cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.8294696
title: Prediction of volume of distribution in humans: analysis of eight methods and their application in drug discovery

description: The performance of eight different methods to predict human volume of distribution (VD<sub>ss</sub>) using a large data set (<i>N</i> &gt; 100) was evaluated.The accuracy was assessed by the end points % within two-fold and absolute average fold error (AAFE). The ability to rank order was accessed by the σ and bias was examined using average fold error. Significance of observed differences was established using statistical permutation testing.The Rodgers-Lukova equation, a tissue composition model, for acids and single species scaling based on rat for other ion classes showed the best results in absence of non-rodent data.The semimechanistic Øie-Tozer model based on all thee preclinical species showed the best performance overall (81% within two-fold, AAFE 1.55, σ 0.62). This was not statistically significantly better at the 95% confidence level than the same model based on two preclinical species or single species scaling from monkey. Thus, the use of primates appears difficult to justify when the sole goal is to extrapolate human volume of distribution. The performance of eight different methods to predict human volume of distribution (VD<sub>ss</sub>) using a large data set (<i>N</i> &gt; 100) was evaluated. The accuracy was assessed by the end points % within two-fold and absolute average fold error (AAFE). The ability to rank order was accessed by the σ and bias was examined using average fold error. Significance of observed differences was established using statistical permutation testing. The Rodgers-Lukova equation, a tissue composition model, for acids and single species scaling based on rat for other ion classes showed the best results in absence of non-rodent data. The semimechanistic Øie-Tozer model based on all thee preclinical species showed the best performance overall (81% within two-fold, AAFE 1.55, σ 0.62). This was not statistically significantly better at the 95% confidence level than the same model based on two preclinical species or single species scaling from monkey. Thus, the use of primates appears difficult to justify when the sole goal is to extrapolate human volume of distribution.
DOI: 10.6084/m9.figshare.8294696.v1
title: Prediction of volume of distribution in humans: analysis of eight methods and their application in drug discovery

description: The performance of eight different methods to predict human volume of distribution (VD<sub>ss</sub>) using a large data set (<i>N</i> &gt; 100) was evaluated.The accuracy was assessed by the end points % within two-fold and absolute average fold error (AAFE). The ability to rank order was accessed by the σ and bias was examined using average fold error. Significance of observed differences was established using statistical permutation testing.The Rodgers-Lukova equation, a tissue composition model, for acids and single species scaling based on rat for other ion classes showed the best results in absence of non-rodent data.The semimechanistic Øie-Tozer model based on all thee preclinical species showed the best performance overall (81% within two-fold, AAFE 1.55, σ 0.62). This was not statistically significantly better at the 95% confidence level than the same model based on two preclinical species or single species scaling from monkey. Thus, the use of primates appears difficult to justify when the sole goal is to extrapolate human volume of distribution. The performance of eight different methods to predict human volume of distribution (VD<sub>ss</sub>) using a large data set (<i>N</i> &gt; 100) was evaluated. The accuracy was assessed by the end points % within two-fold and absolute average fold error (AAFE). The ability to rank order was accessed by the σ and bias was examined using average fold error. Significance of observed differences was established using statistical permutation testing. The Rodgers-Lukova equation, a tissue composition model, for acids and single species scaling based on rat for other ion classes showed the best results in absence of non-rodent data. The semimechanistic Øie-Tozer model based on all thee preclinical species showed the best performance overall (81% within two-fold, AAFE 1.55, σ 0.62). This was not statistically significantly better at the 95% confidence level than the same model based on two preclinical species or single species scaling from monkey. Thus, the use of primates appears difficult to justify when the sole goal is to extrapolate human volume of distribution.
DOI: 10.6084/m9.figshare.8294669
title: Uptake and pharmacokinetics of cefuroxime in rabbits after intravitreal, intracameral, and topical dosing: relevance to human ocular injection of cefuroxime

