cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1463374.v1
title: Discovery of a latent calcineurin inhibitory peptide from its auto inhibitory domain by docking, dynamic simulation and <i>in vitro</i> methods

description: Auto Inhibitory Domain (AID) of calcineurin (CN) was discovered two decades ago. Fewer investigations are reported to find out shortest possible peptide from the AID for CN inhibition. Hence, the current study has focused on screening of nearly 150 peptide fragments derived from the AID using in silico method. Therefore, we have employed docking studies, aiming to analyze the best pose of AID derived peptides on CN active site. We also analyzed binding free energy (ΔG) of docked complex using Molecular Mechanics/Generalized Born Surface Area (MM/GBSA). MM/GBSA predicts two short peptides P1and P2 found to be lowest binding free energy. Two peptides exhibit better binding affinity with CN, suggests that the possible candidates for potential CN inhibition. Further, the stability of the docked complex was analyzed using Molecular Dynamic (MD) simulation. MD study shows that CNA:P2 is most stable complex than CN A:P1 and CN A:AID. Besides, we have synthesized and purified P1 and P2 peptides over High Performance Liquid Chromatography (HPLC) found to be 90.31% and 98.93% of purity respectively. In addition, AID peptides were characterized over mass spectral analysis. Peptides were subjected to CN inhibitory assay using malachite green method. Where, P1 and P2 exhibit CN inhibition better than AID. In particular, shortest peptide P2 shows highest inhibitory activity than AID. Enzyme assay reveals CN inhibitory activity of P2 peptide is consistent with in silico results. In silico and in vitro results corroborated each other to confirm short peptide P2 can be used as a potential CN inhibitor.
DOI: 10.6084/m9.figshare.1463374
title: Discovery of a latent calcineurin inhibitory peptide from its autoinhibitory domain by docking, dynamic simulation, and <i>in vitro</i> methods

description: Autoinhibitory domain (AID) of calcineurin (CN) was discovered two decades ago. Fewer investigations are reported to find out shortest possible peptide from the AID for CN inhibition. Hence, this study has focused on screening of nearly 150 peptide fragments derived from the AID using in silico method. Therefore, we have employed docking studies, aiming to analyze the best pose of AID-derived peptides on CN active site. We also analyzed binding free energy (Δ<i>G</i>) of docked complex using molecular mechanics/generalized Born surface area (MM/GBSA). MM/GBSA predicts two short peptides P1 and P2 found to be lowest binding free energy. Two peptides exhibit better binding affinity with CN, suggests that the possible candidates for potential CN inhibition. Further, the stability of the docked complex was analyzed using molecular dynamic (MD) simulation. MD study shows that CNA:P2 is the most stable complex than CN A:P1 and CN A:AID. Besides, we have synthesized and purified P1 and P2 peptides over high performance liquid chromatography (HPLC) found to be 90.31% and 98.93% of purity, respectively. In addition, AID peptides were characterized over mass spectral analysis. Peptides were subjected to CN inhibitory assay using malachite green method. Where, P1 and P2 exhibit CN inhibition better than AID. In particular, shortest peptide P2 shows highest inhibitory activity than AID. Enzyme assay reveals CN inhibitory activity of P2 peptide is consistent within silico results. In silico and <i>in vitro,</i> results corroborated each other to confirm short peptide P2 can be used as a potential CN inhibitor.
DOI: 10.6084/m9.figshare.1463356
title: VU University | PhD records without on-line PhD thesis publications | @ 24/5/2015

description: Via e-Library VU University Amsterdam.
DOI: 10.6084/m9.figshare.1463374.v3
title: Discovery of a latent calcineurin inhibitory peptide from its autoinhibitory domain by docking, dynamic simulation, and <i>in vitro</i> methods

