cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.4750798.v1
title: Supplementary Material for: Increased Survival in the Red Flour Beetle after Oral Priming with Bacteria-Conditioned Media

description: Immune priming is defined as enhanced protection upon secondary exposure to a pathogen. Such enhanced resistance after prior exposure has been demonstrated for a number of insect species including the red flour beetle, <i>Tribolium castaneum</i>. In testing this phenomenon, the majority of studies have focused on introducing the pathogen into the insect's hemocoel via septic wounding through the cuticle. Although such septic injury can occur in nature, many pathogens enter their hosts via the oral route, i.e. by ingestion. <i>Bacillus thuringiensis</i> bacteria are well-known insect pathogens that infect their host orally. We found that <i>T. castaneum</i> larvae showed increased survival after oral exposure to <i>B. thuringiensis</i>, when they had been orally primed with filter-sterilized media in which spores of <i>B. thuringiensis</i> had been raised. Such priming was achieved only with a naturally pathogenic strain of <i>B. thuringiensis</i> and a strain that was made pathogenic by transfer of plasmids. Moreover, primed larvae were smaller in size 24 h after priming and had a longer developmental time, indicating that investment in such a response comes at a cost. However, the increased survival in primed larvae was not caused by larval size differences upon challenge.
DOI: 10.6084/m9.figshare.4750786
title: Supplementary Material for: The EFEMP1 Gene: A Frequent Target for Epigenetic Silencing in Multiple Human Pituitary Adenoma Subtypes

description: <strong><em>Background/Aims:</em></strong> In a genome-wide investigation we recently identified the EGF-containing fibulin-like extracellular matrix protein 1 gene, <i>EFEMP1</i>, as hypermethylated in growth hormone-secreting adenoma. <b><i>Methods:</i></b> In an independent cohort we determined expression of EFEMP1, CpG island methylation and histone tail modification status. The causal consequences of epigenetic modification were determined through epidrug-induced reversal and enforced EFEMP1 expression in GH3 cells. <b><i>Results:</i></b> The majority of adenomas, irrespective of subtype, show reduced EFEMP1 expression. However, epigenetic change, as determined by CpG island methylation, was not invariantly associated with decreased EFEMP1 expression. Conversely, chromatin immunoprecipitation assays revealed enrichment for modifications associated with either active or silenced genes in adenoma that did or did not express EFEMP1 respectively. In AtT-20 and GH3 cells a causal relationship between epigenetic silencing and expression of EFEMP1 was established where co-incubation with the epidrugs zebularine and TSA induced expression of EFEMP1 and concomitant histone tail modifications toward those associated with expressed genes. Enforced expression of EFEMP1 in GH3 cells was without effect on cell proliferation or apoptotic end-points, however inhibition of endogenous matrix metalloproteinase (MMP)-2 expression was apparent. Primary adenomas did not show this relationship, however a positive correlation was apparent with the MMP7 transcript and perhaps reflects cell or species differences. <b><i>Conclusions:</i></b> The protein product of the <i>EFEMP1</i> gene, fibulin-3, is reported to impact on multiple pathways in a cell-specific context. Subtype-independent loss of EFEMP1 expression in the majority of primary adenomas should prompt more detailed investigation in this tumour type.
DOI: 10.6084/m9.figshare.4750777
title: Supplementary Material for: Gene Expression Analysis and Urinary Biomarker Assays Reveal Activation of Tubulointerstitial Injury Pathways in a Rodent Model of Chronic Proteinuria (Doxorubicin Nephropathy)

description: <strong><em>Background:</em></strong> Tubular atrophy and interstitial fibrosis are well-recognized sequelae of chronic proteinuria; however, little is known regarding the molecular pathways activated within tubulointerstitium in chronic proteinuric nephropathies. <b><i>Methods:</i></b> To investigate the molecular mechanisms of proteinuria-associated tubulointerstitial (TI) disease, doxorubicin nephropathy was induced in rats. Progression of disease was monitored with weekly urinary biomarker assays. Because histopathology revealed multifocal TI injury, immunodirected laser capture microdissection was used to identify and isolate injured proximal tubules, as indicated by kidney injury molecule-1 immunolabeling. Adjacent interstitial cells were harvested separately. Gene expression microarray, manual annotation of gene lists, and Gene Set Enrichment Analysis were performed. A subset of the regulated transcripts was validated by quantitative PCR and immunohistochemistry. <b><i>Results:</i></b> Severe proteinuria preceded tubular injury biomarkers by 1 week. Histology revealed multifocal, mild TI damage at 3 weeks, which progressed in severity at 5 weeks. Affymetrix microarray analysis revealed tissue-specific regulation of gene expression. Manual annotation of gene lists, gene set enrichment analysis, and urinary biomarker assays revealed similarities to pathways activated in direct TI injuries. This suggests commonalities amongst the molecular mechanisms of TI injury secondary to proteinuria, ischemia-reperfusion, and nephrotoxicity.
DOI: 10.6084/m9.figshare.4750783
title: Supplementary Material for: Analysis of Germline Gene Copy Number Variants of Patients with Sporadic Pancreatic Adenocarcinoma Reveals Specific Variations

