cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.5747184
title: DeepSpot

description: Simulated smFISH datasets for DeepSpot paper
DOI: 10.5281/zenodo.5724465
title: DeepSpot

description: Simulated smFISH datasets for DeepSpot paper
DOI: 10.6084/m9.figshare.17105132
title: Supplementary Material for: ESCAPE: An Open-Label Trial of Personalized Immunotherapy in Critically lll COVID-19 Patients

description: <b><i>Background:</i></b> Macrophage activation-like syndrome (MALS) and complex immune dysregulation (CID) often underlie acute respiratory distress (ARDS) in COVID-19. We aimed to investigate the effect of personalized immunotherapy on clinical improvement of critical COVID-19. <b><i>Methods:</i></b> In this open-label prospective trial, 102 patients with ARDS by SARS-CoV-2 were screened for MALS (ferritin &gt;4,420 ng/mL) and CID (ferritin ≤4,420 ng/mL and low human leukocyte antigen (HLA)-DR expression on CD14-monocytes). Patients with MALS or CID with increased aminotransferases received intravenous anakinra; those with CID and normal aminotransferases received tocilizumab. The primary outcome was ≥25% decrease in the Sequential Organ Failure Assessment (SOFA) score and/or 50% increase in the respiratory ratio by day 8; 28-day mortality, change of SOFA score by day 28, serum biomarkers, and cytokine production by mononuclear cells were secondary endpoints. <b><i>Results:</i></b> The primary study endpoint was met in 58.3% of anakinra-treated patients and in 33.3% of tocilizumab-treated patients (<i>p</i>: 0.01). Most patients in both groups received dexamethasone as standard of care. No differences were found in secondary outcomes, mortality, and SOFA score changes. Ferritin decreased among anakinra-treated patients; interleukin-6, soluble urokinase plasminogen activator receptor, and HLA-DR expression increased among tocilizumab-treated patients. Survivors by day 28 who received anakinra were distributed to lower severity levels of the WHO clinical progression scale. Greater incidence of secondary infections was found with tocilizumab treatment. <b><i>Conclusion:</i></b> Immune assessment resulted in favorable anakinra responses among critically ill patients with COVID-19 and features of MALS<i>.</i>
DOI: 10.6084/m9.figshare.12579152.v2
title: Potentilla_anserina.gff3

description: Genes structure annotation file
DOI: 10.6084/m9.figshare.13705231
title: Order-preserving dynamics in one dimension – single-file diffusion and caging from the perspective of dynamical density functional theory

description: Dynamical density functional theory (DDFT) is a powerful variational framework to study the nonequilibrium properties of colloids by only considering a time-dependent one-body number density. Despite the large number of recent successes, properly modelling the long-time dynamics in interacting systems within DDFT remains a notoriously difficult problem, since structural information, accounting for temporary or permanent particle cages, gets lost. Here we address such a caging scenario by reducing it to a clean one-dimensional problem, where the particles are naturally ordered (arranged on a line) by perfect cages created by their two next neighbours. In particular, we construct a DDFT approximation based on an equilibrium system with an asymmetric pair potential, such that the corresponding one-body densities still carry the footprint of particle order. Applied to a system of confined hard rods, this order-preserving dynamics (OPD) yields exact results at the system boundaries, in addition to the imprinted correct long-time behaviour of density profiles representing individual particles. In an open system, our approach correctly reproduces the reduced long-time diffusion coefficient and subdiffusion, characteristic for a single-file setup. These observations cannot be made using current forms of DDFT without particle order.
DOI: 10.6084/m9.figshare.13705231.v3
title: Order-preserving dynamics in one dimension – single-file diffusion and caging from the perspective of dynamical density functional theory

