cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.4475261
title: Files for publication "Microseek: A Protein-Based Metagenomic Pipeline for Virus Diagnostic and Discovery"

description: <strong>Context</strong> These files correspond to the article “Microseek: A Protein-Based Metagenomic Pipeline for Virus Diagnostic and Discovery” submitted to Genes. <strong>File content</strong> empty_matrices: 50M-read Tissues and Plasma matrices, no spike; matrices_spiked_known_viruses: 50M-read Tissues and Plasma matrices spiked with six known virus at d1, d10, d100; matrices_spiked_neo_viruses: 50M-read Tissues and Plasma matrices spiked with 3 Neopneumoviruses at d1 and d10; neo_viruses: Nucleotide and protein sequences of 3 Neopeumoviruses output_microseek: Microseek outputs, raw results and results after background filtration <strong>File listing </strong> <pre><code class="language-bash">empty_matrices.tar.xz ├── plasma.fastq └── tissue.fastq matrices_spiked_known_viruses ├── d1 │ ├── spiked_plasma.fastq │ └── spiked_tissue.fastq ├── d10 │ ├── spiked_plasma.fastq │ └── spiked_tissue.fastq └── d100 ├── spiked_plasma.fastq └── spiked_tissue.fastq matrices_spiked_neo_viruses.tar.xz ├── d1 │ ├── plasma_spiked_with_neo1.fastq │ ├── plasma_spiked_with_neo2.fastq │ ├── plasma_spiked_with_neo3.fastq │ ├── tissue_spiked_with_neo1.fastq │ ├── tissue_spiked_with_neo2.fastq │ └── tissue_spiked_with_neo3.fastq └── d10 ├── plasma_spiked_with_neo1.fastq ├── plasma_spiked_with_neo2.fastq ├── plasma_spiked_with_neo3.fastq ├── tissue_spiked_with_neo1.fastq ├── tissue_spiked_with_neo2.fastq └── tissue_spiked_with_neo3.fastq neo_viruses.tar.xz ├── genes │ ├── neo_1.fasta │ ├── neo_2.fasta │ └── neo_3.fasta └── proteins ├── neo_1.fasta ├── neo_2.fasta └── neo_3.fasta output_microseek.tar.xz ├── empty_matrices │ ├── matrix_plasma │ └── matrix_tissue ├── matrices_spiked_known_viruses │ ├── filtered │ │ ├── d100_plasma │ │ ├── d100_tissue │ │ ├── d10_plasma │ │ ├── d10_tissue │ │ ├── d1_plasma │ │ └── d1_tissue │ └── non_filtered │ ├── d100_plasma │ ├── d100_tissue │ ├── d10_plasma │ ├── d10_tissue │ ├── d1_plasma │ └── d1_tissue └── matrices_spiked_neo_viruses ├── filtered │ ├── plasma_spiked_with_neo1_at_d1 │ ├── plasma_spiked_with_neo1_at_d10 │ ├── plasma_spiked_with_neo2_at_d1 │ ├── plasma_spiked_with_neo2_at_d10 │ ├── plasma_spiked_with_neo3_at_d1 │ ├── plasma_spiked_with_neo3_at_d10 │ ├── tissue_spiked_with_neo1_at_d1 │ ├── tissue_spiked_with_neo1_at_d10 │ ├── tissue_spiked_with_neo2_at_d1 │ ├── tissue_spiked_with_neo2_at_d10 │ ├── tissue_spiked_with_neo3_at_d1 │ └── tissue_spiked_with_neo3_at_d10 └── non-filtered ├── plasma_spiked_with_neo1_at_d1 ├── plasma_spiked_with_neo1_at_d10 ├── plasma_spiked_with_neo2_at_d1 ├── plasma_spiked_with_neo2_at_d10 ├── plasma_spiked_with_neo3_at_d1 ├── plasma_spiked_with_neo3_at_d10 ├── tissue_spiked_with_neo1_at_d1 ├── tissue_spiked_with_neo1_at_d10 ├── tissue_spiked_with_neo2_at_d1 ├── tissue_spiked_with_neo2_at_d10 ├── tissue_spiked_with_neo3_at_d1 └── tissue_spiked_with_neo3_at_d10 </code></pre>
DOI: 10.21227/jz39-0292
title: Dr.

