cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.21903879.v3
title: The diagnostic yield of CGH and WES in neurodevelopmental disorders

description: The diagnostic yield of CGH and WES in neurodevelopmental disorders.
DOI: 10.6084/m9.figshare.21903879.v2
title: The diagnostic yield of CGH and WES in neurodevelopmental disorders

description: The diagnostic yield of CGH and WES in neurodevelopmental disorders.
DOI: 10.6084/m9.figshare.21903879
title: The diagnostic yield of CGH and WES in neurodevelopmental disorders

description: The diagnostic yield of CGH and WES in neurodevelopmental disorders.
DOI: 10.5281/zenodo.7540354
title: Raw data files for the manuscript entitled "Solid-state synthesis of a MOF/polymer composite for hydrodeoxygenation of vanillin"

description: Datasets for the manuscript entitled "Solid-state synthesis of a MOF/polymer composite for hydrodeoxygenation of vanillin" published in Chemical Communications.
DOI: 10.5281/zenodo.7540353
title: Raw data files for the manuscript entitled "Solid-state synthesis of a MOF/polymer composite for hydrodeoxygenation of vanillin"

description: Datasets for the manuscript entitled "Solid-state synthesis of a MOF/polymer composite for hydrodeoxygenation of vanillin" published in Chemical Communications.
DOI: 10.6084/m9.figshare.21904071
title: Percentages - descriptive analysis.pdf

description: Descriptive analysis- percetanges included in the analysis of the students peer-feedback
DOI: 10.6084/m9.figshare.21904080
title: Means and SD.pdf

description: Means and SD refering to the analysis of peer-assessment of university students
DOI: 10.5281/zenodo.7538189
title: MUSES Fractional Vegetation Coverage (FVC) 8-Day Global 250m SIN Grid in 2008 (185–361)

description: The MUltiscale Satellite remotE Sensing (MUSES) product suite includes products with different spatial and temporal resolutions for parameters such as Normalized Difference Vegetation Index (NDVI), Near-Infrared Reflectance of Vegetation (NIRv), Leaf Area Index (LAI), Fraction of Absorbed Photosynthetically Active Radiation (FAPAR), Fractional Vegetation Coverage (FVC), Gross Primary Production (GPP), Net Primary Production (NPP). For more information about the MUSES products, please refer to this website (https://muses.bnu.edu.cn/). This dataset is the MUSES global FVC product at 250m spatial resolution and 8-day temporal resolution. The MUSES FVC product is provided on a Sinusoidal grid and spans from 2000 to 2019 (continuously updated). It was generated from the MUSES LAI product at 250m resolution and other ancillary information using the complement to unity of the transmittance of light through the entire canopy in the nadir viewing direction (Xiao <em>et al</em>., 2016). The MUSES FVC values are physically consistent with the corresponding MUSES LAI values. The MUSES FVC product is spatially complete and temporally continuous. This dataset is the MUSES FVC product in 2008 (185–361). <em>Please <strong>click here</strong> to download the MUSES FVC product <strong>in 2008 (001–177)</strong> and <em><strong>click here</strong> to download the MUSES FVC produ</em>ct <strong>in 2009 (001–177)</strong></em>. <strong>Dataset Characteristics:</strong> Spatial Coverage: Global Temporal Coverage: 2008 (185–361) Spatial Resolution: 250m Temporal Resolution: 8 days Projection: Sinusoidal Data Format: HDF Scale: 0.01 Valid Range: 0 – 100 <strong>Citation </strong>(Please cite this paper whenever these data are used)<strong>:</strong> Xiao Zhiqiang, <em>et a</em>l. (2016). Estimating the Fractional Vegetation Cover from GLASS Leaf Area Index Product. <em>Remote Sensing</em>, 8, 337. If you have any questions, please contact Prof. Zhiqiang Xiao (zhqxiao@bnu.edu.cn).
DOI: 10.5281/zenodo.7538188
title: MUSES Fractional Vegetation Coverage (FVC) 8-Day Global 250m SIN Grid in 2008 (185–361)

