cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.9585275.v1
title: Interaction_test_reQTL_Monocytes.txt

description: These files contain the summary statistics of the eQTL analysis in the manuscript titled “Neonatal genetics of gene expression reveal the origins of autoimmune and allergic disease risk”. Read https://www.biorxiv.org/content/10.1101/683086v1for detailed methods. The four files named with “Full_summary_stat_eQTL” contains full summary statistics of eQTL analysis in the following four experimental conditions: resting monocytes, LPS-stimulated monocytes, resting T cells, and PHA-stimulated T cells. The statistics were calculated using the <i>Matrix eQTL</i>R package. Significant eGenes are listed in Table S1–4. The two files named with “Interaction_test_reQTL” contains fulll summary statistics of the interaction tests used for response eQTL (reQTL) detection in monocytes and in T cells. Significant reQTLs (FDR ≤0.05) are listed in Table S7–8. Table legend is similar to that for Table S7–8.
DOI: 10.6084/m9.figshare.9585410.v2
title: Data for "Characterization of the Airflow within an Average Geometry of the Healthy Human Nasal Cavity?"

description: This repository contains the data described in the manuscript "Characterization of the Airflow within an Average Geometry of the Healthy Human Nasal Cavity?" published in Nature Scientific Reports (doi: will be added when available).An extensive description of the published data is given in the readme.txt.<br>- Average geometry of the healthy nasal cavity: The average geometry of the healthy nasal cavity generated using the statistical shape model described in the manuscript is provided in two file formats. An .stl-file with ASCII encoding and a .surf-file in ASCII encoding. The formatting of the latter file is specified in the readme file.<br>- Individual wall-bound distributions: All 25 patient-specific distributions of the wall shear stress and static pressure that were calculated during inspiration and expiraton respectively are made available via the individualDistributions.zip archive. All individual files are written in as ASCII files. More details regarding the formatting of those files is given in the readme file.<br>- Average Distributions: The averages of the individual distributions are made available via the averageDistributions.zip archive.<br>- SSM Distributions: The distributions of wall shear stresses and static pressure calculated for the average geometry during inspiration and expiration are made available via the SSMDistributions.zip archive.<br>- Integral measures: A table containing all integral measures calculated and reported within the manuscript can be found in the Excel file "integralMeasures_healthySubjects.xlsx".<br>- MATLAB Files for Data Processing: MATLAB functions for reading the surface and data files are made available via the MATLAB_readAMIRA.zip archive.<br>- data that might be added later: We are currently discussing whether we are allowed to publish the patient-specific geometries. If we get the required permissions, this data will also be added. <br><br>If any additional data is required or if you have questions regarding the data, don't hestitate to ask.<br><br><br>
DOI: 10.6084/m9.figshare.9584744
title: Malignant lymphoma in granulomatosis with polyangiitis: subtypes, clinical characteristics and prognosis

description: Malignant lymphoma in granulomatosis with polyangiitis: subtypes, clinical characteristics and prognosis
DOI: 10.6084/m9.figshare.9584828
title: CSSS Participant Data—Cleaned and Anonymized

description: A cleaned and anonymized version of participant data collected for analysis of collaboration of the history of the Santa Fe Institute's Summer School in Complex Systems<br>
DOI: 10.6084/m9.figshare.9584828.v1
title: CSSS Participant Data—Cleaned and Anonymized

description: A cleaned and anonymized version of participant data collected for analysis of collaboration of the history of the Santa Fe Institute's Summer School in Complex Systems<br>
DOI: 10.6084/m9.figshare.9584744.v1
title: Malignant lymphoma in granulomatosis with polyangiitis: subtypes, clinical characteristics and prognosis

description: Malignant lymphoma in granulomatosis with polyangiitis: subtypes, clinical characteristics and prognosis
DOI: 10.6084/m9.figshare.9585410.v3
title: Data for "Characterization of the Airflow within an Average Geometry of the Healthy Human Nasal Cavity?"