description: Simulated data: dual-polarized antenna array in GNSS
DOI: 10.6084/m9.figshare.13312427
title: DKD dataset for repository.csv

description: Data set of patients of Diabetic Kidney Disease and controls with parameters of renal funcion and concentrations of arachidonic acid-derived eicasanoids in plasma and urine
DOI: 10.5517/ccdc.csd.cc258k56
title: CCDC 2004217: Experimental Crystal Structure Determination

description: Related Article: Jincheng Xu, Aishun Ding, Yanbin Zhang, Hao Guo|2021|J.Org.Chem.|86|3656|doi:10.1021/acs.joc.0c02781
DOI: 10.5517/ccdc.csd.cc25f51v
title: CCDC 2008646: Experimental Crystal Structure Determination

description: Related Article: Emilien Le Saux, Dengke Ma, Pablo Bonilla, Catherine M. Holden, Danilo Lustosa, Paolo Melchiorre|2021|Angew.Chem.,Int.Ed.|60|5357|doi:10.1002/anie.202014876
DOI: 10.6084/m9.figshare.14139632
title: HG00096 liftover files

description: Liftover results of HG00096 for TT-Mars
DOI: 10.6084/m9.figshare.14139632.v1
title: HG00096 liftover files

description: Liftover results of HG00096 for TT-Mars
DOI: 10.5517/ccdc.csd.cc25zxrv
title: CCDC 2025718: Experimental Crystal Structure Determination

description: Related Article: Philipp Holtkamp, Dario Poier, Beate Neumann, Hans-Georg Stammler, Norbert W. Mitzel|2021|Chem.-Eur.J.|27|3793|doi:10.1002/chem.202004600
DOI: 10.5517/ccdc.csd.cc25zxsw
title: CCDC 2025719: Experimental Crystal Structure Determination

description: Related Article: Philipp Holtkamp, Dario Poier, Beate Neumann, Hans-Georg Stammler, Norbert W. Mitzel|2021|Chem.-Eur.J.|27|3793|doi:10.1002/chem.202004600
DOI: 10.5517/ccdc.csd.cc25zxvy
title: CCDC 2025721: Experimental Crystal Structure Determination

description: Related Article: Philipp Holtkamp, Dario Poier, Beate Neumann, Hans-Georg Stammler, Norbert W. Mitzel|2021|Chem.-Eur.J.|27|3793|doi:10.1002/chem.202004600
DOI: 10.5517/ccdc.csd.cc25zxx0
title: CCDC 2025723: Experimental Crystal Structure Determination

description: Related Article: Philipp Holtkamp, Dario Poier, Beate Neumann, Hans-Georg Stammler, Norbert W. Mitzel|2021|Chem.-Eur.J.|27|3793|doi:10.1002/chem.202004600
DOI: 10.5517/ccdc.csd.cc25zxy1
title: CCDC 2025724: Experimental Crystal Structure Determination

description: Related Article: Philipp Holtkamp, Dario Poier, Beate Neumann, Hans-Georg Stammler, Norbert W. Mitzel|2021|Chem.-Eur.J.|27|3793|doi:10.1002/chem.202004600
DOI: 10.5517/ccdc.csd.cc25zxz2
title: CCDC 2025725: Experimental Crystal Structure Determination

description: Related Article: Philipp Holtkamp, Dario Poier, Beate Neumann, Hans-Georg Stammler, Norbert W. Mitzel|2021|Chem.-Eur.J.|27|3793|doi:10.1002/chem.202004600
DOI: 10.5517/ccdc.csd.cc26gg16
title: CCDC 2039677: Experimental Crystal Structure Determination

description: Related Article: Sonia Bruña, Alan. R. Kennedy, Michael Fairley, Charles T. O'Hara|2021|Chem.-Eur.J.|27|4134|doi:10.1002/chem.202004696
DOI: 10.5517/ccdc.csd.cc25zxtx
title: CCDC 2025720: Experimental Crystal Structure Determination

description: Related Article: Philipp Holtkamp, Dario Poier, Beate Neumann, Hans-Georg Stammler, Norbert W. Mitzel|2021|Chem.-Eur.J.|27|3793|doi:10.1002/chem.202004600
DOI: 10.5517/ccdc.csd.cc25zxwz
title: CCDC 2025722: Experimental Crystal Structure Determination

