cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.14333381
title: Supplementary Material for: MASP-1 and MASP-3 Bind Directly to <b><i>Aspergillus fumigatus</i></b> and Promote Complement Activation and Phagocytosis

description: Activation of the complement system is mediated by the interaction between pathogens and pattern recognition molecules (PRMs); mannose-binding lectin (MBL), ficolins, and collectin-10/-11 from the lectin pathway and C1q from the classical pathway. Lectin pathway activation specifically depends on proteases named MBL-associated serine proteases (MASPs) that are found in complexes with PRMs. In this study, we hypothesize that MASPs can recognize selected pathogens independently of PRMs. Using different clinical strains of opportunistic fungi, we have observed that MASPs directly recognize certain fungal pathogens in a way that can facilitate complement activation. Among these were <i>Aspergillus fumigatus</i> – a dangerous pathogen, especially for immunocompromised patients. In flow cytometry and fluorescence microscopy, we found that MASP-1 and -3 bound to all <i>A. fumigatus</i> growth stages (conidia, germ tubes, and hyphae), whereas rMASP-2 and the nonproteolytic rMAP-1 did not. Bound rMASPs could recruit rMBL and rficolin-3 to <i>A. fumigatus</i> conidia in a nonclassical manner and activate complement via rMASP-2. In experiments using recombinant and purified components, rMASP-1 increased the neutrophilic phagocytosis of conidia. In serum where known complement activation pathways were blocked, phagocytosis could be mediated by rMASP-3. We have encountered an unknown pathway for complement activation and found that MASP-1 and MASP-3 have dual functions as enzymes and as PRMs.
DOI: 10.15468/y3mkt2
title: Taxonomy of the genus Duolandrevus Kirby, 1906 (Orthoptera: Gryllidae; Landrevinae) from China with a new species of the subgenus Eulandrevus Gorochov, 1988

description: This dataset contains the digitized treatments in Plazi based on the original journal article Zheng, Yanna, Ma, Libin (2021): Taxonomy of the genus Duolandrevus Kirby, 1906 (Orthoptera: Gryllidae; Landrevinae) from China with a new species of the subgenus Eulandrevus Gorochov, 1988. Zootaxa 4942 (2): 252-268, DOI: https://doi.org/10.11646/zootaxa.4942.2.7
DOI: 10.25392/leicester.data.7636268
title: Protein preference and photometry I

description: These data files are from an experiment investigating protein preference behaviour and associated neural activity in ventral tegmental area.<br>Data files are acquired via Tucker Davis Tech. hardware and represent fluorescent signals recorded in a fibre photometry experiment with associated timestamps showing licking behaviour and sipper presentation. Full description of the methods is published on bioRxiv (https://www.biorxiv.org/content/10.1101/542340v3).<br>The raw data files from TDT which include all signals and videos are archived in three 7zip-compressed files - PPP1_tdtfiles.7z, PPP3_tdtfiles.7z, and PPP4_tdtfiles.7z - and require the accompanying .xlsx metafiles to know details of each file (e.g. rat ID, dietary condition etc).<br>Partially analysed files (.pickle) in which signals have been aligned to behavioural events of interest and all cohorts of rats are combined are also provided and can be imported into Python using the dill module.<br>Finally, the pandas dataframes used to make all figures and perform stats are also included as .pickle files, which is the smallest and easiest to download (e.g. ppp_dfs_pref.pickle). These dataframes are also available from the following link: http://www.mccutcheonlab.com/s/data.zip<br>All analysis scripts for this dataset can be found on Github (https://github.com/mccutcheonlab/PPP_analysis).<br>
DOI: 10.25392/leicester.data.7636268.v1
title: Protein preference and photometry I

