cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7889741
title: den.npy

description: Numpy array for the circle pack geometry for 3,553 images. Shape of the den array is [3553,256,256,1]
DOI: 10.6084/m9.figshare.7889735
title: gVCF_HG01302

description: 1000 Genomes gVCF mapped to hs37d5 for HG01302. Complete collection: https://doi.org/10.6084/m9.figshare.c.4414307
DOI: 10.6084/m9.figshare.7889723
title: gVCF_NA18616

description: 1000 Genomes gVCF mapped to hs37d5 for NA18616. Complete collection: https://doi.org/10.6084/m9.figshare.c.4414307
DOI: 10.6084/m9.figshare.7889732
title: gVCF_HG01286

description: 1000 Genomes gVCF mapped to hs37d5 for HG01286. Complete collection: https://doi.org/10.6084/m9.figshare.c.4414307
DOI: 10.6084/m9.figshare.7889735.v1
title: gVCF_HG01302

description: 1000 Genomes gVCF mapped to hs37d5 for HG01302. Complete collection: https://doi.org/10.6084/m9.figshare.c.4414307
DOI: 10.6084/m9.figshare.7889738.v1
title: gVCF_HG01303

description: 1000 Genomes gVCF mapped to hs37d5 for HG01303. Complete collection: https://doi.org/10.6084/m9.figshare.c.4414307
DOI: 10.6084/m9.figshare.7889720
title: gVCF_HG02947

description: 1000 Genomes gVCF mapped to hs37d5 for HG02947. Complete collection: https://doi.org/10.6084/m9.figshare.c.4414307
DOI: 10.6084/m9.figshare.7889729
title: gVCF_HG01284

description: 1000 Genomes gVCF mapped to hs37d5 for HG01284. Complete collection: https://doi.org/10.6084/m9.figshare.c.4414307
DOI: 10.6084/m9.figshare.7889732.v1
title: gVCF_HG01286

description: 1000 Genomes gVCF mapped to hs37d5 for HG01286. Complete collection: https://doi.org/10.6084/m9.figshare.c.4414307
DOI: 10.6084/m9.figshare.7889720.v1
title: gVCF_HG02947

description: 1000 Genomes gVCF mapped to hs37d5 for HG02947. Complete collection: https://doi.org/10.6084/m9.figshare.c.4414307
DOI: 10.6084/m9.figshare.7889723.v1
title: gVCF_NA18616

description: 1000 Genomes gVCF mapped to hs37d5 for NA18616. Complete collection: https://doi.org/10.6084/m9.figshare.c.4414307
DOI: 10.6084/m9.figshare.7889648
title: Gender parity in medical authorship

description: Author lists from published papers for the years 2002-2014 across a large range of medical subspecialties collected from PubMed. Each name is assigned gender automatically.<br>- Analysis and writeup: https://jflournoy.github.io/gender-in-medical-authorship/gender_parity.html- