cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1210740
title: Archisargoid flies (Diptera, Brachycera, Archisargidae and Kovalevisargidae) from the Jurassic Daohugou biota of China, and the related biostratigraphical correlation and geological age

description: Nine impression fossils of archisargoid flies were examined, described here as eight species (seven new), in seven genera (two new): <i>Archirhagio mostovskii</i> sp. nov., <i>Archirhagio varius</i> sp. nov., <i>Mesosolva huabeiensis</i> (Hong, 1983), <i>Novisargus rarus</i> gen. et sp. nov., <i>Ovisargus</i> (<i>Ovisargus</i>) <i>singulus</i> sp. nov., <i>Sharasargus maculus</i> sp. nov., <i>Tabanisargus daohugouensis</i> gen. et sp. nov. (Archisargidae) and <i>Kovalevisargus haifanggouensis</i> sp. nov. (Kovalevisargidae). These findings suggest that archisargoid flies were already highly diverse in the Daohugou biota. Furthermore, there is a very close resemblance between the Daohugou and Karatau biotas, consistent with the numerous other genera of insects shared between the Daohugou and Karabastau formations. The geological age for the archisargoid-bearing non-marine volcano-sedimentary rocks is reassessed as latest Middle Jurassic (Callovian) – earliest Late Jurassic (Oxfordian) related to that of the Karabastau Formation, rather than Middle Jurassic Jiulongshan Formation or the Early Cretaceous Dabeigou and/or Yixian formations.http://zoobank.org/urn:lsid:zoobank.org:pub:6B735695-DE37-4933-B449-B5EDE7A8A73A
DOI: 10.6084/m9.figshare.1210740.v1
title: Archisargoid flies (Diptera, Brachycera, Archisargidae and Kovalevisargidae) from the Jurassic Daohugou biota of China, and the related biostratigraphical correlation and geological age

description: Nine impression fossils of archisargoid flies were examined, described here as eight species (seven new), in seven genera (two new): <i>Archirhagio mostovskii</i> sp. nov., <i>Archirhagio varius</i> sp. nov., <i>Mesosolva huabeiensis</i> (Hong, 1983), <i>Novisargus rarus</i> gen. et sp. nov., <i>Ovisargus</i> (<i>Ovisargus</i>) <i>singulus</i> sp. nov., <i>Sharasargus maculus</i> sp. nov., <i>Tabanisargus daohugouensis</i> gen. et sp. nov. (Archisargidae) and <i>Kovalevisargus haifanggouensis</i> sp. nov. (Kovalevisargidae). These findings suggest that archisargoid flies were already highly diverse in the Daohugou biota. Furthermore, there is a very close resemblance between the Daohugou and Karatau biotas, consistent with the numerous other genera of insects shared between the Daohugou and Karabastau formations. The geological age for the archisargoid-bearing non-marine volcano-sedimentary rocks is reassessed as latest Middle Jurassic (Callovian) – earliest Late Jurassic (Oxfordian) related to that of the Karabastau Formation, rather than Middle Jurassic Jiulongshan Formation or the Early Cretaceous Dabeigou and/or Yixian formations.http://zoobank.org/urn:lsid:zoobank.org:pub:6B735695-DE37-4933-B449-B5EDE7A8A73A
DOI: 10.6084/m9.figshare.1210740.v2
title: Archisargoid flies (Diptera, Brachycera, Archisargidae and Kovalevisargidae) from the Jurassic Daohugou biota of China, and the related biostratigraphical correlation and geological age

description: Nine impression fossils of archisargoid flies were examined, described here as eight species (seven new), in seven genera (two new): <i>Archirhagio mostovskii</i> sp. nov., <i>Archirhagio varius</i> sp. nov., <i>Mesosolva huabeiensis</i> (Hong, 1983), <i>Novisargus rarus</i> gen. et sp. nov., <i>Ovisargus</i> (<i>Ovisargus</i>) <i>singulus</i> sp. nov., <i>Sharasargus maculus</i> sp. nov., <i>Tabanisargus daohugouensis</i> gen. et sp. nov. (Archisargidae) and <i>Kovalevisargus haifanggouensis</i> sp. nov. (Kovalevisargidae). These findings suggest that archisargoid flies were already highly diverse in the Daohugou biota. Furthermore, there is a very close resemblance between the Daohugou and Karatau biotas, consistent with the numerous other genera of insects shared between the Daohugou and Karabastau formations. The geological age for the archisargoid-bearing non-marine volcano-sedimentary rocks is reassessed as latest Middle Jurassic (Callovian) – earliest Late Jurassic (Oxfordian) related to that of the Karabastau Formation, rather than Middle Jurassic Jiulongshan Formation or the Early Cretaceous Dabeigou and/or Yixian formations.http://zoobank.org/urn:lsid:zoobank.org:pub:6B735695-DE37-4933-B449-B5EDE7A8A73A
DOI: 10.6084/m9.figshare.1210740.v3
title: Archisargoid flies (Diptera, Brachycera, Archisargidae and Kovalevisargidae) from the Jurassic Daohugou biota of China, and the related biostratigraphical correlation and geological age