description: <strong><em>Objectives:</em></strong> The rapid fatality of pancreatic cancer is, in large part, the result of diagnosis at an advanced stage in the majority of patients. Identification of individuals at risk of developing pancreatic adenocarcinoma would be useful to improve the prognosis of this disease. There is presently no biological or genetic indicator allowing the detection of patients at risk. Our main goal was to identify copy number variants (CNVs) common to all patients with sporadic pancreatic cancer. <b><i>Methods:</i></b> We analyzed gene CNVs in leukocyte DNA from 31 patients with sporadic pancreatic adenocarcinoma and from 93 matched controls. Genotyping was performed with the use of the GeneChip Human Mapping 500K Array Set (Affymetrix). <b><i>Results:</i></b> We identified 431 single nucleotide polymorphism (SNP) probes with abnormal hybridization signal present in the DNA of all 31 patients. Of these SNP probes, 284 corresponded to 3 or more copies and 147 corresponded to 1 or 0 copies. Several cancer-associated genes were amplified in all patients. Conversely, several genes supposed to oppose cancer development were present as single copy. <b><i>Conclusions:</i></b> These data suggest that a set of 431 CNVs could be associated with the disease. This set could be useful for early diagnosis.
DOI: 10.6084/m9.figshare.4750807.v1
title: Small carnivore ecosystem services data

description: Data analysed in Williams, S.T., Maree, N., Taylor, P., Belmain, S.R., Keith, M. and Swanepoel, L.H. (in review) Predation by small mammalian carnivores in rural agro-ecosystems: An undervalued ecosystem service? Ecosystem Services. <br><br>
DOI: 10.7910/dvn/pkjufn/fl3zoj
title: FCC2001.055.ran

description: :unav
DOI: 10.6084/m9.figshare.4750777.v1
title: Supplementary Material for: Gene Expression Analysis and Urinary Biomarker Assays Reveal Activation of Tubulointerstitial Injury Pathways in a Rodent Model of Chronic Proteinuria (Doxorubicin Nephropathy)

description: <strong><em>Background:</em></strong> Tubular atrophy and interstitial fibrosis are well-recognized sequelae of chronic proteinuria; however, little is known regarding the molecular pathways activated within tubulointerstitium in chronic proteinuric nephropathies. <b><i>Methods:</i></b> To investigate the molecular mechanisms of proteinuria-associated tubulointerstitial (TI) disease, doxorubicin nephropathy was induced in rats. Progression of disease was monitored with weekly urinary biomarker assays. Because histopathology revealed multifocal TI injury, immunodirected laser capture microdissection was used to identify and isolate injured proximal tubules, as indicated by kidney injury molecule-1 immunolabeling. Adjacent interstitial cells were harvested separately. Gene expression microarray, manual annotation of gene lists, and Gene Set Enrichment Analysis were performed. A subset of the regulated transcripts was validated by quantitative PCR and immunohistochemistry. <b><i>Results:</i></b> Severe proteinuria preceded tubular injury biomarkers by 1 week. Histology revealed multifocal, mild TI damage at 3 weeks, which progressed in severity at 5 weeks. Affymetrix microarray analysis revealed tissue-specific regulation of gene expression. Manual annotation of gene lists, gene set enrichment analysis, and urinary biomarker assays revealed similarities to pathways activated in direct TI injuries. This suggests commonalities amongst the molecular mechanisms of TI injury secondary to proteinuria, ischemia-reperfusion, and nephrotoxicity.
DOI: 10.6084/m9.figshare.4750783.v1
title: Supplementary Material for: Analysis of Germline Gene Copy Number Variants of Patients with Sporadic Pancreatic Adenocarcinoma Reveals Specific Variations