description: Dynamical density functional theory (DDFT) is a powerful variational framework to study the nonequilibrium properties of colloids by only considering a time-dependent one-body number density. Despite the large number of recent successes, properly modelling the long-time dynamics in interacting systems within DDFT remains a notoriously difficult problem, since structural information, accounting for temporary or permanent particle cages, gets lost. Here we address such a caging scenario by reducing it to a clean one-dimensional problem, where the particles are naturally ordered (arranged on a line) by perfect cages created by their two next neighbours. In particular, we construct a DDFT approximation based on an equilibrium system with an asymmetric pair potential, such that the corresponding one-body densities still carry the footprint of particle order. Applied to a system of confined hard rods, this order-preserving dynamics (OPD) yields exact results at the system boundaries, in addition to the imprinted correct long-time behaviour of density profiles representing individual particles. In an open system, our approach correctly reproduces the reduced long-time diffusion coefficient and subdiffusion, characteristic for a single-file setup. These observations cannot be made using current forms of DDFT without particle order.
DOI: 10.6084/m9.figshare.17105090.v1
title: Genomic sequences of Omicron variants of SARS-CoV-2 from November 9 to November 28, 2021

description: Genomic sequences of Omicron variants of SARS-CoV-2 from November 9 to November 28, 2021 from GISAID
DOI: 10.5519/qd.htoknv3o
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (165 records)
DOI: 10.6084/m9.figshare.15169362
title: Supplemental Material: Behind teaching-learning strategies in physiology: perceptions of students and teachers of Brazilian medical courses

description: Appendix 1_Students' questionnaireAppendix 2_Teachers' questionnaireAppendix 3_TablesFigure S1Figure S2
DOI: 10.5281/zenodo.5745862
title: Processed Data and codes for visualization

description: Processed Data and codes for visualization
DOI: 10.5281/zenodo.5745861
title: Processed Data and codes for visualization

description: Processed Data and codes for visualization
DOI: 10.6084/m9.figshare.16610892
title: Isoflurane not at the expense of postoperative nausea and vomiting in cardiac anesthesia – an observational study

description: Inhalative anesthesia is of common use, but is generally known to potentiate postoperative nausea and vomiting (PONV). With an internal change of anesthesia regimen from total intravenous anesthesia (TIVA) to isoflurane (in terms of myocardial protection) in cardiac anesthesia a higher incidence of PONV was to be expected. Therefore, we evaluated the incidence of PONV after the simultaneous implementation of PONV prophylaxis. The incidence of PONV, prospectively assessed in 197 cardiac surgery patients (68 <i>y</i> ± 10.4, 66.5% male) having isoflurane plus dual PONV prophylaxis with dexamethasone and droperidol, was compared with previous data of 190 controls (67 <i>y</i> ± 9.6, 71% male) having TIVA without and with single or dual PONV prophylaxis (<i>n</i> = 64 dexamethasone and droperidol, <i>n</i> = 25 dexamethasone, <i>n</i> = 101 only TIVA), and the Apfel-scoring (0–4 depending on PONV-risk). DRKS00014275. Statistics: Chi<sup>2</sup>-test, <i>p</i> The incidence of PONV under isoflurane with antiemetic prophylaxis was 20.8% (95% confidence interval (CI) 15.4; 27.4) compared to 30.5% (95%CI 24; 37.6) under TIVA (<i>p</i> = .029; dexamethasone and droperidol 23.4% (95%CI 13.8; 35.7); dexamethasone 32% (95%CI 14.9; 53.5); only TIVA 34.7% (95%CI 25.5; 44.8)), but was not lower in high-risk patients than predicted according to Apfel-scoring 4 (71.4 vs. 78%). In cardiac anesthesia, the use of isoflurane is not at the expense of PONV when using a risk-independent two-drug-prophylaxis. It is even beneficial resulting surprisingly in a lower incidence of PONV than under TIVA unless with and without prophylaxis. Patients with the highest risk for PONV and receiving isoflurane should receive a third antiemetic prophylactic drug.
DOI: 10.6084/m9.figshare.16610892.v2
title: Isoflurane not at the expense of postoperative nausea and vomiting in cardiac anesthesia – an observational study

