cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.8976026
title: <i>Scheenstia bernissartensis</i> (Actinopterygii: Ginglymodi) from the Early Cretaceous of Bernissart, Belgium, with an appraisal of ginglymodian evolutionary history

description: <i>Lepidotes bernissartensis</i> is a species of holostean ray-finned fish from the Barremian–Aptian of Bernissart, Belgium, described by Traquair in 1911. We provide here a revision of its anatomy, which led us to include this species in the genus <i>Scheenstia</i>, and to consider <i>L. brevifulcratus</i> and <i>L. arcuatus</i>, both from the same site, synonymous with <i>S. bernissartensis</i>. We performed two cladistic analyses in order to assess the phylogenetic position of <i>S. bernissartensis</i> and to do an updated appraisal of the evolutionary history of the ginglymodians. <i>Scheenstia</i> is included in the Lepidotidae, and placed in a pectinated position between the basal genus <i>Lepidotes</i> and the more derived members of the family (other species of <i>Scheenstia</i>, <i>Isanichthys</i> and <i>Camerichthys</i>). The nodes within the lepidotids are weakly supported. Although <i>S. bernissartensis</i> is not directly related to <i>S. mantelli</i> from the Wealden of Europe, the two species have similar palaeoenvironments and stratigraphical ranges. Taken as a whole, the ginglymodians experienced several episodes of diversification that are spatially and temporally restricted. The oldest episode involved basal ginglymodians and occurred in the Middle Triassic, in marine environments along the northern margin of the Tethys. A second episode affected the Semionotidae and occurred in freshwater environments of North America and Europe in the Late Triassic and Early Jurassic. The remaining Semionotiformes, Macrosemiidae and Callipurbeckidae, ranged from the Triassic to the Early Cretaceous and were mostly marine. Among the Lepisosteiformes, two clades, the Lepidotidae and the Lepisosteoidi, show episodes of diversification, first in marine and then in freshwater environments.
DOI: 10.6084/m9.figshare.8976026.v1
title: <i>Scheenstia bernissartensis</i> (Actinopterygii: Ginglymodi) from the Early Cretaceous of Bernissart, Belgium, with an appraisal of ginglymodian evolutionary history

description: <i>Lepidotes bernissartensis</i> is a species of holostean ray-finned fish from the Barremian–Aptian of Bernissart, Belgium, described by Traquair in 1911. We provide here a revision of its anatomy, which led us to include this species in the genus <i>Scheenstia</i>, and to consider <i>L. brevifulcratus</i> and <i>L. arcuatus</i>, both from the same site, synonymous with <i>S. bernissartensis</i>. We performed two cladistic analyses in order to assess the phylogenetic position of <i>S. bernissartensis</i> and to do an updated appraisal of the evolutionary history of the ginglymodians. <i>Scheenstia</i> is included in the Lepidotidae, and placed in a pectinated position between the basal genus <i>Lepidotes</i> and the more derived members of the family (other species of <i>Scheenstia</i>, <i>Isanichthys</i> and <i>Camerichthys</i>). The nodes within the lepidotids are weakly supported. Although <i>S. bernissartensis</i> is not directly related to <i>S. mantelli</i> from the Wealden of Europe, the two species have similar palaeoenvironments and stratigraphical ranges. Taken as a whole, the ginglymodians experienced several episodes of diversification that are spatially and temporally restricted. The oldest episode involved basal ginglymodians and occurred in the Middle Triassic, in marine environments along the northern margin of the Tethys. A second episode affected the Semionotidae and occurred in freshwater environments of North America and Europe in the Late Triassic and Early Jurassic. The remaining Semionotiformes, Macrosemiidae and Callipurbeckidae, ranged from the Triassic to the Early Cretaceous and were mostly marine. Among the Lepisosteiformes, two clades, the Lepidotidae and the Lepisosteoidi, show episodes of diversification, first in marine and then in freshwater environments.
DOI: 10.6084/m9.figshare.8976116.v1
title: Revision of the subfamily Pitarinae Stewart, 1930 (<i>Eucallista</i> Dall, 1902; <i>Austrocallista</i> Erdmann & Morra, 1985; <i>Proteopitar</i> gen. nov.) from Cenozoic southern South America: systematic and phylogenetic analyses

