cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.14350265
title: Supplementary Material for: Risk Factors for Olfactory and Gustatory Dysfunctions in Patients with SARS-CoV-2 Infection

description: <b><i>Introduction:</i></b> Smell and taste loss are characteristic symptoms of SARS-CoV-2 infection. The aim of this study is to investigate the prevalence and risk factors associated with olfactory and gustatory dysfunctions in coronavirus disease (COVID-19) patients. <b><i>Methods:</i></b> We conducted an observational, retrospective study on 376 patients with documented SARS-CoV-2 infection admitted to the San Gerardo Hospital in Monza, Italy, from March to July 2020. All patients answered a phone questionnaire providing information on age, sex, smoking status, and clinical characteristics. Adjusted odds ratios (ORs) and corresponding 95% confidence intervals (CIs) were estimated through logistic regression models including relevant covariates. <b><i>Results:</i></b> The prevalence of olfactory and gustatory dysfunctions in COVID-19 patients was 33.5 and 35.6%, respectively. Olfactory dysfunctions were significantly directly associated with current smoking and history of allergy, the multivariable ORs being 6.53 (95% CI 1.16–36.86) for current smokers versus never smokers, and 1.89 (95% CI 1.05–3.39) for those with an allergy compared to those without any allergy. Respiratory allergy in particular was significantly associated with olfactory dysfunctions (multivariable OR 2.30, 95% CI 1.02–5.17). Significant inverse associations were observed for patients aged 60 years or more (multivariable OR 0.33, 95% CI 0.19–0.57) and hospitalization (multivariable OR 0.22, 95% CI 0.06–0.89). Considering gustatory dysfunctions, after allowance of other variables a significant direct association was found for respiratory allergies (OR 2.24, 95% CI 1.03–4.86), and an inverse association was found only for hospitalization (OR 0.21, 95% CI 0.06–0.76). <b><i>Conclusion:</i></b> Our study indicates that current smoking and history of allergy (particularly respiratory) significantly increase the risk for smell loss in COVID-19 patients; the latter is also significantly associated to taste loss. Hospitalization has an inverse association with the risk of olfactory and gustatory dysfunctions, suggesting that these may be symptoms characteristics of less severe SARS-CoV-2 infection.
DOI: 10.25909/12818834.v1
title: Observation Sessions in Prague: L1 English Expatriates

description: This dataset contains seven observation sessions. Seven groups of L1 English expatriates/immigrants living in the Czech Republic are speaking together about basic topics including travel, food and life in the Czech Republic vs their home countries.<br>The data is in English. It was used for analysis of language contact and grammatical borrowing. <br>In Observation Session 2, there was a Czech participant present (PCZ) who had lived in Australia for several years as an adult. Her data was not used for analysis in this study. <br><br><br>
DOI: 10.6084/m9.figshare.14350265.v1
title: Supplementary Material for: Risk Factors for Olfactory and Gustatory Dysfunctions in Patients with SARS-CoV-2 Infection

