cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5845020
title: Can carcinoembryonic antigen replace computed tomography in response evaluation of metastatic colorectal cancer?

description: <b>Introduction:</b> Response Evaluation Criteria in Solid Tumours (RECISTs 1.1) define computed tomography (CT) as the gold standard in response evaluation of patients with metastatic colorectal cancer (mCRC) who are undergoing chemotherapy. The aim of this study was to evaluate whether carcinoembryonic antigen (CEA), which is cheaper and easier to perform, can replace repeated CT. <b>Material and methods:</b> The study included 66 patients with non-resectable mCRC participating in a phase I–II study. CEA values were determined, and CT images were taken every 2 months. CT images were externally and retrospectively reviewed according to the RECIST 1.1 criteria. Different cut-off values for CEA change in percent (DeltaCEA%) compared with baseline or nadir value underwent testing to find patients with disease control (that is stable disease, partial or complete response) at 2, 4, 6 and 8 months, in order to identify those who could have continued with chemotherapy based on CEA values alone. CT verification is needed in progressive disease (PD), and therefore identifying PD patients was our secondary endpoint. <b>Results:</b> The results showed that by using a cut-off value of 0 for DeltaCEA%, disease control was seen in all patients at all measuring points (negative predictive value (NPV) = 1.0). Secondarily, increasing CEA was able to identify all PD patients (sensitivity (Se) = 1.0) and in 50–74% of the patients increasing CEA provided a lead time to PD on upcoming CT. It was possible to replace CT with CEA in all patients with decreasing CEA, meaning that 23–47% of CT scans could have been avoided at any given time point. <b>Conclusion:</b> When the CEA level at a certain measuring point is the same or lower than CEA at baseline or at nadir (the measuring point with the lowest CEA value) during treatment, CEA can replace CT.
DOI: 10.6084/m9.figshare.5845020.v1
title: Can carcinoembryonic antigen replace computed tomography in response evaluation of metastatic colorectal cancer?

description: <b>Introduction:</b> Response Evaluation Criteria in Solid Tumours (RECISTs 1.1) define computed tomography (CT) as the gold standard in response evaluation of patients with metastatic colorectal cancer (mCRC) who are undergoing chemotherapy. The aim of this study was to evaluate whether carcinoembryonic antigen (CEA), which is cheaper and easier to perform, can replace repeated CT. <b>Material and methods:</b> The study included 66 patients with non-resectable mCRC participating in a phase I–II study. CEA values were determined, and CT images were taken every 2 months. CT images were externally and retrospectively reviewed according to the RECIST 1.1 criteria. Different cut-off values for CEA change in percent (DeltaCEA%) compared with baseline or nadir value underwent testing to find patients with disease control (that is stable disease, partial or complete response) at 2, 4, 6 and 8 months, in order to identify those who could have continued with chemotherapy based on CEA values alone. CT verification is needed in progressive disease (PD), and therefore identifying PD patients was our secondary endpoint. <b>Results:</b> The results showed that by using a cut-off value of 0 for DeltaCEA%, disease control was seen in all patients at all measuring points (negative predictive value (NPV) = 1.0). Secondarily, increasing CEA was able to identify all PD patients (sensitivity (Se) = 1.0) and in 50–74% of the patients increasing CEA provided a lead time to PD on upcoming CT. It was possible to replace CT with CEA in all patients with decreasing CEA, meaning that 23–47% of CT scans could have been avoided at any given time point. <b>Conclusion:</b> When the CEA level at a certain measuring point is the same or lower than CEA at baseline or at nadir (the measuring point with the lowest CEA value) during treatment, CEA can replace CT.
DOI: 10.6084/m9.figshare.5845014
title: Normative data for the Rey Auditory Verbal Learning Test in the older French-Quebec population

description: <b>Objective</b>: The aim of this study was to establish normative data for the Rey Auditory Verbal Learning Test, a test assessing verbal episodic memory, in the older French-Quebec population. <b>Method</b>: A total of 432 French-speaking participants aged between 55 and 93 years old, from the Province of Quebec (Canada), were included in the study. Using multiple regression analyses, normative data were developed for five variable of interest, namely scores on trial 1, sum of trials 1 to 5, interference list B, immediate recall of list A, and delayed recall of list A. <b>Results</b>: Results showed that age, education, and sex were associated with performance on all variables. Equations to calculate the expected score for a participant based on sex, age, and education level as well as the <i>Z</i> score were developed. <b>Conclusion</b>: This study provides clinicians with normative data that take into account the participants’ sociodemographic characteristics, thus giving a more accurate interpretation of the results.
DOI: 10.6084/m9.figshare.5845014.v2
title: Normative data for the Rey Auditory Verbal Learning Test in the older French-Quebec population

