cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.24661110.v2
title: <b>Data and code from: </b><b>Crop cover and nutrient levels mediate the effects of land management type on aquatic invertebrate richness in prairie potholes</b>

description: <b>Abstract from paper: </b><b>Crop cover and nutrient levels mediate the effects of land management type on aquatic invertebrate richness in prairie potholes</b>Aquatic invertebrates provide important ecosystem services, including decomposition and nutrient cycling, and provide nutrition for birds, fish, amphibians, and bats. Thus, the effects of agricultural land management practices on aquatic invertebrates are relevant to farmers, wildlife biologists, and policymakers. Here, we used data on aquatic invertebrates (159 taxa, 73 to species, 75 to genus/family) collected in 40 wetlands in the Canadian prairies to test for direct and indirect relationships among land management types (perennial cover, organic, minimum tillage, conventional), landscape structure (cropland and wetland cover within the surrounding landscape), and water quality (total nutrient levels, turbidity) on species richness of invertebrates using structural equation modelling. Additionally, we assessed variation in community composition within and among wetlands in different land use management types using a direct gradient analysis and variance partitioning. The direct effects of land management type were not supported but we found strong supportive evidence that effects of land management on richness were significantly mediated through cropland cover, nutrient levels, and turbidity. After controlling for these indirect effects, aquatic invertebrate richness decreased along a gradient from the lowest to the highest farming intensity, i.e., richness decreased from perennial cover sites to organic to minimum tillage to conventional sites. Support was also found for negative effects of nutrient levels and turbidity on richness. We did not find significant support for differences in gamma diversity or a simple test (homogeneity of multivariate dispersions) of differences in turnover among land management types; however, land management had a significant effect in distance-based redundancy analysis. Taken together, these results suggest that focusing conservation efforts on reducing cropland erosion and nutrient inputs to wetlands and creating more permanent cover may be effective strategies for conserving richness of aquatic invertebrates in agricultural landscapes in this region.
DOI: 10.6084/m9.figshare.24661110.v1
title: <b>Data and code from: </b><b>Crop cover and nutrient levels mediate the effects of land management type on aquatic invertebrate richness in prairie potholes</b>

description: <b>Abstract from paper: </b><b>Crop cover and nutrient levels mediate the effects of land management type on aquatic invertebrate richness in prairie potholes</b>Aquatic invertebrates provide important ecosystem services, including decomposition and nutrient cycling, and provide nutrition for birds, fish, amphibians, and bats. Thus, the effects of agricultural land management practices on aquatic invertebrates are relevant to farmers, wildlife biologists, and policymakers. Here, we used data on aquatic invertebrates (159 taxa, 73 to species, 75 to genus/family) collected in 40 wetlands in the Canadian prairies to test for direct and indirect relationships among land management types (perennial cover, organic, minimum tillage, conventional), landscape structure (cropland and wetland cover within the surrounding landscape), and water quality (total nutrient levels, turbidity) on species richness of invertebrates using structural equation modelling. Additionally, we assessed variation in community composition within and among wetlands in different land use management types using a direct gradient analysis and variance partitioning. The direct effects of land management type were not supported but we found strong supportive evidence that effects of land management on richness were significantly mediated through cropland cover, nutrient levels, and turbidity. After controlling for these indirect effects, aquatic invertebrate richness decreased along a gradient from the lowest to the highest farming intensity, i.e., richness decreased from perennial cover sites to organic to minimum tillage to conventional sites. Support was also found for negative effects of nutrient levels and turbidity on richness. We did not find significant support for differences in gamma diversity or a simple test (homogeneity of multivariate dispersions) of differences in turnover among land management types; however, land management had a significant effect in distance-based redundancy analysis. Taken together, these results suggest that focusing conservation efforts on reducing cropland erosion and nutrient inputs to wetlands and creating more permanent cover may be effective strategies for conserving richness of aquatic invertebrates in agricultural landscapes in this region.
DOI: 10.6073/pasta/26a46cc8f400bf9809f5210a94aacd72
title: Community and Ecosystem Impacts in Hemlock Removal Experiment at Harvard Forest since 2003

