cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1230122
title: Molecular docking and dynamics simulation analyses unraveling the differential enzymatic catalysis by plant and fungal laccases with respect to lignin biosynthesis and degradation

description: Laccase, widely distributed in bacteria, fungi, and plants, catalyzes the oxidation of wide range of compounds. With regards to one of the important physiological functions, plant laccases are considered to catalyze lignin biosynthesis while fungal laccases are considered for lignin degradation. The present study was undertaken to explain this dual function of laccases using <i>in-silico</i> molecular docking and dynamics simulation approaches. Modeling and superimposition analyses of one each representative of plant and fungal laccases, namely, <i>Populus trichocarpa</i> and <i>Trametes versicolor</i>, respectively, revealed low level of similarity in the folding of two laccases at 3D levels. Docking analyses revealed significantly higher binding efficiency for lignin model compounds, in proportion to their size, for fungal laccase as compared to that of plant laccase. Residues interacting with the model compounds at the respective enzyme active sites were found to be in conformity with their role in lignin biosynthesis and degradation. Molecular dynamics simulation analyses for the stability of docked complexes of plant and fungal laccases with lignin model compounds revealed that tetrameric lignin model compound remains attached to the active site of fungal laccase throughout the simulation period, while it protrudes outwards from the active site of plant laccase. Stability of these complexes was further analyzed on the basis of binding energy which revealed significantly higher stability of fungal laccase with tetrameric compound than that of plant. The overall data suggested a situation favorable for the degradation of lignin polymer by fungal laccase while its synthesis by plant laccase.
DOI: 10.6084/m9.figshare.1230106
title: Protected areas threats and conservation activities accross tropical Africa

description: Data from STranquilli et al. 2014 Plos One: Protected areas in tropical Africa: assessing threats and conservation activities.
DOI: 10.6084/m9.figshare.1230121.v1
title: iUbiq-Lys: prediction of lysine ubiquitination sites in proteins by extracting sequence evolution information via a gray system model

description: As one of the most important posttranslational modifications (PTMs), ubiquitination plays an important role in regulating varieties of biological processes, such as signal transduction, cell division, apoptosis, and immune response. Ubiquitination is also named “lysine ubiquitination” because it occurs when an ubiquitin is covalently attached to lysine (K) residues of targeting proteins. Given an uncharacterized protein sequence that contains many lysine residues, which one of them is the ubiquitination site, and which one is of non-ubiquitination site? With the avalanche of protein sequences generated in the postgenomic age, it is highly desired for both basic research and drug development to develop an automated method for rapidly and accurately annotating the ubiquitination sites in proteins. In view of this, a new predictor called “iUbiq-Lys” was developed based on the evolutionary information, gray system model, as well as the general form of pseudo-amino acid composition. It was demonstrated via the rigorous cross-validations that the new predictor remarkably outperformed all its counterparts. As a web-server, iUbiq-Lys is accessible to the public at http://www.jci-bioinfo.cn/iUbiq-Lys. For the convenience of most experimental scientists, we have further provided a protocol of step-by-step guide, by which users can easily get their desired results without the need to follow the complicated mathematics that were presented in this paper just for the integrity of its development process.
DOI: 10.6084/m9.figshare.1230122.v2
title: Molecular docking and dynamics simulation analyses unraveling the differential enzymatic catalysis by plant and fungal laccases with respect to lignin biosynthesis and degradation

