cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.24627844
title: Examination of newborn DNA methylation among women with polycystic ovary syndrome/hirsutism

description: Research suggests that polycystic ovary syndrome (PCOS) traits (e.g., hyperandrogenism) may create a suboptimal intrauterine environment and induce epigenetic modifications. Therefore, we assessed the associations of PCOS traits with neonatal DNA methylation (DNAm) using two independent cohorts. DNAm was measured in both cohorts using the Infinium MethylationEPIC array. Multivariable robust linear regression was used to determine associations of maternal PCOS exposure or preconception testosterone with methylation β-values at each CpG probe and corrected for multiple testing by false-discovery rate (FDR). In the birth cohort, 12% (102/849) had a PCOS diagnosis (8.1% PCOS without hirsutism; 3.9% PCOS with hirsutism). Infants exposed to maternal PCOS with hirsutism compared to no PCOS had differential DNAm at cg02372539 [β(SE): −0.080 (0.010); FDR <i>p</i> = 0.009], cg08471713 [β(SE):0.077 (0.014); FDR <i>p</i> = 0.016] and cg17897916 [β(SE):0.050 (0.009); FDR <i>p</i> = 0.009] with adjustment for maternal characteristics including pre-pregnancy BMI. PCOS with hirsutism was also associated with 8 differentially methylated regions (DMRs). PCOS without hirsutism was not associated with individual CpGs. In an independent preconception cohort, total testosterone concentrations were associated with 3 DMRs but not with individual CpGs, though the top quartile of testosterone compared to the lowest was marginally associated with increased DNAm at cg21472377 near an uncharacterized locus (FDR <i>p</i> = 0.09). Examination of these probes and DMRs indicate they may be under foetal genetic control. Overall, we found several associations among newborns exposed to PCOS, specifically when hirsutism was reported, and among newborns of women with relatively higher testosterone around conception.
DOI: 10.6084/m9.figshare.24627844.v1
title: Examination of newborn DNA methylation among women with polycystic ovary syndrome/hirsutism

description: Research suggests that polycystic ovary syndrome (PCOS) traits (e.g., hyperandrogenism) may create a suboptimal intrauterine environment and induce epigenetic modifications. Therefore, we assessed the associations of PCOS traits with neonatal DNA methylation (DNAm) using two independent cohorts. DNAm was measured in both cohorts using the Infinium MethylationEPIC array. Multivariable robust linear regression was used to determine associations of maternal PCOS exposure or preconception testosterone with methylation β-values at each CpG probe and corrected for multiple testing by false-discovery rate (FDR). In the birth cohort, 12% (102/849) had a PCOS diagnosis (8.1% PCOS without hirsutism; 3.9% PCOS with hirsutism). Infants exposed to maternal PCOS with hirsutism compared to no PCOS had differential DNAm at cg02372539 [β(SE): −0.080 (0.010); FDR <i>p</i> = 0.009], cg08471713 [β(SE):0.077 (0.014); FDR <i>p</i> = 0.016] and cg17897916 [β(SE):0.050 (0.009); FDR <i>p</i> = 0.009] with adjustment for maternal characteristics including pre-pregnancy BMI. PCOS with hirsutism was also associated with 8 differentially methylated regions (DMRs). PCOS without hirsutism was not associated with individual CpGs. In an independent preconception cohort, total testosterone concentrations were associated with 3 DMRs but not with individual CpGs, though the top quartile of testosterone compared to the lowest was marginally associated with increased DNAm at cg21472377 near an uncharacterized locus (FDR <i>p</i> = 0.09). Examination of these probes and DMRs indicate they may be under foetal genetic control. Overall, we found several associations among newborns exposed to PCOS, specifically when hirsutism was reported, and among newborns of women with relatively higher testosterone around conception.
DOI: 10.6084/m9.figshare.24628001
title: Documenting birds over two centuries of deforestation in an Atlantic Forest region of Brazil

