cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.3159496.v1
title: Atomistic molecular dynamics simulations of typical and atypical antipsychotic drugs at the dopamine D2 receptor (D2R) elucidates their inhibition mechanism

description: Dopamine D2 receptor (D2R) plays a pivotal role in nervous systems. Its dysfunction leads to the schizophrenia, Parkinson’s diseases and drug addiction. Since the crystal structure of the D2R was not solved yet, discovering of potent and highly selective anti-psychotic drugs carry challenges for different neurodegenerative diseases. In the current study, we modeled the three-dimensional (3D) structure of the D2R based on a recently crystallized structure of the dopamine D3 receptor. These two receptors share a high amino acid sequence homology (&gt;70%). The interaction of the modeled receptor with well-known atypical and typical anti-psychotic drugs and the inhibition mechanisms of drugs at the catalytic domain were studied via atomistic molecular dynamics simulations. Our results revealed that, class-I and class-II forms of atypical and typical D2R antagonists follow different pathways in the inhibition of the D2Rs.
DOI: 10.6084/m9.figshare.3159487
title: Patterns of failure and optimal radiotherapy target volumes in primary intradural extramedullary Ewing sarcoma

description: Patterns of failure and optimal radiotherapy target volumes in primary intradural extramedullary Ewing sarcoma
DOI: 10.6084/m9.figshare.3159523.v2
title: Functional characterization of hypothetical proteins of <i>Mycobacterium tuberculosis</i> with possible esterase/lipase signature: a cumulative <i>in silico</i> and <i>in vitro</i> approach

description: The functional aspect of several mycobacterium proteins annotated as hypothetical are yet to be discovered. In the present investigation, <i>in silico</i> approaches were used to predict the biological function of some of the unknown <i>Mtb</i> proteins, which were further validated by wet lab experiments. After screening thousands of <i>Mtb</i> proteins, functionally unknown hypothetical proteins Rv0421c, Rv0519c, Rv0774c, Rv1191, Rv1592c, and Rv3591c were chosen on the basis of their importance in <i>Mtb</i> life cycle. All these proteins posses the α/β-hydrolase topological fold, characteristic of lipases/esterases, with serine, aspartate, and histidine as the putative members of the catalytic triad. The catalytic serine is located in pentapeptide motif “GXSXG” and oxyanion residue is in dipeptide motif HG. To further support our observation, molecular docking was performed with conventional synthetic lipolytic substrates (pNP-esterss) and specific lipase/esterase inhibitors (tetrahydrolipstatin and phenylmethanesulfonyl fluoride (PMSF)). Significant docking score and strong interaction of substrates/inhibitors with these proteins revealed that these could be possible lipases/esterases. To validate the <i>in silico</i> studies, these genes were cloned from <i>Mtb</i> genome and the proteins were over-expressed in pQE-30/<i>Escherichia coli</i> M15 system. The expressed proteins were purified to homogeneity and enzymatic activity was determined using pNP esters as substrate. The enzyme activity of recombinant proteins was inhibited by tetrahydrolipstatin and PMSF pre-treatment. Outcome of the present investigation provided a basic platform to analyze and characterize unknown hypothetical proteins.
DOI: 10.6084/m9.figshare.3159523.v1
title: Functional characterization of hypothetical proteins of <i>Mycobacterium tuberculosis</i> with possible esterase/lipase signature: A Cumulative <i>in silico</i> and <i>in vitro</i> approach

description: The functional aspect of several mycobacterium proteins annotated as hypothetical are yet to be discovered. In the present investigation, <i>in silico</i> approaches were used to predict the biological function of some of the unknown <i>Mtb</i> proteins, which were further validated by wet lab experiments. After screening thousands of <i>Mtb</i> proteins, functionally unknown hypothetical proteins Rv0421c, Rv0519c, Rv0774c, Rv1191, Rv1592c and Rv3591c were chosen on the basis of their importance in <i>Mtb</i> life cycle. All these proteins posses the α/β-hydrolase topological fold, characteristic of lipases/esterases, with serine, aspartate, and histidine as the putative members of the catalytic triad. The catalytic serine is located in pentapeptide motif “GXSXG” and oxyanion residue is in dipeptide motif HG. To further support our observation, molecular docking was performed with conventional synthetic lipolytic substrates (pNP-esterss) and specific lipase/esterase inhibitors (tetrahydrolipstatin, PMSF). Significant docking score and strong interaction of substrates/inhibitors with these proteins revealed that these could be possible lipases/esterases. To validate the <i>in silico</i> studies, these genes were cloned from <i>Mtb</i> genome and the proteins were over-expressed in pQE-30/<i>Escherichia coli</i> M15 system. The expressed proteins were purified to homogeneity and enzymatic activity was determined by using pNP esters as substrate. The enzyme activity of recombinant proteins was inhibited by tetrahydrolipstatin and PMSF pre-treatment. Outcome of the present investigation provided a basic platform to analyse and characterize unknown hypothetical proteins.
DOI: 10.6084/m9.figshare.3159478
title: Chromosome diversity and evolution in <i>Allium</i> (Allioideae, Amaryllidaceae)