description: The MUltiscale Satellite remotE Sensing (MUSES) product suite includes products with different spatial and temporal resolutions for parameters such as Normalized Difference Vegetation Index (NDVI), Near-Infrared Reflectance of Vegetation (NIRv), Leaf Area Index (LAI), Fraction of Absorbed Photosynthetically Active Radiation (FAPAR), Fractional Vegetation Coverage (FVC), Gross Primary Production (GPP), Net Primary Production (NPP). For more information about the MUSES products, please refer to this website (https://muses.bnu.edu.cn/). This dataset is the MUSES global FVC product at 250m spatial resolution and 8-day temporal resolution. The MUSES FVC product is provided on a Sinusoidal grid and spans from 2000 to 2019 (continuously updated). It was generated from the MUSES LAI product at 250m resolution and other ancillary information using the complement to unity of the transmittance of light through the entire canopy in the nadir viewing direction (Xiao <em>et al</em>., 2016). The MUSES FVC values are physically consistent with the corresponding MUSES LAI values. The MUSES FVC product is spatially complete and temporally continuous. This dataset is the MUSES FVC product in 2008 (185–361). <em>Please <strong>click here</strong> to download the MUSES FVC product <strong>in 2008 (001–177)</strong> and <em><strong>click here</strong> to download the MUSES FVC produ</em>ct <strong>in 2009 (001–177)</strong></em>. <strong>Dataset Characteristics:</strong> Spatial Coverage: Global Temporal Coverage: 2008 (185–361) Spatial Resolution: 250m Temporal Resolution: 8 days Projection: Sinusoidal Data Format: HDF Scale: 0.01 Valid Range: 0 – 100 <strong>Citation </strong>(Please cite this paper whenever these data are used)<strong>:</strong> Xiao Zhiqiang, <em>et a</em>l. (2016). Estimating the Fractional Vegetation Cover from GLASS Leaf Area Index Product. <em>Remote Sensing</em>, 8, 337. If you have any questions, please contact Prof. Zhiqiang Xiao (zhqxiao@bnu.edu.cn).
DOI: 10.5281/zenodo.7539461
title: MUSES Fractional Vegetation Coverage (FVC) 8-Day Global 250m SIN Grid in 2008 (001–177)

description: The MUltiscale Satellite remotE Sensing (MUSES) product suite includes products with different spatial and temporal resolutions for parameters such as Normalized Difference Vegetation Index (NDVI), Near-Infrared Reflectance of Vegetation (NIRv), Leaf Area Index (LAI), Fraction of Absorbed Photosynthetically Active Radiation (FAPAR), Fractional Vegetation Coverage (FVC), Gross Primary Production (GPP), Net Primary Production (NPP). For more information about the MUSES products, please refer to this website (https://muses.bnu.edu.cn/). This dataset is the MUSES global FVC product at 250m spatial resolution and 8-day temporal resolution. The MUSES FVC product is provided on a Sinusoidal grid and spans from 2000 to 2019 (continuously updated). It was generated from the MUSES LAI product at 250m resolution and other ancillary information using the complement to unity of the transmittance of light through the entire canopy in the nadir viewing direction (Xiao <em>et al</em>., 2016). The MUSES FVC values are physically consistent with the corresponding MUSES LAI values. The MUSES FVC product is spatially complete and temporally continuous. This dataset is the MUSES FVC product in 2008 (001–177). <em>Please <strong><em>click</em> here</strong> to download the MUSES FVC product <strong>in 2007 (185–361)</strong></em>, and <em><strong>click here</strong> to download the MUSES FVC product <strong>in 2008 (185–361</strong></em><em><strong>)</strong></em>. <strong>Dataset Characteristics:</strong> Spatial Coverage: Global Temporal Coverage: 2008 (001–177) Spatial Resolution: 250m Temporal Resolution: 8 days Projection: Sinusoidal Data Format: HDF Scale: 0.01 Valid Range: 0 – 100 <strong>Citation </strong>(Please cite this paper whenever these data are used)<strong>:</strong> Xiao Zhiqiang, <em>et a</em>l. (2016). Estimating the Fractional Vegetation Cover from GLASS Leaf Area Index Product. <em>Remote Sensing</em>, 8, 337. If you have any questions, please contact Prof. Zhiqiang Xiao (zhqxiao@bnu.edu.cn).
DOI: 10.6084/m9.figshare.17696696
title: Phytochemical rich Himalayan <i>Rhododendron arboreum</i> petals inhibit SARS-CoV-2 infection <i>in vitro</i>

