cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5517/ccdc.csd.cc24w5dm
title: CCDC 1992320: Experimental Crystal Structure Determination

description: Related Article: Kristof Pota, Enikő Molnár, Ferenc Krisztián Kálmán, David M. Freire, Gyula Tircsó, Kayla N. Green|2020|Inorg.Chem.|59|11366|doi:10.1021/acs.inorgchem.0c01053
DOI: 10.5517/ccdc.csd.cc24w5gp
title: CCDC 1992322: Experimental Crystal Structure Determination

description: Related Article: Kristof Pota, Enikő Molnár, Ferenc Krisztián Kálmán, David M. Freire, Gyula Tircsó, Kayla N. Green|2020|Inorg.Chem.|59|11366|doi:10.1021/acs.inorgchem.0c01053
DOI: 10.5517/ccdc.csd.cc2498sj
title: CCDC 1975127: Experimental Crystal Structure Determination

description: Related Article: Huan He, Ruiyuan Cao, Ruidi Cao, Xiao-Yu Liu, Wei Li, Di Yu, Yuexiang Li, Miaomiao Liu, Yanmei Wu, Pingzhou Wu, Jin-Song Yang, Yunzheng Yan, Jingjing Yang, Zhi-Bing Zheng, Wu Zhong, Yong Qin|2020|Org.Biomol.Chem.|18|6155|doi:10.1039/D0OB01172J
DOI: 10.6084/m9.figshare.9888425
title: Reappraisal of FDA approved drugs against Alzheimer’s disease based on differential gene expression and protein interaction network analysis: an in silico approach

description: Alzheimer’s disease (AD), a most prevailing neurodegenerative disorder with turbulence in cognitive and behavioural abilities, epitomizes one of the highest unmet medical requirements. The current AD treatment focuses merely on symptomatic relief, this explains a dearth in drug research oriented towards unwinding of disease specific druggable targets. On the other hand, toxicity and poor bioavailability hamper the evolution of novel chemical entities (NCE) in clinical trials. Drug repurposing offers a gateway to rejuvenate new therapeutic applications for existing approved drugs. This study concentrates on the identification of potential druggable AD targets and screening of FDA approved drugs with a concept of drug repurposing. differentially expressed genes (DEGs) were identified in frontal cortex, temporal cortex and hippocampus in AD patients from Gene Expression Omnibus (GEO) dataset GSE36980. Protein-protein interaction (PPI) analysis revealed SERPINA3 and BDNF to possess high node degree interaction with literature derived candidate genes (LDGs) in AD males and females, respectively, thus were selected as potential AD targets. Subsequently, FDA approved drugs were screened through the above shortlisted targets and were ranked based on molecular docking and MM-GBSA energy calculations using Glide and Prime tools, respectively. Drugs possessing best docking score and maximum binding energy were further evaluated through molecular dynamics simulation studies, which revealed the affinity of Tiludronic acid and Olsalazine towards SERPINA3 and BDNF, respectively. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.9888416
title: Ribonucleic acid (RNA) condensation by thermal cycling with metal cations: yield of nanoparticles and their applicability for transfection

description: To the present, different efficient but expensive, multistage, and time-consuming technologies have been developed to deliver ribonucleic acids (RNA) into eukaryotic cells. Here, we report a simple and feasible solution to design RNA nanocarriers based on nucleic acid condensation by bi- and trivalent metal ions during thermal cycling. Efficient RNA conversion to nanoparticles with small size (10–50 nm) suitable for transfection was achieved using cations Ni<sup>2+</sup>, Co<sup>2+</sup> or Cu<sup>2+</sup> alone or in combination with Ca<sup>2+</sup> at the specially selected concentrations (2.0 mM–3.5 mM), low ionic strength, and narrow pH range (8.0–8.5). Other ions – Mn<sup>2+</sup>, Zn<sup>2+</sup>, Tb<sup>3+</sup>, or Gd<sup>3+</sup> – caused RNA-cleaving effect that was abolished in the presence of Ni<sup>2+</sup>, Co<sup>2+</sup>, Zn<sup>2+</sup>, or Cu<sup>2+</sup>. Naked RNA-metal ion nanoparticles were extremely unstable in phosphate buffer and sensitive to serum ribonucleases (RNases), and this problem was solved by treatment with polyarginines-16 and 8. Polyarginine-stabilized nanoparticles, containing malachite green (MG) aptamer RNA and metal cations, crossed the cell membrane, dissociated in the cytoplasm, and preserved the functionality of transported RNA, as judged from efficient transfection of human embryonic kidney 293 cells. The technology, involving RNA condensation by metal cations, can be used as a cheap alternative to produce nanoscale carriers to deliver various RNAs into cells <i>in vitro</i> and <i>in vivo</i>. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.9888425.v2
title: Reappraisal of FDA approved drugs against Alzheimer’s disease based on differential gene expression and protein interaction network analysis: an in silico approach

