cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12082200
title: Additional file 3 of Assessment of viral RNA in idiopathic pulmonary fibrosis using RNA-seq

description: Additional file 3: Table S3. Counts for virus mapped non-poly(A) selected RNA-seq reads for IPF and control lung RNA.
DOI: 10.6084/m9.figshare.12082200.v1
title: Additional file 3 of Assessment of viral RNA in idiopathic pulmonary fibrosis using RNA-seq

description: Additional file 3: Table S3. Counts for virus mapped non-poly(A) selected RNA-seq reads for IPF and control lung RNA.
DOI: 10.6084/m9.figshare.12082209
title: Additional file 4 of Assessment of viral RNA in idiopathic pulmonary fibrosis using RNA-seq

description: Additional file 4: Table S4. Counts for HERV mapped non-poly(A) selected RNA-seq reads for IPF and control lung RNA.
DOI: 10.6084/m9.figshare.12082209.v1
title: Additional file 4 of Assessment of viral RNA in idiopathic pulmonary fibrosis using RNA-seq

description: Additional file 4: Table S4. Counts for HERV mapped non-poly(A) selected RNA-seq reads for IPF and control lung RNA.
DOI: 10.6084/m9.figshare.12082218
title: Additional file 5 of Assessment of viral RNA in idiopathic pulmonary fibrosis using RNA-seq

description: Additional file 5: Table S5. Counts for virus mapped SRA RNA-seq reads for IPF and control lung RNA.
DOI: 10.6084/m9.figshare.12082218.v1
title: Additional file 5 of Assessment of viral RNA in idiopathic pulmonary fibrosis using RNA-seq

description: Additional file 5: Table S5. Counts for virus mapped SRA RNA-seq reads for IPF and control lung RNA.
DOI: 10.6084/m9.figshare.12082242
title: Additional file 10 of A novel virtual barcode strategy for accurate panel-wide variant calling in circulating tumor DNA

description: Additional file 10. Table S1. (Table S1): Panel-wide statistics for 30 BGs, 3 HWTs and 2 tumor samples.
DOI: 10.6084/m9.figshare.25151393
title: Data available.xlsx

description: we evaluated the the prognosis impact of monocyte percentage at diagnosis in newly diagnosed DLBCL patients. This retrospective cohort study firstly displayed a significant association between elevated monocyte percentage and a poor survival outcome. The data of monocytes percentage, achieved from CBC, may be widely used and easily incorporated into clinical practice. In addition, monocyte percentage presented prognostic information independent of NCCN-IPI and is also able to provide additional prognostic information when combined with NCCN-IPI.
DOI: 10.6084/m9.figshare.25151393.v1
title: Data available.xlsx

description: we evaluated the the prognosis impact of monocyte percentage at diagnosis in newly diagnosed DLBCL patients. This retrospective cohort study firstly displayed a significant association between elevated monocyte percentage and a poor survival outcome. The data of monocytes percentage, achieved from CBC, may be widely used and easily incorporated into clinical practice. In addition, monocyte percentage presented prognostic information independent of NCCN-IPI and is also able to provide additional prognostic information when combined with NCCN-IPI.
DOI: 10.6084/m9.figshare.12082242.v1
title: Additional file 10 of A novel virtual barcode strategy for accurate panel-wide variant calling in circulating tumor DNA

description: Additional file 10. Table S1. (Table S1): Panel-wide statistics for 30 BGs, 3 HWTs and 2 tumor samples.
DOI: 10.6084/m9.figshare.9985097
title: <i>Phialophora</i> section <i>Catenulatae</i> disassembled: New genera, species, and combinations and a new family encompassing taxa with cleistothecial ascomata and phialidic asexual states