description: This repository contains the data described in the manuscript "Characterization of the Airflow within an Average Geometry of the Healthy Human Nasal Cavity?" published in Nature Scientific Reports (doi: will be added when available).An extensive description of the published data is given in the readme.txt.<br>- Average geometry of the healthy nasal cavity: The average geometry of the healthy nasal cavity generated using the statistical shape model described in the manuscript is provided in two file formats. An .stl-file with ASCII encoding and a .surf-file in ASCII encoding. The formatting of the latter file is specified in the readme file.<br>- Individual wall-bound distributions: All 25 patient-specific distributions of the wall shear stress and static pressure that were calculated during inspiration and expiraton respectively are made available via the individualDistributions.zip archive. All individual files are written in as ASCII files. More details regarding the formatting of those files is given in the readme file.<br>- Average Distributions: The averages of the individual distributions are made available via the averageDistributions.zip archive.<br>- SSM Distributions: The distributions of wall shear stresses and static pressure calculated for the average geometry during inspiration and expiration are made available via the SSMDistributions.zip archive.<br>- Integral measures: A table containing all integral measures calculated and reported within the manuscript can be found in the Excel file "integralMeasures_healthySubjects.xlsx".<br>- MATLAB Files for Data Processing: MATLAB functions for reading the surface and data files are made available via the MATLAB_readAMIRA.zip archive.<br>- data that might be added later: We are currently discussing whether we are allowed to publish the patient-specific geometries. If we get the required permissions, this data will also be added. <br><br>If any additional data is required or if you have questions regarding the data, don't hestitate to ask.<br><br><br>
DOI: 10.6084/m9.figshare.9582962
title: Monitored data on occupants’ presence and actions in an office building (dataset)

description: The present contribution includes occupant presence and behaviour data along with indoor and outdoor environmental data monitored over a period of one year (from 2013-01-01 to 2013-12-31) in an office area of around 200 square meter in a university building in Vienna. Specifically, the data set includes the following: 1. Presence at work station [0:vacant, 1:occupied]2. Window state [0:open, 1:closed]3. Light state [0:off, 1:on]4. Equipment power [W]5. Indoor air temperature [°C]6. Indoor air relative humidity [%]7. Global radiation [W.m-2]8. Air temperature [°C]9. Air relative humidity [%]10. Wind speed [m.s-1]11. Wind direction [degree]<br>Occupant behaviour data and indoor environmental data streams (items 1-6) are stored in 15-min time intervals. Outdoor environmental data streams (items 7-11) are stored in hourly intervals.
DOI: 10.6084/m9.figshare.9582674
title: Supplementary Material for: Sahamalaza Sportive Lemur, <b><i>Lepilemur sahamalaza</i></b>, Vocal Communication: Call Use, Context and Gradation

description: Stereotypical vocalisations can facilitate long-distance communication in dense and, thus, sound-degrading forest habitats. Despite this, primate vocal repertoires often also include gradations between different call types that are used in social interactions. Because many nocturnal primates show a solitary social structure, it has been difficult to assess the role vocalisations play in mediating their social encounters. Here we aim to expand on the call types of Sahamalaza sportive lemurs, <i>Lepilemur sahamalaza</i>, as well as investigate their variability and use in social contexts. Through long-term behavioural observations with concurrent recording of vocalisations of known and unknown individuals between 2015 and 2016, we described three previously unrecorded calls and expanded the vocal repertoire to 12 different call types that were used in both targeted social and broadcast solitary contexts. Linear discriminant function and cluster analysis supported initial observations that vocalisations within call types were variable and that at least two call types can be classified as “graded,” contrary to expectations. Despite variations in call-context connections, no clear patterns of call use could be established. However, measurable differences in vocal behaviour between the seasons and the sexes indicate that calling is used in a reproductive context, similar to other nocturnal and diurnal primates.
DOI: 10.6084/m9.figshare.9580022
title: Supplementary Material for: Ultraviolet Radiation Exposure of One Eye Stimulates Sympathizing Expression of Neurokinin-1 Receptor but Not Monocyte Chemoattractant Protein-1 in the Partner Eye