description: Nine impression fossils of archisargoid flies were examined, described here as eight species (seven new), in seven genera (two new): <i>Archirhagio mostovskii</i> sp. nov., <i>Archirhagio varius</i> sp. nov., <i>Mesosolva huabeiensis</i> (Hong, 1983), <i>Novisargus rarus</i> gen. et sp. nov., <i>Ovisargus</i> (<i>Ovisargus</i>) <i>singulus</i> sp. nov., <i>Sharasargus maculus</i> sp. nov., <i>Tabanisargus daohugouensis</i> gen. et sp. nov. (Archisargidae) and <i>Kovalevisargus haifanggouensis</i> sp. nov. (Kovalevisargidae). These findings suggest that archisargoid flies were already highly diverse in the Daohugou biota. Furthermore, there is a very close resemblance between the Daohugou and Karatau biotas, consistent with the numerous other genera of insects shared between the Daohugou and Karabastau formations. The geological age for the archisargoid-bearing non-marine volcano-sedimentary rocks is reassessed as latest Middle Jurassic (Callovian) – earliest Late Jurassic (Oxfordian) related to that of the Karabastau Formation, rather than Middle Jurassic Jiulongshan Formation or the Early Cretaceous Dabeigou and/or Yixian formations.http://zoobank.org/urn:lsid:zoobank.org:pub:6B735695-DE37-4933-B449-B5EDE7A8A73A
DOI: 10.6084/m9.figshare.1210740.v5
title: Archisargoid flies (Diptera, Brachycera, Archisargidae and Kovalevisargidae) from the Jurassic Daohugou biota of China, and the related biostratigraphical correlation and geological age

description: Nine impression fossils of archisargoid flies were examined, described here as eight species (seven new), in seven genera (two new): <i>Archirhagio mostovskii</i> sp. nov., <i>Archirhagio varius</i> sp. nov., <i>Mesosolva huabeiensis</i> (Hong, 1983), <i>Novisargus rarus</i> gen. et sp. nov., <i>Ovisargus</i> (<i>Ovisargus</i>) <i>singulus</i> sp. nov., <i>Sharasargus maculus</i> sp. nov., <i>Tabanisargus daohugouensis</i> gen. et sp. nov. (Archisargidae) and <i>Kovalevisargus haifanggouensis</i> sp. nov. (Kovalevisargidae). These findings suggest that archisargoid flies were already highly diverse in the Daohugou biota. Furthermore, there is a very close resemblance between the Daohugou and Karatau biotas, consistent with the numerous other genera of insects shared between the Daohugou and Karabastau formations. The geological age for the archisargoid-bearing non-marine volcano-sedimentary rocks is reassessed as latest Middle Jurassic (Callovian) – earliest Late Jurassic (Oxfordian) related to that of the Karabastau Formation, rather than Middle Jurassic Jiulongshan Formation or the Early Cretaceous Dabeigou and/or Yixian formations.http://zoobank.org/urn:lsid:zoobank.org:pub:6B735695-DE37-4933-B449-B5EDE7A8A73A
DOI: 10.6084/m9.figshare.1210740.v4
title: Archisargoid flies (Diptera, Brachycera, Archisargidae and Kovalevisargidae) from the Jurassic Daohugou biota of China, and the related biostratigraphical correlation and geological age

