cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.3725881
title: Eigen scores for human genome assembly GRCh38 Part 1 (Chr12 - Chr22)

description: Eigen is a spectral approach to the functional annotation of genetic variants in coding and noncoding regions. Eigen makes use of a variety of functional annotations in both coding and noncoding regions (such as protein function scores, evolutionary conservation scores, and epigenetic annotations from ENCODE and Roadmap Epigenomics projects), and combines them into one single measure of functional importance. Eigen is an unsupervised approach, and, unlike many existing methods, is not based on any labelled training data. Eigen produces estimates of predictive accuracy for each functional annotation score, and subsequently uses these estimates of accuracy to derive the aggregate functional score for variants of interest as a weighted linear combination of individual annotations.
description: Uploading errors
DOI: 10.5281/zenodo.3726145
title: Eigen scores for human genome assembly GRCh38 Part 1 (Chr12 - Chr22)

description: Eigen is a spectral approach to the functional annotation of genetic variants in coding and noncoding regions. Eigen makes use of a variety of functional annotations in both coding and noncoding regions (such as protein function scores, evolutionary conservation scores, and epigenetic annotations from ENCODE and Roadmap Epigenomics projects), and combines them into one single measure of functional importance. Eigen is an unsupervised approach, and, unlike many existing methods, is not based on any labelled training data. Eigen produces estimates of predictive accuracy for each functional annotation score, and subsequently uses these estimates of accuracy to derive the aggregate functional score for variants of interest as a weighted linear combination of individual annotations.
description: Uploading errors
DOI: 10.5281/zenodo.3257464
title: Eigen scores for human genome assembly GRCh38 Part 2 (Chr6 - Chr11)

description: Eigen is a spectral approach to the functional annotation of genetic variants in coding and noncoding regions. Eigen makes use of a variety of functional annotations in both coding and noncoding regions (such as protein function scores, evolutionary conservation scores, and epigenetic annotations from ENCODE and Roadmap Epigenomics projects), and combines them into one single measure of functional importance. Eigen is an unsupervised approach, and, unlike many existing methods, is not based on any labelled training data. Eigen produces estimates of predictive accuracy for each functional annotation score, and subsequently uses these estimates of accuracy to derive the aggregate functional score for variants of interest as a weighted linear combination of individual annotations.
DOI: 10.5281/zenodo.3257463
title: Eigen scores for human genome assembly GRCh38 Part 2 (Chr6 - Chr11)

description: Eigen is a spectral approach to the functional annotation of genetic variants in coding and noncoding regions. Eigen makes use of a variety of functional annotations in both coding and noncoding regions (such as protein function scores, evolutionary conservation scores, and epigenetic annotations from ENCODE and Roadmap Epigenomics projects), and combines them into one single measure of functional importance. Eigen is an unsupervised approach, and, unlike many existing methods, is not based on any labelled training data. Eigen produces estimates of predictive accuracy for each functional annotation score, and subsequently uses these estimates of accuracy to derive the aggregate functional score for variants of interest as a weighted linear combination of individual annotations.
DOI: 10.5281/zenodo.3725020
title: Eigen scores for human genome assembly GRCh38 Part 2 (Chr6 - Chr11)

description: Eigen is a spectral approach to the functional annotation of genetic variants in coding and noncoding regions. Eigen makes use of a variety of functional annotations in both coding and noncoding regions (such as protein function scores, evolutionary conservation scores, and epigenetic annotations from ENCODE and Roadmap Epigenomics projects), and combines them into one single measure of functional importance. Eigen is an unsupervised approach, and, unlike many existing methods, is not based on any labelled training data. Eigen produces estimates of predictive accuracy for each functional annotation score, and subsequently uses these estimates of accuracy to derive the aggregate functional score for variants of interest as a weighted linear combination of individual annotations.
DOI: 10.6084/m9.figshare.22739690.v1
title: Growth hormone releasing hormone signaling promotes Th17 cell differentiation and autoimmune inflammation