description: <strong><em>Objectives:</em></strong> The rapid fatality of pancreatic cancer is, in large part, the result of diagnosis at an advanced stage in the majority of patients. Identification of individuals at risk of developing pancreatic adenocarcinoma would be useful to improve the prognosis of this disease. There is presently no biological or genetic indicator allowing the detection of patients at risk. Our main goal was to identify copy number variants (CNVs) common to all patients with sporadic pancreatic cancer. <b><i>Methods:</i></b> We analyzed gene CNVs in leukocyte DNA from 31 patients with sporadic pancreatic adenocarcinoma and from 93 matched controls. Genotyping was performed with the use of the GeneChip Human Mapping 500K Array Set (Affymetrix). <b><i>Results:</i></b> We identified 431 single nucleotide polymorphism (SNP) probes with abnormal hybridization signal present in the DNA of all 31 patients. Of these SNP probes, 284 corresponded to 3 or more copies and 147 corresponded to 1 or 0 copies. Several cancer-associated genes were amplified in all patients. Conversely, several genes supposed to oppose cancer development were present as single copy. <b><i>Conclusions:</i></b> These data suggest that a set of 431 CNVs could be associated with the disease. This set could be useful for early diagnosis.
DOI: 10.6084/m9.figshare.4750786.v1
title: Supplementary Material for: The EFEMP1 Gene: A Frequent Target for Epigenetic Silencing in Multiple Human Pituitary Adenoma Subtypes

description: <strong><em>Background/Aims:</em></strong> In a genome-wide investigation we recently identified the EGF-containing fibulin-like extracellular matrix protein 1 gene, <i>EFEMP1</i>, as hypermethylated in growth hormone-secreting adenoma. <b><i>Methods:</i></b> In an independent cohort we determined expression of EFEMP1, CpG island methylation and histone tail modification status. The causal consequences of epigenetic modification were determined through epidrug-induced reversal and enforced EFEMP1 expression in GH3 cells. <b><i>Results:</i></b> The majority of adenomas, irrespective of subtype, show reduced EFEMP1 expression. However, epigenetic change, as determined by CpG island methylation, was not invariantly associated with decreased EFEMP1 expression. Conversely, chromatin immunoprecipitation assays revealed enrichment for modifications associated with either active or silenced genes in adenoma that did or did not express EFEMP1 respectively. In AtT-20 and GH3 cells a causal relationship between epigenetic silencing and expression of EFEMP1 was established where co-incubation with the epidrugs zebularine and TSA induced expression of EFEMP1 and concomitant histone tail modifications toward those associated with expressed genes. Enforced expression of EFEMP1 in GH3 cells was without effect on cell proliferation or apoptotic end-points, however inhibition of endogenous matrix metalloproteinase (MMP)-2 expression was apparent. Primary adenomas did not show this relationship, however a positive correlation was apparent with the MMP7 transcript and perhaps reflects cell or species differences. <b><i>Conclusions:</i></b> The protein product of the <i>EFEMP1</i> gene, fibulin-3, is reported to impact on multiple pathways in a cell-specific context. Subtype-independent loss of EFEMP1 expression in the majority of primary adenomas should prompt more detailed investigation in this tumour type.
DOI: 10.7910/dvn/pkjufn/fardvj
title: FCC2003.146.ran

description: :unav
DOI: 10.6084/m9.figshare.4750768
title: Tables S11 and S13 from Population genetics of immune-related multilocus copy number variation in Native Americans

description: Genotyping of 53 trios and Reference samples with known copy numbers from the European Collection of Cell Cultures.
DOI: 10.6084/m9.figshare.4750807.v2
title: Small carnivore ecosystem services data

description: This file set contains the data analysed in Williams, S.T., Maree, N., Taylor, P., Belmain, S.R., Keith, M. and Swanepoel, L.H. (in review) Predation by small mammalian carnivores in rural agro-ecosystems: An undervalued ecosystem service? Ecosystem Services. <br><br>There are two types of data included:1. data fom a camera trap survey of small carnivores in a rural agro-ecosystem South Africa 2. data from a questionnaire survey of perceptions of small carnivores and the potential ecosystems services they could provide. <br>R scripts are also included, showing how we analysed the data. Please see the article for further details. Please contact Sam Williams (samual.t.williams@gmail.com) or Lourens Swanepoel (lourens.swanepoel.univen@gmail.com) if you have any questions. <br>The files provided in this file set are as follows:<br>## Camera trap data <br>- CameraTraps.xlsContains attributes of camera trap sites used for the camera trap survey.<br>- occudatatest1.csvData analysed in occupancy analysis<br>- Occupancy Analysis.RR code used to conduct occupancy analysis<br><br>## Questionnaire data<br>- questionRaw.csvAll questionnaire data in a raw form, before processing for analysis<br>- chi.csvData analysed using chi square tests<br>- chickensWide.csvData on poultry holdings<br>- posNeg.csvData on positive and negative perceptions of small carnivores in the community<br>- questionSummaryLong.csvSummarised questionnaire data used for analysis <br>- Questionnaire analysis.RR code used to analyse questionnaire data
DOI: 10.7910/dvn/pkjufn/vy9kh8
title: FCC2002.104.ran