description: Cefuroxime is one of the widely used antibiotics. The objective of this study was to determine pharmacokinetics and disposition in various ocular tissues following topical (TOP), intracameral (IC) and intravitreal (IVT) administration of cefuroxime to rabbits.Following TOP, IC and IVT dosing plasma and various ocular tissues (aqueous humor (AH), vitreous humor (VH), conjunctiva, trabecular mesh (TM), lens and retina-choroid (RC)) were collected and analyzed to understand the disposition of cefuroxime. Postintravenous administration plasma samples were collected to determine the systemic pharmacokinetics.Post-TOP dosing cefuroxime concentrations were observed only in conjunctiva up to 48 h. IC administration showed cefuroxime concentrations in AH up to 8 h; in conjunctiva, TM and plasma, the concentration lasted up to 4 h and in RC and VH till 1 h. IVT administration of cefuroxime showed concentrations in all ocular tissues (up to 8 h) and lasted up to 48 h except in conjunctiva and RC.There was evidence that the mechanism(s) of cefuroxime entry into the eye by via IVT, IC and TOP routes is clearly different. The present ocular tissue data may aid clinicians for considering appropriate choice in the treatment of post-operative ocular complications due to bacterial infections including endophthalmitis. Cefuroxime is one of the widely used antibiotics. The objective of this study was to determine pharmacokinetics and disposition in various ocular tissues following topical (TOP), intracameral (IC) and intravitreal (IVT) administration of cefuroxime to rabbits. Following TOP, IC and IVT dosing plasma and various ocular tissues (aqueous humor (AH), vitreous humor (VH), conjunctiva, trabecular mesh (TM), lens and retina-choroid (RC)) were collected and analyzed to understand the disposition of cefuroxime. Postintravenous administration plasma samples were collected to determine the systemic pharmacokinetics. Post-TOP dosing cefuroxime concentrations were observed only in conjunctiva up to 48 h. IC administration showed cefuroxime concentrations in AH up to 8 h; in conjunctiva, TM and plasma, the concentration lasted up to 4 h and in RC and VH till 1 h. IVT administration of cefuroxime showed concentrations in all ocular tissues (up to 8 h) and lasted up to 48 h except in conjunctiva and RC. There was evidence that the mechanism(s) of cefuroxime entry into the eye by via IVT, IC and TOP routes is clearly different. The present ocular tissue data may aid clinicians for considering appropriate choice in the treatment of post-operative ocular complications due to bacterial infections including endophthalmitis.
DOI: 10.6084/m9.figshare.8294669.v1
title: Uptake and pharmacokinetics of cefuroxime in rabbits after intravitreal, intracameral, and topical dosing: relevance to human ocular injection of cefuroxime

description: Cefuroxime is one of the widely used antibiotics. The objective of this study was to determine pharmacokinetics and disposition in various ocular tissues following topical (TOP), intracameral (IC) and intravitreal (IVT) administration of cefuroxime to rabbits.Following TOP, IC and IVT dosing plasma and various ocular tissues (aqueous humor (AH), vitreous humor (VH), conjunctiva, trabecular mesh (TM), lens and retina-choroid (RC)) were collected and analyzed to understand the disposition of cefuroxime. Postintravenous administration plasma samples were collected to determine the systemic pharmacokinetics.Post-TOP dosing cefuroxime concentrations were observed only in conjunctiva up to 48 h. IC administration showed cefuroxime concentrations in AH up to 8 h; in conjunctiva, TM and plasma, the concentration lasted up to 4 h and in RC and VH till 1 h. IVT administration of cefuroxime showed concentrations in all ocular tissues (up to 8 h) and lasted up to 48 h except in conjunctiva and RC.There was evidence that the mechanism(s) of cefuroxime entry into the eye by via IVT, IC and TOP routes is clearly different. The present ocular tissue data may aid clinicians for considering appropriate choice in the treatment of post-operative ocular complications due to bacterial infections including endophthalmitis. Cefuroxime is one of the widely used antibiotics. The objective of this study was to determine pharmacokinetics and disposition in various ocular tissues following topical (TOP), intracameral (IC) and intravitreal (IVT) administration of cefuroxime to rabbits. Following TOP, IC and IVT dosing plasma and various ocular tissues (aqueous humor (AH), vitreous humor (VH), conjunctiva, trabecular mesh (TM), lens and retina-choroid (RC)) were collected and analyzed to understand the disposition of cefuroxime. Postintravenous administration plasma samples were collected to determine the systemic pharmacokinetics. Post-TOP dosing cefuroxime concentrations were observed only in conjunctiva up to 48 h. IC administration showed cefuroxime concentrations in AH up to 8 h; in conjunctiva, TM and plasma, the concentration lasted up to 4 h and in RC and VH till 1 h. IVT administration of cefuroxime showed concentrations in all ocular tissues (up to 8 h) and lasted up to 48 h except in conjunctiva and RC. There was evidence that the mechanism(s) of cefuroxime entry into the eye by via IVT, IC and TOP routes is clearly different. The present ocular tissue data may aid clinicians for considering appropriate choice in the treatment of post-operative ocular complications due to bacterial infections including endophthalmitis.
DOI: 10.6084/m9.figshare.8294630
title: R Code. Completeness of the known graptoloid palaeontological record

