in <i>Drosophila</i> humoral immunity, mediating the killing of the fungal pathogen <i>Candida glabrata</i> in an in vitro assay of cell-free hemolymph. In addition, we find that the level of antifungal activity both in vivo and in vitro is linked to the level of <i>Bom</i> gene expression. Although Toll dictates expression of the antimicrobial peptides (AMPs) drosomycin and metchnikowin, we find no evidence that Boms act by modifying the expression of the mature forms of these antifungal AMPs.
DOI: 10.6084/m9.figshare.6604799.v1
title: Supplementary Material for: Short-Form Bomanins Mediate Humoral Immunity in <b><i>Drosophila</i></b>

description: The Bomanins (Boms) are a family of a dozen secreted peptides that mediate the innate immune response governed by the <i>Drosophila</i> Toll receptor. We recently showed that deleting a cluster of 10 <i>Bom</i> genes blocks Toll-mediated defenses against a range of fungi and gram-positive bacteria. Here, we characterize the activity of individual Bom family members. We provide evidence that the Boms overlap in function and that a single <i>Bom</i> gene encoding a mature peptide of just 16 amino acids can act largely or entirely independent of other family members to provide phenotypic rescue in vivo. We further demonstrate that the <i>Boms</i> function in <i>Drosophila</i> humoral immunity, mediating the killing of the fungal pathogen <i>Candida glabrata</i> in an in vitro assay of cell-free hemolymph. In addition, we find that the level of antifungal activity both in vivo and in vitro is linked to the level of <i>Bom</i> gene expression. Although Toll dictates expression of the antimicrobial peptides (AMPs) drosomycin and metchnikowin, we find no evidence that Boms act by modifying the expression of the mature forms of these antifungal AMPs.
DOI: 10.6084/m9.figshare.6604763
title: The ergosterol X-ray data

description: The ergosterol X-ray data
DOI: 10.7284/133258
title: Multibeam Echosounder data collected during research cruise NA105 using a Kongsberg EM302 instrument system onboard the platform EV Nautilus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.34740/kaggle/dsv/1448951
title: COVID-19 Indonesia Dataset
DOI: 10.6084/m9.figshare.6603404
title: C.militaris Transcriptome data

description: The cordyceps militarris transcriptome data of single molecular real time sequencing
DOI: 10.6084/m9.figshare.6603404.v1
title: C.militaris Transcriptomic data

description: The cordyceps militarris transcriptome data of single molecular real time sequencing
DOI: 10.6084/m9.figshare.6603404.v2
title: C.militaris Transcriptome data

description: The cordyceps militarris transcriptome data of single molecular real time sequencing
DOI: 10.6084/m9.figshare.6603335
title: Morphological data.csv

description: This file correspond to the data used in the paper entitled "Sexual dimorphism in the dermal armour of cordyline lizards (Squamata: Cordylinae)" (BJLS-5481.R1). For each species, the body size is shown, as well as the average osteoderm expression (either volume in mm³ or thickness in mm). <br>
DOI: 10.6084/m9.figshare.6603302
title: C. militaris Genomic data

description: The Cordyceps militaris genomic DNA data of single molecular real time sequencing
DOI: 10.6084/m9.figshare.6603155
title: Database_Skiers_snowboarders.sav

description: All patients with Alpine sports-related injuries reported to a leading medical assistance organization in the Netherlands in the period of 2013-2016 were contacted. Medical data were collected from the patient files. Injuries were classified according to the Abbreviated Injury Scale (AIS) and Injury Severity Scale (ISS). Data on the accident conditions, i.e. risk factors, were collected using retrospective patient-reported questionnaires. Risk factors for serious injury (ISS≥9) were analysed by multivariate modelling.
DOI: 10.6084/m9.figshare.6603008
title: Myocardial motion dataset (raw data)

description: Myocardial motion raw dataset containing text files with recordings of accelerometer/gyro sensor readings in addition to other measures like left ventricular pressure.<br>File name convention:MKCMSxx yy zzzzzzzzzzz.ssa/lvm <br>[experiment ID][recording #][intervention]<br><br><br>
DOI: 10.6084/m9.figshare.6603008.v1
title: Myocardial motion dataset (raw data)

