cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.24648039
title: Supplementary Material for: Neurodevelopmental outcomes prediction in newborns with seizures caused by KCNQ2 gene defects

description: Introduction: Pathogenic variant in the KCNQ2 gene is a common genetic etiology of neonatal convulsion. However, it remains a question in KCNQ2-related disorders that who will develop into atypical developmental outcomes. Methods: We established a prediction model for the neurodevelopmental outcomes of newborns with seizures caused by KCNQ2 gene defects based on the Gradient Boosting Machine (GBM) model with a training set obtained from the Human Gene Mutation Database (HGMD, public training dataset). The features used in the prediction model were respectively based on clinical features only and optimized features. The validation set was obtained from the China Neonatal Genomes Project (CNGP, internal validation dataset). Results: With the HGMD training set, the prediction results showed that the area under the receiver operating characteristic curve (AUC) for predicting atypical developmental outcomes was 0.723 when using clinical features only, and was improved to 0.986 when using optimized features, respectively. In feature importance ranking, both variants pathogenicity and protein functional/structural features played an important role in the prediction model. For the CNGP validation set, the AUC was 0.596 when using clinical features only, and was improved to 0.736 when using optimized features. Conclusion: In our study, functional/structural features and variant pathogenicity have higher feature importance compared with clinical information. This prediction model for the neurodevelopmental outcomes of newborns with seizures caused by KCNQ2 gene defects is a promising alternative that could prove to be valuable in clinical practice.
DOI: 10.6084/m9.figshare.24648039.v1
title: Supplementary Material for: Neurodevelopmental outcomes prediction in newborns with seizures caused by KCNQ2 gene defects

description: Introduction: Pathogenic variant in the KCNQ2 gene is a common genetic etiology of neonatal convulsion. However, it remains a question in KCNQ2-related disorders that who will develop into atypical developmental outcomes. Methods: We established a prediction model for the neurodevelopmental outcomes of newborns with seizures caused by KCNQ2 gene defects based on the Gradient Boosting Machine (GBM) model with a training set obtained from the Human Gene Mutation Database (HGMD, public training dataset). The features used in the prediction model were respectively based on clinical features only and optimized features. The validation set was obtained from the China Neonatal Genomes Project (CNGP, internal validation dataset). Results: With the HGMD training set, the prediction results showed that the area under the receiver operating characteristic curve (AUC) for predicting atypical developmental outcomes was 0.723 when using clinical features only, and was improved to 0.986 when using optimized features, respectively. In feature importance ranking, both variants pathogenicity and protein functional/structural features played an important role in the prediction model. For the CNGP validation set, the AUC was 0.596 when using clinical features only, and was improved to 0.736 when using optimized features. Conclusion: In our study, functional/structural features and variant pathogenicity have higher feature importance compared with clinical information. This prediction model for the neurodevelopmental outcomes of newborns with seizures caused by KCNQ2 gene defects is a promising alternative that could prove to be valuable in clinical practice.
DOI: 10.17909/300a-ns91
title: HST ACS/WFC3 imaging of BST1047+1156
DOI: 10.6084/m9.figshare.24518422.v1
title: Supplementary Material for: Stratifying future stroke risk with incidentally-discovered white matter disease severity and covert brain infarct site

description: Background: Covert cerebrovascular disease (CCD) includes white matter disease (WMD) and covert brain infarction (CBI). Incidentally-discovered CCD is associated with increased risk of subsequent symptomatic stroke. However, it is unknown whether the severity of WMD or the location of CBI predicts risk. Objectives: To examine the association of incidentally-discovered WMD severity and CBI location with risk of subsequent symptomatic stroke. Method: This retrospective cohort study includes patients 50 years old in the Kaiser Permanente Southern California health system who received neuroimaging for a non-stroke indication between 2009-2019. Incidental CBI and WMD were identified via natural language processing of the neuroimage report, and WMD severity was classified into grades. Results: 261,960 patients received neuroimaging; 78,555 (30.0%) were identified to have incidental WMD, and 12,857 (4.9%) to have incidental CBI. Increasing WMD severity is associated with increased incidence rate of future stroke. However, the stroke incidence rate in CT-identified WMD is higher at each level of severity compared to rates in MRI-identified WMD. Patients with mild WMD via CT have a stroke incidence rate of 24.9 per 1,000 person-years, similar to that of patients with severe WMD via MRI. Among incidentally-discovered CBI patients with a determined CBI location, 97.9% are subcortical rather than cortical infarcts. CBI confers a similar risk of future stroke, whether cortical or subcortical, or whether MRI- or CT-detected. Conclusions: Increasing severity of incidental WMD is associated with an increased risk of future symptomatic stroke, dependent on the imaging modality. Subcortical and cortical CBI conferred similar risks.
DOI: 10.6084/m9.figshare.24711663
title: <b>Variations and estimation models of dead fuel loading at five typical forest ecosystems in</b><b>the middle subtropical area</b>