description: The Pleuroascaceae (Leotiomycetes) is introduced for <i>Phialophora hyalina</i> (section <i>Catenulatae</i>) and its closest relatives based on analyses of DNA sequences of five gene regions and the comparison of cultural and micromorphological characters. The family is resolved as a strongly supported clade that encompasses <i>Pleuroascus</i> and the new anamorph genera <i>Entimomentora</i> and <i>Venustampulla</i>. The latter includes <i>V. parva</i>, a species placed formerly in <i>Scopulariopsis</i>, and <i>V. echinocandica</i>, which is established for the echinocandin-producing isolate BP-5553. <i>Entimomentora</i> includes <i>E. hyalina</i>, a species based on the ex-type strain of <i>Ph. hyalina</i>. Additional isolates identified as <i>Ph. hyalina</i> are distantly related to the Pleuroacaceae and include <i>Psychrophila antarctica</i> (Arachnopezizaceae) and <i>Cryonesomyces dreyfussii</i>, the sole member of the new genus <i>Cryonesomyces</i> (incertae sedis). Isolates identified or deposited as <i>Ph. alba</i> are also not closely related; they include a species for which we propose the name <i>Neobulgaria koningiana</i> (Gelatinodiscaceae) and a second psychrophilic species that we describe as <i>Psychrophila lagodekhiensis</i>. Of the 13 isolates assessed for in vitro antifungal activity, only <i>V. echinocandica</i> inhibited the growth of <i>Candida albicans</i>.
DOI: 10.6084/m9.figshare.9985097.v1
title: <i>Phialophora</i> section <i>Catenulatae</i> disassembled: New genera, species, and combinations and a new family encompassing taxa with cleistothecial ascomata and phialidic asexual states

description: The Pleuroascaceae (Leotiomycetes) is introduced for <i>Phialophora hyalina</i> (section <i>Catenulatae</i>) and its closest relatives based on analyses of DNA sequences of five gene regions and the comparison of cultural and micromorphological characters. The family is resolved as a strongly supported clade that encompasses <i>Pleuroascus</i> and the new anamorph genera <i>Entimomentora</i> and <i>Venustampulla</i>. The latter includes <i>V. parva</i>, a species placed formerly in <i>Scopulariopsis</i>, and <i>V. echinocandica</i>, which is established for the echinocandin-producing isolate BP-5553. <i>Entimomentora</i> includes <i>E. hyalina</i>, a species based on the ex-type strain of <i>Ph. hyalina</i>. Additional isolates identified as <i>Ph. hyalina</i> are distantly related to the Pleuroacaceae and include <i>Psychrophila antarctica</i> (Arachnopezizaceae) and <i>Cryonesomyces dreyfussii</i>, the sole member of the new genus <i>Cryonesomyces</i> (incertae sedis). Isolates identified or deposited as <i>Ph. alba</i> are also not closely related; they include a species for which we propose the name <i>Neobulgaria koningiana</i> (Gelatinodiscaceae) and a second psychrophilic species that we describe as <i>Psychrophila lagodekhiensis</i>. Of the 13 isolates assessed for in vitro antifungal activity, only <i>V. echinocandica</i> inhibited the growth of <i>Candida albicans</i>.
DOI: 10.6084/m9.figshare.12082248
title: Additional file 11 of A novel virtual barcode strategy for accurate panel-wide variant calling in circulating tumor DNA

description: Additional file 11. Table S2. (Table S2).
DOI: 10.6084/m9.figshare.12082248.v1
title: Additional file 11 of A novel virtual barcode strategy for accurate panel-wide variant calling in circulating tumor DNA

description: Additional file 11. Table S2. (Table S2).
DOI: 10.6084/m9.figshare.12082251
title: Additional file 12 of A novel virtual barcode strategy for accurate panel-wide variant calling in circulating tumor DNA

description: Additional file 12. Table S3. (Table S3).
DOI: 10.6084/m9.figshare.12082251.v1
title: Additional file 12 of A novel virtual barcode strategy for accurate panel-wide variant calling in circulating tumor DNA

