cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.17632/ryn6wdgckf.1
title: Database of incorrect R equations

description: This database contains information on studies (conducted since 1989) that used incorrect R equations to calculate rainfall erosivity. We spent numerous hours manually combing through Scopus, Google Scholar, and other Internet sources to locate these articles. The literature search was initially limited to English-language papers and later expanded to Chinese publications in order to determine the origin of the misuse of R equations. A total of 125 papers were discovered and entered into this database, and it is easy to add studies if more are found.
DOI: 10.17632/cprmgk9584.1
title: LINF_300022700

description: cdc2-related protein kinase 11 | CRK11
Leishmania infantum (strain JPCM5)
DOI: 10.17632/cbjp83r99w.1
title: LINF_300022800

description: DnaJ domain-containing protein | JDP24 | J24
Leishmania infantum (strain JPCM5)
DOI: 10.17632/2z3t52wdy8.1
title: Monitoring of the SARS-CoV-2 Omicron BA.1/BA.2 lineage transition in the Swedish population reveals increased viral RNA levels in BA.2 cases; Lentini et al 2022

description: Table S1-6. Excel spreadsheets. Lentini 2022.
DOI: 10.17632/rz98xx625v.1
title: LINF_300022900

description: queuine tRNA-ribosyltransferase
Leishmania infantum (strain JPCM5)
DOI: 10.17632/gvc7df7btk.1
title: Solutions and Gantt charts in Tables 2.3.5.6.7

description: Solutions and Gantt charts in Tables 2.3.5.6.7 are used to verify correctness of the established models.
DOI: 10.17632/3ky2nf6dts.1
title: LINF_300023000

description: hydin
Leishmania infantum (strain JPCM5)
DOI: 10.17632/mfj7t3wfk3.1
title: Antibody therapy reverses biological signatures of COVID-19 progression_Maher et al.

description: Supplementary Files 1 and 2
DOI: 10.5281/zenodo.6865934
title: Data and R-code belonging to Manuscript: "Prior experience of captivity affects behavioural responses to 'novel' environments"

description: Data and R-code belonging to Manuscript:"Prior experience of captivity affects behavioural responses to 'novel' environments" 1) the data can be found in an excel file named: datafile_explorationGT2022.xlsx 2) the R-code used to do the analysis in the MS can be found in an R-markdown file: Rmd_file_MS_GTexploration_R2.Rmd
DOI: 10.5281/zenodo.6023093
title: Data and R-code belonging to Manuscript: "Prior experience of captivity affects behavioural responses to 'novel' environments"

description: Data and R-code belonging to Manuscript:"Prior experience of captivity affects behavioural responses to 'novel' environments" 1) the data can be found in an excel file named: datafile_explorationGT2022.xlsx 2) the R-code used to do the analysis in the MS can be found in an R-markdown file: Rmd_file_MS_GTexploration_R2.Rmd
DOI: 10.6084/m9.figshare.19591021
title: MALAT1-dependent hsa_circ_0076611 regulates translation rate in triple-negative breast cancer

description: Vascular Endothelial Growth Factor A (VEGFA) is the most commonly expressed angiogenic growth factor in solid tumors and is generated as multiple isoforms through alternative mRNA splicing. Here, we show that lncRNA <em>MALAT1</em> (metastasis-associated lung adenocarcinoma transcript 1) and ID4 (inhibitor of DNA-binding 4) protein, previously referred to as regulators of linear isoforms of <em>VEGFA</em>, induce back-splicing of <em>VEGFA</em> exon 7, producing circular RNA circ_0076611. Circ_0076611 is detectable in triple-negative breast cancer (TNBC) cells and tissues, in exosomes released from TNBC cells and in the serum of breast cancer patients. Circ_0076611 interacts with a variety of proliferation-related transcripts, included <em>MYC</em> and <em>VEGFA</em> mRNAs, and increases cell proliferation and migration of TNBC cells. Mechanistically, circ_0076611 favors the expression of its target mRNAs by facilitating their interaction with components of the translation initiation machinery. These results add further complexity to the multiple <em>VEGFA</em> isoforms expressed in cancer cells and highlight the relevance of post-transcriptional regulation of <em>VEGFA</em> expression in TNBC cells.
DOI: 10.6084/m9.figshare.19591021.v1
title: MALAT1-dependent hsa_circ_0076611 regulates translation rate in triple-negative breast cancer