description: Myocardial motion raw dataset containing text files with recordings of accelerometer/gyro sensor readings in addition to other measures like left ventricular pressure.<br>File name convention:MKCMSxx yy zzzzzzzzzzz.ssa/lvm <br>[experiment ID][recording #][intervention]<br><br><br>
DOI: 10.6084/m9.figshare.6602900
title: C. militaris DNA methylation data.xlsx

description: The C. militaris DNA methylation data of single molecular real time sequencing
DOI: 10.6084/m9.figshare.6602708
title: Internship proposal for BSc or MSc student at VU University Amsterdam: studying metabolism of Lactobacillus crispatus

description: Internship proposal for BSc or MSc student at VU University Amsterdam: studying metabolism of <i>Lactobacillus crispatus</i><br>
DOI: 10.6084/m9.figshare.6602705
title: Supplementary Material for: Tobacco Cessation in Oncology Care

description: Globally, tobacco use is a major modifiable risk factor and leading cause of many forms of cancer and cancer death. Tobacco use contributes to poorer prognosis in cancer care. This article reviews the current state of tobacco cessation treatment in oncology. Effective behavioral and pharmacological treatments exist for tobacco cessation, but are not being widely used in oncology treatment settings. Comprehensive tobacco treatment increases success with quitting smoking and can improve oncological and overall health outcomes. This article describes the components of a model treatment program, which includes automatic referrals for all current tobacco users and recent quitters, motivational interviewing during initial and follow-up contacts, combined behavioral and pharmacological interventions for cessation, and systematic follow-up phone calls for relapse prevention.
DOI: 10.6084/m9.figshare.6602684
title: Inoculation and cultivation protocol for Lactobacillus crispatus

description: Method used to inoculate and cultivate <i>Lactobacillus crispatus</i> strains.<br>Used in http://www.reblab.org/ongoing-experiments-log/carbohydrate-active-enzymes-in-lactobacillus-crispatus-a-possible-link-between-the-pullulanase-gene-and-growth-on-glycogen/
DOI: 10.6084/m9.figshare.6601085
title: MOESM4 of RNA-Seq based transcriptome of whole blood from immunocompetent pigs (Sus scrofa) experimentally infected with Mycoplasma suis strain Illinois

description: Additional file 4. Gene ontology (GO) categories of all 55 differentially expressed (DE) genes of Mycoplasma suis infected pigs. First tab describes raw results of GO analysis, with all DE genes and their correspondent GO categories (and functions). Second tab shows the identified functions of the “biological process” category of all 55 DE genes and the number of reported genes for each function. Functional categories with the largest number of genes are highlighted in yellow. GO analysis was performed using Blast2Go software [39].
DOI: 10.6084/m9.figshare.6601085.v1
title: MOESM4 of RNA-Seq based transcriptome of whole blood from immunocompetent pigs (Sus scrofa) experimentally infected with Mycoplasma suis strain Illinois

description: Additional file 4. Gene ontology (GO) categories of all 55 differentially expressed (DE) genes of Mycoplasma suis infected pigs. First tab describes raw results of GO analysis, with all DE genes and their correspondent GO categories (and functions). Second tab shows the identified functions of the “biological process” category of all 55 DE genes and the number of reported genes for each function. Functional categories with the largest number of genes are highlighted in yellow. GO analysis was performed using Blast2Go software [39].
DOI: 10.6084/m9.figshare.6601067
title: MOESM2 of RNA-Seq based transcriptome of whole blood from immunocompetent pigs (Sus scrofa) experimentally infected with Mycoplasma suis strain Illinois

description: Additional file 2. Results of RNA-Seq analyses. List of differentially expressed (DE) genes identified in whole blood of Mycoplasma suis-infected pigs (when compared to sham-infected group) separated by all three methods of RNA-Seq analyses (DESeq2, edgeR, Cufflinks). First tab describes all DE genes (p-value ≤ 0.1) that were detected in all three methods, in two methods, followed by each individual method. The following tabs report the statistics of each evaluated gene for each method. Highlighted in grey are statistically significant DE genes (dark grey: p-value ≤ 0.05; light grey p-value ≤ 0.1).
DOI: 10.6084/m9.figshare.6601067.v1
title: MOESM2 of RNA-Seq based transcriptome of whole blood from immunocompetent pigs (Sus scrofa) experimentally infected with Mycoplasma suis strain Illinois

