cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.4872875.v1
title: Supplementary Material for: Combining Cystatin C and Creatinine Yields a Reliable Glomerular Filtration Rate Estimation in Older Adults in Contrast to β-Trace Protein and β2-Microglobulin

description: <b><i>Background:</i></b> The glomerular filtration rate (GFR) is the most important measure of kidney function and chronic kidney disease (CKD). This study aims to validate commonly used equations for estimated GFR (eGFR) based on creatinine (cr), cystatin C (cys), β-trace protein (BTP), and β2-microglobulin (B2M) in older adults. <b><i>Method:</i></b> We conducted a validation study with 126 participants aged between 72 and 98 with a mean measured GFR (mGFR) by iohexol clearance of 54 mL/min/1.73 m<sup>2</sup>. The eGFR equations (CKD-Epidemiology collaboration [CKD-EPI], Berlin Initiative Study [BIS], Full Age Spectrum [FAS], Modification of Diet in Renal Disease [MDRD]<sub>cr</sub>, Caucasian-Asian-Pediatric-Adult [CAPA]<sub>cys</sub>, Lund-Malmö Revised [LM-REV]<sub>cr</sub>, and MEAN-LM-CAPA<sub>cr-cys</sub>), were assessed in terms of bias (median difference: eGFR-mGFR), precision (interquartile range of the differences), and accuracy (P30: percentage of estimates ±30% of mGFR). The equations were compared to a benchmark equation: CKD-EPI<sub>cr-cys</sub>. <b><i>Results:</i></b> All cystatin C-based equations underestimated the GFR compared to mGFR, whereas bias was mixed for the equations based only on creatinine. Accuracy was the highest for CKD-EPI<sub>cr-cys</sub> (98%) and lowest for MDRD (82%). Below mGFR 45 mL/min/1.73 m<sup>2</sup> only equations incorporating cystatin C reached P30 accuracy &gt;90%. CKD-EPI<sub>cr-cys</sub> was not significantly more accurate than the other cystatin C-based equations. In contrast, CKD-EPI<sub>cr-cys</sub> was significantly more accurate than all creatinine-based equations except LM-REV<sub>cr</sub>. <b><i>Conclusion:</i></b> This study confirms that it is reasonable to use equations incorporating cystatin C and creatinine in older patients across a wide spectrum of GFR. However, the results call into question the use of creatinine alone below mGFR 45 mL/min/1.73 m<sup>2</sup>. B2M and BTP do not demonstrate additional value in eGFR determination in older adults.
DOI: 10.6084/m9.figshare.4872785
title: One-domain approach for studying multiphase transport phenomena in biofilm growing systems

description: The one-domain approach (ODA) was used as an alternative to solve fluid–biofilm interfacial behavior in a 2-D model for diffusion–reaction–convection coupled with prediction of irregular growth of biofilms <i>via</i> a cellular automaton strategy. The simulations exhibited errors of &lt;7% compared with the porosity of a previously reported capillary experimental system. Additionally, biofilm surface geometrical aspects were satisfactorily compared with reports of experimental and similar rigorously simulated benchmark systems. The method developed was applied to simulate typical biofilm systems predicting recirculation flow patterns, interface concentration profiles, and clogging of the inlet section of the capillary tube, which are phenomena that affect the efficiency of diverse biotechnological applications, including membrane bioreactors and biofilters. The ODA method applied to the governing equations of momentum and mass transfer combined with a cellular automaton algorithm is a suitable and straightforward approach for modeling solid-state fermentation at different sophistication levels.
DOI: 10.6084/m9.figshare.4872785.v2
title: One-domain approach for studying multiphase transport phenomena in biofilm growing systems

description: The one-domain approach (ODA) was used as an alternative to solve fluid–biofilm interfacial behavior in a 2-D model for diffusion–reaction–convection coupled with prediction of irregular growth of biofilms <i>via</i> a cellular automaton strategy. The simulations exhibited errors of &lt;7% compared with the porosity of a previously reported capillary experimental system. Additionally, biofilm surface geometrical aspects were satisfactorily compared with reports of experimental and similar rigorously simulated benchmark systems. The method developed was applied to simulate typical biofilm systems predicting recirculation flow patterns, interface concentration profiles, and clogging of the inlet section of the capillary tube, which are phenomena that affect the efficiency of diverse biotechnological applications, including membrane bioreactors and biofilters. The ODA method applied to the governing equations of momentum and mass transfer combined with a cellular automaton algorithm is a suitable and straightforward approach for modeling solid-state fermentation at different sophistication levels.
DOI: 10.6084/m9.figshare.4872785.v1
title: One-domain approach for studying multiphase transport phenomena in biofilm growing systems

