cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.9162152
title: Whole Genome Sequence Alignments and Phylogenetic Trees

description: Includes intermediate files and custom scripts used to create the WGS tree. Also includes a list of GC#s specifying genomes used in the creation of the tree.
DOI: 10.6084/m9.figshare.9162143
title: Type 1 Secretion System Component Alignments in FASTA Format

description: Alignments of Type 1 Secretion System components from Legionella species.
DOI: 10.6084/m9.figshare.9162140
title: pat 15 MRI

description: Admire, Pinnacle, and Velocity denote structure sets after a deformable or rigid registration was applied to the MRI holding the CT as primary.
DOI: 10.6084/m9.figshare.9162143.v1
title: Type 1 Secretion System Component Alignments in FASTA Format

description: Alignments of Type 1 Secretion System components from Legionella species.
DOI: 10.6084/m9.figshare.9162146.v1
title: T1SS BLAST Results and Sequence IDs

description: Blast Results describing T1SSs in the Legionella genus.
DOI: 10.6084/m9.figshare.9162137
title: pat 15 CT

description: Admire, Pinnacle, and Velocity denote structure sets after a deformable or rigid registration was applied to the MRI holding the CT as primary.
DOI: 10.6084/m9.figshare.9162140.v1
title: pat 15 MRI

description: Admire, Pinnacle, and Velocity denote structure sets after a deformable or rigid registration was applied to the MRI holding the CT as primary.
DOI: 10.6084/m9.figshare.9162152.v1
title: Whole Genome Sequence Alignments and Phylogenetic Trees

description: Includes intermediate files and custom scripts used to create the WGS tree. Also includes a list of GC#s specifying genomes used in the creation of the tree.
DOI: 10.6084/m9.figshare.9162131
title: pat 14 CT

description: Admire, Pinnacle, and Velocity denote structure sets after a deformable or rigid registration was applied to the MRI holding the CT as primary.
DOI: 10.6084/m9.figshare.9162134
title: pat 14 MRI

description: Admire, Pinnacle, and Velocity denote structure sets after a deformable or rigid registration was applied to the MRI holding the CT as primary.
DOI: 10.6084/m9.figshare.9162131.v1
title: pat 14 CT

description: Admire, Pinnacle, and Velocity denote structure sets after a deformable or rigid registration was applied to the MRI holding the CT as primary.
DOI: 10.6084/m9.figshare.9162134.v1
title: pat 14 MRI

description: Admire, Pinnacle, and Velocity denote structure sets after a deformable or rigid registration was applied to the MRI holding the CT as primary.
DOI: 10.6084/m9.figshare.9162014
title: Bins_Vigneron_SAS2A_Ano_Ster.rar

description: Genomic bins associated with <b>Ultra-small and abundant: Candidate Phyla Radiation members are potential catalysts of carbon transformation in a thermokarst lake ecosystem </b> Adrien Vigneron,<sup>1,2,3</sup>* Perrine Cruaud,<sup>3,5</sup> Valérie Langlois,<sup>2,3,5</sup> Connie Lovejoy,<sup>1,2,3,4</sup> Alexander I. Culley,<sup>2,3,5</sup> Warwick F. Vincent<sup>1,2,3</sup> <sup>1</sup>Département de Biologie, Université Laval, Québec, QC, Canada <sup>2</sup>Centre d’études nordiques (CEN), Takuvik Joint International Laboratory, Université Laval, Québec, QC, Canada <sup>3</sup>Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC, Canada <sup>4</sup>Québec Océan, Université Laval, Québec, QC Canada <sup>5</sup>Département de Biochimie, de Microbiologie et de Bio-informatique, Université Laval, Québec, QC, Canada
DOI: 10.6084/m9.figshare.9162014.v1
title: Bins_Vigneron_SAS2A_Ano_Ster.rar

