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669 results for “substitution”
Hydrogen storage properties of Mn and Cu for Fe substitution in TiFe0.9 intermetallic compound - Dataset related to publication.
<p>Data type: Experimental measurements, correlations and Van't Hoff plot. Date format: .opj. Origin of the data: Experimental pressure composition isotherm measurements. Data generated by a home-made Sieverts’ type apparatus from CNRS, ICMPE, Thiais, France. Software needed to plot the data: Origin.</p>
Magnetism of Topological Boundary States Induced by Boron Substitution in Graphene Nanoribbons
<p>OPEN DATA related to the research publication:</p> <p>Niklas Friedrich, Pedro Brandimarte, Jingcheng Li, Shohei Saito, Shigehiro Yamaguchi, Iago Pozo, Diego Peña, Thomas Frederiksen, Aran Garcia-Lekue, Daniel Sánchez-Portal, and José Ignacio Pascual, <em>Magnetism of Topological Boundary States Induced by Boron Substitution in Graphene Nanoribbons</em>, Phys. Rev. Lett. <strong>125</strong>, 146801 (2020) [arXiv:2004.10280]</p> <p>Abstract: Graphene nanoribbons (GNRs), low-dimensional platforms for carbon-based electronics, show the promising perspective to also incorporate spin polarization in their conjugated electron system. However, magnetism in GNRs is generally associated with localized states around zigzag edges, difficult to fabricate and with high reactivity. Here we demonstrate that magnetism can also be induced away from physical GNR zigzag edges through atomically precise engineering topological defects in its interior. A pair of substitutional boron atoms inserted in the carbon backbone breaks the conjugation of their topological bands and builds two spin-polarized boundary states around them. The spin state was detected in electrical transport measurements through boron-substituted GNRs suspended between the tip and the sample of a scanning tunneling microscope. First-principle simulations find that boron pairs induce a spin 1, which is modified by tuning the spacing between pairs. Our results demonstrate a route to embed spin chains in GNRs, turning them into basic elements of spintronic devices.</p>
Fundamental hydrogen storage properties of TiFe-alloy with partial substitution of Fe by Ti and Mn - Dataset related to publication
<p>Data type: Experimental measurements, correlations and Van't Hoff plot. Date format: .opj. Origin of the data: Experimental pressure composition isotherm measurements. Data generated by a home-made Sieverts’ type apparatus from CNRS, ICMPE, Thiais, France. Software needed to plot the data: Origin.</p>
In-situ neutron diffraction during reversible deuterium loading in Ti-rich and Mn-substituted Ti(Fe,Mn)0.90 alloys - Dataset related to publication
<p>Data type: resume of Rietveld refinement outputs and original refinements</p> <p>Date format: .zip, .opj; .xlsm, .dat, .pcr (Software FullProf package outputs), .inp (Software Topas package outputs)</p> <p>Origin of the data: neutron diffraction patterns from ILL and ISIS, and manual Sievert measurements (PCI curves from home-made Sieverts’ type apparatus from CNRS, ICMPE, Thiais, France)</p> <p>Software needed to plot the data: folders need to be unzipped, Origin, FullProf package and Topas package.</p>
S108 | SINLIST | SIN (Substitute It Now) list of hazardous chemicals by ChemSec
<p>This is the collection associated with list S108 SINLIST SIN (Substitute It Now) list of hazardous chemicals by ChemSec on the NORMAN Suspect List Exchange.</p> <p><a href="https://www.norman-network.com/nds/SLE/">https://www.norman-network.com/nds/SLE/</a></p> <p>SIN (Substitute It Now) list of hazardous chemicals used in a wide variety of articles, products and manufacturing processes around the globe.The SIN List consists of chemicals that have been identified by the non-profit <a href="https://sinlist.chemsec.org/">ChemSec</a> as being Substances of Very High Concern, based on the criteria defined within REACH, the EU chemicals legislation.The SIN abbreviation – Substitute It Now – implies that these chemicals should be removed as soon as possible as they pose a threat to human health and the environment.<br>The list was kindly provided by Anna Lennquist (ChemSec, Sweden) and Hans Peter Arp (NGI,NTNU, Norway).</p> <p>List updated with new substances on 08 May 2024</p>