description: Inhalative anesthesia is of common use, but is generally known to potentiate postoperative nausea and vomiting (PONV). With an internal change of anesthesia regimen from total intravenous anesthesia (TIVA) to isoflurane (in terms of myocardial protection) in cardiac anesthesia a higher incidence of PONV was to be expected. Therefore, we evaluated the incidence of PONV after the simultaneous implementation of PONV prophylaxis. The incidence of PONV, prospectively assessed in 197 cardiac surgery patients (68 <i>y</i> ± 10.4, 66.5% male) having isoflurane plus dual PONV prophylaxis with dexamethasone and droperidol, was compared with previous data of 190 controls (67 <i>y</i> ± 9.6, 71% male) having TIVA without and with single or dual PONV prophylaxis (<i>n</i> = 64 dexamethasone and droperidol, <i>n</i> = 25 dexamethasone, <i>n</i> = 101 only TIVA), and the Apfel-scoring (0–4 depending on PONV-risk). DRKS00014275. Statistics: Chi<sup>2</sup>-test, <i>p</i> The incidence of PONV under isoflurane with antiemetic prophylaxis was 20.8% (95% confidence interval (CI) 15.4; 27.4) compared to 30.5% (95%CI 24; 37.6) under TIVA (<i>p</i> = .029; dexamethasone and droperidol 23.4% (95%CI 13.8; 35.7); dexamethasone 32% (95%CI 14.9; 53.5); only TIVA 34.7% (95%CI 25.5; 44.8)), but was not lower in high-risk patients than predicted according to Apfel-scoring 4 (71.4 vs. 78%). In cardiac anesthesia, the use of isoflurane is not at the expense of PONV when using a risk-independent two-drug-prophylaxis. It is even beneficial resulting surprisingly in a lower incidence of PONV than under TIVA unless with and without prophylaxis. Patients with the highest risk for PONV and receiving isoflurane should receive a third antiemetic prophylactic drug.
DOI: 10.6084/m9.figshare.16610892.v1
title: Isoflurane not at the expense of postoperative nausea and vomiting in cardiac anesthesia – an observational study

description: Inhalative anesthesia is of common use, but is generally known to potentiate postoperative nausea and vomiting (PONV). With an internal change of anesthesia regimen from total intravenous anesthesia (TIVA) to isoflurane (in terms of myocardial protection) in cardiac anesthesia a higher incidence of PONV was to be expected. Therefore, we evaluated the incidence of PONV after the simultaneous implementation of PONV prophylaxis. The incidence of PONV, prospectively assessed in 197 cardiac surgery patients (68y ± 10.4, 66.5% male) having isoflurane plus dual PONV prophylaxis with dexamethasone and droperidol, was compared with previous data of 190 controls (67y ± 9.6, 71% male) having TIVA without and with single or dual PONV prophylaxis (n = 64 dexamethasone and droperidol, n= 25 dexamethasone, n = 101 only TIVA), and the Apfel-scoring (0-4 depending on PONV-risk). DRKS00014275. Statistics: Chi<sup>2</sup>-test, p The incidence of PONV under isoflurane with antiemetic prophylaxis was 20.8% (95% confidence interval (CI) 15.4; 27.4) compared to 30.5% (95%CI 24; 37.6) under TIVA (p = 0.029; dexamethasone and droperidol 23.4% (95%CI 13.8; 35.7); dexamethasone 32% (95%CI 14.9; 53.5); only TIVA 34.7% (95%CI 25.5; 44.8)), but was not lower in high-risk patients than predicted according to Apfel-scoring 4 (71.4 vs. 78%). In cardiac anesthesia, the use of isoflurane is not at the expense of PONV when using a risk-independent two-drug-prophylaxis. It is even beneficial resulting surprisingly in a lower incidence of PONV than under TIVA unless with and without prophylaxis. Patients with the highest risk for PONV and receiving isoflurane should receive a third antiemetic prophylactic drug.
DOI: 10.6084/m9.figshare.14401729.v1
title: Segmental Lennard-Jones interactions for semi-flexible polymer networks