description: <b>Objective</b>: The aim of this study was to establish normative data for the Rey Auditory Verbal Learning Test, a test assessing verbal episodic memory, in the older French-Quebec population. <b>Method</b>: A total of 432 French-speaking participants aged between 55 and 93 years old, from the Province of Quebec (Canada), were included in the study. Using multiple regression analyses, normative data were developed for five variable of interest, namely scores on trial 1, sum of trials 1 to 5, interference list B, immediate recall of list A, and delayed recall of list A. <b>Results</b>: Results showed that age, education, and sex were associated with performance on all variables. Equations to calculate the expected score for a participant based on sex, age, and education level as well as the <i>Z</i> score were developed. <b>Conclusion</b>: This study provides clinicians with normative data that take into account the participants’ sociodemographic characteristics, thus giving a more accurate interpretation of the results.
DOI: 10.6084/m9.figshare.5845014.v1
title: Normative data for the Rey Auditory Verbal Learning Test in the older French-Quebec population

description: <b>Objective</b>: The aim of this study was to establish normative data for the Rey Auditory Verbal Learning Test, a test assessing verbal episodic memory, in the older French-Quebec population. <b>Method</b>: A total of 432 French-speaking participants aged between 55 and 93 years old, from the Province of Quebec (Canada), were included in the study. Using multiple regression analyses, normative data were developed for five variable of interest, namely scores on trial 1, sum of trials 1 to 5, interference list B, immediate recall of list A, and delayed recall of list A. <b>Results</b>: Results showed that age, education, and sex were associated with performance on all variables. Equations to calculate the expected score for a participant based on sex, age, and education level as well as the <i>Z</i> score were developed. <b>Conclusion</b>: This study provides clinicians with normative data that take into account the participants’ sociodemographic characteristics, thus giving a more accurate interpretation of the results.
DOI: 10.6084/m9.figshare.5844966
title: Preparation of affordable and multifunctional clay-based ceramic filter matrix for treatment of drinking water

description: Affordable clay-based ceramic filters with multifunctional properties were prepared using low-cost and active ingredients. The characterization results clearly revealed well crystallinity, structural elucidation, extensive porosity, higher surface area, higher stability, and durability which apparently enhance the treatment efficiency. The filtration rates of ceramic filter were evaluated under gravity and the results obtained were compared with a typical gravity slow sand filter (GSSF). All ceramic filters showed significant filtration rates of about 50–180 m/h, which is comparatively higher than the typical GSSF. Further, purification efficiency of clay-based ceramic filters was evaluated by considering important drinking water parameters and contaminants. A significant removal potential was achieved by the clay-based ceramic filter with 25% and 30% activated carbon along with active agents. Desired drinking water quality parameters were achieved by potential removal of nitrite (98.5%), nitrate (80.5%), total dissolved solids (62%), total hardness (55%), total organic pollutants (89%), and pathogenic microorganisms (100%) using ceramic filters within a short duration. The remarkable purification and disinfection efficiencies were attributed to the extensive porosity (0.202 cm<sup>3</sup> g<sup>−1</sup>), surface area (124.61 m<sup>2</sup> g<sup>−1</sup>), stability, and presence of active nanoparticles such as Cu, TiO<sub>2</sub>, and Ag within the porous matrix of the ceramic filter.
DOI: 10.6084/m9.figshare.5844966.v1
title: Preparation of affordable and multifunctional clay-based ceramic filter matrix for treatment of drinking water