description: <b><i>Introduction:</i></b> Smell and taste loss are characteristic symptoms of SARS-CoV-2 infection. The aim of this study is to investigate the prevalence and risk factors associated with olfactory and gustatory dysfunctions in coronavirus disease (COVID-19) patients. <b><i>Methods:</i></b> We conducted an observational, retrospective study on 376 patients with documented SARS-CoV-2 infection admitted to the San Gerardo Hospital in Monza, Italy, from March to July 2020. All patients answered a phone questionnaire providing information on age, sex, smoking status, and clinical characteristics. Adjusted odds ratios (ORs) and corresponding 95% confidence intervals (CIs) were estimated through logistic regression models including relevant covariates. <b><i>Results:</i></b> The prevalence of olfactory and gustatory dysfunctions in COVID-19 patients was 33.5 and 35.6%, respectively. Olfactory dysfunctions were significantly directly associated with current smoking and history of allergy, the multivariable ORs being 6.53 (95% CI 1.16–36.86) for current smokers versus never smokers, and 1.89 (95% CI 1.05–3.39) for those with an allergy compared to those without any allergy. Respiratory allergy in particular was significantly associated with olfactory dysfunctions (multivariable OR 2.30, 95% CI 1.02–5.17). Significant inverse associations were observed for patients aged 60 years or more (multivariable OR 0.33, 95% CI 0.19–0.57) and hospitalization (multivariable OR 0.22, 95% CI 0.06–0.89). Considering gustatory dysfunctions, after allowance of other variables a significant direct association was found for respiratory allergies (OR 2.24, 95% CI 1.03–4.86), and an inverse association was found only for hospitalization (OR 0.21, 95% CI 0.06–0.76). <b><i>Conclusion:</i></b> Our study indicates that current smoking and history of allergy (particularly respiratory) significantly increase the risk for smell loss in COVID-19 patients; the latter is also significantly associated to taste loss. Hospitalization has an inverse association with the risk of olfactory and gustatory dysfunctions, suggesting that these may be symptoms characteristics of less severe SARS-CoV-2 infection.
DOI: 10.6084/m9.figshare.14350244
title: Supplementary Material for: Clinical Characteristics, Management, and Natural History of Chronic Inducible Urticaria in a Pediatric Cohort

description: <b><i>Background:</i></b> Some forms of chronic urticaria (CU) can be specifically attributed to a response to a definite trigger, referred to as chronic inducible urticaria (CIndU). We aimed to assess the demographics, clinical characteristics, comorbidities, natural history, and management of pediatric patients with CIndU. <b><i>Methods:</i></b> Over a 6-year period, children presenting to the allergy clinic at the Montreal Children’s Hospital (MCH) with CIndU were prospectively recruited. CU was defined as the presence of wheals and/or angioedema, occurring for at least 6 weeks. A standardized diagnostic test was used to establish the presence of a specific form of urticaria. Resolution was defined as the absence of hives for 1 year without treatment. <b><i>Results:</i></b> Sixty-four patients presented with CIndU, of which 51.6% were male, with a median age of 12.5 (interquartile range 7.3, 15.9) years. Cold CU and cholinergic CU were the most common subtypes (60.3 and 41.3%, respectively). Basophil counts were undetectable in 48.4% of the cases, and C-reactive protein levels were elevated in 7.8% of patients. Of all cases, 71.4% were controlled with second-generation antihistamines. The resolution rate was of 45.3% (95% confidence interval 33.1–57.5%), based on per-protocol population within the 6-year course of the study. Resolution was more likely in patients who presented with well-controlled urticaria control test scores and elevated CD63 counts and in those suffering from thyroid comorbidity. <b><i>Conclusion:</i></b> The natural history of CIndU resolution in pediatric patients was relatively low and was associated with elevated CD63 levels, as well as thyroid comorbidity.
DOI: 10.25909/12818849.v1
title: Interview Sessions in Prague: L1 English Expatriates

description: This dataset contains thirteen interviews. Thirteen participants are speaking with their researcher about their experiences with borrowing between languages.<br><br>The data is in English. It was used for analysis of the language contact situation between English and Czech for L1 English L2 Czech speakers living in the Czech Republic.
DOI: 10.6084/m9.figshare.14350226
title: Supplementary Material for: Chitin, Chitin Oligosaccharide, and Chitin Disaccharide Metabolism of <b><i>Escherichia coli</i></b> Revisited: Reassignment of the Roles of ChiA, ChbR, ChbF, and ChbG