description: Systematic and phylogenetic analyses of fossil and extant Pitarinae of the South-Western Atlantic Ocean and Chile have been performed. The group is represented by <i>Eucallista</i> Dall, 1902 (early Miocene–Recent), <i>Austrocallista</i> Erdmann & Morra, 1985 (Eocene–Pliocene) and <i>Proteopitar</i> gen. nov. (middle Miocene–Recent). <i>Eucallista</i> and <i>Austrocallista</i> have sculptured nymphs and include species previously assigned to <i>Amiantis</i> Carpenter, 1864. <i>Eucallista</i> is represented by three species: the extant <i>E. purpurata</i> (Lamarck, 1818) (Pleistocene–Recent, South-Western Atlantic Ocean from Golfo San Matías [Argentina] to Espirito Santo [Brazil]) and two fossil taxa, <i>E. laziarina</i> (Ihering, 1907) from the Miocene and Pliocene of Chile, Argentina and Uruguay, and <i>E. domeykoana</i> (Philippi, 1887) from the Miocene and Pliocene of Chile and Peru. <i>Austrocallista</i> has four taxa: <i>Austrocallista</i> sp. from the Eocene of Santa Cruz Province, <i>A. iheringi</i> (Cossmann, 1898) from the late Oligocene–middle Miocene of Patagonia, <i>A. australis</i> (Feruglio, 1935) (lectotype MGGC 607) from the early Miocene of Santa Cruz Province, and <i>A. boliviana</i> (Philippi, 1887) from the Miocene and Pliocene of Chile and Peru. <i>Proteopitar</i> gen. nov. is erected to incorporate two species previously assigned to <i>Pitar</i> Römer, 1857: <i>Proteopitar mutabilis</i> (del Río & Martínez, 1998) from the middle Miocene–late Miocene of Argentina and the Pleistocene–Recent species <i>Proteopitar patagonicus</i> (d’Orbigny, 1835–1847) (from Rio de Janeiro [Brazil] to Bahía Vera [Chubut, Argentina]). These systematic hypotheses are corroborated by the phylogenetic analysis performed, which is the first one of the subfamily that includes fossil and extant taxa based on morphological characters of the shell. In addition, a new site on the coast of Río Negro Province which contains shells of the extant species is dated as 830 Ka BP (MIS21), being the oldest record of both extant species. http://www.zoobank.org/urn:lsid:zoobank.org:pub:16519263-4F9E-41AB-A009-EAC030681826
DOI: 10.6084/m9.figshare.8975948
title: A ninth bibliography of fractional programming

description: A ninth bibliography of fractional programming
DOI: 10.6084/m9.figshare.8975951
title: Development and rigorous validation of antimalarial predictive models using machine learning approaches

description: The large collection of known and experimentally verified compounds from the ChEMBL database was used to build different classification models for predicting the antimalarial activity against <i>Plasmodium falciparum</i>. Four different machine learning methods, namely the support vector machine (SVM), random forest (RF), k-nearest neighbour (kNN) and XGBoost have been used for the development of models using the diverse antimalarial dataset from ChEMBL. A well-established feature selection framework was used to select the best subset from a larger pool of descriptors. Performance of the models was rigorously evaluated by evaluation of the applicability domain, Y-scrambling and AUC-ROC curve. Additionally, the predictive power of the models was also assessed using probability calibration and predictiveness curves. SVM and XGBoost showed the best performances, yielding an accuracy of ~85% on the independent test set. In term of probability prediction, SVM and XGBoost were well calibrated. Total gain (TG) from the predictiveness curve was more related to SVM (TG = 0.67) and XGBoost (TG = 0.75). These models also predict the high-affinity compounds from PubChem antimalarial bioassay (as external validation) with a high probability score. Our findings suggest that the selected models are robust and can be potentially useful for facilitating the discovery of antimalarial agents.
DOI: 10.6084/m9.figshare.8975951.v1
title: Development and rigorous validation of antimalarial predictive models using machine learning approaches