description: R Code.
DOI: 10.6084/m9.figshare.8294627
title: Stratigraphic ranges of Ordovician species. Completeness of the known graptoloid palaeontological record

description: Stratigraphic ranges of Ordovician species.
DOI: 10.6084/m9.figshare.8294630.v1
title: R Code. Completeness of the known graptoloid palaeontological record

description: R Code.
DOI: 10.6084/m9.figshare.8294624
title: Stratigraphic ranges of Silurian species. Completeness of the known graptoloid palaeontological record

description: Stratigraphic ranges of Silurian species.
DOI: 10.6084/m9.figshare.8294624.v1
title: Stratigraphic ranges of Silurian species. Completeness of the known graptoloid palaeontological record

description: Stratigraphic ranges of Silurian species.
DOI: 10.6084/m9.figshare.8294627.v1
title: Stratigraphic ranges of Ordovician species. Completeness of the known graptoloid palaeontological record

description: Stratigraphic ranges of Ordovician species.
DOI: 10.6084/m9.figshare.8294591
title: MOESM2 of Identification of a new vector species of avian haemoproteids, with a description of methodology for the determination of natural vectors of haemosporidian parasites

description: Additional file 2: Table S2. Measurements of sporozoites detected in Culicoides kibunensis biting midges. Widths, lengths (μm) and areas of Haemoproteus pallidus sporozoites detected in Culicoides kibunensis biting midges are provided.
DOI: 10.6084/m9.figshare.8294591.v1
title: MOESM2 of Identification of a new vector species of avian haemoproteids, with a description of methodology for the determination of natural vectors of haemosporidian parasites

description: Additional file 2: Table S2. Measurements of sporozoites detected in Culicoides kibunensis biting midges. Widths, lengths (μm) and areas of Haemoproteus pallidus sporozoites detected in Culicoides kibunensis biting midges are provided.
DOI: 10.6084/m9.figshare.8294570
title: Additional file 1: of Ear biometrics for patient identification in global health: a field study to test the effectiveness of an image stabilization device in improving identification accuracy

description: Matlab functions and main script. (ZIP 4 kb)
DOI: 10.6084/m9.figshare.8294570.v1
title: Additional file 1: of Ear biometrics for patient identification in global health: a field study to test the effectiveness of an image stabilization device in improving identification accuracy

description: Matlab functions and main script. (ZIP 4 kb)
DOI: 10.6084/m9.figshare.8294561
title: Additional file 1 of Expression analysis of the osteoarthritis genetic susceptibility mapping to the matrix Gla protein gene MGP

description: Table S1. Details of the 165 osteoarthritis patients included in this study. (XLSX 15 kb)
DOI: 10.6084/m9.figshare.8294561.v1
title: Additional file 1 of Expression analysis of the osteoarthritis genetic susceptibility mapping to the matrix Gla protein gene MGP

description: Table S1. Details of the 165 osteoarthritis patients included in this study. (XLSX 15 kb)
DOI: 10.6084/m9.figshare.8294513
title: Additional file 1: of Multiple independent L-gulonolactone oxidase (GULO) gene losses and vitamin C synthesis reacquisition events in non-Deuterostomian animal species

description: Table S1. Summary of the annotation process on the downloaded non-Bilaterian and Protostomian genomes. The rows display information on the analysed species taxonomic groups and names, while the columns present information on the annotations steps performed on the species genomes and the obtained final results. The annotation steps were performed in succession from left to right, and show respectively if any sequences were retrieved from the initial tblastn, if the obtained sequences had a conserved HWXK motif, if the obtained alignment was residual or considerable, if the sequences had exons spread across several scaffolds, if the final obtained coding sequence had stop codons, and the final CDS alignment coverage. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.8294513.v1
title: Additional file 1: of Multiple independent L-gulonolactone oxidase (GULO) gene losses and vitamin C synthesis reacquisition events in non-Deuterostomian animal species

description: Table S1. Summary of the annotation process on the downloaded non-Bilaterian and Protostomian genomes. The rows display information on the analysed species taxonomic groups and names, while the columns present information on the annotations steps performed on the species genomes and the obtained final results. The annotation steps were performed in succession from left to right, and show respectively if any sequences were retrieved from the initial tblastn, if the obtained sequences had a conserved HWXK motif, if the obtained alignment was residual or considerable, if the sequences had exons spread across several scaffolds, if the final obtained coding sequence had stop codons, and the final CDS alignment coverage. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.8294480
title: Additional file 7: of Insights into Klebsiella pneumoniae type VI secretion system transcriptional regulation