description: <i>Escherichia coli</i> is unable to grow on polymeric and oligomeric chitin, but grows on chitin disaccharide (GlcNAc-GlcNAc; <i>N,N</i>′-diacetylchitobiose) and chitin trisaccharide (GlcNAc-GlcNAc-GlcNAc; <i>N,N</i>′<i>,N</i>′′-triacetylchitotriose) via expression of the <i>chb</i> operon (<i>chbBCARFG</i>). The phosphotransferase system (PTS) transporter ChbBCA facilitates transport of both saccharides across the inner membrane and their concomitant phosphorylation at the non-reducing end, intracellularly yielding GlcNAc 6-phosphate-GlcNAc (GlcNAc6P-GlcNAc) and GlcNAc6P-GlcNAc-GlcNAc, respectively. We revisited the intracellular catabolism of the PTS products, thereby correcting the reported functions of the 6-phospho-glycosidase ChbF, the monodeacetylase ChbG, and the transcriptional regulator ChbR. Intracellular accumulation of glucosamine 6P-GlcNAc (GlcN6P-GlcNAc) and GlcN6P-GlcNAc-GlcNAc in a <i>chbF</i> mutant unraveled a role for ChbG as a monodeacetylase that removes the <i>N-</i>acetyl group at the non-reducing end. Consequently, GlcN6P- but not GlcNAc6P-containing saccharides likely function as coactivators of ChbR. Furthermore, ChbF removed the GlcN6P from the non-reducing terminus of the former saccharides, thereby degrading the inducers of the <i>chb</i> operon and facilitating growth on the saccharides. Consequently, ChbF was unable to hydrolyze GlcNAc6P-residues from the non-reducing end, contrary to previous assumptions but in agreement with structural modeling data and with the unusual catalytic mechanism of the family 4 of glycosidases, to which ChbF belongs. We also refuted the assumption that ChiA is a bifunctional endochitinase/lysozyme ChiA, and show that it is unable to degrade peptidoglycans but acts as a bona fide chitinase in vitro and in vivo, enabling growth of <i>E. coli</i> on chitin oligosaccharides when ectopically expressed. Overall, this study revises our understanding of the chitin, chitin oligosaccharide, and chitin disaccharide metabolism of <i>E. coli</i>.
DOI: 10.48370/ofd/9kptss
title: Trędownik bulwiasty (Scrophularia nodosa L.), 8182

description: Herbarium
DOI: 10.6084/m9.figshare.14350271.v1
title: Raw Data - Atopic Biomarker Changes after Exposure to Porphyromonas gingivalis Lipopolysaccharide: A Small Experimental Study in Wistar Rat

description: <i>Background</i>. IgE and IgG<sub>4</sub> are implicated in atopic development and clinically utilized as major biomarkers. Atopic responses followingcertain pathogens such as <i>Porphyromonas gingivalis </i>is currently an area of interest for further research. <i>Purpose</i>. The aim of this study is to measure the level of IgE, IgG<sub>4</sub>, and IgG<sub>4</sub>/IgE ratio periodically after exposure of periodontal pathogen <i>Porphyromonas gingivalis</i>(Pg) lipopolysaccharide (LPS). <i>Methods</i>. We used 16 wistar rats (<i>Rattus norvegicus</i>) randomly subdivided into 4 groups, group 1 were injected by placebo, group 2 by LPS Pg 0.3 µg/mL,group 3 by LPS Pg 1 µg/mL, and group 4 by LPS Pg 3 µg/mL. Sera from both groups were taken from retro-orbital plexus before and after exposure. <i>Results</i>. Level of IgE and IgG<sub>4</sub> increased significantly following exposure of LPS Pg at day-4 and day-11. Greater increase of IgE rather than IgG<sub>4</sub> contributes to rapid decline of IgG<sub>4</sub>/IgE ratio, detected in the peripheral blood at day-4 and day-11. <i>Conclusion</i>. Modulation of atopic responses following exposure to LPS Pg is reflected bydecrease in IgG<sub>4</sub>/IgE ratio that accompanies an increase of IgE.
DOI: 10.6084/m9.figshare.14350271
title: Raw Data - Atopic Biomarker Changes after Exposure to Porphyromonas gingivalis Lipopolysaccharide: A Small Experimental Study in Wistar Rat