description: Based on a dataset of 150 forest plots in subtropical China, we examined the relationship between forest dead fuel loading and stand and topographic factors.<br>
DOI: 10.6084/m9.figshare.24711663.v2
title: <b>Variations and estimation models of dead fuel loading at five typical forest ecosystems in</b><b>the middle subtropical area</b>

description: Based on a dataset of 150 forest plots in subtropical China, we examined the relationship between forest dead fuel loading and stand and topographic factors.<br>
DOI: 10.6084/m9.figshare.24711663.v1
title: data_.xlsx

description: Based on a dataset of 150 forest plots in subtropical China, we examined the relationship between forest dead fuel loading and stand and topographic factors.<br>
DOI: 10.6084/m9.figshare.24711927
title: Supplementary Table 1 from Reduced social function in experimentally evolved <i>Dictyostelium discoideum</i> implies selection for social conflict in nature

description: Table of strains used
DOI: 10.6084/m9.figshare.24711927.v1
title: Supplementary Table 1 from Reduced social function in experimentally evolved <i>Dictyostelium discoideum</i> implies selection for social conflict in nature

description: Table of strains used
DOI: 10.4121/152663fc-0e02-46bf-a0c7-2ebb7b509f68
title: Data underlying the PhD thesis: BresDefender, An experimental study on an emergency response measure for levee breaches

description: Dataset of raw data used within the PhD thesis: BresDefender, An experimental study on an emergency response measure for levee breaches. The aim of the thesis is to find the effectiveness and the reliability of emergency measures, specifically the BresDefender. The acquired data is applied in different chapters in the thesis, each consisting of unique experiments on different scales:<br>Chapter 2 - Phreatic surface measurementsData gathered in the TU Delft hydraulic laboratoryData gathered at Flood Proof Holland, DelftChapter 3 - Leakage discharge measurementsData gathered at Flood Proof Holland, DelftData gathered at the Hedwige-ProsperpolderChapter 4 - Logistical considerations emergency measure based on expert opinionsExpert judgement data
DOI: 10.4121/152663fc-0e02-46bf-a0c7-2ebb7b509f68.v1
title: Data underlying the PhD thesis: BresDefender, An experimental study on an emergency response measure for levee breaches

description: Dataset of raw data used within the PhD thesis: BresDefender, An experimental study on an emergency response measure for levee breaches. The aim of the thesis is to find the effectiveness and the reliability of emergency measures, specifically the BresDefender. The acquired data is applied in different chapters in the thesis, each consisting of unique experiments on different scales:<br>Chapter 2 - Phreatic surface measurementsData gathered in the TU Delft hydraulic laboratoryData gathered at Flood Proof Holland, DelftChapter 3 - Leakage discharge measurementsData gathered at Flood Proof Holland, DelftData gathered at the Hedwige-ProsperpolderChapter 4 - Logistical considerations emergency measure based on expert opinionsExpert judgement data
DOI: 10.6084/m9.figshare.24624252
title: Supplementary Material for: Smartphone photographs of chronic urticaria taken by patients are of good quality and useful in the clinic