description: The file contains all raw data presented in all Figures.
DOI: 10.6084/m9.figshare.22739690
title: Growth hormone releasing hormone signaling promotes Th17 cell differentiation and autoimmune inflammation

description: The file contains all raw data presented in all Figures.
DOI: 10.6084/m9.figshare.22770776.v1
title: Eye accommodation-inspired neuro-metasurface focusing

description: The relevant 1-D result data are provided as Source Data File.
DOI: 10.6084/m9.figshare.22770776
title: Eye accommodation-inspired neuro-metasurface focusing

description: The relevant 1-D result data are provided as Source Data File.
DOI: 10.7488/ds/7459
title: Scottish Young People's Survey Cohort 1985-86, Sweep 2 (SYPS 1989 autumn)
title: SYPS1989 autumn

description: The Scottish Young People's Survey (SYPS) was a nationally-representative survey of young people in Scotland. The first sweep of the survey was carried out when the young people were aged 16/17, with a subsequent sweep at age 18/19. The SYPS1989autumn survey was the 2nd sweep of the cohort who were in the SYPS 1987 (also held in Datashare), and describes the experiences of young people in jobs, training or unemployed, as well as those continuing their education at school, college or university. In addition to factual questions about attainment and destinations, family background, social class, school and region, each of the surveys included questions about attitudes, aspirations and choices.
DOI: 10.6084/m9.figshare.22644298
title: Supplementary Material for: Formyl peptide receptor type 2 (FPR2) deficiency in myeloid cells amplifies sepsis-induced cardiac dysfunction

description: Using a global formyl-peptide receptor (Fpr)2 knockout mouse colony, we have reported the modulatory properties of this pro-resolving receptor in polymicrobial sepsis. Herein, we have used a humanized FPR2 (hFPR2) mouse colony bearing an intact or a selective receptor deficiency in myeloid cells to dwell on the cellular mechanisms. hFPR2 mice and myeloid cell-specific hFPR2 KO (abbreviated to KO) mice were subjected to cecal ligation and puncture (CLP)-induced polymicrobial sepsis. Compared with hFPR2 mice, CLP caused exacerbated cardiac dysfunction (assessed by echocardiography), worsened clinical outcome and impaired bacteria clearance in KO mice. This pathological scenario was paralleled by increased recruitment of pro-inflammatory monocytes and reduced M2-like macrophages within the KO hearts. In peritoneal exudates of KO mice, we quantified increased neutrophil and MHC II+ macrophage numbers, but decreased monocyte/macrophage and MHC II- macrophage recruitment. hFPR2 up-regulation was absent in myeloid cells and local production of lipoxin A4 was reduced in septic KO mice. Administration of the FPR2 agonist Annexin A1 (AnxA1) improved cardiac function in hFPR2 septic mice, but had limited beneficial effects in KO mice, in which the FPR2 ligand failed to polarize macrophages towards an MHC II- phenotype. In conclusion, FPR2 deficiency in myeloid cells exacerbates cardiac dysfunction and worsens clinical outcome in polymicrobial sepsis. The improvement of cardiac function and the host immune response by AnxA1 is more effective in hFPR2 competent septic mice.
DOI: 10.6084/m9.figshare.22644298.v1
title: Supplementary Material for: Formyl peptide receptor type 2 (FPR2) deficiency in myeloid cells amplifies sepsis-induced cardiac dysfunction