description: Genomic bins associated with <b>Ultra-small and abundant: Candidate Phyla Radiation members are potential catalysts of carbon transformation in a thermokarst lake ecosystem </b> Adrien Vigneron,<sup>1,2,3</sup>* Perrine Cruaud,<sup>3,5</sup> Valérie Langlois,<sup>2,3,5</sup> Connie Lovejoy,<sup>1,2,3,4</sup> Alexander I. Culley,<sup>2,3,5</sup> Warwick F. Vincent<sup>1,2,3</sup> <sup>1</sup>Département de Biologie, Université Laval, Québec, QC, Canada <sup>2</sup>Centre d’études nordiques (CEN), Takuvik Joint International Laboratory, Université Laval, Québec, QC, Canada <sup>3</sup>Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC, Canada <sup>4</sup>Québec Océan, Université Laval, Québec, QC Canada <sup>5</sup>Département de Biochimie, de Microbiologie et de Bio-informatique, Université Laval, Québec, QC, Canada
DOI: 10.6084/m9.figshare.9159869
title: Data_File_9.docx

description: List of primers used for pol II ChIP-qPCR in HEK293, HEK293-Flp, CFIm25KD, and CFIm68KD.
DOI: 10.6084/m9.figshare.9159869.v1
title: Data_File_9.docx

description: List of primers used for pol II ChIP-qPCR in HEK293, HEK293-Flp, CFIm25KD, and CFIm68KD.
DOI: 10.6084/m9.figshare.9159824
title: Risk of bias assessments for Cochrane Review 'Altering the availability or proximity of food, alcohol, and tobacco products to change their selection and consumption' (2019)

description: Risk of bias assessments for Cochrane Review 'Altering the availability or proximity of food, alcohol, and tobacco products to change their selection and consumption' (2019)
DOI: 10.6084/m9.figshare.9159746
title: Allplex vs Aptima

description: Database of the comparison of Allplex assay and Aptima assay.<br><br>Abbreviations:<br>CT: C. trachomatis;GC: N. gonorrhoeae; MG: M. genitalium TV: T. vaginalis; M: Male; F:Female
DOI: 10.6084/m9.figshare.9159746.v2
title: Allplex vs Aptima

description: Database of the comparison of Allplex assay and Aptima assay.<br><br>Abbreviations:<br>CT: C. trachomatis;GC: N. gonorrhoeae; MG: M. genitalium TV: T. vaginalis; M: Male; F:Female
DOI: 10.6084/m9.figshare.9159530
title: Supplementary Material for: Carboplatin in Combination with Oral or Intravenous Etoposide for Extra-Pulmonary, Poorly-Differentiated Neuroendocrine Carcinomas

description: <b><i>Background:</i></b> Carboplatin-etoposide (CarboEtop) is a 1st-line option for patients with advanced extra-pulmonary (EP), poorly-differentiated (PD) neuroendocrine carcinoma (NEC). Different schedules are used in clinical practice and randomised evidence is lacking. <b><i>Objectives:</i></b> To provide real-life outcomes of carboplatin combined with oral or intravenous (IV) etoposide (Etop) in advanced EP-PD-NEC, from 2 specialist centres. <b><i>Methods:</i></b> Activity/efficacy/toxicity data of CarboEtop were collected retrospectively and analysed. <b><i>Results:</i></b> We identified 113 patients; median age: 65.8 years; male: 64%; gastro-entero-pancreatic origin: 54%; stage IV: 90%; median Ki-67: 70%; median follow-up: 11.5 months. A total of 123 courses of CarboEtop (oral: 45%; IV: 55%) were administered; 106 (86%) 1st-line, 16 (13%) 2nd-line, and 1 (1%) 3rd-line. Disease control rate: 74.5% in 1st-line and 69.2% in 2nd/3rd-line, with no significant difference between oral and IV Etop in 1st-line (69.8 vs. 80.8%, <i>p</i> = 0.237). Median progression-free survival (PFS): 6.0 and 4.5 months in 1st-line and 2nd/3rd-line, respectively. Overall survival (OS): 11.5 and 12.5 months in 1st-line and 2nd/3rd-line, respectively. The schedule (oral versus IV Etop) did not impact on 1st-line PFS (5.6 vs. 6.2 months, <i>p</i> = 0.179), although there was a trend towards shorter OS (8.9 vs. 12.1 months, <i>p</i> = 0.069). Liver metastases correlated with worse 1st-line PFS (<i>p</i> = 0.015) and 1st-line OS (<i>p</i> &lt; 0.001) on multivariable analysis. The commonest grade 3–4 adverse event was myelosuppression (49%), with comparable toxicity between oral and IV Etop, except for venous thromboembolism (12.5 vs. 1.7%, <i>p</i> = 0.04). <b><i>Conclusions:</i></b> CarboEtop for advanced EP-PD-NEC is active, effective, and well-tolerated. Oral and IV Etop schedules are associated with comparable toxicity; activity should be compared in larger cohorts.
DOI: 10.6084/m9.figshare.9159530.v1
title: Supplementary Material for: Carboplatin in Combination with Oral or Intravenous Etoposide for Extra-Pulmonary, Poorly-Differentiated Neuroendocrine Carcinomas