description: Related Article: Philipp Holtkamp, Dario Poier, Beate Neumann, Hans-Georg Stammler, Norbert W. Mitzel|2021|Chem.-Eur.J.|27|3793|doi:10.1002/chem.202004600
DOI: 10.5517/ccdc.csd.cc26q7nv
title: CCDC 2047167: Experimental Crystal Structure Determination

description: Related Article: José-Antonio García-López, María-José Oliva-Madrid, Delia Bautista, José Vicente, Isabel Saura-Llamas|2021|Organometallics|40|539|doi:10.1021/acs.organomet.0c00787
DOI: 10.5517/ccdc.csd.cc26q7pw
title: CCDC 2047168: Experimental Crystal Structure Determination

description: Related Article: José-Antonio García-López, María-José Oliva-Madrid, Delia Bautista, José Vicente, Isabel Saura-Llamas|2021|Organometallics|40|539|doi:10.1021/acs.organomet.0c00787
DOI: 10.5517/ccdc.csd.cc26q7qx
title: CCDC 2047169: Experimental Crystal Structure Determination

description: Related Article: José-Antonio García-López, María-José Oliva-Madrid, Delia Bautista, José Vicente, Isabel Saura-Llamas|2021|Organometallics|40|539|doi:10.1021/acs.organomet.0c00787
DOI: 10.5517/ccdc.csd.cc26q7v1
title: CCDC 2047173: Experimental Crystal Structure Determination

description: Related Article: José-Antonio García-López, María-José Oliva-Madrid, Delia Bautista, José Vicente, Isabel Saura-Llamas|2021|Organometallics|40|539|doi:10.1021/acs.organomet.0c00787
DOI: 10.5517/ccdc.csd.cc26q7x3
title: CCDC 2047175: Experimental Crystal Structure Determination

description: Related Article: José-Antonio García-López, María-José Oliva-Madrid, Delia Bautista, José Vicente, Isabel Saura-Llamas|2021|Organometallics|40|539|doi:10.1021/acs.organomet.0c00787
DOI: 10.5517/ccdc.csd.cc26q7z5
title: CCDC 2047177: Experimental Crystal Structure Determination

description: Related Article: José-Antonio García-López, María-José Oliva-Madrid, Delia Bautista, José Vicente, Isabel Saura-Llamas|2021|Organometallics|40|539|doi:10.1021/acs.organomet.0c00787
DOI: 10.5517/ccdc.csd.cc26q807
title: CCDC 2047178: Experimental Crystal Structure Determination

description: Related Article: José-Antonio García-López, María-José Oliva-Madrid, Delia Bautista, José Vicente, Isabel Saura-Llamas|2021|Organometallics|40|539|doi:10.1021/acs.organomet.0c00787
DOI: 10.5517/ccdc.csd.cc26rf6m
title: CCDC 2048300: Experimental Crystal Structure Determination

description: Related Article: Lihui Fan, Shengjie Lin, Xinxin Wang, Lianglan Yue, Tingting Xu, Zhenzhen Jiang, Yabing He|2021|Inorg.Chem.|60|2704|doi:10.1021/acs.inorgchem.0c03583
DOI: 10.5517/ccdc.csd.cc26rf5l
title: CCDC 2048299: Experimental Crystal Structure Determination

description: Related Article: Lihui Fan, Shengjie Lin, Xinxin Wang, Lianglan Yue, Tingting Xu, Zhenzhen Jiang, Yabing He|2021|Inorg.Chem.|60|2704|doi:10.1021/acs.inorgchem.0c03583
DOI: 10.5517/ccdc.csd.cc26rf7n
title: CCDC 2048301: Experimental Crystal Structure Determination

description: Related Article: Lihui Fan, Shengjie Lin, Xinxin Wang, Lianglan Yue, Tingting Xu, Zhenzhen Jiang, Yabing He|2021|Inorg.Chem.|60|2704|doi:10.1021/acs.inorgchem.0c03583
DOI: 10.6084/m9.figshare.14139683
title: Supplementary Material for: Topical Applications of a Heparinoid-Containing Product Attenuate Glucocorticoid-Induced Alterations in Epidermal Permeability Barrier in Mice