description: Autoinhibitory domain (AID) of calcineurin (CN) was discovered two decades ago. Fewer investigations are reported to find out shortest possible peptide from the AID for CN inhibition. Hence, this study has focused on screening of nearly 150 peptide fragments derived from the AID using in silico method. Therefore, we have employed docking studies, aiming to analyze the best pose of AID-derived peptides on CN active site. We also analyzed binding free energy (Δ<i>G</i>) of docked complex using molecular mechanics/generalized Born surface area (MM/GBSA). MM/GBSA predicts two short peptides P1 and P2 found to be lowest binding free energy. Two peptides exhibit better binding affinity with CN, suggests that the possible candidates for potential CN inhibition. Further, the stability of the docked complex was analyzed using molecular dynamic (MD) simulation. MD study shows that CNA:P2 is the most stable complex than CN A:P1 and CN A:AID. Besides, we have synthesized and purified P1 and P2 peptides over high performance liquid chromatography (HPLC) found to be 90.31% and 98.93% of purity, respectively. In addition, AID peptides were characterized over mass spectral analysis. Peptides were subjected to CN inhibitory assay using malachite green method. Where, P1 and P2 exhibit CN inhibition better than AID. In particular, shortest peptide P2 shows highest inhibitory activity than AID. Enzyme assay reveals CN inhibitory activity of P2 peptide is consistent within silico results. In silico and <i>in vitro,</i> results corroborated each other to confirm short peptide P2 can be used as a potential CN inhibitor.
DOI: 10.6084/m9.figshare.1466767.v49
title: Program for keeping into account the solar reflections from obstructions in ESP-r on the basis of the irradiance ratios

description: Modish is a program for bringing into account the reflective effect of solar obstructions on solar gains in an ESP-r building model on the basis of the irradiance ratios combining the direct unreflected radiation on a surface, as calculated by ESP-r, and the total radiation on the same surface calculated by the means of Radiance. <br><br>
DOI: 10.6084/m9.figshare.1463374.v2
title: Discovery of a latent calcineurin inhibitory peptide from its autoinhibitory domain by docking, dynamic simulation, and <i>in vitro</i> methods

description: Autoinhibitory domain (AID) of calcineurin (CN) was discovered two decades ago. Fewer investigations are reported to find out shortest possible peptide from the AID for CN inhibition. Hence, this study has focused on screening of nearly 150 peptide fragments derived from the AID using in silico method. Therefore, we have employed docking studies, aiming to analyze the best pose of AID-derived peptides on CN active site. We also analyzed binding free energy (Δ<i>G</i>) of docked complex using molecular mechanics/generalized Born surface area (MM/GBSA). MM/GBSA predicts two short peptides P1 and P2 found to be lowest binding free energy. Two peptides exhibit better binding affinity with CN, suggests that the possible candidates for potential CN inhibition. Further, the stability of the docked complex was analyzed using molecular dynamic (MD) simulation. MD study shows that CNA:P2 is the most stable complex than CN A:P1 and CN A:AID. Besides, we have synthesized and purified P1 and P2 peptides over high performance liquid chromatography (HPLC) found to be 90.31% and 98.93% of purity, respectively. In addition, AID peptides were characterized over mass spectral analysis. Peptides were subjected to CN inhibitory assay using malachite green method. Where, P1 and P2 exhibit CN inhibition better than AID. In particular, shortest peptide P2 shows highest inhibitory activity than AID. Enzyme assay reveals CN inhibitory activity of P2 peptide is consistent within silico results. In silico and <i>in vitro,</i> results corroborated each other to confirm short peptide P2 can be used as a potential CN inhibitor.
DOI: 10.6084/m9.figshare.1463328
title: Costs of Rabies Post-Exposure Prophylaxis According to Pre-Exposure Prophylaxis Status

description: Costs of PrEP were assessed for the cohort of 4,666 children in the study at the time of PreP administration. PrEP schedule followed the WHO guidelines, with intradermal administration of 0.1 ml volume per site (one site each day) given on days 0, 7 and 28. The direct medical costs included cost of biologicals (rabies vaccine), cost per shipment, considered as 2% of the vaccine cost, cost of needles, alcohol and cotton used. Costs related to health care staff were not included. The number of doses per vial assumed for the analysis is 4, although in theory 1 vial could be used to deliver 5 x 0.1 mL doses, thus 20% vaccine wastage is built into the calculations.In addition, to explore further the benefits of such vaccination program, projected costs of two hypothetical cohorts of children bitten by a dog were assessed according to two scenarios: (i) Scenario 1, no PrEP: Assessment of the costs related to the expected annual number of children among the study cohort bitten by a dog, assuming they did not have PrEP. These children were considered to follow the standard of care for Post-Exposure Prophylaxis (PEP) defined as 2-site intradermal method (2-2-2-0-1) for use with PVRV (complete PEP), with RIG given for category III bites. (ii) Scenario 2, with PrEP Assessment of the costs related to the expected annual number of children among the study cohort bitten by a dog benefiting from PrEP. Following the national guidelines, such patients should be given only two booster doses on days 0 and 3, but no RIG. Costs associated with wound care (e.g. antibiotics, tetanus immunization) were not included in the analysis since these do not depend on rabies vaccination status of the patient. Indirect costs were also not included in the analysis. Time horizon for the comparison of the economic benefit of the two strategies was projected to 1 year, 5 years and 10 years. All medical costs were expressed in terms of Philippine peso (PhP), and converted to US dollars (USD) using the average exchange rate of USD 1 = PhP 43. <br>
DOI: 10.6084/m9.figshare.1463337
title: Air quality dataset

