cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.4738825
title: Design, synthesis, and evaluation of pyrazolo-pyrazole derivatives on Methylisocitratelyase of <i>Pseudomonas aeruginosa</i>: <i>in silico</i> and <i>in vitro</i> study

description: <i>Pseudomonas aeruginosa</i> is an opportunistic micro-organism causing diseases both in animals and humans. In case of human pathology, the role of <i>P. aeruginosa</i> is one of the major concerns in intensive care septicemia. Presently, the drug resistance strains of <i>P. aeruginosa</i> are arising mainly by developing multiple mechanisms due to its natural and acquired resistance to many of the antimicrobial agents commonly used in clinical practice. As a result, there is a direct need to invent new drugs so that they may restrict the outbreak of multidrug resistant strains. Virtual high-throughput <i>insilico</i> screening, which helps to identify the chemical ligands that bind to the enzymes, is an important tool in drug discovery and the drugs discovered in this way are clinically tested. In this study, Methylisocitratelyase (MICL), which is essential for the survival of the bacterium and which doesn’t show any similarity with the humans, was selected to evaluate the functions of high-afﬁnity inhibitors (PPI-analogs) that are identified using the virtual screening approach. By adopting the computational analysis tools, structural, functional, and inhibitor interactions of MICL against <i>P. aeruginosa</i> were identified. The PPIA-32 is found to be the best binding interactions with MICL. PPIA-32 reduces the binding afﬁnity for substrate to residues required for MICL enzyme activity and also Root Mean Square Deviation simulations show the most stable nature of PPA32-MICL(complex) than that of MICL alone, thereby effectively inhibiting the growth of virulent <i>P. aeruginosa</i>. To our surprise, the same phenomenon is also identified with other gram-negative bacteria like <i>Escherichia coli</i>, <i>Klebsiella pneumoniae</i>, and <i>Salmonella typhi</i>.
DOI: 10.6084/m9.figshare.4738825.v1
title: Design, synthesis, and evaluation of pyrazolo-pyrazole derivatives on Methylisocitratelyase of <i>Pseudomonas aeruginosa</i>: <i>in silico</i> and <i>in vitro</i> study

description: <i>Pseudomonas aeruginosa</i> is an opportunistic micro-organism causing diseases both in animals and humans. In case of human pathology, the role of <i>P. aeruginosa</i> is one of the major concerns in intensive care septicemia. Presently, the drug resistance strains of <i>P. aeruginosa</i> are arising mainly by developing multiple mechanisms due to its natural and acquired resistance to many of the antimicrobial agents commonly used in clinical practice. As a result, there is a direct need to invent new drugs so that they may restrict the outbreak of multidrug resistant strains. Virtual high-throughput <i>insilico</i> screening, which helps to identify the chemical ligands that bind to the enzymes, is an important tool in drug discovery and the drugs discovered in this way are clinically tested. In this study, Methylisocitratelyase (MICL), which is essential for the survival of the bacterium and which doesn’t show any similarity with the humans, was selected to evaluate the functions of high-afﬁnity inhibitors (PPI-analogs) that are identified using the virtual screening approach. By adopting the computational analysis tools, structural, functional, and inhibitor interactions of MICL against <i>P. aeruginosa</i> were identified. The PPIA-32 is found to be the best binding interactions with MICL. PPIA-32 reduces the binding afﬁnity for substrate to residues required for MICL enzyme activity and also Root Mean Square Deviation simulations show the most stable nature of PPA32-MICL(complex) than that of MICL alone, thereby effectively inhibiting the growth of virulent <i>P. aeruginosa</i>. To our surprise, the same phenomenon is also identified with other gram-negative bacteria like <i>Escherichia coli</i>, <i>Klebsiella pneumoniae</i>, and <i>Salmonella typhi</i>.
DOI: 10.6084/m9.figshare.3807678.v1
title: Exploring the interactions of a DNA aptamer with human serum albumins: simulation studies

description: Exploring the interactions of a DNA aptamer with human serum albumins: simulation studies
DOI: 10.6084/m9.figshare.3569631
title: Computational analysis of the glutamate receptor gene family of <i>Arabidopsis thaliana</i>