description: Despite extensive literature on the diversity of karyotypes in <i>Allium</i> is available, no attempt to analyse these data together, within a robust phylogenetic framework, has been carried out so far. Thus, we examined patterns and trends in chromosome evolution across the genus. Based on literature survey, karyo-morphometric features for 207 species belonging to 12 subgenera of <i>Allium</i> were obtained. Included in the data-set were basic chromosome number (<i>x</i>), somatic chromosome number (2<i>n</i>), total haploid (monoploid) chromosome length (THL) and three different measures defining karyotype structure: CV<sub>CI</sub>, measuring how heterogeneous are centromeres positions in a karyotype, CV<sub>CL</sub> and M<sub>CA</sub>, quantifying interchromosomal and intrachromosomal karyotype asymmetry, respectively. Trends in karyotype evolution were analysed by phylogenetic regressions and independent contrasts. Mean karyotypes highlighted differences and similarities in karyotype structure between the 12 subgenera. Further differences were noted when the two parameters for analysing karyotype asymmetry were assessed. In addition, by examining the effects of increasing karyotype dimensions (a proxy for genome size) on karyotype structure and asymmetry, it was shown that in <i>Allium</i> species, the DNA was added proportionally to their arm lengths. Overall, <i>p</i> = 8 and somehow intermediate karyotype asymmetry levels seem to represent plesiomorphic character-states in <i>Allium</i>.
DOI: 10.6084/m9.figshare.3159487.v1
title: Patterns of failure and optimal radiotherapy target volumes in primary intradural extramedullary Ewing sarcoma

description: Patterns of failure and optimal radiotherapy target volumes in primary intradural extramedullary Ewing sarcoma
DOI: 10.6084/m9.figshare.3159430
title: Age estimation of African lions Panthera leo by ratio of tooth areas

description: X-ray images of PM<sup>2</sup> of known aged African lions<br>
DOI: 10.6084/m9.figshare.3159409
title: Long-term risk of colorectal cancer by gender after positive colonoscopy: population-based cohort study

description: <b>Background:</b> Evidence for surveillance intervals of colonoscopy are primarily based on adenoma recurrence rate rather than on colorectal cancer (C.R.C.) incidence. Little is known about long-term risk of C.R.C. after positive colonoscopy. In view of men have significantly higher C.R.C. risk than women, we aimed to estimate the gender-specific C.R.C. incidence after positive colonoscopy (adenoma or malignant lesion) at follow-up colonoscopy. <b>Methods:</b> A retrospective cohort study was conducted using data from a database of colonoscopy screening and surveillance. Patients having had a colonoscopy (January 2010–March 2014) were selected as study subjects and the history of prior colonoscopies was reviewed. Multivariable Weibull regression models were used to estimate the incidence of C.R.C. at follow-up colonoscopy for subjects who were assigned a stratified risk level. The benchmark risk was defined according to a national survey. <b>Results:</b> The interval incidence of C.R.C. at a 10 year follow-up was 164 (95% C.I. 63–343) and 79 (95% C.I. 26–188) per 100,000 person-years for low-risk men and women respectively, which tallied with our benchmark risk. Men exceeded the benchmark risk in 3–5 years if they had an incomplete polyp removal, ≥3 adenomas during their last colonoscopy or a personal C.R.C. history, and in 7–8 years if they only had familial C.R.C. history. Women had a lower risk of C.R.C., and reached a same risk level 3–5 years later than men. Coexisting above risk factors resulted in a sharp increase in the incidence of C.R.C. at follow-up exceeding the benchmark much earlier. <b>Conclusion:</b> Surveillance intervals for men based on incidence of C.R.C. are in line with that recommended by the current guidelines for colonoscopy. However, an extension of 3–5 years may be appropriate for women. To target personalized medicine, a risk predictive model could be used to identify an appropriate surveillance interval for each individual in the future.
DOI: 10.6084/m9.figshare.3159478.v1
title: Chromosome diversity and evolution in <i>Allium</i> (Allioideae, Amaryllidaceae)