Discovery and characterization of pyridine and furan substituted ligands of choline acetyltransferase
<p><span>This repository contains datasets for the manuscript "Discovery and characterization of pyridine and furan substituted ligands of choline acetyltransferase"</span></p> <ul> <li><span>Data set of 1.4 million compounds used for virtual screening are freely available at </span><span><a href="https://vitasmlab.biz/downloads"><span>https://vitasmlab.biz/downloads</span></a></span><span>. Vina-MPI used for the virtual screening protocol is freely available at </span><span><a href="https://github.com/mokarrom/mpi-vina"><span>https://github.com/mokarrom/mpi-vina</span></a></span><span>. </span></li> <li><span>The docking pose and docking score for the screened library with Vina-MPI is available in PDBQT format with their docking scores in the folder “vitas_virtual_screening_800K”.</span></li> <li><span>Selected 5958 compounds from the virtual screening are given as PDBQT with docking scores in folder “top_5K_hits”.</span></li> <li><span>Re-docked docking score (Top_5K_re_docking.sdf) and MMGBSA (Top_250_MMGBSA.sdf) calculation are also available with the structures in SDF format.</span></li> </ul>
Data for "Meat and dairy substitutes – better for health and the environment? Impacts on nutrition and sustainability; consumer perspectives; ethical and legal considerations"
<p>Combined data reposatory for the output of the project "Meat and dairy substitutes – better for health and the environment? Impacts on nutrition and sustainability; consumer perspectives; ethical and legal considerations"</p> <p><em>Kombiniertes Datenarchiv für die Ergebnisse des Projekts "Fleisch- und Milchersatzprodukte – besser für Gesundheit und Umwelt? Auswirkungen auf Ernährung und Nachhaltigkeit, die Sicht der Konsumentinnen und Konsumenten sowie ethische und rechtliche Überlegungen"</em></p> <p>The project was funded by the Foundation for Technology Assessment (TA-Swiss) "<a href="https://ror.org/02shtak05">ror.org/02shtak05</a>".</p> <p><em>Das Projekt wurde von der Stiftung für Technologiefolgen-Abschätzung (TA-Swiss) finanziert "<a href="https://ror.org/02shtak05">ror.org/02shtak05</a>". </em></p>
Figures - Vat photopolymerization of biomimetic bone scaffolds based on Mg, Sr, Zn-substituted hydroxyapatite: Effect of sintering temperature
<p>Figures of publication "<span>Vat photopolymerization of biomimetic bone scaffolds based on Mg, Sr, Zn-substituted hydroxyapatite: Effect of sintering temperature</span>".</p> <p><a title="Persistent link using digital object identifier" href="https://doi.org/10.1016/j.ceramint.2024.05.038" target="_blank" rel="noreferrer noopener"><span><span>https://doi.org/10.1016/j.ceramint.2024.05.038</span></span></a></p>
Data for: BetaScan2: Standardized Statistics to Detect Balancing Selection Utilizing Substitution Data
<p>Genome-wide scan using BetaScan2 in 1KG populations report in:</p> <p><a href="https://pubmed.ncbi.nlm.nih.gov/32011695/">BetaScan2: Standardized Statistics to Detect Balancing Selection Utilizing Substitution Data.</a></p> <p>Siewert KM, Voight BF.Genome Biol Evol. 2020 Feb 1;12(2):3873-3877. doi: 10.1093/gbe/evaa013.</p> <p>PMID: 32011695 </p> <p>Code available at: https://github.com/ksiewert/BetaScan</p>
Dataset for "Phenolic Substitution in Fidaxomicin: A Semisynthetic Approach to Antibiotic Activity Across Species"