description: Ionotropic glutamate receptors (iGluRs) function as glutamate-activated ion channels in rapid synaptic transmission in animals. <i>Arabidopsis thaliana</i> possess 20 glutamate receptor-like genes (AtGLRs) in its genome which are involved in many functions including light signal transduction and calcium homeostasis. However, little is known about the physico-chemical, functional and structural properties of AtGLRs. In this study, glutamate receptor-like genes of <i>A. thaliana</i> have been studied <i>in silico</i>. Exon–intron structures revealed common origin of majority of these genes. The presence of several phosphorylation and myristoilation sites indicate the involvement of AtGLRs in various signaling processes. Gene ontology analysis showed the participation of AtGLRs in various biological processes including different stress responses. In two genes namely AT2G17260 and AT4G35290, presence of RAV1-A binding site motif in the promoter coupled with results from gene ontology annotation indicate their role in stomatal movement through abscisic acid signaling. Expression analysis showed differential expression of several tandemly arranged genes which indicates neo or sub-functionalization. Two genes namely AT5G48400 and AT5G48410 showed significantly more expression in response to <i>Botrytis cinerea</i> infection. Five of these genes have shown G-protein-coupled γ-aminobutyric acid (GABA) receptor activity indicating a possible interaction between AtGLRs and GABA. Structurally, all of them were similar while differences were found regarding electrostatic surfaces as well as surface hydrophobicity. Results of this study provide a comprehensive reference regarding AtGLRs for further analysis regarding the structure, function, and evolution of the glutamate receptors in plants.
DOI: 10.6084/m9.figshare.3569631.v2
title: Computational analysis of the glutamate receptor gene family of <i>Arabidopsis thaliana</i>

description: Ionotropic glutamate receptors (iGluRs) function as glutamate-activated ion channels in rapid synaptic transmission in animals. <i>Arabidopsis thaliana</i> possess 20 glutamate receptor-like genes (AtGLRs) in its genome which are involved in many functions including light signal transduction and calcium homeostasis. However, little is known about the physico-chemical, functional and structural properties of AtGLRs. In this study, glutamate receptor-like genes of <i>A. thaliana</i> have been studied <i>in silico</i>. Exon–intron structures revealed common origin of majority of these genes. The presence of several phosphorylation and myristoilation sites indicate the involvement of AtGLRs in various signaling processes. Gene ontology analysis showed the participation of AtGLRs in various biological processes including different stress responses. In two genes namely AT2G17260 and AT4G35290, presence of RAV1-A binding site motif in the promoter coupled with results from gene ontology annotation indicate their role in stomatal movement through abscisic acid signaling. Expression analysis showed differential expression of several tandemly arranged genes which indicates neo or sub-functionalization. Two genes namely AT5G48400 and AT5G48410 showed significantly more expression in response to <i>Botrytis cinerea</i> infection. Five of these genes have shown G-protein-coupled γ-aminobutyric acid (GABA) receptor activity indicating a possible interaction between AtGLRs and GABA. Structurally, all of them were similar while differences were found regarding electrostatic surfaces as well as surface hydrophobicity. Results of this study provide a comprehensive reference regarding AtGLRs for further analysis regarding the structure, function, and evolution of the glutamate receptors in plants.
DOI: 10.6084/m9.figshare.3807678
title: Exploring the interactions of a DNA aptamer with human serum albumins: simulation studies

description: Exploring the interactions of a DNA aptamer with human serum albumins: simulation studies
DOI: 10.6084/m9.figshare.17702362.v1
title: Physicochemical sequence characteristics that influence <i>S</i>-palmitoylation propensity

description: Over the past 30 years, several hundred eukaryotic proteins spanning from yeast to man have been shown to be <i>S</i>-palmitoylated. This post-translational modification involves the reversible addition of a 16-carbon saturated fatty acyl chain onto the cysteine residue of a protein where it regulates protein membrane association and distribution, conformation, and stability. However, the large-scale proteome-wide discovery of new palmitoylated proteins has been hindered by the difficulty of identifying a palmitoylation consensus sequence. Using a bioinformatics approach, we show that the enrichment of hydrophobic and basic residues, the cellular context of the protein, and the structural features of the residues surrounding the palmitoylated cysteine all influence the likelihood of palmitoylation. We developed a new palmitoylation predictor that incorporates these identified features, and this predictor achieves a Matthews Correlation Coefficient of .74 using 10-fold cross validation, and significantly outperforms existing predictors on unbiased testing sets. This demonstrates that palmitoylation sites can be predicted with accuracy by taking into account not only physiochemical properties of the modified cysteine and its surrounding residues, but also structural parameters and the subcellular localization of the modified cysteine. This will allow for improved predictions of palmitoylated residues in uncharacterized proteins. A web-based version of this predictor is currently under development.
DOI: 10.6084/m9.figshare.17702362
title: Physicochemical sequence characteristics that influence <i>S</i>-palmitoylation propensity