description: <b><i>Purpose:</i></b> To investigate the influence of unilateral ultraviolet radiation (UVR) exposure on the unexposed, partner eye in vivo. To characterize the immunological cross-talk between the eyes and verify a sympathizing reaction of the partner eye via a neurokinin-dependent signaling pathway of substance P and its neurokinin-1 receptor (NKR-1) and/or monocyte chemoattractant protein-1 (MCP-1). <b><i>Methods:</i></b> C57BL/6 mice were unilaterally exposed in vivo to UVR-B to a 5-fold cataract threshold equivalent dose of 14.5 kJ/m<sup>2</sup> with a UV irradiation Bio-Spectra system. The unexposed contralateral eye was completely shielded during irradiation. After 3 and 7 days post exposure, eyes were stained with fluorescence-coupled antibody for substance P NKR-1. The same was performed in control animals receiving only anesthesia but no UVR-B exposure. NKR-1 and MCP-1 levels in ocular tissue lysates were quantified by enzyme-linked immunosorbent assay. <b><i>Results:</i></b> UVR-B induces NKR-1 upregulation after 3 and 7 days in the exposed and in the unexposed, contralateral mouse eye. NKR-1 protein level was upregulated in the exposed and contralateral iris/ciliary body complex, choroidea and in the contralateral retina as well as in the exposed cornea. MCP-1 levels were elevated in the exposed cornea, iris/ciliary body complex, and aqueous humor but not in contralateral ocular tissues. <b><i>Conclusions:</i></b> UVR-B exposure triggers NKR-1 upregulation not only in the exposed but also in the unexposed, partner eye in various ocular tissues. Following UVR-B exposure, MCP-1 protein levels are upregulated in the exposed eye, but the contralateral side remains unaffected.
DOI: 10.6084/m9.figshare.9580022.v1
title: Supplementary Material for: Ultraviolet Radiation Exposure of One Eye Stimulates Sympathizing Expression of Neurokinin-1 Receptor but Not Monocyte Chemoattractant Protein-1 in the Partner Eye

description: <b><i>Purpose:</i></b> To investigate the influence of unilateral ultraviolet radiation (UVR) exposure on the unexposed, partner eye in vivo. To characterize the immunological cross-talk between the eyes and verify a sympathizing reaction of the partner eye via a neurokinin-dependent signaling pathway of substance P and its neurokinin-1 receptor (NKR-1) and/or monocyte chemoattractant protein-1 (MCP-1). <b><i>Methods:</i></b> C57BL/6 mice were unilaterally exposed in vivo to UVR-B to a 5-fold cataract threshold equivalent dose of 14.5 kJ/m<sup>2</sup> with a UV irradiation Bio-Spectra system. The unexposed contralateral eye was completely shielded during irradiation. After 3 and 7 days post exposure, eyes were stained with fluorescence-coupled antibody for substance P NKR-1. The same was performed in control animals receiving only anesthesia but no UVR-B exposure. NKR-1 and MCP-1 levels in ocular tissue lysates were quantified by enzyme-linked immunosorbent assay. <b><i>Results:</i></b> UVR-B induces NKR-1 upregulation after 3 and 7 days in the exposed and in the unexposed, contralateral mouse eye. NKR-1 protein level was upregulated in the exposed and contralateral iris/ciliary body complex, choroidea and in the contralateral retina as well as in the exposed cornea. MCP-1 levels were elevated in the exposed cornea, iris/ciliary body complex, and aqueous humor but not in contralateral ocular tissues. <b><i>Conclusions:</i></b> UVR-B exposure triggers NKR-1 upregulation not only in the exposed but also in the unexposed, partner eye in various ocular tissues. Following UVR-B exposure, MCP-1 protein levels are upregulated in the exposed eye, but the contralateral side remains unaffected.
DOI: 10.6084/m9.figshare.9579707
title: Fragilaria radians multiplication validation

description: The experimental validation data for the Fragilaria radians intragenic multiplications. For all the candidate genes this includes IDs (according to https://lin.irk.ru/sacus), primers, PCR temperature and whether or not the sequence was successfully amplified, confirmed via amplicon sequencing on PacBio RSII, or found in the transcriptomic data.<br>
DOI: 10.17028/rd.lboro.9579659
title: Information management applied to bioinformatics. Appendices B, C, and D.

description: Appendix B. Stakeholder identification Exercise: • Raw interview data from stakeholder identification. • Analysis of the interviews with potential stakeholders. Appendix C: Raw interview data from Sanger Institute case study. Appendix D: Raw interview data from AstraZeneca case study<br>Abstract:<br>Bioinformatics, the discipline concerned with biological information management is essential in the post-genome era, where the complexity of data processing allows for contemporaneous multi level research including that at the genome level, transcriptome level, proteome level, the metabolome level, and the integration of these -omic studies towards gaining an understanding of biology at the systems level. This research is also having a major impact on disease research and drug discovery, particularly through pharmacogenomics studies. In this study innovative resources have been generated via the use of two case studies. One was of the Research & Development Genetics (RDG) department at AstraZeneca, Alderley Park and the other was of the Pharmacogenomics Group at the Sanger Institute in Cambridge UK. In the AstraZeneca case study senior scientists were interviewed using semi-structured interviews to determine information behaviour through the study scientific workflows. Document analysis was used to generate an understanding of the underpinning concepts and fonned one of the sources of context-dependent information on which the interview questions were based. The objectives of the Sanger Institute case study were slightly different as interviews were carried out with eight scientists together with the use of participation observation, to collect data to develop a database standard for one process of their Pharmacogenomics workflow. The results indicated that AstraZeneca would benefit through upgrading their data management solutions in the laboratory and by development of resources for the storage of data from larger scale projects such as whole genome scans. These studies will also generate very large amounts of data and the analysis of these will require more sophisticated statistical methods. At the Sanger Institute a minimum information standard was reported for the manual design of primers and included in a decision making tree developed for Polymerase Chain Reactions (PCRs). This tree also illustrates problems that can be encountered when designing primers along with procedures that can be taken to address such issues
DOI: 10.6084/m9.figshare.9579707.v1
title: Fragilaria radians multiplication validation

description: The experimental validation data for the Fragilaria radians intragenic multiplications. For all the candidate genes this includes IDs (according to https://lin.irk.ru/sacus), primers, PCR temperature and whether or not the sequence was successfully amplified, confirmed via amplicon sequencing on PacBio RSII, or found in the transcriptomic data.<br>
DOI: 10.17028/rd.lboro.9579659.v1
title: Information management applied to bioinformatics. Appendices B, C, and D.

description: Appendix B. Stakeholder identification Exercise: • Raw interview data from stakeholder identification. • Analysis of the interviews with potential stakeholders. Appendix C: Raw interview data from Sanger Institute case study. Appendix D: Raw interview data from AstraZeneca case study<br>Abstract:<br>Bioinformatics, the discipline concerned with biological information management is essential in the post-genome era, where the complexity of data processing allows for contemporaneous multi level research including that at the genome level, transcriptome level, proteome level, the metabolome level, and the integration of these -omic studies towards gaining an understanding of biology at the systems level. This research is also having a major impact on disease research and drug discovery, particularly through pharmacogenomics studies. In this study innovative resources have been generated via the use of two case studies. One was of the Research & Development Genetics (RDG) department at AstraZeneca, Alderley Park and the other was of the Pharmacogenomics Group at the Sanger Institute in Cambridge UK. In the AstraZeneca case study senior scientists were interviewed using semi-structured interviews to determine information behaviour through the study scientific workflows. Document analysis was used to generate an understanding of the underpinning concepts and fonned one of the sources of context-dependent information on which the interview questions were based. The objectives of the Sanger Institute case study were slightly different as interviews were carried out with eight scientists together with the use of participation observation, to collect data to develop a database standard for one process of their Pharmacogenomics workflow. The results indicated that AstraZeneca would benefit through upgrading their data management solutions in the laboratory and by development of resources for the storage of data from larger scale projects such as whole genome scans. These studies will also generate very large amounts of data and the analysis of these will require more sophisticated statistical methods. At the Sanger Institute a minimum information standard was reported for the manual design of primers and included in a decision making tree developed for Polymerase Chain Reactions (PCRs). This tree also illustrates problems that can be encountered when designing primers along with procedures that can be taken to address such issues
DOI: 10.6084/m9.figshare.9578318
title: Supplementary Material for: Effectiveness of Combined External Ventricular Drainage with Intraventricular Fibrinolysis for the Treatment of Intraventricular Haemorrhage with Acute Obstructive Hydrocephalus