description: Dataset
DOI: 10.6084/m9.figshare.1463356.v1
title: VU University | PhD records without on-line PhD thesis publications | @ 24/5/2015

description: Via e-Library VU University Amsterdam.
DOI: 10.17632/ytst4kss9p.2
title: Fidgety Philip and the Suggested Clinical Immobilization Test: Annotation Dataset

description: To facilitate ‘structured behavioral observations’ in clinical practice, we are interested in analyzing movement patterns, mainly voluntary and involuntary motions, during sitting. We developed a clinical protocol for analyzing characteristics of voluntary movements during sitting with the goal to capture disorder specific movement patterns and contribute to the phenotypic characterization of H-behaviors. To enhance our understanding, we conducted this phenotyping exercise independent of discipline-related boundaries and applied a pictogram guided-phenotyping language (PG-PL). Phase 1, Step 1: Annotation/analysis concept naïve research assistants (RAs) were trained. They then annotated three original Fidgety Philip cartoons and were instructed to ‘describe, but not interpret’. The dataset contains RAs' annotations of the cartoons. Phase 1, Step 2: RAs then annotated snapshots from suggested clinical immobilization tests (SCIT) to work out the distinction between ‘interpretive’ and ‘neutral, non-interpretive’ PG-PL descriptions in the analysis of snapshots from the SCIT with free-hand and then PG-PL annotations. The dataset contains RAs' free-hand and pictogram annotations of 12 SCIT snapshots. Phase 2: The goal of this phase was to apply the PG-PL to SCIT videos and to develop the first machine learning algorithm for automated movement detection. The dataset contains RAs' pictogram annotations of 1-minute long SCIT video clips. The data are available in raw and processed formats.​
DOI: 10.6084/m9.figshare.1463318
title: Multilocus sequence analysis of Streptococcus anginosus group

description: This fileset contains individual FASTA files for the unique alleles at each of the loci considered in the Multilocus Sequence Analysis method used and two supplementary tables with the information of individual strains.
DOI: 10.6084/m9.figshare.1463319
title: Identification of genes containing expanded purine repeats in the human genome and their apparent protective role against cancer

description: Purine repeat sequences present in a gene are unique as they have high propensity to form unusual DNA-triple helix structures. Friedreich’s ataxia is the only human disease that is well known to be associated with DNA-triplexes formed by purine repeats. The purpose of this study was to recognize the expanded purine repeats (EPRs) in human genome and find their correlation with cancer pathogenesis. We developed “<i>PuRepeatFinder.pl</i>” algorithm to identify non-overlapping EPRs without pyrimidine interruptions in the human genome and customized for searching repeat lengths, <i>n</i> ≥ 200. A total of 1158 EPRs were identified in the genome which followed <i>Wakeby</i> distribution. Two hundred and ninety-six EPRs were found in geneic regions of 282 genes (EPR-genes). Gene clustering of EPR-genes was done based on their cellular function and a large number of EPR-genes were found to be enzymes/enzyme modulators. Meta-analysis of 282 EPR-genes identified only 63 EPR-genes in association with cancer, mostly in breast, lung, and blood cancers. Protein–protein interaction network analysis of all 282 EPR-genes identified proteins including those in cadherins and VEGF. The two observations, that EPRs can induce mutations under malignant conditions and that identification of some EPR-gene products in vital cell signaling-mediated pathways, together suggest the crucial role of EPRs in carcinogenesis. The new link between EPR-genes and their functionally interacting proteins throws a new dimension in the present understanding of cancer pathogenesis and can help in planning therapeutic strategies. Validation of present results using techniques like NGS is required to establish the role of the EPR genes in cancer pathology.
DOI: 10.6084/m9.figshare.1463319.v1
title: Identification of genes containing expanded purine repeats in the human genome and their apparent protective role against cancer