description: Over the past 30 years, several hundred eukaryotic proteins spanning from yeast to man have been shown to be <i>S</i>-palmitoylated. This post-translational modification involves the reversible addition of a 16-carbon saturated fatty acyl chain onto the cysteine residue of a protein where it regulates protein membrane association and distribution, conformation, and stability. However, the large-scale proteome-wide discovery of new palmitoylated proteins has been hindered by the difficulty of identifying a palmitoylation consensus sequence. Using a bioinformatics approach, we show that the enrichment of hydrophobic and basic residues, the cellular context of the protein, and the structural features of the residues surrounding the palmitoylated cysteine all influence the likelihood of palmitoylation. We developed a new palmitoylation predictor that incorporates these identified features, and this predictor achieves a Matthews Correlation Coefficient of .74 using 10-fold cross validation, and significantly outperforms existing predictors on unbiased testing sets. This demonstrates that palmitoylation sites can be predicted with accuracy by taking into account not only physiochemical properties of the modified cysteine and its surrounding residues, but also structural parameters and the subcellular localization of the modified cysteine. This will allow for improved predictions of palmitoylated residues in uncharacterized proteins. A web-based version of this predictor is currently under development.
DOI: 10.5281/zenodo.5809060
title: Epizoanthus illoricatus decontaminated FSCR

description: .
DOI: 10.5281/zenodo.5809059
title: Epizoanthus illoricatus decontaminated FSCR

description: .
DOI: 10.5519/qd.qxtbn02q
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (4992893 records)
DOI: 10.5281/zenodo.5808324
title: Sen2CHRIS dataset for training and test

description: Compact High Resolution Imaging Spectrometer, namely CHRIS, is carried on PRoject for On Board Autonomy 1 (PROBA-1) satellite and provides hyperspectral images.However, CHRIS images are always accompanied by hybrid noise, stripe gap, and high cloud cover. Furthermore, all satellite passes are systematically acquired according to a fixed acquisition plan. Observation over a new specific area should be performed by submitting the request to add a new site to the acquisition plan, which costs much money and time. To verify the model performance of solving generalized spectral super-resolution, Sen2CHRIS data set is generated from three freely available data subsets, including Xiong'an, Washington DC Mall, and Chikusei, by downsampling the spectral channels of free hyperspectral data to the same of CHRIS and Sentinel-2 using Hysure. The file named "Chikusei_CHRIS.h5" contains 1016 training samples where the high-resolution multispectral images are with size of 128×128×4 while the size of low-resolution multispectral images is 64×64×4. Moreover, we also give some test images in the "Chikusei_test.mat". The file named "DCMall_CHRIS.h5" contains 2424 training samples where the high-resolution multispectral images are with size of 64×64×4 while the size of low-resolution multispectral images is 32×32×4. Moreover, we also give some test images in the "DCMall_test.mat". The file named "Xiongan_CHRIS.h5" contains 1216 training samples where the high-resolution multispectral images are with size of 128×128×4 while the size of low-resolution multispectral images is 64×64×4. Moreover, we also give some test images in the "Xiongan_test.mat". Details about generalized spectral super-resolution can be found in the following paper. Paper: J. He, Q. Yuan, J. Li, and L. Zhang, "PoNet: A universal physical optimization-based spectral super-resolution network for arbitrary multispectral images," <em>Information Fusion</em>, vol. 80, pp. 205–225, 2022. More information about the author can be found at https://jianghe96.github.io/ If this dataset is helpful please cite as: <pre>@article{He2022PoNet, title={PoNet: A universal physical optimization-based spectral super-resolution network for arbitrary multispectral images}, author={He, Jiang and Yuan, Qiangqiang and Li, Jie and Zhang, Liangpei}, journal={Information Fusion}, volume={80}, pages={205--225}, year={2022}, }</pre>
DOI: 10.5281/zenodo.5808323
title: Sen2CHRIS dataset for training and test

