cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5531698.v1
title: Dataset for: Estrogen receptor mutations and splice variants determined in liquid biopsies from metastatic breast cancer patients

description: Mutations and splice variants in the estrogen receptor (ER) gene, ESR1, may yield endocrine resistance in metastatic breast cancer (MBC) patients. These putative endocrine resistance markers are likely to emerge during treatment and therefore its detection in liquid biopsies, such as circulating tumor cells (CTCs) and cell-free DNA (cfDNA), is of great interest. This research aimed to determine if ESR1 mutations and splice variants occur more frequently in CTCs of MBC patients progressing on endocrine treatment. In addition, the presence of ESR1 mutations was evaluated in matched cfDNA and compared to CTCs. CellSearch-enriched CTC fractions (≥5/7.5 mL) of two MBC cohorts were evaluated, including 1) patients starting first-line endocrine therapy (n=43, baseline cohort) and 2) patients progressing on any line of endocrine therapy (n=40, progressing cohort). ESR1 hotspot mutations (D538G and Y537S/N/C) were evaluated in CTC-enriched DNA using digital PCR and compared with matched cfDNA (n=18 baseline cohort; n=26 progressing cohort). Expression of ESR1 full-length and 4 of its splice variants (∆5, ∆7, 36KD and 46KD) was evaluated in CTC-enriched mRNA. It was observed that in the CTCs, the ESR1 mutations were not enriched in the progressing cohort (8%), when compared to the baseline cohort (5%) (P=0.66). In the cfDNA, however, ESR1 mutations were more prevalent in the progressing cohort (42%) than in the baseline cohort (11%) (P=0.04). Three of the same mutations were observed in both CTCs and cfDNA, 1 mutation in CTCs only and 11 in cfDNA only. Only the ∆5 ESR1 splice variant was CTC-specific expressed, but was not enriched in the progressing cohort. In conclusion, sensitivity for detecting ESR1 mutations in CTC-enriched fractions was lower than for cfDNA. ESR1 mutations detected in cfDNA, rarely present at start of first-line endocrine therapy, were enriched at progression, strongly suggesting a role in conferring endocrine resistance in MBC.
DOI: 10.6084/m9.figshare.5531224
title: Exponential Integrators for Weather and Climate Simulations using Global Spectral Methods

description: This work studies exponential integrator (EI) methods in the context of climate and weather simulations. We put our focus on a rational approximation of exponential integrators (REXI) which can be expressed via U (∆t) ≈ n β n (∆tL + α n ) −1 U (0) where α, β ∈ C, L a linear operator (with oscillatory or diffusive stiffness) and the initial conditions, U (0) (see e.g. [Clancy and Lynch, 2011; Haut et al., 2015]). The additional degrees of freedom for parallelization are made available by the independent terms in the sum which can be solved in parallel. This formulation enables us to overcome the time step limitation due to the linear stiffness. A special focus is put on PDEs relevant for climate and weather simulations.<br>Such EI methods have a rich history (see e.g. [Moler and Van Loan, 2003; Hochbruck and Ostermann, 2010]) and are of increasing interest in the parallel-in-time (PinT) community. In the context of PinT methods, these EI formulations were first mentioned by [Gander and Guettel, 2013] as the ParaEXP method. In the context of the development of dynamical cores for climate and weather simulations, recent research [Clancy and Lynch, 2011; Garcia et al., 2014; Clancy and Pudykiewicz, 2013] exploited EI formulations and also showed promising results regarding higher accuracy. Additionally, EI are a crucial component when applying the asymptotic PinT approach [Haut and Wingate, 2014] to a more realistic problem. Parallel performance and numerical accuracy studies of the REXI method were conducted for the linear shallow-water equations (SWE) on the plane [Schreiber et al., 2016] using spectral solvers for Fourier space and finite-difference formulations. Up to two orders of magnitude of speedup for oscillatory linear stiff problems were presented in this work. The successful application of spectral solvers to solve for each REXI term motivated an investigation of EI to the linearized SWE including the effect of a rotating sphere. Spherical Harmonics are used which exploit the low-bandwidth structure of the linear rotational SWE in spectral space[Schreiber and Loft, 2017].<br>In this talk, we will present our current research on extending our previous work to the full non-linear PDEs. First, we will give a brief overview of the results to solve the linear SWE on the plane and rotating sphere with EI. Second, we will discuss time splitting approaches and study the direct application of EI formulations which can be expressed via the aforementioned sum and their extension to non-linearities (see e.g. [Cox and Matthews, 2002; Luan and Ostermann, 2016]). Finally, we will compare EI formulations with state-of-the art time stepping methods which are currently used in operational weather forecasts.<br>ERRATA:page 21: \leq =&gt; \geqpage 21: exp(i) =&gt; exp(i0)
DOI: 10.6084/m9.figshare.5531170
title: Deltapodus 3D models from Belvedere & Mietto 2010