description: Purine repeat sequences present in a gene are unique as they have high propensity to form unusual DNA-triple helix structures. Friedreich’s ataxia is the only human disease that is well known to be associated with DNA-triplexes formed by purine repeats. The purpose of this study was to recognize the expanded purine repeats (EPRs) in human genome and find their correlation with cancer pathogenesis. We developed “<i>PuRepeatFinder.pl</i>” algorithm to identify non-overlapping EPRs without pyrimidine interruptions in the human genome and customized for searching repeat lengths, <i>n</i> ≥ 200. A total of 1158 EPRs were identified in the genome which followed <i>Wakeby</i> distribution. Two hundred and ninety-six EPRs were found in geneic regions of 282 genes (EPR-genes). Gene clustering of EPR-genes was done based on their cellular function and a large number of EPR-genes were found to be enzymes/enzyme modulators. Meta-analysis of 282 EPR-genes identified only 63 EPR-genes in association with cancer, mostly in breast, lung, and blood cancers. Protein–protein interaction network analysis of all 282 EPR-genes identified proteins including those in cadherins and VEGF. The two observations, that EPRs can induce mutations under malignant conditions and that identification of some EPR-gene products in vital cell signaling-mediated pathways, together suggest the crucial role of EPRs in carcinogenesis. The new link between EPR-genes and their functionally interacting proteins throws a new dimension in the present understanding of cancer pathogenesis and can help in planning therapeutic strategies. Validation of present results using techniques like NGS is required to establish the role of the EPR genes in cancer pathology.
DOI: 10.6084/m9.figshare.1463311
title: <i>In</i>-<i>silico</i> analysis of Sirt2 from <i>Schistosoma mansoni</i>: structures, conformations, and interactions with inhibitors

description: Sirtuins are NAD+-dependent lysine deacetylases member of the class III HDAC family. These are demonstrated to be therapeutic targets in parasitic diseases like schistosomiasis. Observations suggested that sirtuin enzyme is necessary for the functionality of fe/male reproductive system, due to which SmSirt2 is treated as a potential therapeutic target. There are no structural and molecular features of SmSirt2 have been reported yet. In this study, homology modeling has been used to determine the three-dimensional features of the SmSITRT2. Further, structure validation has been performed by energy minimization and Ramachandran plot. Validated structures are further subjected to molecular docking and virtual screening to find the best lead molecules for downstream analysis. Ten lead molecules were selected while comparing virtual screening of hSirt2 and SmSirt2 both. These leads are further compared with AKG2 which is known inhibitor of hSirt2 (−8.8 kcal/mol). Out of selected 10 leads, four of them (ZINC23995485 (−9.5 kcal/mol), ZINC53298162 (−9.4 kcal/mol), ZINC70927268 (−10.0 kcal/mol), ZINC89878705 (−11.2 kcal/mol)) have shown better interaction with SmSirt2, in which ZINC89878705 (−11.2 kcal/mol) shows a more compact packing as compared to AKG2 and rest of ligands. These molecules could be further subject to <i>in vitro</i> study and model of SmSirt2 has been proposed for further structure-based drug design projects concerning sirtuins from <i>Schistosoma mansoni</i>.
DOI: 10.6084/m9.figshare.1463328.v1
title: Costs of Rabies Post-Exposure Prophylaxis According to Pre-Exposure Prophylaxis Status

description: Costs of PrEP were assessed for the cohort of 4,666 children in the study at the time of PreP administration. PrEP schedule followed the WHO guidelines, with intradermal administration of 0.1 ml volume per site (one site each day) given on days 0, 7 and 28. The direct medical costs included cost of biologicals (rabies vaccine), cost per shipment, considered as 2% of the vaccine cost, cost of needles, alcohol and cotton used. Costs related to health care staff were not included. The number of doses per vial assumed for the analysis is 4, although in theory 1 vial could be used to deliver 5 x 0.1 mL doses, thus 20% vaccine wastage is built into the calculations.In addition, to explore further the benefits of such vaccination program, projected costs of two hypothetical cohorts of children bitten by a dog were assessed according to two scenarios: (i) Scenario 1, no PrEP: Assessment of the costs related to the expected annual number of children among the study cohort bitten by a dog, assuming they did not have PrEP. These children were considered to follow the standard of care for Post-Exposure Prophylaxis (PEP) defined as 2-site intradermal method (2-2-2-0-1) for use with PVRV (complete PEP), with RIG given for category III bites. (ii) Scenario 2, with PrEP Assessment of the costs related to the expected annual number of children among the study cohort bitten by a dog benefiting from PrEP. Following the national guidelines, such patients should be given only two booster doses on days 0 and 3, but no RIG. Costs associated with wound care (e.g. antibiotics, tetanus immunization) were not included in the analysis since these do not depend on rabies vaccination status of the patient. Indirect costs were also not included in the analysis. Time horizon for the comparison of the economic benefit of the two strategies was projected to 1 year, 5 years and 10 years. All medical costs were expressed in terms of Philippine peso (PhP), and converted to US dollars (USD) using the average exchange rate of USD 1 = PhP 43. <br>
DOI: 10.6084/m9.figshare.1463311.v2
title: <i>In</i>-<i>silico</i> analysis of Sirt2 from <i>Schistosoma mansoni</i>: structures, conformations, and interactions with inhibitors