description: Affordable clay-based ceramic filters with multifunctional properties were prepared using low-cost and active ingredients. The characterization results clearly revealed well crystallinity, structural elucidation, extensive porosity, higher surface area, higher stability, and durability which apparently enhance the treatment efficiency. The filtration rates of ceramic filter were evaluated under gravity and the results obtained were compared with a typical gravity slow sand filter (GSSF). All ceramic filters showed significant filtration rates of about 50–180 m/h, which is comparatively higher than the typical GSSF. Further, purification efficiency of clay-based ceramic filters was evaluated by considering important drinking water parameters and contaminants. A significant removal potential was achieved by the clay-based ceramic filter with 25% and 30% activated carbon along with active agents. Desired drinking water quality parameters were achieved by potential removal of nitrite (98.5%), nitrate (80.5%), total dissolved solids (62%), total hardness (55%), total organic pollutants (89%), and pathogenic microorganisms (100%) using ceramic filters within a short duration. The remarkable purification and disinfection efficiencies were attributed to the extensive porosity (0.202 cm<sup>3</sup> g<sup>−1</sup>), surface area (124.61 m<sup>2</sup> g<sup>−1</sup>), stability, and presence of active nanoparticles such as Cu, TiO<sub>2</sub>, and Ag within the porous matrix of the ceramic filter.
DOI: 10.6084/m9.figshare.5844909
title: Dataset from Successful escape of bombardier beetles from predator digestive systems

description: Dataset
DOI: 10.6084/m9.figshare.5844909.v1
title: Dataset from Successful escape of bombardier beetles from predator digestive systems

description: Dataset
DOI: 10.6084/m9.figshare.5844873
title: Supplementary Material for: Upregulation of Vascular Endothelial Growth Factor in Amniotic Fluid Stem Cells Enhances Their Potential to Attenuate Lung Injury in a Preterm Rabbit Model of Bronchopulmonary Dysplasia

description: <b><i>Background:</i></b> Bronchopulmonary dysplasia (BPD) is a chronic lung disease that affects extremely preterm infants and remains – despite improvements in neonatal intensive care – a major cause of neonatal mortality and morbidity. Cell-therapeutic strategies employing mesenchymal stem cells (MSC) have been shown to modulate lung development in BPD models. <b><i>Objective:</i></b> Herein, we evaluate the potential of human amniotic fluid (hAF)-SC and hAF-SC with upregulated expression of vascular endothelial growth factor (VEGF) as cell-therapeutic agents for BPD. <b><i>Methods:</i></b> Preterm rabbit pups were raised in normoxia (21% O<sub>2</sub>) or hyperoxia (≥95% O<sub>2</sub>). Hyperoxia-exposed pups randomly received an intraperitoneal injection of fibroblasts, naïve hAF-SC, or hAF-SC-VEGF on postnatal day (PN) 0. On PN7, surviving pups were tested for pulmonary (forced oscillation technique) and vascular (pulmonary artery Doppler ultrasound) function, and lungs were processed for morphometric measurements of parenchymal and vascular structure and inflammation. <b><i>Results:</i></b> Intraperitoneal injection of cells resulted in homing to the lungs. The lungs of hyperoxia-exposed animals displayed parenchymal and vascular structural and functional damage reminiscent of BPD, which was significantly improved after treatment with hAF-SC-VEGF. Treating hyperoxia-exposed animals with naïve AF-SC attenuated only the lung inflammation and the vascular structural defect. Treatment with fibroblasts, which were used as a cellular control, did not lead to any improvements. <b><i>Conclusion:</i></b> hAF-SC with upregulated VEGF expression display enhanced potential to prevent/reverse lung injury in preterm rabbits, whereas naïve hAF-SC only show a moderate therapeutic potential. These results point towards an added value of VEGF delivered by hAF-SC in the treatment of BPD.
DOI: 10.6084/m9.figshare.5844873.v1
title: Supplementary Material for: Upregulation of Vascular Endothelial Growth Factor in Amniotic Fluid Stem Cells Enhances Their Potential to Attenuate Lung Injury in a Preterm Rabbit Model of Bronchopulmonary Dysplasia