description: Alzheimer’s disease (AD), a most prevailing neurodegenerative disorder with turbulence in cognitive and behavioural abilities, epitomizes one of the highest unmet medical requirements. The current AD treatment focuses merely on symptomatic relief, this explains a dearth in drug research oriented towards unwinding of disease specific druggable targets. On the other hand, toxicity and poor bioavailability hamper the evolution of novel chemical entities (NCE) in clinical trials. Drug repurposing offers a gateway to rejuvenate new therapeutic applications for existing approved drugs. This study concentrates on the identification of potential druggable AD targets and screening of FDA approved drugs with a concept of drug repurposing. differentially expressed genes (DEGs) were identified in frontal cortex, temporal cortex and hippocampus in AD patients from Gene Expression Omnibus (GEO) dataset GSE36980. Protein-protein interaction (PPI) analysis revealed SERPINA3 and BDNF to possess high node degree interaction with literature derived candidate genes (LDGs) in AD males and females, respectively, thus were selected as potential AD targets. Subsequently, FDA approved drugs were screened through the above shortlisted targets and were ranked based on molecular docking and MM-GBSA energy calculations using Glide and Prime tools, respectively. Drugs possessing best docking score and maximum binding energy were further evaluated through molecular dynamics simulation studies, which revealed the affinity of Tiludronic acid and Olsalazine towards SERPINA3 and BDNF, respectively. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.9888416.v2
title: Ribonucleic acid (RNA) condensation by thermal cycling with metal cations: yield of nanoparticles and their applicability for transfection

description: To the present, different efficient but expensive, multistage, and time-consuming technologies have been developed to deliver ribonucleic acids (RNA) into eukaryotic cells. Here, we report a simple and feasible solution to design RNA nanocarriers based on nucleic acid condensation by bi- and trivalent metal ions during thermal cycling. Efficient RNA conversion to nanoparticles with small size (10–50 nm) suitable for transfection was achieved using cations Ni<sup>2+</sup>, Co<sup>2+</sup> or Cu<sup>2+</sup> alone or in combination with Ca<sup>2+</sup> at the specially selected concentrations (2.0 mM–3.5 mM), low ionic strength, and narrow pH range (8.0–8.5). Other ions – Mn<sup>2+</sup>, Zn<sup>2+</sup>, Tb<sup>3+</sup>, or Gd<sup>3+</sup> – caused RNA-cleaving effect that was abolished in the presence of Ni<sup>2+</sup>, Co<sup>2+</sup>, Zn<sup>2+</sup>, or Cu<sup>2+</sup>. Naked RNA-metal ion nanoparticles were extremely unstable in phosphate buffer and sensitive to serum ribonucleases (RNases), and this problem was solved by treatment with polyarginines-16 and 8. Polyarginine-stabilized nanoparticles, containing malachite green (MG) aptamer RNA and metal cations, crossed the cell membrane, dissociated in the cytoplasm, and preserved the functionality of transported RNA, as judged from efficient transfection of human embryonic kidney 293 cells. The technology, involving RNA condensation by metal cations, can be used as a cheap alternative to produce nanoscale carriers to deliver various RNAs into cells <i>in vitro</i> and <i>in vivo</i>. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.9888164
title: IBRAHIM DATA.xlsx