description: These data files are from an experiment investigating protein preference behaviour and associated neural activity in ventral tegmental area.<br>Data files are acquired via Tucker Davis Tech. hardware and represent fluorescent signals recorded in a fibre photometry experiment with associated timestamps showing licking behaviour and sipper presentation. Full description of the methods is published on bioRxiv (https://doi.org/10.1101/542340).<br>The raw data files from TDT which include all signals and videos are archived in two 7zip-compressed files - PPP1_tdtfiles.7z and PPP3_tdtfiles.7z - and require the accompanying .xls workbooks to know details of each file (e.g. rat ID, dietary condition etc).<br>Files in which data streams and timestamps have been extracted into Matlab (.mat) files are also provided - PPP1_matfiles.7z and PPP3_matfiles.7z - and are considerably less bulky.<br>Partially analysed files (.pickle) in which signals have been aligned to behavioural events of interest and both cohorts of rats are combined are also provided and can be imported into Python using the dill module.<br>Finally, the pandas dataframes used to make all figures and perform stats are also included as a .pickle file, which is the smallest and easiest to download (ppp_dfs_pref.pickle).<br>All analysis scripts for this dataset can be found on Github (https://github.com/mccutcheonlab/PPP_analysis/tree/Submission1 and https://github.com/mccutcheonlab/tdt-convert).<br>
DOI: 10.5281/zenodo.4644182
title: The Association between BMI self-selection, self-reported BMI and objectively measured BMI

description: <strong><em>Background</em></strong> It is challenging to measure BMI accurately in population studies because it is an expensive and time-consuming task. As a result, subjectively measured BMI, calculated from self-reported height and weight, is often used which we know to be inaccurate. The purpose of this study is to determine whether using a different, subjective method of measuring BMI, BMI self-selection, would be more accurate. BMI self-selection is determined by asking participants to place themselves in one of the BMI categories, underweight, normal weight, overweight or obese. <strong><em>Methods</em></strong> A quantitative survey with the addition of open-ended questions conducted in the outpatient departments of two hospitals in the South West of Ireland. Participants &gt;18 years were included. Pregnant women were excluded. The final sample included 70 subjects. Survey completion, including self-reported height and weight and BMI self-selection, preceded the objectively measured weight and height using calibrated SECA scales and stadiometer. Demographic and lifestyle factors were also recorded. <strong><em>Results</em></strong> 59% of the sample were overweight or obese – 54% of males and 63% of females. The sensitivity for correct BMI self-selection for normal weight, overweight and obese categories was 90%, 36% and 33% respectively. The sensitivity for BMI categories calculated from self-reported height and weight was 83%, 57% and 59% respectively. In analyses, age, regular alcohol consumption, unhealthy diet and lower levels of physical activity were all associated with underestimation of BMI. <strong><em>Conclusion</em></strong> BMI self-selection is an accurate tool when used with normal weight individuals but shows poorer ability to demonstrate accurate measurement in overweight and obese BMI categories. It is inferior to the traditional self-reported BMI method for measuring BMI levels in the general population. Presently, we recommend continuing with self-reported BMI for BMI measurement in large population studies. However, further testing of BMI classification in larger studies is suggested and investigation into alternative objective methods of measurement is warranted.
DOI: 10.5281/zenodo.4633931
title: The Association between BMI self-selection, self-reported BMI and objectively measured BMI

description: <strong><em>Background</em></strong> It is challenging to measure BMI accurately in population studies because it is an expensive and time-consuming task. As a result, subjectively measured BMI, calculated from self-reported height and weight, is often used which we know to be inaccurate. The purpose of this study is to determine whether using a different, subjective method of measuring BMI, BMI self-selection, would be more accurate. BMI self-selection is determined by asking participants to place themselves in one of the BMI categories, underweight, normal weight, overweight or obese. <strong><em>Methods</em></strong> A quantitative survey with the addition of open-ended questions conducted in the outpatient departments of two hospitals in the South West of Ireland. Participants &gt;18 years were included. Pregnant women were excluded. The final sample included 70 subjects. Survey completion, including self-reported height and weight and BMI self-selection, preceded the objectively measured weight and height using calibrated SECA scales and stadiometer. Demographic and lifestyle factors were also recorded. <strong><em>Results</em></strong> 59% of the sample were overweight or obese – 54% of males and 63% of females. The sensitivity for correct BMI self-selection for normal weight, overweight and obese categories was 90%, 36% and 33% respectively. The sensitivity for BMI categories calculated from self-reported height and weight was 83%, 57% and 59% respectively. In analyses, age, regular alcohol consumption, unhealthy diet and lower levels of physical activity were all associated with underestimation of BMI. <strong><em>Conclusion</em></strong> BMI self-selection is an accurate tool when used with normal weight individuals but shows poorer ability to demonstrate accurate measurement in overweight and obese BMI categories. It is inferior to the traditional self-reported BMI method for measuring BMI levels in the general population. Presently, we recommend continuing with self-reported BMI for BMI measurement in large population studies. However, further testing of BMI classification in larger studies is suggested and investigation into alternative objective methods of measurement is warranted.
DOI: 10.6084/m9.figshare.14333423
title: Supplementary Material for: Use of Composite Outcomes in Neonatal Trials: An Analysis of the Cochrane Reviews