<p>ZIP File:</p> <p>Characterisation data (such as e.g. NMR, IR, MS spectra)</p> <p>NMR raw data, .mnova files</p> <p>ChemDraw drawings (.cdx files)</p> <p>PDF file:</p> <p>Supporting information for</p> <p><strong>Phenolic Substitution in Fidaxomicin: A Semisynthetic Approach to Antibiotic Activity Across Species</strong></p> <p><br> Erik Jung,[a] Anastassia Kraimps,[a] Silvia Dittmann,[b] Tizian Griesser,[c] Jordan Costafrolaz,[d] Yves Mattenberger,[d] Simon Jurt,[a] Patrick H. Viollier,[d] Peter Sander,[c] Susanne Sievers,[b] and Karl Gademann*[a]</p> <p>[a] E. Jung, A. Kraimps, S. Jurt, Prof. Dr. K. Gademann Department of Chemistry, University of Zurich 8057 Zürich (Switzerland)<br> E-mail: karl.gademann@uzh.ch<br> [b] S. Dittmann, Dr. S. Sievers<br> Department of Microbial Physiology and Molecular Biology Institute of Microbiology<br> Center for Functional Genomics of Microbes<br> University of Greifswald<br> Greifswald (Germany)<br> [c] T. Griesser, Prof. Dr. P. Sander Institute of Medical Microbiology University of Zurich<br> Zurich (Switzerland)<br> [d] J. Costafrolaz, Dr. Y. Mattenberger, Prof. Dr. P. H. Viollier Department of Microbiology and Molecular Medicine Faculty of Medicine, University of Geneva<br> Geneva (Switzerland)<br> </p> <p>Abstract of the corresponding publication:</p> <p>Fidaxomicin (Fdx) is a natural product antibiotic with potent activity against Clostridioides difficile and other Gram-positive bacteria such as Mycobacterium tuberculosis. Only a few Fdx derivatives have been synthesized and examined for their biological activity in the 50 years since its discovery. Fdx has a well-studied mechanism of action, namely inhibition of the bacterial RNA polymerase. Yet, the targeted organisms harbor different target protein sequences, which poses a challenge for the rational development of new semisynthetic Fdx derivatives. We introduced substituents on the two phenolic hydroxy<br> groups of Fdx and evaluated the resulting trends in antibiotic activity against M. tuberculosis, C. difficile, and the Gram-neg- ative model organism Caulobacter crescentus. As suggested by the target protein structures, we identified the preferable derivatisation site for each organism. The derivative ortho- methyl Fdx also exhibited activity against the Gram-negative C. crescentus wild type, a first for fidaxomicin antibiotics. These insights will guide the synthesis of next-generation fidaxomicin antibiotics.</p>
Dataset for study "Band gap engineering by cationic substitution in Sn(Zr1-xTix)Se3 alloy for bottom sub-cell application in solar cells"
<p>This dataset contains raw and processed data that were used to for the study entilted "Band gap engineering by cationic substitution in Sn(Zr1-xTix)Se3 alloy for bottom sub-cell application in solar cells". </p>
Figure 2 in Cicada minimum age tree: Cryptic speciation and exponentially increasing base substitution rates in recent geologic time
Figure 2. Cicada timetree built by BEAST v1.X, applying 1,534 bp COI sequence. OUTs with isolate number: our own analyzed specimens shown in Table 1, and others: from GenBank/DDJB. In outgroup Hemiptera; #: analyzed family by Johnson et al. (2018); % analyzed family by Misof et al. (2014). Inserted figure: Base substitution rate (= rate median shown at each node; substitutions per site per million year; s/s/myr) vs age (= posterior age shown at each node) diagram. Red approximate curve with its formula was drawn by Excel function, with the intersection for the curve = 0.0128 s/s/myr, the rate median shown on Tracer.
Figure 4 in Cicada minimum age tree: Cryptic speciation and exponentially increasing base substitution rates in recent geologic time
Figure 4. Number of base changes of transition and tansversion vs corrected pairwide distance diagram for whole mitochondrial gene.
Figure 1 in Cicada minimum age tree: Cryptic speciation and exponentially increasing base substitution rates in recent geologic time
Figure 1. Simplified cicada timetree built by BEAST v1.X, applying a 1,534 bp in maximum COI sequence. Inserted figure: Base substitution rate (= ratemedian shown at each node; substitutions per siteper millionyear; s/s/ myr) vsage (= posterior age shown at each node) diagram. Red approximate curve with its formula was drawn by an Excel function, with the intersection for the curve = 0.0128 s/s/myr, the rate median shown on Tracer.