description: Background: Chronic urticaria (CU) is characterized by transient wheals and angioedema, which are often not present when patients see their treating physician. Aim: To evaluate the diagnostic value of smartphone photographs captured by patients prior to their first visit at an urticaria outpatient clinic. Methods: A survey regarding the quality and utility of smartphone photographs of urticarial skin lesions in patients with CU attending the outpatient clinic for the first time was conducted. Up to three random patient-selected photographs of skin lesions were evaluated by a physician. Results: Of 148 patients, 118 (79.7%) had taken photographs of their skin lesions prior to the consultation, and 75% took photographs with the intention of presenting it to their physician. The photographs were of wheals in 90% of the cases, and angioedema in 8%. In total, 72% of the smartphone photographs had the skin lesion in focus, 64% had good resolution, 48% had good lighting. Only 9% of the smartphone photographs were blurred, 10% had bad lighting, 4% had bad resolution, and 8% did not have the lesion in focus. Moreover, 86% of the smartphone photographs were found to be useful for clinical evaluation. At least one photograph of good/very good quality was presented by 86% of the patients, and 97% had at least one photograph that was useful for clinical evaluation. Conclusion: Patients with CU often take smartphone photographs of their skin lesions on their own initiative prior to their first consultation to present the photographs to their physician. These smartphone photographs are very often of good quality and suitable for clinical evaluation.
DOI: 10.6084/m9.figshare.24624252.v1
title: Supplementary Material for: Smartphone photographs of chronic urticaria taken by patients are of good quality and useful in the clinic

description: Background: Chronic urticaria (CU) is characterized by transient wheals and angioedema, which are often not present when patients see their treating physician. Aim: To evaluate the diagnostic value of smartphone photographs captured by patients prior to their first visit at an urticaria outpatient clinic. Methods: A survey regarding the quality and utility of smartphone photographs of urticarial skin lesions in patients with CU attending the outpatient clinic for the first time was conducted. Up to three random patient-selected photographs of skin lesions were evaluated by a physician. Results: Of 148 patients, 118 (79.7%) had taken photographs of their skin lesions prior to the consultation, and 75% took photographs with the intention of presenting it to their physician. The photographs were of wheals in 90% of the cases, and angioedema in 8%. In total, 72% of the smartphone photographs had the skin lesion in focus, 64% had good resolution, 48% had good lighting. Only 9% of the smartphone photographs were blurred, 10% had bad lighting, 4% had bad resolution, and 8% did not have the lesion in focus. Moreover, 86% of the smartphone photographs were found to be useful for clinical evaluation. At least one photograph of good/very good quality was presented by 86% of the patients, and 97% had at least one photograph that was useful for clinical evaluation. Conclusion: Patients with CU often take smartphone photographs of their skin lesions on their own initiative prior to their first consultation to present the photographs to their physician. These smartphone photographs are very often of good quality and suitable for clinical evaluation.
DOI: 10.6084/m9.figshare.24623946
title: Supplementary Material for: The Effects of Mindfulness for Youth (MYmind) versus Group Cognitive Behavioral Therapy (CBT) in Improving Attention and Reducing Behavioral Problems among Children with Attention Deficit Hyperactivity Disorder (ADHD) and Their Parents: A Randomized Controlled Trial

description: Introduction There is a lack of studies evaluating mindfulness-based interventions for children with ADHD compared with an evidence-based control. This randomized controlled trial (RCT) evaluated the effects of Mindfulness for Youth (MYmind) in improving children’s attention, behavior and parent related outcomes versus cognitive behavioral therapy (CBT). Method A total of 138 families of children with ADHD aged 8-12 years were recruited from the community with 69 randomized to MYmind and 69 to CBT. Participants were assessed at baseline, immediately after intervention, at 3 months and 6 months. The primary outcome was the attention score of the Sky Search subtest of the Test of Everyday Attention for Children (TEA-Ch). Secondary outcomes were child behavior and parent-related assessments. Linear mixed models (LMMs) were used to assess the efficacy of MYmind compared with CBT. Results Both MYmind and CBT significantly improved children’s attention score at 6 months (MYmind: β = 1.48, p = 0.013, Cohen’s d = 0.32; CBT: β = 1.46, p = 0.008, d = 0.27). There were significant within-group improvements in most secondary outcomes. No significant difference was shown for both primary or secondary outcomes between the two arms at any time point. Conclusions Both MYmind and CBT appeared to improve children’s attention and behavior outcomes, although no difference was found between these two interventions. This is the largest RCT so far comparing MYmind and CBT although there was loss of follow-up assessments during the pandemic. Further RCTs adopting a non-inferiority design are needed to validate the results.
DOI: 10.25835/25dccboy
title: Modelled habitat suitability for wild bees in the Hannover region

