cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12276830
title: Additional file 1 of Cone-beam computed tomography investigation of middle mesial canals and isthmuses in mandibular first molars in a Chinese population

description: Additional file 1. Raw data.
DOI: 10.6084/m9.figshare.19092718
title: Additional file 6 of Identification and development of the novel 7-genes diagnostic signature by integrating multi cohorts based on osteoarthritis

description: Additional file 6. Informationon the annotation of the methylation sites and the distance between the probeCpG site and the transcription start site
DOI: 10.6084/m9.figshare.19092732
title: Additional file 2 of Subtyping of sarcomas based on pathway enrichment scores in bulk and single cell transcriptomes

description: Additional file 2: Table S2. Pathways, immune signatures, and biological processes and their marker genes.
DOI: 10.6084/m9.figshare.19092738.v1
title: Additional file 4 of Subtyping of sarcomas based on pathway enrichment scores in bulk and single cell transcriptomes

description: Additional file 4: Table S3. Pearson correlations between the methylation levels and expression levels of the genes having significantly different methylation levels among the sarcoma subtypes.
DOI: 10.6084/m9.figshare.19097051.v1
title: Combining pangenome analysis to identify potential cross-protective antigens against avian pathogenic <i>Escherichia coli</i>

description: Avian pathogenic <i>Escherichia coli</i> (APEC) is the bacterial pathogen of poultry colibacillosis, which causes significant economic losses to the poultry industry. The lack of an effective vaccine against multiple serotypes and the emergence of multi-resistant isolates have made the control of avian colibacillosis troublesome. To identify conserved potential vaccine candidates, 58 genomes of APEC were obtained (54 sequenced by our laboratory and four downloaded from NCBI). A reverse vaccinology (RV) method based on the pangenome – called Pan-RV analysis – was performed in APEC-protective protein mining for the first time. Finally, four proteins were selected, and their immunoreactivity with anti-O1, O2, and O78 serum was verified by western blotting. Our <i>in silico</i> method of analysis will pave the way for rapid screening of vaccine candidates and will lay the foundation for the development of a highly effective subunit vaccine controlling APEC infection. RESEARCH HIGHLIGHTSPan-RV analysis was used for the first time in the discovery of APEC-protective proteins.A total of 53 potential protective proteins were screened out.Four proteins were verified as potential vaccine candidates using western blotting. Pan-RV analysis was used for the first time in the discovery of APEC-protective proteins. A total of 53 potential protective proteins were screened out. Four proteins were verified as potential vaccine candidates using western blotting.
DOI: 10.6084/m9.figshare.19092684
title: Additional file 2 of Risk stratification of lung adenocarcinoma using a nomogram combined with ferroptosis-related LncRNAs and subgroup analysis with immune and N6-methyladenosine modification

description: Additional file 2. The data analysis.
DOI: 10.6084/m9.figshare.12276830.v1
title: Additional file 1 of Cone-beam computed tomography investigation of middle mesial canals and isthmuses in mandibular first molars in a Chinese population

description: Additional file 1. Raw data.
DOI: 10.6084/m9.figshare.22630754
title: Elucidation of conserved multi-epitope vaccine against <i>Leishmania donovani</i> using reverse vaccinology

description: Visceral leishmaniasis (VL) is a tropical disease that causes severe public health problems in humans when untreated. As no licensed vaccine exists against VL, we aimed to formulate a potential MHC-restricted chimeric vaccine construct against this dreadful parasitic disease. Amastin-like protein derived from <i>L. donovani</i> is considered to be stable, immunogenic and non-allergic. A comprehensive established framework was used to explore the set of immunogenic epitopes with estimated population coverage of 96.08% worldwide. The rigorous assessment revealed 6 promiscuous T-epitopes which can plausibly be presented by more than 66 diverse HLA alleles. Further docking and simulation study of peptide receptor complexes identified a strong and stable binding interaction with better structural compactness. The predicted epitopes were combined with appropriate linkers and adjuvant molecules and their translation efficiency was evaluated in pET28+(a), an bacterial expression vector using in-silico cloning. Molecular docking followed by MD simulation study revealed a stable interaction between chimeric vaccine construct with TLRs. Immune simulation of the chimeric vaccine constructs showed an elevated Th1 immune response against both B and T epitopes. With this, the detailed computational analysis suggested that the chimeric vaccine construct can evoke a robust immune response against <i>Leishmania donovani</i> infection. Future studies are required to validate the role of amastin as a promising vaccine target. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.22665369.v1
title: Molecular modeling of ARF6 dysregulation caused by mutations in IQSEC2

