cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.6510077.v1
title: Toxicity assessment of cobalt ferrite nanoparticles on wheat plants

description: Cobalt ferrite nanoparticles (NPs) have received increasing attention due to their widespread therapeutic and agricultural applicability. In the environmental field, dry powder- and ferrofluid-suspended cobalt ferrite NPs were found to be useful for removing heavy metals and metalloids from water, while diluted suspensions of cobalt ferrite NP have been promisingly applied in medicine. However, the potential toxicological implications of widespread exposure are still unknown. Since cobalt ferrite NPs are considered residual wastes of environmental or medical applications, plants may serve as a point-of-entry for engineered nanomaterials as a result of consumption of these plants. Thus, the aim of this study was to assess the effects of dry powder and fresh cobalt ferrite NP on wheat plants. Seven-day assays were conducted, using quartz sand as the plant growth substrate. The toxicity end points measured were seed germination, root and shoot lengths, total cobalt (Co) and iron (Fe) accumulation, photosynthetic pigment production, protein (PRT) production, and activities of catalase (CAT), ascorbate peroxidase (APX), and guaiacol peroxidase (GPX). Increasing total Co and Fe in plant tissues indicated that wheat plants were exposed to cobalt ferrite NP. Seed germination and shoot length were not sufficiently sensitive toxicity end points. The effective concentration (EC<sub>50</sub>) that diminished root length of plants by 50% was 1963 mg/kg for fresh ferrite NPs and 5023 mg/kg for powder ferrite NP. Hence, fresh ferrite NPs were more toxic than powder NP. Plant stress was indicated by a significant decrease in photosynthetic pigments. CAT, APX, and GPX antioxidant enzymatic activity suggested the generation of reactive oxygen species and oxidative damage induced by cobalt ferrite NP. More studies are thus necessary to determine whether the benefits of using these NPs outweigh the risks.
DOI: 10.6084/m9.figshare.6509984
title: Blueschist-facies overprint of a Late Triassic Tethyan oceanic crust in a subduction-accretion complex in north-central Anatolia, Turkey

description: These supplementary materials are related to the paper entitled 'Blueschist-facies overprint of a Late Triassic Tethyan oceanic crust in a subduction-accretion complex in north-central Anatolia, Turkey'
DOI: 10.6084/m9.figshare.6509984.v1
title: Late Triassic crystallization ages from meta-plagiogranites of Tethyan oceanic crust and HP-LT overprint on metamorphic rocks in the subduction - accretion complex of north-central Anatolia, Turkey

description: These supplementary materials are related to the paper entitled 'Late Triassic crystallization ages from meta-plagiogranites of Tethyan oceanic crust and HP-LT overprint on metamorphic rocks in the subduction - accretion complex of north-central Anatolia, Turkey'
DOI: 10.6084/m9.figshare.6509816
title: On-demand release of <i>Candida albicans</i> biofilms from urinary catheters by mechanical surface deformation

description: <i>Candida albicans</i> is a leading cause of catheter-associated urinary tract infections and elimination of these biofilm-based infections without antifungal agents would constitute a significant medical advance. A novel urinary catheter prototype that utilizes on-demand surface deformation is effective at eliminating bacterial biofilms and here the broader applicability of this prototype to remove fungal biofilms has been demonstrated. <i>C. albicans</i> biofilms were debonded from prototypes by selectively inflating four additional intralumens surrounding the main lumen of the catheters to provide the necessary surface strain to remove the adhered biofilm. Deformable catheters eliminated significantly more biofilm than the controls (&gt;90% eliminated <i>vs</i> 10% control; <i>p</i> −2. This study underscores the potential of mechanical disruption as a materials design strategy to combat fungal device-associated infections.
DOI: 10.6084/m9.figshare.6509816.v1
title: On-demand release of <i>Candida albicans</i> biofilms from urinary catheters by mechanical surface deformation

description: <i>Candida albicans</i> is a leading cause of catheter-associated urinary tract infections and elimination of these biofilm-based infections without antifungal agents would constitute a significant medical advance. A novel urinary catheter prototype that utilizes on-demand surface deformation is effective at eliminating bacterial biofilms and here the broader applicability of this prototype to remove fungal biofilms has been demonstrated. <i>C. albicans</i> biofilms were debonded from prototypes by selectively inflating four additional intralumens surrounding the main lumen of the catheters to provide the necessary surface strain to remove the adhered biofilm. Deformable catheters eliminated significantly more biofilm than the controls (&gt;90% eliminated <i>vs</i> 10% control; <i>p</i> −2. This study underscores the potential of mechanical disruption as a materials design strategy to combat fungal device-associated infections.
DOI: 10.6084/m9.figshare.6509765
title: Iron-deficiency response and expression of genes related to iron homeostasis in poplars

