cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.8057540
title: MOESM5 of Retrotransposon expression in response to in vitro inoculation with two fungal pathogens of Scots pine (Pinus sylvestris L.)

description: Additional file 5. a. Relative expression of 9 retrotransposon families across the ramets of three pine clones (Ja3, Sm3, Sm9) after inoculation with LS. Tissue type: needles. b. PsBs antimicrobial gene mean relative expression in Ja3, Sm9 pine ramets after LS inoculation (3dpi, 14dpi and 31dpi). c. Mean and overall mean Conagree transcript copy numbers after LS inoculation, absolute quantification.
DOI: 10.6084/m9.figshare.8057543
title: Additional file 2: of Transcriptomic reprogramming of barley seminal roots by combined water deficit and salt stress

description: Overview of RNA-Seq output and mapping results. (XLSX 16 kb)
DOI: 10.6084/m9.figshare.8057540.v1
title: MOESM5 of Retrotransposon expression in response to in vitro inoculation with two fungal pathogens of Scots pine (Pinus sylvestris L.)

description: Additional file 5. a. Relative expression of 9 retrotransposon families across the ramets of three pine clones (Ja3, Sm3, Sm9) after inoculation with LS. Tissue type: needles. b. PsBs antimicrobial gene mean relative expression in Ja3, Sm9 pine ramets after LS inoculation (3dpi, 14dpi and 31dpi). c. Mean and overall mean Conagree transcript copy numbers after LS inoculation, absolute quantification.
DOI: 10.6084/m9.figshare.8057543.v1
title: Additional file 2: of Transcriptomic reprogramming of barley seminal roots by combined water deficit and salt stress

description: Overview of RNA-Seq output and mapping results. (XLSX 16 kb)
DOI: 10.6084/m9.figshare.8057498
title: Additional file 1: of Factors associated with syphilis infection: a cross-sectional survey among outpatients in Asikuma Odoben Brakwa District, Ghana

description: Syphilis Prevalence Study-AOBD. Raw data of Syphilis Prevalence Study-AOBD. (XLSX 52 kb)
DOI: 10.6084/m9.figshare.8057498.v1
title: Additional file 1: of Factors associated with syphilis infection: a cross-sectional survey among outpatients in Asikuma Odoben Brakwa District, Ghana

description: Syphilis Prevalence Study-AOBD. Raw data of Syphilis Prevalence Study-AOBD. (XLSX 52 kb)
DOI: 10.6084/m9.figshare.8057468
title: MOESM2 of Remote ischemic preconditioning attenuates intestinal mucosal damage: insight from a rat model of ischemiaâ reperfusion injury

description: Additional file 2. Effects of I/R and RIPC on phosphorylation of cellular signaling kinases.
DOI: 10.6084/m9.figshare.8057468.v1
title: MOESM2 of Remote ischemic preconditioning attenuates intestinal mucosal damage: insight from a rat model of ischemiaâ reperfusion injury

description: Additional file 2. Effects of I/R and RIPC on phosphorylation of cellular signaling kinases.
DOI: 10.6084/m9.figshare.8057459
title: MOESM3 of Plasmodium knowlesi clinical isolates from Malaysia show extensive diversity and strong differential selection pressure at the merozoite surface protein 7D (MSP7D)

description: Additional file 3. Neucleotide polymorphism across the full-length pkmsp7D genes. Hyper-variable SNPs are marked in bold and white and SNPs withÂ deletions marked in red.
DOI: 10.6084/m9.figshare.8057459.v1
title: MOESM3 of Plasmodium knowlesi clinical isolates from Malaysia show extensive diversity and strong differential selection pressure at the merozoite surface protein 7D (MSP7D)

description: Additional file 3. Neucleotide polymorphism across the full-length pkmsp7D genes. Hyper-variable SNPs are marked in bold and white and SNPs withÂ deletions marked in red.
DOI: 10.6084/m9.figshare.8057444
title: Additional file 1: of Susceptibility for varicella and factors associated with immunity among pregnant women in a tertiary care hospital in Sri Lanka- a cross-sectional study