description: Despite extensive literature on the diversity of karyotypes in <i>Allium</i> is available, no attempt to analyse these data together, within a robust phylogenetic framework, has been carried out so far. Thus, we examined patterns and trends in chromosome evolution across the genus. Based on literature survey, karyo-morphometric features for 207 species belonging to 12 subgenera of <i>Allium</i> were obtained. Included in the data-set were basic chromosome number (<i>x</i>), somatic chromosome number (2<i>n</i>), total haploid (monoploid) chromosome length (THL) and three different measures defining karyotype structure: CV<sub>CI</sub>, measuring how heterogeneous are centromeres positions in a karyotype, CV<sub>CL</sub> and M<sub>CA</sub>, quantifying interchromosomal and intrachromosomal karyotype asymmetry, respectively. Trends in karyotype evolution were analysed by phylogenetic regressions and independent contrasts. Mean karyotypes highlighted differences and similarities in karyotype structure between the 12 subgenera. Further differences were noted when the two parameters for analysing karyotype asymmetry were assessed. In addition, by examining the effects of increasing karyotype dimensions (a proxy for genome size) on karyotype structure and asymmetry, it was shown that in <i>Allium</i> species, the DNA was added proportionally to their arm lengths. Overall, <i>p</i> = 8 and somehow intermediate karyotype asymmetry levels seem to represent plesiomorphic character-states in <i>Allium</i>.
DOI: 10.6084/m9.figshare.3159430.v1
title: Age estimation of African lions Panthera leo by ratio of tooth areas

description: X-ray images of PM<sup>2</sup> of known aged African lions<br>
DOI: 10.6084/m9.figshare.3159349
title: R code to reproduce the analyses from Dallas, Hall, and Drake 2015 "Competition-mediated feedbacks in experimental multi-species epizootics". Ecology

description: This repository contains all the data and code necessary to reproduce all analyses and recreate figures from the following publication:<br><b>Publication:</b><br>&gt; Dallas, T, R Hall, and JM Drake. 2015. Competition-mediated feedbacks in experimentalmulti-species epizootics. Ecology. http://dx.doi.org/10.1890/15-0305.1<br><b>Project description:</b><br>This project examined how competition with a non-susceptible host species (<i>Daphnia pulicaria</i>) influenced infection dynamics in a focal host. The `Rmd` file in this directory contains both epidemiological model, and analysis of experimental data.<br>
DOI: 10.6084/m9.figshare.3159364
title: Parasite sharing networks short talk (UGA GSS 2016)

description: Presentation given as part of the 2016 Graduate Student Symposium at University of Georgia's Odum School of Ecology. I present on some developing work examining the identifiability of important nodes in networks of parasite sharing.
DOI: 10.6084/m9.figshare.3159349.v1
title: R code to reproduce the analyses from Dallas, Hall, and Drake 2015 "Competition-mediated feedbacks in experimental multi-species epizootics". Ecology

description: This repository contains all the data and code necessary to reproduce all analyses and recreate figures from the following publication:<br><b>Publication:</b><br>&gt; Dallas, T, R Hall, and JM Drake. 2015. Competition-mediated feedbacks in experimentalmulti-species epizootics. Ecology. http://dx.doi.org/10.1890/15-0305.1<br><b>Project description:</b><br>This project examined how competition with a non-susceptible host species (<i>Daphnia pulicaria</i>) influenced infection dynamics in a focal host. The `Rmd` file in this directory contains both epidemiological model, and analysis of experimental data.<br>
DOI: 10.6084/m9.figshare.3159280
title: PLOS One Supplment Archive Data.zip

description: Dataset from single TCR alpha mice. Data is sequencing data from the TCR beta repertoire from Tconv and Tregs from 5 mice in the periphery and 3 mice from the thymus.
DOI: 10.6084/m9.figshare.3159364.v2
title: Parasite sharing networks short talk (UGA GSS 2016)

description: Presentation given as part of the 2016 Graduate Student Symposium at University of Georgia's Odum School of Ecology. I present on some developing work examining the identifiability of important nodes in networks of parasite sharing.
DOI: 10.6084/m9.figshare.3159409.v2
title: Long-term risk of colorectal cancer by gender after positive colonoscopy: population-based cohort study