description: Nine impression fossils of archisargoid flies were examined, described here as eight species (seven new), in seven genera (two new): <i>Archirhagio mostovskii</i> sp. nov., <i>Archirhagio varius</i> sp. nov., <i>Mesosolva huabeiensis</i> (Hong, 1983), <i>Novisargus rarus</i> gen. et sp. nov., <i>Ovisargus</i> (<i>Ovisargus</i>) <i>singulus</i> sp. nov., <i>Sharasargus maculus</i> sp. nov., <i>Tabanisargus daohugouensis</i> gen. et sp. nov. (Archisargidae) and <i>Kovalevisargus haifanggouensis</i> sp. nov. (Kovalevisargidae). These findings suggest that archisargoid flies were already highly diverse in the Daohugou biota. Furthermore, there is a very close resemblance between the Daohugou and Karatau biotas, consistent with the numerous other genera of insects shared between the Daohugou and Karabastau formations. The geological age for the archisargoid-bearing non-marine volcano-sedimentary rocks is reassessed as latest Middle Jurassic (Callovian) – earliest Late Jurassic (Oxfordian) related to that of the Karabastau Formation, rather than Middle Jurassic Jiulongshan Formation or the Early Cretaceous Dabeigou and/or Yixian formations.http://zoobank.org/urn:lsid:zoobank.org:pub:6B735695-DE37-4933-B449-B5EDE7A8A73A
DOI: 10.6084/m9.figshare.1221225
title: Identification of DNA-binding proteins by incorporating evolutionary information into pseudo amino acid composition via the top-n-gram approach

description: DNA-binding proteins are crucial for various cellular processes and hence have become an important target for both basic research and drug development. With the avalanche of protein sequences generated in the postgenomic age, it is highly desired to establish an automated method for rapidly and accurately identifying DNA-binding proteins based on their sequence information alone. Owing to the fact that all biological species have developed beginning from a very limited number of ancestral species, it is important to take into account the evolutionary information in developing such a high-throughput tool. In view of this, a new predictor was proposed by incorporating the evolutionary information into the general form of pseudo amino acid composition via the top-n-gram approach. It was observed by comparing the new predictor with the existing methods via both jackknife test and independent data-set test that the new predictor outperformed its counterparts. It is anticipated that the new predictor may become a useful vehicle for identifying DNA-binding proteins. It has not escaped our notice that the novel approach to extract evolutionary information into the formulation of statistical samples can be used to identify many other protein attributes as well.
DOI: 10.6084/m9.figshare.1221225.v1
title: Identification of DNA-binding proteins by incorporating evolutionary information into pseudo amino acid composition via the top-n-gram approach

description: DNA-binding proteins are crucial for various cellular processes and hence have become an important target for both basic research and drug development. With the avalanche of protein sequences generated in the postgenomic age, it is highly desired to establish an automated method for rapidly and accurately identifying DNA-binding proteins based on their sequence information alone. Owing to the fact that all biological species have developed beginning from a very limited number of ancestral species, it is important to take into account the evolutionary information in developing such a high-throughput tool. In view of this, a new predictor was proposed by incorporating the evolutionary information into the general form of pseudo amino acid composition via the top-n-gram approach. It was observed by comparing the new predictor with the existing methods via both jackknife test and independent data-set test that the new predictor outperformed its counterparts. It is anticipated that the new predictor may become a useful vehicle for identifying DNA-binding proteins. It has not escaped our notice that the novel approach to extract evolutionary information into the formulation of statistical samples can be used to identify many other protein attributes as well.
DOI: 10.6084/m9.figshare.1232120
title: Statistically and Computationally Efficient Estimating Equations for Large Spatial Datasets

description: For Gaussian process models, likelihood based methods are often difficult to use with large irregularly spaced spatial datasets, because exact calculations of the likelihood for <i>n</i> observations require <i>O</i>(<i>n</i><sup>3</sup>) operations and <i>O</i>(<i>n</i><sup>2</sup>) memory. Various approximation methods have been developed to address the computational difficulties. In this paper, we propose new unbiased estimating equations based on score equation approximations that are both computationally and statistically efficient. We replace the inverse covariance matrix that appears in the score equations by a sparse matrix to approximate the quadratic forms, then set the resulting quadratic forms equal to their expected values to obtain unbiased estimating equations. The sparse matrix is constructed by a sparse inverse Cholesky approach to approximate the inverse covariance matrix. The statistical efficiency of the resulting unbiased estimating equations are evaluated both in theory and by numerical studies. Our methods are applied to nearly 90,000 satellite-based measurements of water vapor levels over a region in the Southeast Pacific Ocean.
DOI: 10.6084/m9.figshare.1232120.v1
title: Statistically and Computationally Efficient Estimating Equations for Large Spatial Datasets