description: This dataset (GRID) contains the modelled habitat suitability for wild bees in the Hannover region modelled with ESTIMAP and InVEST and based on the biotope types of the Hannover region (to be requested at GISBuero@Region-Hannover.de) and the CORINE Landcover 2018 (https://land.copernicus.eu/en/products/corine-land-cover) and Urban Atlas 2018 (https://land.copernicus.eu/en/products/urban-atlas). Furthermore, the similarity maps between the results based on the different model & dataset combinations are included.
DOI: 10.6084/m9.figshare.24540859
title: Supplementary Material for: Functional analysis of a novel complement C5a receptor 1-blocking monoclonal antibody

description: Introduction The complement system anaphylatoxin C5a is a critical player in inflammation. By binding to complement C5a receptor 1 (C5aR1/CD88), C5a regulates many cellular functions, mainly as a potent pro-inflammatory inducer, such as cytokine release, cellular motility, and homeostasis. We describe the generation and selection of a potent antagonistic C5aR1 mouse monoclonal antibody (mAb). Methods and results Initial C5aR1 hybridoma clone selection was performed with a cell binding study on human whole blood. The iLite® C5a assay was used to assess C5aR1 inhibition of isolated C5aR1 mAbs, which led to the selection of a particular C5aR1 mAb (clone 18-41-6). Specificity of mAb 18-41-6 for C5aR1 was demonstrated on C5aR1his- and C5aR2his-expressing Flp-In™-CHO cells. C5aR1 mAb 18-41-6 directly inhibited C5a-mediated C5aR1 receptor activation in a PMN calcium flux assay. Full-size and/or F(ab’)2 preparations of mAb 18-41-6 were found to significantly reduce the expression of the activation markers CD11b and CD66b in both a PMN C5a stimulation assay and a whole blood model stimulated with Escherichia coli. Conclusion Our results demonstrate that mAb 18-41-6 is a valuable tool for investigating the C5a-C5aR1 axis and a potential therapeutic candidate for inflammatory disease treatment.
DOI: 10.6084/m9.figshare.24540859.v1
title: Supplementary Material for: Functional analysis of a novel complement C5a receptor 1-blocking monoclonal antibody

description: Introduction The complement system anaphylatoxin C5a is a critical player in inflammation. By binding to complement C5a receptor 1 (C5aR1/CD88), C5a regulates many cellular functions, mainly as a potent pro-inflammatory inducer, such as cytokine release, cellular motility, and homeostasis. We describe the generation and selection of a potent antagonistic C5aR1 mouse monoclonal antibody (mAb). Methods and results Initial C5aR1 hybridoma clone selection was performed with a cell binding study on human whole blood. The iLite® C5a assay was used to assess C5aR1 inhibition of isolated C5aR1 mAbs, which led to the selection of a particular C5aR1 mAb (clone 18-41-6). Specificity of mAb 18-41-6 for C5aR1 was demonstrated on C5aR1his- and C5aR2his-expressing Flp-In™-CHO cells. C5aR1 mAb 18-41-6 directly inhibited C5a-mediated C5aR1 receptor activation in a PMN calcium flux assay. Full-size and/or F(ab’)2 preparations of mAb 18-41-6 were found to significantly reduce the expression of the activation markers CD11b and CD66b in both a PMN C5a stimulation assay and a whole blood model stimulated with Escherichia coli. Conclusion Our results demonstrate that mAb 18-41-6 is a valuable tool for investigating the C5a-C5aR1 axis and a potential therapeutic candidate for inflammatory disease treatment.
DOI: 10.6084/m9.figshare.24511456.v1
title: Supplementary Material for: Radiographic signs of advanced cerebral venous thrombosis negatively modulate the effectiveness of endovascular treatments