description: Data set for sero-prevalence of varicella immunity among pregnant mothers at DMH. This is the final data set used to generate the submitted article. (SAV 28 kb)
DOI: 10.6084/m9.figshare.8057444.v1
title: Additional file 1: of Susceptibility for varicella and factors associated with immunity among pregnant women in a tertiary care hospital in Sri Lanka- a cross-sectional study

description: Data set for sero-prevalence of varicella immunity among pregnant mothers at DMH. This is the final data set used to generate the submitted article. (SAV 28 kb)
DOI: 10.6084/m9.figshare.8057420
title: Songs used for the supplemental figure (.wav files) from The variability of song variability in zebra finch (<i>Taeniopygia guttata</i>) populations

description: The song files are the 9 individuals used to make the figure.
DOI: 10.6084/m9.figshare.8057420.v1
title: Songs used for the supplemental figure (.wav files) from The variability of song variability in zebra finch (<i>Taeniopygia guttata</i>) populations

description: The song files are the 9 individuals used to make the figure.
DOI: 10.6084/m9.figshare.8057378
title: A new scincid lizard from the Miocene of northern Australia, and the evolutionary history of social skinks (Scincidae: Egerniinae)

description: The Egerniinae (formerly the <i>Egernia</i> group) is a morphologically diverse clade of skinks comprising 61 extant species from eight genera, spread across Australia, New Guinea, and the Solomon Islands. The relatively large size and robustness of many egerniines has meant that they fossilize more readily than other Australian skinks and have been more frequently recorded from paleontological excavations. The Riversleigh World Heritage Area of northeastern Australia has yielded multiple egerniine fossils, but most are isolated jaw elements, and only one taxon (‘<i>Tiliqua’ pusilla</i>) has been formally described. Articulated remains recently recovered from the mid-Miocene AL90 site (14.8 Ma) at Riversleigh are here described as <i>Egernia gillespieae</i> and represent the first opportunity to describe the morphology of a significant portion of a single individual of a fossil member of the Egerniinae. We include this fossil and ‘<i>T.</i>’ <i>pusilla</i> in an integrated analysis of morphology and published molecular data to assess their relationships and to provide calibration points for the timing of the egerniine radiation. Our calibrated tree combining molecular and morphological data suggests that the modern Australian radiation dates to the end of the Eocene (34.1 Ma). Both fossils are within the Australian crown clade Egerniinae: <i>Egernia gillespieae</i> is placed close to species of the living genus <i>Egernia</i>, whereas ‘<i>Tiliqua</i>’ <i>pusilla</i> likely sits basal to the divergence of the clade inclusive of <i>Tiliqua</i> and <i>Cyclodomorphus</i>. The fossils thus provide direct evidence that the Australian radiation of the Egerniinae was well underway by the mid-Miocene.
DOI: 10.26180/5cc80de987113
title: Intervention data and data dictionary

description: These data comprise those for an intervention of hypertension conducted in rural India. The intervention was delivered by health workers in a group setting, every 2 weeks for 3 months. The primary outcome was control of blood pressure after the end of the 3-month intervention period.<br>
DOI: 10.6084/m9.figshare.8057378.v1
title: A new scincid lizard from the Miocene of Northern Australia, and the evolutionary history of social skinks (Scincidae: Egerniinae)

description: The Egerniinae (formerly the <i>Egernia</i> group) is a morphologically diverse clade of skinks comprising 61 extant species from eight genera, spread across Australia, New Guinea, and the Solomon Islands. The relatively large size and robustness of many egerniines has meant that they fossilize more readily than other Australian skinks and have been more frequently recorded from paleontological excavations. The Riversleigh World Heritage Area of northeastern Australia has yielded multiple egerniine fossils, but most are isolated jaw elements, and only one taxon (‘<i>Tiliqua’ pusilla</i>) has been formally described. Articulated remains recently recovered from the mid-Miocene AL90 site (14.8 Ma) at Riversleigh are here described as <i>Egernia gillespieae</i> and represent the first opportunity to describe the morphology of a significant portion of a single individual of a fossil member of the Egerniinae. We include this fossil and ‘<i>T.</i>’ <i>pusilla</i> in an integrated analysis of morphology and published molecular data to assess their relationships and to provide calibration points for the timing of the egerniine radiation. Our calibrated tree combining molecular and morphological data suggests that the modern Australian radiation dates to the end of the Eocene (34.1 Ma). Both fossils are within the Australian crown clade Egerniinae: <i>Egernia gillespieae</i> is placed close to species of the living genus <i>Egernia</i>, whereas ‘<i>Tiliqua</i>’ <i>pusilla</i> likely sits basal to the divergence of the clade inclusive of <i>Tiliqua</i> and <i>Cyclodomorphus</i>. The fossils thus provide direct evidence that the Australian radiation of the Egerniinae was well underway by the mid-Miocene.
DOI: 10.6084/m9.figshare.8057378.v3
title: A new scincid lizard from the Miocene of northern Australia, and the evolutionary history of social skinks (Scincidae: Egerniinae)

