cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.4622023
title: Conformation-dependent QSAR approach for the prediction of inhibitory activity of bromodomain modulators

description: Epigenetic drug discovery is a promising research field with growing interest in the scientific community, as evidenced by the number of publications and the large amount of structure-epigenetic activity information currently available in the public domain. Computational methods are valuable tools to analyse and understand the activity of large compound collections from their structural information. In this manuscript, QSAR models to predict the inhibitory activity of a diverse and heterogeneous set of 88 organic molecules against the bromodomains BRD2, BRD3 and BRD4 are presented. A conformation-dependent representation of the chemical structures was established using the RDKit software and a training and test set division was performed. Several two-linear and three-linear QuBiLS-MIDAS molecular descriptors (www.tomocomd.com) were computed to extract the geometric structural features of the compounds studied. QuBiLS-MIDAS-based features sets, to be used in the modelling, were selected using dimensionality reduction strategies. The multiple linear regression procedure coupled with a genetic algorithm were employed to build the predictive models. Regression models containing between 6 to 9 variables were developed and assessed according to several internal and external validation methods. Analyses of outlier compounds and the applicability domain for each model were performed. As a result, the models against BRD2 and BRD3 with 8 variables and the model with 9 variables against BRD4 were those with the best overall performance according to the criteria accounted for. The results obtained suggest that the models proposed will be a good tool for studying the inhibitory activities of drug candidates against the bromodomains considered during epigenetic drug discovery.
DOI: 10.6084/m9.figshare.4622029.v1
title: Biochemical synthesis of uniformly <sup>13</sup>C-labeled diterpene hydrocarbons and their bioconversion to diterpenoid phytoalexins <i>in planta</i>

description: Phytocassanes and momilactones are the major diterpenoid phytoalexins inductively produced in rice as bioactive substances. Regardless of extensive studies on the biosynthetic pathways of these phytoalexins, bioconversion of diterpene hydrocarbons is not shown <i>in planta</i>. To elucidate the entire biosynthetic pathways of these phytoalexins, uniformly <sup>13</sup>C-labeled <i>ent</i>-cassadiene and <i>syn</i>-pimaradiene were enzymatically synthesized with structural verification by GC–MS and <sup>13</sup>C-NMR. Application of the <sup>13</sup>C-labeled substrates on rice leaves led to the detection of <sup>13</sup>C-labeled metabolites using LC-MS/MS. Further application of this method in the moss <i>Hypnum plumaeforme</i> and the nearest out-group of <i>Oryza</i> species <i>Leersia perrieri</i>, respectively, resulted in successful bioconversion of these labeled substrates into phytoalexins in these plants. These results demonstrate that genuine biosynthetic pathways from these diterpene hydrocarbons to the end product phytoalexins occur in these plants and that enzymatically synthesized [U-<sup>13</sup>C<sub>20</sub>] diterpene substrates are a powerful tool for chasing endogenous metabolites without dilution with naturally abundant unlabeled compounds. Uniformly labeled <sup>13</sup>C-diterpene: A powerful tool for tracing endogenous metabolites without dilution with naturally abundant unlabeled compounds
DOI: 10.6084/m9.figshare.4622032.v1
title: <i>n</i>-Hexanal and (<i>Z</i>)-3-hexenal are generated from arachidonic acid and linolenic acid by a lipoxygenase in <i>Marchantia polymorpha</i> L.

description: Most terrestrial plants form green leaf volatiles (GLVs), which are mainly composed of six-carbon (C6) compounds. In our effort to study the distribution of the ability of lipoxygenase (LOX) to form GLVs, we found that a liverwort, <i>Marchantia polymorpha</i>, formed <i>n</i>-hexanal and (<i>Z</i>)-3-hexenal. Some LOXs execute a secondary reaction to form short chain volatiles. One of the LOXs from <i>M. polymorpha</i> (MpLOX7) oxygenized arachidonic and α-linolenic acids at almost equivalent efficiency and formed C6-aldehydes during its catalysis; these are likely formed from hydroperoxides of arachidonic and α-linolenic acids, with a cleavage of the bond between carbon at the base of the hydroperoxy group and carbon of double bond, which is energetically unfavorable. These lines of evidence suggest that one of the LOXs in liverwort employs an unprecedented reaction to form C6 aldehydes as by-products of its reaction with fatty acid substrates. One of <i>Marchantia polymorpha</i> lipoxygenases forms six-carbon aldehydes as by-products.
DOI: 10.6084/m9.figshare.4622017
title: Reconstructing the Cryogenian–Ediacaran evolution of the Porongos fold and thrust belt, Southern Brasiliano Orogen, based on Zircon U–Pb–Hf–O isotopes