description: Here we provide the 3D models used to generate the false-colour maps, the contour-lines and the cross-sections in Belvedere and Mietto, 2010.<br>The two tracks were moulded in the field with silicon rubber (Silical 110 – CTS srl), from which fibreglass casts were made. A triangulation-based laser scanner ShapeGrabberSG1002 was used to digitize the two fiberglass casts, and all the subsequent data manipulation was carried out with Innovmetric Polyworks, following the method of Petti et al. (2008).For each fspecimen, we performed five scans at 0.3-mm resolution, which were then combined, achieving a final standard deviation of 0.11 mm.<br><b>References</b><br>Belvedere M. and Mietto P. 2010. First evidence of stegosaurian <i>Deltapodus </i>footprints in North Africa (Iouaridène Formation, Upper Jurassic, Morocco). Palaeontology, 53 (1), 233-240. doi: 10.1111/j.1475-4983.2009.00928.x.<br> Petti F.M., Avanzini M., Belvedere M., De Gasperi M., Ferretti P. Girardi S., Remondino F. and Tomasoni R. 2008. Digital 3D modelling of dinosaur footprints by photogrammetry and laser scanning techniques: evaluation of the integrated approach at the Coste dell’Anglone tracksite (Lower Jurassic, Southern Alps, Northern Italy). Studi Tridentini Scienze Naturali, Acta Geologica, 83, 303-315.
DOI: 10.6084/m9.figshare.5531155
title: An Examination of the Perceptions of Men Exposed to Trauma

description: This study was conducted by interviewing men between the ages of 18-35 who had been exposed to trauma in early childhood. Many things became clear in this study, Firstly, perception affected how badly the people were affected by the trauma. Also, we found that thorough discussion of trauma and perception examination is very therapeutic. Moreover, we found that those with stronger faith had less PTSD symptoms as defined by the DSM-V diagnostic criteria. This was a qualitative study known as a phenomenology and the results may not be generalizeable to other populations.
DOI: 10.6084/m9.figshare.5531032
title: Ancestrular morphology in cyclostome bryozoans and the quest for phylogenetically informative skeletal characters

description: Cyclostomes are an ancient order of bryozoans with more than 500 living species. Traditionally, cyclostome taxonomy has depended almost entirely on characters of the calcareous skeletons of mature colonies. However, the taxonomic distribution of these characters is largely incongruent with well-supported molecular phylogenetic trees, implying the need for major revisions if cyclostome taxonomy is to reflect phylogeny. While far more taxa must be sequenced to ascertain their molecular relationships, there is also a need to discover morphological characters that can be used to support molecular clades, not least to allow these clades to be inferred among fossil cyclostomes for which molecular data will never be available. Here we survey the skeletal morphology of the first-formed part of the skeleton – the protoecium of the founding zooid (ancestrula) – in a variety of Recent and well-preserved fossil cyclostomes, motivated by the recent discovery of a morphologically disparate molecular clade that can be distinguished by protoecial characters. The distribution of pseudopores on the protoecium is shown to vary between species, with eight patterns recognizable, offering a new source of skeletal characters in both living and fossil taxa. However, the patterns seem not to be fully congruent with the cyclostome molecular tree and more data and analyses are required before these patterns can be used to recognize cyclostome clades.
DOI: 10.6084/m9.figshare.5531032.v1
title: Ancestrular morphology in cyclostome bryozoans and the quest for phylogenetically informative skeletal characters