description: Additional file 12. Table S3. (Table S3).
DOI: 10.6084/m9.figshare.12082254
title: Additional file 13 of A novel virtual barcode strategy for accurate panel-wide variant calling in circulating tumor DNA

description: Additional file 13. Table S4. (Table S4).
DOI: 10.6084/m9.figshare.12082254.v1
title: Additional file 13 of A novel virtual barcode strategy for accurate panel-wide variant calling in circulating tumor DNA

description: Additional file 13. Table S4. (Table S4).
DOI: 10.6084/m9.figshare.12082257
title: Additional file 14 of A novel virtual barcode strategy for accurate panel-wide variant calling in circulating tumor DNA

description: Additional file 14. Table S5. (Table S5): Annotations for left sites in controls.
DOI: 10.6084/m9.figshare.12082257.v1
title: Additional file 14 of A novel virtual barcode strategy for accurate panel-wide variant calling in circulating tumor DNA

description: Additional file 14. Table S5. (Table S5): Annotations for left sites in controls.
DOI: 10.6084/m9.figshare.12082260
title: Additional file 15 of A novel virtual barcode strategy for accurate panel-wide variant calling in circulating tumor DNA

description: Additional file 15. Table S6. (Table S6): Distribution of controls’ left sites with AF values in multiplexing samples at same sequencing line.
DOI: 10.6084/m9.figshare.12082260.v1
title: Additional file 15 of A novel virtual barcode strategy for accurate panel-wide variant calling in circulating tumor DNA

description: Additional file 15. Table S6. (Table S6): Distribution of controls’ left sites with AF values in multiplexing samples at same sequencing line.
DOI: 10.6084/m9.figshare.19422326
title: Exosomes from human adipose-derived mesenchymal stem cells inhibit production of extracellular matrix in keloid fibroblasts via downregulating transforming growth factor-β2 and Notch-1 expression

description: Keloids are an excessive tissue response to dermal damage, characterized by uncontrolled growth and a high recurrence rate after various treatments. Abnormalities with the extracellular matrix (ECM) are one of the most important contributing factors to the formation of keloids. Although exosomes from human adipose-derived mesenchymal stem cells (adMSC-Exos) have been shown to promote repair and regeneration in wounds, they have seldom been studied for the treatment of keloids. In this study, we aimed to investigate the effects of adMSC-Exos on ECM remodeling in keloids using both <i>in vitro</i> and <i>ex vivo</i> models. The results showed that adMSC-Exos inhibited gene and protein expression of collagen I (<i>COL-1</i>), collagen III (<i>COL-3</i>), fibronectin (<i>FN</i>), and α-smooth muscle actin (<i>α-SMA</i>) in keloid fibroblasts (KFs). Furthermore, using an <i>ex vivo</i> tissue explant model, we found that adMSC-Exos significantly suppressed COL production and disrupted the microvessel stucture. We also demonstrated that adMSC-Exos inhibited the protein expression of Smad3 and Notch-1, and the expression of transforming growth factor β2 (<i>TGF-β2</i>) in KFs, and promoted the expression of <i>TGF-β3</i>. These findings largely explain the mechanisms underlying the inhibition of ECM production in keloids by adMSC-Exos. In conclusion, our results revealed that adMSC-Exos effectively inhibited the production of ECM in keloids, which provides a new potential alternative for the systemic treatment of keloids.
DOI: 10.6084/m9.figshare.19422326.v1
title: Exosomes from human adipose-derived mesenchymal stem cells inhibit production of extracellular matrix in keloid fibroblasts via downregulating transforming growth factor-β2 and Notch-1 expression