description: <b><i>Introduction:</i></b> Composite outcomes are used to increase the power of a study by combining event rates. Many composite outcomes in adult clinical trials have components that differ substantially in patient importance, event rate, and effect size, making interpretation challenging. Little is known about the use of composite outcomes in neonatal randomized controlled trials (RCTs). <b><i>Methods:</i></b> We assessed the use of composite outcomes in neonatal RCTs included in Cochrane Neonatal reviews published till November 2017. Two authors reviewed the components of the composite outcomes to compare their patient importance and computed the ratios of effect sizes and event rates between the components, with an a priori threshold of 1.5, indicating a substantial difference. Descriptive statistics were presented. <b><i>Results:</i></b> We extracted 7,766 outcomes in 2,134 RCTs in 312 systematic reviews. Among them, 55 composite outcomes (0.7%) were identified in 46 RCTs. The vast majority (92.7%) of composite outcomes had 2 components, with death being the most common component (included 51 times [92.7%]). The components in nearly three-quarters of the composite outcomes (<i>n</i> = 40 [72.7%]) had different patient importance, while the effect sizes and event rates differed substantially between the components in 27 (49.1%) and 35 (63.6%) outcomes, respectively, with up to 43-fold difference in the event rates observed. <b><i>Conclusions:</i></b> The majority of composite outcomes in neonatal RCTs had different patient importance with contrasting effect sizes and event rates between the components. In patient communication, clinicians should highlight individual components, rather than the composites, with explanation on the relationship between the components, to avoid misleading impression on the effect of the intervention. Future trials should report the estimates of all individual components alongside the composite outcomes presented.
DOI: 10.6084/m9.figshare.14333423.v1
title: Supplementary Material for: Use of Composite Outcomes in Neonatal Trials: An Analysis of the Cochrane Reviews

description: <b><i>Introduction:</i></b> Composite outcomes are used to increase the power of a study by combining event rates. Many composite outcomes in adult clinical trials have components that differ substantially in patient importance, event rate, and effect size, making interpretation challenging. Little is known about the use of composite outcomes in neonatal randomized controlled trials (RCTs). <b><i>Methods:</i></b> We assessed the use of composite outcomes in neonatal RCTs included in Cochrane Neonatal reviews published till November 2017. Two authors reviewed the components of the composite outcomes to compare their patient importance and computed the ratios of effect sizes and event rates between the components, with an a priori threshold of 1.5, indicating a substantial difference. Descriptive statistics were presented. <b><i>Results:</i></b> We extracted 7,766 outcomes in 2,134 RCTs in 312 systematic reviews. Among them, 55 composite outcomes (0.7%) were identified in 46 RCTs. The vast majority (92.7%) of composite outcomes had 2 components, with death being the most common component (included 51 times [92.7%]). The components in nearly three-quarters of the composite outcomes (<i>n</i> = 40 [72.7%]) had different patient importance, while the effect sizes and event rates differed substantially between the components in 27 (49.1%) and 35 (63.6%) outcomes, respectively, with up to 43-fold difference in the event rates observed. <b><i>Conclusions:</i></b> The majority of composite outcomes in neonatal RCTs had different patient importance with contrasting effect sizes and event rates between the components. In patient communication, clinicians should highlight individual components, rather than the composites, with explanation on the relationship between the components, to avoid misleading impression on the effect of the intervention. Future trials should report the estimates of all individual components alongside the composite outcomes presented.
DOI: 10.17028/rd.lboro.14333447
title: Supplementary information files for Elucidating the electronic structure of a delayed fluorescence emitter via orbital interactions, excitation energy components, charge-transfer numbers, and vibrational reorganization energies