description: <b><i>Background:</i></b> Carboplatin-etoposide (CarboEtop) is a 1st-line option for patients with advanced extra-pulmonary (EP), poorly-differentiated (PD) neuroendocrine carcinoma (NEC). Different schedules are used in clinical practice and randomised evidence is lacking. <b><i>Objectives:</i></b> To provide real-life outcomes of carboplatin combined with oral or intravenous (IV) etoposide (Etop) in advanced EP-PD-NEC, from 2 specialist centres. <b><i>Methods:</i></b> Activity/efficacy/toxicity data of CarboEtop were collected retrospectively and analysed. <b><i>Results:</i></b> We identified 113 patients; median age: 65.8 years; male: 64%; gastro-entero-pancreatic origin: 54%; stage IV: 90%; median Ki-67: 70%; median follow-up: 11.5 months. A total of 123 courses of CarboEtop (oral: 45%; IV: 55%) were administered; 106 (86%) 1st-line, 16 (13%) 2nd-line, and 1 (1%) 3rd-line. Disease control rate: 74.5% in 1st-line and 69.2% in 2nd/3rd-line, with no significant difference between oral and IV Etop in 1st-line (69.8 vs. 80.8%, <i>p</i> = 0.237). Median progression-free survival (PFS): 6.0 and 4.5 months in 1st-line and 2nd/3rd-line, respectively. Overall survival (OS): 11.5 and 12.5 months in 1st-line and 2nd/3rd-line, respectively. The schedule (oral versus IV Etop) did not impact on 1st-line PFS (5.6 vs. 6.2 months, <i>p</i> = 0.179), although there was a trend towards shorter OS (8.9 vs. 12.1 months, <i>p</i> = 0.069). Liver metastases correlated with worse 1st-line PFS (<i>p</i> = 0.015) and 1st-line OS (<i>p</i> &lt; 0.001) on multivariable analysis. The commonest grade 3–4 adverse event was myelosuppression (49%), with comparable toxicity between oral and IV Etop, except for venous thromboembolism (12.5 vs. 1.7%, <i>p</i> = 0.04). <b><i>Conclusions:</i></b> CarboEtop for advanced EP-PD-NEC is active, effective, and well-tolerated. Oral and IV Etop schedules are associated with comparable toxicity; activity should be compared in larger cohorts.
DOI: 10.6084/m9.figshare.9159533.v1
title: Model Mis-Specification of Generalized Gamma Distribution for Accelerated Lifetime Censored Data