description: Using a global formyl-peptide receptor (Fpr)2 knockout mouse colony, we have reported the modulatory properties of this pro-resolving receptor in polymicrobial sepsis. Herein, we have used a humanized FPR2 (hFPR2) mouse colony bearing an intact or a selective receptor deficiency in myeloid cells to dwell on the cellular mechanisms. hFPR2 mice and myeloid cell-specific hFPR2 KO (abbreviated to KO) mice were subjected to cecal ligation and puncture (CLP)-induced polymicrobial sepsis. Compared with hFPR2 mice, CLP caused exacerbated cardiac dysfunction (assessed by echocardiography), worsened clinical outcome and impaired bacteria clearance in KO mice. This pathological scenario was paralleled by increased recruitment of pro-inflammatory monocytes and reduced M2-like macrophages within the KO hearts. In peritoneal exudates of KO mice, we quantified increased neutrophil and MHC II+ macrophage numbers, but decreased monocyte/macrophage and MHC II- macrophage recruitment. hFPR2 up-regulation was absent in myeloid cells and local production of lipoxin A4 was reduced in septic KO mice. Administration of the FPR2 agonist Annexin A1 (AnxA1) improved cardiac function in hFPR2 septic mice, but had limited beneficial effects in KO mice, in which the FPR2 ligand failed to polarize macrophages towards an MHC II- phenotype. In conclusion, FPR2 deficiency in myeloid cells exacerbates cardiac dysfunction and worsens clinical outcome in polymicrobial sepsis. The improvement of cardiac function and the host immune response by AnxA1 is more effective in hFPR2 competent septic mice.
DOI: 10.5281/zenodo.7989871
title: Dataset for 'Phytoplankton community response to episodic wet and dry aerosol deposition in the subtropical North Atlantic' by Yuan et al. 2023. Limnology and Oceanography.

description: Dataset for 'Phytoplankton community response to episodic wet and dry aerosol deposition in the subtropical North Atlantic' by Yuan et al. 2023. Limnology and Oceanography.
DOI: 10.5281/zenodo.7989870
title: Dataset for 'Phytoplankton community response to episodic wet and dry aerosol deposition in the subtropical North Atlantic' by Yuan et al. 2023. Limnology and Oceanography.

description: Dataset for 'Phytoplankton community response to episodic wet and dry aerosol deposition in the subtropical North Atlantic' by Yuan et al. 2023. Limnology and Oceanography.
DOI: 10.6084/m9.figshare.22434010
title: BASALT models

description: BASALT models for neural networks
DOI: 10.6084/m9.figshare.22434010.v2
title: BASALT models

description: BASALT models for neural networks
DOI: 10.48329/4wmr-x234
title: CPRD GOLD June 2023

description: The CPRD GOLD database contains longitudinal routinely-collected electronic health records (EHR data) from UK primary care practices using Vision® general practice patient management software. The database captures information on demographic characteristics; diagnoses and symptoms; drug exposures; vaccination history; laboratory tests; and referrals to hospital and specialist care. Access to anonymised data from CPRD is subject to a full licence agreement containing detailed terms and conditions of use. Anonymised patient datasets can be extracted for researchers against specific study specifications, following protocol approval. Further information is available at https://www.cprd.com/data-access.
DOI: 10.6084/m9.figshare.22732634
title: Penile cancer: long-term infectious and thromboembolic complications following lymph node dissection – a population-based study (Sweden)

description: To assess the long-term risks of infectious and thromboembolic events following inguinal (ILND) and pelvic (PLND) lymph node dissection in men with penile cancer. A total of 364 men subjected to ILND with or without PLND for penile cancer between 2000 and 2012 were identified in the Swedish National Penile Cancer Register. Each patient was matched based on age and county of residence with six penile cancer-free men. The Swedish Cancer Register and other population-based registers were used to retrieve information on treatment and hospitalisation for selected infectious and thromboembolic events. Hazard ratios (HRs) with 95% confidence intervals (CIs) were estimated using Cox proportional hazard models with multiple imputation. The risk of infectious events remained increased for more than five years postoperatively in men with penile cancer compared with matched controls. The palpable nodal disease was the only predictor of these events, with risk increasing with the cN stage. The HR at one, three and five years and six months postoperatively was 8.60 (95% CI 5.16–14.34), 4.02 (95% CI 2.65–6.09) and 1.93 (95% CI 1.11–3.38), respectively. An increased risk of thromboembolic events persisted for three years postoperatively. The HR at one and three years postoperatively was 13.51 (95% CI 6.53–27.93) and 2.12 (95% CI 1.07–4.20). The results correspond well with the over-prescription of anticoagulants observed during this period. An association with bulky disease (cN3) was observed. Lymph node dissection for penile cancer is associated with an increased risk of infectious and thromboembolic events. The findings of this population-based study show that the risks of these events remain increased more than five years for infectious and three years for thromboembolic events. Improved awareness of long-term complications following ILND is of importance both among patients and care givers to ensure early detection and treatment.
DOI: 10.6084/m9.figshare.22933849
title: Role of immune checkpoint inhibitors in metastatic uveal melanoma: a single-center retrospective cohort study