description: This is the raw and permuted data for the paper; effect of financial globalization uncertainty on financial development on selected African countries.
DOI: 10.6084/m9.figshare.9888155
title: Acceptability and sensory qualities of fortified rice in Nepal

description: The data sets have enough information to replicate the results of our study on acceptability of fortified rice in Nepal.
DOI: 10.6084/m9.figshare.9888155.v1
title: Acceptability and sensory qualities of fortified rice in Nepal

description: The data sets have enough information to replicate the results of our study on acceptability of fortified rice in Nepal.
DOI: 10.6084/m9.figshare.9888059
title: MOESM1 of Microbial biosynthesis of lactate esters

description: Additional file 1: Table S1. Summary of high cell density cultures of EcJW101, EcJW102, EcJW103, EcJW104, and EcJW105 with addition of glucose and various alcohols after 24 h. The subscripts i and f are referred to the initial (0 h) and final (24 h) time of the culture, respectively. Table S2. Summary of titer, specific productivity, and yield of esters in high cell density cultures of EcJW101, EcJW102, EcJW103, EcJW104, and EcJW105 with addition of glucose and various alcohols after 24 h. The acyl acetate and acyl lactate columns correspond to the acyl alcohols added. For example, with the exogenous addition of ethanol, the acyl acetate, and acyl lactate columns represent ethyl acetate, and ethyl lactate, respectively. Table S3. (A) Summary of high cell density cultures of EcDL002, EcJW201, and EcJW202 after 24 h. (B) Summary of bioreactor batch fermentation of EcJW201 after 18 h. The subscripts i and f are referred to the initial (0 h) and final (24 h) time of the culture, respectively. Table S4. Summary of high cell density cultures of EcJW106-108 and EcJW203-208 with different concentrations of IPTG (0.01, 0.1, or 1.0 mM) after 24 h. The subscripts i and f are referred to the initial (0 h) and final (24 h) time of the culture, respectively. Table S5. Summary of titer, specific productivity, and yield of esters in high cell density cultures of EcJW106-108 and EcJW203-208 with different concentrations of IPTG (0.01, 0.1, or 1.0 mM) after 24 h. Table S6. Summary of high cell density cultures of EcJW209-212 with or without addition of ethanol (2 or 10 g/L) after 24 h. (A) OD600, pH, glucose, lactate, and ethanol. (B) Titer, specific productivity, and yield of esters. The subscripts i and f are referred to the initial (0 h) and final (24 h) time of the culture, respectively. Table S7. Summary of high cell density cultures of EcJW213-221 after 24 h. (A) OD600, pH, glucose, lactate, and ethanol. (B) Titer, specific productivity, and yield of esters. The subscripts i and f are referred to the initial (0 h) and final (24 h) time of the culture, respectively. Table S8. Summary of high cell density cultures of EcJW109-117 after 24 h. (A) OD600, pH, glucose, lactate, and ethanol. (B) Titer, specific productivity, and yield of esters. The subscripts i and f are referred to the initial (0 h) and final (24 h) time of the culture, respectively.
DOI: 10.6084/m9.figshare.9888059.v1
title: MOESM1 of Microbial biosynthesis of lactate esters