description: Vascular Endothelial Growth Factor A (VEGFA) is the most commonly expressed angiogenic growth factor in solid tumors and is generated as multiple isoforms through alternative mRNA splicing. Here, we show that lncRNA <em>MALAT1</em> (metastasis-associated lung adenocarcinoma transcript 1) and ID4 (inhibitor of DNA-binding 4) protein, previously referred to as regulators of linear isoforms of <em>VEGFA</em>, induce back-splicing of <em>VEGFA</em> exon 7, producing circular RNA circ_0076611. Circ_0076611 is detectable in triple-negative breast cancer (TNBC) cells and tissues, in exosomes released from TNBC cells and in the serum of breast cancer patients. Circ_0076611 interacts with a variety of proliferation-related transcripts, included <em>MYC</em> and <em>VEGFA</em> mRNAs, and increases cell proliferation and migration of TNBC cells. Mechanistically, circ_0076611 favors the expression of its target mRNAs by facilitating their interaction with components of the translation initiation machinery. These results add further complexity to the multiple <em>VEGFA</em> isoforms expressed in cancer cells and highlight the relevance of post-transcriptional regulation of <em>VEGFA</em> expression in TNBC cells.
DOI: 10.5281/zenodo.6860705
title: Dynamics of the euphotic zone in the Black Sea: The synergy of data from profiling floats, machine learning and numerical modeling

description: The datasets contain input data and data emulated by Neural networks (NN) used in the study 'Dynamics of the euphotic zone in the Black Sea: The synergy of data from profiling floats, machine learning and numerical modeling' - <strong>NN2018_CMEMS_ARGO.tar.gz</strong>: archive contains Matlab binary files consisting of NN-derived BGC variables (Chlorophyll-a, Oxygen and backscatter at 700nm) along ARGO float paths in 2018 with vertical resolution taken from CMEMS (13 depth levels in the depth range studied here); NN was applied either on CMEMS physics ('C') or on ARGO physics ('A'); additionally, CMEMS BGC model data (Chlorophyll-a and Oxygen) along these paths are included; (filenames follow the names of floats given in Table 1:<em> floatname</em>_2018_NNARGOCMEMS.mat) - <strong>NNalongARGO.tar.gz</strong>: archive contains Matlab binary files consisting of NN-derived BGC variables (Chlorophyll-a, Oxygen and backscatter at 700 nm) along ARGO float paths together with input ARGO data (time, latitude, longitude, salinity, temperature, sigma_T and BGC variables); all variables are mapped with 1m vertical resolution; depth range is [1m 150m] ; additionally, float ogs7 data include NO3, float hzg1 data does not contain Chlorophyll-a and backscatter at 700 nm; (filenames follow the names of floats given in Table 1:<em> floatname</em>_euph_1mRes_150mALLINCLNN.mat) - <strong>NNReconBlackSea.tar.gz</strong>: archive contains Matlab binary files consisting of basin wide NN derived BGC variables (Chlorophyll-a, Oxygen and backscatter at 700nm) for the years 2015-19 and 2010/11 (weekly mean data); additionally CMEMS data (time, latitude, longitude, salinity, temperature, sea surface height) are provided for the photic zone; (filenames are reconNNCMEMS_2015_2019.mat and reconNNCMEMS_2010_2011.mat, respectively)
DOI: 10.5281/zenodo.6855471
title: Dynamics of the euphotic zone in the Black Sea: The synergy of data from profiling floats, machine learning and numerical modeling

description: The datasets contain input data and data emulated by Neural networks (NN) used in the study 'Dynamics of the euphotic zone in the Black Sea: The synergy of data from profiling floats, machine learning and numerical modeling' - <strong>NN2018_CMEMS_ARGO.tar.gz</strong>: archive contains Matlab binary files consisting of NN-derived BGC variables (Chlorophyll-a, Oxygen and backscatter at 700nm) along ARGO float paths in 2018 with vertical resolution taken from CMEMS (13 depth levels in the depth range studied here); NN was applied either on CMEMS physics ('C') or on ARGO physics ('A'); additionally, CMEMS BGC model data (Chlorophyll-a and Oxygen) along these paths are included; (filenames follow the names of floats given in Table 1:<em> floatname</em>_2018_NNARGOCMEMS.mat) - <strong>NNalongARGO.tar.gz</strong>: archive contains Matlab binary files consisting of NN-derived BGC variables (Chlorophyll-a, Oxygen and backscatter at 700 nm) along ARGO float paths together with input ARGO data (time, latitude, longitude, salinity, temperature, sigma_T and BGC variables); all variables are mapped with 1m vertical resolution; depth range is [1m 150m] ; additionally, float ogs7 data include NO3, float hzg1 data does not contain Chlorophyll-a and backscatter at 700 nm; (filenames follow the names of floats given in Table 1:<em> floatname</em>_euph_1mRes_150mALLINCLNN.mat) - <strong>NNReconBlackSea.tar.gz</strong>: archive contains Matlab binary files consisting of basin wide NN derived BGC variables (Chlorophyll-a, Oxygen and backscatter at 700nm) for the years 2015-19 and 2010/11 (weekly mean data); additionally CMEMS data (time, latitude, longitude, salinity, temperature, sea surface height) are provided for the photic zone; (filenames are reconNNCMEMS_2015_2019.mat and reconNNCMEMS_2010_2011.mat, respectively)
DOI: 10.6084/m9.figshare.20342670
title: Research Date.sav