description: The large collection of known and experimentally verified compounds from the ChEMBL database was used to build different classification models for predicting the antimalarial activity against <i>Plasmodium falciparum</i>. Four different machine learning methods, namely the support vector machine (SVM), random forest (RF), k-nearest neighbour (kNN) and XGBoost have been used for the development of models using the diverse antimalarial dataset from ChEMBL. A well-established feature selection framework was used to select the best subset from a larger pool of descriptors. Performance of the models was rigorously evaluated by evaluation of the applicability domain, Y-scrambling and AUC-ROC curve. Additionally, the predictive power of the models was also assessed using probability calibration and predictiveness curves. SVM and XGBoost showed the best performances, yielding an accuracy of ~85% on the independent test set. In term of probability prediction, SVM and XGBoost were well calibrated. Total gain (TG) from the predictiveness curve was more related to SVM (TG = 0.67) and XGBoost (TG = 0.75). These models also predict the high-affinity compounds from PubChem antimalarial bioassay (as external validation) with a high probability score. Our findings suggest that the selected models are robust and can be potentially useful for facilitating the discovery of antimalarial agents.
DOI: 10.6084/m9.figshare.8975948.v2
title: A ninth bibliography of fractional programming

description: A ninth bibliography of fractional programming
DOI: 10.6084/m9.figshare.8975948.v1
title: A ninth bibliography of fractional programming

description: A ninth bibliography of fractional programming
DOI: 10.6084/m9.figshare.8975756
title: Supplementary Material for: A Higher Rate of Pulmonary Fungal Infection in Chronic Obstructive Pulmonary Disease Patients with Influenza in a Large Tertiary Hospital

description: <b><i>Background:</i></b> Influenza is considered a self-limiting disease. However, in patients with chronic obstructive pulmonary disease (COPD), it may result in serious outcomes during the flu season. <b><i>Objectives:</i></b> The aims of this retrospective study were to explore the characteristics of hospitalized patients with COPD complicated by influenza and determine the factors affecting the prognosis of these patients. <b><i>Method:</i></b> Demographic and clinical data were collected for 278 patients totally from the West China Hospital between January 1, 2016 and February 28, 2018. <b><i>Results:</i></b> Among the patients with influenza, the positive fungal culture rate, and the rates of antifungal drug and systemic corticosteroids use were higher for those with COPD than for those without COPD. Respiratory failure was more common in patients with influenza and COPD than in patients with influenza only, while the proportion of severe cases was higher among the former than among the latter. Among the patients with COPD, the positive fungal culture rate, particularly for <i>Aspergillus</i>, and the rate of systemic corticosteroids use were higher for those with influenza than for those without influenza. Multivariate analysis revealed that a COPD history of &gt;20 years and smoking for &gt;20 pack-years were independent factors for susceptibility of COPD patients to influenza. <b><i>Conclusions:</i></b> <i>Aspergillus</i> infection seems to be more common in patients with influenza and COPD. In addition, COPD complicated by influenza during the seasonal outbreak can easily progress to a severe disease state. Heavy smokers and patients with a prolonged COPD history are more likely to be infected by influenza.
DOI: 10.6084/m9.figshare.8975756.v1
title: Supplementary Material for: A Higher Rate of Pulmonary Fungal Infection in Chronic Obstructive Pulmonary Disease Patients with Influenza in a Large Tertiary Hospital