description: <b>Background:</b> Evidence for surveillance intervals of colonoscopy are primarily based on adenoma recurrence rate rather than on colorectal cancer (C.R.C.) incidence. Little is known about long-term risk of C.R.C. after positive colonoscopy. In view of men have significantly higher C.R.C. risk than women, we aimed to estimate the gender-specific C.R.C. incidence after positive colonoscopy (adenoma or malignant lesion) at follow-up colonoscopy. <b>Methods:</b> A retrospective cohort study was conducted using data from a database of colonoscopy screening and surveillance. Patients having had a colonoscopy (January 2010–March 2014) were selected as study subjects and the history of prior colonoscopies was reviewed. Multivariable Weibull regression models were used to estimate the incidence of C.R.C. at follow-up colonoscopy for subjects who were assigned a stratified risk level. The benchmark risk was defined according to a national survey. <b>Results:</b> The interval incidence of C.R.C. at a 10 year follow-up was 164 (95% C.I. 63–343) and 79 (95% C.I. 26–188) per 100,000 person-years for low-risk men and women respectively, which tallied with our benchmark risk. Men exceeded the benchmark risk in 3–5 years if they had an incomplete polyp removal, ≥3 adenomas during their last colonoscopy or a personal C.R.C. history, and in 7–8 years if they only had familial C.R.C. history. Women had a lower risk of C.R.C., and reached a same risk level 3–5 years later than men. Coexisting above risk factors resulted in a sharp increase in the incidence of C.R.C. at follow-up exceeding the benchmark much earlier. <b>Conclusion:</b> Surveillance intervals for men based on incidence of C.R.C. are in line with that recommended by the current guidelines for colonoscopy. However, an extension of 3–5 years may be appropriate for women. To target personalized medicine, a risk predictive model could be used to identify an appropriate surveillance interval for each individual in the future.
DOI: 10.6084/m9.figshare.3159409.v1
title: Long-term Risk of Colorectal Cancer by Gender after Positive Colonoscopy: Population-Based Cohort Study

description: <b>Background:</b> Evidence for surveillance intervals of colonoscopy are primarily based on adenoma recurrence rate rather than on colorectal cancer (CRC) incidence. Little is known about a long-term risk of CRC after positive colonoscopy. In view of men have significantly higher CRC risk than women, we aimed to estimate the gender-specific CRC incidence after positive colonoscopy (adenoma or malignant lesion) at follow-up colonoscopy. <b>Methods:</b> A retrospective cohort study was conducted using data from a database of colonoscopy screening and surveillance. Patients having had a colonoscopy (January 2010-March 2014) were selected as study subjects and the history of prior colonoscopies were reviewed. Multivariable Weibull regression models were used to estimate the incidence of CRC at follow-up colonoscopy for subjects who were assigned a stratified risk level. The benchmark risk was defined according to a national survey. <b>Results:</b> The interval incidence of CRC at a 10-year follow-up was 164 (95%CI 63-343) and 79 (95%CI 26-188) per 100,000 person-years for low-risk men and women respectively, which tallied with our benchmark risk. Men exceeded the benchmark risk in 3-5 years if they had an incomplete polyp removal, ≥3 adenomas during their last colonoscopy or a personal CRC history, while in 7-8 years if only they had a familial CRC history. Women had a lower risk of CRC, and reached a same risk level in 3-5 years later than men. Coexisting above risk factors resulted in a sharp increase in the incidence of CRC at follow-up exceeding the benchmark much earlier. <b>Conclusion:</b> Surveillance intervals for men based on incidence of CRC are in line with that recommended by the current guidelines for colonoscopy. But, an additional extension of 3-5 years may be appropriate for women. To target personalized medicine, a risk predictive model could be used to identify an appropriate surveillance interval for each individual in the future.
DOI: 10.6084/m9.figshare.3159280.v1
title: PLOS One Supplment Archive Data.zip

description: Dataset from single TCR alpha mice. Data is sequencing data from the TCR beta repertoire from Tconv and Tregs from 5 mice in the periphery and 3 mice from the thymus.
DOI: 10.6084/m9.figshare.3159208
title: Geodynamics of Late Carboniferous-Early Permian forearc in north Chile (28°30'-29°30'S)

description: Table 2 U-Pb geochronologic analyses.
DOI: 10.6084/m9.figshare.3159205
title: Geodynamics of Late Carboniferous-Early Permian forearc in north Chile (28°30'-29°30'S)