description: The Egerniinae (formerly the <i>Egernia</i> group) is a morphologically diverse clade of skinks comprising 61 extant species from eight genera, spread across Australia, New Guinea, and the Solomon Islands. The relatively large size and robustness of many egerniines has meant that they fossilize more readily than other Australian skinks and have been more frequently recorded from paleontological excavations. The Riversleigh World Heritage Area of northeastern Australia has yielded multiple egerniine fossils, but most are isolated jaw elements, and only one taxon (‘<i>Tiliqua’ pusilla</i>) has been formally described. Articulated remains recently recovered from the mid-Miocene AL90 site (14.8 Ma) at Riversleigh are here described as <i>Egernia gillespieae</i> and represent the first opportunity to describe the morphology of a significant portion of a single individual of a fossil member of the Egerniinae. We include this fossil and ‘<i>T.</i>’ <i>pusilla</i> in an integrated analysis of morphology and published molecular data to assess their relationships and to provide calibration points for the timing of the egerniine radiation. Our calibrated tree combining molecular and morphological data suggests that the modern Australian radiation dates to the end of the Eocene (34.1 Ma). Both fossils are within the Australian crown clade Egerniinae: <i>Egernia gillespieae</i> is placed close to species of the living genus <i>Egernia</i>, whereas ‘<i>Tiliqua</i>’ <i>pusilla</i> likely sits basal to the divergence of the clade inclusive of <i>Tiliqua</i> and <i>Cyclodomorphus</i>. The fossils thus provide direct evidence that the Australian radiation of the Egerniinae was well underway by the mid-Miocene.
DOI: 10.6084/m9.figshare.8057378.v2
title: A new scincid lizard from the Miocene of Northern Australia, and the evolutionary history of social skinks (Scincidae: Egerniinae)

description: The Egerniinae (formerly the <i>Egernia</i> group) is a morphologically diverse clade of skinks comprising 61 extant species from eight genera, spread across Australia, New Guinea, and the Solomon Islands. The relatively large size and robustness of many egerniines has meant that they fossilize more readily than other Australian skinks and have been more frequently recorded from paleontological excavations. The Riversleigh World Heritage Area of northeastern Australia has yielded multiple egerniine fossils, but most are isolated jaw elements, and only one taxon (‘<i>Tiliqua’ pusilla</i>) has been formally described. Articulated remains recently recovered from the mid-Miocene AL90 site (14.8 Ma) at Riversleigh are here described as <i>Egernia gillespieae</i> and represent the first opportunity to describe the morphology of a significant portion of a single individual of a fossil member of the Egerniinae. We include this fossil and ‘<i>T.</i>’ <i>pusilla</i> in an integrated analysis of morphology and published molecular data to assess their relationships and to provide calibration points for the timing of the egerniine radiation. Our calibrated tree combining molecular and morphological data suggests that the modern Australian radiation dates to the end of the Eocene (34.1 Ma). Both fossils are within the Australian crown clade Egerniinae: <i>Egernia gillespieae</i> is placed close to species of the living genus <i>Egernia</i>, whereas ‘<i>Tiliqua</i>’ <i>pusilla</i> likely sits basal to the divergence of the clade inclusive of <i>Tiliqua</i> and <i>Cyclodomorphus</i>. The fossils thus provide direct evidence that the Australian radiation of the Egerniinae was well underway by the mid-Miocene.
DOI: 10.6084/m9.figshare.8057258
title: Spring is in the air: seasonal profiles indicate vernal change of miRNA activity