description: Additional file 1: Table S1. Summary of high cell density cultures of EcJW101, EcJW102, EcJW103, EcJW104, and EcJW105 with addition of glucose and various alcohols after 24 h. The subscripts i and f are referred to the initial (0 h) and final (24 h) time of the culture, respectively. Table S2. Summary of titer, specific productivity, and yield of esters in high cell density cultures of EcJW101, EcJW102, EcJW103, EcJW104, and EcJW105 with addition of glucose and various alcohols after 24 h. The acyl acetate and acyl lactate columns correspond to the acyl alcohols added. For example, with the exogenous addition of ethanol, the acyl acetate, and acyl lactate columns represent ethyl acetate, and ethyl lactate, respectively. Table S3. (A) Summary of high cell density cultures of EcDL002, EcJW201, and EcJW202 after 24 h. (B) Summary of bioreactor batch fermentation of EcJW201 after 18 h. The subscripts i and f are referred to the initial (0 h) and final (24 h) time of the culture, respectively. Table S4. Summary of high cell density cultures of EcJW106-108 and EcJW203-208 with different concentrations of IPTG (0.01, 0.1, or 1.0 mM) after 24 h. The subscripts i and f are referred to the initial (0 h) and final (24 h) time of the culture, respectively. Table S5. Summary of titer, specific productivity, and yield of esters in high cell density cultures of EcJW106-108 and EcJW203-208 with different concentrations of IPTG (0.01, 0.1, or 1.0 mM) after 24 h. Table S6. Summary of high cell density cultures of EcJW209-212 with or without addition of ethanol (2 or 10 g/L) after 24 h. (A) OD600, pH, glucose, lactate, and ethanol. (B) Titer, specific productivity, and yield of esters. The subscripts i and f are referred to the initial (0 h) and final (24 h) time of the culture, respectively. Table S7. Summary of high cell density cultures of EcJW213-221 after 24 h. (A) OD600, pH, glucose, lactate, and ethanol. (B) Titer, specific productivity, and yield of esters. The subscripts i and f are referred to the initial (0 h) and final (24 h) time of the culture, respectively. Table S8. Summary of high cell density cultures of EcJW109-117 after 24 h. (A) OD600, pH, glucose, lactate, and ethanol. (B) Titer, specific productivity, and yield of esters. The subscripts i and f are referred to the initial (0 h) and final (24 h) time of the culture, respectively.
DOI: 10.6084/m9.figshare.9887984
title: GCMS files for Pathria et al., Nat Cell Biol 2019

description: raw data in netCDF format for figures in Pathria et al, Nature Cell Biology, 2019
DOI: 10.6084/m9.figshare.9887609
title: XLEAP XTCAV phase space measurements

description: Calibrated XLEAP electron beam longitudinal phase space measured with the LCLS X-band deflecting cavity and energy spectrometer at the dump after all undulators<br><br>amolu0017_run_46_xtcav_dataset.npz - XLEAP wiggler out and XLEAP chicane off used in Figure 1e<br>amolu0017_run_47_xtcav_dataset.npz - XLEAP wiggler in and XLEAP chicane off used in Figure 1d<br>amolu0017_run_48_xtcav_dataset.npz - XLEAP wiggler in and XLEAP chicane on used in Figure 1b,c<br><br>plot_saved_xtcav.py - example of how to read and plot the XTCAV datasets above<br>xtcav_get_und_entrance.py - dependency of plot_saved_xtcav.py used to "dewake" the phase space in order to estimate the phase space at the entrance to the LCLS undulator line
DOI: 10.6084/m9.figshare.9887627
title: Helechos y Licofitas de la Reserva de Biosfera Yabotí, Misiones, Argentina: Parque Provincial Moconá

description: <b>Tabla S1</b> – Especies de helechos y licofitas presentes en el Parque Provincial Moconá, Misiones, Argentina. <b>Table S1</b> – Ferns and lycophytes species from Moconá Provincial Park, Misiones, Argentina.
DOI: 10.6084/m9.figshare.9887528
title: Human Nasal Cavity - Male 33 years old - Septal Deviation - CT-Data

description: In this data set the computed tomography image data of a 33 year old patient with deviation of the nasal septum is provided. Additional information, as for example the segmentation of the nasal cavity will be provided subsequently.
DOI: 10.6084/m9.figshare.9887438
title: Transcriptomic analysis of brain hypometabolism links the cholinergic and gingipain hypotheses of Alzheimer’s disease pathogenesis