description: The one-domain approach (ODA) was used as an alternative to solve fluid–biofilm interfacial behavior in a 2-D model for diffusion–reaction–convection coupled with prediction of irregular growth of biofilms <i>via</i> a cellular automaton strategy. The simulations exhibited errors of &lt;7% compared with the porosity of a previously reported capillary experimental system. Additionally, biofilm surface geometrical aspects were satisfactorily compared with reports of experimental and similar rigorously simulated benchmark systems. The method developed was applied to simulate typical biofilm systems predicting recirculation flow patterns, interface concentration profiles, and clogging of the inlet section of the capillary tube, which are phenomena that affect the efficiency of diverse biotechnological applications, including membrane bioreactors and biofilters. The ODA method applied to the governing equations of momentum and mass transfer combined with a cellular automaton algorithm is a suitable and straightforward approach for modeling solid-state fermentation at different sophistication levels.
DOI: 10.6084/m9.figshare.4872668
title: Supplementary Material for: The Inhibitory Effect of Eplerenone on Cell Proliferation in the Contralateral Kidneys of Rats with Unilateral Ureteral Obstruction

description: <b><i>Background:</i></b> The unilateral ureteral obstruction (UUO) model not only induces renal interstitial fibrosis in the obstructed kidney but also induces injury in the contralateral kidney. We hypothesized that activation of the mineralocorticoid receptor (MR) may induce fibrosis in the early stage of UUO. <b><i>Methods:</i></b> Thirty male Sprague-Dawley rats weighting 200 ± 10 g were used in this study and randomly divided into 3 groups: a UUO group, a UUO and eplerenone group, and a sham group. The contralateral kidney and plasma were harvested for further study 10 days after surgery. <b><i>Results:</i></b> The level of plasma aldosterone (869.95 ± 55.851 pg/mL) was significantly higher in the UUO group than that in the sham group (478.581 ± 36.186 pg/mL vs. UUO, <i>p</i> &lt; 0.05). The infiltrated inflammatory cells (F4/80) and deposited collagens were increased significantly in the contralateral kidneys in the UUO group compared to those in the sham group, which were decreased by eplerenone. However, proliferating cell nuclear antigen was increased 2.47 times in the UUO group compared to the sham group in the contralateral kidney (<i>p</i> &lt; 0.01), and those changes are attenuated by eplerenone. The expression of SGK-1 protein and mRNA was upregulated in the contralateral kidney in the UUO group, which is suppressed by eplerenone treatment. NF-κB pathway effecters were also changed markedly in the contralateral kidney in the UUO group and partly reversed by eplerenone. <b><i>Conclusion:</i></b> Aldosterone induces inflammatory cell proliferation via the MR/SGK-1 and NF-κB pathways and eventually leads to fibrosis in the contralateral kidney.
DOI: 10.6084/m9.figshare.4872665
title: Supplementary Material for: Comparison of pro re nata versus Bimonthly Injection of Intravitreal Aflibercept for Typical Neovascular Age-Related Macular Degeneration

description: <b><i>Purpose:</i></b> The aim of this study was to clarify the 1-year outcomes of pro re nata (PRN) and bimonthly intravitreal injections of aflibercept (IVA) for typical neovascular age-related macular degeneration (tAMD) after the initial 3 monthly IVA. <b><i>Methods:</i></b> We conducted a prospective, interventional study. Fifty-eight treatment-naïve patients with tAMD were randomly assigned to the PRN (30 patients) or the bimonthly (28 patients) treatment group. Both groups initially received 3 monthly IVA. Visual acuity, central macular retinal thickness (CRT), and central choroidal thickness (CCT) were evaluated at 12 months. Subanalysis was performed to identify factors associated with the best-corrected visual acuity (BCVA). <b><i>Results:</i></b> BCVA was significantly improved only in the bimonthly group at 12 months. CRT and CCT were significantly decreased in both groups. Subanalysis showed that the only factor associated with BCVA improvement at 12 months was the existence of pigment epithelial detachment at baseline. <b><i>Conclusions:</i></b> BCVA showed significant improvement only in the bimonthly group but not in the PRN group at 12 months.
DOI: 10.6084/m9.figshare.4872656
title: Analysis of the implementation of a personalized care model in diabetes mellitus as an example of chronic disease with information and communication technology support