description: Cyclostomes are an ancient order of bryozoans with more than 500 living species. Traditionally, cyclostome taxonomy has depended almost entirely on characters of the calcareous skeletons of mature colonies. However, the taxonomic distribution of these characters is largely incongruent with well-supported molecular phylogenetic trees, implying the need for major revisions if cyclostome taxonomy is to reflect phylogeny. While far more taxa must be sequenced to ascertain their molecular relationships, there is also a need to discover morphological characters that can be used to support molecular clades, not least to allow these clades to be inferred among fossil cyclostomes for which molecular data will never be available. Here we survey the skeletal morphology of the first-formed part of the skeleton – the protoecium of the founding zooid (ancestrula) – in a variety of Recent and well-preserved fossil cyclostomes, motivated by the recent discovery of a morphologically disparate molecular clade that can be distinguished by protoecial characters. The distribution of pseudopores on the protoecium is shown to vary between species, with eight patterns recognizable, offering a new source of skeletal characters in both living and fossil taxa. However, the patterns seem not to be fully congruent with the cyclostome molecular tree and more data and analyses are required before these patterns can be used to recognize cyclostome clades.
DOI: 10.6084/m9.figshare.5531116
title: My medication education data

description: A national representative sample of 6,226 students from 99 primary, middle, and high schools completed an online self-administered questionnaire. Multiple logistic regression analysis was used to examine factors related to inappropriate self-medication.
DOI: 10.6084/m9.figshare.5531023.v1
title: Dataset for: Cellwise robust regularized discriminant analysis

description: Quadratic and Linear Discriminant Analysis (QDA/LDA) are the most often applied classiﬁcation rules under normality. In QDA, a separate covariance matrix is estimated for each group. If there are more variables than observations in the groups, the usual estimates are singular and cannot be used anymore. Assuming homoscedasticity, as in LDA, reduces the number of parameters to estimate. This rather strong assumption is however rarely veriﬁed in practice. Regularized discriminant techniques that are computable in high-dimension and cover the path between the two extremes QDA and LDA have been proposed in the literature. However, these procedures rely on sample covariance matrices. As such, they become inappropriate in presence of cellwise outliers, a type of outliers that is very likely to occur in high-dimensional datasets. In this paper, we propose cellwise robust counterparts of these regularized discriminant techniques by inserting cellwise robust covariance matrices. Our methodology results in a family of discriminant methods that (i) are robust against outlying cells, (ii) cover the gap between LDA and QDA and (iii) are computable in high-dimension. The good performance of the new methods is illustrated through simulated and real data examples. As a by-product, visual tools are provided for the detection of outliers.
DOI: 10.6084/m9.figshare.5530498
title: FGB alignment

description: Alignment of FGB gene sequences from representatives of Oligoryzomys
DOI: 10.6084/m9.figshare.5530483
title: cytb alignment

description: Alignment of cytb gene sequences from representatives of Oligoryzomys
DOI: 10.6084/m9.figshare.5530510
title: 17-loci Y-STR data for Northern Iraqi Arabs, Kurds, Turkmens, Syriacs and Yazidis

description: In an effort to contribute to a better understanding of the genetic basis of the Northern Iraqi ethnic diversity, a total of 500 samples were collected from volunteers belonging to five major ethnic groups, namely: Arabs (<i>n</i>=102), Kurds (<i>n</i>=104), Turkmens (<i>n</i>=102), Yazidis (<i>n</i>=106) and Syriacs (<i>n</i>=86). 17-loci Y-STR analyses were carried out using the AmpF<i>l</i>STR Yfiler system.
DOI: 10.6084/m9.figshare.5530498.v1
title: FGB alignment

description: Alignment of FGB gene sequences from representatives of Oligoryzomys
DOI: 10.6084/m9.figshare.5530423
title: Table S5

description: Supplemental Table S5. Annotations for eight FUnkFams with a protein sequence whose function is annotated in the UniProt xref database (despite having no annotated domains). From manuscript:A most wanted list of conserved protein families with no known domainsStacia K. Wyman, Aram Avila-Herrera, Stephen Nayfach, Katherine S. Pollard
DOI: 10.6084/m9.figshare.5530411
title: Table S3

description: Supplemental Table S3. Results of statistical tests for associations between environmental variables and FUnkFams presence across Tara Oceans samples. From manuscript: A most wanted list of conserved protein families with no known domains. Stacia K. Wyman, Aram Avila-Herrera, Stephen Nayfach, Katherine S. Pollard<br>
DOI: 10.6084/m9.figshare.5530414
title: Table S4

description: Supplemental Table S4. Results of statistical tests for associations between host phenotype variables and FUnkFams presence across Human Microbiome Project samples. From manuscript:A most wanted list of conserved protein families with no known domainsStacia K. Wyman, Aram Avila-Herrera, Stephen Nayfach, Katherine S. Pollard
DOI: 10.6084/m9.figshare.5530423.v1
title: Table S5