description: Keloids are an excessive tissue response to dermal damage, characterized by uncontrolled growth and a high recurrence rate after various treatments. Abnormalities with the extracellular matrix (ECM) are one of the most important contributing factors to the formation of keloids. Although exosomes from human adipose-derived mesenchymal stem cells (adMSC-Exos) have been shown to promote repair and regeneration in wounds, they have seldom been studied for the treatment of keloids. In this study, we aimed to investigate the effects of adMSC-Exos on ECM remodeling in keloids using both <i>in vitro</i> and <i>ex vivo</i> models. The results showed that adMSC-Exos inhibited gene and protein expression of collagen I (<i>COL-1</i>), collagen III (<i>COL-3</i>), fibronectin (<i>FN</i>), and α-smooth muscle actin (<i>α-SMA</i>) in keloid fibroblasts (KFs). Furthermore, using an <i>ex vivo</i> tissue explant model, we found that adMSC-Exos significantly suppressed COL production and disrupted the microvessel stucture. We also demonstrated that adMSC-Exos inhibited the protein expression of Smad3 and Notch-1, and the expression of transforming growth factor β2 (<i>TGF-β2</i>) in KFs, and promoted the expression of <i>TGF-β3</i>. These findings largely explain the mechanisms underlying the inhibition of ECM production in keloids by adMSC-Exos. In conclusion, our results revealed that adMSC-Exos effectively inhibited the production of ECM in keloids, which provides a new potential alternative for the systemic treatment of keloids.
DOI: 10.20363/rif511-1.0
title: Fauna in Phoenix palm trees – results from a full year monitoring in southern Spain

description: This study aimed to monitor the invertebrate and vertebrate fauna occurring on and associated with ornamental palms of the genus Phoenix, over the course of one year. The term ‘ornamental palm’ in this context refers to the type of trees (i.e. non-native, planted palm trees) rather than their current use at the study sites. Five different locations and settings were chosen in southern Spain, as a representative Mediterranean region where ornamental palms are commonly used. Monitoring methods were applied monthly in order to assess the vertebrates and invertebrates associated with the full seasonal cycle of palms, including flowering and fruiting.
DOI: 10.5281/zenodo.10619729
title: Coelacanth transcriptome from SRR391920

description: Coelacanth transcriptome which was archived on NCBI GenBank (Run accession: SRR391920).

The sequence read archive was downloaded and reads were assembled with Trinity with default settings.
DOI: 10.5281/zenodo.10469583
title: Data from: From death comes life: Large vertebrate carrion enhances seedling establishment in clonal ericaceous shrubs

description: 1.     Carrion can have disproportionally large effects on ecological processes and community dynamics. During decomposition, the influx of growth-limiting nutrients can create small-scale disturbances with high soil cover known as ‘cadaver decomposition islands’ (CDIs). Such disturbances can allow for altered plant species composition, increased biomass production or provide microsites for regeneration. Carcasses also provide a resource for omnivorous scavengers, which have the potential to direct endozoochorous seed dispersal towards developing CDIs.

2.     In this study, we investigated functional links between the scavenger community, carcass induced-disturbances in vegetation, and seedling establishment of berry-producing ericaceous species. We experimentally placed out 30 vertebrate carcasses of various species in a boreal forest ecosystem, each paired with a control and a mechanically disturbed plot to track vertebrate animal activity (i.e. dispersal vectors), vegetation changes (i.e. recruitment windows) and seedling establishment. We hypothesized that carcass size and season of experimental deposition would affect (H1) scavenger community composition and (H2) formation of CDIs, and that (H3) seedling establishment of ericaceous species is more abundant at CDIs compared with control or disturbed plots without carcass deposition. 

3.     We found that carcass presence effectively created a spatiotemporal hotspot of animal activity and that 94 % of observations of vertebrates at carcasses were of species with the potential for ericaceous seed dispersal. Larger carcasses (e.g. moose, reindeer) attracted similar and abundant vertebrate communities whereas observations at small carcasses (e.g. red fox) resembled those at control plots (H1). Only larger carcasses led to CDI formation (i.e. potential recruitment microsites) while plots with small carcasses resembled control plots (H2). Surprisingly, season of carcass deposition did not influence vertebrate composition at carcass plots or CDI formation (H1-2). Seedlings were significantly more abundant in CDIs compared with mechanical disturbance and control plots (H3). Overall, CDIs contained about 4 and 19 times more seedlings compared with disturbed and controls, respectively.