description: IQSEC2 gene mutations are associated with epilepsy, autism, and intellectual disability. The primary function IQSEC2, mediated via its Sec 7 domain, is to act as a guanine nucleotide exchange factor for ARF6. We sought to develop a molecular model, which may explain the aberrant Sec 7 activity on ARF6 of different human IQSEC2 mutations. We integrated experimental data of IQSEC2 mutants with protein structure prediction by the RaptorX server combined with molecular modeling and molecular dynamics simulations. Normally, apocalmodulin (apoCM) binds to IQSEC2 resulting in its N-terminal fragment inhibiting access of its Sec 7 domain to ARF6. An increase in Ca2+ concentration destabilizes the interaction of IQSEC2 with apoCM and removes steric hindrance of Sec 7 binding with ARF6. Mutations at amino acid residue 350 of IQSEC2 result in loss of steric hindrance of Sec 7 binding with ARF6 leading to constitutive activation of ARF6 by Sec 7. On the other hand, a mutation at amino acid residue 359 of IQSEC2 results in constitutive hindrance of Sec 7 binding to ARF6 leading to the loss of the ability of IQSEC2 to activate ARF6. These studies provide a model for dysregulation of IQSEC2 Sec 7 activity by mutant IQSEC2 proteins. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.22593044
title: Clinical side-effects based drug repositioning for anti-epileptic activity

description: Several generations of anti-epileptic drugs (AEDs) are available but have several associated side effects apart from a limited success rate. Drug repositioning strategies have gained importance in the last two decades owing to lower failure rates and economic burden. Drugs with similar side effect profiles may share a common mechanism of action and thus can be linked to other disease treatments. The present study was carried out to identify the newly approved drug candidate(s) as AEDs using clinical side-effects drug repositioning strategy. The clinical side effect similarity of drugs available in the SIDER v4.1 database was estimated against common side effects of 5 major marketed AEDs, using the ‘dplyr’ package library in the R. Further drugs were filtered based on Blood Brain Barrier permeability prediction and FDA-approval status. Molecular docking studies were performed for selected 26 hits (drugs) against previously identified epilepsy target receptors: Voltage-gated sodium channel α2 (Nav1.2), GABA receptor α1-β1 (GABAr α1-β1), and Voltage-gated calcium channel α-1 G (Cav3.1). Only 2 drugs (Ziprasidone and Paroxetine) showed better binding affinities against studied epilepsy receptors Nav1.2, GABAr α1-β1, and Cav3.1, than their corresponding standard AEDs, i.e. Carbamazepine, Clonazepam, and Pregabalin, respectively. Ziprasidone reportedly showed seizure-like symptoms in ∼3% of patients and was hence omitted from further study. The MDS study of docked complexes of Paroxetine with selected epilepsy target receptors showed stable RMSD values and better interaction energies. The study reveals Paroxetine as a potential candidate to be repurposed for 1st line epileptic seizure medication. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.22665369
title: Molecular modeling of ARF6 dysregulation caused by mutations in IQSEC2