description: Simulating soft matter systems such as the cytoskeleton can enable deep understanding of experimentally observed phenomena. One challenge of modelling such systems is realistic description of the steric repulsion between nearby polymers. Previous models of the polymeric excluded volume interaction have the deficit of being non-analytic, being computationally expensive, or allowing polymers to erroneously cross each other. A recent solution to these issues, implemented in the MEDYAN simulation platform, uses analytical expressions obtained from integrating an interaction kernel along the lengths of two polymer segments to describe their repulsion. Here, we extend this model by re-deriving it for lower-dimensional geometrical configurations, deriving similar expressions using a steeper interaction kernel, comparing it to other commonly used potentials, and showing how to parameterise these models. We also generalise this new integrated style of potential by introducing a segmental Lennard-Jones potential, which enables modelling both attractive and repulsive interactions in semi-flexible polymer networks. These results can be further generalised to facilitate the development of effective interaction potentials for other finite elements in simulations of softmatter systems.
DOI: 10.6084/m9.figshare.14401729
title: Segmental Lennard-Jones interactions for semi-flexible polymer networks

description: Simulating soft matter systems such as the cytoskeleton can enable deep understanding of experimentally observed phenomena. One challenge of modelling such systems is realistic description of the steric repulsion between nearby polymers. Previous models of the polymeric excluded volume interaction have the deficit of being non-analytic, being computationally expensive, or allowing polymers to erroneously cross each other. A recent solution to these issues, implemented in the MEDYAN simulation platform, uses analytical expressions obtained from integrating an interaction kernel along the lengths of two polymer segments to describe their repulsion. Here, we extend this model by re-deriving it for lower-dimensional geometrical configurations, deriving similar expressions using a steeper interaction kernel, comparing it to other commonly used potentials, and showing how to parameterise these models. We also generalise this new integrated style of potential by introducing a segmental Lennard-Jones potential, which enables modelling both attractive and repulsive interactions in semi-flexible polymer networks. These results can be further generalised to facilitate the development of effective interaction potentials for other finite elements in simulations of softmatter systems.
DOI: 10.25345/c51z9w
title: MassIVE MSV000088482 - CETSA MS melt curve dataset of Arabidopsis thaliana
title: CETSA MS melt curve dataset of Arabidopsis thaliana. Two replicates per condition, i.e DMSO and treated samples, each ran in a TMT10 plex in a temperature gradient of 25-70 degrees Celsius
DOI: 10.5517/ccdc.csd.cc28hl3h
title: CCDC 2100346: Experimental Crystal Structure Determination

description: Related Article: Jackson S. Henneveld, Selena C. L. Gilmer, Nigel T. Lucas, Bill C. Hawkins|2021|Asian J.Org.Chem|10|2553|doi:10.1002/ajoc.202100500
DOI: 10.5281/zenodo.5746114
title: Wikidata Dump

description: RDF dump of wikidata produced with wdumps. <br> View on wdumper <b>entity count</b>: 0, <b>statement count</b>: 0, <b>triple count</b>: 0
DOI: 10.5281/zenodo.5746113
title: Wikidata Dump

description: RDF dump of wikidata produced with wdumps. <br> View on wdumper <b>entity count</b>: 0, <b>statement count</b>: 0, <b>triple count</b>: 0
DOI: 10.6073/pasta/0a8c468823bef79b515c6d2db181b114
title: Primary Production Data for lakes and lake inlets/outlets samples collected summer 2000, Arctic LTER, Toolik Research Station, Alaska