description: Uveal melanoma is an orphan malignancy with very limited data on treatment options in metastatic setting. In this single<b>-</b>center retrospective study, we describe real-world epidemiological and survival data on 121 metastatic uveal melanoma (MUM) patients registered in our institution. As a large tertiary referral center, almost 30% of all diagnoses in the Flemish region of Belgium were covered. Primarily, we determined whether introduction of immune checkpoint inhibitors (ICI) led to improved overall survival (OS) in MUM patients. Secondarily, response rates to ICI were assessed and we evaluated whether first-line ICI could be a valid alternative to liver-directed therapy (LDT) in liver-only disease. The initially perceived 10.8 months survival benefit from treatment with ICI disappeared after correction for immortality bias. By analyzing treatment type as time-varying covariate on OS, no significant benefit of ICI over other systemic therapies (HR = 0.771) or best supportive care (BSC) (HR = 0.780) was found. Also comparison of the pre-ICI versus ICI era showed no OS improvement after introduction of ICI in our center (<i>p</i> = 0.7994). Only liver-directed and local oligometastatic approaches were associated with a lower chance of mortality when compared to ICI (<i>p</i> = 0.0025), other systemic therapies (<i>p</i> = 0.0001) and BSC (<i>p</i> = 0.0003), yet without correction for selection bias. We reported overall response rates on ICI ranging from 8–15% and we found some support for neoadjuvant strategies with ICI resulting in remission or downsizing, allowing oligometastatic approaches later on. In first-line liver-only disease, median real-world progression-free survival and OS did not significantly differ between patients treated with LDT or ICI upfront (<i>p</i> = 0.2930 and <i>p</i> = 0.5461 respectively). Although we documented responses to ICI, our analyses do not demonstrate an OS benefit of ICI over alternative treatment strategies for MUM. However, local treatment options, whether liver-directed or for oligometastatic disease, may be beneficial and should be considered.
DOI: 10.6084/m9.figshare.22732634.v1
title: Penile cancer: long-term infectious and thromboembolic complications following lymph node dissection – a population-based study (Sweden)

description: To assess the long-term risks of infectious and thromboembolic events following inguinal (ILND) and pelvic (PLND) lymph node dissection in men with penile cancer. A total of 364 men subjected to ILND with or without PLND for penile cancer between 2000 and 2012 were identified in the Swedish National Penile Cancer Register. Each patient was matched based on age and county of residence with six penile cancer-free men. The Swedish Cancer Register and other population-based registers were used to retrieve information on treatment and hospitalisation for selected infectious and thromboembolic events. Hazard ratios (HRs) with 95% confidence intervals (CIs) were estimated using Cox proportional hazard models with multiple imputation. The risk of infectious events remained increased for more than five years postoperatively in men with penile cancer compared with matched controls. The palpable nodal disease was the only predictor of these events, with risk increasing with the cN stage. The HR at one, three and five years and six months postoperatively was 8.60 (95% CI 5.16–14.34), 4.02 (95% CI 2.65–6.09) and 1.93 (95% CI 1.11–3.38), respectively. An increased risk of thromboembolic events persisted for three years postoperatively. The HR at one and three years postoperatively was 13.51 (95% CI 6.53–27.93) and 2.12 (95% CI 1.07–4.20). The results correspond well with the over-prescription of anticoagulants observed during this period. An association with bulky disease (cN3) was observed. Lymph node dissection for penile cancer is associated with an increased risk of infectious and thromboembolic events. The findings of this population-based study show that the risks of these events remain increased more than five years for infectious and three years for thromboembolic events. Improved awareness of long-term complications following ILND is of importance both among patients and care givers to ensure early detection and treatment.
DOI: 10.6084/m9.figshare.22933849.v1
title: Role of immune checkpoint inhibitors in metastatic uveal melanoma: a single-center retrospective cohort study