description: Supplementary files for article Elucidating the electronic structure of a delayed fluorescence emitter via orbital interactions, excitation energy components, charge-transfer numbers, and vibrational reorganization energies. Recently, Wang and co-workers carried out frontier molecule orbital engineering in the design of m-Cz-BNCz, a thermally activated delayed fluorescence (TADF) molecule that emits pure green light at an external quantum efficiency of 27%. To further understand the underlying molecular design principles, we employed four advanced electronic structure analysis tools. First, an absolutely localized molecular orbitals (ALMO-) based analysis indicates an antibonding combination between the highest occupied molecular orbitals (HOMOs) of the donor 3,6-di-tert-butylcarbazole fragment and the acceptor BNCz fragment, which raises the HOMO energy and red-shifts the fluorescence emission wavelength. Second, excitation energy component analysis reveals that the S<sub>1</sub>-T<sub>1</sub> gap is dominated by two-electron components of the excitation energies. Third, charge transfer number analysis, which is extended to use fragment-based Hirshfeld weights, indicates that the S<sub>1</sub> and T<sub>1</sub> excited states of m-Cz-BNCz (within time-dependent density functional theory) have notable charge transfer characters (27% for S<sub>1</sub> and 12% for T<sub>1</sub>). This provides a balance between a small single-triplet gap and a substantial fluorescence intensity. Last, a vibrational reorganization energy analysis pinpoints the torsional motion between the BNCz and Cz moieties of m-Cz-BNCz as the source for its wider emission peak than that of p-Cz-BNCz. These four types of analyses are expected to be very valuable in the study and design of other TADF and functional dye molecules.
DOI: 10.17028/rd.lboro.14333447.v1
title: Supplementary information files for Elucidating the electronic structure of a delayed fluorescence emitter via orbital interactions, excitation energy components, charge-transfer numbers, and vibrational reorganization energies

description: Supplementary files for article Elucidating the electronic structure of a delayed fluorescence emitter via orbital interactions, excitation energy components, charge-transfer numbers, and vibrational reorganization energies. Recently, Wang and co-workers carried out frontier molecule orbital engineering in the design of m-Cz-BNCz, a thermally activated delayed fluorescence (TADF) molecule that emits pure green light at an external quantum efficiency of 27%. To further understand the underlying molecular design principles, we employed four advanced electronic structure analysis tools. First, an absolutely localized molecular orbitals (ALMO-) based analysis indicates an antibonding combination between the highest occupied molecular orbitals (HOMOs) of the donor 3,6-di-tert-butylcarbazole fragment and the acceptor BNCz fragment, which raises the HOMO energy and red-shifts the fluorescence emission wavelength. Second, excitation energy component analysis reveals that the S<sub>1</sub>-T<sub>1</sub> gap is dominated by two-electron components of the excitation energies. Third, charge transfer number analysis, which is extended to use fragment-based Hirshfeld weights, indicates that the S<sub>1</sub> and T<sub>1</sub> excited states of m-Cz-BNCz (within time-dependent density functional theory) have notable charge transfer characters (27% for S<sub>1</sub> and 12% for T<sub>1</sub>). This provides a balance between a small single-triplet gap and a substantial fluorescence intensity. Last, a vibrational reorganization energy analysis pinpoints the torsional motion between the BNCz and Cz moieties of m-Cz-BNCz as the source for its wider emission peak than that of p-Cz-BNCz. These four types of analyses are expected to be very valuable in the study and design of other TADF and functional dye molecules.
DOI: 10.5286/isis.e.rb2010240-2
title: Investigation of magnetism in layered two-dimensional triangular lattice oxide LixCoO2

description: The compound LiCoO2 has attracted lots of attention in the recent years because of its application in Li-ion batteries. Investigation of the magnetism in LixCoO2, using the single crystals have not been reported thus far. The crystal structure contains CoO2 layers arranged on a 2D triangular lattice. The presence of antiferromagentic interaction between the magnetic Co ions is expected to give rise to a geometrical frustration (due to the triangular geometry) and novel magnetic states are expected. For both samples, an anomaly in the dc susceptibility measurements is observed around 50 K indicating the onset of a long-range magnetic order. We propose to carry out neutron diffraction experiments on single crystal of LixCoO2 (x = 0.7 and 0.9) to investigate the nature of spin correlations and measure diffuse magnetic scattering to get the information about short-range magnetic order.
DOI: 10.25345/c5sr54
title: MassIVE MSV000087122 - Analysis of four natural resins from trees
title: LC-MS based untargeted metabolomics analysis of natural resins
DOI: 10.5281/zenodo.4643774
title: Fluorescence lifetime imaging of pH along the secretory pathway