description: Hypothetical binding sites for transcriptional regulators predicted in putative promoter sequence of T6SS genes in HS11286. Position Weight Matrix (PWM), Start and End position, Strand, Score and Sequence binding for transcriptional regulators. (XLS 42 kb)
DOI: 10.6084/m9.figshare.8294486
title: Additional file 8: of Insights into Klebsiella pneumoniae type VI secretion system transcriptional regulation

description: Hypothetical binding sites for transcriptional regulators predicted in putative promoter sequence of T6SS genes in NTUH-K2044. Position Weight Matrix (PWM), Start and End position, Strand, Score and Sequence binding for transcriptional regulators. (XLS 47 kb)
DOI: 10.6084/m9.figshare.8294480.v1
title: Additional file 7: of Insights into Klebsiella pneumoniae type VI secretion system transcriptional regulation

description: Hypothetical binding sites for transcriptional regulators predicted in putative promoter sequence of T6SS genes in HS11286. Position Weight Matrix (PWM), Start and End position, Strand, Score and Sequence binding for transcriptional regulators. (XLS 42 kb)
DOI: 10.6084/m9.figshare.8294486.v1
title: Additional file 8: of Insights into Klebsiella pneumoniae type VI secretion system transcriptional regulation

description: Hypothetical binding sites for transcriptional regulators predicted in putative promoter sequence of T6SS genes in NTUH-K2044. Position Weight Matrix (PWM), Start and End position, Strand, Score and Sequence binding for transcriptional regulators. (XLS 47 kb)
DOI: 10.6084/m9.figshare.8294465
title: Additional file 5: of Insights into Klebsiella pneumoniae type VI secretion system transcriptional regulation

description: Putative promoter sequence of T6SS genes. 250 bp upstream those transcriptional start sites of T6SS genes in genome of Klebsiella pneumoniae Kp52.145, HS11286 and NTUH-K2044. (TXT 11 kb)
DOI: 10.6084/m9.figshare.8294471
title: Additional file 6: of Insights into Klebsiella pneumoniae type VI secretion system transcriptional regulation

description: Hypothetical binding sites for transcriptional regulators predicted in putative promoter sequence of T6SS genes in Kp52.145. Position Weight Matrix (PWM), Start and End position, Strand, Score and Sequence binding for transcriptional regulators. (XLS 55 kb)
DOI: 10.6084/m9.figshare.8294462
title: Additional file 4: of Insights into Klebsiella pneumoniae type VI secretion system transcriptional regulation

description: Predicted 휎70 promoter sequences of T6SS genes. Binding sites − 10, spacer region, − 35 and Transcriptional Start Site upstream the CDSs coding for the T6SS-related genes in genome of Klebsiella pneumoniae Kp52.145, HS11286 and NTUH-K2044. (XLS 98 kb)
DOI: 10.6084/m9.figshare.8294471.v1
title: Additional file 6: of Insights into Klebsiella pneumoniae type VI secretion system transcriptional regulation

description: Hypothetical binding sites for transcriptional regulators predicted in putative promoter sequence of T6SS genes in Kp52.145. Position Weight Matrix (PWM), Start and End position, Strand, Score and Sequence binding for transcriptional regulators. (XLS 55 kb)
DOI: 10.6084/m9.figshare.8294465.v1
title: Additional file 5: of Insights into Klebsiella pneumoniae type VI secretion system transcriptional regulation

description: Putative promoter sequence of T6SS genes. 250 bp upstream those transcriptional start sites of T6SS genes in genome of Klebsiella pneumoniae Kp52.145, HS11286 and NTUH-K2044. (TXT 11 kb)
DOI: 10.6084/m9.figshare.8294462.v1
title: Additional file 4: of Insights into Klebsiella pneumoniae type VI secretion system transcriptional regulation

description: Predicted 휎70 promoter sequences of T6SS genes. Binding sites − 10, spacer region, − 35 and Transcriptional Start Site upstream the CDSs coding for the T6SS-related genes in genome of Klebsiella pneumoniae Kp52.145, HS11286 and NTUH-K2044. (XLS 98 kb)
DOI: 10.6084/m9.figshare.8294450
title: Additional file 2: of Insights into Klebsiella pneumoniae type VI secretion system transcriptional regulation