description: Laccase, widely distributed in bacteria, fungi, and plants, catalyzes the oxidation of wide range of compounds. With regards to one of the important physiological functions, plant laccases are considered to catalyze lignin biosynthesis while fungal laccases are considered for lignin degradation. The present study was undertaken to explain this dual function of laccases using <i>in-silico</i> molecular docking and dynamics simulation approaches. Modeling and superimposition analyses of one each representative of plant and fungal laccases, namely, <i>Populus trichocarpa</i> and <i>Trametes versicolor</i>, respectively, revealed low level of similarity in the folding of two laccases at 3D levels. Docking analyses revealed significantly higher binding efficiency for lignin model compounds, in proportion to their size, for fungal laccase as compared to that of plant laccase. Residues interacting with the model compounds at the respective enzyme active sites were found to be in conformity with their role in lignin biosynthesis and degradation. Molecular dynamics simulation analyses for the stability of docked complexes of plant and fungal laccases with lignin model compounds revealed that tetrameric lignin model compound remains attached to the active site of fungal laccase throughout the simulation period, while it protrudes outwards from the active site of plant laccase. Stability of these complexes was further analyzed on the basis of binding energy which revealed significantly higher stability of fungal laccase with tetrameric compound than that of plant. The overall data suggested a situation favorable for the degradation of lignin polymer by fungal laccase while its synthesis by plant laccase.
DOI: 10.6084/m9.figshare.1230122.v1
title: Molecular docking and dynamics simulation analyses unraveling the differential enzymatic catalysis by plant and fungal laccases with respect to lignin biosynthesis and degradation

description: Laccase, widely distributed in bacteria, fungi, and plants, catalyzes the oxidation of wide range of compounds. With regards to one of the important physiological functions, plant laccases are considered to catalyze lignin biosynthesis while fungal laccases are considered for lignin degradation. The present study was undertaken to explain this dual function of laccases using <i>in-silico</i> molecular docking and dynamics simulation approaches. Modeling and superimposition analyses of one each representative of plant and fungal laccases, namely, <i>Populus trichocarpa</i> and <i>Trametes versicolor</i>, respectively, revealed low level of similarity in the folding of two laccases at 3D levels. Docking analyses revealed significantly higher binding efficiency for lignin model compounds, in proportion to their size, for fungal laccase as compared to that of plant laccase. Residues interacting with the model compounds at the respective enzyme active sites were found to be in conformity with their role in lignin biosynthesis and degradation. Molecular dynamics simulation analyses for the stability of docked complexes of plant and fungal laccases with lignin model compounds revealed that tetrameric lignin model compound remains attached to the active site of fungal laccase throughout the simulation period, while it protrudes outwards from the active site of plant laccase. Stability of these complexes was further analyzed on the basis of binding energy which revealed significantly higher stability of fungal laccase with tetrameric compound than that of plant. The overall data suggested a situation favorable for the degradation of lignin polymer by fungal laccase while its synthesis by plant laccase.
DOI: 10.6084/m9.figshare.1230106.v1
title: new fileset

description: Data from STranquilli et al. 2014 Plos One: Protected areas in tropical Africa: assessing threats and conservation activities.
DOI: 10.6084/m9.figshare.1230106.v2
title: STranquilli et al. 2014 Plos One

description: Data from STranquilli et al. 2014 Plos One: Protected areas in tropical Africa: assessing threats and conservation activities.
DOI: 10.6084/m9.figshare.1230086
title: The Spatial LASSO With Applications to Unmixing Hyperspectral Biomedical Images

description: Hyperspectral imaging (HSI) is a spectroscopic method that uses densely sampled measurements along the electromagnetic spectrum to identify the unique molecular composition of an object. Traditionally HSI has been associated with remote sensing-type applications, but recently has found increased use in biomedicine, from investigations at the cellular to the tissue level. One of the main challenges in the analysis of HSI is estimating the proportions, also called abundance fractions of each of the molecular signatures. While there is great promise for HSI in the area of biomedicine, large variability in the measurements and artifacts related to the instrumentation has slow adoption into more widespread practice. In this article, we propose a novel regularization and variable selection method called the spatial LASSO (SPLASSO). The SPLASSO incorporates spatial information via a graph Laplacian-based penalty to help improve the model estimation process for multivariate response data. We show the strong performance of this approach on a benchmark HSI dataset with considerable improvement in predictive accuracy over the standard LASSO. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.1230106.v3
title: Protected areas in tropical Africa: assessing threats and conservation activities