4.     Our study demonstrates how individual carcasses in a boreal forest landscape can facilitate sexual reproduction in ericaceous keystone species. We suggest that this pathway also occurs in other ecosystems and that it may contribute to genetic diversity of plant populations.
DOI: 10.5281/zenodo.10469582
title: Data from: From death comes life: Large vertebrate carrion enhances seedling establishment in clonal ericaceous shrubs

description: 1.     Carrion can have disproportionally large effects on ecological processes and community dynamics. During decomposition, the influx of growth-limiting nutrients can create small-scale disturbances with high soil cover known as ‘cadaver decomposition islands’ (CDIs). Such disturbances can allow for altered plant species composition, increased biomass production or provide microsites for regeneration. Carcasses also provide a resource for omnivorous scavengers, which have the potential to direct endozoochorous seed dispersal towards developing CDIs.

2.     In this study, we investigated functional links between the scavenger community, carcass induced-disturbances in vegetation, and seedling establishment of berry-producing ericaceous species. We experimentally placed out 30 vertebrate carcasses of various species in a boreal forest ecosystem, each paired with a control and a mechanically disturbed plot to track vertebrate animal activity (i.e. dispersal vectors), vegetation changes (i.e. recruitment windows) and seedling establishment. We hypothesized that carcass size and season of experimental deposition would affect (H1) scavenger community composition and (H2) formation of CDIs, and that (H3) seedling establishment of ericaceous species is more abundant at CDIs compared with control or disturbed plots without carcass deposition. 

3.     We found that carcass presence effectively created a spatiotemporal hotspot of animal activity and that 94 % of observations of vertebrates at carcasses were of species with the potential for ericaceous seed dispersal. Larger carcasses (e.g. moose, reindeer) attracted similar and abundant vertebrate communities whereas observations at small carcasses (e.g. red fox) resembled those at control plots (H1). Only larger carcasses led to CDI formation (i.e. potential recruitment microsites) while plots with small carcasses resembled control plots (H2). Surprisingly, season of carcass deposition did not influence vertebrate composition at carcass plots or CDI formation (H1-2). Seedlings were significantly more abundant in CDIs compared with mechanical disturbance and control plots (H3). Overall, CDIs contained about 4 and 19 times more seedlings compared with disturbed and controls, respectively.

4.     Our study demonstrates how individual carcasses in a boreal forest landscape can facilitate sexual reproduction in ericaceous keystone species. We suggest that this pathway also occurs in other ecosystems and that it may contribute to genetic diversity of plant populations.
DOI: 10.6084/m9.figshare.25151429
title: Supplementary Material for: Diagnostic Accuracy of Point-Of-Care Testing of C-Reactive Protein, Interleukin-6, And Procalcitonin in Neonates with Clinically Suspected Sepsis: A Prospective Observational Study

description: Objective: Sepsis often prompts clinicians to start empirical antibiotics in suspected neonates while awaiting diagnosis. The next-generation testing with point-of-care techniques offers a lead time advantage that could bridge the gap by providing a timely diagnosis. Materials and Methods: We conducted a prospective diagnostic study in 82 neonates enrolled between May and October 2022 in a level III neonatal intensive care unit. All neonates with a new episode of clinically suspected sepsis were included. Diagnostic accuracy of point-of-care (POC) testing of C-reactive protein (CRP), interleukin-6 (IL-6), and procalcitonin with standard laboratory methods was performed. Results: The mean gestation age and birth weight of the neonates were 33.17 ± 4.25 weeks and 1695.4 ± 700.74 grams respectively. Most neonates were preterm (75%) with nearly equal proportions of early (51.22%) and late-onset (48.78%) sepsis. The point-of-care CRP correlated well with standard CRP (r = 0.8001, 95% CI: 0.706 - 0.867, p &lt; 0.0001). Amongst the three biomarkers, CRP had the maximum diagnostic accuracy (AUC - 0.73) followed by procalcitonin (AUC - 0.65) and IL-6 (0.55). There was no significant difference in the diagnostic accuracy of CRP (p = 0.46), procalcitonin (p = 0.29), and IL-6 (p = 0.60) in early and late-onset sepsis. The mean time for point-of-care estimation of IL-6, PCT, and CRP was 12 ± 3 minutes which was significantly less compared to 366 ± 61 minutes for standard techniques. (p &lt; 0.001). Conclusion: Point-of-care CRP correlates well with standard techniques of estimation, and CRP alone and in combination with procalcitonin has good diagnostic accuracy in neonatal sepsis.
DOI: 10.6084/m9.figshare.25151429.v1
title: Supplementary Material for: Diagnostic Accuracy of Point-Of-Care Testing of C-Reactive Protein, Interleukin-6, And Procalcitonin in Neonates with Clinically Suspected Sepsis: A Prospective Observational Study