description: <i>Background</i>. IgE and IgG<sub>4</sub> are implicated in atopic development and clinically utilized as major biomarkers. Atopic responses followingcertain pathogens such as <i>Porphyromonas gingivalis </i>is currently an area of interest for further research. <i>Purpose</i>. The aim of this study is to measure the level of IgE, IgG<sub>4</sub>, and IgG<sub>4</sub>/IgE ratio periodically after exposure of periodontal pathogen <i>Porphyromonas gingivalis</i>(Pg) lipopolysaccharide (LPS). <i>Methods</i>. We used 16 wistar rats (<i>Rattus norvegicus</i>) randomly subdivided into 4 groups, group 1 were injected by placebo, group 2 by LPS Pg 0.3 µg/mL,group 3 by LPS Pg 1 µg/mL, and group 4 by LPS Pg 3 µg/mL. Sera from both groups were taken from retro-orbital plexus before and after exposure. <i>Results</i>. Level of IgE and IgG<sub>4</sub> increased significantly following exposure of LPS Pg at day-4 and day-11. Greater increase of IgE rather than IgG<sub>4</sub> contributes to rapid decline of IgG<sub>4</sub>/IgE ratio, detected in the peripheral blood at day-4 and day-11. <i>Conclusion</i>. Modulation of atopic responses following exposure to LPS Pg is reflected bydecrease in IgG<sub>4</sub>/IgE ratio that accompanies an increase of IgE.
DOI: 10.6084/m9.figshare.14350289
title: Supplementary Material for: Relationship between Immunophenotype and Clinicopathological Findings for Superficial Nonampullary Duodenal Epithelial Tumor

description: <b><i>Introduction:</i></b> The natural history and prognosis of superficial nonampullary duodenal epithelial tumors (SNADETs) remain uncertain. We elucidated the relationship between immunophenotype and clinicopathological features. <b><i>Materials and Methods:</i></b> A total of 98 SNADETs were divided into 3 groups according to immunohistochemical findings: gastric phenotype (G type), gastrointestinal phenotype (GI type), and intestinal phenotype (I type). Cellular dysplasia was divided into low-grade dysplasia and high-grade dysplasia/adenocarcinoma (≥HGD). White opaque substance (WOS) deposition was categorized into diffuse WOS, partial WOS, and no WOS, based on endoscopic findings. <b><i>Results:</i></b> Of the 98 SNADETs, 4 lesions (4.1%) were G type, 32 lesions (32.7%) were GI type, and 62 lesions (63.2%) were I type. All G-type SNADETs were located in the oral side of the papilla including the bulb, and the rate of bulbar lesions was significantly higher in the G type than in the GI and I types (<i>p</i> = 0.004). The most frequent type of WOS was no WOS (4/4, 100%) for G type, partial WOS (19/32, 59.4%) for GI type, and diffuse WOS (34/62, 54.8%) for I type (<i>p</i> &lt; 0.001), and loss of intestinal character was significantly correlated with WOS deficiency. GI/I-type SNADETs with partial or no WOS and G-type SNADETs were associated with ≥HGD. Additionally, the frequency of ≥HGD lesion was significantly higher in the CD10-negative group than in the CD10-positive group (57.1 vs. 19.8%, <i>p</i> = 0.043). <b><i>Conclusion:</i></b> Pathological intestinal character was correlated with the presence of WOS, and CD10 loss was associated with malignant potential of SNADETs.
DOI: 10.6084/m9.figshare.14350289.v1
title: Supplementary Material for: Relationship between Immunophenotype and Clinicopathological Findings for Superficial Nonampullary Duodenal Epithelial Tumor