description: <b><i>Background:</i></b> Influenza is considered a self-limiting disease. However, in patients with chronic obstructive pulmonary disease (COPD), it may result in serious outcomes during the flu season. <b><i>Objectives:</i></b> The aims of this retrospective study were to explore the characteristics of hospitalized patients with COPD complicated by influenza and determine the factors affecting the prognosis of these patients. <b><i>Method:</i></b> Demographic and clinical data were collected for 278 patients totally from the West China Hospital between January 1, 2016 and February 28, 2018. <b><i>Results:</i></b> Among the patients with influenza, the positive fungal culture rate, and the rates of antifungal drug and systemic corticosteroids use were higher for those with COPD than for those without COPD. Respiratory failure was more common in patients with influenza and COPD than in patients with influenza only, while the proportion of severe cases was higher among the former than among the latter. Among the patients with COPD, the positive fungal culture rate, particularly for <i>Aspergillus</i>, and the rate of systemic corticosteroids use were higher for those with influenza than for those without influenza. Multivariate analysis revealed that a COPD history of &gt;20 years and smoking for &gt;20 pack-years were independent factors for susceptibility of COPD patients to influenza. <b><i>Conclusions:</i></b> <i>Aspergillus</i> infection seems to be more common in patients with influenza and COPD. In addition, COPD complicated by influenza during the seasonal outbreak can easily progress to a severe disease state. Heavy smokers and patients with a prolonged COPD history are more likely to be infected by influenza.
DOI: 10.6084/m9.figshare.8974817
title: HBCx_95_scChIPseq_mm10_50kb.tsv

description: The samples correspond to the mouse cells from patient-derived xenograft (PDX) originating from two different human donors. The HBCx-22 and HBCx-22-TamR datasets correspond to mouse cells from a pair of luminal ER<sup>+</sup> breast PDXs: HBCx-22, responsive to Tamoxifen and HBCx-22-TamR, resistant to Tamoxifen. The HBCx-95 and HBCx-95-CapaR correspond to a triple-negative breast cancer (TNBC) tumor model of acquired resistance to chemotherapy. Row names of the matrices are 50,000-bp binned regions; Column names are barcodes corresponding to single cell; Cells contains raw counts, in mm10 reference.
DOI: 10.6084/m9.figshare.8974814
title: HBCx_22_TamR_scChIPseq_mm10_50kb.tsv

description: The samples correspond to the mouse cells from patient-derived xenograft (PDX) originating from two different human donors. The HBCx-22 and HBCx-22-TamR datasets correspond to mouse cells from a pair of luminal ER<sup>+</sup> breast PDXs: HBCx-22, responsive to Tamoxifen and HBCx-22-TamR, resistant to Tamoxifen. The HBCx-95 and HBCx-95-CapaR correspond to a triple-negative breast cancer (TNBC) tumor model of acquired resistance to chemotherapy. Row names of the matrices are 50,000-bp binned regions; Column names are barcodes corresponding to single cell; Cells contains raw counts, in mm10 reference.
DOI: 10.6084/m9.figshare.8974811
title: HBCx_95_CapaR_scChIPseq_mm10_50kb.tsv

description: The samples correspond to the mouse cells from patient-derived xenograft (PDX) originating from two different human donors. The HBCx-22 and HBCx-22-TamR datasets correspond to mouse cells from a pair of luminal ER<sup>+</sup> breast PDXs: HBCx-22, responsive to Tamoxifen and HBCx-22-TamR, resistant to Tamoxifen. The HBCx-95 and HBCx-95-CapaR correspond to a triple-negative breast cancer (TNBC) tumor model of acquired resistance to chemotherapy. Row names of the matrices are 50,000-bp binned regions; Column names are barcodes corresponding to single cell; Cells contains raw counts, in mm10 reference.
DOI: 10.6084/m9.figshare.8974250
title: ChromSCape_single_cell_ChIP_seq_matrices

