cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7791845
title: Decoupling facilitative effects in a temperate subhumid grassland: photosynthetic metabolism matters

description: <b>Background</b>: Abiotic microhabitat amelioration and protection from herbivores are two of the main mechanisms associated with facilitative interactions in plant communities. <b>Aims</b>: We investigated the effect of the shrub <i>Acanthostyles buniifolius</i> on the herbaceous community of a subhumid grassland in order to disentangle the protective role of the shrub from its effect on ameliorating the abiotic conditions of microhabitats. <b>Methods</b>: In two contiguous areas, one continuously grazed and the other excluded from livestock for 3 years, we determined floristic composition and species cover under the shrub canopy and in paired open sites. We calculated the Relative Interaction Index (RII) for cover of plant functional types and species. <b>Results</b>: Under grazing, C<sub>3</sub> grass richness was higher under the shrub canopy than in open plots. Also, the RII was higher in the grazed area for most functional types. Inside the exclosure, the cover of C<sub>3</sub> grasses was higher in the presence of the shrub. Conversely, the richness and cover of C<sub>4</sub> grasses was lower under the shrub canopy. <b>Conclusions</b>: We found evidence of facilitation in a subhumid grassland. The shrub may protect grasses from grazers and may benefit C<sub>3</sub> grasses through microclimatic amelioration. Therefore, photosynthetic pathway should be considered when analysing facilitative interactions in mesic environments.
DOI: 10.6084/m9.figshare.7791845.v1
title: Decoupling facilitative effects in a temperate subhumid grassland: photosynthetic metabolism matters

description: <b>Background</b>: Abiotic microhabitat amelioration and protection from herbivores are two of the main mechanisms associated with facilitative interactions in plant communities. <b>Aims</b>: We investigated the effect of the shrub <i>Acanthostyles buniifolius</i> on the herbaceous community of a subhumid grassland in order to disentangle the protective role of the shrub from its effect on ameliorating the abiotic conditions of microhabitats. <b>Methods</b>: In two contiguous areas, one continuously grazed and the other excluded from livestock for 3 years, we determined floristic composition and species cover under the shrub canopy and in paired open sites. We calculated the Relative Interaction Index (RII) for cover of plant functional types and species. <b>Results</b>: Under grazing, C<sub>3</sub> grass richness was higher under the shrub canopy than in open plots. Also, the RII was higher in the grazed area for most functional types. Inside the exclosure, the cover of C<sub>3</sub> grasses was higher in the presence of the shrub. Conversely, the richness and cover of C<sub>4</sub> grasses was lower under the shrub canopy. <b>Conclusions</b>: We found evidence of facilitation in a subhumid grassland. The shrub may protect grasses from grazers and may benefit C<sub>3</sub> grasses through microclimatic amelioration. Therefore, photosynthetic pathway should be considered when analysing facilitative interactions in mesic environments.
DOI: 10.6084/m9.figshare.7791797
title: Incidence and survival of laryngeal cancer in Denmark: a nation-wide study from 1980 to 2014

description: <b>Background:</b> The purpose of this registry study was to evaluate trends in incidence and survival of laryngeal cancer in the Danish population from 1980 to 2014. <b>Methods:</b> This study includes all patients with laryngeal cancer registered in the Danish Cancer Registry (DCR) in the period 1980–2014. The age-adjusted incidence rate (AAIR) per 100,000 and average annual percent change (AAPC) were calculated. We evaluated the relative survival at five years in relation to gender, anatomical location, year at diagnosis, and histological type. Further, an age-period-cohort (APC) model of incidence was constructed. <b>Results:</b> A total of 8748 patients (82% males) were included. The median age at diagnosis was 60 years, range 18–101 years. The AAIR decreased from 3.6 per 100,000 in 1980 to 2.3 per 100,000 in 2014 with an AAPC of –0.8% (<i>p</i> <b>Conclusions:</b> This nation-wide study reports a significant decrease in the incidence of laryngeal cancer. Glottic cancer had a significantly better survival at five years compared to other locations.
DOI: 10.6084/m9.figshare.7791725
title: Don’t brush off buccal data heterogeneity