description: Data from STranquilli et al. 2014 Plos One: Protected areas in tropical Africa: assessing threats and conservation activities.
DOI: 10.6084/m9.figshare.1230086.v2
title: The Spatial LASSO With Applications to Unmixing Hyperspectral Biomedical Images

description: Hyperspectral imaging (HSI) is a spectroscopic method that uses densely sampled measurements along the electromagnetic spectrum to identify the unique molecular composition of an object. Traditionally HSI has been associated with remote sensing-type applications, but recently has found increased use in biomedicine, from investigations at the cellular to the tissue level. One of the main challenges in the analysis of HSI is estimating the proportions, also called abundance fractions of each of the molecular signatures. While there is great promise for HSI in the area of biomedicine, large variability in the measurements and artifacts related to the instrumentation has slow adoption into more widespread practice. In this article, we propose a novel regularization and variable selection method called the spatial LASSO (SPLASSO). The SPLASSO incorporates spatial information via a graph Laplacian-based penalty to help improve the model estimation process for multivariate response data. We show the strong performance of this approach on a benchmark HSI dataset with considerable improvement in predictive accuracy over the standard LASSO. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.1230106.v4
title: Protected areas in tropical Africa: threats and conservation activities.

description: Data from STranquilli et al. 2014 Plos One: Protected areas in tropical Africa: assessing threats and conservation activities.
DOI: 10.6084/m9.figshare.1230083
title: Results from the BASS Survey for Brown Dwarfs in Young Moving Groups

description: In this talk I present the latest results of a near-infrared spectroscopic follow-up of brown dwarf candidate members that were uncovered from the BANYAN All-Sky Survey (BASS), to identify signs of low-gravity (youth) in their spectra. The BASS survey has unveiled a significant population of young brown dwarfs with potential age constraints and distance estimates that can be obtained from their moving group candidacy. I show how this new population can already give us useful insight on the empirical properties of young L dwarfs.
DOI: 10.6084/m9.figshare.1230086.v1
title: The Spatial LASSO with Applications to Unmixing Hyperspectral Biomedical Images

description: Hyperspectral imaging (HSI) is a spectroscopic method which uses densely sampled measurements along the electromagnetic spectrum to identify the unique molecular composition of an object. Traditionally HSI has been associated with remote sensing type applications, but recently has found increased use in biomedicine, from investigations at the cellular to the tissue level. One of the main challenges in the analysis of HSI is estimating the proportions, also called abundance fractions of each of the molecular signatures. While there is great promise for HSI in the area of biomedicine, large variability in the measurements and artifacts related to the instrumentation have slown adoption into more widespread practice. In this paper we propose a novel regularization and variable selection method called the spatial LASSO (SPLASSO). The SPLASSO incorporates spatial information via a graph Laplacian based penalty to help improve the model estimation process for multivariate response data. We show the strong performance of this approach on a benchmark HSI data set with considerable improvement in predictive accuracy over the standard LASSO.
DOI: 10.6084/m9.figshare.1230083.v1
title: Results from the BASS Survey for Brown Dwarfs in Young Moving Groups

description: In this talk I present the latest results of a near-infrared spectroscopic follow-up of brown dwarf candidate members that were uncovered from the BANYAN All-Sky Survey (BASS), to identify signs of low-gravity (youth) in their spectra. The BASS survey has unveiled a significant population of young brown dwarfs with potential age constraints and distance estimates that can be obtained from their moving group candidacy. I show how this new population can already give us useful insight on the empirical properties of young L dwarfs.
DOI: 10.6084/m9.figshare.1230080
title: Insect Responses to Odour Stimulus