description: Hemlock decline in New England is caused by direct and indirect effects of invasion of the hemlock woolly adelgid. Direct damage from the insect is causing gradual mortality of hemlock, and widespread harvesting of hemlock in advance of mortality creates a contrasting disturbance. Although both processes affect thousands of acres of forest annually, we have only a limited understanding of their effects on forest ecosystem function and productivity and the nature of the subsequent forest community. We anticipate that harvesting will yield different consequences than gradual mortality from the insect. Therefore we have designed an experiment to simulate the impact of both in order to contrast them. To simulate some of the effects of the adelgid (e.g., progressive mortality, retention of the wood on the site) we are girdling all hemlocks in a hemlock-dominated stand. In the adjacent area we are conducting a commercial harvesting of hemlock. Results from both experimental treatments will be compared to the changes observed in forests that are being infested by the adelgid, and can also be included in integrated analyses of a suite of large experiments that form a core component of the Harvard Forest LTER program.
DOI: 10.5281/zenodo.1442765
title: Choro Songbook Corpus

description: Initial release of the Choro Songbook Corpus

The repository contains the original transcription and a .TSV with the complete data.
DOI: 10.5281/zenodo.8229125
title: Choro Songbook Corpus
DOI: 10.14459/2023mp1728246
title: Trace water in lead iodide affecting perovskite crystal nucleation limits the performance of perovskite solar cells

description: All data for the paper entitled with 'Trace water in lead iodide affecting perovskite crystal nucleation limits the performance of perovskite solar cells' published by Advanced Materials
DOI: 10.6084/m9.figshare.24721386
title: Input hydrographs (Probabilistic flood plains)

description: This dataset contains water level hydrographs as Matlab files for Travemünde, Germany with extreme sea level (ESL) magnitudes ranging from 1.60 m to 3.40 m in 5 cm increments. Each ESL hydrograph is available at the 5th, 50th and 95th hydrograph intensity. The first number in the datatitle corresponds to the ESl while the second number stands for the hydrograph intensity.
DOI: 10.6084/m9.figshare.24721524
title: 50-year Hydrographs (Intensities)

description: This dataset contains 100 hydrographs as Matlab files for Travemünde, Germany at an extreme sea level (ESL) height of 2.24 m (50-year return period) where each of the 100 different hydrographs has a different intensity.
DOI: 10.6084/m9.figshare.24721524.v1
title: 50-year Hydrographs (Intensities)

description: This dataset contains 100 hydrographs as Matlab files for Travemünde, Germany at an extreme sea level (ESL) height of 2.24 m (50-year return period) where each of the 100 different hydrographs has a different intensity.
DOI: 10.6084/m9.figshare.24721530
title: 200-year Hydrographs (Intensities)

description: This dataset contains 100 hydrographs as Matlab files for Travemünde, Germany at an extreme sea level (ESL) height of 2.55 m (100-year return period) where each of the 100 different hydrographs has a different intensity.
DOI: 10.6084/m9.figshare.24721539
title: Flood Extents

description: This dataset contains the maximum flood extents from the annual probabilistic analysis, resulting from an ESL of 3.40 m and for each of the three analysed hydrograph intensities (5th, 50th and 95th). Names of the files start with 340_. Moreover, it contains three samples of flood extents from the hydrograph intensity analysis of the 50-year ESL and the 200-year ESL. Names of the 50-year flood extents start with 224_ and the 200-year flood extents with 255_. All flood extents are provided as matlab files.
DOI: 10.6073/pasta/ed3d3fecd5d653507192f506ccac7650
title: Historical GIS Data for Prospect Hill Tract at Harvard Forest 1733-1986

description: This dataset contains elevation, 1986 forest type, land-use history, and soils maps for the Prospect Hill Tract, digitized from paper maps in the Harvard Forest Archives. File format = Idrisi 4.1 binary. Resolution = 10m x 10m. Coordinates = UTM zone 18. Datum = 1927 North American. This dataset has been replaced with a new vector series for the entire Harvard Forest (see HF110).
DOI: 10.6084/m9.figshare.21842549
title: A knowledge-based protein-protein interaction inhibition (KPI) pipeline: an insight from drug repositioning for COVID-19 inhibition