description: Sirtuins are NAD+-dependent lysine deacetylases member of the class III HDAC family. These are demonstrated to be therapeutic targets in parasitic diseases like schistosomiasis. Observations suggested that sirtuin enzyme is necessary for the functionality of fe/male reproductive system, due to which SmSirt2 is treated as a potential therapeutic target. There are no structural and molecular features of SmSirt2 have been reported yet. In this study, homology modeling has been used to determine the three-dimensional features of the SmSITRT2. Further, structure validation has been performed by energy minimization and Ramachandran plot. Validated structures are further subjected to molecular docking and virtual screening to find the best lead molecules for downstream analysis. Ten lead molecules were selected while comparing virtual screening of hSirt2 and SmSirt2 both. These leads are further compared with AKG2 which is known inhibitor of hSirt2 (−8.8 kcal/mol). Out of selected 10 leads, four of them (ZINC23995485 (−9.5 kcal/mol), ZINC53298162 (−9.4 kcal/mol), ZINC70927268 (−10.0 kcal/mol), ZINC89878705 (−11.2 kcal/mol)) have shown better interaction with SmSirt2, in which ZINC89878705 (−11.2 kcal/mol) shows a more compact packing as compared to AKG2 and rest of ligands. These molecules could be further subject to <i>in vitro</i> study and model of SmSirt2 has been proposed for further structure-based drug design projects concerning sirtuins from <i>Schistosoma mansoni</i>.
DOI: 10.6084/m9.figshare.1463311.v1
title: <i>In-silico</i> analysis of Sirt2 from <i>Schistosoma monsoni</i>: Structures, Conformations and Interactions with Inhibitors

description: Sirtuins are NAD+ dependent lysine deacetylases member of the class III HDAC family. These are demonstrated to be therapeutic targets in parasitic diseases like Schistosomiasis. Observations suggested that sirtuin enzyme is necessary for the functionality of fe/male reproductive system, due to which SmSirt2 is treated as a potential therapeutic target. There are no structural and molecular features of SmSirt2 have been reported yet.In this study, homology modeling has been used to determine the three-dimensional features of the SmSITRT2. Further, structure validation has been performed by energy minimization and Ramachandran plot. Validated structures are further subjected to molecular docking and virtual screening to find the best lead molecules for downstream analysis.Ten lead molecules were selected while comparing virtual screening of hSirt2 and SmSirt2 both. These leads are further compared with AKG2 which is known inhibitor of hSirt2 (-8.8kcal/mol). Out of selected 10 leads, four of them (ZINC23995485 (-9.5kcal/mol), ZINC53298162 (-9.4 kcal/mol), ZINC70927268 (-10.0 kcal/mol), ZINC89878705 (-11.2 kcal/mol)) have shown better interaction with SmSirt2, in which ZINC89878705 (-11.2 kcal/mol) shows a more compact packing as compared to AKG2 and rest of ligands.These molecules could be further subject to <i>in vitro</i> study and model of SmSirt2 has been proposed for further structure-based drug design projects concerning sirtuins from <i>S. monsoni</i>.
DOI: 10.6084/m9.figshare.1462278
title: Average Leaf Nutrient Levels in Sweetpotato Varieties

description: Average leaf nutrient levels in sweetpotato varieties at the early storage root bulking stage (25-30 days).
DOI: 10.6084/m9.figshare.1461856
title: Koala skull MRI

description: This is an MRI of a koala (Phascolarctos cinereus) skull, PD weighted.
DOI: 10.6084/m9.figshare.1461856.v1
title: Koala skull MRI

description: This is an MRI of a koala (Phascolarctos cinereus) skull, PD weighted.
DOI: 10.6084/m9.figshare.1461816
title: Low Temperature Reactive Sputtering of Thin Aluminum Nitride Films on Metallic Nanocomposites

description: This fileset contains all raw data and figures related to the article "Low Temperature Reactive Sputtering of Thin Aluminum Nitride Films on Metallic Nanocomposites", submitted by Ramadan and Evoy to PLOS ONE, in March 2015