description: Phytochemicals with potential to competitively bind to the host receptors or inhibit SARS-CoV-2 replication, may prove to be useful as adjunct therapeutics for COVID-19. We profiled and investigated the phytochemicals of <i>Rhododendron arboreum</i> petals sourced from Himalayan flora, undertook <i>in vitro</i> studies and found it as a promising candidate against SARS-CoV-2. The phytochemicals were reported in various scientific investigations to act against a range of virus <i>in vitro</i> and <i>in vivo,</i> which prompted us to test against SARS-CoV-2. <i>In vitro</i> assays of <i>R. arboreum</i> petals hot aqueous extract confirmed dose dependent reduction in SARS-CoV-2 viral load in infected Vero E6 cells (80% inhibition at 1 mg/ml; IC50 = 173 µg/ml) and phytochemicals profiled were subjected to molecular docking studies against SARS CoV-2 target proteins. The molecules 5-O-Feruloyl-quinic acid, 3-Caffeoyl-quinic acid, 5-O-Coumaroyl-D-quinic acid, Epicatechin and Catechin showed promising binding affinity with SARS-CoV-2 Main protease (M<sup>Pro</sup>; PDB ID: 6LU7; responsible for viral replication) and Human Angiotensin Converting Enzyme-2 (ACE2; PDB ID: 1R4L; mediate viral entry in the host). Molecular dynamics (MD) simulation of 5-O-Feruloyl-quinic acid, an abundant molecule in the extract complexed with the target proteins showed stable interactions. Taken together, the phytochemical profiling, <i>in silico</i> analysis and <i>in vitro</i> anti-viral assay revealed that the petals extract act upon M<sup>Pro</sup> and may be inhibiting SARS-CoV-2 replication. This is the first report highlighting <i>R. arboreum</i> petals as a reservoir of antiviral phytochemicals with potential anti-SARS-CoV-2 activity using an <i>in vitro</i> system. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.17702089
title: DNA-binding, cleavage, antibacterial and <i>in vitro</i> anticancer activity of copper(II) mixed ligand complexes of 2-(((6-chloro-1H-benzo[d]imidazol-2-yl)methyl)amino)aceticacid and polypyridyl ligands

description: A tridentate ligand(A), 2-(((6-chloro-1H-benzo[d]imidazol-2-yl)methyl)amino) aceticacid (Cl-BIGH) was synthesised by the Phillips condensation of 4-chlorobenzene-1,2-diamine and iminodiaceticacid in 1:2 molar ratio. Its Cu(II) mixed ligand complexes[Cu(II)-A-L] were obtained by involving other co-ligands(L): 2,2΄-bipyridine(L<sub>1</sub>), 4,4΄-dimethyl-2,2΄-bipyridyl(L<sub>2</sub>), 5,5΄-dimethyl-2,2΄-bipyridyl(L<sub>3</sub>) and 1,10 phenanthroline(L<sub>4</sub>). The complexes were characterized by elemental analysis, thermal analysis, molar conductance, magnetic moment measurements, X-ray diffraction, FTIR, UV–Visible, ESR spectroscopy, mass spectrometry and cyclic voltammetry. From the spectral and analytical data, the ternary complexes [Cu(Cl-BIGH)(L<sub>1-4</sub>)]ClO<sub>4</sub> were found to form in 1:1:1(Cu(II): Cl-BIGH: L) molar ratio. The geometry of the mixed-ligand complexes were found to be 5-coordinated square pyramidal or trigonal bipyramidal with polycrystalline natures. The DNA binding and cleaving abilities, antibacterial and the <i>in vitro</i> cytotoxicity of the complexes were explored. The molecular docking was used to predict the efficiency of binding of the metal complexes with COX- 2. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.17702089.v1
title: DNA-binding, cleavage, antibacterial and <i>in vitro</i> anticancer activity of copper(II) mixed ligand complexes of 2-(((6-chloro-1H-benzo[d]imidazol-2-yl)methyl)amino)aceticacid and polypyridyl ligands

description: A tridentate ligand(A), 2-(((6-chloro-1H-benzo[d]imidazol-2-yl)methyl)amino) aceticacid (Cl-BIGH) was synthesised by the Phillips condensation of 4-chlorobenzene-1,2-diamine and iminodiaceticacid in 1:2 molar ratio. Its Cu(II) mixed ligand complexes[Cu(II)-A-L] were obtained by involving other co-ligands(L): 2,2΄-bipyridine(L<sub>1</sub>), 4,4΄-dimethyl-2,2΄-bipyridyl(L<sub>2</sub>), 5,5΄-dimethyl-2,2΄-bipyridyl(L<sub>3</sub>) and 1,10 phenanthroline(L<sub>4</sub>). The complexes were characterized by elemental analysis, thermal analysis, molar conductance, magnetic moment measurements, X-ray diffraction, FTIR, UV–Visible, ESR spectroscopy, mass spectrometry and cyclic voltammetry. From the spectral and analytical data, the ternary complexes [Cu(Cl-BIGH)(L<sub>1-4</sub>)]ClO<sub>4</sub> were found to form in 1:1:1(Cu(II): Cl-BIGH: L) molar ratio. The geometry of the mixed-ligand complexes were found to be 5-coordinated square pyramidal or trigonal bipyramidal with polycrystalline natures. The DNA binding and cleaving abilities, antibacterial and the <i>in vitro</i> cytotoxicity of the complexes were explored. The molecular docking was used to predict the efficiency of binding of the metal complexes with COX- 2. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.18012329.v1
title: Modeling, molecular dynamics and docking studies of a full-length <i>Echinococcus granulosus</i> 2DBD nuclear receptor