description: Additional file 2. Results of RNA-Seq analyses. List of differentially expressed (DE) genes identified in whole blood of Mycoplasma suis-infected pigs (when compared to sham-infected group) separated by all three methods of RNA-Seq analyses (DESeq2, edgeR, Cufflinks). First tab describes all DE genes (p-value ≤ 0.1) that were detected in all three methods, in two methods, followed by each individual method. The following tabs report the statistics of each evaluated gene for each method. Highlighted in grey are statistically significant DE genes (dark grey: p-value ≤ 0.05; light grey p-value ≤ 0.1).
DOI: 10.6084/m9.figshare.6601058
title: MOESM1 of RNA-Seq based transcriptome of whole blood from immunocompetent pigs (Sus scrofa) experimentally infected with Mycoplasma suis strain Illinois

description: Additional file 1. Results of Mycoplasma suis microbead immunoassay (MIA). Median Fluorescence Intensity (MFI) of Mycoplasma suis-infected and sham-inoculated pigs as detected in serum samples collected along the experiment. Serum antibodies were measured using recombinant GrpE (rGrpE) protein in a MIA [30]. Sham-inoculated group (control group): pig #1, pig #2 and pig #3. M. suis-inoculated group (infected group): pig #5, pig #6, pig #7. Day 0 corresponds to inoculation day. MFI cut-off was 74.07. It is important to note that a high cut-off may have been encountered due to the low number of animals to determine a cut-off, which increases the standard deviation. MFI values in bold correspond to positive results based on cut-off values for each group. ND: not done.
DOI: 10.6084/m9.figshare.6601058.v1
title: MOESM1 of RNA-Seq based transcriptome of whole blood from immunocompetent pigs (Sus scrofa) experimentally infected with Mycoplasma suis strain Illinois

description: Additional file 1. Results of Mycoplasma suis microbead immunoassay (MIA). Median Fluorescence Intensity (MFI) of Mycoplasma suis-infected and sham-inoculated pigs as detected in serum samples collected along the experiment. Serum antibodies were measured using recombinant GrpE (rGrpE) protein in a MIA [30]. Sham-inoculated group (control group): pig #1, pig #2 and pig #3. M. suis-inoculated group (infected group): pig #5, pig #6, pig #7. Day 0 corresponds to inoculation day. MFI cut-off was 74.07. It is important to note that a high cut-off may have been encountered due to the low number of animals to determine a cut-off, which increases the standard deviation. MFI values in bold correspond to positive results based on cut-off values for each group. ND: not done.
DOI: 10.6084/m9.figshare.6601007
title: Additional file 2: of Experimental folate deficiency in human subjects: what is the influence of vitamin C status on time taken to develop megaloblastic anaemia?

description: Microsoft Excel table and chart for Fig. 5. (XLSX 21 kb)
DOI: 10.6084/m9.figshare.6601007.v1
title: Additional file 2: of Experimental folate deficiency in human subjects: what is the influence of vitamin C status on time taken to develop megaloblastic anaemia?

description: Microsoft Excel table and chart for Fig. 5. (XLSX 21 kb)
DOI: 10.6084/m9.figshare.6600986
title: Additional file 1: of Experimental folate deficiency in human subjects: what is the influence of vitamin C status on time taken to develop megaloblastic anaemia?

description: Microsoft Excel table and chart for Fig. 3. (XLSX 43 kb)
DOI: 10.6084/m9.figshare.6600986.v1
title: Additional file 1: of Experimental folate deficiency in human subjects: what is the influence of vitamin C status on time taken to develop megaloblastic anaemia?

description: Microsoft Excel table and chart for Fig. 3. (XLSX 43 kb)
DOI: 10.6084/m9.figshare.6600974
title: Additional file 2: of Clinical trials involving positron emission tomography and prostate cancer: an analysis of the ClinicalTrials.gov database

description: Trials Endpoints. (XLSX 56 kb)
DOI: 10.6084/m9.figshare.6600974.v1
title: Additional file 2: of Clinical trials involving positron emission tomography and prostate cancer: an analysis of the ClinicalTrials.gov database

description: Trials Endpoints. (XLSX 56 kb)
DOI: 10.6084/m9.figshare.6600926
title: Additional file 1: of Clinical trials involving positron emission tomography and prostate cancer: an analysis of the ClinicalTrials.gov database

description: Annotated Dataset. (XLSX 54 kb)