description: The first ornithological record from Paraná State, Southern Brazil, dates from 1820, when forests covered 83% of the area. There is a lack of studies evaluating how knowledge on species richness increased over time, together with a massive deforestation process. We aimed to describe the changes, by decade, in forest species richness since that time, and to determine how field effort hours were distributed. We reviewed published studies using online databases. We compared forest bird communities between decades with Jaccard Dissimilarity Indices and compared communities’ composition among decades with Analysis of Similarity. In 200 years, 421 forest bird species were mentioned. Most of the species were detected until 1980, a likely subset of the avifauna before habitat loss; fewer species (108) were recorded afterward. An increasing number of species (8–20) stopped being recorded by decade from the 1980s. Field effort hours were mentioned in 1984, remaining temporally and spatially uneven. More than 1,000 localities have been inventoried, but most species reports are from Eastern municipalities. Areas within Serra do Mar, Curitiba, and Londrina stand out as protected forests and well-known academic centers. Cerrado endemics corroborated the relevance of exploring different regions, but further studies in this domain are strongly recommended.
DOI: 10.6084/m9.figshare.24628001.v1
title: Documenting birds over two centuries of deforestation in an Atlantic Forest region of Brazil

description: The first ornithological record from Paraná State, Southern Brazil, dates from 1820, when forests covered 83% of the area. There is a lack of studies evaluating how knowledge on species richness increased over time, together with a massive deforestation process. We aimed to describe the changes, by decade, in forest species richness since that time, and to determine how field effort hours were distributed. We reviewed published studies using online databases. We compared forest bird communities between decades with Jaccard Dissimilarity Indices and compared communities’ composition among decades with Analysis of Similarity. In 200 years, 421 forest bird species were mentioned. Most of the species were detected until 1980, a likely subset of the avifauna before habitat loss; fewer species (108) were recorded afterward. An increasing number of species (8–20) stopped being recorded by decade from the 1980s. Field effort hours were mentioned in 1984, remaining temporally and spatially uneven. More than 1,000 localities have been inventoried, but most species reports are from Eastern municipalities. Areas within Serra do Mar, Curitiba, and Londrina stand out as protected forests and well-known academic centers. Cerrado endemics corroborated the relevance of exploring different regions, but further studies in this domain are strongly recommended.
DOI: 10.6084/m9.figshare.24628003
title: R code from Global warming intensifies the interference competition by a poleward-expanding invader on a native dragonfly species

description: Rapid climate warming has boosted biological invasions and the distribution or expansion polewards of many species: this can cause serious impacts on local ecosystems within the invaded areas. Subsequently, native species may be exposed to threats of both interspecific competition with invaders and temperature rises. However, effects of warming on interspecific interactions, especially competition between invader and native species remains unclear. To better understand the combined threats of biological invasions and warming, the effect of temperature on competitive interactions between two dragonfly species, the expanding <i>Trithemis aurora</i> from Southeast Asia and the Japanese native <i>Orthetrum albistylum speciosum</i> were assessed based on their foraging capacity. Although the stand-alone effect of temperature on foraging intake of the native dragonfly was not apparent, its intake significantly decreased with increasing temperatures when the invader <i>T. aurora</i> was present. Such reductions in foraging might lead to displacement of the native species through competition for food resources. This suggests that impacts of invader species against native species are expected to be more severe when interspecific competition is exacerbated by temperature rises.
DOI: 10.6084/m9.figshare.24628003.v1
title: R code from Global warming intensifies the interference competition by a poleward-expanding invader on a native dragonfly species

description: Rapid climate warming has boosted biological invasions and the distribution or expansion polewards of many species: this can cause serious impacts on local ecosystems within the invaded areas. Subsequently, native species may be exposed to threats of both interspecific competition with invaders and temperature rises. However, effects of warming on interspecific interactions, especially competition between invader and native species remains unclear. To better understand the combined threats of biological invasions and warming, the effect of temperature on competitive interactions between two dragonfly species, the expanding <i>Trithemis aurora</i> from Southeast Asia and the Japanese native <i>Orthetrum albistylum speciosum</i> were assessed based on their foraging capacity. Although the stand-alone effect of temperature on foraging intake of the native dragonfly was not apparent, its intake significantly decreased with increasing temperatures when the invader <i>T. aurora</i> was present. Such reductions in foraging might lead to displacement of the native species through competition for food resources. This suggests that impacts of invader species against native species are expected to be more severe when interspecific competition is exacerbated by temperature rises.
DOI: 10.5281/zenodo.7866256
title: Supplemental Datasets for 'A novel tool kit to study effector recognition and cell-autonomous defense signaling in wheat'