description: The Neoproterozoic geotectonic triad of the Brasiliano Orogen is reconstructed in southern Brazil from studies focused on the Porongos fold and thrust belt. We integrate field geology with isotopic studies of zircon U–Pb SHRIMP and Lu–Hf–O laser determinations in seven metasedimentary and three metavolcanic rock samples. The results indicate that the Porongos palaeo-basin was derived from mixed sources (3200–550 Ma), with major contributions from Rhyacian (2170 Ma) and Ediacaran (608 Ma) sources. Minor contributions from Archaean to Tonian sources are also registered. The maximum depositional age of the Porongos palaeo-basin is established by the age range of 650–550 Ma with <i>T</i><sub>DM</sub> model ages between 2.5 and 1.3 Ga. The reworked signature (<i>ε</i><sub>Hf</sub> values = −34 to −4) and the characteristic crustal magma reservoirs (<i>δ</i><sup>18</sup>O ≥5.3 ‰) indicate that these sediments are equivalent to Neoproterozoic granites of the Dom Feliciano Belt. The episodic depositional history started in the Cryogenian (650 Ma) and lasted until the Ediacaran (most likely 570 Ma). A magmatic event of Tonian age is recorded in rhyodacite samples interleaved with the metasedimentary rocks and dated at 773, 801, and 809 Ma. The crustal evolution of the Sul-Riograndense Shield included mountain building, folding and thrusting and flexural subsidence in the foreland. An orogenic triad is revealed as the Pelotas Batholith, the Porongos fold and thrust belt and the Camaquã Basin, all part of the Dom Feliciano Belt.
DOI: 10.6084/m9.figshare.4622023.v1
title: Conformation-dependent QSAR approach for the prediction of inhibitory activity of bromodomain modulators

description: Epigenetic drug discovery is a promising research field with growing interest in the scientific community, as evidenced by the number of publications and the large amount of structure-epigenetic activity information currently available in the public domain. Computational methods are valuable tools to analyse and understand the activity of large compound collections from their structural information. In this manuscript, QSAR models to predict the inhibitory activity of a diverse and heterogeneous set of 88 organic molecules against the bromodomains BRD2, BRD3 and BRD4 are presented. A conformation-dependent representation of the chemical structures was established using the RDKit software and a training and test set division was performed. Several two-linear and three-linear QuBiLS-MIDAS molecular descriptors (www.tomocomd.com) were computed to extract the geometric structural features of the compounds studied. QuBiLS-MIDAS-based features sets, to be used in the modelling, were selected using dimensionality reduction strategies. The multiple linear regression procedure coupled with a genetic algorithm were employed to build the predictive models. Regression models containing between 6 to 9 variables were developed and assessed according to several internal and external validation methods. Analyses of outlier compounds and the applicability domain for each model were performed. As a result, the models against BRD2 and BRD3 with 8 variables and the model with 9 variables against BRD4 were those with the best overall performance according to the criteria accounted for. The results obtained suggest that the models proposed will be a good tool for studying the inhibitory activities of drug candidates against the bromodomains considered during epigenetic drug discovery.
DOI: 10.6084/m9.figshare.4622014
title: Genesis of late carboniferous granitoid intrusions in the Dayinsu area, West Junggar, Northwest China: evidence of an arc setting for the western CAOB

description: The Dayinsu area is located in the northern part of the West Junggar district near the border between China and Kazakhstan and is an important component of the Central Asian Orogenic Belt (CAOB). The Dayinsu area hosts numerous granitoid plutons in Devonian–Carboniferous volcano–sedimentary strata. The older Laodayinsu and Kubei (345–330 Ma) plutons are located in the west with the younger Bayimuzha and Qianfeng (330–325 Ma) plutons in the east. The whole-rock SiO<sub>2</sub> contents of the four granitoid plutons range from 52.22 to 68.42 wt.% and total alkaline contents (K<sub>2</sub>O + Na<sub>2</sub>O) range from 4.94 to 9.16 wt.%. The granites are enriched in large ion lithophile elements and light rare earth elements with depletions in Nb, Ta, Ce, Pr, P, and Ti. The plutons are metaluminous with I-type signatures. The geochemistry of the intrusions suggests that they formed in a subduction zone setting, and subsequently underwent fractional crystallization during emplacement, with higher degrees of fractionation in the eastern sector than in the west. Similarities in the geochronology and geochemical characteristics of the granitoid plutons in Dayinsu to those in the Tabei district (west to Dayinsu area) suggest that both districts are part of the Carboniferous Tarbagatay Mountain intrusive event. The early Carboniferous (345–324 Ma) granitoid intrusions in the Tarbagatay Mountain likely formed in an island arc subduction setting during the evolution of the CAOB.
DOI: 10.6084/m9.figshare.4621963
title: Data and code to describe Carlia johnstonei and C. triacantha