description: <b><i>Introduction:</i></b> The natural history and prognosis of superficial nonampullary duodenal epithelial tumors (SNADETs) remain uncertain. We elucidated the relationship between immunophenotype and clinicopathological features. <b><i>Materials and Methods:</i></b> A total of 98 SNADETs were divided into 3 groups according to immunohistochemical findings: gastric phenotype (G type), gastrointestinal phenotype (GI type), and intestinal phenotype (I type). Cellular dysplasia was divided into low-grade dysplasia and high-grade dysplasia/adenocarcinoma (≥HGD). White opaque substance (WOS) deposition was categorized into diffuse WOS, partial WOS, and no WOS, based on endoscopic findings. <b><i>Results:</i></b> Of the 98 SNADETs, 4 lesions (4.1%) were G type, 32 lesions (32.7%) were GI type, and 62 lesions (63.2%) were I type. All G-type SNADETs were located in the oral side of the papilla including the bulb, and the rate of bulbar lesions was significantly higher in the G type than in the GI and I types (<i>p</i> = 0.004). The most frequent type of WOS was no WOS (4/4, 100%) for G type, partial WOS (19/32, 59.4%) for GI type, and diffuse WOS (34/62, 54.8%) for I type (<i>p</i> &lt; 0.001), and loss of intestinal character was significantly correlated with WOS deficiency. GI/I-type SNADETs with partial or no WOS and G-type SNADETs were associated with ≥HGD. Additionally, the frequency of ≥HGD lesion was significantly higher in the CD10-negative group than in the CD10-positive group (57.1 vs. 19.8%, <i>p</i> = 0.043). <b><i>Conclusion:</i></b> Pathological intestinal character was correlated with the presence of WOS, and CD10 loss was associated with malignant potential of SNADETs.
DOI: 10.5281/zenodo.4651305
title: mpeg-miv-database-A

description: This database contains a couple of multiview YUV 4:2:0 Texture and Depth sequence files with a json view parameters file, as it is used by MPEG Immersive Video (MIV) working group for the investigation on future ISO/IEC 23090- part 12 specification. Each zip file also contains a specific copyright license file. Cf www.mpeg-miv.org for further details.
DOI: 10.5281/zenodo.4651304
title: mpeg-miv-database-A

description: This database contains a couple of multiview YUV 4:2:0 Texture and Depth sequence files with a json view parameters file, as it is used by MPEG Immersive Video (MIV) working group for the investigation on future ISO/IEC 23090- part 12 specification. Each zip file also contains a specific copyright license file. Cf www.mpeg-miv.org for further details.
DOI: 10.5281/zenodo.4556885
title: RNA dataset generated by Taiyaki

description: RNA training data generated using Oxford Nanopore's research software Taiyaki. Instructions used to generate this data are available at: https://github.com/nanoporetech/taiyaki/blob/master/docs/walkthrough.rst This HDF5 file is comprised of 116,072 reads. Arabidopsis thaliana: 24,370, Epinano synthetic: 29,728, Homo Sapiens: 30,048, C. Elegans: 24,192, and E. Coli: 7,734. Arabidopsis data is from an in house, unreleased dataset. FLO-MIN106 SQK-RNA002 r9.4.1 Homo Sapiens data is from the Nanopore WGS Consortium (BHAM_RUN1), NA12878. FLO-MIN106 SQK-RNA001 r9.4 Epinano synthetic construct data is from SRA accession SRX5177013. FLO-MIN106 SQK-RNA001 r9.4.1 C. Elegans data is from ENA accession ERX3290223. FLO-MIN106 SQK-RNA001 r9.4 E.Coli data is from SRA accession SRX8495663<strong>. </strong>Unknown SQK-RNA001 r9.4
description: This work was supported by grants from the National Science Foundation (DGE-1450032 and DBI-1949036). Any opinions, findings, conclusions or recommendations expressed are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.
DOI: 10.5281/zenodo.4556884
title: RNA dataset generated by Taiyaki