description: Researchers performed this experiment on York University's grassland on campus beside Danby Woods.The purpose of this research was to see if insects were attracted to different types of odour stimuli. This experiment was replicated on 2 seperate days to account for temperature and sunlight differences. The experiments were performed on Day 1 (15/10/2014) and Day 2 (22/10/2014). Day 1 was cloudy and rainy (12 degrees Celsius), Day 2 was sunny and not cloudy (15 degrees Celsius). Also on both days the treatment was placed on different colours of paper to also account for insect prefrence on colour (Day 1 was white and Day 2 was brown). Grass was soaked in water (control), perfume, salt, or sugar (5% concentration) and placed on white paper (Day 1) and brown paper (Day 2). These treatments were placed together in a random area in a grassland in a random order. Each station was seperated by 8 meters. And there was 3 stations per day for more accurate results. At 20 minute intervals researchers recorded the number of insects present on each treatment.
DOI: 10.6084/m9.figshare.1230080.v1
title: Insect Responses to Odour Stimulus

description: Researchers performed this experiment on York University's grassland on campus beside Danby Woods.The purpose of this research was to see if insects were attracted to different types of odour stimuli. This experiment was replicated on 2 seperate days to account for temperature and sunlight differences. The experiments were performed on Day 1 (15/10/2014) and Day 2 (22/10/2014). Day 1 was cloudy and rainy (12 degrees Celsius), Day 2 was sunny and not cloudy (15 degrees Celsius). Also on both days the treatment was placed on different colours of paper to also account for insect prefrence on colour (Day 1 was white and Day 2 was brown). Grass was soaked in water (control), perfume, salt, or sugar (5% concentration) and placed on white paper (Day 1) and brown paper (Day 2). These treatments were placed together in a random area in a grassland in a random order. Each station was seperated by 8 meters. And there was 3 stations per day for more accurate results. At 20 minute intervals researchers recorded the number of insects present on each treatment.
DOI: 10.6084/m9.figshare.1230077
title: Planar bifunctional Luneburg-fisheye lens made of an anisotropic metasurface

description: Luneburg-fisheye lens made of anisotropic metasurface, which features as Luneburg along the horizontal optical axis while as fisheye along the vertical optical axis. We propose a method to control the inhomogeneous indexes of refraction independently along the two optical axes by designing anisotropic and non-uniform metasurface, which can provide the required distributions of refractive indexes approximately for Luneburg and fisheye lenses watching from the two optical axes. Experiments in the microwave frequency demonstrate very good performance of the planar bi-functional Luneburg-fisheye lens. The proposed method opens a venue to design other kinds of bi-functional devices using metasurfaces in the microwave, terahertz, and even optical frequencies.
DOI: 10.6084/m9.figshare.1230073
title: Relationship in levels of disturbance within a power line near York University to the species richness and diversity of the community

description: Meta-data and raw data for the <em>Relationship in levels of disturbance within a power line near York University to the species richness and diversity of the community</em> article
DOI: 10.6084/m9.figshare.1230074
title: Characteristics of White Aster in a Powerline Corridor