description: Buccal epithelial cells are among the most clinically accessible tissues and are increasingly being used to identify epigenetic disease patterns. However, substantial variation in buccal DNA methylation patterns indicates heterogeneity of cell types within and between samples, raising questions of data quality. We systematically estimated cell-type composition for a large collection of buccal and saliva samples from 11 published studies of DNA methylation. In these we identified numerous cases of buccal samples with questionable purity, which may be affected by sampling from individuals with neurodevelopmental disorders, and by the brushes used for sample collection. Further challenges are involved in comparisons with tissues such as saliva, in which buccal component varies widely. We propose a reference-based method of correcting for buccal purity that reduces unwanted variation while preserving cross-tissue differences. Our work demonstrates the wide variation of buccal quality in epigenetic studies and suggests a possible approach to overcome this issue.
DOI: 10.6084/m9.figshare.7791797.v1
title: Incidence and survival of laryngeal cancer in Denmark: a nation-wide study from 1980 to 2014

description: <b>Background:</b> The purpose of this registry study was to evaluate trends in incidence and survival of laryngeal cancer in the Danish population from 1980 to 2014. <b>Methods:</b> This study includes all patients with laryngeal cancer registered in the Danish Cancer Registry (DCR) in the period 1980–2014. The age-adjusted incidence rate (AAIR) per 100,000 and average annual percent change (AAPC) were calculated. We evaluated the relative survival at five years in relation to gender, anatomical location, year at diagnosis, and histological type. Further, an age-period-cohort (APC) model of incidence was constructed. <b>Results:</b> A total of 8748 patients (82% males) were included. The median age at diagnosis was 60 years, range 18–101 years. The AAIR decreased from 3.6 per 100,000 in 1980 to 2.3 per 100,000 in 2014 with an AAPC of –0.8% (<i>p</i> <b>Conclusions:</b> This nation-wide study reports a significant decrease in the incidence of laryngeal cancer. Glottic cancer had a significantly better survival at five years compared to other locations.
DOI: 10.6084/m9.figshare.7791659
title: Placial analysis of events: a case study on criminological places

description: The contrast of space and place has long been an active topic of scholarly discussions in many disciplines. While spatial analysis enjoys a multitude of quantitative methods, the study of place remains mostly conceptual and descriptive. This paper expands upon the rich concepts of place in the literature to propose a quantitative framework for placial analysis based on events. Central to the proposed framework are three assumptions: (1) human experiences transform space to place; (2) events build human experiences in space; and (3) places emerge organically and may change characters, spatial extent and location over time through the shifts in occurrences and types of events in space and time. The proposed framework consists of three elements: clustering events, decomposing event distributions, and identifying the similarity of event clusters. We applied the framework to identify criminological places in the City of Dallas in the United States and the changes of these places from 1 June 2014 to 30 May 2018.
DOI: 10.6084/m9.figshare.7791659.v1
title: Placial analysis of events: a case study on criminological places

description: The contrast of space and place has long been an active topic of scholarly discussions in many disciplines. While spatial analysis enjoys a multitude of quantitative methods, the study of place remains mostly conceptual and descriptive. This paper expands upon the rich concepts of place in the literature to propose a quantitative framework for placial analysis based on events. Central to the proposed framework are three assumptions: (1) human experiences transform space to place; (2) events build human experiences in space; and (3) places emerge organically and may change characters, spatial extent and location over time through the shifts in occurrences and types of events in space and time. The proposed framework consists of three elements: clustering events, decomposing event distributions, and identifying the similarity of event clusters. We applied the framework to identify criminological places in the City of Dallas in the United States and the changes of these places from 1 June 2014 to 30 May 2018.
DOI: 10.6084/m9.figshare.7791413
title: AFM_RawData_Succinyltransferase_Eskandarian

description: Preparation conditions and the technical setup for AFM experiments were conducted as per Eskandarian <i>et al</i>. 2017. Cells of <i>M. smegmatis</i>wildtype expressing Wag31-GFP were mixed with non-fluorescent <i>MSMEG_3187</i>and deposited on a PDMS-coated coverslip. WT cells were distinguished from <i>MSMEG_3187</i>cells by optical fluorescence microscopy. AFM measurements were made using a Dimension Icon scan head (Bruker) using ScanAsyst fluid cantilevers (Bruker) with a nominal spring constant of 0.7 N m<sup>-1</sup>in Peak Force QNM mode at a force setpoint ~1 nN and typical scan rates of 0.3 Hz. Indentation on the cell surface was estimated to be ~10 nm with a range of ~5 nm in the Z-axis. Height, peak force error, and DMT modulus channels were recorded for all scanned images in the trace and retrace directions. Images were processed using Gwyddion (Department of Nanometrology, Czech Metrology Institute – http://gwyddion.net). ImageJ was used for extracting bacterial cell profiles from height and DMT modulus images in a tabular format. A two-sided Wilcoxon rank sum U test was used to analyze the data with a continuity correction and confidence level of 95% using MatLab.<br>
DOI: 10.6084/m9.figshare.7791413.v1
title: AFM_RawData_Succinyltransferase_Eskandarian