description: :unav
DOI: 10.6084/m9.figshare.4750762
title: Tables S8 and S9 from Population genetics of immune-related multilocus copy number variation in Native Americans

description: Diploid copy number distributions of DEFB and FCGR3B loci for worldwide populations (Human Genome Diversity Project panel) and allele frequencies and fCNV inferred using CoNVEM (A) and CNVice (B).
DOI: 10.6084/m9.figshare.4750768.v1
title: Tables S11 and S13 from Population genetics of immune-related multilocus copy number variation in Native Americans

description: Genotyping of 53 trios and Reference samples with known copy numbers from the European Collection of Cell Cultures.
DOI: 10.7910/dvn/pkjufn/vw0raj
title: FCC2003.268.ran

description: :unav
DOI: 10.6084/m9.figshare.4750762.v1
title: Tables S8 and S9 from Population genetics of immune-related multilocus copy number variation in Native Americans

description: Diploid copy number distributions of DEFB and FCGR3B loci for worldwide populations (Human Genome Diversity Project panel) and allele frequencies and fCNV inferred using CoNVEM (A) and CNVice (B).
DOI: 10.6084/m9.figshare.4750807.v3
title: Small carnivore ecosystem services data

description: This file set contains the data analysed in Williams, S.T., Maree, N., Taylor, P., Belmain, S.R., Keith, M. and Swanepoel, L.H. (in review) Predation by small mammalian carnivores in rural agro-ecosystems: An undervalued ecosystem service? Ecosystem Services.
DOI: 10.7910/dvn/pkjufn/brhim5
title: FCC2003.078.ran

description: :unav
DOI: 10.6084/m9.figshare.4750807.v4
title: Small carnivore ecosystem services data

description: This file set contains the data analysed in Williams, S.T., Maree, N., Taylor, P., Belmain, S.R., Keith, M. and Swanepoel, L.H. (in review) Predation by small mammalian carnivores in rural agro-ecosystems: An undervalued ecosystem service? Ecosystem Services. <br><br>There are two types of data included:1. data from a camera trap survey of small carnivores in a rural agro-ecosystem South Africa. 2. data from a questionnaire survey of perceptions of small carnivores and the potential ecosystems services they could provide. <br>Both raw and processed data are included, along with an R script is also included, showing how we analysed the camera trap data. Please see the article for further details. Please contact Sam Williams (samual.t.williams@gmail.com) or Lourens Swanepoel (lourens.swanepoel.univen@gmail.com) if you have any questions. <br>The files provided in this file set are as follows:<br>## Camera trap data <br>- Raw Camtrap data.csvThe raw data from the camera traps.<br>- CameraTraps.xlsContains attributes of camera trap sites used for the camera trap survey.<br>- The following processed dat were used in the occupancy analysis - SpData.txt - box1.txt - species names.csv - LUTdetailed.shp (land use shapefile used for plotting maps) <br>- analysis code.RR code used to analyse camera trap data<br><br>## Questionnaire data<br>- questionRaw.csvAll questionnaire data in a raw form
DOI: 10.6084/m9.figshare.4750750
title: Tables S3 to S7 from Population genetics of immune-related multilocus copy number variation in Native Americans

description: Diplotype distributions for all loci and inferred allelic frequency in populations and subpopulations with CoNVEM (A) and CNVice (B).
DOI: 10.7910/dvn/pkjufn/mluqd9
title: FCC2001.220.ran

description: :unav
DOI: 10.6084/m9.figshare.4750750.v1
title: Tables S3 to S7 from Population genetics of immune-related multilocus copy number variation in Native Americans

description: Diplotype distributions for all loci and inferred allelic frequency in populations and subpopulations with CoNVEM (A) and CNVice (B).
DOI: 10.7910/dvn/pkjufn/wfr4ne
title: FCC2003.321.ran

description: :unav
DOI: 10.7910/dvn/pkjufn/x2jrvm
title: FCC2001.185.ran

description: :unav
DOI: 10.6084/m9.figshare.4750723
title: Copy Number Data from Population genetics of immune-related multilocus copy number variation in Native Americans

description: Individual copy number data
DOI: 10.6084/m9.figshare.4750723.v1
title: Copy Number Data from Population genetics of immune-related multilocus copy number variation in Native Americans