description: <b><i>Background:</i></b> Bronchopulmonary dysplasia (BPD) is a chronic lung disease that affects extremely preterm infants and remains – despite improvements in neonatal intensive care – a major cause of neonatal mortality and morbidity. Cell-therapeutic strategies employing mesenchymal stem cells (MSC) have been shown to modulate lung development in BPD models. <b><i>Objective:</i></b> Herein, we evaluate the potential of human amniotic fluid (hAF)-SC and hAF-SC with upregulated expression of vascular endothelial growth factor (VEGF) as cell-therapeutic agents for BPD. <b><i>Methods:</i></b> Preterm rabbit pups were raised in normoxia (21% O<sub>2</sub>) or hyperoxia (≥95% O<sub>2</sub>). Hyperoxia-exposed pups randomly received an intraperitoneal injection of fibroblasts, naïve hAF-SC, or hAF-SC-VEGF on postnatal day (PN) 0. On PN7, surviving pups were tested for pulmonary (forced oscillation technique) and vascular (pulmonary artery Doppler ultrasound) function, and lungs were processed for morphometric measurements of parenchymal and vascular structure and inflammation. <b><i>Results:</i></b> Intraperitoneal injection of cells resulted in homing to the lungs. The lungs of hyperoxia-exposed animals displayed parenchymal and vascular structural and functional damage reminiscent of BPD, which was significantly improved after treatment with hAF-SC-VEGF. Treating hyperoxia-exposed animals with naïve AF-SC attenuated only the lung inflammation and the vascular structural defect. Treatment with fibroblasts, which were used as a cellular control, did not lead to any improvements. <b><i>Conclusion:</i></b> hAF-SC with upregulated VEGF expression display enhanced potential to prevent/reverse lung injury in preterm rabbits, whereas naïve hAF-SC only show a moderate therapeutic potential. These results point towards an added value of VEGF delivered by hAF-SC in the treatment of BPD.
DOI: 10.6084/m9.figshare.5844795
title: Comparative toxicity of three differently shaped carbon nanomaterials on <i>Daphnia magna</i>: does a shape effect exist?

description: The acute toxicity of three differently shaped carbon nanomaterials (CNMs) was studied on <i>Daphnia magna</i>, comparing the induced effects and looking for the toxic mechanisms. We used carbon nano-powder (CNP), with almost spherical primary particle morphology, multi-walled carbon nanotubes (CNTs), tubes of multi-graphitic sheets, and cubic-shaped carbon nanoparticles (CNCs), for which no ecotoxicological data are available so far. Daphnids were exposed to six suspensions (1, 2, 5, 10, 20 and 50 mg L<sup>−1</sup>) of each CNM, and then microscopically analyzed. Ultrastructural analyses evidenced cellular uptake of nanoparticle in CNP and CNT exposed groups, but not in samples exposed to CNCs. Despite this difference, very similar effects were observed in tissues exposed to the three used CNMs: empty spaces between cells, cell detachment from the basal lamina, many lamellar bodies and autophagy vacuoles. These pathological figures were qualitatively similar among the three groups, but they differed in frequency and severity. CNCs caused the most severe effects, such as partial or complete dissolution of the brush border and thinning of the digestive epithelium. Being the cubic shape not allowed to be internalized into cells, but more effective than others in determining physical damages, we can conclude that shape is an important factor for driving nanoparticle uptake by cells and for determining the acute toxicological endpoints. Shape also plays a key role in determining the kind and the severity of pathologies, which are linked to the physical interactions of CNMs with the exposed tissues.
DOI: 10.6084/m9.figshare.5844795.v1
title: Comparative toxicity of three differently shaped carbon nanomaterials on <i>Daphnia magna</i>: does a shape effect exist?

description: The acute toxicity of three differently shaped carbon nanomaterials (CNMs) was studied on <i>Daphnia magna</i>, comparing the induced effects and looking for the toxic mechanisms. We used carbon nano-powder (CNP), with almost spherical primary particle morphology, multi-walled carbon nanotubes (CNTs), tubes of multi-graphitic sheets, and cubic-shaped carbon nanoparticles (CNCs), for which no ecotoxicological data are available so far. Daphnids were exposed to six suspensions (1, 2, 5, 10, 20 and 50 mg L<sup>−1</sup>) of each CNM, and then microscopically analyzed. Ultrastructural analyses evidenced cellular uptake of nanoparticle in CNP and CNT exposed groups, but not in samples exposed to CNCs. Despite this difference, very similar effects were observed in tissues exposed to the three used CNMs: empty spaces between cells, cell detachment from the basal lamina, many lamellar bodies and autophagy vacuoles. These pathological figures were qualitatively similar among the three groups, but they differed in frequency and severity. CNCs caused the most severe effects, such as partial or complete dissolution of the brush border and thinning of the digestive epithelium. Being the cubic shape not allowed to be internalized into cells, but more effective than others in determining physical damages, we can conclude that shape is an important factor for driving nanoparticle uptake by cells and for determining the acute toxicological endpoints. Shape also plays a key role in determining the kind and the severity of pathologies, which are linked to the physical interactions of CNMs with the exposed tissues.
DOI: 10.6084/m9.figshare.5844789
title: NaPiRE Data Set 2013Naming the Pain in Requirements Engineering Survey Data 2013