description: <b><i>Introduction:</i></b> Either systemic or topical glucocorticoids (GCs) can cause significant adverse effects on cutaneous structure and function. Although some products and ingredients can improve GC-induced abnormalities in epidermal permeability barrier, the efficacy is moderate. Prior studies in normal mice showed that topical applications of a heparinoid-containing product, Hirudoid® cream, improve epidermal barrier function by upregulation of epidermal proliferation, expression of mRNA for epidermal differentiation, and lipid production. <b><i>Objective:</i></b> The objective of this study was to assess whether topical applications of this product could prevent GC-induced changes in epidermal function in murine skin. <b><i>Materials and Methods:</i></b> One group of C57BL/6J mice was treated topically with 0.05% clobetasol propionate twice daily for 6 days, while another group was treated topically with Hirudoid® cream 30 min after each application of clobetasol propionate. Untreated mice served as normal controls. Transepidermal water loss (TEWL) rates, stratum corneum hydration, and skin surface pH were measured using respective probes connected to an MPA5 physiology monitor. qPCR was used to measure the expression levels of mRNA for keratinocyte differentiation-related proteins and lipid synthetic enzymes. <b><i>Results:</i></b> Co-applications of Hirudoid® cream with GC minimally, but significantly, increased skin thickness in comparison to GC treatment alone (<i>p</i> &lt; 0.05), in parallel with increased expression levels of mRNA for PCNA in both the dermis and the epidermis. Moreover, Hirudoid® cream largely prevented GC-induced elevation in basal TEWL (<i>p</i> &lt; 0.001) and delay in barrier recovery (<i>p</i> &lt; 0.05), accompanied by upregulation in the expression levels of mRNA for epidermal involucrin, HMGCoA, and SPT1. However, both stratum corneum hydration and skin surface pH were comparable in the skin treated with GC alone versus GC + Hirudoid® cream. <b><i>Conclusion:</i></b> Topical heparinoid-containing product can partially prevent GC-induced alterations in some epidermal functions.
DOI: 10.6084/m9.figshare.14139683.v1
title: Supplementary Material for: Topical Applications of a Heparinoid-Containing Product Attenuate Glucocorticoid-Induced Alterations in Epidermal Permeability Barrier in Mice

description: <b><i>Introduction:</i></b> Either systemic or topical glucocorticoids (GCs) can cause significant adverse effects on cutaneous structure and function. Although some products and ingredients can improve GC-induced abnormalities in epidermal permeability barrier, the efficacy is moderate. Prior studies in normal mice showed that topical applications of a heparinoid-containing product, Hirudoid® cream, improve epidermal barrier function by upregulation of epidermal proliferation, expression of mRNA for epidermal differentiation, and lipid production. <b><i>Objective:</i></b> The objective of this study was to assess whether topical applications of this product could prevent GC-induced changes in epidermal function in murine skin. <b><i>Materials and Methods:</i></b> One group of C57BL/6J mice was treated topically with 0.05% clobetasol propionate twice daily for 6 days, while another group was treated topically with Hirudoid® cream 30 min after each application of clobetasol propionate. Untreated mice served as normal controls. Transepidermal water loss (TEWL) rates, stratum corneum hydration, and skin surface pH were measured using respective probes connected to an MPA5 physiology monitor. qPCR was used to measure the expression levels of mRNA for keratinocyte differentiation-related proteins and lipid synthetic enzymes. <b><i>Results:</i></b> Co-applications of Hirudoid® cream with GC minimally, but significantly, increased skin thickness in comparison to GC treatment alone (<i>p</i> &lt; 0.05), in parallel with increased expression levels of mRNA for PCNA in both the dermis and the epidermis. Moreover, Hirudoid® cream largely prevented GC-induced elevation in basal TEWL (<i>p</i> &lt; 0.001) and delay in barrier recovery (<i>p</i> &lt; 0.05), accompanied by upregulation in the expression levels of mRNA for epidermal involucrin, HMGCoA, and SPT1. However, both stratum corneum hydration and skin surface pH were comparable in the skin treated with GC alone versus GC + Hirudoid® cream. <b><i>Conclusion:</i></b> Topical heparinoid-containing product can partially prevent GC-induced alterations in some epidermal functions.
DOI: 10.6084/m9.figshare.14139626
title: Supplementary Material for: Association between Down Syndrome and Disorders of Sex Development: Report of Three Cases and Review of 188 Cases in the Literature