description: The envisioned application of miRNAs as diagnostic or prognostic biomarkers calls for an in-depth understanding of their distribution and variability in different physiological states. While effects with respect to ethnic origin, age, or gender are known, the inter-individual variability of miRNAs across the four seasons remained largely hidden. We sequentially profiled the complete repertoire of blood-borne miRNAs for 25 physiologically normal individuals in spring, summer, fall, and winter (altogether 95 samples) and validated the results on 292 individuals (919 samples collected with the Mitra home sampling device) by RT-qPCR. Principal variance component analysis suggests that the largest variability observed in miRNA expression is due to individual variability and the individuals’ gender. But the results also highlight a deviation of miRNA activity in samples collected during spring time. Following adjustment for multiple testing, remarkable differences are observed between spring and fall (77 miRNAs). The two most dys-regulated miRNAs were miR-181c-5p and miR-106b-5p (adjusted p-value of 0.007). Other significant miRNAs include miR-140-3p, miR-21-3p, and let-7c-5p. The dys-regulation was validated by RT-qPCR. Systems biology analysis further provides strong evidence for the immunological origin of the signals: dys-regulated miRNAs are enriched in CD56 cells and belong to various signalling and immune-system-related pathways. Our data suggest that besides known confounding factors such as age and sex, also the season in which a test is conducted might have a considerable influence on the expression of blood-borne miRNAs and subsequently might interfere with diagnosis based on such signatures.
DOI: 10.6084/m9.figshare.8057270.v1
title: Lymphocytes upregulate CD36 in adipose tissue and liver

description: CD36 is a multifunctional scavenger receptor and lipid transporter implicated in metabolic and inflammatory pathologies, as well as cancer progression. CD36 is known to be expressed by adipocytes and monocytes/macrophages, but its expression by T cells is not clearly established. We found that CD4 and CD8 T cells in adipose tissue and liver of humans, monkeys, and mice upregulated CD36 expression (ranging from ~5–40% CD36+), whereas little to no CD36 was expressed by T cells in blood, spleen, and lymph nodes. CD36 was expressed predominantly by resting CD38-, HLA.DR-, and PD-1- adipose tissue T cells in monkeys, and increased during high-fat feeding in mice. Adipose tissue and liver promote a distinct phenotype in resident T cells characterized by CD36 upregulation.
DOI: 10.6084/m9.figshare.8057258.v2
title: Spring is in the air: seasonal profiles indicate vernal change of miRNA activity

description: The envisioned application of miRNAs as diagnostic or prognostic biomarkers calls for an in-depth understanding of their distribution and variability in different physiological states. While effects with respect to ethnic origin, age, or gender are known, the inter-individual variability of miRNAs across the four seasons remained largely hidden. We sequentially profiled the complete repertoire of blood-borne miRNAs for 25 physiologically normal individuals in spring, summer, fall, and winter (altogether 95 samples) and validated the results on 292 individuals (919 samples collected with the Mitra home sampling device) by RT-qPCR. Principal variance component analysis suggests that the largest variability observed in miRNA expression is due to individual variability and the individuals’ gender. But the results also highlight a deviation of miRNA activity in samples collected during spring time. Following adjustment for multiple testing, remarkable differences are observed between spring and fall (77 miRNAs). The two most dys-regulated miRNAs were miR-181c-5p and miR-106b-5p (adjusted p-value of 0.007). Other significant miRNAs include miR-140-3p, miR-21-3p, and let-7c-5p. The dys-regulation was validated by RT-qPCR. Systems biology analysis further provides strong evidence for the immunological origin of the signals: dys-regulated miRNAs are enriched in CD56 cells and belong to various signalling and immune-system-related pathways. Our data suggest that besides known confounding factors such as age and sex, also the season in which a test is conducted might have a considerable influence on the expression of blood-borne miRNAs and subsequently might interfere with diagnosis based on such signatures.
DOI: 10.6084/m9.figshare.8057141
title: Supplementary Material for: Sex-Specific Effects of Stress on Mood-Related Gene Expression