description: IQSEC2 gene mutations are associated with epilepsy, autism, and intellectual disability. The primary function IQSEC2, mediated via its Sec 7 domain, is to act as a guanine nucleotide exchange factor for ARF6. We sought to develop a molecular model, which may explain the aberrant Sec 7 activity on ARF6 of different human IQSEC2 mutations. We integrated experimental data of IQSEC2 mutants with protein structure prediction by the RaptorX server combined with molecular modeling and molecular dynamics simulations. Normally, apocalmodulin (apoCM) binds to IQSEC2 resulting in its N-terminal fragment inhibiting access of its Sec 7 domain to ARF6. An increase in Ca2+ concentration destabilizes the interaction of IQSEC2 with apoCM and removes steric hindrance of Sec 7 binding with ARF6. Mutations at amino acid residue 350 of IQSEC2 result in loss of steric hindrance of Sec 7 binding with ARF6 leading to constitutive activation of ARF6 by Sec 7. On the other hand, a mutation at amino acid residue 359 of IQSEC2 results in constitutive hindrance of Sec 7 binding to ARF6 leading to the loss of the ability of IQSEC2 to activate ARF6. These studies provide a model for dysregulation of IQSEC2 Sec 7 activity by mutant IQSEC2 proteins. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.22691882
title: Identification of potential natural products derived from fungus growing termite, inhibiting <i>Pseudomonas aeruginosa</i> quorum sensing protein LasR using molecular docking and molecular dynamics simulation approach

description: <i>Pseudomonas aeruginosa</i>, the most common opportunistic pathogen, is becoming antibiotic-resistant worldwide. The fate of <i>P. aeruginosa</i>, a multidrug-resistant strain, can be determined by multidrug efflux pumps, enzyme synthesis, outer membrane protein depletion, and target alterations. Microbial niches have long used quorum sensing (QS) to synchronize virulence gene expression. Computational methods can aid in the development of novel <i>P. aeruginosa</i> drug-resistant treatments. The tripartite symbiosis in termites that grow fungus may help special microbes find new antimicrobial drugs. To find anti-quorum sensing natural products that could be used as alternative therapies, a library of 376 fungal-growing termite-associated natural products (NPs) was screened for their physicochemical properties, pharmacokinetics, and drug-likeness. Using GOLD, the top 74 NPs were docked to the QS transcriptional regulator LasR protein. The five lead NPs with the highest gold score and drug-like properties were chosen for a 200-ns molecular dynamics simulation to test the competitive activity of different compounds against negative catechin. Fridamycin and Daidzein had stable conformations, with mean RMSDs of 2.48 and 3.67 Å, respectively, which were similar to Catechin’s 3.22 Å. Fridamycin and Daidzein had absolute binding energies of −71.186 and −52.013 kcal/mol, respectively, which were higher than the control’s −42.75 kcal/mol. All the compounds within the active site of the LasR protein were kept intact by Trp54, Arg55, Asp67, and Ser123. These findings indicate that termite gut and fungus-associated NPs, specifically Fridamycin and Daidzein, are potent QS antagonists that can be used to treat <i>P. aeruginosa</i>’s multidrug resistance. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.22691882.v1
title: Identification of potential natural products derived from fungus growing termite, inhibiting <i>Pseudomonas aeruginosa</i> quorum sensing protein LasR using molecular docking and molecular dynamics simulation approach

description: <i>Pseudomonas aeruginosa</i>, the most common opportunistic pathogen, is becoming antibiotic-resistant worldwide. The fate of <i>P. aeruginosa</i>, a multidrug-resistant strain, can be determined by multidrug efflux pumps, enzyme synthesis, outer membrane protein depletion, and target alterations. Microbial niches have long used quorum sensing (QS) to synchronize virulence gene expression. Computational methods can aid in the development of novel <i>P. aeruginosa</i> drug-resistant treatments. The tripartite symbiosis in termites that grow fungus may help special microbes find new antimicrobial drugs. To find anti-quorum sensing natural products that could be used as alternative therapies, a library of 376 fungal-growing termite-associated natural products (NPs) was screened for their physicochemical properties, pharmacokinetics, and drug-likeness. Using GOLD, the top 74 NPs were docked to the QS transcriptional regulator LasR protein. The five lead NPs with the highest gold score and drug-like properties were chosen for a 200-ns molecular dynamics simulation to test the competitive activity of different compounds against negative catechin. Fridamycin and Daidzein had stable conformations, with mean RMSDs of 2.48 and 3.67 Å, respectively, which were similar to Catechin’s 3.22 Å. Fridamycin and Daidzein had absolute binding energies of −71.186 and −52.013 kcal/mol, respectively, which were higher than the control’s −42.75 kcal/mol. All the compounds within the active site of the LasR protein were kept intact by Trp54, Arg55, Asp67, and Ser123. These findings indicate that termite gut and fungus-associated NPs, specifically Fridamycin and Daidzein, are potent QS antagonists that can be used to treat <i>P. aeruginosa</i>’s multidrug resistance. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.22630755
title: Identification and mechanistic exploration of structural and conformational dynamics of NF-kB inhibitors: rationale insights from <i>in silico</i> and <i>in vitro</i> studies