description: Nuclear receptors are ligand-activated transcription factors capable of regulating the expression of complex gene networks. The family includes seven subfamilies of protein with a wide phylogenetic distribution. A novel subfamily with two DNA-binding domains (2DBDs) has been first reported in <i>Schistosoma mansoni</i> (Platyhelminth, Trematoda). Employing an ab initio protocol and homology modeling methods, the full-length 3D structure of the Eg2DBDα.1 nuclear receptor from <i>Echinococcus granulosus</i> (Platyhelminth, Cestoda) was generated. The model analysis reveals the presence of the conserved three-layered alpha-helical sandwich structure in the ligand binding domain, and a particularly long and flexible hinge region. Molecular dynamics simulations were performed previous to dock a conformational library of fatty acids and retinoic acids. Our results indicate that oleic and linoleic acids are suitable ligands to this receptor. The ligand-protein complex is stabilized mainly by hydrogen bonds and hydrophobic interactions. The fact that 2DBD nuclear receptors have not been identified in vertebrates confers particular interest to these nuclear receptors, not only concerning their structure and function but as targets of new anthelmintic drugs. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.17705133.v1
title: Serine 106 preserves the tertiary structure, function, and stability of a cyclophilin from <i>Staphylococcus aureus</i>

description: SaCyp, a staphylococcal cyclophilin involved in both protein folding and pathogenesis, has a Ser residue at position 106 and a Trp residue at position 136. While Ser 106 of SaCyp aligned with a cyclosporin A (CsA) binding Ala residue, its Trp 136 aligned with a Trp or a Phe residue of most other cyclophilins. To demonstrate the exact roles of Ser 106 and Trp 136 in SaCyp, we have elaborately studied rCyp[S106A] and rCyp[W136A], two-point mutants of a recombinant SaCyp (rCyp) harboring an Ala substitution at positions 106 and 136, respectively. Of the mutants, rCyp[W136A] showed the rCyp-like CsA binding affinity and peptidyl-prolyl <i>cis</i>-<i>trans</i> isomerase (PPIase) activity. Conversely, the PPIase activity, CsA binding affinity, stability, tertiary structure, surface hydrophobicity, and Trp accessibility of rCyp[S106A] notably differed from those of rCyp. The computational experiments also reveal that the structure, dimension, and fluctuation of SaCyp are not identical to those of SaCyp[S106A]. Furthermore, Ser at position 106 of SaCyp, compared to Ala at the same position, formed a higher number of non-covalent bonds with CsA. Collectively, Ser 106 is an indispensable residue for SaCyp that keeps its tertiary structure, function, and stability intact. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.17708682
title: Computational refinement identifies functional destructive single nucleotide polymorphisms associated with human retinoid X receptor gene

description: Alterations in the nuclear retinoid X receptor (RXRs) signalling have been implicated in neurodegenerative disorders such as Alzheimer’s disease, Parkinson’s disease, stroke, multiple sclerosis and glaucoma. Single nucleotide polymorphisms (SNPs) are the main cause underlying single nucleic acid variations which in turn determine heterogeneity within various populations. These genetic polymorphisms have been suggested to associate with various degenerative disorders in population-wide analysis. This bioinformatics study was designed to investigate, search, retrieve and identify deleterious SNPs which may affect the structure and function of various RXR isoforms through a computational and molecular modelling approach. Amongst the 1,813 retrieved SNPs several were found to be deleterious with rs140464195_G139R, rs368400425_R358W and rs368586400_L383F <i>RXRα</i> mutant variants being the most detrimental ones causing changes in the interatomic interactions and decreasing the flexibility of the mutant proteins. Molecular genetics analysis identified seven missense mutations in RXRα/β/γ isoforms. Two novel mutations SNP IDs (rs1588299621 and rs1057519958) were identified in <i>RXRα</i> isoform. We used several <i>in silico</i> prediction tools such as SIFT, PolyPhen, I-Mutant, Protein Variation Effect Analyzer (PROVEAN), PANTHER, SNP&Go, PhD-SNP and SNPeffect to predict pathogenicity and protein stability associated with RXR mutations. The structural assessment by DynaMut tool revealed that hydrogen bonds were affected along with hydrophobic and carbonyl interactions resulting in reduced flexibility at the mutated residue positions but ultimately stabilizing the molecule as a whole. Summarizing, analysis of the missense mutations in RXR isoforms showed a mix of conclusive and inconclusive genotype–phenotype correlations suggesting the use of sophisticated computational analysis tools for studying RXR variants. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.17708682.v1
title: Computational refinement identifies functional destructive single nucleotide polymorphisms associated with human retinoid X receptor gene