description: Identification and location of T6SS components in the genome of KP Kp52.145, HS11286 and NTUH-K2044. Table describing locus tag, previous annotation and indicated if T6SS components to belong in loci or are orphan. (XLS 284 kb)
DOI: 10.25345/c5kj1p
title: MassIVE MSV000086021 - Selective Labeling and Identification of the Tumor Cell Proteome of Pancreatic Cancer In Vivo
title: Pancreatic ductal adenocarcinoma (PDAC) is among the deadliest cancers. Dissecting the tumor cell proteome from that of the non-tumor cells in the PDAC tumor bulk is critical for tumorigenesis studies, biomarker discovery, and development of therapeutics. However, investigating the tumor cell proteome has proven evasive due to the tumor's extremely complex cellular composition. To circumvent this technical barrier, we have combined bioorthogonal non-canonical amino acid tagging (BONCAT) and data-independent acquisition mass spectrometry (DIA-MS) in an orthotopic PDAC model to specifically identify the tumor cell proteome in vivo. Utilizing the tumor cell-specific expression of a mutant tRNA synthetase transgene, this approach provides tumor cells with the exclusive ability to incorporate an azide-bearing methionine analog into newly synthesized proteins. The azide-tagged tumor cell proteome is subsequently enriched and purified via a bioorthogonal reaction, and then identified and quantified using DIA-MS. Applying this workflow to the orthotopic PDAC model, we have identified thousands of proteins expressed by the tumor cells. Furthermore, by comparing the tumor cell and tumor bulk proteomes, we showed that the approach can distinctly differentiate proteins produced by tumor-cells from non-tumor cells within the tumor microenvironment. Our study, for the first time, reveals the tumor cell proteome of PDAC under physiological conditions, providing broad applications for tumorigenesis, therapeutics, and biomarker studies in various human cancers.
DOI: 10.6084/m9.figshare.8294441
title: Additional file 1: of Insights into Klebsiella pneumoniae type VI secretion system transcriptional regulation

description: Summary of Secret6 and VRprofile results contributing to the annotation of T6SS genes in KP. Table describing T6SS genes in KP genomes: old and current locus-tag, genomic coordinates, gene orientation, gene size, gene product, SecreT6 and VRprofile predictions. (XLS 56 kb)
DOI: 10.6084/m9.figshare.8294450.v1
title: Additional file 2: of Insights into Klebsiella pneumoniae type VI secretion system transcriptional regulation

description: Identification and location of T6SS components in the genome of KP Kp52.145, HS11286 and NTUH-K2044. Table describing locus tag, previous annotation and indicated if T6SS components to belong in loci or are orphan. (XLS 284 kb)
DOI: 10.6084/m9.figshare.8294441.v1
title: Additional file 1: of Insights into Klebsiella pneumoniae type VI secretion system transcriptional regulation

description: Summary of Secret6 and VRprofile results contributing to the annotation of T6SS genes in KP. Table describing T6SS genes in KP genomes: old and current locus-tag, genomic coordinates, gene orientation, gene size, gene product, SecreT6 and VRprofile predictions. (XLS 56 kb)
DOI: 10.6084/m9.figshare.8294348
title: Additional file 5: of Comparative genomics of Mycobacterium mucogenicum and Mycobacterium neoaurum clade members emphasizing tRNA and non-coding RNA

description: Introduction. Figure legends. Figure S14a, b. Comparing positioning of tRNA genes in MmucT, MtbH37Rv and MsmegMC2-155. Figure S15a, b. Frequency of the identity of the nucleobase at position -1 in tRNA genes [35]. (ZIP 3300 kb)
DOI: 10.6084/m9.figshare.8294348.v1
title: Additional file 5: of Comparative genomics of Mycobacterium mucogenicum and Mycobacterium neoaurum clade members emphasizing tRNA and non-coding RNA

description: Introduction. Figure legends. Figure S14a, b. Comparing positioning of tRNA genes in MmucT, MtbH37Rv and MsmegMC2-155. Figure S15a, b. Frequency of the identity of the nucleobase at position -1 in tRNA genes [35]. (ZIP 3300 kb)
DOI: 10.6084/m9.figshare.8294339
title: Additional file 4: of Comparative genomics of Mycobacterium mucogenicum and Mycobacterium neoaurum clade members emphasizing tRNA and non-coding RNA

description: Introduction. Table and Figure legends. Table S7. Rfam non-coding RNA annotations. Figure S8a, b. ncRNA genes. Figure S9a-i. RNase P RNA (rnpB), tmRNA and 4.5S RNA. Figure S10. Northern blot analysis of selected tRNAs and ncRNAs with size markers. Figure S11a, b. Analysis of GOLLD RNA. Figure S12a-d. Comparison of Ms1 RNA and 6C RNA genes in mycobacteria. Figure S13a, b. Comparison of a intron Group II gene cluster. (ZIP 7530 kb)