description: The inhibition of protein-protein interactions (PPIs) by small molecules is an exciting drug discovery strategy. Here, we aimed to develop a pipeline to identify candidate small molecules to inhibit PPIs. Therefore, KPI, a Knowledge-based Protein-Protein Interaction Inhibition pipeline, was introduced to improve the discovery of PPI inhibitors. Then, phytochemicals from a collection of known Middle Eastern antiviral herbs were screened to identify potential inhibitors of key PPIs involved in COVID-19. Here, the following investigations were sequenced: 1) Finding the binding partner and the interface of the proteins in PPIs, 2) Performing the blind ligand-protein inhibition (LPI) simulations, 3) Performing the local LPI simulations, 4) Simulating the interactions of the proteins and their binding partner in the presence and absence of the ligands, and 5) Performing the molecular dynamics simulations. The pharmacophore groups involved in the LPI were also characterized. Aloin, Genistein, Neoglucobrassicin, and Rutin are our new pipeline candidates for inhibiting PPIs involved in COVID-19. We also propose KPI for drug repositioning studies. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.21842549.v1
title: A knowledge-based protein-protein interaction inhibition (KPI) pipeline: an insight from drug repositioning for COVID-19 inhibition

description: The inhibition of protein-protein interactions (PPIs) by small molecules is an exciting drug discovery strategy. Here, we aimed to develop a pipeline to identify candidate small molecules to inhibit PPIs. Therefore, KPI, a Knowledge-based Protein-Protein Interaction Inhibition pipeline, was introduced to improve the discovery of PPI inhibitors. Then, phytochemicals from a collection of known Middle Eastern antiviral herbs were screened to identify potential inhibitors of key PPIs involved in COVID-19. Here, the following investigations were sequenced: 1) Finding the binding partner and the interface of the proteins in PPIs, 2) Performing the blind ligand-protein inhibition (LPI) simulations, 3) Performing the local LPI simulations, 4) Simulating the interactions of the proteins and their binding partner in the presence and absence of the ligands, and 5) Performing the molecular dynamics simulations. The pharmacophore groups involved in the LPI were also characterized. Aloin, Genistein, Neoglucobrassicin, and Rutin are our new pipeline candidates for inhibiting PPIs involved in COVID-19. We also propose KPI for drug repositioning studies. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.21814682
title: Phenolic compounds from <i>Tradescantia pallida</i> ameliorate diabetes by inhibiting enzymatic and non-enzymatic pathways

description: Diabetes is a chronic metabolic disorder marked by postprandial hyperglycemia due to several etiologies including abnormal carbohydrate digestion and glycation of hemoglobin. The prolong use of synthetic drugs results in characteristic side effects which necessitates the discovery of safe and cost-effective substitutes. The aim of the current study is to isolate and evaluate the antidiabetic potential of the phenolic compounds from the leaves of <i>Tradescantia pallida</i>. Syringic acid, <i>p</i>-coumaric acid, morin and catechin (compounds <b>1</b>–<b>4</b>) were isolated and characterized from <i>Tradescantia pallida</i> leaves using column chromatography and spectroscopic techniques. The <i>in vitro</i> antidiabetic potential of the phenolic compounds were assessed using α-amylase and non-enzymatic glycosylation of hemoglobin protein assays. A mechanistic insight of interactions between phenolic compounds and human α-amylase and hemoglobin protein were scrutinized by employing molecular docking method. Prime Molecular Mechanics/Generalized Born Surface Area (MM-GBSA) calculations were carried out to find the binding energies of the ligand-protein complexes. Morin and catechin were further analyzed to find the dynamic and thermodynamic constraints of the complexes under specific biological conditions using molecular dynamic simulation trajectories. The stability and flexibility of the complexes were justified by fluctuation of α-carbon chain, Root Mean Square Deviation (RMSD), Root Mean Square Fluctuation (RMSF) and type of interactions involved which authenticated the <i>in vitro</i> inhibitory potential of morin and catechin against enzymatic and non-enzymatic pathways. The current study could be fruitful in rational designing of safe antidiabetic drugs of natural origin. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.21814682.v1
title: Phenolic compounds from <i>Tradescantia pallida</i> ameliorate diabetes by inhibiting enzymatic and non-enzymatic pathways