description: Supplemental Table S5. Annotations for eight FUnkFams with a protein sequence whose function is annotated in the UniProt xref database (despite having no annotated domains). From manuscript:A most wanted list of conserved protein families with no known domainsStacia K. Wyman, Aram Avila-Herrera, Stephen Nayfach, Katherine S. Pollard
DOI: 10.6084/m9.figshare.5530408
title: Table S2

description: Supplemental Table S2. Annotations for 1 045 FUnkFams with a protein sequence in the UniProt xref database. From manuscript:<br>A most wanted list of conserved protein families with no known domainsStacia K. Wyman, Aram Avila-Herrera, Stephen Nayfach, Katherine S. Pollard
DOI: 10.6084/m9.figshare.5530411.v1
title: Table S3

description: Supplemental Table S3. Results of statistical tests for associations between environmental variables and FUnkFams presence across Tara Oceans samples. From manuscript: A most wanted list of conserved protein families with no known domains. Stacia K. Wyman, Aram Avila-Herrera, Stephen Nayfach, Katherine S. Pollard<br>
DOI: 10.6084/m9.figshare.5530399
title: Table S1

description: Supplemental Table S1: Characteristics of FUnkFams, including phylogenetic distribution and prevalence in TO and HMP samples. <br>From manuscript: <b>A most wanted list of conserved protein families with no known domains</b><br>Stacia K. Wyman, Aram Avila-Herrera, Stephen Nayfach, Katherine S. Pollard<br>
DOI: 10.6084/m9.figshare.5530414.v1
title: Table S4

description: Supplemental Table S4. Results of statistical tests for associations between host phenotype variables and FUnkFams presence across Human Microbiome Project samples. From manuscript:A most wanted list of conserved protein families with no known domainsStacia K. Wyman, Aram Avila-Herrera, Stephen Nayfach, Katherine S. Pollard
DOI: 10.6084/m9.figshare.5530285
title: Two-Step Estimation of Incomplete Information Social Interaction Models With Sample Selection

description: This article considers linear social interaction models under incomplete information that allow for missing outcome data due to sample selection. For model estimation, assuming that each individual forms his/her belief about the other members’ outcomes based on rational expectations, we propose a two-step series nonlinear least squares estimator. Both the consistency and asymptotic normality of the estimator are established. As an empirical illustration, we apply the proposed model and method to National Longitudinal Study of Adolescent Health (Add Health) data to examine the impacts of friendship interactions on adolescents’ academic achievements. We provide empirical evidence that the interaction effects are important determinants of grade point average and that controlling for sample selection bias has certain impacts on the estimation results. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.5530402
title: Data from "Intraocular lens power calculation for the equine eye."

description: The data set describe refractive state, corneal curvature (keratometry) and the axial location of all optical interfaces (biometry) of the eyes of the evaluated horses.<br>
DOI: 10.6084/m9.figshare.5530408.v1
title: Table S2

description: Supplemental Table S2. Annotations for 1 045 FUnkFams with a protein sequence in the UniProt xref database. From manuscript:<br>A most wanted list of conserved protein families with no known domainsStacia K. Wyman, Aram Avila-Herrera, Stephen Nayfach, Katherine S. Pollard
DOI: 10.6084/m9.figshare.5530243
title: FUnkFams Protein Sequences

description: These 6,668 Function Unknown Families (FUnkFams) are homologous, full-length protein sequences that derive from genomes in at least two taxonomic classes but with no annotated protein domains. They are a subset of the SFams Protein Families, described in this manuscript: <br>T.J. Sharpton, G. Jospin, D. Wu, M.G. Langille, K.S. Pollard, J.A. Eisen (2012). Sifting through genomes with iterative-sequence clustering produces a large, phylogenetically diverse protein-family resource, BMC Bioinformatics, 13(1): 264. <br>The family ID format is taxonomicspan_familyID_proteinID.
DOI: 10.6084/m9.figshare.5530399.v1
title: Table S1

description: Supplemental Table S1: Characteristics of FUnkFams, including phylogenetic distribution and prevalence in TO and HMP samples. <br>From manuscript: <b>A most wanted list of conserved protein families with no known domains</b><br>Stacia K. Wyman, Aram Avila-Herrera, Stephen Nayfach, Katherine S. Pollard<br>
DOI: 10.6084/m9.figshare.5530402.v1
title: Data from "Intraocular lens power calculation for the equine eye."