description: Supplemental Datasets: <strong>Number </strong> <strong>File name </strong> <strong>Description </strong> S1 S1_Figure1_Data.csv Luminescence data for Figure 1, protoplast time course experiment S2 S2_RNAseqSampleTable.csv List of samples and treatment groups for RNAseq experiment S3 S3_LFC_1_genes.xlsx Lists of Gabo/GaboSr50, Fielder and all cultivar genes upregulated by log fold threshold of 1 S4 S4_GOTerms_Table.xlsx GO terms analysis Query tables and g:profiler results tables S5 S5_LFC2_genes.xlsx Lists of Gabo/GaboSr50, Fielder and all cultivar genes upregulated by log fold threshold of 2 S6 S6_Primers.xlsx List of primers used S7 S7_PlasmidList.xlsx List of plasmids used S8 S8_Figures3-5Data.xlsx Luminescence data used for generating Figures 3, 4 and 5
DOI: 10.5281/zenodo.7844446
title: Supplemental Datasets for 'Multiplexed effector screening for recognition by endogenous resistance genes using positive defense reporters in wheat protoplasts'

description: Supplemental Datasets:
Number 
File name 
Description 
S1 
S1_Figure1_Data.csv 
Luminescence data for Figure 1, protoplast time course experiment 
S2 
S2_RNAseqSampleTable.csv 
List of samples and treatment groups for RNAseq experiment 
S3 
S3_LFC_1_genes.xlsx 
Lists of Gabo/GaboSr50, Fielder and all cultivar genes upregulated by log fold threshold of 1 
S4 
S4_GOTerms_Table.xlsx 
GO terms analysis Query tables and g:profiler results tables 
S5 
S5_LFC2_genes.xlsx 
Lists of Gabo/GaboSr50, Fielder and all cultivar genes upregulated by log fold threshold of 2 
 
S6 
S6_Primers.xlsx 
List of primers used 
S7 
S7_PlasmidList.xlsx 
List of plasmids used 
S8 
S8_Figures3-5Data.xlsx 
Luminescence data used for generating Figures 3 - 7
S9
 
S9_Figures3-7Stat.xlsx
 
Stats output for Figures 3 - 7
 
S10
 
S10_SuppFiguresData.xlsx
 
Data for Supplementary Figures S1 and S2
DOI: 10.5281/zenodo.7844447
title: Supplemental Datasets for 'A novel tool kit to study effector recognition and cell-autonomous defense signaling in wheat'

description: Supplemental Datasets: <strong>name</strong> <strong>description</strong> AvrRupGenePool_lfc2.txt list of genes from RNAseq upregulated by log2 fold change of 2 in all cultivars Data_Figure1AB.csv data used to make figure 1 plots, section A and B Data_Figure3.csv data used to make figure 3 plots Data_Figure4.csv data used to make figure 4 plots Data_Figure5.csv data used to make figure 5 plots Fielder_AvrRupregGenePool_lfc1.txt list of genes from RNAseq upregulated by log2 fold change of 1 in Fielder Gabo_AvrRupregGenePool_lfc1.txt list of genes from RNAseq upregulated by log2 fold change of 1 in Gabo/GaboSr50 Plasmid_list.csv list of plasmids generated Primers.csv list of primers used WheatProtoplastsRNAseqSamples.csv list of samples and conditions for RNAseq experiment
DOI: 10.5281/zenodo.7847800
title: Supplemental Datasets for 'A novel tool kit to study effector recognition and cell-autonomous defense signaling in wheat'

description: Supplemental Datasets: <strong>name</strong> <strong>description</strong> AvrRupGenePool_lfc2.txt list of genes from RNAseq upregulated by log2 fold change of 2 in all cultivars Data_Figure1AB.csv data used to make figure 1 plots, section A and B Data_Figure3.csv data used to make figure 3 plots Data_Figure4.csv data used to make figure 4 plots Data_Figure5.csv data used to make figure 5 plots Fielder_AvrRupregGenePool_lfc1.txt list of genes from RNAseq upregulated by log2 fold change of 1 in Fielder Gabo_AvrRupregGenePool_lfc1.txt list of genes from RNAseq upregulated by log2 fold change of 1 in Gabo/GaboSr50 Plasmid_list.csv list of plasmids generated Primers.csv list of primers used WheatProtoplastsRNAseqSamples.csv list of samples and conditions for RNAseq experiment
DOI: 10.5281/zenodo.7880015
title: Supplemental Datasets for 'A novel tool kit to study effector recognition and cell-autonomous defense signaling in wheat'