description: Compact High Resolution Imaging Spectrometer, namely CHRIS, is carried on PRoject for On Board Autonomy 1 (PROBA-1) satellite and provides hyperspectral images.However, CHRIS images are always accompanied by hybrid noise, stripe gap, and high cloud cover. Furthermore, all satellite passes are systematically acquired according to a fixed acquisition plan. Observation over a new specific area should be performed by submitting the request to add a new site to the acquisition plan, which costs much money and time. To verify the model performance of solving generalized spectral super-resolution, Sen2CHRIS data set is generated from three freely available data subsets, including Xiong'an, Washington DC Mall, and Chikusei, by downsampling the spectral channels of free hyperspectral data to the same of CHRIS and Sentinel-2 using Hysure. The file named "Chikusei_CHRIS.h5" contains 1016 training samples where the high-resolution multispectral images are with size of 128×128×4 while the size of low-resolution multispectral images is 64×64×4. Moreover, we also give some test images in the "Chikusei_test.mat". The file named "DCMall_CHRIS.h5" contains 2424 training samples where the high-resolution multispectral images are with size of 64×64×4 while the size of low-resolution multispectral images is 32×32×4. Moreover, we also give some test images in the "DCMall_test.mat". The file named "Xiongan_CHRIS.h5" contains 1216 training samples where the high-resolution multispectral images are with size of 128×128×4 while the size of low-resolution multispectral images is 64×64×4. Moreover, we also give some test images in the "Xiongan_test.mat". Details about generalized spectral super-resolution can be found in the following paper. Paper: J. He, Q. Yuan, J. Li, and L. Zhang, "PoNet: A universal physical optimization-based spectral super-resolution network for arbitrary multispectral images," <em>Information Fusion</em>, vol. 80, pp. 205–225, 2022. More information about the author can be found at https://jianghe96.github.io/ If this dataset is helpful please cite as: <pre>@article{He2022PoNet, title={PoNet: A universal physical optimization-based spectral super-resolution network for arbitrary multispectral images}, author={He, Jiang and Yuan, Qiangqiang and Li, Jie and Zhang, Liangpei}, journal={Information Fusion}, volume={80}, pages={205--225}, year={2022}, }</pre>
DOI: 10.5281/zenodo.4715544
title: Deep tissue localization and sensing using optical microcavity probes

description: Data and code for publication Deep tissue localization and sensing using optical microcavity probes.
DOI: 10.6084/m9.figshare.17702453
title: Dataset for bank credit shocks

description: Dataset for the paper on bank credit shocks
DOI: 10.5281/zenodo.5809096
title: Dataset related to article "New composite physico-chemical indicators constructed by Bayesian inference for water quality monitoring"

description: These dataset are associated with the paper being submitted entitled: <strong>New composite physico-chemical indicators constructed by Bayesian inference for water quality monitoring.</strong> Data collection covered an 8-year period divided into two sets of years: 2002 to 2006 and 2014 to 2016. All data were acquired from several comparable scientific studies using the same methods (AFNOR,1997). Imputation of missing data was performed to complete this dataset using the non-parametric "missForest" algorithm for mixed-type data. Physico-chemical parameters were extracted from publications (Gnohossou, 2006; Odountan et al., 2019, Zandagba et al., 2016a, 2016b). 17 variables were measured: water temperature, transparency, turbidity, conductivity, salinity, pH, dissolved oxygen (DO), BOD, COD, Kjeldahl nitrogen (TKN), ammonium , nitrates , nitrites , dry organic matter (DM) content, orthophosphates, total phosphorus (TP), suspended solids (SS). The geographical distribution of the sampling points is made to cover the whole Nokoué lagoon complex. A total of 20 sampling points were surveyed. The parameters were measured according to the four seasons of the year and/or at the succession of high water, low water, high water, and low water-stretch transitions. Nine driving forces described as factors likely to induce pressures were retained to explain the physico-chemical characteristics of the Nokoué and complete this data set. The data resulting from the land use maps and relative to the distances between the considered stations and the tributaries can be improved in the future (Lead to other versions of this data set). As natural forcing variables, we have the sampling years, the seasons (SWS: short wet season or flood period; SDS: short dry season; LWS: long wet season; LDS: long dry season), the average monthly water level (MAWL) and the average wind speed (AWS), which is important in the context of Nokoué... **Minor modifications<br> -Modification of the name of the variables of the initial dataset<br> -Modification of the name of the original dataset (lac_Nokoue.csv)<br> - Added the dataset used for the article being submitted (lac_Nokoue.csv)
description: *lac_Nokoue_brute : Real data ; *lac_Nokoue_missForest : Data generated after imputation from the missForest algorithm; *lac_Nokoue : dataset used for the article being submitted
DOI: 10.5281/zenodo.5809094
title: Deep tissue localization and sensing using optical microcavity probes