description: Table 3: Ar-Ar geochronological data. Relative isotope abundances in Mol units
DOI: 10.6084/m9.figshare.3159208.v1
title: Geodynamics of Late Carboniferous-Early Permian forearc in north Chile (28°30'-29°30'S)

description: Table 2 U-Pb geochronologic analyses.
DOI: 10.6084/m9.figshare.3159094
title: 3D models of the TBSV replication platform as visualized by Metal-Tagging Transmission Electron Microscopy (METTEM) and Electron Tomography (ET)

description: <b>Movies S1-S2. </b>3D models of the TBSV replication platform as visualized by METTEM and ET (from tomograms in Fig. 5A and Fig. 6A). <br> <b>Movie S3. </b>3D model of a TBSV replication platform as visualized by METTEM immunogold labeling with anti-dsRNA antibodies and ET (from volume in Fig. 5B). The computational slices of the tomogram are first swept upwards (first third of the movie) then backwards (second third), revealing the 3D isosurface representation. The last third of the movie rotates the 3D representation. <br><br> <b>Movie S4.</b> 3D model of a TBSV replication platform as visualized by METTEM immunogold labeling with anti-dsRNA antibodies and ET (from volume in Fig. 7). The computational slices of the tomogram are first swept upwards (first third of the movie) then backwards (second third), revealing the 3D isosurface representation. The last third of the movie rotates the 3D representation.
DOI: 10.6084/m9.figshare.3159205.v1
title: Geodynamics of Late Carboniferous-Early Permian forearc in north Chile (28°30'-29°30'S)

description: Table 3: Ar-Ar geochronological data. Relative isotope abundances in Mol units
DOI: 10.6084/m9.figshare.3159043
title: Raw data for the role of acetyl phosphate in bypassing the cell membrane electrical potential sensor LytS

description: Data 1<br>Autophosphorylation of LytS.<br>Quantification of phosphorylated LytS bands by NIH Image J. Average of two trials. Data 2<br>Phosphorylation of LytR by acetyl phosphate.<br>Quantification of phosphorylated LytR bands by NIH ImageJ. Data 3<br>Phosphorylation of LytR-N by acetyl phosphate.<br>Quantification of phosphorylated LytR-N bands by NIH ImageJ. Data 4<br>Quantification of LytR bands in native-PAGEs (Figure 6A and B) by NIH Image J. LytR protein was phosphorylated by acetyl phosphate and its dephosphorylation by LytS was monitored by native-PAGE, whereby the phosphorylated dimer LytR becomes monomer after dephosphorylation. The column “corrected” represents the data after correcting for background signal at 0 min, and considering the band labeled “Monomer”, in the absence of LytS and ATP, as 100% unphosphorylated LytR.
DOI: 10.6084/m9.figshare.3158827
title: Micromeasure Data.zip

description: Micromeasure data
DOI: 10.6084/m9.figshare.3159094.v2
title: 3D models of the TBSV replication platform as visualized by Metal-Tagging Transmission Electron Microscopy (METTEM) and Electron Tomography (ET)

description: <b>Movies S1-S2. </b>3D models of the TBSV replication platform as visualized by METTEM and ET (from tomograms in Fig. 5A and Fig. 6A). <br> <b>Movie S3. </b>3D model of a TBSV replication platform as visualized by METTEM immunogold labeling with anti-dsRNA antibodies and ET (from volume in Fig. 5B). The computational slices of the tomogram are first swept upwards (first third of the movie) then backwards (second third), revealing the 3D isosurface representation. The last third of the movie rotates the 3D representation. <br><br> <b>Movie S4.</b> 3D model of a TBSV replication platform as visualized by METTEM immunogold labeling with anti-dsRNA antibodies and ET (from volume in Fig. 7). The computational slices of the tomogram are first swept upwards (first third of the movie) then backwards (second third), revealing the 3D isosurface representation. The last third of the movie rotates the 3D representation.
DOI: 10.6084/m9.figshare.3158836
title: Wagner-Fischer Demo

description: This is a demo-application illustrating how the Wagner-Fischer alignment (Wagner and Fischer 1974) between two sequences is computed. The interactive application which computes this code has been tested on Google Chrome and Firefox and should work out of the box by simply opening the HTML file in your browser. The screen video gives an additional illustration of the appearance of the application. The script was originally written for education purposes and may turn out to be useful in this context, since it allows the users to review each step of the Wagner-Fischer algorithm in different pastes.<br>