description: Supplemental Datasets: <strong>Number </strong> <strong>File name </strong> <strong>Description </strong> S1 S1_Figure1_Data.csv Luminescence data for Figure 1, protoplast time course experiment S2 S2_RNAseqSampleTable.csv List of samples and treatment groups for RNAseq experiment S3 S3_LFC_1_genes.xlsx Lists of Gabo/GaboSr50, Fielder and all cultivar genes upregulated by log fold threshold of 1 S4 S4_GOTerms_Table.xlsx GO terms analysis Query tables and g:profiler results tables S5 S5_LFC2_genes.xlsx Lists of Gabo/GaboSr50, Fielder and all cultivar genes upregulated by log fold threshold of 2 S6 S6_Primers.xlsx List of primers used S7 S7_PlasmidList.xlsx List of plasmids used S8 S8_Figures3-5Data.xlsx Luminescence data used for generating Figures 3, 4 and 5
DOI: 10.5281/zenodo.8135161
title: Supplemental Datasets for 'Multiplexed effector screening for recognition by endogenous resistance genes using positive defense reporters in wheat protoplasts'

description: Supplemental Datasets:
Number 
File name 
Description 
S1 
S1_Figure1_Data.csv 
Luminescence data for Figure 1, protoplast time course experiment 
S2 
S2_RNAseqSampleTable.csv 
List of samples and treatment groups for RNAseq experiment 
S3 
S3_LFC_1_genes.xlsx 
Lists of Gabo/GaboSr50, Fielder and all cultivar genes upregulated by log fold threshold of 1 
S4 
S4_GOTerms_Table.xlsx 
GO terms analysis Query tables and g:profiler results tables 
S5 
S5_LFC2_genes.xlsx 
Lists of Gabo/GaboSr50, Fielder and all cultivar genes upregulated by log fold threshold of 2 
 
S6 
S6_Primers.xlsx 
List of primers used 
S7 
S7_PlasmidList.xlsx 
List of plasmids used 
S8 
S8_Figures3-5Data.xlsx 
Luminescence data used for generating Figures 3 - 7
S9
 
S9_Figures3-7Stat.xlsx
 
Stats output for Figures 3 - 7
 
S10
 
S10_SuppFiguresData.xlsx
 
Data for Supplementary Figures S1 and S2
DOI: 10.6084/m9.figshare.24628097
title: Additional file 1 of Lactate receptor GPR81 drives breast cancer growth and invasiveness through regulation of ECM properties and Notch ligand DLL4

description: Additional file 1.
DOI: 10.6084/m9.figshare.24628097.v1
title: Additional file 1 of Lactate receptor GPR81 drives breast cancer growth and invasiveness through regulation of ECM properties and Notch ligand DLL4

description: Additional file 1.
DOI: 10.6084/m9.figshare.24523243
title: Virtual reality interventions to reduce psychological distress during colonoscopy: a rapid review

description: Colonoscopy can cause psychological distress in patients, consequently discouraging patients from undergoing an unpleasant procedure or reducing compliance with follow-up examinations. This rapid review aimed to assess the feasibility and efficacy of Virtual Reality (VR) interventions during colonoscopy on patients’ perceived psychological distress and procedure satisfaction. We searched PubMed, CINAHL, ProQuest/All Databases, and Cochrane Library databases on 1 December 2022, with a date limiter of 2002–2022 for articles that investigated the effect and feasibility of any type of immersive VR-based intervention on patients’ pain, anxiety, discomfort, and procedure satisfaction immediately before, during, and/or post-procedure of colonoscopy. Initially, 118 articles were identified, of which seven were eligible and included in this rapid review. Our findings demonstrate that VR interventions during colonoscopy were feasible, significantly reduced participant pain and anxiety, and significantly increased participant satisfaction with the procedure. VR interventions appear to be an effective alternative for patients who prefer to avoid analgetic medications or as an adjunct to routine sedation during colonoscopy. Directions of research design should focus on an optimized blinding process, using the high-end technology of 3-dimensional devices, considering an audiovisual distracting intervention, and designing multicenter and high-quality Randomized Controlled Trials.
DOI: 10.6084/m9.figshare.24523243.v1
title: Virtual reality interventions to reduce psychological distress during colonoscopy: a rapid review