description: This file has been updated and combined in a multi-year file. See: Giblin, A., Kling, G. 1992. Chlorophyll a and primary productivity data for various lakes near Toolik Research Station, Arctic LTER. Summer 2000 to 2009. Environmental Data Initiative. http://dx.doi.org/10.6073/pasta/c14fe6e5bb0e2a2c6a74d51a6943c667Yearly Yearly file detailing rates of primary production in various surface waters near Toolik Research Station (68 38'N, 149 36'W). Sample site descriptors include an assigned number (sortchem), site, date, time, depth. Dates of analysis (incubation), and rates of primary production are also included.
DOI: 10.6073/pasta/c3350f2ba7c0ed8c9a02b381d11a60df
title: Primary Production Data for lakes and lake inlets/outlets samples collected summer 2005, Arctic LTER, Toolik Research Station, Alaska

description: This file has been updated and combined in a multi-year file. See: Giblin, A., Kling, G. 1992. Chlorophyll a and primary productivity data for various lakes near Toolik Research Station, Arctic LTER. Summer 2000 to 2009. Environmental Data Initiative. http://dx.doi.org/10.6073/pasta/c14fe6e5bb0e2a2c6a74d51a6943c667Yearly Yearly file detailing rates of primary production in various surface waters near Toolik Research Station (68 38'N, 149 36'W). Sample site descriptors include an assigned number (sortchem), site, date, time, depth. Dates of analysis (incubation), and rates of primary production are also included.
DOI: 10.6073/pasta/2d02b7227b5f0a0b24ec1a30e539ea3f
title: Primary Production Data for lakes and lake inlets/outlets samples collected summer 2001, Arctic LTER, Toolik Research Station, Alaska

description: This file has been updated and combined in a multi-year file. See: Giblin, A., Kling, G. 1992. Chlorophyll a and primary productivity data for various lakes near Toolik Research Station, Arctic LTER. Summer 2000 to 2009. Environmental Data Initiative. http://dx.doi.org/10.6073/pasta/c14fe6e5bb0e2a2c6a74d51a6943c667Yearly Yearly file detailing rates of primary production in various surface waters near Toolik Research Station (68 38'N, 149 36'W). Sample site descriptors include an assigned number (sortchem), site, date, time, depth. Dates of analysis (incubation), and rates of primary production are also included.
DOI: 10.6073/pasta/58c04c752406dd7d99fd3857ad0cf3a1
title: Primary Production Data for lakes and lake inlets/outlets samples collected summer 2002, Arctic LTER, Toolik Research Station, Alaska

description: This file has been updated and combined in a multi-year file. See: Giblin, A., Kling, G. 1992. Chlorophyll a and primary productivity data for various lakes near Toolik Research Station, Arctic LTER. Summer 2000 to 2009. Environmental Data Initiative. http://dx.doi.org/10.6073/pasta/c14fe6e5bb0e2a2c6a74d51a6943c667Yearly Yearly file detailing rates of primary production in various surface waters near Toolik Research Station (68 38'N, 149 36'W). Sample site descriptors include an assigned number (sortchem), site, date, time, depth. Dates of analysis (incubation), and rates of primary production are also included.
DOI: 10.6073/pasta/b9fa474f6e3ba19e82df45a32b3b3106
title: Primary Production Data for lakes and lake inlets/outlets samples collected summer 2007, Arctic LTER, Toolik Research Station, Alaska

description: This file has been updated and combined in a multi-year file. See: Giblin, A., Kling, G. 1992. Chlorophyll a and primary productivity data for various lakes near Toolik Research Station, Arctic LTER. Summer 2000 to 2009. Environmental Data Initiative. http://dx.doi.org/10.6073/pasta/c14fe6e5bb0e2a2c6a74d51a6943c667 file detailing rates of primary production in various surface waters near Toolik Research Station (68 38'N, 149 36'W). Sample site descriptors include an assigned number (sortchem), site, date, time, depth. Dates of analysis (incubation), and rates of primary production are also included.
DOI: 10.6073/pasta/ef144ce05767cc0d4c5884c8c8ac4c88
title: Primary Production Data for lakes and lake inlets/outlets samples collected summer 2003, Arctic LTER, Toolik Research Station, Alaska