description: With the increasing popularity of Internet devices, the rate of Internet addiction, particularly among adolescents, is rising dramatically. IA causes adolescents to short-sightedness, resulting in a dramatic increase in delayed discounting. However, the effects and potential mechanisms of IA on adolescent delay discounting remain largely unknown. To our knowledge, this is the first study to examine the relationship between IA and delay discounting in Chinese adolescents. The sample comprised 2245 adolescents (49.70% male; <em>M(SD)age</em> = 14.86(2.18) years) completed questionnaires anonymously regarding IA, delayed discounting, time perception, and future self-continuity (FSC). The results indicated that: (a) IA showed a positive association with adolescent delay discounting. (b) time perception mediated the association between IA and delay discounting, and the mediating effect was smaller for older adolescents compared to younger adolescents. (c) FSC only moderates the relationship between IA and delay discounting in older adolescents. Specifically, the relationship between IA and delay discounting was weaker in older adolescents with higher levels of FSC. These findings show that IA distorts adolescents' perceptions of future time, which affects delay discounting. We need to use more targeted intervention strategies to prevent and mitigate the effects of IA on delay discounting in adolescents of various ages.
DOI: 10.5281/zenodo.6645820
title: Intratumoural heterogeneity and immune modulation in lung adenocarcinoma of female smokers and never smokers

description: Count matrix and associated meta data for single nucleus transcriptomics of healthy and tumour lung tissue from lung adenocarcinoma patients. Cohort includes young and elderly, female and male, smokers and never smokers.
DOI: 10.5281/zenodo.6645819
title: Intratumoural heterogeneity and immune modulation in lung adenocarcinoma of female smokers and never smokers

description: Count matrix and associated meta data for single nucleus transcriptomics of healthy and tumour lung tissue from lung adenocarcinoma patients. Cohort includes young and elderly, female and male, smokers and never smokers.
DOI: 10.6084/m9.figshare.20296695
title: ALS raw data.xlsx

description: Meta-analysis of CSF TDP-43 levels raw data, Prisma flow diagram, Forest plot- TDP 43 levels in ALS patients, TDP-43 p.N345K gene in ALS Patients <br> <br>
DOI: 10.6084/m9.figshare.20296695.v2
title: ALS raw data.xlsx

description: Meta-analysis of CSF TDP-43 levels raw data, Prisma flow diagram, Forest plot- TDP 43 levels in ALS patients, TDP-43 p.N345K gene in ALS Patients <br> <br>
DOI: 10.6084/m9.figshare.13627580
title: Virtual screening of epalrestat mimicking selective ALR2 inhibitors from natural product database: auto pharmacophore, ADMET prediction and molecular dynamics approach