description: Objective: Sepsis often prompts clinicians to start empirical antibiotics in suspected neonates while awaiting diagnosis. The next-generation testing with point-of-care techniques offers a lead time advantage that could bridge the gap by providing a timely diagnosis. Materials and Methods: We conducted a prospective diagnostic study in 82 neonates enrolled between May and October 2022 in a level III neonatal intensive care unit. All neonates with a new episode of clinically suspected sepsis were included. Diagnostic accuracy of point-of-care (POC) testing of C-reactive protein (CRP), interleukin-6 (IL-6), and procalcitonin with standard laboratory methods was performed. Results: The mean gestation age and birth weight of the neonates were 33.17 ± 4.25 weeks and 1695.4 ± 700.74 grams respectively. Most neonates were preterm (75%) with nearly equal proportions of early (51.22%) and late-onset (48.78%) sepsis. The point-of-care CRP correlated well with standard CRP (r = 0.8001, 95% CI: 0.706 - 0.867, p &lt; 0.0001). Amongst the three biomarkers, CRP had the maximum diagnostic accuracy (AUC - 0.73) followed by procalcitonin (AUC - 0.65) and IL-6 (0.55). There was no significant difference in the diagnostic accuracy of CRP (p = 0.46), procalcitonin (p = 0.29), and IL-6 (p = 0.60) in early and late-onset sepsis. The mean time for point-of-care estimation of IL-6, PCT, and CRP was 12 ± 3 minutes which was significantly less compared to 366 ± 61 minutes for standard techniques. (p &lt; 0.001). Conclusion: Point-of-care CRP correlates well with standard techniques of estimation, and CRP alone and in combination with procalcitonin has good diagnostic accuracy in neonatal sepsis.
DOI: 10.24403/jp.1318894
title: Kritische Revision der "Thlaspi''-Arten Europas, Vorderasiens und Afrikas. Spezieller Teil : VII. Callothlaspi / Friedrich Karl Meyer
DOI: 10.5517/ccdc.csd.cc28khdr
title: CCDC 2102184: Experimental Crystal Structure Determination

description: Related Article: Su Yong Go, Hyunho Chung, Samuel Jaeho Shin, Sohee An, Ju Hyun Youn, Tae Yeong Im, Ji Yong Kim, Taek Dong Chung, Hong Geun Lee|2022|J.Am.Chem.Soc.|144|9149|doi:10.1021/jacs.2c03213
DOI: 10.5517/ccdc.csd.cc298l9h
title: CCDC 2123416: Experimental Crystal Structure Determination

description: Related Article: Ningchao Liu, Hirofumi Morimoto, Fan Wu, Xiaojuan Lv, Bentian Xiao, Daiki Kuzuhara, Jianming Pan, Fengxian Qiu, Naoki Aratani, Zhen Shen, Hiroko Yamada, Songlin Xue|2022|Org.Lett.|24|3609|doi:10.1021/acs.orglett.2c01147