description: In this study, we present 3 cases of Down syndrome (DS) associated with disorders/differences of sex development (DSD) and review the literature on this topic. Case 1: 1-year-old child with male genitalia and DS phenotype, 47,XX,+21 karyotype and testicular DSD. Case 2: 11-month-old child with male genitalia and few DS dysmorphisms, 45,X/47,XY,+21 karyotype, and mixed gonadal dysgenesis. Case 3: 4-month-old child with female genitalia and DS phenotype, 47,XY,+21 karyotype and XY complete gonadal dysgenesis. In the literature, among 188 patients, 107 (57%) had Klinefelter syndrome and 61 (33%) Turner syndrome, 12 (6%) had mixed gonadal dysgenesis, 2 (1%) had partial androgen insensitivity, 2 (1%) ovotesticular DSD, and the others had congenital adrenal hyperplasia, XY partial gonadal dysgenesis, XY complete gonadal dysgenesis, and complete androgen insensitivity (1 case each). A typical DS phenotype was found in all individuals of the revision, with the exception of one case, but DSD features were not always reported. In conclusion, the association of DS with sex chromosome DSD is the most frequently observed, whereas associations with 46,XX and 46,XY DSD is extremely rare.
DOI: 10.6084/m9.figshare.12191898
title: Darwinian Selection Discriminates Young Athletes: The Relative Age Effect in Relation to Sporting Performance

description: Jakobsson, J., Julin, A.L., Persson, G. <i>et al.</i> Darwinian Selection Discriminates Young Athletes: the Relative Age Effect in Relation to Sporting Performance. <i>Sports Med - Open</i> 7, 16 (2021). <br>DOI <br>https://doi.org/10.1186/s40798-021-00300-2<br><br><br><br>Supplementary data files 1 to 5 <br><br>Including raw data sets and additional tables with extended statistical information.
DOI: 10.5281/zenodo.3948424
title: On the donor substrate dependence of group transfer reactions by hydrolytic enzymes: insight from kinetic analysis of sucrose phosphorylase-catalyzed transglycosylation

description: We provide here the underlying data of the publication "On the donor substrate dependence of group transfer reactions by hydrolytic enzymes: insight from kinetic analysis of sucrose phosphorylase-catalyzed transglycosylation". Please find the abstract below. Chemical group-transfer reactions by hydrolytic enzymes have considerable importance in biocatalytic synthesis and are exploited broadly in commercial-scale chemical production. Mechanistically, these reactions have in common the involvement of a covalent enzyme intermediate which is formed upon enzyme reaction with the donor substrate and is subsequently intercepted by a suitable acceptor. Here, we studied the glycosylation of glycerol from sucrose by sucrose phosphorylase (SucP) to clarify a peculiar, yet generally important characteristic of this reaction: partitioning between glycosylation of glycerol and hydrolysis depends on the type and the concentration of the donor substrate used (here: sucrose, α-D-glucose 1-phosphate (G1P)). We develop a kinetic framework to analyze the effect and provide evidence that, when G1P is used as donor substrate, hydrolysis occurs not only from the β-glucosyl-enzyme intermediate (E-Glc), but additionally from a noncovalent complex of E-Glc and substrate which unlike E-Glc is unreactive to glycerol. Depending on the relative rates of hydrolysis of free and substrate-bound E-Glc, inhibition (Leuconostoc mesenteroides SucP) or apparent activation (Bifidobacterium adolescentis SucP) is observed at high donor substrate concentration. At a G1P concentration that excludes the substrate-bound E-Glc, the transfer/hydrolysis ratio changes to a value consistent with reaction exclusively through E-Glc, independent of the donor substrate used. Collectively, these results give explanation for a kinetic behavior of SucP not previously accounted for, provide essential basis for design and optimization of the synthetic reaction, and establish a theoretical framework for the analysis of kinetically analogous group transfer reactions by hydrolytic enzymes.
DOI: 10.5281/zenodo.3948423
title: On the donor substrate dependence of group transfer reactions by hydrolytic enzymes: insight from kinetic analysis of sucrose phosphorylase-catalyzed transglycosylation