description: Data and code for publication Deep tissue localization and sensing using optical microcavity probes.
DOI: 10.5281/zenodo.4715543
title: Deep tissue localization and sensing using optical microcavity probes

description: Data and code for publication Deep tissue localization and sensing using optical microcavity probes.
DOI: 10.6084/m9.figshare.13946903
title: Supplementary data and research materials for "Early-stage spatial disease surveillance of novel SARS-CoV-2 variants of concern in Germany with crowdsourced data"

description: This folder contains study data, protocols and STATA programming codes to replicate the empirical analysis presented in:<br>"Early-stage spatial disease surveillance of novel SARS-CoV-2 variants of concern in Germany with crowdsourced data"<br>by Timo Mitze and Johannes Rode.<br>Accepted for publication in "Scientific Reports" (with DOI: 10.1038/s41598-021-04573-1)<br>Please see the README file before using the study data and replication codes. In the case of questions contact: Timo Mitze (tmitze@sam.sdu.dk)<br>
DOI: 10.6084/m9.figshare.13946903.v1
title: Supplementary data and research materials for "Early-stage spatial disease surveillance of novel SARS-CoV-2 variants of concern in Germany with crowdsourced data"

description: This folder contains study data, protocols and STATA programming codes to replicate the empirical analysis presented in:<br>"Early-stage spatial disease surveillance of novel SARS-CoV-2 variants of concern in Germany with crowdsourced data"<br>by Timo Mitze and Johannes Rode.<br>Accepted for publication in "Scientific Reports" (with DOI: 10.1038/s41598-021-04573-1)<br>Please see the README file before using the study data and replication codes. In the case of questions contact: Timo Mitze (tmitze@sam.sdu.dk)<br>
DOI: 10.5281/zenodo.5809089
title: Erythroxylum foetidum decontaminated FSCR

description: .
DOI: 10.5281/zenodo.5809088
title: Erythroxylum foetidum decontaminated FSCR

description: .
DOI: 10.5281/zenodo.5809102
title: Penthetria funebris decontaminated FSCR

description: .
DOI: 10.5281/zenodo.5809101
title: Penthetria funebris decontaminated FSCR

description: .
DOI: 10.6084/m9.figshare.17702492
title: Supplementary Material for: The Dynamics of Circulating Heparin-Binding Protein: Implications for Its Use as a Biomarker

description: Heparin-binding protein (HBP) is a promising biomarker for the development and severity of sepsis. To guide its use, it is important to understand the factors that could lead to false-positive or negative results, such as inappropriate release and inadequate clearance of HBP. HBP is presumably released only by neutrophils, and the organs responsible for its elimination are unknown. In this study, we aimed to determine whether non-neutrophil cells can be a source of circulating HBP and which organs are responsible for its removal. We found that in two cohorts of neutropenic patients, 12% and 19% of patients in each cohort, respectively, had detectable plasma HBP levels. In vitro, three leukemia-derived monocytic cell lines and healthy CD14+ monocytes constitutively released detectable levels of HBP. When HBP was injected intravenously in rats, we found that plasma levels of HBP decreased rapidly, with a distribution half-life below 10 min and an elimination half-life of 1–2 h. We measured HBP levels in the liver, spleen, kidneys, lungs, and urine using both ELISA and immunofluorescence quantitation, and found that the majority of HBP was present in the liver, and a small amount was present in the spleen. Immunofluorescence imaging indicated that HBP is associated mainly with hepatocytes in the liver and monocytes/macrophages in the spleen. The impact of hematologic malignancies and liver diseases on plasma HBP levels should be explored further in clinical studies.