description: Uveal melanoma is an orphan malignancy with very limited data on treatment options in metastatic setting. In this single<b>-</b>center retrospective study, we describe real-world epidemiological and survival data on 121 metastatic uveal melanoma (MUM) patients registered in our institution. As a large tertiary referral center, almost 30% of all diagnoses in the Flemish region of Belgium were covered. Primarily, we determined whether introduction of immune checkpoint inhibitors (ICI) led to improved overall survival (OS) in MUM patients. Secondarily, response rates to ICI were assessed and we evaluated whether first-line ICI could be a valid alternative to liver-directed therapy (LDT) in liver-only disease. The initially perceived 10.8 months survival benefit from treatment with ICI disappeared after correction for immortality bias. By analyzing treatment type as time-varying covariate on OS, no significant benefit of ICI over other systemic therapies (HR = 0.771) or best supportive care (BSC) (HR = 0.780) was found. Also comparison of the pre-ICI versus ICI era showed no OS improvement after introduction of ICI in our center (<i>p</i> = 0.7994). Only liver-directed and local oligometastatic approaches were associated with a lower chance of mortality when compared to ICI (<i>p</i> = 0.0025), other systemic therapies (<i>p</i> = 0.0001) and BSC (<i>p</i> = 0.0003), yet without correction for selection bias. We reported overall response rates on ICI ranging from 8–15% and we found some support for neoadjuvant strategies with ICI resulting in remission or downsizing, allowing oligometastatic approaches later on. In first-line liver-only disease, median real-world progression-free survival and OS did not significantly differ between patients treated with LDT or ICI upfront (<i>p</i> = 0.2930 and <i>p</i> = 0.5461 respectively). Although we documented responses to ICI, our analyses do not demonstrate an OS benefit of ICI over alternative treatment strategies for MUM. However, local treatment options, whether liver-directed or for oligometastatic disease, may be beneficial and should be considered.
DOI: 10.5517/ccdc.csd.cc261gtk
title: CCDC 2027208: Experimental Crystal Structure Determination

description: Related Article: Harmeet Bhoday, Audrey Schuman, Kaidi Yang, Steven P. Kelley, Rainer Glaser|2020|CSD Communication|||
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5281/zenodo.7892012
title: AgriSen-COG.LPIS.GT.

description: AgriSen-COG - a large-scale dataset for crop type mapping. This repository includes the original and processed LPIS files and the rasterized corresponding tiles in Geotiff format.
DOI: 10.5281/zenodo.7892011
title: AgriSen-COG.LPIS.GT.

description: AgriSen-COG - a large-scale dataset for crop type mapping. This repository includes the original and processed LPIS files and the rasterized corresponding tiles in Geotiff format.
DOI: 10.5281/zenodo.8005289
title: Theoretical and numerical comparison of quantum- and classical embedding models for optical spectra

description: This repository contains the files for the computational study on "Theoretical and numerical comparison of quantum- and classical embedding models for optical spectra".<br> The repository is organized into different folders as described below: ====================================================================================================<br> 1_pna<br> This folder contains the configuration structures for p-nitroaniline extracted from the Molecular Dynamics (MD) simulations in *.xyz format that were used for any further calculations.<br> ====================================================================================================<br> 2_pftaa<br> This folder contains the configuration structures for pentameric formyl thiophene acetic acid extracted from the Molecular Dynamics (MD) simulations in *.xyz format that were used for any further calculations.<br> ==================================================================================================== <br> We acknowledge funding by the German Research Foundation (DFG) through the Emmy Noether Young Group Leader Programme (CK, project KO 5423/1-1), The Villum Foundation, Young Investigator Program (EDH, grant no. 29412), the Swedish Research Council (EDH, grant no. 2019-04205), and Independent Research Fund Denmark (EDH, grant no. 0252-00002B and grant no. 2064-00002B) for support.<br>