description: <b>Introduction</b>: Diabetes mellitus affects 13.8% of the adult population in Spain, representing some 8.2% of total Spanish health spending, which may be reduced by optimizing treatment and disease monitoring. <b>Areas covered</b>: This perspective article aims to evaluate the possible clinical and economic outcomes of implementing a theoretical personalized care model in diabetes supported by information and communications technology in Spain vs. conventional care. Moreover, we assessed the value of emminens® eConecta, a solution designed to support the operational implementation of this model, which enables the connection and participation of patients and health professionals, facilitates patient education, decision-making, access to information, and data analysis. We carried out a review of the available evidence, consultations with experts and a clinical and cost estimation. <b>Expert commentary</b>: The experts consulted considered that the proposed model is consistent with Spanish strategies on chronicity, supports the management of chronicity/diabetes, and may improve the most important aspects of disease management. In the literature, this type of care models improved or provided equal disease control compared with conventional care, potentiated self-management strategies and reduced the high use of resources. Cost estimation showed a reduction of −12% in total direct costs and around −34% in the costs of outpatient visits.
DOI: 10.6084/m9.figshare.4872656.v1
title: Analysis of the implementation of a personalized care model in diabetes mellitus as an example of chronic disease with information and communication technology support

description: <b>Introduction</b>: Diabetes mellitus affects 13.8% of the adult population in Spain, representing some 8.2% of total Spanish health spending, which may be reduced by optimizing treatment and disease monitoring. <b>Areas covered</b>: This perspective article aims to evaluate the possible clinical and economic outcomes of implementing a theoretical personalized care model in diabetes supported by information and communications technology in Spain vs. conventional care. Moreover, we assessed the value of emminens® eConecta, a solution designed to support the operational implementation of this model, which enables the connection and participation of patients and health professionals, facilitates patient education, decision-making, access to information, and data analysis. We carried out a review of the available evidence, consultations with experts and a clinical and cost estimation. <b>Expert commentary</b>: The experts consulted considered that the proposed model is consistent with Spanish strategies on chronicity, supports the management of chronicity/diabetes, and may improve the most important aspects of disease management. In the literature, this type of care models improved or provided equal disease control compared with conventional care, potentiated self-management strategies and reduced the high use of resources. Cost estimation showed a reduction of −12% in total direct costs and around −34% in the costs of outpatient visits.
DOI: 10.17608/k6.auckland.4872419
title: Laser-ultrasound waves generated with various energy densities and recorded with GCLAD

description: Laser-ultrasound waves are generated on a solid tissue phantom and recorded with GCLAD on the opposite side of the sample. The pulse energy is varied from 70, 80, 90, and 100 mJ/cm^2. Python script is used to determine the proportionality between pulse energy and measured laser-ultrasound amplitude with GCLAD.
DOI: 10.17608/k6.auckland.4872419.v1
title: Laser-ultrasound waves generated with various energy densities and recorded with GCLAD

description: Laser-ultrasound waves are generated on a solid tissue phantom and recorded with GCLAD on the opposite side of the sample. The pulse energy is varied from 70, 80, 90, and 100 mJ/cm^2. Python script is used to determine the proportionality between pulse energy and measured laser-ultrasound amplitude with GCLAD.
DOI: 10.5281/zenodo.4010121
title: Vertex-transitive Graphs On Fewer Than 48 Vertices

description: <strong><em>Vertex-transitive Graphs On Fewer Than 48 Vertices</em></strong> This dataset contains all the vertex-transitive graphs on 10-47 vertices. It consists of a collection of tar files, with names like alltrans26.tar meaning that this tar file contains all the vertex-transitive graphs on 26 vertices. Once the tar file is unpacked (using "tar xf alltrans26.tar") this will create a number of smaller gzipped files with names such as alltrans26_k=03.gz meaning that this file contains all the transitive graphs on 26 vertices with degree (valency) 3. Once the gzip file is unpacked using "gunzip alltrans26_k=03.gz" the resulting file contains all the graphs, one per line, in graph6 format (this format was invented by Brendan McKay and is recognised by SageMath). The first five lines of the file alltrans26_k=03 are as follows: <pre>Ys???C????_CA?@?`?_GO?c?@_?Q??K??O@CG?aA?GAG@?OCCG?GGC?? Ys??WO@?O??O?J?E?A_H??A?C??O?????_?DC?AQ?AAA??oG?C_O?I?? Ys??WWG@?@?A?W?c??g?S?@??G???G??O??S??I?_?Ac??SS??OW??_? Ys?GGSG@?@?A?W?c??g?S?@??G???G??O??S??I?_?Ac??SS??OW??_? Ys?GOO?????c?Q?c?B?@_?I?A??G??A?@?CCC?OP?CCC?C_O?AOC?C_? </pre> These can be directly used as input to SageMath with commands such as g = Graph("Ys???C????_CA?@?`?_GO?c?@_?Q??K??O@CG?aA?GAG@?OCCG?GGC??") No attempt has been made to reduce data storage by removing redundancy. So the tar file for vertex-transitive graphs on n vertices contains files for each feasible valency from 0 to n-1, despite the redundancy inherent in storing both a graph and its complement, and in storing both disconnected and connected graphs.
description: {"references": ["Derek Holt and Gordon Royle, A census of small transitive groups and vertex-transitive graphs, https://arxiv.org/abs/1811.09015"]}
DOI: 10.6084/m9.figshare.4872011
title: HGT in Archaea-part II