description: Increased expression of target genes that code for proinflammatory chemical mediators results from a series of intracellular cascades triggered by activation of dysregulated NF-κB signaling pathway. Dysfunctional NF-kB signaling amplifies and perpetuates autoimmune responses in inflammatory diseases, including psoriasis. This study aimed to identify therapeutically relevant NF-kB inhibitors and elucidate the mechanistic aspects behind NF-kB inhibition. After virtual screening and molecular docking, five hit NF-kB inhibitors opted, and their therapeutic efficacy was examined using cell-based assays in TNF-α stimulated human keratinocyte cells. To investigate the conformational changes of target protein and inhibitor-protein interaction mechanisms, molecular dynamics (MD) simulations, binding free energy calculations together with principal component (PC) analysis, dynamics cross-correlation matrix analysis (DCCM), free energy landscape (FEL) analysis and quantum mechanical calculations were carried out. Among identified NF-kB inhibitors, myricetin and hesperidin significantly scavenged intracellular ROS and inhibited NF-kB activation. Analysis of the MD simulation trajectories of ligand–protein complexes revealed that myricetin and hesperidin formed energetically stabilized complexes with the target protein and were able to lock NF-kB in a closed conformation. Myricetin and hesperidin binding to the target protein significantly impacted conformational changes and internal dynamics of amino acid residues in protein domains. Tyr57, Glu60, Lys144 and Asp239 residues majorly contributed to locking the NF-kB in a closed conformation. The combinatorial approach employing <i>in silico</i> tools integrated with cell-based approaches substantiated the binding mechanism and NF-kB active site inhibition by the lead molecule myricetin, which can be explored as a viable antipsoriatic drug candidate associated with dysregulated NF-kB. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.22692258
title: SPP1, a potential therapeutic target and biomarker for lung cancer: functional insights through computational studies

description: NIH reported 128 different types of cancer of which lung cancer is the leading cause of mortality. Globally, it is estimated that on average one in every seventeen hospitalized patients was deceased. There are plenty of studies that have been reported on lung cancer draggability and therapeutics, but yet a protein that plays a central specific to cure the disease remains unclear. So, this study is designed to identify the possible therapeutic targets and biomarkers that can be used for the potential treatment of lung cancers. In order to identify differentially expressed genes, 39 microarray datasets of lung cancer patients were obtained from various demographic regions of the GEO database available at NCBI. After annotating statistically, 6229 up-regulated genes and 10324 down-regulated genes were found. Out of 17 up-regulated genes and significant genes, we selected SPP1 (osteopontin) through virtual screening studies. We found functional interactions with the other cancer-associated genes such as VEGF, FGA, JUN, EGFR, and TGFB1. For the virtual screening studies,198 biological compounds were retrieved from the ACNPD database and docked with SPP1 protein (PDBID: 3DSF). In the results, two highly potential compounds secoisolariciresinol diglucoside (-12.9 kcal/mol), and Hesperidin (-12.0 kcal/mol) showed the highest binding affinity. The stability of the complex was accessed by 100 ns simulation in an SPC water model. From the functional insights obtained through these computational studies, we report that SPP1 could be a potential biomarker and successive therapeutic protein target for lung cancer treatment. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.8092034
title: Integrated Guidance and Control of Multiple Interceptor Missiles Based on Improved Distributed Cooperative Control Strategy