description: We provide here the underlying data of the publication "On the donor substrate dependence of group transfer reactions by hydrolytic enzymes: insight from kinetic analysis of sucrose phosphorylase-catalyzed transglycosylation". Please find the abstract below. Chemical group-transfer reactions by hydrolytic enzymes have considerable importance in biocatalytic synthesis and are exploited broadly in commercial-scale chemical production. Mechanistically, these reactions have in common the involvement of a covalent enzyme intermediate which is formed upon enzyme reaction with the donor substrate and is subsequently intercepted by a suitable acceptor. Here, we studied the glycosylation of glycerol from sucrose by sucrose phosphorylase (SucP) to clarify a peculiar, yet generally important characteristic of this reaction: partitioning between glycosylation of glycerol and hydrolysis depends on the type and the concentration of the donor substrate used (here: sucrose, α-D-glucose 1-phosphate (G1P)). We develop a kinetic framework to analyze the effect and provide evidence that, when G1P is used as donor substrate, hydrolysis occurs not only from the β-glucosyl-enzyme intermediate (E-Glc), but additionally from a noncovalent complex of E-Glc and substrate which unlike E-Glc is unreactive to glycerol. Depending on the relative rates of hydrolysis of free and substrate-bound E-Glc, inhibition (Leuconostoc mesenteroides SucP) or apparent activation (Bifidobacterium adolescentis SucP) is observed at high donor substrate concentration. At a G1P concentration that excludes the substrate-bound E-Glc, the transfer/hydrolysis ratio changes to a value consistent with reaction exclusively through E-Glc, independent of the donor substrate used. Collectively, these results give explanation for a kinetic behavior of SucP not previously accounted for, provide essential basis for design and optimization of the synthetic reaction, and establish a theoretical framework for the analysis of kinetically analogous group transfer reactions by hydrolytic enzymes.
DOI: 10.6084/m9.figshare.14139671
title: Data of Energy from computational chemistry calculation and the total vapour pressure data from the experiment

description: Energy, enthalpy, and Gibbs free energy data are obtained from computational chemistry calculations. The total vapour pressure data of the benzene-toluene and the acetonitrile-methanol mixture.
DOI: 10.6084/m9.figshare.14139671.v1
title: Data of Energy from computational chemistry calculation and the total vapour pressure data from the experiment

description: Energy, enthalpy, and Gibbs free energy data are obtained from computational chemistry calculations. The total vapour pressure data of the benzene-toluene and the acetonitrile-methanol mixture.
DOI: 10.6084/m9.figshare.14139713
title: <i>In silico</i> identification of epitope-based vaccine candidates against HTLV-1

description: Human T cell leukemia virus type-1 (HTLV-1) is the cause of adult T cell leukemia/lymphoma (ATL), uveitis, and certain pulmonary diseases. In recent decades, many scientists have proposed the development of different treatment and prevention strategies to combat HTLV-1 infection. In this study, we used bioinformatics tools to predict peptide and protein vaccine candidates against HTLV-1 that can potentially induce antibody production and both CD4+ and CD8+ T cell immune responses. Five critical proteins, viz., <i>Hbz, Tax, Pol, Gag</i>, and <i>Env, were</i> analyzed for predicting immunogenic T and B cell epitopes and subsequently evaluated using bioinformatics tools. Based on the predictions, the most antigenic epitopes were selected, and their interaction with immune receptors was investigated. We also designed a protein vaccine candidate with an eight-epitopes-rich domain, including <b>overlapping epitopes detected on both B and T cells.</b> Then, the interaction of the epitope and the designed protein with immune receptors was validated in an <i>in silico</i> docking study. The docking analysis showed that the O2 epitope and D8 protein interact strongly with immune receptors, especially the HLA-A*02:01 receptor. The stability of the interactions was investigated by molecular dynamics (MD) for 100 ns. The root mean square deviation, radius of gyration, hydrogen bonds, and solvent-accessible surface area were calculated for the 100 ns trajectory period. MD studies demonstrated that the O2–HLA-A*02:01 and D8–HLA-A*02:01 complexes were stable during the simulation. Analysis of <i>in silico</i> results showed that the peptide and the designed protein could elicit humoral and cell-mediated immune responses. Communicated by Ramaswamy H. Sarma