description: This file has been updated and combined in a multi-year file. See: Giblin, A., Kling, G. 1992. Chlorophyll a and primary productivity data for various lakes near Toolik Research Station, Arctic LTER. Summer 2000 to 2009. Environmental Data Initiative. http://dx.doi.org/10.6073/pasta/c14fe6e5bb0e2a2c6a74d51a6943c667Yearly Yearly file detailing rates of primary production in various surface waters near Toolik Research Station (68 38'N, 149 36'W). Sample site descriptors include an assigned number (sortchem), site, date, time, depth. Dates of analysis (incubation), and rates of primary production are also included.
DOI: 10.6073/pasta/9ee2a3713b5946d30819971a2ce7a81a
title: Primary Production Data for lakes and lake inlets/outlets samples collected summer 2006, Arctic LTER, Toolik Research Station, Alaska

description: This file has been updated and combined in a multi-year file. See: Giblin, A., Kling, G. 1992. Chlorophyll a and primary productivity data for various lakes near Toolik Research Station, Arctic LTER. Summer 2000 to 2009. Environmental Data Initiative. http://dx.doi.org/10.6073/pasta/c14fe6e5bb0e2a2c6a74d51a6943c667Yearly Yearly file detailing rates of primary production in various surface waters near Toolik Research Station (68 38'N, 149 36'W). Sample site descriptors include an assigned number (sortchem), site, date, time, depth. Dates of analysis (incubation), and rates of primary production are also included.
DOI: 10.5281/zenodo.5747200
title: Dataset related to the article: Exercise Intolerance and Oxygen Desaturation in Patients with Parkinson's Disease: Triggers for Respiratory Rehabilitation?

description: Dataset related to the article: Vitacca, M.; Olivares, A.; Comini, L.; Vezzadini, G.; Langella, A.; Luisa, A.; Petrolati, A.; Frigo, G.; Paneroni, M. Exercise Intolerance and Oxygen Desaturation in Patients with Parkinson’s Disease: Triggers for Respiratory Rehabilitation? <em>Int. J. Environ. Res. Public Health</em> <strong>2021</strong>, <em>18</em>, 12298. Abstract: The role that oxygen desaturation plays in exercise tolerance and its rehabilitative implications<br> in patients with Parkinson’s disease (PD) are unclear. We aimed to test exercise tolerance and<br> oxygen saturation levels both during exercise and at night in PD patients to better define their rehabilitative<br> needs. In clinically stable PD patients, undergoing inpatient rehabilitation, and in “ON” phase,<br> we prospectively assessed clinical data, sleepiness, comorbidities, PD severity (Hoehn&Yahr, HY),<br> motor function (ADLs, UPDRSII and UPDRSIII, Barthel Index, Functional Independence Measure),<br> balance, spirometry, respiratory muscles (MIP/MEP), peak cough expiratory flow (PCEF), continuous<br> night oxygen monitoring, and meters at 6MWT. Of 55 patients analyzed (28 with moderate–severe PD,<br> HY 2.5), 37% and 23% showed moderate–severe impairment on UPDRSII and UPDRSIII, respectively;<br> 96% had reduced exercise tolerance and severe respiratory muscles impairment (MIP/MEP<br> &lt; 45% pred.); 21.8% showed desaturations during exercise; and 12.7% showed nocturnal desaturations.<br> At multiple regression, low exercise tolerance and low mean nocturnal and exercise-induced<br> saturation correlated with several respiratory and motor function and disability indices (all p &lt;<br> 0.03). Exercise tolerance, exercise-induced desaturations, and nocturnal desaturations were extremely<br> frequent in PD patients and were worse in more severe PD patients. This suggests considering a<br> combined role for motor and respiratory rehabilitation in these patients.