description: Diabetes is a chronic metabolic disorder marked by postprandial hyperglycemia due to several etiologies including abnormal carbohydrate digestion and glycation of hemoglobin. The prolong use of synthetic drugs results in characteristic side effects which necessitates the discovery of safe and cost-effective substitutes. The aim of the current study is to isolate and evaluate the antidiabetic potential of the phenolic compounds from the leaves of <i>Tradescantia pallida</i>. Syringic acid, <i>p</i>-coumaric acid, morin and catechin (compounds <b>1</b>–<b>4</b>) were isolated and characterized from <i>Tradescantia pallida</i> leaves using column chromatography and spectroscopic techniques. The <i>in vitro</i> antidiabetic potential of the phenolic compounds were assessed using α-amylase and non-enzymatic glycosylation of hemoglobin protein assays. A mechanistic insight of interactions between phenolic compounds and human α-amylase and hemoglobin protein were scrutinized by employing molecular docking method. Prime Molecular Mechanics/Generalized Born Surface Area (MM-GBSA) calculations were carried out to find the binding energies of the ligand-protein complexes. Morin and catechin were further analyzed to find the dynamic and thermodynamic constraints of the complexes under specific biological conditions using molecular dynamic simulation trajectories. The stability and flexibility of the complexes were justified by fluctuation of α-carbon chain, Root Mean Square Deviation (RMSD), Root Mean Square Fluctuation (RMSF) and type of interactions involved which authenticated the <i>in vitro</i> inhibitory potential of morin and catechin against enzymatic and non-enzymatic pathways. The current study could be fruitful in rational designing of safe antidiabetic drugs of natural origin. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.21972984
title: pH modulates the role of SP6 RNA polymerase in transcription process: an <i>in silico</i> study

description: SP6 RNA polymerase (SP6 RNAP) is an essential enzyme for the transcription process in SP6 bacteriophage. SP6 RNAP plays a vital role in mRNA vaccine designing technology and other translational biotechnology research due to the high specificity towards its promoter. The self-replicating performance also put this polymerase to study extensively. Despite of the reports emphasizing the function of this enzyme, a detailed structural and functional understanding of RNA polymerase is not reported so far. Here, we report the first-ever information about SP6RNAP structure and its effect on promoter binding at different pH environments using molecular docking and molecular dynamics simulation (MDS) study. We also report the changes in polymerase conformations in different pH conditions using <i>in-silico</i> approach. The docking study was also performed for SP6 RNAP with SP6 promoter at different pH environments using the <i>in-silico</i> docking tools and conducted the MDS study for complexes. MM/PBSA and per residue energy contribution has been performed at three different pH environments. The structural aspects confirmed that the pH 7.9 state favors the polymerase functional activity in the transcription process which was in the range reported using transcription assay. This polymerase’s unique features may play its emerging role as an efficient transcription factor in translational biological research. Communicated by Ramaswamy H. Sarma The PRL and PBL of polymerase maintain a minimum distance from the promoter site at pH 7.9, leading to a possible transcription model for SP6 bacteriophage. HIGHLIGHTSThe structure of SP6 RNA polymerase (SP6RNAP) was modelled using <i>in silico</i> tools. This model is essential as no structure was solved for this enzyme using any of the standard structural biology techniques.The modelled structure was used to understand the interactions between SP6 RNAP and its promoter.The structure of the SP6 RNAP-SP6 promoter was subjected to various pH states to analyze the stability of the complex using <i>in silico</i> tools.The model was successfully able to explain the pH-dependent activity of the polymerase reported in the literature.A possible mechanism for the change in the activity of the polymerase was proposed. The structure of SP6 RNA polymerase (SP6RNAP) was modelled using <i>in silico</i> tools. This model is essential as no structure was solved for this enzyme using any of the standard structural biology techniques. The modelled structure was used to understand the interactions between SP6 RNAP and its promoter. The structure of the SP6 RNAP-SP6 promoter was subjected to various pH states to analyze the stability of the complex using <i>in silico</i> tools. The model was successfully able to explain the pH-dependent activity of the polymerase reported in the literature. A possible mechanism for the change in the activity of the polymerase was proposed.
DOI: 10.6084/m9.figshare.21972984.v2
title: pH modulates the role of SP6 RNA polymerase in transcription process: an <i>in silico</i> study