description: Preparation conditions and the technical setup for AFM experiments were conducted as per Eskandarian <i>et al</i>. 2017. Cells of <i>M. smegmatis</i>wildtype expressing Wag31-GFP were mixed with non-fluorescent <i>MSMEG_3187</i>and deposited on a PDMS-coated coverslip. WT cells were distinguished from <i>MSMEG_3187</i>cells by optical fluorescence microscopy. AFM measurements were made using a Dimension Icon scan head (Bruker) using ScanAsyst fluid cantilevers (Bruker) with a nominal spring constant of 0.7 N m<sup>-1</sup>in Peak Force QNM mode at a force setpoint ~1 nN and typical scan rates of 0.3 Hz. Indentation on the cell surface was estimated to be ~10 nm with a range of ~5 nm in the Z-axis. Height, peak force error, and DMT modulus channels were recorded for all scanned images in the trace and retrace directions. Images were processed using Gwyddion (Department of Nanometrology, Czech Metrology Institute – http://gwyddion.net). ImageJ was used for extracting bacterial cell profiles from height and DMT modulus images in a tabular format. A two-sided Wilcoxon rank sum U test was used to analyze the data with a continuity correction and confidence level of 95% using MatLab.<br>
DOI: 10.6084/m9.figshare.7791413.v2
title: AFM_RawData_Succinyltransferase_Eskandarian

description: Preparation conditions and the technical setup for AFM experiments were conducted as per Eskandarian <i>et al</i>. 2017. Cells of <i>M. smegmatis</i>wildtype expressing Wag31-GFP were mixed with non-fluorescent <i>MSMEG_3187</i>and deposited on a PDMS-coated coverslip. WT cells were distinguished from <i>MSMEG_3187</i>cells by optical fluorescence microscopy. AFM measurements were made using a Dimension Icon scan head (Bruker) using ScanAsyst fluid cantilevers (Bruker) with a nominal spring constant of 0.7 N m<sup>-1</sup>in Peak Force QNM mode at a force setpoint ~1 nN and typical scan rates of 0.3 Hz. Indentation on the cell surface was estimated to be ~10 nm with a range of ~5 nm in the Z-axis. Height, peak force error, and DMT modulus channels were recorded for all scanned images in the trace and retrace directions. Images were processed using Gwyddion (Department of Nanometrology, Czech Metrology Institute – http://gwyddion.net). ImageJ was used for extracting bacterial cell profiles from height and DMT modulus images in a tabular format. A two-sided Wilcoxon rank sum U test was used to analyze the data with a continuity correction and confidence level of 95% using MatLab.<br>
DOI: 10.6084/m9.figshare.7791335
title: data.rar

description: <i>锁阳（Cynomorium songaricum</i> Rupr。）对卵巢切除大鼠的神经保护作用具有潜在的治疗作用
DOI: 10.6084/m9.figshare.7791314
title: Recapitulating Parkinson's disease pathology in a three-dimensional human neural cell culture model

description: Extensive loss of dopaminergic neurons and aggregation of the protein α-synuclein, into ubiquitin-positive Lewy bodies represents major neuropathological hallmarks of Parkinson's disease. At present, the generation of large nuclear associated Lewy bodies from endogenous wild-type α-synuclein, translationally regulated under its own promoter in human cell culture models requires costly and time-consuming protocols. Here, we demonstrate that fully differentiated human SH-SY5Y neuroblastoma cells grown in three-dimensional cell culture develop Lewy body pathology upon exposure to exogenous α-synuclein species. In contrast to most cell- and rodent-based models that exhibit multiple diffuse α-synuclein aggregates throughout the cytoplasm, a single large nuclear inclusion immuno-positive for α-synuclein and ubiquitin is rapidly obtained in our model without the need for over-expression of α-synuclein or genetic modification of the cell line. However, phosphorylation of α-synuclein within these inclusions was not observed. The system described here provides an ideal tool to screen compounds to therapeutically intervene in Lewy body formation and to investigate the mechanisms involved in disease progression in synucleinopathies.<br>Repository contains raw qPCR and image J analysis data.
DOI: 10.6084/m9.figshare.7791314.v1
title: Recapitulating Parkinson's disease pathology in a three-dimensional human neural cell culture model