description: This experiment took place in a powerline corridor functioning as an urban greenway (Figure 5), which is an open field north of Steeles Avenue West (43.779291, -79.504367), Concord, ON L4K 3C8, across from York University. This field is located along a busy roadside, and extends behind buildings along the street. Sampling was done in the powerline corridor directly behind the buildings which are separated from the field by a fence. We used a shallow drainage ditch with steep sides as our area of focus, which is located parallel to a fence. This drainage ditch is a main source of water in the immediate area, since most of the field is open and flat on one side, and has buildings on the other side. Therefore most runoff in this area will accumulate in the drainage ditch. Data collection occurred on 3 days (October 2nd, 9th and 16th, 2014), from 2:30 pm to 5:30 pm. The weather on the first day was 16°C and sunny, on the second day it was 13°C and partly cloudy, and the last day was 12°C and it rained. Sets of quadrats (1m x 1m) were taken along the edge of the drainage ditch at 1.5 meters apart to allow for enough replicates, and they were taken at 3 different distances along a transect perpendicular to the ditch that extended away from the road and buildings: the first quadrat was 0 meters (at the very edge of the ditch), the second was 10 meters from the ditch, and the third 20 meters from the ditch. Plants were only considered to be in the quadrat if their roots resided within its perimeter. This process was repeated until 7 sets, n = 21 quadrats were completed. For this experiment, we looked at how the drainage ditch is an important source of water for plants in the powerline corridor. This was done by measuring different variables at different distances from the ditch, focusing specifically on the white aster plant. The factors measured in each quadrat were height of the white aster plants, density, number of flowers per plant and species richness. The height of plants was taken using measuring tape from the soil to the top of the plant. The density was visually evaluated, and the percentage of white aster plants in the quadrat was estimated. The number of flowers per plant was counted on each stem individually, and only open flowers at the time of sampling were counted. In the last 2 weeks the majority of flowers closed and some stems fell off, so all flowers were counted. Species richness was counted by observing morphology and using a plant guide book to identify species. The data collected was analyzed using a 1 way ANOVA test with α=0.05 to determine the variance of each variable at different distances. Bar graphs with standard deviation bars were made for each variable in relation to the 3 distances from the ditch.
DOI: 10.6084/m9.figshare.1230067
title: Biol2050 Group Experiment

description: experiment was designed and held on thursday oct23, 2014 at york university, keel campus. the purpose of the experiment was to study factors affecting the number and richness of insects (dependent factors) in different environments. independent factors being temperature, vegetation crowding and pan colours were alternating in order to study their influence on dependent factors. 15pans of 3 different colour were placed 3 meter apart from each other in 3 different environment being the grass field, woodlot and parking/disturbed. soapy water was added to each pan. data was collected and recorded after 2hours. the experiment was repeated one week later on thursday oct30, 2014, in order to increase the liability of information.
DOI: 10.6084/m9.figshare.1230073.v1
title: Relationship in levels of disturbance within a power line near York University to the species richness and diversity of the community

description: Meta-data and raw data for the <em>Relationship in levels of disturbance within a power line near York University to the species richness and diversity of the community</em> article
DOI: 10.6084/m9.figshare.1230060
title: Intentionally Blank Pages

description: Retreived from ScienceDirect, November 4 2014.
DOI: 10.6084/m9.figshare.1230058
title: Ecology Lab 5: The Effects of Density and Sunlight Exposure to a Maple Trees Growth

description: <strong>Hypothesis:</strong> Testing the effects of density and sunlight availability on a trees growth or its diameter at breast height (DBH). <strong>Methods</strong>: Observations and data were collected at the York University Keele campus in the woodlot. A target species was selected to be Maple trees. The target tree to be observed was selected randomly by walking 10 steps north and 5 steps east. A 10 meter radius was laid around the target tree, the number of plants within the radius were counted and recorded in order to determine the density. This includes adult trees and saplings, which were defined to be any tree at least 3 meters in height. The diameter at breast height was measured and recorded as well as the percentage of sunlight coverage. This was done by standing directly against the tree facing towards the direction of sunlight, using a 4′ by 6″ quadrant to estimate the amount of sunlight the tree is exposed to. A new tree was selected at least 5 meters away from the outside of previous radius to avoid recounting. A random maple tree was selected once again by walking 10 steps north and 5 steps east and selecting the closest maple tree outside the previous radius. The process was repeated for a total sample size of 35 maple trees. <strong>Predictions</strong>: Assuming that the density and sunlight availability are independent of each other the following predictions can be made. - High density creates competition amongst species for resources (water, space, nutrients), negatively effecting the tree growth (small dbh) - High density can mean there is an abundance of resources available in that location which positively effects the trees growth (large dbh) - Large canopy coverage means there is competition for sunlight, negatively effects growth (small dbh) - Small canopy coverage, low competition, high exposure to sunlight which positively effects growth (large dbh)