Figure 3 in Cicada minimum age tree: Cryptic speciation and exponentially increasing base substitution rates in recent geologic time
Figure 3. Cicada timetree built by BEAST v1.X, applying 1,534 bp COI and 874 bp 18S rRNA sequences. OUTswith isolate number: our own analyzed specimens shown in Table 1, and others: from GenBank/DDJB. In outgroup Hemiptera; #: analyzed family by Johnson et al. (2018); % analyzed family by Misof et al. (2014). Inserted figure: Base substitution rate (= rate median shown at each node; substitutions per site per million year; s/s/myr) vs age (= posterior age shown at each node) diagram. Red approximatecurve with its formulawas drawn by Excel function, with the intersection for the curve = 0.0114 s/s/myr, the rate median shown on Tracer. Note that this rate is a little slower than thatsolely of COI in Figures 1 and 2, reflecting slowerrate of 18S rRNAthan COI (see Osozawa et al. 2017a).
Data for "Impact of Ligand Substitution and Metal Node Exchange in the Electronic Properties of Scandium Terephthalate Frameworks"
<p>The AiiDA archives of the high-throughput calculations presented in the paper "Impact of Ligand Substitution and Metal Node Exchange in the Electronic Properties of Scandium Terephthalate Frameworks".</p><p>The file "MOF_workflows.aiida" contains the actual calculation data and the files with suffix "*.yaml" contain configuration files of the workflows.</p>
Quantitative results of the analysis of relevant components of artificial bilayered substitutes developed by tissue engineering
<p>This dataset corresponds to the quantification results carried out for artificial bilayered substitutes developed by tissue engineering and control tissues analyzed in the manuscript entitled "<span>Spatiotemporal characterization of extracellular matrix maturation in human artificial stromal-epithelial tissue substitutes</span>". Tissue engineering techniques offer new strategies to understand complex processes in a controlled and reproducible system. In this study, we generated bilayered human tissue substitutes consisting of a cellular connective tissue with a suprajacent epithelium (full-thickness stromal-epithelial substitutes or SESS), and human tissue substitutes with an epithelial layer generated on top of an acellular biomaterial (epithelial substitutes or ESS). Both types of artificial tissues were studied at sequential time periods to analyze the maturation process of the extracellular matrix (ECM) using histochemical and immunohistochemical techniques. Results showed that both models were able to exhibit a partial development of the epithelial layer. ESS cells showed active proliferation, positive expression of KRT5 and low expression of differentiation markers, whereas SESS epithelium showed higher differentiation levels, with a progressive positive expression of KRT10 and claudin, although the differentiation levels of control native tissues were not reached. Despite the typical rete-ridges and papillae of native tissues were not found, stromal cells in SESS tended to accumulate and actively synthetize ECM components such as collagens and proteoglycans in the stromal area in direct contact with the epithelium (Z1 zone), whereas these components were very scarce in ESS. Regarding the basement membrane (BM), ESS showed a partially-differentiated structure containing fibronectin-1 (FN1) and perlecan (HSPG2), although the PAS staining signal was significantly lower than control native tissues. However, SESS showed higher BM differentiation, with positive expression of FN1, HSPG2, nidogen 1 (NID1), chondroitin-6-sulfate proteoglycans (CH6S), agrin (AGRN), and collagens types IV (COL-IV) and VII (COL-VII), although this structure was negative for lumican (LUM). These results confirm the relevance of epithelial-stromal interaction for ECM development and differentiation, especially regarding BM components, and suggest the usefulness of bilayered artificial tissue substitutes to reproduce ex vivo the ECM maturation and development process of human tissues. The original data obtained for the quantitative analyses of each component are shown in this dataset.</p> <p> </p>
Main model fits and substitution rate predictions for: A quantitative genetic model of background selection in humans