description: @page { margin: 0.79in } p { margin-bottom: 0.1in; direction: ltr; line-height: 120%; text-align: left; orphans: 2; widows: 2 } a:link { so-language: zxx } a.western:visited { so-language: fr-FR } a.cjk:visited { so-language: zh-CN } a.ctl:visited { so-language: hi-IN } @page { margin: 0.79in } p { margin-bottom: 0.1in; direction: ltr; line-height: 120%; text-align: left; orphans: 2; widows: 2 } a:link { so-language: zxx } a.western:visited { so-language: fr-FR } a.cjk:visited { so-language: zh-CN } a.ctl:visited { so-language: hi-IN } Mouse stromal cells from PDX count matrices reformatted to be inputed in ChromSCape (https://github.com/vallotlab/ChromSCape), two of which had not been analyzed in our previous study (Grosselin et al., 2019, https://www.nature.com/articles/s41588-019-0424-9). @page { margin: 0.79in } p { margin-bottom: 0.1in; direction: ltr; line-height: 120%; text-align: left; orphans: 2; widows: 2 } a:link { so-language: zxx } a.western:visited { so-language: fr-FR } a.cjk:visited { so-language: zh-CN } a.ctl:visited { so-language: hi-IN } The samples correspond to the mouse cells from patient-derived xenograft (PDX) originating from two different human donors. The HBCx-22 and HBCx-22-TamR datasets correspond to mouse cells from a pair of luminal ER<sup>+</sup> breast PDXs: HBCx-22, responsive to Tamoxifen and HBCx-22-TamR, resistant to Tamoxifen. The HBCx-95 and HBCx-95-CapaR correspond to a triple-negative breast cancer (TNBC) tumor model of acquired resistance to chemotherapy. Row names of the matrices are 50,000-bp binned regions; Column names are barcodes corresponding to single cell; Cells contains raw counts, in mm10 reference.
DOI: 10.6084/m9.figshare.8974808
title: HBCx_22_scChIPseq_mm10_50kb.tsv

description: The samples correspond to the mouse cells from patient-derived xenograft (PDX) originating from two different human donors. The HBCx-22 and HBCx-22-TamR datasets correspond to mouse cells from a pair of luminal ER<sup>+</sup> breast PDXs: HBCx-22, responsive to Tamoxifen and HBCx-22-TamR, resistant to Tamoxifen. The HBCx-95 and HBCx-95-CapaR correspond to a triple-negative breast cancer (TNBC) tumor model of acquired resistance to chemotherapy. Row names of the matrices are 50,000-bp binned regions; Column names are barcodes corresponding to single cell; Cells contains raw counts, in mm10 reference.
DOI: 10.6084/m9.figshare.8974808.v1
title: HBCx_22_scChIPseq_mm10_50kb.tsv

description: The samples correspond to the mouse cells from patient-derived xenograft (PDX) originating from two different human donors. The HBCx-22 and HBCx-22-TamR datasets correspond to mouse cells from a pair of luminal ER<sup>+</sup> breast PDXs: HBCx-22, responsive to Tamoxifen and HBCx-22-TamR, resistant to Tamoxifen. The HBCx-95 and HBCx-95-CapaR correspond to a triple-negative breast cancer (TNBC) tumor model of acquired resistance to chemotherapy. Row names of the matrices are 50,000-bp binned regions; Column names are barcodes corresponding to single cell; Cells contains raw counts, in mm10 reference.
DOI: 10.6084/m9.figshare.8974250.v1
title: ChromSCape_single_cell_ChIP_seq_matrices