description: SP6 RNA polymerase (SP6 RNAP) is an essential enzyme for the transcription process in SP6 bacteriophage. SP6 RNAP plays a vital role in mRNA vaccine designing technology and other translational biotechnology research due to the high specificity towards its promoter. The self-replicating performance also put this polymerase to study extensively. Despite of the reports emphasizing the function of this enzyme, a detailed structural and functional understanding of RNA polymerase is not reported so far. Here, we report the first-ever information about SP6RNAP structure and its effect on promoter binding at different pH environments using molecular docking and molecular dynamics simulation (MDS) study. We also report the changes in polymerase conformations in different pH conditions using <i>in-silico</i> approach. The docking study was also performed for SP6 RNAP with SP6 promoter at different pH environments using the <i>in-silico</i> docking tools and conducted the MDS study for complexes. MM/PBSA and per residue energy contribution has been performed at three different pH environments. The structural aspects confirmed that the pH 7.9 state favors the polymerase functional activity in the transcription process which was in the range reported using transcription assay. This polymerase’s unique features may play its emerging role as an efficient transcription factor in translational biological research. Communicated by Ramaswamy H. Sarma The PRL and PBL of polymerase maintain a minimum distance from the promoter site at pH 7.9, leading to a possible transcription model for SP6 bacteriophage. HIGHLIGHTSThe structure of SP6 RNA polymerase (SP6RNAP) was modelled using <i>in silico</i> tools. This model is essential as no structure was solved for this enzyme using any of the standard structural biology techniques.The modelled structure was used to understand the interactions between SP6 RNAP and its promoter.The structure of the SP6 RNAP-SP6 promoter was subjected to various pH states to analyze the stability of the complex using <i>in silico</i> tools.The model was successfully able to explain the pH-dependent activity of the polymerase reported in the literature.A possible mechanism for the change in the activity of the polymerase was proposed. The structure of SP6 RNA polymerase (SP6RNAP) was modelled using <i>in silico</i> tools. This model is essential as no structure was solved for this enzyme using any of the standard structural biology techniques. The modelled structure was used to understand the interactions between SP6 RNAP and its promoter. The structure of the SP6 RNAP-SP6 promoter was subjected to various pH states to analyze the stability of the complex using <i>in silico</i> tools. The model was successfully able to explain the pH-dependent activity of the polymerase reported in the literature. A possible mechanism for the change in the activity of the polymerase was proposed.
DOI: 10.6084/m9.figshare.21864666
title: Vitamin derivatives as potential drugs for Influenza Hemagglutinin

description: The objective of the study was to identify potential inhibitors of Influenza surface Hemagglutinin (HA), which plays key role in the entry and replication of Influenza virus into the host cell. As ligands, seven vitamins and their derivatives were selected after initial screening based on their metabolizable capacity with no reported side effects, for <i>in silico</i> studies. Docking, and Post docking analysis (X Score and Ligplot+) were performed against nine Influenza HA targets for the vitamins and its derivatives. ‘Vitamin Derivatives’ with top docking score were further analysed by MD Simulations and free energy was calculated using MMGBSA module. FMNNa and FMNCa displayed high binding free energy with Influenza HA, thereby exhibiting potential as HA inhibitors. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.21864666.v1
title: Vitamin derivatives as potential drugs for Influenza Hemagglutinin

description: The objective of the study was to identify potential inhibitors of Influenza surface Hemagglutinin (HA), which plays key role in the entry and replication of Influenza virus into the host cell. As ligands, seven vitamins and their derivatives were selected after initial screening based on their metabolizable capacity with no reported side effects, for <i>in silico</i> studies. Docking, and Post docking analysis (X Score and Ligplot+) were performed against nine Influenza HA targets for the vitamins and its derivatives. ‘Vitamin Derivatives’ with top docking score were further analysed by MD Simulations and free energy was calculated using MMGBSA module. FMNNa and FMNCa displayed high binding free energy with Influenza HA, thereby exhibiting potential as HA inhibitors. Communicated by Ramaswamy H. Sarma