description: For Gaussian process models, likelihood based methods are often difficult to use with large irregularly spaced spatial datasets, because exact calculations of the likelihood for <i>n</i> observations require <i>O</i>(<i>n</i><sup>3</sup>) operations and <i>O</i>(<i>n</i><sup>2</sup>) memory. Various approximation methods have been developed to address the computational difficulties. In this paper, we propose new unbiased estimating equations based on score equation approximations that are both computationally and statistically efficient. We replace the inverse covariance matrix that appears in the score equations by a sparse matrix to approximate the quadratic forms, then set the resulting quadratic forms equal to their expected values to obtain unbiased estimating equations. The sparse matrix is constructed by a sparse inverse Cholesky approach to approximate the inverse covariance matrix. The statistical efficiency of the resulting unbiased estimating equations are evaluated both in theory and by numerical studies. Our methods are applied to nearly 90,000 satellite-based measurements of water vapor levels over a region in the Southeast Pacific Ocean.
DOI: 10.5281/zenodo.10864837
title: Improved Inception-based Neural Network for Real-time Prediction of  Displacement Field in Nonlinear Seismic Response of Ultra-High-Rise  Structures

description: Training sets, validation sets, network architecture, and running code for a comming research paper.
DOI: 10.6084/m9.figshare.1232161
title: miR-214-mediated downregulation of RNF8 induces chromosomal instability in ovarian cancer cells

description: Defective DNA damage response (DDR) is frequently associated with carcinogenesis. Abrogation of DDR leads to chromosomal instability, a most common characteristic of tumors. However, the molecular mechanisms underlying regulation of DDR are still elusive. The ubiquitin ligase RNF8 mediates the ubiquitination of γH2AX and recruits 53BP1 and BRCA1 to DNA damage sites which promotes DDR and inhibits chromosomal instability. Though RNF8 is a key player involved in DDR, regulation of its expression is still poorly understood. Here, we show that miR-214 could abrogate DDR by repressing RNF8 expression through direct binding to 3′-untranslated region (3′ UTR) of RNF8 mRNA in human ovarian cancer cells. Antagonizing miR-214 by expressing its inhibitors in A2780 cells significantly increased RNF8 expression and thus promoted DNA damage repair. Consistent with the role of miR-214 in regulating RNF8 expression, the impaired DNA repair induced by miR-214 overexpression can be rescued by overexpressing RNF8 mRNA lacking the 3′ UTR. Together, our results indicate that down-regulation of RNF8 mediated by miR-214 impedes DNA damage response to induce chromosomal instability in ovarian cancers, which may facilitate the understanding of mechanisms underlying chromosomal instability.
DOI: 10.6084/m9.figshare.1232161.v1
title: miR-214-mediated downregulation of RNF8 induces chromosomal instability in ovarian cancer cells

description: Defective DNA damage response (DDR) is frequently associated with carcinogenesis. Abrogation of DDR leads to chromosomal instability, a most common characteristic of tumours. However, the molecular mechanisms underlying regulation of DDR are still elusive. The ubiquitin ligase RNF8 mediates the ubiquitination of γH2AX and recruits 53BP1 and BRCA1 to DNA damage sites which promotes DDR and inhibits chromosomal instability. Though RNF8 is a key player involved in DDR, regulation of its expression is still poorly understood. Here, we show that miR-214 could abrogate DDR by repressing RNF8 expression through direct binding to 3´-untranslated region (3´ UTR) of RNF8 mRNA in human ovarian cancer cells. Antagonizing miR-214 by expressing its inhibitors in A2780 cells significantly increased RNF8 expression and thus promoted DNA damage repair. Consistent with the role of miR-214 in regulating RNF8 expression, the impaired DNA repair induced by miR-214 over-expression can be rescued by over-expressing RNF8 mRNA lacking the 3´ UTR. Together, our results indicate that down-regulation of RNF8 mediated by miR-214 impedes DNA damage response to induce chromosomal instability in ovarian cancers, which may facilitate the understanding of mechanisms underlying chromosomal instability.
DOI: 10.6084/m9.figshare.1232161.v2
title: miR-214-mediated downregulation of RNF8 induces chromosomal instability in ovarian cancer cells

description: Defective DNA damage response (DDR) is frequently associated with carcinogenesis. Abrogation of DDR leads to chromosomal instability, a most common characteristic of tumors. However, the molecular mechanisms underlying regulation of DDR are still elusive. The ubiquitin ligase RNF8 mediates the ubiquitination of γH2AX and recruits 53BP1 and BRCA1 to DNA damage sites which promotes DDR and inhibits chromosomal instability. Though RNF8 is a key player involved in DDR, regulation of its expression is still poorly understood. Here, we show that miR-214 could abrogate DDR by repressing RNF8 expression through direct binding to 3′-untranslated region (3′ UTR) of RNF8 mRNA in human ovarian cancer cells. Antagonizing miR-214 by expressing its inhibitors in A2780 cells significantly increased RNF8 expression and thus promoted DNA damage repair. Consistent with the role of miR-214 in regulating RNF8 expression, the impaired DNA repair induced by miR-214 overexpression can be rescued by overexpressing RNF8 mRNA lacking the 3′ UTR. Together, our results indicate that down-regulation of RNF8 mediated by miR-214 impedes DNA damage response to induce chromosomal instability in ovarian cancers, which may facilitate the understanding of mechanisms underlying chromosomal instability.
DOI: 10.6084/m9.figshare.1232161.v3
title: miR-214-mediated downregulation of RNF8 induces chromosomal instability in ovarian cancer cells