description: Iron (Fe) deficiency is a serious agricultural problem, especially in calcareous soils, which are distributed worldwide. Poplar trees are an important biomass plant, and overcoming Fe deficiency in poplars will increase biomass productivity worldwide. The poplar Fe-deficiency response and the genes involved in poplar Fe homeostasis remain largely unknown. To identify these genes and processes, we cultivated poplar plants under Fe-deficient conditions, both in calcareous soil and hydroponically, and analyzed their growth rates, leaf Soil and Plant Analyzer Development (SPAD) values, and metal concentrations. The data clearly showed that poplars have notable growth defects in both calcareous soil and a Fe-deficient hydroponic culture. They exhibited serious chlorosis of young leaves after 3 weeks of Fe-deficient hydroponic culture. The Fe concentrations in old leaves with high SPAD values were markedly lower in Fe-deficient poplars, suggesting that poplars may have good translocation capability from old to new leaves. The Zn concentration in new leaves increased in Fe-deficient poplars. The pH of the hydroponic solution decreased in the Fe-deficient culture compared to the Fe-sufficient culture. This finding shows that poplars may be able to adjust the pH of a culture solution to better take up Fe. We also analyzed the expression of Fe homeostasis-related genes in the roots and leaves of Fe-sufficient and Fe-deficient poplars. Our results demonstrate that <i>PtIRT1, PtNAS2, PtFRO2, PtFRO5</i>, and <i>PtFIT</i> were induced in Fe-deficient roots. <i>PtYSL2</i> and <i>PtNAS4</i> were induced in Fe-deficient leaves. <i>PtYSL3</i> was induced in both Fe-deficient leaves and roots. These genes may be involved in the Fe uptake and/or translocation mechanisms in poplars under Fe-deficient conditions. Our results will increase a better understanding of the Fe-deficiency response of poplars and hence improve the breeding of Fe-deficiency-tolerant poplars for improved biomass production, the greening of high pH soils, and combatting global warming.
DOI: 10.6084/m9.figshare.6509765.v1
title: Iron-deficiency response and expression of genes related to iron homeostasis in poplars

description: Iron (Fe) deficiency is a serious agricultural problem, especially in calcareous soils, which are distributed worldwide. Poplar trees are an important biomass plant, and overcoming Fe deficiency in poplars will increase biomass productivity worldwide. The poplar Fe-deficiency response and the genes involved in poplar Fe homeostasis remain largely unknown. To identify these genes and processes, we cultivated poplar plants under Fe-deficient conditions, both in calcareous soil and hydroponically, and analyzed their growth rates, leaf Soil and Plant Analyzer Development (SPAD) values, and metal concentrations. The data clearly showed that poplars have notable growth defects in both calcareous soil and a Fe-deficient hydroponic culture. They exhibited serious chlorosis of young leaves after 3 weeks of Fe-deficient hydroponic culture. The Fe concentrations in old leaves with high SPAD values were markedly lower in Fe-deficient poplars, suggesting that poplars may have good translocation capability from old to new leaves. The Zn concentration in new leaves increased in Fe-deficient poplars. The pH of the hydroponic solution decreased in the Fe-deficient culture compared to the Fe-sufficient culture. This finding shows that poplars may be able to adjust the pH of a culture solution to better take up Fe. We also analyzed the expression of Fe homeostasis-related genes in the roots and leaves of Fe-sufficient and Fe-deficient poplars. Our results demonstrate that <i>PtIRT1, PtNAS2, PtFRO2, PtFRO5</i>, and <i>PtFIT</i> were induced in Fe-deficient roots. <i>PtYSL2</i> and <i>PtNAS4</i> were induced in Fe-deficient leaves. <i>PtYSL3</i> was induced in both Fe-deficient leaves and roots. These genes may be involved in the Fe uptake and/or translocation mechanisms in poplars under Fe-deficient conditions. Our results will increase a better understanding of the Fe-deficiency response of poplars and hence improve the breeding of Fe-deficiency-tolerant poplars for improved biomass production, the greening of high pH soils, and combatting global warming.
DOI: 10.6084/m9.figshare.6509609
title: FitnessSubsamplingSimulations.R from Little plant, big city: a test of adaptation to urban environments in common ragweed (<i>Ambrosia artemisiifolia</i>)

description: A full understanding of how cities shape adaptation requires characterizing genetically-based phenotypic and fitness differences between urban and rural populations under field conditions. We used a reciprocal transplant experiment with the native plant common ragweed, (<i>Ambrosia artemisiifolia</i>), and found that urban and rural populations have diverged in flowering time, a trait that strongly affects fitness. Although urban populations flowered earlier than rural populations, plants growing in urban field sites flowered later than plants in rural field sites. This counter-gradient variation is consistent adaptive divergence between urban and rural populations. Also consistent with local adaptation, both urban and rural genotypes experienced stronger net selection in the foreign than in the local habitat, but this pattern was not significant for male fitness. Despite the evidence for local adaptation, rural populations had higher lifetime fitness at all sites, suggesting that selection has been stronger or more uniform in rural than urban populations. We also found that inter-population differences in both flowering time and fitness tended to be greater among urban than rural populations, which is consistent with greater drift or spatial variation in selection within urban environments. In sum, our results are consistent with adaptive divergence of urban and rural populations, but also suggest there may be greater environmental heterogeneity in urban environments which also affects evolution in urban landscapes.
DOI: 10.6084/m9.figshare.6509609.v1
title: FitnessSubsamplingSimulations.R from Little plant, big city: a test of adaptation to urban environments in common ragweed (<i>Ambrosia artemisiifolia</i>)

description: A full understanding of how cities shape adaptation requires characterizing genetically-based phenotypic and fitness differences between urban and rural populations under field conditions. We used a reciprocal transplant experiment with the native plant common ragweed, (<i>Ambrosia artemisiifolia</i>), and found that urban and rural populations have diverged in flowering time, a trait that strongly affects fitness. Although urban populations flowered earlier than rural populations, plants growing in urban field sites flowered later than plants in rural field sites. This counter-gradient variation is consistent adaptive divergence between urban and rural populations. Also consistent with local adaptation, both urban and rural genotypes experienced stronger net selection in the foreign than in the local habitat, but this pattern was not significant for male fitness. Despite the evidence for local adaptation, rural populations had higher lifetime fitness at all sites, suggesting that selection has been stronger or more uniform in rural than urban populations. We also found that inter-population differences in both flowering time and fitness tended to be greater among urban than rural populations, which is consistent with greater drift or spatial variation in selection within urban environments. In sum, our results are consistent with adaptive divergence of urban and rural populations, but also suggest there may be greater environmental heterogeneity in urban environments which also affects evolution in urban landscapes.
DOI: 10.6084/m9.figshare.6508808
title: Supplementary Material for: Endotracheal Intubation and In-Hospital Mortality after Intracerebral Hemorrhage

description: <b><i>Background:</i></b> Many patients with acute intracerebral hemorrhages (ICHs) undergo endotracheal intubation with subsequent mechanical ventilation (MV) for “airway protection” with the intent to prevent aspiration, pneumonias, and its related mortality. Conversely, these procedures may independently promote pneumonia, laryngeal trauma, dysphagia, and adversely affect patient outcomes. The net benefit of intubation and MV in this patient cohort has not been systematically investigated. <b><i>Methods:</i></b> We conducted a large single-center observational cohort study to examine the independent association between endotracheal intubation and MV, hospital-acquired pneumonia (HAP), and in-hospital mortality (HM) in patients with ICH. All consecutive patients admitted with a primary diagnosis of a spontaneous ICH to a tertiary care hospital in Boston, Massachusetts, from June 2000 through January 2014, who were ≥18 years of age and hospitalized for ≥2 days were eligible for inclusion. Patients with pneumonia on admission, or those having brain or lung neoplasms were excluded. Our exposure of interest was endotracheal intubation and MV during hospitalization; our primary outcomes were incidence of HAP and HM, ascertained using International Classification of Diseases-9 and administrative discharge disposition codes, respectively, in patients who underwent endotracheal intubation and MV versus those who did not. Multivariable logistic regression was used to control for confounders. <b><i>Results:</i></b> Of the 2,386 hospital admissions screened, 1,384 patients fulfilled study criteria and were included in the final analysis. A total of 507 (36.6%) patients were intubated. Overall 133 (26.23%) patients in the intubated group developed HAP versus 41 (4.67%) patients in the non-intubated group (<i>p</i> &lt; 0.0001); 195 (38.5%) intubated patients died during hospitalization compared to 48 (5.5%) non-intubated patients (<i>p</i> &lt; 0.0001). After confounder adjustments, OR for HAP and HM, were 4.23 (95% CI 2.48–7.22; <i>p</i> &lt; 0.0001) and 4.32 (95% CI 2.5–7.49; <i>p</i> &lt; 0.0001) with c-statistics of 0.79 and 0.89, in the intubated versus non-intubated patients, respectively. <b><i>Conclusion:</i></b> In this large hospital-based cohort of patients presenting with an acute spontaneous ICH, endotracheal intubation and MV were associated with increased odds of HAP and HM. These findings urge further examination of the practice of intubation in prospective studies.
DOI: 10.6084/m9.figshare.6508808.v1
title: Supplementary Material for: Endotracheal Intubation and In-Hospital Mortality after Intracerebral Hemorrhage