description: HGT in human gut microbes: Horizontally transferred genes received by Archaea species.
DOI: 10.6084/m9.figshare.4872008
title: Dataset for: Bayesian estimation of physiological parameters governing a dynamic two-compartment model of exhaled nitric oxide

description: The fractional concentration of nitric oxide in exhaled breath (FᴇNO) is a biomarker of airway inflammation with applications in clinical asthma management and environmental epidemiology. FᴇNO concentration depends on the expiratory flow rate. Standard FᴇNO is assessed at 50 ml/s, but “extended NO analysis” uses FᴇNO measured at multiple different flow rates to estimate parameters quantifying proximal and distal sources of NO in the lower respiratory tract. Most approaches to modeling multiple flow FᴇNO assume the concentration of NO throughout the airway has achieved a “steady-state”. In practice, this assumption demands that subjects maintain sustained flow rate exhalations, during which both FᴇNO and expiratory flow rate must remain constant, and the FᴇNO maneuver is summarized by the average FᴇNO concentration and average flow during a small interval. In this work, we drop the steady-state assumption in the classic two-compartment model. Instead, we have developed a new parameter estimation approach based on measuring and adjusting for a continuously varying flow rate over the entire FᴇNO maneuver. We have developed a Bayesian inference framework for the parameters of the partial differential equation underlying this model. Based on multiple flow FᴇNO data from the Southern California Children’s Health Study, we use observed and simulated NO concentrations to demonstrate that our approach has reasonable computation time and is consistent with existing steady state approaches, while our inferences consistently offer greater precision than current methods.
DOI: 10.6084/m9.figshare.4872011.v1
title: HGT in Archaea-part II

description: HGT in human gut microbes: Horizontally transferred genes received by Archaea species.
DOI: 10.17608/k6.auckland.4871993
title: Laser-ultrasound measurements with GCLAD for various air-gaps

description: Laser-ultrasound waves were generated on absorbing tape on the surface of a tissue phantom with high-energy (200mJ) laser pulses at 1064 nm. The resulting waves were recorded through many different propagation distances through air with GCLAD in transmission mode.
DOI: 10.6084/m9.figshare.4872008.v1
title: Dataset for: Bayesian estimation of physiological parameters governing a dynamic two-compartment model of exhaled nitric oxide

description: The fractional concentration of nitric oxide in exhaled breath (FᴇNO) is a biomarker of airway inflammation with applications in clinical asthma management and environmental epidemiology. FᴇNO concentration depends on the expiratory flow rate. Standard FᴇNO is assessed at 50 ml/s, but “extended NO analysis” uses FᴇNO measured at multiple different flow rates to estimate parameters quantifying proximal and distal sources of NO in the lower respiratory tract. Most approaches to modeling multiple flow FᴇNO assume the concentration of NO throughout the airway has achieved a “steady-state”. In practice, this assumption demands that subjects maintain sustained flow rate exhalations, during which both FᴇNO and expiratory flow rate must remain constant, and the FᴇNO maneuver is summarized by the average FᴇNO concentration and average flow during a small interval. In this work, we drop the steady-state assumption in the classic two-compartment model. Instead, we have developed a new parameter estimation approach based on measuring and adjusting for a continuously varying flow rate over the entire FᴇNO maneuver. We have developed a Bayesian inference framework for the parameters of the partial differential equation underlying this model. Based on multiple flow FᴇNO data from the Southern California Children’s Health Study, we use observed and simulated NO concentrations to demonstrate that our approach has reasonable computation time and is consistent with existing steady state approaches, while our inferences consistently offer greater precision than current methods.
DOI: 10.17608/k6.auckland.4871993.v1
title: Laser-ultrasound measurements with GCLAD for various air-gaps