description: Data from the NaPiRE run 2012 in Germany, codebook and instrument printout. Further information can be taken from the website www.re-survey.orgSurvey Data on practices and problems in Requirements Engineering
DOI: 10.6084/m9.figshare.5844783
title: Dataset for: Structural mechanisms for the S-nitrosylation-derived protection of mouse galectin-2 from oxidation-induced inactivation revealed by NMR

description: Galectin-2 (Gal-2) is a lectin thought to play protective roles in the gastrointestinal tract. Oxidation of mouse Gal-2 (mGal-2) by hydrogen peroxide (H<sub>2</sub>O<sub>2</sub>) results in the loss of sugar-binding activity, whereas S-nitrosylation of mGal-2, which does not change its sugar-binding profile, has been shown to protect the protein from H<sub>2</sub>O<sub>2</sub>-induced inactivation. One of the two cysteine residues, C57, has been identified as being responsible for controlling H<sub>2</sub>O<sub>2</sub>-induced inactivation; however, the underlying molecular mechanism has not been elucidated. We performed structural analyses of mGal-2 using NMR and found that residues near C57 experienced significant chemical shift changes following S-nitrosylation, and that S-nitrosylation slowed the H<sub>2</sub>O<sub>2</sub>-induced aggregation of mGal-2. We also revealed that S-nitrosylation improves the thermal stability of mGal-2, and that the solvent accessibility and/or local dynamics of residues near C57 and the local dynamics of the core-forming residues in mGal-2 are reduced by S-nitrosylation. Structural models of Gal-2 indicated that C57 is located in a hydrophobic pocket that can be plugged by S-nitrosylation, which was supported by the NMR experiments. Based on these results, we propose two structural mechanisms by which S-nitrosylation protects mGal-2 from H<sub>2</sub>O<sub>2</sub>-induced aggregation without changing its sugar-binding profile: (1) steric prevention of H<sub>2</sub>O<sub>2</sub> access to C57 by filling the hydrophobic pocket where the residue is located, and (2) dynamic prevention of H<sub>2</sub>O<sub>2</sub> access to C57 by reducing the population of the transiently unfolded state of the protein, in which the residue is exposed to H<sub>2</sub>O<sub>2</sub>.
DOI: 10.6084/m9.figshare.5844783.v1
title: Dataset for: Structural mechanisms for the S-nitrosylation-derived protection of mouse galectin-2 from oxidation-induced inactivation revealed by NMR

description: Galectin-2 (Gal-2) is a lectin thought to play protective roles in the gastrointestinal tract. Oxidation of mouse Gal-2 (mGal-2) by hydrogen peroxide (H<sub>2</sub>O<sub>2</sub>) results in the loss of sugar-binding activity, whereas S-nitrosylation of mGal-2, which does not change its sugar-binding profile, has been shown to protect the protein from H<sub>2</sub>O<sub>2</sub>-induced inactivation. One of the two cysteine residues, C57, has been identified as being responsible for controlling H<sub>2</sub>O<sub>2</sub>-induced inactivation; however, the underlying molecular mechanism has not been elucidated. We performed structural analyses of mGal-2 using NMR and found that residues near C57 experienced significant chemical shift changes following S-nitrosylation, and that S-nitrosylation slowed the H<sub>2</sub>O<sub>2</sub>-induced aggregation of mGal-2. We also revealed that S-nitrosylation improves the thermal stability of mGal-2, and that the solvent accessibility and/or local dynamics of residues near C57 and the local dynamics of the core-forming residues in mGal-2 are reduced by S-nitrosylation. Structural models of Gal-2 indicated that C57 is located in a hydrophobic pocket that can be plugged by S-nitrosylation, which was supported by the NMR experiments. Based on these results, we propose two structural mechanisms by which S-nitrosylation protects mGal-2 from H<sub>2</sub>O<sub>2</sub>-induced aggregation without changing its sugar-binding profile: (1) steric prevention of H<sub>2</sub>O<sub>2</sub> access to C57 by filling the hydrophobic pocket where the residue is located, and (2) dynamic prevention of H<sub>2</sub>O<sub>2</sub> access to C57 by reducing the population of the transiently unfolded state of the protein, in which the residue is exposed to H<sub>2</sub>O<sub>2</sub>.