description: ABSTRACT In this study, an improved cooperative integrated guidance and control (IGC) design method is proposed based on distributed networks to address the guidance and control problem of multiple interceptor missiles. An IGC model for a leading interceptor is constructed based on the relative kinematic relations between missiles and a target and the kinematic equations of the missiles in a pitch channel. The unknown disturbances of the model are estimated using a finite-time disturbance observer (FTDO). Then, the control algorithm for the leading interceptor is designed according to the disturbance estimation and nonsingular fast dynamic surface sliding mode control (SMC). To enhance the rate of convergence of the cooperative control commands for the interceptors, an improved cooperative control strategy is proposed based on the leader-follower distributed network. Consequently, the two velocity components of the interceptor in the pitch channel can be obtained, which are subsequently converted to the total velocity and flight path angle commands of the interceptor using kinematic relations. The control algorithm for the following interceptor is similarly designed using an FTDO and dynamic surface SMC. The effectiveness of the improved distributed cooperative control strategy for multiple interceptors is validated through simulations.
DOI: 10.4121/5e40ecd6-98c4-423c-bd1c-d24f0f7a7a59.v5
title: 20211109 20211215 Main deployment - Nearshore - RealDune/REFLEX

description: Nearshore field measurements of the main November - December deployment of the RealDune/REFLEX experiments at the Dutch coast in Autumn/Winter 2021/2022. The lidar and GoPro data are stored separately. This dataset is part of the data collection 'Nearshore coastal measurements of calm, moderate, and storm conditions at two artificial dunes along the Dutch Coast during the RealDune/REFLEX experiments'.
DOI: 10.6084/m9.figshare.7038083.v1
title: Additional file 2: of Assessing the sensitivity of placental growth factor and soluble fms-like tyrosine kinase 1 at 36 weeks’ gestation to predict small-for-gestational-age infants or late-onset preeclampsia: a prospective nested case-control study

description: S2. Study data. (XLSX 104 kb)
DOI: 10.6084/m9.figshare.8092148
title: Crystallization Behavior and Mechanical Properties of Cu-based Bulk Metallic Glass Composites

description: This work highlights the relationship between the preparation, crystallization behavior, microstructures, and mechanical properties of Cu-based bulk metallic glasses (BMGs) and their composites (BMGCs). (Cu47Zr45Al8)97.5Y1.5Nb in-situ BMGCs were prepared using isothermal annealing, and the experimental results indicate tunable mechanical properties of the alloys by processing parameter manipulation. The crystallinity of (Cu47Zr45Al8)97.5Y1.5Nb BMGCs increases with extended annealing temperature and time, while their phase transition with rising temperature follows Am (amorphous state) → Am + Cu10Zr7 →Am + Cu10Zr7 + AlCu2Zr + Al2Zr. Precipitation strengthening during annealing above 720 K (447 ºC) can enhance the alloy microhardness remarkably and achieve an optimum of 712 HV by annealing at 800 K (527 ºC) for 60 min. TEM results show that Cu10Zr7 with sizes of 12~15 nm precipitates out upon crystallization and thereby accounts for the superior compressive property. The alloy exhibits a fracture strength up to 2080 MPa after annealing at 680 K (407 ºC) for 30 min. Morphological observation of the fracture surface reveals a transition of fracture characteristics from the typical amorphous ductile manner to a brittle manner with further annealing. The investigation provides novel thoughts of BMGs processing for further performance improvement.
DOI: 10.4121/b3cc08f1-cc3e-4b16-b007-72a421435f2c
title: 20220105 20220107 Storm deployment - Nearshore - RealDune/REFLEX

description: Nearshore field measurements of the January storm deployment of the RealDune/REFLEX experiments at the Dutch coast in Autumn/Winter 2021/2022. This dataset is part of the data collection 'Nearshore coastal measurements of calm, moderate, and storm conditions at two artificial dunes along the Dutch Coast during the RealDune/REFLEX experiments'.
DOI: 10.4121/b3cc08f1-cc3e-4b16-b007-72a421435f2c.v3
title: 20220105 20220107 Storm deployment - Nearshore - RealDune/REFLEX

description: Nearshore field measurements of the January storm deployment of the RealDune/REFLEX experiments at the Dutch coast in Autumn/Winter 2021/2022. This dataset is part of the data collection 'Nearshore coastal measurements of calm, moderate, and storm conditions at two artificial dunes along the Dutch Coast during the RealDune/REFLEX experiments'.
DOI: 10.34740/kaggle/dsv/7623620
title: 📒 Meta Kaggle ported to MS SQL SERVER 2022 DB