description: RNA training data generated using Oxford Nanopore's research software Taiyaki. Instructions used to generate this data are available at: https://github.com/nanoporetech/taiyaki/blob/master/docs/walkthrough.rst This HDF5 file is comprised of 116,072 reads. Arabidopsis thaliana: 24,370, Epinano synthetic: 29,728, Homo Sapiens: 30,048, C. Elegans: 24,192, and E. Coli: 7,734. Arabidopsis data is from an in house, unreleased dataset. FLO-MIN106 SQK-RNA002 r9.4.1 Homo Sapiens data is from the Nanopore WGS Consortium (BHAM_RUN1), NA12878. FLO-MIN106 SQK-RNA001 r9.4 Epinano synthetic construct data is from SRA accession SRX5177013. FLO-MIN106 SQK-RNA001 r9.4.1 C. Elegans data is from ENA accession ERX3290223. FLO-MIN106 SQK-RNA001 r9.4 E.Coli data is from SRA accession SRX8495663<strong>. </strong>Unknown SQK-RNA001 r9.4
description: This work was supported by grants from the National Science Foundation (DGE-1450032 and DBI-1949036). Any opinions, findings, conclusions or recommendations expressed are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.
DOI: 10.5281/zenodo.4556951
title: RNA training and validation data

description: RNA training and validation data randomly selected from the Taiyaki formatted data available at https://doi.org/10.5281/zenodo.4556884 Chunk size 4096. All chunks were confined to a maximum of 70 samples per base.
description: This work was supported by grants from the National Science Foundation (DGE-1450032 and DBI-1949036). Any opinions, findings, conclusions or recommendations expressed are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.
DOI: 10.5281/zenodo.4556950
title: RNA training and validation data

description: RNA training and validation data randomly selected from the Taiyaki formatted data available at https://doi.org/10.5281/zenodo.4556884 Chunk size 4096. All chunks were confined to a maximum of 70 samples per base.
description: This work was supported by grants from the National Science Foundation (DGE-1450032 and DBI-1949036). Any opinions, findings, conclusions or recommendations expressed are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.
DOI: 10.5281/zenodo.4557005
title: RNA test dataset

description: Raw RNA sequencing data from Oxford Nanopore. Each dataset is comprised of 100k randomly selected reads. Arabidopsis data is from ENA accession ERX3766448. FLO-MIN106 SQK-RNA001 r9.4.1 Homo Sapiens data is from the Nanopore WGS Consortium (HOPKINS_RUN1), NA12878. FLO-MIN106 SQK-RNA001 r9.4 Mouse data is from ENA accession ERX3444723. FLO-MIN106 SQK-RNA001 r9.4.1 Poplar data is from SRA accession SRX9347134. FLO-MIN106 SQK-RNA001 r9.4.1 Yeast data is from SRA access SRX8120036. FLO-MIN106 SQK-RNA002 r9.4.1 Note: The yeast fast5 data (heatshock control) is stored here (https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?study=SRP166020)
description: This work was supported by grants from the National Science Foundation (DGE-1450032 and DBI-1949036). Any opinions, findings, conclusions or recommendations expressed are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.
DOI: 10.5281/zenodo.4557004
title: RNA test dataset

description: Raw RNA sequencing data from Oxford Nanopore. Each dataset is comprised of 100k randomly selected reads. Arabidopsis data is from ENA accession ERX3766448. FLO-MIN106 SQK-RNA001 r9.4.1 Homo Sapiens data is from the Nanopore WGS Consortium (HOPKINS_RUN1), NA12878. FLO-MIN106 SQK-RNA001 r9.4 Mouse data is from ENA accession ERX3444723. FLO-MIN106 SQK-RNA001 r9.4.1 Poplar data is from SRA accession SRX9347134. FLO-MIN106 SQK-RNA001 r9.4.1 Yeast data is from SRA access SRX8120036. FLO-MIN106 SQK-RNA002 r9.4.1 Note: The yeast fast5 data (heatshock control) is stored here (https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?study=SRP166020)
description: This work was supported by grants from the National Science Foundation (DGE-1450032 and DBI-1949036). Any opinions, findings, conclusions or recommendations expressed are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.