description: <b><i>Background:</i></b> Intraventricular haemorrhage (IVH) patients with acute obstructive hydrocephalus (AOH) who require external ventricular drainage (EVD) are at high risk for poor outcomes. Intraventricular fibrinolysis (IVF) with low-dose recombinant tissue plasminogen activator (rtPA) can be used to improve patient outcomes. Here, we evaluated the impact of IVF on the risk of death and the functional outcomes in IVH patients with AOH. <b><i>Methods:</i></b> This prospective cohort study included IVH patients with hypertensive intracranial haemorrhage complicated by AOH who required EVD. We evaluated the risk of death and the functional outcomes at 1 and 3 months, with a specific focus on the impact of combined EVD with IVF by low-dose rtPA. <b><i>Results:</i></b> Between November 30, 2011 and December 30, 2014, 80 patients were included. Forty-five patients were treated with EVD alone (EVD group) and 35 received IVF (EVD+IVF group). The 30- and 90-day mortality rates were lower in the EVD+IVF group than in the EVD group (42.2 vs. 11.4%, <i>p</i> = 0.003, and 62.2 vs. 20%, <i>p</i> &lt; 0.001, respectively). The Graeb scores were significantly lower in the EVD+IVF group than in the EVD group (<i>p</i> ≤ 0.001) during the first 3 days and on day 7 after assignment. The 30-day good functional outcome (modified Rankin Scale [mRS] score 0–3) was also higher in the EVD+IVF group than in the EVD group (6.7 vs. 28.6%, <i>p</i> = 0.008). However, the 90-day good functional outcome (mRS score 0–3) did not significantly increase in the EVD+IVF group (30.8% in the EVD group vs. 51.6% in the EVD+IVF group, <i>p</i> = 0.112). <b><i>Conclusions:</i></b> In our prospective observational study, EVD+IVF was associated with a lower risk of death in IVH patients. EVD+IVF improved the chance of having a good functional outcome at 1 month; however, this result was no longer observed at 3 months.
DOI: 10.6084/m9.figshare.9578081
title: RT Modelling Output Images

description: Hyperion RT output images and radial profiles presented in the paper as well as the scripts used to generate them from the model output.
DOI: 10.6084/m9.figshare.9578174
title: RT Modelling Output SEDs

description: Output SEDs and scripts used to generate SEDs from the Hyperion model output.
DOI: 10.6084/m9.figshare.9578318.v1
title: Supplementary Material for: Effectiveness of Combined External Ventricular Drainage with Intraventricular Fibrinolysis for the Treatment of Intraventricular Haemorrhage with Acute Obstructive Hydrocephalus

description: <b><i>Background:</i></b> Intraventricular haemorrhage (IVH) patients with acute obstructive hydrocephalus (AOH) who require external ventricular drainage (EVD) are at high risk for poor outcomes. Intraventricular fibrinolysis (IVF) with low-dose recombinant tissue plasminogen activator (rtPA) can be used to improve patient outcomes. Here, we evaluated the impact of IVF on the risk of death and the functional outcomes in IVH patients with AOH. <b><i>Methods:</i></b> This prospective cohort study included IVH patients with hypertensive intracranial haemorrhage complicated by AOH who required EVD. We evaluated the risk of death and the functional outcomes at 1 and 3 months, with a specific focus on the impact of combined EVD with IVF by low-dose rtPA. <b><i>Results:</i></b> Between November 30, 2011 and December 30, 2014, 80 patients were included. Forty-five patients were treated with EVD alone (EVD group) and 35 received IVF (EVD+IVF group). The 30- and 90-day mortality rates were lower in the EVD+IVF group than in the EVD group (42.2 vs. 11.4%, <i>p</i> = 0.003, and 62.2 vs. 20%, <i>p</i> &lt; 0.001, respectively). The Graeb scores were significantly lower in the EVD+IVF group than in the EVD group (<i>p</i> ≤ 0.001) during the first 3 days and on day 7 after assignment. The 30-day good functional outcome (modified Rankin Scale [mRS] score 0–3) was also higher in the EVD+IVF group than in the EVD group (6.7 vs. 28.6%, <i>p</i> = 0.008). However, the 90-day good functional outcome (mRS score 0–3) did not significantly increase in the EVD+IVF group (30.8% in the EVD group vs. 51.6% in the EVD+IVF group, <i>p</i> = 0.112). <b><i>Conclusions:</i></b> In our prospective observational study, EVD+IVF was associated with a lower risk of death in IVH patients. EVD+IVF improved the chance of having a good functional outcome at 1 month; however, this result was no longer observed at 3 months.
DOI: 10.6084/m9.figshare.9578081.v2
title: RT Modelling Output Images

description: Hyperion RT output images and radial profiles presented in the paper as well as the scripts used to generate them from the model output.
DOI: 10.6084/m9.figshare.9578081.v1
title: RT Modelling Output Images

description: Hyperion RT output images and radial profiles presented in the paper as well as the scripts used to generate them from the model output.
DOI: 10.6084/m9.figshare.9578174.v1
title: RT Modelling Output SEDs

description: Output SEDs and scripts used to generate SEDs from the Hyperion model output.