description: The data set describe refractive state, corneal curvature (keratometry) and the axial location of all optical interfaces (biometry) of the eyes of the evaluated horses.<br>
DOI: 10.6084/m9.figshare.5530231
title: TRES Settlement 2016_FigShare.xlsx

description: This data is from a breeding population of tree swallows, nesting in nest boxes in Davis, CA. Data from adults and nestlings was recorded during the 2016 breeding season. <br>Measurements were taken from bird exposed to traffic noise playbacks and control conditions. <br>There are 2 sheets in the Excel file. The first sheet contains the data and the second sheet contains the descriptions of each column.
DOI: 10.6084/m9.figshare.5530243.v1
title: FUnkFams Protein Sequences

description: These 6,668 Function Unknown Families (FUnkFams) are homologous, full-length protein sequences that derive from genomes in at least two taxonomic classes but with no annotated protein domains. They are a subset of the SFams Protein Families, described in this manuscript: <br>T.J. Sharpton, G. Jospin, D. Wu, M.G. Langille, K.S. Pollard, J.A. Eisen (2012). Sifting through genomes with iterative-sequence clustering produces a large, phylogenetically diverse protein-family resource, BMC Bioinformatics, 13(1): 264. <br>The family ID format is taxonomicspan_familyID_proteinID.
DOI: 10.6084/m9.figshare.5530285.v2
title: Two-Step Estimation of Incomplete Information Social Interaction Models With Sample Selection

description: This article considers linear social interaction models under incomplete information that allow for missing outcome data due to sample selection. For model estimation, assuming that each individual forms his/her belief about the other members’ outcomes based on rational expectations, we propose a two-step series nonlinear least squares estimator. Both the consistency and asymptotic normality of the estimator are established. As an empirical illustration, we apply the proposed model and method to National Longitudinal Study of Adolescent Health (Add Health) data to examine the impacts of friendship interactions on adolescents’ academic achievements. We provide empirical evidence that the interaction effects are important determinants of grade point average and that controlling for sample selection bias has certain impacts on the estimation results. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.5528038
title: Integrated quality by design (QbD) and design of experiments (DoE) approach for UFLC determination of telaprevir in rat serum

description: An ultrafast liquid chromatographic bioanalytical method was developed and validated for the determination of telaprevir in Wistar albino rat serum. Principles of quality by design (QbD) were implemented for enhancing the bioanalytical liquid–liquid extraction of telaprevir from rat serum. A Box–Behnken design was utilized in the studies by selecting extraction time, centrifugation speed, and vortex time as the critical method variables for evaluating their effect on the critical analytical attribute, i.e., %recovery of telaprevir. Chromatographic separation was achieved within a run time of 10 min using a C-18 column and mobile phase comprising of methanol:borate buffer of pH 9 (90:10 v/v) flowing at 1.2 mL/min. Photodiode array detection was performed at 270 nm. Results of validation studies were satisfactory. The method was linear over a concentration of 25–10,000 ng/mL. Limit of detection for the developed method was 10 ng/mL. Further, design of experiments (DoE) used for inter-day accuracy and precision study suggested superior method reliability. This integrated QbD- and DoE-based approach ensured the development of a validated and reliable analytical method for optimum bioanalysis of telaprevir in biological matrix.
DOI: 10.6084/m9.figshare.5528038.v2
title: Integrated quality by design (QbD) and design of experiments (DoE) approach for UFLC determination of telaprevir in rat serum

description: An ultrafast liquid chromatographic bioanalytical method was developed and validated for the determination of telaprevir in Wistar albino rat serum. Principles of quality by design (QbD) were implemented for enhancing the bioanalytical liquid–liquid extraction of telaprevir from rat serum. A Box–Behnken design was utilized in the studies by selecting extraction time, centrifugation speed, and vortex time as the critical method variables for evaluating their effect on the critical analytical attribute, i.e., %recovery of telaprevir. Chromatographic separation was achieved within a run time of 10 min using a C-18 column and mobile phase comprising of methanol:borate buffer of pH 9 (90:10 v/v) flowing at 1.2 mL/min. Photodiode array detection was performed at 270 nm. Results of validation studies were satisfactory. The method was linear over a concentration of 25–10,000 ng/mL. Limit of detection for the developed method was 10 ng/mL. Further, design of experiments (DoE) used for inter-day accuracy and precision study suggested superior method reliability. This integrated QbD- and DoE-based approach ensured the development of a validated and reliable analytical method for optimum bioanalysis of telaprevir in biological matrix.