description: <b><i>Background:</i></b> Many patients with acute intracerebral hemorrhages (ICHs) undergo endotracheal intubation with subsequent mechanical ventilation (MV) for “airway protection” with the intent to prevent aspiration, pneumonias, and its related mortality. Conversely, these procedures may independently promote pneumonia, laryngeal trauma, dysphagia, and adversely affect patient outcomes. The net benefit of intubation and MV in this patient cohort has not been systematically investigated. <b><i>Methods:</i></b> We conducted a large single-center observational cohort study to examine the independent association between endotracheal intubation and MV, hospital-acquired pneumonia (HAP), and in-hospital mortality (HM) in patients with ICH. All consecutive patients admitted with a primary diagnosis of a spontaneous ICH to a tertiary care hospital in Boston, Massachusetts, from June 2000 through January 2014, who were ≥18 years of age and hospitalized for ≥2 days were eligible for inclusion. Patients with pneumonia on admission, or those having brain or lung neoplasms were excluded. Our exposure of interest was endotracheal intubation and MV during hospitalization; our primary outcomes were incidence of HAP and HM, ascertained using International Classification of Diseases-9 and administrative discharge disposition codes, respectively, in patients who underwent endotracheal intubation and MV versus those who did not. Multivariable logistic regression was used to control for confounders. <b><i>Results:</i></b> Of the 2,386 hospital admissions screened, 1,384 patients fulfilled study criteria and were included in the final analysis. A total of 507 (36.6%) patients were intubated. Overall 133 (26.23%) patients in the intubated group developed HAP versus 41 (4.67%) patients in the non-intubated group (<i>p</i> &lt; 0.0001); 195 (38.5%) intubated patients died during hospitalization compared to 48 (5.5%) non-intubated patients (<i>p</i> &lt; 0.0001). After confounder adjustments, OR for HAP and HM, were 4.23 (95% CI 2.48–7.22; <i>p</i> &lt; 0.0001) and 4.32 (95% CI 2.5–7.49; <i>p</i> &lt; 0.0001) with c-statistics of 0.79 and 0.89, in the intubated versus non-intubated patients, respectively. <b><i>Conclusion:</i></b> In this large hospital-based cohort of patients presenting with an acute spontaneous ICH, endotracheal intubation and MV were associated with increased odds of HAP and HM. These findings urge further examination of the practice of intubation in prospective studies.
DOI: 10.6084/m9.figshare.6508796
title: Supplementary Material for: Comparison of Verapamil versus Heparin as Adjunctive Treatment for Transradial Coronary Procedures: The VERMUT Study

description: <b><i>Objective:</i></b> We sought to demonstrate that the combination of a local vasodilator (verapamil), modern materials, patent hemostasis, and intravenous anticoagulant only in the case of percutaneous coronary intervention, as compared to default heparin administration after sheath insertion, may optimize a combined endpoint, including radial artery oc­clusion (RAO), radial artery spasm (RAS), and access site complication. <b><i>Methods:</i></b> This is a prospective, single-center, double-blind randomized trial. Overall, 418 patients undergoing a transradial approach (TRA) for coronary procedures were randomized 1: 1 to receive intraradial verapamil (5 mg) or heparin (5,000 IU) after a 6-Fr sheath insertion. The primary outcome was the 24-h occurrence of RAO (ultrasound confirmation), access site complication, and RAS requiring the bailout administration of vasodilators. <b><i>Results:</i></b> The combined primary outcome occurred in 127 (30%) patients. It was significantly lower in patients randomized to verapamil as compared to others (26 vs. 35%, <i>p</i> = 0.03). This was mainly due to a significant reduction in RAS (3 vs. 10%, <i>p</i> = 0.006). The 24-h and 30-day occurrence of RAO did not differ between the study groups. <b><i>Conclusion:</i></b> Local administration of verapamil versus heparin reduces RAS, without increasing RAO, which appears to be strictly related to radial artery diameter and hemostasis time.
DOI: 10.6084/m9.figshare.6508754
title: Supplementary Material for: Patient’s Skeletal Muscle Radiation Attenuation and Sarcopenic Obesity are Associated with Postoperative Morbidity after Neoadjuvant Chemoradiation and Resection for Rectal Cancer

description: <b><i>Background/Aims:</i></b> To investigate the relation between skeletal muscle measurements (muscle mass, radiation attenuation, and sarcopenic obesity), postoperative morbidity, and survival after treatment of locally advanced rectal cancer. <b><i>Methods:</i></b> This explorative retrospective study identified 99 consecutive patients who underwent neoadjuvant chemoradiation and surgery between January 2007 and May 2012. Skeletal muscle mass was measured as total psoas area and total abdominal muscle area (TAMA) at 3 anatomical levels using the patient’s preoperative computed tomography scan. Radiation attenuation was measured using corresponding mean Hounsfield units for TAMA. Sarcopenic obesity was defined as body mass index above 25 kg·m<sup>–2</sup> combined with skeletal muscle mass index below the sex-specific median. Postoperative complications were graded by using the ­Clavien-Dindo classification. <b><i>Results:</i></b> Twenty-five patients (25.3%) developed a grade 3–5 complication. Lower radiation attenuation was independently associated with overall (<i>p</i> = 0.003) and grade 3–5 complications (<i>p</i> = 0.002). Sarcopenic obesity was associated with overall complications (all <i>p</i> &lt; 0.05). Skeletal muscle measurements and survival were not significantly related. <b><i>Conclusion:</i></b> Radiation attenuation was associated with overall and grade 3–5 postoperative morbidity after neoadjuvant chemoradiation and non-laparoscopic resection for rectal cancer. Sarcopenic obesity was associated with overall complications.
DOI: 10.6084/m9.figshare.6508754.v1
title: Supplementary Material for: Patient’s Skeletal Muscle Radiation Attenuation and Sarcopenic Obesity are Associated with Postoperative Morbidity after Neoadjuvant Chemoradiation and Resection for Rectal Cancer

description: <b><i>Background/Aims:</i></b> To investigate the relation between skeletal muscle measurements (muscle mass, radiation attenuation, and sarcopenic obesity), postoperative morbidity, and survival after treatment of locally advanced rectal cancer. <b><i>Methods:</i></b> This explorative retrospective study identified 99 consecutive patients who underwent neoadjuvant chemoradiation and surgery between January 2007 and May 2012. Skeletal muscle mass was measured as total psoas area and total abdominal muscle area (TAMA) at 3 anatomical levels using the patient’s preoperative computed tomography scan. Radiation attenuation was measured using corresponding mean Hounsfield units for TAMA. Sarcopenic obesity was defined as body mass index above 25 kg·m<sup>–2</sup> combined with skeletal muscle mass index below the sex-specific median. Postoperative complications were graded by using the ­Clavien-Dindo classification. <b><i>Results:</i></b> Twenty-five patients (25.3%) developed a grade 3–5 complication. Lower radiation attenuation was independently associated with overall (<i>p</i> = 0.003) and grade 3–5 complications (<i>p</i> = 0.002). Sarcopenic obesity was associated with overall complications (all <i>p</i> &lt; 0.05). Skeletal muscle measurements and survival were not significantly related. <b><i>Conclusion:</i></b> Radiation attenuation was associated with overall and grade 3–5 postoperative morbidity after neoadjuvant chemoradiation and non-laparoscopic resection for rectal cancer. Sarcopenic obesity was associated with overall complications.
DOI: 10.6084/m9.figshare.6508745
title: Publishing margins modelling tool

description: A financial modelling tool built for self-publishing Societies, taking into consideration publication rates, Open Access, and other matters.
DOI: 10.6084/m9.figshare.6508745.v1
title: Publishing margins modelling tool

description: A financial modelling tool built for self-publishing Societies, taking into consideration publication rates, Open Access, and other matters.