description: Supplement data and figures from "Transcriptomic analysis of brain hypometabolism links the cholinergic and gingipain hypotheses of Alzheimer’s disease pathogenesis"<br>Preprint:https://www.biorxiv.org/content/10.1101/2019.12.23.887364v2<br><br>Github:https://github.com/leonfrench/AD-Allen-FDG<br><br>Supplement Figure 1: Differential expression of ER translocation genes in microglia from individuals with Alzheimer’s disease. In the top row, ROC curves show the proportion of ER translocation genes (y-axis, true positive fraction) across the genes tested for differential expression in microglia. The tested genes were ranked from the most overexpressed in early-pathology compared to no-pathology (A) and overexpressed in late-pathology compared to early-pathology (B). Subpanels C and D show the corresponding distributions with a black lines marking ER translocation genes across the differential expression rankings.
DOI: 10.6084/m9.figshare.9887438.v1
title: Transcriptomic analysis of brain hypometabolism links the cholinergic and gingipain hypotheses of Alzheimer’s disease pathogenesis

description: Supplement data and figures from "Transcriptomic analysis of brain hypometabolism links the cholinergic and gingipain hypotheses of Alzheimer’s disease pathogenesis"<br>Preprint:https://www.biorxiv.org/content/10.1101/2019.12.23.887364v2<br><br>Github:https://github.com/leonfrench/AD-Allen-FDG<br><br>Supplement Figure 1: Differential expression of ER translocation genes in microglia from individuals with Alzheimer’s disease. In the top row, ROC curves show the proportion of ER translocation genes (y-axis, true positive fraction) across the genes tested for differential expression in microglia. The tested genes were ranked from the most overexpressed in early-pathology compared to no-pathology (A) and overexpressed in late-pathology compared to early-pathology (B). Subpanels C and D show the corresponding distributions with a black lines marking ER translocation genes across the differential expression rankings.
DOI: 10.6084/m9.figshare.9886064
title: Lai_JGR_submission_2019JC015283.zip

description: data and program for paper "The generation of nonlinear internal waves in the South China Sea: A three-dimensional, nonhydrostatic numerical study" submitted to JGR<br>
DOI: 10.6084/m9.figshare.9886004
title: Metadata record for: Mercury concentrations in biota in the Mediterranean Sea, a compilation of 40 years of surveys

description: This dataset contains key characteristics about the data described in the Data Descriptor Mercury concentrations in biota in the Mediterranean Sea, a compilation of 40 years of surveys. <br> Contents: <br> 1. human readable metadata summary table in CSV format 2. machine readable metadata file in JSON format <br> <br> Versioning Note:Version 2 was generated when the metadata format was updated from JSON to JSON-LD. This was an automatic process that changed only the format, not the contents, of the metadata.<br>
DOI: 10.6084/m9.figshare.9886064.v1
title: Lai_JGR_submission_2019JC015283.zip

description: data and program for paper "The generation of nonlinear internal waves in the South China Sea: A three-dimensional, nonhydrostatic numerical study" submitted to JGR<br>
DOI: 10.15468/ed653s
title: A new species of Eulagius M, 1845 (Coleoptera: Mycetophagidae) from Iran

description: This dataset contains the digitized treatments in Plazi based on the original journal article Esser, Jens, Varandi, Hassan Barimani, Farashiani, Mohammad Ebrahim (2018): A new species of Eulagius M, 1845 (Coleoptera: Mycetophagidae) from Iran. Linzer biologische Beiträge 50 (1): 239-243, DOI: http://doi.org/10.5281/zenodo.4001997
DOI: 10.6084/m9.figshare.9886004.v2
title: Metadata record for: Mercury concentrations in biota in the Mediterranean Sea, a compilation of 40 years of surveys

description: This dataset contains key characteristics about the data described in the Data Descriptor Mercury concentrations in biota in the Mediterranean Sea, a compilation of 40 years of surveys. <br> Contents: <br> 1. human readable metadata summary table in CSV format 2. machine readable metadata file in JSON format <br> <br> Versioning Note:Version 2 was generated when the metadata format was updated from JSON to JSON-LD. This was an automatic process that changed only the format, not the contents, of the metadata.<br>
DOI: 10.6084/m9.figshare.9885641
title: Human platelet antigen polymorphisms and the risk of chronic Chagas disease cardiomyopathy