description: Colonoscopy can cause psychological distress in patients, consequently discouraging patients from undergoing an unpleasant procedure or reducing compliance with follow-up examinations. This rapid review aimed to assess the feasibility and efficacy of Virtual Reality (VR) interventions during colonoscopy on patients’ perceived psychological distress and procedure satisfaction. We searched PubMed, CINAHL, ProQuest/All Databases, and Cochrane Library databases on 1 December 2022, with a date limiter of 2002–2022 for articles that investigated the effect and feasibility of any type of immersive VR-based intervention on patients’ pain, anxiety, discomfort, and procedure satisfaction immediately before, during, and/or post-procedure of colonoscopy. Initially, 118 articles were identified, of which seven were eligible and included in this rapid review. Our findings demonstrate that VR interventions during colonoscopy were feasible, significantly reduced participant pain and anxiety, and significantly increased participant satisfaction with the procedure. VR interventions appear to be an effective alternative for patients who prefer to avoid analgetic medications or as an adjunct to routine sedation during colonoscopy. Directions of research design should focus on an optimized blinding process, using the high-end technology of 3-dimensional devices, considering an audiovisual distracting intervention, and designing multicenter and high-quality Randomized Controlled Trials.
DOI: 10.6084/m9.figshare.20461303
title: Utilizing subsonic vibration in cryogenic quenching for heat flux enhancement

description: An active method for heat transfer enhancement is proposed and thoroughly characterized for the first time for cryogenic quenching, in which mechanical vibrations are directly induced onto the sample to be quenched, employing a compact modular system composed of a pneumatic plunging device along with a DC motor/eccentric cam mechanism, generating oscillations on three different axes at a wide array of amplitude-frequency combinations. The quenching performance was investigated from both flow-field and thermal standpoints, through numerical simulations of the flow behavior, high-speed imaging of the process, and experimentally generated transient quenching and boiling curves under the influence of the governing parameters, underlining their combined effect on the mechanism of heat transfer augmentation. Under optimal conditions of amplitude and frequency, a remarkable CHF enhancement of 270% was obtained and the quenching time was reduced from 5 seconds to 1.8 seconds compared to the non-vibration case, where the vibration frequency was found to be the primary factor involved in the increase of oscillation-driven pressure drop and subsequent cavitation-induced CHF enhancement. Consequently, we are providing researchers in the field of cryogenics a method that not only provides enhanced performance but also offers flexibility enabling active control of the governing parameters of the system.
DOI: 10.6084/m9.figshare.20461303.v1
title: Utilizing subsonic vibration in cryogenic quenching for heat flux enhancement

description: An active method for heat transfer enhancement is proposed and thoroughly characterized for the first time for cryogenic quenching, in which mechanical vibrations are directly induced onto the sample to be quenched, employing a compact modular system composed of a pneumatic plunging device along with a DC motor/eccentric cam mechanism, generating oscillations on three different axes at a wide array of amplitude-frequency combinations. The quenching performance was investigated from both flow-field and thermal standpoints, through numerical simulations of the flow behavior, high-speed imaging of the process, and experimentally generated transient quenching and boiling curves under the influence of the governing parameters, underlining their combined effect on the mechanism of heat transfer augmentation. Under optimal conditions of amplitude and frequency, a remarkable CHF enhancement of 270% was obtained and the quenching time was reduced from 5 seconds to 1.8 seconds compared to the non-vibration case, where the vibration frequency was found to be the primary factor involved in the increase of oscillation-driven pressure drop and subsequent cavitation-induced CHF enhancement. Consequently, we are providing researchers in the field of cryogenics a method that not only provides enhanced performance but also offers flexibility enabling active control of the governing parameters of the system.
DOI: 10.6084/m9.figshare.24626907
title: Data_ Engineered pine endophytic Bacillus toyonensis with nematocidal and colonization abilities for pine wilt disease control

description: Data of the article Engineered pine endophytic Bacillus toyonensis with nematocidal and colonization abilities for pine wilt disease control
DOI: 10.6084/m9.figshare.24626907.v2
title: Data_ Engineered pine endophytic Bacillus toyonensis with nematocidal and colonization abilities for pine wilt disease control

description: Data of the article Engineered pine endophytic Bacillus toyonensis with nematocidal and colonization abilities for pine wilt disease control
DOI: 10.6084/m9.figshare.24626907.v1
title: Data_ Engineered pine endophytic Bacillus toyonensis with nematocidal and colonization abilities for pine wilt disease control

description: Data of the article Engineered pine endophytic Bacillus toyonensis with nematocidal and colonization abilities for pine wilt disease control