description: Input files for analysis with BPP, StarBEAST2 and SNAPP for species delimitation with genetic data as well code and raw data for Morphological analysis.
DOI: 10.6084/m9.figshare.4622014.v1
title: Genesis of late carboniferous granitoid intrusions in the Dayinsu area, West Junggar, Northwest China: evidence of an arc setting for the western CAOB

description: The Dayinsu area is located in the northern part of the West Junggar district near the border between China and Kazakhstan and is an important component of the Central Asian Orogenic Belt (CAOB). The Dayinsu area hosts numerous granitoid plutons in Devonian–Carboniferous volcano–sedimentary strata. The older Laodayinsu and Kubei (345–330 Ma) plutons are located in the west with the younger Bayimuzha and Qianfeng (330–325 Ma) plutons in the east. The whole-rock SiO<sub>2</sub> contents of the four granitoid plutons range from 52.22 to 68.42 wt.% and total alkaline contents (K<sub>2</sub>O + Na<sub>2</sub>O) range from 4.94 to 9.16 wt.%. The granites are enriched in large ion lithophile elements and light rare earth elements with depletions in Nb, Ta, Ce, Pr, P, and Ti. The plutons are metaluminous with I-type signatures. The geochemistry of the intrusions suggests that they formed in a subduction zone setting, and subsequently underwent fractional crystallization during emplacement, with higher degrees of fractionation in the eastern sector than in the west. Similarities in the geochronology and geochemical characteristics of the granitoid plutons in Dayinsu to those in the Tabei district (west to Dayinsu area) suggest that both districts are part of the Carboniferous Tarbagatay Mountain intrusive event. The early Carboniferous (345–324 Ma) granitoid intrusions in the Tarbagatay Mountain likely formed in an island arc subduction setting during the evolution of the CAOB.
DOI: 10.6084/m9.figshare.4622017.v1
title: Reconstructing the Cryogenian–Ediacaran evolution of the Porongos fold and thrust belt, Southern Brasiliano Orogen, based on Zircon U–Pb–Hf–O isotopes

description: The Neoproterozoic geotectonic triad of the Brasiliano Orogen is reconstructed in southern Brazil from studies focused on the Porongos fold and thrust belt. We integrate field geology with isotopic studies of zircon U–Pb SHRIMP and Lu–Hf–O laser determinations in seven metasedimentary and three metavolcanic rock samples. The results indicate that the Porongos palaeo-basin was derived from mixed sources (3200–550 Ma), with major contributions from Rhyacian (2170 Ma) and Ediacaran (608 Ma) sources. Minor contributions from Archaean to Tonian sources are also registered. The maximum depositional age of the Porongos palaeo-basin is established by the age range of 650–550 Ma with <i>T</i><sub>DM</sub> model ages between 2.5 and 1.3 Ga. The reworked signature (<i>ε</i><sub>Hf</sub> values = −34 to −4) and the characteristic crustal magma reservoirs (<i>δ</i><sup>18</sup>O ≥5.3 ‰) indicate that these sediments are equivalent to Neoproterozoic granites of the Dom Feliciano Belt. The episodic depositional history started in the Cryogenian (650 Ma) and lasted until the Ediacaran (most likely 570 Ma). A magmatic event of Tonian age is recorded in rhyodacite samples interleaved with the metasedimentary rocks and dated at 773, 801, and 809 Ma. The crustal evolution of the Sul-Riograndense Shield included mountain building, folding and thrusting and flexural subsidence in the foreland. An orogenic triad is revealed as the Pelotas Batholith, the Porongos fold and thrust belt and the Camaquã Basin, all part of the Dom Feliciano Belt.
DOI: 10.6084/m9.figshare.4621963.v2
title: Data and code to describe Carlia johnstonei and C. triacantha

description: Input files for analysis with BPP, StarBEAST2 and SNAPP for species delimitation with genetic data as well code and raw data for Morphological analysis.
DOI: 10.6084/m9.figshare.12909565.v1
title: A doxycycline-inducible C17.2 neural stem cell-based combination of differentiation and suicide gene therapy for an <i>in vitro</i> tumorigenic C6 glioma model

description: Neural stem cell (NSC)-based gene therapies have been recently developed as effective strategies for treating brain tumors through inherent tumor tropism. However, this methodology has two considerable challenges: preventing NSCs from dying from the therapeutic agents encoded by their equipped genes before reaching tumor sites and the clearance of exogenous NSCs after therapeutic treatments. For these purposes, we established a novel doxycycline-inducible retroviral plasmid pTRE3G-TKGFP. A herpes simplex type 1 thymidine kinase (HSV1TK)-green fluorescent protein (GFP) fusion protein coding sequence was integrated into the multiple cloning site II (MCS II) of the pQcXIX vector, and the CMV IE promoter (P<sub>CMV IE</sub>) of pQcXIX was replaced with the doxycycline-inducible TRE3G promoter (P<sub>TRE3G</sub>). We then cloned the coding sequences of tumor necrosis factor-α (TNF-α), interleukin 6 (IL-6) and soluble interleukin 6 receptor (sIL-6R) into MCS I to combine HSV1TK (TK)/ganciclovir (GCV)-based suicide gene therapy against tumorigenic C6 glioma cells. TNF-α, IL-6 and sIL6R could efficiently induce tumorigenic C6 glioma cell differentiation, resulted in down-regulating the cell proliferation rate and the tumorigenicity of glioma cells and up-regulating the production of differentiation markers, such as connexin-43. Furthermore, gap junctions could enhance the bystander effect in suicide gene therapy. Consequently, we found that the retroviral plasmid transfected NSCs exerted stronger remedial effects on tumorigenic C6 glioma cells through the combination of differentiation and suicide gene therapy than by suicide gene therapy alone. This study is also the first case applying NSCs to conduct the combination of differentiation and TK/GCV-based suicide gene therapy on glioma cells.
DOI: 10.6084/m9.figshare.12909565
title: A doxycycline-inducible C17.2 neural stem cell-based combination of differentiation and suicide gene therapy for an <i>in vitro</i> tumorigenic C6 glioma model

description: Neural stem cell (NSC)-based gene therapies have been recently developed as effective strategies for treating brain tumors through inherent tumor tropism. However, this methodology has two considerable challenges: preventing NSCs from dying from the therapeutic agents encoded by their equipped genes before reaching tumor sites and the clearance of exogenous NSCs after therapeutic treatments. For these purposes, we established a novel doxycycline-inducible retroviral plasmid pTRE3G-TKGFP. A herpes simplex type 1 thymidine kinase (HSV1TK)-green fluorescent protein (GFP) fusion protein coding sequence was integrated into the multiple cloning site II (MCS II) of the pQcXIX vector, and the CMV IE promoter (P<sub>CMV IE</sub>) of pQcXIX was replaced with the doxycycline-inducible TRE3G promoter (P<sub>TRE3G</sub>). We then cloned the coding sequences of tumor necrosis factor-α (TNF-α), interleukin 6 (IL-6) and soluble interleukin 6 receptor (sIL-6R) into MCS I to combine HSV1TK (TK)/ganciclovir (GCV)-based suicide gene therapy against tumorigenic C6 glioma cells. TNF-α, IL-6 and sIL6R could efficiently induce tumorigenic C6 glioma cell differentiation, resulted in down-regulating the cell proliferation rate and the tumorigenicity of glioma cells and up-regulating the production of differentiation markers, such as connexin-43. Furthermore, gap junctions could enhance the bystander effect in suicide gene therapy. Consequently, we found that the retroviral plasmid transfected NSCs exerted stronger remedial effects on tumorigenic C6 glioma cells through the combination of differentiation and suicide gene therapy than by suicide gene therapy alone. This study is also the first case applying NSCs to conduct the combination of differentiation and TK/GCV-based suicide gene therapy on glioma cells.
DOI: 10.6084/m9.figshare.12769826.v4
title: Bone health in patients with asthma: A systematic review and meta-analysis

description: Form used to extract all the relevant data from each eligible article.
DOI: 10.6084/m9.figshare.12769826
title: Bone health in patients with asthma: A systematic review and meta-analysis

description: Form used to extract all the relevant data from each eligible article.
DOI: 10.6084/m9.figshare.12769826.v6
title: Bone health in patients with asthma: A systematic review and meta-analysis

description: Form used to extract all the relevant data from each eligible article.
DOI: 10.6084/m9.figshare.12769826.v5
title: Bone health in patients with asthma: A systematic review and meta-analysis

description: Form used to extract all the relevant data from each eligible article.
DOI: 10.6084/m9.figshare.12909557
title: demographic and clinical characteristics and serum cytokine levels of participants in HS study.xlsx

description: Demographic and clinical characteristics and serum hs-CRP, TNF-a, IL-1b, IL-17A, IL-23 levels of 26 HS patient and 24 controls.
DOI: 10.6084/m9.figshare.12909557.v1
title: demographic and clinical characteristics and serum cytokine levels of participants in HS study.xlsx

description: Demographic and clinical characteristics and serum hs-CRP, TNF-a, IL-1b, IL-17A, IL-23 levels of 26 HS patient and 24 controls.
DOI: 10.6084/m9.figshare.4621315
title: final version.doc

description: <br>
DOI: 10.6084/m9.figshare.4621315.v1
title: final version.doc

description: <br>
DOI: 10.6084/m9.figshare.4621042
title: The Effect Computers Have on Our Future Generations

description: With new advances of technology in recent years and upcoming research, it is certain that artificial intelligence will be making its way into the lives of many with accessible computers. As our younger generations are and will be greatly part of a technological world, it can be hypothesized that in the education systems, computer usage is prominent in learning, projects, and activities. This may affect the youth's mental and physical health and even their lifestyles, because being exposed to technology at a young age affects the way they do work and business grown-up. Overall, this is all about how, if computers are providing so much automatic service, aid, and information to children and teens, then they will probably be less productive, physically and mentally. As well, although the youth is constantly being given quick answers from the Internet, the overload of knowledge cannot help the fact that they will not be able to apply anything they learned to work. Given this information and the fact that we have an aging population, we hypothesize that words related to this aspect of society would be found among the results.
DOI: 10.6084/m9.figshare.4621036
title: Statistical Analysis on Interdisciplinary Papers in 2016

description: The goal of the project is to analyze altmetric data regarding published scientific papers in 2016, and to specifically determine which interdisciplinary fields are impactful. After taking some random samples, the program designed uses data clustering as well as data representation techniques to analyze the altmetric data. Trying to classify the papers into different levels of impact, k-means clustering is applied in a creative way. With the focus on the interdisciplinary fields, three kinds of matrices are now calculated to illustrate the strength of the connection between every possible pairing combination: average altmetric score, percentage of published papers in this interdisciplinary field, and total altmetric score. Sorting based on the values obtained in the matrices and comparing three matrices can yield insightful results and help people understand the connections between different subjects better.
DOI: 10.6084/m9.figshare.4621039
title: Disease and the Steps to the Cure

description: An average of 56 million deaths occur worldwide each year and nearly 62% are caused by disease. Although research, awareness, and funding has increased significantly over the past century, it still might not be enough. After a small investigation it was revealed that the top three fatal diseases of Canadian citizens in 2015 were malignant neoplasms, heart diseases, and cerebrovascular diseases. A program which outputs Key words, including ones related to health and medical sciences, was designed to quickly analyze the relevance of the aforementioned diseases. This program uses an input of data sets from 2016. Through analyzing the 2015 Top 100 articles and the 2016 data, we were able to infer the amount of research and funding that these topics receive, and its associated trends. Since these three diseases are leading causes of mortality rates, it is important that more research and funding goes towards these diseases, but more specifically the field of health and medical sciences.
DOI: 10.6084/m9.figshare.4621036.v1
title: Statistical Analysis on Interdisciplinary Papers in 2016

description: The goal of the project is to analyze altmetric data regarding published scientific papers in 2016, and to specifically determine which interdisciplinary fields are impactful. After taking some random samples, the program designed uses data clustering as well as data representation techniques to analyze the altmetric data. Trying to classify the papers into different levels of impact, k-means clustering is applied in a creative way. With the focus on the interdisciplinary fields, three kinds of matrices are now calculated to illustrate the strength of the connection between every possible pairing combination: average altmetric score, percentage of published papers in this interdisciplinary field, and total altmetric score. Sorting based on the values obtained in the matrices and comparing three matrices can yield insightful results and help people understand the connections between different subjects better.