description: Alterations in the nuclear retinoid X receptor (RXRs) signalling have been implicated in neurodegenerative disorders such as Alzheimer’s disease, Parkinson’s disease, stroke, multiple sclerosis and glaucoma. Single nucleotide polymorphisms (SNPs) are the main cause underlying single nucleic acid variations which in turn determine heterogeneity within various populations. These genetic polymorphisms have been suggested to associate with various degenerative disorders in population-wide analysis. This bioinformatics study was designed to investigate, search, retrieve and identify deleterious SNPs which may affect the structure and function of various RXR isoforms through a computational and molecular modelling approach. Amongst the 1,813 retrieved SNPs several were found to be deleterious with rs140464195_G139R, rs368400425_R358W and rs368586400_L383F <i>RXRα</i> mutant variants being the most detrimental ones causing changes in the interatomic interactions and decreasing the flexibility of the mutant proteins. Molecular genetics analysis identified seven missense mutations in RXRα/β/γ isoforms. Two novel mutations SNP IDs (rs1588299621 and rs1057519958) were identified in <i>RXRα</i> isoform. We used several <i>in silico</i> prediction tools such as SIFT, PolyPhen, I-Mutant, Protein Variation Effect Analyzer (PROVEAN), PANTHER, SNP&Go, PhD-SNP and SNPeffect to predict pathogenicity and protein stability associated with RXR mutations. The structural assessment by DynaMut tool revealed that hydrogen bonds were affected along with hydrophobic and carbonyl interactions resulting in reduced flexibility at the mutated residue positions but ultimately stabilizing the molecule as a whole. Summarizing, analysis of the missense mutations in RXR isoforms showed a mix of conclusive and inconclusive genotype–phenotype correlations suggesting the use of sophisticated computational analysis tools for studying RXR variants. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.17702088.v1
title: Genome-wide identification and analysis of the <i>PAL</i> genes from the orchids <i>Apostasia shenzhenica, Dendrobium catenatum</i> and <i>Phalaenopsis equestris</i>

description: Phenylalanine ammonia-lyase (PAL) is a key gateway enzyme that connects the phenylpropanoid pathway to primary metabolism. The phenylpropanoid pathway plays a vital role in the growth and environmental adaptation of many plants leading to the production of valuable bioactive compounds with industrial and medical applications. In the present study, nine putative <i>PAL</i> genes from three orchids were identified; five in <i>Apostasia shenzhenica</i> and two each in <i>Dendrobium catenatum</i> and <i>Phalaenopsis equestris</i>. Eighteen motifs and four major conserved functional domains were identified as reported in PAL proteins of other species. All the nine PALs were stable based on their computed physicochemical properties and localized in the cytoplasm. The three-dimensional structures of PALs revealed a homo-tetrameric structure consisting of four identical subunits. A total of 21 cis-regulatory elements with known functions were identified from the promoter regions of all PALs which are responsible for various plant responses to light, stress and growth regulators like auxins, gibberellins and abscisic acid. Phylogenetic analysis showed that the studied PAL proteins clustered in two major clades (clade I and II), placing dicot and monocot PALs in two separate monophyletic clades. <i>In silico</i> gene expression of the identified <i>PALs</i> in different vegetative and reproductive tissues revealed the differential expressions based on tissue type and disclosed that the expression of <i>PAL</i> genes was upregulated in all the tissues examined with an exception of <i>PePAL</i> leaf samples where no expression was detected, however, the same being highly expressed in reproductive tissues (<i>PePAL1</i>-labellum; <i>PePAL2</i>-sepal). In case of <i>AsPALs</i>, the expression was found to be highest in reproductive tissues (<i>AsPAL</i>4-maximum in inflorescence). On the other hand, the expression of <i>DcPALs</i> was found to be highest in vegetative tissues (<i>DcPAL2-</i>maximum in root). Based on the medicinal importance of orchids and the significant role of <i>PAL</i> genes in synthesis of bioactive compounds, the functional characterization of <i>PAL</i> genes can be further exploited in genetic improvement of medicinal orchids. Communicated by Ramaswamy H. Sarma