description: Defective DNA damage response (DDR) is frequently associated with carcinogenesis. Abrogation of DDR leads to chromosomal instability, a most common characteristic of tumors. However, the molecular mechanisms underlying regulation of DDR are still elusive. The ubiquitin ligase RNF8 mediates the ubiquitination of γH2AX and recruits 53BP1 and BRCA1 to DNA damage sites which promotes DDR and inhibits chromosomal instability. Though RNF8 is a key player involved in DDR, regulation of its expression is still poorly understood. Here, we show that miR-214 could abrogate DDR by repressing RNF8 expression through direct binding to 3′-untranslated region (3′ UTR) of RNF8 mRNA in human ovarian cancer cells. Antagonizing miR-214 by expressing its inhibitors in A2780 cells significantly increased RNF8 expression and thus promoted DNA damage repair. Consistent with the role of miR-214 in regulating RNF8 expression, the impaired DNA repair induced by miR-214 overexpression can be rescued by overexpressing RNF8 mRNA lacking the 3′ UTR. Together, our results indicate that down-regulation of RNF8 mediated by miR-214 impedes DNA damage response to induce chromosomal instability in ovarian cancers, which may facilitate the understanding of mechanisms underlying chromosomal instability.
DOI: 10.6084/m9.figshare.1232161.v4
title: miR-214-mediated downregulation of RNF8 induces chromosomal instability in ovarian cancer cells

description: Defective DNA damage response (DDR) is frequently associated with carcinogenesis. Abrogation of DDR leads to chromosomal instability, a most common characteristic of tumors. However, the molecular mechanisms underlying regulation of DDR are still elusive. The ubiquitin ligase RNF8 mediates the ubiquitination of γH2AX and recruits 53BP1 and BRCA1 to DNA damage sites which promotes DDR and inhibits chromosomal instability. Though RNF8 is a key player involved in DDR, regulation of its expression is still poorly understood. Here, we show that miR-214 could abrogate DDR by repressing RNF8 expression through direct binding to 3′-untranslated region (3′ UTR) of RNF8 mRNA in human ovarian cancer cells. Antagonizing miR-214 by expressing its inhibitors in A2780 cells significantly increased RNF8 expression and thus promoted DNA damage repair. Consistent with the role of miR-214 in regulating RNF8 expression, the impaired DNA repair induced by miR-214 overexpression can be rescued by overexpressing RNF8 mRNA lacking the 3′ UTR. Together, our results indicate that down-regulation of RNF8 mediated by miR-214 impedes DNA damage response to induce chromosomal instability in ovarian cancers, which may facilitate the understanding of mechanisms underlying chromosomal instability.
DOI: 10.34740/kaggle/dsv/7929313
title: ⏳ endoflife.date database (duckdb)
DOI: 10.6084/m9.figshare.1241552
title: Histone H3 K27 acetylation marks a potent enhancer element on the adipogenic master regulator gene Pparg2

description: PPARγ2 is expressed almost exclusively in adipose tissue and plays a central role in adipogenesis. Despite intensive studies over the last 2 decades, the mechanism regulating the expression of the Pparg2 gene, especially the role of cis-regulatory elements, is still not completely understood. Here, we report a comprehensive investigation of the enhancer elements within the murine Pparg2 gene. Utilizing the combined techniques of sequence conservation analysis and chromatin marker examination, we identified a potent enhancer element that augmented the expression of a reporter gene under the control of the Pparg2 promoter by 20-fold. This enhancer element was first identified as highly conserved non-coding sequence 10 (CNS10) and was later shown to be enriched with the enhancer marker H3 K27 acetylation. Further studies identified a binding site for p300 as the essential enhancer element in CNS10. Moreover, p300 physically binds to CNS10 and is required for the enhancer activity of CNS10. The depletion of p300 by siRNA resulted in significantly impaired activation of Pparg2 at the early stages of 3T3-L1 adipogenesis. In summary, our study identified a novel enhancer element on the murine Pparg2 gene and suggested a novel mechanism for the regulation of Pparg2 expression by p300 in 3T3-L1 adipogenesis.