description: Introduction: Endovascular treatment (EVT) is a therapeutic option for cerebral venous thrombosis (CVT); however, its benefit over conservative medical management has not been proven. Whether current patient selection practices are appropriate for EVT is unclear. Methods: This was a nationwide study of the 2016-2020 National Inpatient Sample database. Adult CVT patients and EVT treatments were identified. Patient demographics, medical comorbidities, CVT risk factors, and CVT manifestations were identified. Presence of radiographic signs of advanced and severe CVT (venous infarction, cerebral edema, and intracranial hemorrhage) were recorded. Primary and secondary outcomes were good discharge outcomes and in-hospital mortality, respectively. Results: 17,130 CVT patients were identified, and 56.7% had good discharge outcomes while 4.6% died during hospitalization. 945 (5.5%) received EVT, and EVT patients were more likely to have cerebral infarction (35.4% vs. 21.8%, p&lt;0.001), edema (35.4% vs. 20.1%, p&lt;0.001), and hemorrhage (37.6% vs. 19.7%, p&lt;0.001). After multivariable adjustments, EVT for patients without infarction, edema, or hemorrhage was moderately associated with higher odds of good outcomes (OR 1.86 [95%CI 0.98 - 3.53], p=0.059) and resulted in zero deaths. However, with increasing burden of radiographic signs of advanced CVT measured by the cumulative presence of infraction, edema, and hemorrhage, EVT was associated with decreasing odds of good outcomes and increasing odds of in-hospital mortality compared to medical management (interaction p=0.046 and 0.029, respectively). Conclusions: EVT may lead to higher rates of favorable hospitalization outcomes in patients who have not yet developed overt parenchymal manifestations of backpressure changes; presence of infarction, edema, and hemorrhage may diminish the short-term effectiveness of EVT.
DOI: 10.5281/zenodo.10246007
title: scRNA-seq revealed the rules for CDR3 length pairing in TCR beta and alpha chains and BCR heavy and light chains

description: The scRNAseq datasets of CDR3 length pairing in TCR beta and alpha chains which come from human cental and peripheral  samples and mouse peripheral samples.


The scRNAseq datasets of CDR3 length pairing in BCR heavy and light chainsCDR3 length pairing in TCR beta and alpha chains and BCR heavy and light chains human cental and peripheral  samples and mouse cental and peripheral samples.
DOI: 10.5281/zenodo.8152180
title: scRNA-seq revealed the rules for CDR3 length pairing in TCR beta and alpha chains and BCR heavy and light chains

description: The scRNAseq datasets of CDR3 length pairing in TCR beta and alpha chains which come from human cental and peripheral  samples and mouse peripheral samples.


The scRNAseq datasets of CDR3 length pairing in BCR heavy and light chainsCDR3 length pairing in TCR beta and alpha chains and BCR heavy and light chains human cental and peripheral  samples and mouse cental and peripheral samples.
DOI: 10.5281/zenodo.8152181
title: scRNA-seq revealed the rules for CDR3 length pairing in TCR beta and alpha chains and BCR heavy and light chains

description: The scRNAseq datasets of CDR3 length pairing in TCR beta and alpha chains which come from human cental and peripheral samples and mouse peripheral samples. The scRNAseq datasets of CDR3 length pairing in BCR heavy and light chainsCDR3 length pairing in TCR beta and alpha chains and BCR heavy and light chains human cental and peripheral samples and mouse cental and peripheral samples.
description: {"references": ["Park, J. E. et al. (2020). A cell atlas of human thymic development defines T cell repertoire formation.", "Luo, O. J. et al. (2022). Multidimensional single-cell analysis of human peripheral blood reveals characteristic features of the immune system landscape in aging and frailty.", "Bhatt, D. et al. (2021). STARTRAC analyses of scRNAseq data from tumor models reveal T cell dynamics and therapeutic targets.", "Cukalac, T. et al. (2015). Paired TCR\u03b1\u03b2 analysis of virus-specific CD8(+) T cells exposes diversity in a previously defined 'narrow' repertoire.", "Peterson, J. N. et al. (2022). Elevated Detection of Dual Antibody B Cells Identifies Lupus Patients With B Cell-Reactive VH4-34 Autoantibodies.", "Wang, P. et al. (2022). Global Characterization of Peripheral B Cells in Parkinson's Disease by Single-Cell RNA and BCR Sequencing.", "Nguyen, H. T. et al. (2021). Single-cell transcriptome profiling and the use of AID deficient mice reveal that B cell activation combined with antibody class switch recombination and somatic hypermutation do not benefit the control of experimental trypanosomosis.", "Kumar, S. et al. (2022). Structural insights for neutralization of Omicron variants BA.1, BA.2, BA.4, and BA.5 by a broadly neutralizing SARS-CoV-2 antibody.", "Bone--10k_BMMNC_5pv2_nextgem_intron_Multiplex_vdj_b_all_contig; PBMC--vdj_v1_mm_balbc_pbmc_b_all_contig; PBMC--vdj_v1_mm_c57bl6_pbmc_b_all_contig"]}
DOI: 10.5281/zenodo.10210415
title: blood_on_snow_data