description: Women are twice as likely as men to be diagnosed with major depressive disorder (MDD). Recent studies report distinct molecular changes in depressed men and women across mesocorticolimbic brain regions. However, it is unclear which sex-related factors drive distinct MDD-associated pathology. The goal of this study was to use mouse experimental systems to investigate sex-specific mechanisms underlying the distinct molecular profiles of MDD in men and women. We used unpredictable chronic mild stress to induce an elevated anxiety-/depressive-like state and “four core genotypes” (FCG) mice to probe for sex-specific mechanisms. As predicted, based on previous implications in mood, stress impacted the expression of several dopamine-, GABA-, and glutamate-related genes. Some of these effects, specifically in the prefrontal cortex, were genetic sex-specific, with effects in XX mice but not in XY mice. Stress also impacted gene expression differently across the mesocorticolimbic circuit, with increased expression of mood-related genes in the prefrontal cortex and nucleus accumbens, but decreased expression in basolateral amygdala. Our results suggest that females are sensitive to the effects of chronic stress, partly due to their genetic sex, independent of gonadal hormones. Furthermore, these results point to the prefrontal cortex as the node in the mesocorticolimbic circuitry with the strongest female-specific effects.
DOI: 10.6084/m9.figshare.8057258.v1
title: Spring is in the Air: Seasonal Profiles indicate vernal Change of miRNA Activity

description: The envisioned application of miRNAs as diagnostic or prognostic biomarkers calls for an in-depth understanding of their distribution and variability in different physiological states. While effects with respect to ethnic origin, age, or gender are known, the inter-individual variability of miRNAs across the four seasons remained largely hidden. We sequentially profiled the complete repertoire of blood- borne miRNAs for 25 physiologically normal individuals in spring, summer, fall, and winter (altogether 95 samples) and validated the results on 292 individuals (919 samples collected with the Mitra home sampling device) by RT-qPCR. Principal variance component analysis suggests that the largest variability observed in miRNA expression is due to individual variability and the individuals’ gender. But the results also highlight a deviation of miRNA activity in samples collected during spring time. Following adjustment for multiple testing, remarkable differences are observed between spring and fall (77 miRNAs). The two most dys-regulated miRNAs were miR-181c-5p and miR-106b-5p (adjusted p-value of 0.007). Other significant miRNAs include miR-140-3p, miR-21-3p, and let-7c-5p. The dys-regulation was validated by RT-qPCR. Systems biology analysis further provides strong evidence for the immunological origin of the signals: dys-regulated miRNAs are enriched in CD56 cells and belong to various signaling and immune system related pathways. Our data suggest that besides known confounding factors as age and sex, also the season in which a test is conducted might have a considerable influence on expression of blood-borne miRNAs and subsequently might interfere with diagnosis based on such signatures.
DOI: 10.6084/m9.figshare.8057111
title: Role of interim and end of treatment positron emission tomography for response assessment and prediction of relapse in posttransplant lymphoproliferative disorder

description: <b>Background:</b> Fluorine-18-fluorodeoxyglucose positron emission tomography (PET) has an established and central role in diagnosis, staging and response evaluation of lymphoproliferative diseases. It has shown a high sensitivity and specificity at diagnosis in posttransplant lymphoproliferative disorders (PTLDs). However, little is known about the performance of interim and end of treatment (EOT) PET in PTLD patients with regards to response assessment, relapse prediction and outcome. <b>Methods:</b> We performed a single-center retrospective study in which we analyzed consecutive patients diagnosed with CD20-positive PTLD after solid organ transplantation between 2008 and 2017, who all received risk-stratified sequential treatment according to the PTLD-1 phase II trial. Interim and EOT PET studies were scored according to the Deauville criteria. <b>Results:</b> Forty-one patients were included with median follow-up of 41.5 months (range 1–108). Positive and negative predictive values for disease recurrence were 13% and 85% for interim and 33% and 87% for EOT PET, respectively. There was no significant difference in overall survival, progression-free survival nor time to progression between negative versus positive patients on interim and EOT scans. <b>Conclusions:</b> Negative interim and/or negative end of treatment PET identify PTLD patients with low risk of disease recurrence.