description: Laser-ultrasound waves were generated on absorbing tape on the surface of a tissue phantom with high-energy (200mJ) laser pulses at 1064 nm. The resulting waves were recorded through many different propagation distances through air with GCLAD in transmission mode.
DOI: 10.5287/bodleian:6qbky6e2x
title: Leaf Vein CNN Software
DOI: 10.6084/m9.figshare.4871855
title: Supplementary Table S4

description: Genes sequenced as part of the panel design for the Illumina targeted NGS<br>
DOI: 10.6084/m9.figshare.4871867
title: Supplementary Table S5

description: Histo-pathological characteristics of samples in Brown et al.
DOI: 10.6084/m9.figshare.4871855.v1
title: Supplementary Table S4

description: Genes sequenced as part of the panel design for the Illumina targeted NGS<br>
DOI: 10.6084/m9.figshare.4871843
title: Supplementary Table S3

description: Alpha list of genes where mutations occurring with VAF &lt;10% were accepted
DOI: 10.6084/m9.figshare.4871846
title: Tamoxifen-Dependent Induction of <i>AGR2</i> Is Associated with Increased Aggressiveness of Endometrial Cancer Cells

description: Tamoxifen treatment in breast cancer patients is associated with increased risk of endometrial malignancies. Significantly, higher <i>AGR2</i> expression was found in endometrial cancers that developed in women previously treated with tamoxifen compared to those who had not been exposed to tamoxifen. An association of elevated <i>AGR2</i> level with myometrial invasion occurrence and invasion depth was also found. <i>In vitro</i> analyses identified a stimulatory effect of <i>AGR2</i> on cellular proliferation. Although adverse tamoxifen effects on endometrial cells remain elusive, our work identifies elevated <i>AGR2</i> as a candidate tamoxifen-dependent mechanism of action responsible for increased incidence of endometrial cancer.
DOI: 10.6084/m9.figshare.4871867.v1
title: Supplementary Table S5

description: Histo-pathological characteristics of samples in Brown et al.
DOI: 10.6084/m9.figshare.4871834
title: Supplementary Table S2

description: Genes sequenced as part of the panel design for the Ion Torrent targeted NGS
DOI: 10.6084/m9.figshare.4871843.v1
title: Supplementary Table S3

description: Alpha list of genes where mutations occurring with VAF &lt;10% were accepted
DOI: 10.6084/m9.figshare.4871846.v1
title: Tamoxifen-Dependent Induction of <i>AGR2</i> Is Associated with Increased Aggressiveness of Endometrial Cancer Cells

description: Tamoxifen treatment in breast cancer patients is associated with increased risk of endometrial malignancies. Significantly, higher <i>AGR2</i> expression was found in endometrial cancers that developed in women previously treated with tamoxifen compared to those who had not been exposed to tamoxifen. An association of elevated <i>AGR2</i> level with myometrial invasion occurrence and invasion depth was also found. <i>In vitro</i> analyses identified a stimulatory effect of <i>AGR2</i> on cellular proliferation. Although adverse tamoxifen effects on endometrial cells remain elusive, our work identifies elevated <i>AGR2</i> as a candidate tamoxifen-dependent mechanism of action responsible for increased incidence of endometrial cancer.
DOI: 10.6084/m9.figshare.4871828
title: Supplementary Table S1

description: Histo-pathological characteristics of samples in Maetens et al. and Desmedt et al.
DOI: 10.6084/m9.figshare.4871834.v1
title: Supplementary Table S2

description: Genes sequenced as part of the panel design for the Ion Torrent targeted NGS
DOI: 10.6084/m9.figshare.4871756
title: Data for "Long-range temporal correlations in neural narrowband time-series arise due to critical dynamics"

description: Full data to "Long-range temporal correlations in neural narrowbandtime-series arise due to critical dynamics," 2017, PLOSone.Duncan Blythe and Vadim Nikulin
DOI: 10.6084/m9.figshare.4871828.v1
title: Supplementary Table S1

description: Histo-pathological characteristics of samples in Maetens et al. and Desmedt et al.
DOI: 10.6084/m9.figshare.4871690
title: Bibliography for systematic review on learning analytics and learning design.docx

description: bibliography for systematic literature review
DOI: 10.6084/m9.figshare.4871690.v1
title: Bibliography for systematic review on learning analytics and learning design.docx

description: bibliography for systematic literature review