description: The performance of reliability inference strongly depends on the modeling of the product’s lifetime distribution. Many products have complex lifetime distributions whose optimal settings are not easily found. Practitioners prefer to utilize simpler lifetime distribution to facilitate the data modeling process while knowing the true distribution. Therefore, the effects of model mis-specification on the product’s lifetime prediction is an interesting research area. This paper presents some results on the behavior of the relative bias (<i>RB</i>) and relative variability (<i>RV</i>) of <i>p</i>-th quantile of the accelerated lifetime (ALT) experiment when the generalized Gamma (<i>GG</i><sub>3</sub>) distribution is incorrectly specified as Lognormal or Weibull distribution. Both complete and censored ALT models are analyzed. At first, the analytical expressions for the expected log-likelihood function of the mis-specified model with respect to the true model is derived. Consequently, the best parameter for the incorrect model is obtained directly via a numerical optimization to achieve a higher accuracy model than the wrong one for the end-goal task. The results demonstrate that the tail quantiles are significantly overestimated (underestimated) when data is wrongly fitted by Lognormal (Weibull) distribution. Moreover, the variability of the tail quantiles is significantly enlarged when the model is incorrectly specified as Lognormal or Weibull distribution. Precisely, the effect on the tail quantiles is more significant when the sample size and censoring ratio are not large enough. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.9159509
title: How classifiers facilitate predictive processing in L1 and L2 Chinese: the role of semantic and grammatical cues

description: This study examines long-standing claims that L2 learners rely more on non-grammatical than on grammatical information during sentence processing compared to native speakers. Nominal classifiers in Mandarin Chinese offer an ideal opportunity to test this claim, as they simultaneously encode semantic as well as grammatical form-class cues about co-occurring nouns. This paper reports findings from a visual world eye-tracking experiment with L1 and L2 speakers of Mandarin, which was designed to assess listeners’ relative reliance on these two concurrently available cues when creating expectations about an upcoming noun in a sentence. Results show that L2 listeners experienced greater competition than L1 listeners from nouns that were grammatically incompatible with the classifier they heard but shared semantic features associated with it. The greater reliance on semantic cues observed in L2 processing is argued to be an effect of adaptation to the relative reliability of information, serving to maximise L2 processing efficiency.
DOI: 10.6084/m9.figshare.9159509.v2
title: How classifiers facilitate predictive processing in L1 and L2 Chinese: the role of semantic and grammatical cues

description: This study examines long-standing claims that L2 learners rely more on non-grammatical than on grammatical information during sentence processing compared to native speakers. Nominal classifiers in Mandarin Chinese offer an ideal opportunity to test this claim, as they simultaneously encode semantic as well as grammatical form-class cues about co-occurring nouns. This paper reports findings from a visual world eye-tracking experiment with L1 and L2 speakers of Mandarin, which was designed to assess listeners’ relative reliance on these two concurrently available cues when creating expectations about an upcoming noun in a sentence. Results show that L2 listeners experienced greater competition than L1 listeners from nouns that were grammatically incompatible with the classifier they heard but shared semantic features associated with it. The greater reliance on semantic cues observed in L2 processing is argued to be an effect of adaptation to the relative reliability of information, serving to maximise L2 processing efficiency.
DOI: 10.6084/m9.figshare.9159509.v1
title: How classifiers facilitate predictive processing in L1 and L2 Chinese: the role of semantic and grammatical cues

description: This study examines long-standing claims that L2 learners rely more on non-grammatical than on grammatical information during sentence processing compared to native speakers. Nominal classifiers in Mandarin Chinese offer an ideal opportunity to test this claim, as they simultaneously encode semantic as well as grammatical form-class cues about co-occurring nouns. This paper reports findings from a visual world eye-tracking experiment with L1 and L2 speakers of Mandarin, which was designed to assess listeners’ relative reliance on these two concurrently available cues when creating expectations about an upcoming noun in a sentence. Results show that L2 listeners experienced greater competition than L1 listeners from nouns that were grammatically incompatible with the classifier they heard but shared semantic features associated with it. The greater reliance on semantic cues observed in L2 processing is argued to be an effect of adaptation to the relative reliability of information, serving to maximise L2 processing efficiency.
DOI: 10.6084/m9.figshare.9155669
title: Convolved images tagPAINT