description: Epalrestat is the only effective aldose reductase (ALR2) inhibitor available in the market for the treatment of diabetic neuropathy. Clinical effectiveness of epalrestat in diabetic neuropathy encouraged us to develop some more ALR2 inhibitors with a better therapeutic profile. Herein, we utilized the pharmacophoric features of epalrestat to search some novel ALR2 inhibitors from an InterBioScreen database of natural compounds. ADME and PAINS filters were applied to provide drug-likeness and to remove toxicophores from the screened hits. The pharmacophoric features of 4-hydroxy-2-nonenal (HNE), a well-known substrate of ALR1, were also explored to identify selective ALR2 inhibitors. The structure-based analysis was then adopted to find out the molecules showing interactions with ALR2 which are crucial for their therapeutic activity. These interaction patterns and binding modes were compared with that of epalrestat. Molecular dynamics (MD) analysis was also carried out to get more insight into the interactions of screened hits in the catalytic domain of ALR2. Additionally, the top hits were docked and simulated with aldehyde reductase (ALR1) to determine their selectivity for ALR2 over ALR1. Overall, five hits including <b>STOCKIN-44771, STOCKIN-46041, STOCKIN-59369, STOCKIN-69620</b> and <b>STOCKIN-88220</b> were found to possess a good therapeutic profile in terms of key interactions, binding energies and drug-likeness. Two hits, <b>STOCKIN-46041</b> and <b>STOCKIN-59369,</b> were identified as the most selective ALR2 inhibitors when assessed their selectivity profile. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.13621775.v2
title: Promising inhibitors of nsp2 of CHIKV using molecular docking and temperature-dependent molecular dynamics simulations

description: Infection due to the Chikungunya virus (CHIKV) has taken the life of lots of people; and researchers are working to find the vaccine or promisng drug candidates against this viral infection. In this work, the authors have designed one component reaction based on the thia-/oxa-azolidineone and created a library of 2000 molecules based on the product obtained. Further, the compounds were screened through the docking using iGemdock against the non-structural protein 2 (nsp2) of CHIKV. Molecular docking gives the binding energy (BE) or energy for the formation of the complex between the designed compound and nsp2 of CHIKV; and CMPD222 gave the lowest energy. This is based on the energy obtained from van der Waal’s interaction, hydrogen bonding and electrostatic instructions. Further, molecular dynamics simulations (MDS) of nsp2 of CHIKV with and without screened compound (222) were performed to validate the docking results and the change in free energy for the formation of the complex is −10.8327 kcal/mol. To explore the potential of CMPD222, the MDS of the CMPD222-nsp2 of CHIKV were performed at different temperatures (325, 350, 375 and 400 K) to understand the inhibition of the protease. MM-GBSA calculations were performed to determined change in entropy, change in enthalpy and change in free energy to understand the inhibition. Maximum inhibition of nsp2 of CHIKV with CMPD222 is observed at 375 K with a change in free energy of −19.3754 kcal/mol. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.13656128
title: Structural similarity-based prediction of host factors associated with SARS-CoV-2 infection and pathogenesis

description: The current pandemic resulted from SARS-CoV-2 still remains as the major public health concern globally. The precise mechanism of viral pathogenesis is not fully understood, which remains a major hurdle for medical intervention. Here we generated an interactome profile of protein-protein interactions based on host and viral protein structural similarities information. Further computational biological study combined with Gene enrichment analysis predicted key enriched pathways associated with viral pathogenesis. The results show that axon guidance, membrane trafficking, vesicle-mediated transport, apoptosis, clathrin-mediated endocytosis, Vpu mediated degradation of CD4 T cell, and interferon-gamma signaling are key events associated in SARS-CoV-2 life cycle. Further, degree centrality analysis reveals that IRF1/9/7, TP53, and CASP3, UBA52, and UBC are vital proteins for IFN-γ-mediated signaling, apoptosis, and proteasomal degradation of CD4, respectively. We crafted chronological events of the virus life cycle. The SARS-CoV-2 enters through clathrin-mediated endocytosis, and the genome is trafficked to the early endosomes in a RAB5-dependent manner. It is predicted to replicate in a double-membrane vesicle (DMV) composed of the endoplasmic reticulum, autophagosome, and ERAD machinery. The SARS-CoV-2 down-regulates host translational machinery by interacting with protein kinase R, PKR-like endoplasmic reticulum kinase, and heme-regulated inhibitor and can phosphorylate eIF2a. The virion assembly occurs in the ER-Golgi intermediate compartment (ERGIC) organized by the spike and matrix protein. Collectively, we have established a spatial link between viral entry, RNA synthesis, assembly, pathogenesis, and their associated diverse host factors, those could pave the way for therapeutic intervention. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.13656128.v1
title: Structural similarity-based prediction of host factors associated with SARS-CoV-2 infection and pathogenesis