description: @page { margin: 0.79in } p { margin-bottom: 0.1in; direction: ltr; line-height: 120%; text-align: left; orphans: 2; widows: 2 } a:link { so-language: zxx } a.western:visited { so-language: fr-FR } a.cjk:visited { so-language: zh-CN } a.ctl:visited { so-language: hi-IN } @page { margin: 0.79in } p { margin-bottom: 0.1in; direction: ltr; line-height: 120%; text-align: left; orphans: 2; widows: 2 } a:link { so-language: zxx } a.western:visited { so-language: fr-FR } a.cjk:visited { so-language: zh-CN } a.ctl:visited { so-language: hi-IN } Mouse stromal cells from PDX count matrices reformatted to be inputed in ChromSCape (https://github.com/vallotlab/ChromSCape), two of which had not been analyzed in our previous study (Grosselin et al., 2019, https://www.nature.com/articles/s41588-019-0424-9). @page { margin: 0.79in } p { margin-bottom: 0.1in; direction: ltr; line-height: 120%; text-align: left; orphans: 2; widows: 2 } a:link { so-language: zxx } a.western:visited { so-language: fr-FR } a.cjk:visited { so-language: zh-CN } a.ctl:visited { so-language: hi-IN } The samples correspond to the mouse cells from patient-derived xenograft (PDX) originating from two different human donors. The HBCx-22 and HBCx-22-TamR datasets correspond to mouse cells from a pair of luminal ER<sup>+</sup> breast PDXs: HBCx-22, responsive to Tamoxifen and HBCx-22-TamR, resistant to Tamoxifen. The HBCx-95 and HBCx-95-CapaR correspond to a triple-negative breast cancer (TNBC) tumor model of acquired resistance to chemotherapy. Row names of the matrices are 50,000-bp binned regions; Column names are barcodes corresponding to single cell; Cells contains raw counts, in mm10 reference.
DOI: 10.6084/m9.figshare.8972222
title: Supplementary Material for: Survivin Impairs the Apoptotic Machinery in CD4<sup>+</sup> T Cells of Patients with Ulcerative Colitis

description: <b><i>Background:</i></b> The increase in CD4<sup>+</sup> T cell infiltration and overproduction of CD4<sup>+</sup> T cell-associated cytokines have been observed in the inflamed colon mucosa of patients with ulcerative colitis (UC); the underlying mechanisms are not fully understood. Survivin plays a critical role in the interference with apoptotic machinery. This study aims to elucidate the role of survivin in the interference with the apoptotic machinery in CD4<sup>+</sup> T cells of UC patients. <b><i>Methods:</i></b> Peripheral blood samples were collected from UC patients (UC group) and healthy subjects (healthy group). The apoptotic status in CD4<sup>+</sup> T cells was analyzed by flow cytometry. <b><i>Results:</i></b> We observed that the expression of survivin was significantly higher in CD4<sup>+</sup> T cells of UC patients than in healthy subjects. UC CD4<sup>+</sup> T cells were resistant to apoptosis induction. A complex of survivin and c-Myc, the transcription factor of FasL, was detected in CD4<sup>+</sup> T cells in UC patients, which prevented the binding of c-Myc to the FasL promoter and interfered with the expression of FasL. Increased expression of survivin prevented the activation-induced CD4<sup>+</sup> T cells from apoptosis. <b><i>Conclusions:</i></b> The data indicate that UC CD4<sup>+</sup> T cells express high levels of survivin, which impairs the apoptotic machinery in CD4<sup>+</sup> T cells and prevents the activation-induced CD4<sup>+</sup> T cell apoptosis. Therefore, target therapy against survivin has translational potential in the treatment of UC patients.
DOI: 10.26180/5d356d93a2a60
title: Experiment results

description: These data files are for the two experiments of the study presented in "Robotic Hierarchical Graph Neurons. A novel implementation of HGN for swarm robotic behaviour control".
DOI: 10.6084/m9.figshare.8971529
title: original data.rar

description: the original data during constructing three lactose-consuming strains. in addition, the relationship between trehalose and tolerance was studied.
DOI: 10.6084/m9.figshare.8971118
title: melanism and body size in the grass snake

description: Data on the body size (snout vent length) in grass snake of typical and melanistic phenotype from south-eastern Poland.
DOI: 10.6084/m9.figshare.8971529.v1
title: original data.rar

description: the original data during constructing three lactose-consuming strains. in addition, the relationship between trehalose and tolerance was studied.
DOI: 10.6084/m9.figshare.8971118.v1
title: melanism and body size in the grass snake

description: Data on the body size (snout vent length) in grass snake of typical and melanistic phenotype from south-eastern Poland.