description: Human platelet antigen (HPA) polymorphisms are considered to be a risk factor for cardiac and vascular diseases, but the role of HPA in chronic Chagas disease cardiomyopathy (CCC) is not available. Therefore, the aim of this study was to investigate the association of HPA polymorphisms, HPA-1, HPA-2, HPA-3, HPA-5 and HPA-15, in the severity of left ventricular systolic dysfunction (LVSD) in CCC patients. For this, 229 CCC patients were separated into three groups: without LVSD, mild/moderate LVSD and severe LVSD. PCR-SSP was performed for HPA genotyping and the risk was assessed using SNPStats software. HPA-1 allele and genotype frequencies were lower in mild/moderate LVSD patients compared to other groups, without statistical significance. After stratified analyzes, the HPA-3a/3b genotype frequency was lower in women with severe LVSD compared to those without LVSD (OR:0.29; 95% CI: 0.10–0.84). In conclusion, HPA-3 variant could be a protection factor for CCC in the female patients.
DOI: 10.6084/m9.figshare.9886004.v1
title: Metadata record for: Mercury concentrations in biota in the Mediterranean Sea, a compilation of 40 years of surveys

description: This dataset contains key characteristics about the data described in the Data Descriptor Mercury concentrations in biota in the Mediterranean Sea, a compilation of 40 years of surveys. <br> Contents: <br> 1. human readable metadata summary table in CSV format 2. machine readable metadata file in JSON format
DOI: 10.6084/m9.figshare.9885641.v1
title: Human platelet antigen polymorphisms and the risk of chronic Chagas disease cardiomyopathy

description: Human platelet antigen (HPA) polymorphisms are considered to be a risk factor for cardiac and vascular diseases, but the role of HPA in chronic Chagas disease cardiomyopathy (CCC) is not available. Therefore, the aim of this study was to investigate the association of HPA polymorphisms, HPA-1, HPA-2, HPA-3, HPA-5 and HPA-15, in the severity of left ventricular systolic dysfunction (LVSD) in CCC patients. For this, 229 CCC patients were separated into three groups: without LVSD, mild/moderate LVSD and severe LVSD. PCR-SSP was performed for HPA genotyping and the risk was assessed using SNPStats software. HPA-1 allele and genotype frequencies were lower in mild/moderate LVSD patients compared to other groups, without statistical significance. After stratified analyzes, the HPA-3a/3b genotype frequency was lower in women with severe LVSD compared to those without LVSD (OR:0.29; 95% CI: 0.10–0.84). In conclusion, HPA-3 variant could be a protection factor for CCC in the female patients.
DOI: 10.6084/m9.figshare.9885638
title: Development linear and non-linear QSAR models for predicting AXL kinase inhibitory activity of N-[4-(quinolin-4-yloxy)phenyl]benzenesulfonamides

description: In this research, we used CoMFA, LSSVM and FFANN for creating QSAR models for predicting AXL Kinase inhibitory activity of N-[4-(Quinolin-4-yloxy)phenyl]benzenesulfonamides. A CoMFA model with three components was developed and CoMFA contour maps were interpreted to extract chemical features that influence the inhibitory activity of these molecules. <i>R</i><sup>2</sup> for train and test set of CoMFA model were 0.8900 and 0.8171, respectively. Model created by five Dragon descriptors and LSSVM model showed slightly better predictive power with respect to CoMFA model. <i>R</i><sup>2</sup> for train, test set of created LSSVM model were 0.0.8477 and 0.8218, respectively. Also, a FFANN model, using the same five descriptors, was developed with 2 neurons in its hidden layer and <i>R</i><sup>2</sup> for its train and test sets were 0.8314 and 0.8522, respectively. All created models were validated by calculating several statistical parameters and their applicability domain were investigated by calculating leverage. Furthermore, a homology model was built for Axl structure and molecules with the lowest and the greatest activity were docked to it and their interactions with Axl were investigated.