description: Extensive loss of dopaminergic neurons and aggregation of the protein α-synuclein, into ubiquitin-positive Lewy bodies represents major neuropathological hallmarks of Parkinson's disease. At present, the generation of large nuclear associated Lewy bodies from endogenous wild-type α-synuclein, translationally regulated under its own promoter in human cell culture models requires costly and time-consuming protocols. Here, we demonstrate that fully differentiated human SH-SY5Y neuroblastoma cells grown in three-dimensional cell culture develop Lewy body pathology upon exposure to exogenous α-synuclein species. In contrast to most cell- and rodent-based models that exhibit multiple diffuse α-synuclein aggregates throughout the cytoplasm, a single large nuclear inclusion immuno-positive for α-synuclein and ubiquitin is rapidly obtained in our model without the need for over-expression of α-synuclein or genetic modification of the cell line. However, phosphorylation of α-synuclein within these inclusions was not observed. The system described here provides an ideal tool to screen compounds to therapeutically intervene in Lewy body formation and to investigate the mechanisms involved in disease progression in synucleinopathies.<br>Repository contains raw qPCR and image J analysis data.
DOI: 10.6084/m9.figshare.7791335.v1
title: data.rar

description: <i>锁阳（Cynomorium songaricum</i> Rupr。）对卵巢切除大鼠的神经保护作用具有潜在的治疗作用
DOI: 10.6084/m9.figshare.7791263
title: Enhancement of Mass Transfer Intensification for Essential Oil Release from Lavandula pubescence Using Integrated Ultrasonic-Microwave Technique and Enzymatic Pretreatment

description: This work was designed to utilize the integration of ultrasonic-microwave assisted preceded by enzymolysis pretreatment to enhance the extraction efficiency of essential oil (EO) from wild <i>Lavandula pubescens</i> (Lp). Cellulase (C-ase), hemicellulase (H-ase), and mixed enzymes (C-ase/H-ase) were used at 10 mg/100 mL of the liquid phase. Gas chromatography-mass spectrometry (GC-MS) system was used for chemical composition analyses of <i>Lavandula pubescens</i> essential oil (Lp-EO). C-ase pretreatment achieved the highest yield (0.50%) of EO and highest ratio of carvacrol (29.22%) as the main compound in comparison to other treatments. Changes in the morphological structure of Lp tissues were tracked using scanning electron microscopy (SEM). Free radical-scavenging activity was assessed using DPPH<sup>•</sup>-SA and ABTS<sup>•+</sup>-SA assays. The optimal extraction conditions were enzyme concentration of 14.82 mg/100 mL, sonication time of 38.18 min, and microwave power at 333 W. At these conditions, the maximum % yield, % DPPH<sup>•</sup>-SA, and ABTS<sup>•+</sup>SA were 0.67%, 65.40%, and 0.025 (as mM Trolox), respectively. Results exhibited that the isolated Lp-EO could be used as anti-free radical and antibacterial agents in the biological systems.
DOI: 10.6084/m9.figshare.7791251
title: Isolation of essential oil from Lavandula angustifolia by using ultrasonic-microwave assisted method preceded by enzymolysis treatment, and assessment of its biological activities

description: This research study aimed to optimize innovative conditions for enhancing yield and quality of essential oil isolated from <em>Lavandula angustifolia</em> (La) based on rapid and innovative techniques. Ultrasonic-microwave assisted preceded by enzymolysis treatment was used to isolate essential oil (EO) of La. Response Surface Methodology was employed for the same purpose. The yield % of La essential oil (La.EO) obtained from combined enzymes treatment (cellulase and hemicellulase) was higher than that obtained by a single enzyme treatment. Chemical composition analysis of La.EO isolated was carried out using GC-MS. Morphological structure of La tissues was observed using SEM. The anti-free radical activity was assayed using DPPH and ABTS<sup>+</sup> methods The isolation conditions consisted of the concentration of enzymes (12.5 mg) with a range of (5–20 mg), sonication time (52.5 min) with a range of (15–90 min) and microwave power (275W) with a range of (500–50W). The uses of coupling ultrasonic-microwave could be lead to forming of the acoustic cavitation and rupture of plant tissue. This facilitates the flow of liquid phase into the glandular trichomes in plant cells and enhances the absorption from the matrix of plant. Thus, enhances the efficiency of essential oil isolation from aromatic plant based on cavitation phenomenon. The results of the current work found that La.EO which isolated by using ultrasonic-microwave techniques under optimal conditions could be used as food additives in food industries to prevent the oxidation and bacterial spoilage.
DOI: 10.6084/m9.figshare.7791251.v1
title: Isolation of essential oil from Lavandula angustifolia by using ultrasonic-microwave assisted method preceded by enzymolysis treatment, and assessment of its biological activities