description: Many cellular processes are dependent on correct pH levels, and this is especially important for the secretory pathway. Defects in pH homeostasis in distinct organelles cause a wide range of diseases, including disorders of glycosylation and lysosomal storage diseases. Ratiometric imaging of the pH-sensitive mutant of green fluorescent protein (GFP), pHLuorin, has allowed for targeted pH measurements in various organelles, but the required sequential image acquisition is intrinsically slow and therefore the temporal resolution unsuitable to follow the rapid transit of cargo between organelles. We therefore applied fluorescence lifetime imaging microscopy (FLIM) to measure intraorganellar pH with just a single excitation wavelength. We first validated this method by confirming the pH in multiple compartments along the secretory pathway. Then, we analyze the dynamic pH changes within cells treated with Brefeldin A, a COPI coat inhibitor. Finally, we followed the pH changes of newly-synthesized molecules of the inflammatory cytokine tumor necrosis factor (TNF)-α while it was in transit from the endoplasmic reticulum via the Golgi to the plasma membrane. The toolbox we present here can be applied to measure intracellular pH with high spatial and temporal resolution, and can be used to assess organellar pH in disease models.
description: G.v.d.B. is funded by a Young Investigator Grant from the Human Frontier Science Program (HFSP; RGY0080/2018) and a Vidi grant from the Netherlands Organisation for Scientific Research (NWO-ALW VIDI 864.14.001). G.v.d.B has also received funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program (grant agreement No. 862137).
DOI: 10.5281/zenodo.4611465
title: SORTIE MIVM Level 2

description: SORTIE IVM Level 2 data
DOI: 10.21227/1k16-vy42
title: Forecast Result for January 31

description: This csv file contains the load forecasts results on Jan.-31, conducted by Hongqiao Peng.
DOI: 10.5281/zenodo.4644290
title: Prevalence of comorbidities associated with type 2 diabetes in patients attending a disease management program, Medellín, Colombia 2014 - 2019: a descriptive study.

description: Table containing anonymized information about prevalence de comorbidities of diabetes type 2, patients attended in a diseases management program of diabetes, Medellín, Colombia 2014 - 2019.
DOI: 10.5281/zenodo.4644289
title: Prevalence of comorbidities associated with type 2 diabetes in patients attending a disease management program, Medellín, Colombia 2014 - 2019: a descriptive study.

description: Table containing anonymized information about prevalence de comorbidities of diabetes type 2, patients attended in a diseases management program of diabetes, Medellín, Colombia 2014 - 2019.
DOI: 10.5281/zenodo.4643907
title: Which RESTful API Design Rules are Important and How Do They Improve Software Quality? A Delphi Study with Industry Experts

description: The dataset of a Delphi study with 8 industry experts who reached consensus on the perceived importance and positive software quality impact of 82 RESTful API design rules from the catalogue by Mark Massé ("REST API Design Rulebook", O’Reilly Media, 2011). The replication package contains: <strong>rules.csv:</strong> the final consensus results for the 82 rules in CSV format <strong>rule-importance.xlsx</strong>: the detailed results and analysis for rule importance as an Excel spreadsheet <strong>rule-sw-quality-impact.xlsx</strong>: the detailed results and analysis for rule impact on software quality as an Excel spreadsheet
DOI: 10.6084/m9.figshare.12656165.v13
title: COVID-19 Case Reports in China

description: Chinese prefectural level governments started to report daily confirmed COVID-19 cases online, starting from January 2020. The disclosures may contain the mobility, potential exposure scenario, epidemiological characteristics, and other useful information of individual cases. We organized a group of content coders since early March 2020, kept monitoring the information updates, manually extracted useful information from the public disclosures, and compiled these datasets.We welcome any form of collaborations with us and non-commercial reuse of our dataset. We highly encourage interested parties to examine the data, report errors in our coding, and help us to keep the data updated.The detailed data description can be found on SSRN preprint server https://dx.doi.org/10.2139/ssrn.3705815.