description: Gaussian convolved images from ThuderSTORM of tagPAINT data
DOI: 10.6084/m9.figshare.9155207
title: With a little help from my friends: ministerial alignment and public spending composition in parliamentary democracies

description: The determinants of public spending composition have been studied from three broad perspectives in the scholarly literature: functional economic pressures, institutional constraints and party-political determinants. This article engages with the third perspective by placing intra-governmental dynamics in the centre of the analysis. Building on the portfolio allocation approach in the coalition formation literature and the common pool perspective in public budgeting, I theorize that spending ministers with party-political backing from the prime minister or the finance minister are in a privileged position to obtain extra funding for their policy jurisdictions compared to their colleagues without such support or without any partisan affiliation (non-partisan ministers). Via a system of equations on six spending categories using seemingly unrelated regressions as well as Prais–Winsten panel regressions on a sample of 32 parliamentary democracies over two decades, I offer mixed evidence for the impact of party-political alignment. While the relative share of four of the six budget categories systematically increases under the party-political alignment of the prime minister, the impact of finance minister alignment is only significant for the economic budget.
DOI: 10.6084/m9.figshare.9155669.v1
title: Convolved images tagPAINT

description: Gaussian convolved images from ThuderSTORM of tagPAINT data
DOI: 10.6084/m9.figshare.9155207.v1
title: With a little help from my friends: ministerial alignment and public spending composition in parliamentary democracies

description: The determinants of public spending composition have been studied from three broad perspectives in the scholarly literature: functional economic pressures, institutional constraints and party-political determinants. This article engages with the third perspective by placing intra-governmental dynamics in the centre of the analysis. Building on the portfolio allocation approach in the coalition formation literature and the common pool perspective in public budgeting, I theorize that spending ministers with party-political backing from the prime minister or the finance minister are in a privileged position to obtain extra funding for their policy jurisdictions compared to their colleagues without such support or without any partisan affiliation (non-partisan ministers). Via a system of equations on six spending categories using seemingly unrelated regressions as well as Prais–Winsten panel regressions on a sample of 32 parliamentary democracies over two decades, I offer mixed evidence for the impact of party-political alignment. While the relative share of four of the six budget categories systematically increases under the party-political alignment of the prime minister, the impact of finance minister alignment is only significant for the economic budget.
DOI: 10.6084/m9.figshare.9153215
title: Dataset for: UBR5 interacts with the H/ACA RNP complex and regulates ribosomal RNA biogenesis in embryonic stem cells

description: UBR5 protein is involved in distinct processes such as transcriptional regulation and development. UBR5 is highly upregulated in embryonic stem cells (ESCs) whereas its expression decreases with differentiation, suggesting a role of UBR5 in ESC function. However, little is known about how UBR5 regulates ESC identity. Here, we define the protein interactome of UBR5 in ESCs and find interactions with distinct components of the H/ACA ribonucleoprotein complex, which is required for proper maturation of ribosomal RNA (rRNA). Notably, loss of UBR5 induces an abnormal accumulation of rRNA processing intermediates, resulting in diminished ribosomal levels. Consequentially, lack of UBR5 triggers p53 levels and a concomitant decrease in cellular proliferation rates. Thus, our results indicate a link between UBR5 and rRNA maturation.
DOI: 10.6084/m9.figshare.9152393
title: Trip Length Distributions in Nanjing

description: This dataset provides trip length distributions in meters for three type of travelers in Nanjing, which includes the permanent resident, the flowing travelers and the transit travelers.
DOI: 10.6084/m9.figshare.9153215.v1
title: Dataset for: UBR5 interacts with the H/ACA RNP complex and regulates ribosomal RNA biogenesis in embryonic stem cells