description: This research study aimed to optimize innovative conditions for enhancing yield and quality of essential oil isolated from <em>Lavandula angustifolia</em> (La) based on rapid and innovative techniques. Ultrasonic-microwave assisted preceded by enzymolysis treatment was used to isolate essential oil (EO) of La. Response Surface Methodology was employed for the same purpose. The yield % of La essential oil (La.EO) obtained from combined enzymes treatment (cellulase and hemicellulase) was higher than that obtained by a single enzyme treatment. Chemical composition analysis of La.EO isolated was carried out using GC-MS. Morphological structure of La tissues was observed using SEM. The anti-free radical activity was assayed using DPPH and ABTS<sup>+</sup> methods The isolation conditions consisted of the concentration of enzymes (12.5 mg) with a range of (5–20 mg), sonication time (52.5 min) with a range of (15–90 min) and microwave power (275W) with a range of (500–50W). The uses of coupling ultrasonic-microwave could be lead to forming of the acoustic cavitation and rupture of plant tissue. This facilitates the flow of liquid phase into the glandular trichomes in plant cells and enhances the absorption from the matrix of plant. Thus, enhances the efficiency of essential oil isolation from aromatic plant based on cavitation phenomenon. The results of the current work found that La.EO which isolated by using ultrasonic-microwave techniques under optimal conditions could be used as food additives in food industries to prevent the oxidation and bacterial spoilage.
DOI: 10.6084/m9.figshare.7791263.v1
title: Enhancement of Mass Transfer Intensification for Essential Oil Release from Lavandula pubescence Using Integrated Ultrasonic-Microwave Technique and Enzymatic Pretreatment

description: This work was designed to utilize the integration of ultrasonic-microwave assisted preceded by enzymolysis pretreatment to enhance the extraction efficiency of essential oil (EO) from wild <i>Lavandula pubescens</i> (Lp). Cellulase (C-ase), hemicellulase (H-ase), and mixed enzymes (C-ase/H-ase) were used at 10 mg/100 mL of the liquid phase. Gas chromatography-mass spectrometry (GC-MS) system was used for chemical composition analyses of <i>Lavandula pubescens</i> essential oil (Lp-EO). C-ase pretreatment achieved the highest yield (0.50%) of EO and highest ratio of carvacrol (29.22%) as the main compound in comparison to other treatments. Changes in the morphological structure of Lp tissues were tracked using scanning electron microscopy (SEM). Free radical-scavenging activity was assessed using DPPH<sup>•</sup>-SA and ABTS<sup>•+</sup>-SA assays. The optimal extraction conditions were enzyme concentration of 14.82 mg/100 mL, sonication time of 38.18 min, and microwave power at 333 W. At these conditions, the maximum % yield, % DPPH<sup>•</sup>-SA, and ABTS<sup>•+</sup>SA were 0.67%, 65.40%, and 0.025 (as mM Trolox), respectively. Results exhibited that the isolated Lp-EO could be used as anti-free radical and antibacterial agents in the biological systems.
DOI: 10.6084/m9.figshare.7791242
title: Supplementary Table S1-9.xlsx

description: We hypothesized that preterm birth and early feeding affect gut maturation via epigenetic changes. Using piglets as models for infants, preterm and term pigs (n=80) were fed total parenteral nutrition (TPN) or partial enteral feeding (ENT) for 5 days, followed by exclusive enteral feeding until 26 days (weaning age). Small intestinal DNA methylome was compared between preterm and matched term pigs. The differentially methylated regions (DMRs) and the associated genes were listed in this supplementary file.
DOI: 10.6084/m9.figshare.7791242.v1
title: Supplementary Table S1-9.xlsx

description: We hypothesized that preterm birth and early feeding affect gut maturation via epigenetic changes. Using piglets as models for infants, preterm and term pigs (n=80) were fed total parenteral nutrition (TPN) or partial enteral feeding (ENT) for 5 days, followed by exclusive enteral feeding until 26 days (weaning age). Small intestinal DNA methylome was compared between preterm and matched term pigs. The differentially methylated regions (DMRs) and the associated genes were listed in this supplementary file.