description: The current pandemic resulted from SARS-CoV-2 still remains as the major public health concern globally. The precise mechanism of viral pathogenesis is not fully understood, which remains a major hurdle for medical intervention. Here we generated an interactome profile of protein-protein interactions based on host and viral protein structural similarities information. Further computational biological study combined with Gene enrichment analysis predicted key enriched pathways associated with viral pathogenesis. The results show that axon guidance, membrane trafficking, vesicle-mediated transport, apoptosis, clathrin-mediated endocytosis, Vpu mediated degradation of CD4 T cell, and interferon-gamma signaling are key events associated in SARS-CoV-2 life cycle. Further, degree centrality analysis reveals that IRF1/9/7, TP53, and CASP3, UBA52, and UBC are vital proteins for IFN-γ-mediated signaling, apoptosis, and proteasomal degradation of CD4, respectively. We crafted chronological events of the virus life cycle. The SARS-CoV-2 enters through clathrin-mediated endocytosis, and the genome is trafficked to the early endosomes in a RAB5-dependent manner. It is predicted to replicate in a double-membrane vesicle (DMV) composed of the endoplasmic reticulum, autophagosome, and ERAD machinery. The SARS-CoV-2 down-regulates host translational machinery by interacting with protein kinase R, PKR-like endoplasmic reticulum kinase, and heme-regulated inhibitor and can phosphorylate eIF2a. The virion assembly occurs in the ER-Golgi intermediate compartment (ERGIC) organized by the spike and matrix protein. Collectively, we have established a spatial link between viral entry, RNA synthesis, assembly, pathogenesis, and their associated diverse host factors, those could pave the way for therapeutic intervention. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.13621775.v1
title: Promising inhibitors of nsp2 of CHIKV using molecular docking and temperature-dependent molecular dynamics simulations

description: Infection due to the Chikungunya virus (CHIKV) has taken the life of lots of people; and researchers are working to find the vaccine or promisng drug candidates against this viral infection. In this work, the authors have designed one component reaction based on the thia-/oxa-azolidineone and created a library of 2000 molecules based on the product obtained. Further, the compounds were screened through the docking using iGemdock against the non-structural protein 2 (nsp2) of CHIKV. Molecular docking gives the binding energy (BE) or energy for the formation of the complex between the designed compound and nsp2 of CHIKV; and CMPD222 gave the lowest energy. This is based on the energy obtained from van der Waal’s interaction, hydrogen bonding and electrostatic instructions. Further, molecular dynamics simulations (MDS) of nsp2 of CHIKV with and without screened compound (222) were performed to validate the docking results and the change in free energy for the formation of the complex is −10.8327 kcal/mol. To explore the potential of CMPD222, the MDS of the CMPD222-nsp2 of CHIKV were performed at different temperatures (325, 350, 375 and 400 K) to understand the inhibition of the protease. MM-GBSA calculations were performed to determined change in entropy, change in enthalpy and change in free energy to understand the inhibition. Maximum inhibition of nsp2 of CHIKV with CMPD222 is observed at 375 K with a change in free energy of −19.3754 kcal/mol. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.13637312
title: Physicochemical characterization of paclitaxel prodrugs with cytochrome 3A4 to correlate solubility and bioavailability implementing molecular docking and simulation studies

description: Prodrugs are biologically inactive drug molecules that may be developed through rational drug design with an objective to improve a drug’s pharmaceutical and pharmacokinetic properties. Paclitaxel, a highly potent anticancer drug, is directed against many cancers like breast cancer, ovarian cancer, lung cancer, head and neck tumors, non-small cell lung cancer, and Kaposi’s sarcoma, etc. Along with its excellent antitumor activity the drug had a major limitation of low water solubility. To overcome this limitation of this nanomolar active drug many prodrugs were formed in the past. Though increase in the solubility of the drug was obtained but that may or may not account for its increase in bioavailability. CYP3A4 liver enzymes are responsible for the metabolism of fifty percent of the drugs and are major metabolizing enzyme for paclitaxel. Phosphate prodrugs are well known to account the insolubility of many drugs and thus increasing their bioavailability also. In this study, we calculated the ADMET properties of a dataset of twenty phosphate prodrugs of paclitaxel. On the basis of reflection of three favourable properties, ten prodrugs were chosen for further docking studies against CYP3A4. Finally, three prodrugs showing unfavourable binding affinities were selected for Molecular Dynamics Simulations and from this <i>in-silico</i> study we identified that all the three selected prodrugs were unstable as compared to the paclitaxel. The instability of these prodrugs showed their lesser interaction with the CYP3A4 and hence contributing more towards its bioavailability. Thus the three suggested prodrugs those were studied <i>in-silico</i> for oral bioavailability can be further validated for gastrointestinal cancer. Communicated by Ramaswamy H. Sarma