<p>Across the human genome, there are large-scale fluctuations in genetic diversity caused by the indirect effects of selection. This can be thought of as a "linked selection signal" that reflects the impact of selection varying according to the placement of functional regions and recombination rates along the genome. Previous work has shown that negative selection against the steady influx of new deleterious mutations into conserved regions is the predominant mode of selection in humans. However, the theoretic model that underpins these results, classic Background Selection theory, is only applicable when new mutations are so deleterious that they cannot fix in the population. Here, we develop a statistical method based on a quantitative genetics view of the linked selection, which models the effects of weak draft created according to how polygenic additive fitness variance is distributed along the genome. We use a recent model that jointly predicts the equilibrium fitness variance and substitution rates due to both strong and weakly deleterious mutations, we estimate the distribution of fitness effects (DFE) and mutation rate across three human populations. While our model can accommodate weaker selection, we initially find evidence across three human populations of very strong selection against deleterious mutations consistent with previous work. However, the corollary predicted substitution rates for conserved regions are unreasonably low, and in disagreement with observed rates. We hypothesize this could be due to selected sites experiencing a further diminished population size due to selective interference. When we account for this in our method, we find evidence of weakly deleterious mutations in conserved regions which brings the predicted substitution rate into agreement with observations. However, these models lead to implausibly large mutation rate estimates. Overall, while our model of the genomic linked selection signal brings us a step towards uniting population and quantitative genetic selection models with the substitution process, our work suggests considerable uncertainty remains about the processes generating fitness variance in humans.</p>
Quantitative results of the analysis of human native and bioengineered tissues corresponding to the work "Histological, histochemical and immunohistochemical characterization of NANOULCOR nanostructured fibrin-agarose human cornea substitutes generated by tissue engineering"
<p>Dataset containing the quantitative results of the histochemical and immunohistochemical analysis of the following human tissues:</p> <ul> <li>Control native cornea (CTR-C)</li> <li>Control native limbus (CTR-L)</li> <li>Artificial cornea generated by tissue engineering (HAC)</li> </ul> <p>Each tissue type was subjected to histochemical and immunohistochemical analyses and results were quantified using ImageJ software to determine average intensities and area fractions corresponding to positive staining signal for each marker.</p>
Molecular Insights into the Effects of F16L and F19L Substitutions on the Conformation and Aggregation Dynamics of Human Calcitonin
<p><a name="_Hlk145518059"></a><span>Human calcitonin (hCT) regulates calcium-phosphorus metabolism, but its amyloid aggregation disrupts physiological activity, increases thyroid carcinoma risk, and hampers its clinical use for bone-related diseases like osteoporosis and Paget’s disease. Improving hCT with targeted modifications to mitigate amyloid formation while maintaining function holds promise as a strategy. Understanding how each residue in hCT's amyloidogenic core affects its structure and aggregation dynamics is crucial for designing effective analogs. Mutants F16L-hCT and F19L-hCT, where Phe residues in the core are replaced with Leu as in non-amyloidogenic salmon calcitonin, showed different aggregation kinetics. However, the molecular effects of these substitutions in hCT are still unclear. Here, </span><a name="OLE_LINK4"></a><span><span>we systematically investigated the folding and self-assembly conformational dynamics of hCT, F16L-hCT, and F19L-hCT through multiple long-timescale independent atomistic discrete molecular dynamics (DMD) simulations. </span></span><span><span>Our results indicated that the hCT monomer primarily assumed unstructured conformations with dynamic helices around residues 4-12 and 14-21. During self-assembly, the amyloidogenic core of hCT<sub>14-21</sub> converted from dynamic helices to β-sheets. However, substituting F16L did not induce significant conformational changes, as F16L-hCT exhibited similar characteristics to wild-type hCT in both monomeric and oligomeric states. In contrast, F19L-hCT exhibited substantially more helices and fewer β-sheets than hCT, irrespective of their monomers or oligomers. The substitution of F19L significantly enhanced the stability of the helical conformation for hCT<sub>14-21</sub>, thereby suppressing the helix-to-β-sheet conformational conversion. Overall, our findings elucidate the molecular mechanisms underlying hCT aggregation and the effects of F16L and F19L substitutions on the conformational dynamics of hCT, highlighting the critical role of F19 as an important target in the design of amyloid-resistant hCT analogs for future clinical applications.</span></span></p>
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International Brain Laboratory public data
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OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.