description: Individual copy number data
DOI: 10.7910/dvn/pkjufn/5rozwl
title: FCC2003.110.ran

description: :unav
DOI: 10.6084/m9.figshare.4750711
title: Supplementary Material for: Plasticity of the Worker Bumblebee Brain in Relation to Age and Rearing Environment

description: The environment experienced during development can dramatically affect the brain, with possible implications for sensory processing, learning, and memory. Although the effects of single sensory modalities on brain development have been repeatedly explored, the additive or interactive effects of multiple modalities have been less thoroughly investigated. We asked how experience with multisensory stimuli affected brain development in the bumblebee <i>Bombus impatiens</i>. First, to establish the timeline of brain development during early adulthood, we estimated regional brain volumes across a range of ages. We discovered significant age-related volume changes in nearly every region of the brain. Next, to determine whether these changes were dependent upon certain environmental stimuli, we manipulated the visual and olfactory stimuli available to newly emerged bumblebee workers in a factorial manner. Newly emerged bumblebees were maintained in the presence or absence of supplemental visual and/or olfactory stimuli for 7 days, after which the volumes of several brain regions were estimated. We found that the volumes of the mushroom body lobes and calyces were larger in the absence of visual stimuli. Additionally, visual deprivation was associated with the expression of larger antennal lobes, the primary olfactory processing regions of the brain. In contrast, exposure to plant-derived olfactory stimuli did not have a significant effect on brain region volumes. This study is the first to explore the separate and interactive effects of visual and olfactory stimuli on bee brain development. Assessing the timing and sensitivity of brain development is a first step toward understanding how different rearing environments differentially affect regional brain volumes in this species. Our findings suggest that environmental factors experienced during the first week of adulthood can modify bumblebee brain development in many subtle ways.
DOI: 10.6084/m9.figshare.4750702
title: Shiny App - PARV4 prevalence, phylogeny, immunology and coinfection with HIV, HBV and HCV in a multicentre African cohort

description: This deposit provides an interactive treemap for exploring the PARV4 prevalence data made available here: https://doi.org/10.6084/m9.figshare.4707316<br>Martin John Hadley is the data visualisation developer, and Philippa Matthews is the principal investigator and lead author for both the dataset and publications this visualisation is linked to.
DOI: 10.6084/m9.figshare.4750708
title: Supplementary Material for: New Self-Reporting Questionnaire to Assess Urinary Tract Infections and Differential Diagnosis: Acute Cystitis Symptom Score

description: <strong><em>Objective:</em></strong> Development and validation of a simple and standardized self-reporting questionnaire for acute uncomplicated cystitis (AUC) assessing typical and differential symptoms, quality of life and possible changes after therapy in female patients with AUC. <b><i>Materials and Methods:</i></b> Literature research, development and evaluation of the Acute Cystitis Symptom Score (ACSS), an 18-item self-reporting questionnaire including (a) six questions about ‘typical' symptoms of AUC, (b) four questions regarding differential diagnoses, (c) three questions on quality of life and (d) five questions on additional conditions which may affect therapy. The ACSS was evaluated in 286 women (mean age 32.3 ± 12.3 years) in the Russian and Uzbek language. Measurements of reliability, validity, predictive ability and responsiveness were performed. <b><i>Results:</i></b> Cronbach's alpha for the ACSS was 0.89, split-half reliability was 0.92 and correlation between halves was 0.85. Mann-Whitney test revealed significant difference scores of the ‘typical' domain between patients and controls (10.75 vs. 2.02, p &lt; 0.001). The optimal threshold score was 6 points, with a 94% sensitivity and 90% specificity to predict AUC. The symptom score decreased significantly when comparing before and after therapy (10.7 vs. 2.1, p &lt; 0.001). <b><i>Conclusion:</i></b> The new validated ACSS is accurate enough and can be recommended for clinical studies and practice for initial diagnosis and monitoring treatment of AUC. Evaluation in other languages is in progress.
DOI: 10.7910/dvn/pkjufn/vi665j
title: FCC2003.138.ran

description: :unav
DOI: 10.6084/m9.figshare.4750702.v1
title: Shiny App - PARV4 prevalence, phylogeny, immunology and coinfection with HIV, HBV and HCV in a multicentre African cohort

description: This deposit provides an interactive treemap for exploring the PARV4 prevalence data made available here: https://doi.org/10.6084/m9.figshare.4707316<br>Martin John Hadley is the data visualisation developer, and Philippa Matthews is the principal investigator and lead author for both the dataset and publications this visualisation is linked to.