description: UBR5 protein is involved in distinct processes such as transcriptional regulation and development. UBR5 is highly upregulated in embryonic stem cells (ESCs) whereas its expression decreases with differentiation, suggesting a role of UBR5 in ESC function. However, little is known about how UBR5 regulates ESC identity. Here, we define the protein interactome of UBR5 in ESCs and find interactions with distinct components of the H/ACA ribonucleoprotein complex, which is required for proper maturation of ribosomal RNA (rRNA). Notably, loss of UBR5 induces an abnormal accumulation of rRNA processing intermediates, resulting in diminished ribosomal levels. Consequentially, lack of UBR5 triggers p53 levels and a concomitant decrease in cellular proliferation rates. Thus, our results indicate a link between UBR5 and rRNA maturation.
DOI: 10.6084/m9.figshare.9152393.v1
title: Trip Length Distributions in Nanjing

description: This dataset provides trip length distributions in meters for three type of travelers in Nanjing, which includes the permanent resident, the flowing travelers and the transit travelers.
DOI: 10.6084/m9.figshare.9145148
title: Supporting data for figures

description: Halo diameter (mm) of gram positive and gram negative bacteria. Hydro-alcoholic extract (10, 20, 40 and 60 mg/ml) and halo diameter of gram positive (<i>Bacillus subtilis, Staphylococcus aureus</i>) and gram negative (<i>Pseudomonas aeruginosa, Salmonella typhi and Escherica coli</i>) bacteria
DOI: 10.6084/m9.figshare.9145148.v1
title: Supporting data for figures

description: Halo diameter (mm) of gram positive and gram negative bacteria. Hydro-alcoholic extract (10, 20, 40 and 60 mg/ml) and halo diameter of gram positive (<i>Bacillus subtilis, Staphylococcus aureus</i>) and gram negative (<i>Pseudomonas aeruginosa, Salmonella typhi and Escherica coli</i>) bacteria
DOI: 10.6084/m9.figshare.9109160
title: Additional file 3: of Molecular evolution of mammalian genes with epistatic interactions in fertilization

description: Appendix S3. Summary of species names, accession numbers, and Newick strings used in codon model analyses (XLSX 51 kb)
DOI: 10.6084/m9.figshare.9109160.v1
title: Additional file 3: of Molecular evolution of mammalian genes with epistatic interactions in fertilization

description: Appendix S3. Summary of species names, accession numbers, and Newick strings used in codon model analyses (XLSX 51 kb)
DOI: 10.6084/m9.figshare.9109151
title: Additional file 2: of Molecular evolution of mammalian genes with epistatic interactions in fertilization

description: Appendix S2. Input files for codon model analyses (alignments, Newick strings) in fasta format (ZIP 91 kb)
DOI: 10.6084/m9.figshare.9109142
title: Additional file 1: of Molecular evolution of mammalian genes with epistatic interactions in fertilization

description: Appendix S1. aBSREL and MEME output files, and summary of codon model analyses. (ZIP 2616 kb)
DOI: 10.6084/m9.figshare.9109151.v1
title: Additional file 2: of Molecular evolution of mammalian genes with epistatic interactions in fertilization

description: Appendix S2. Input files for codon model analyses (alignments, Newick strings) in fasta format (ZIP 91 kb)
DOI: 10.6084/m9.figshare.9109142.v1
title: Additional file 1: of Molecular evolution of mammalian genes with epistatic interactions in fertilization

description: Appendix S1. aBSREL and MEME output files, and summary of codon model analyses. (ZIP 2616 kb)
DOI: 10.6084/m9.figshare.9109130
title: Additional file 8: of Prediction of advanced colonic neoplasm in symptomatic patients: a scoring system to prioritize colonoscopy (COLONOFIT study)

description: Dataset supporting the conclusions of this article. (ZIP 1179 kb)
DOI: 10.6084/m9.figshare.9109130.v1
title: Additional file 8: of Prediction of advanced colonic neoplasm in symptomatic patients: a scoring system to prioritize colonoscopy (COLONOFIT study)

description: Dataset supporting the conclusions of this article. (ZIP 1179 kb)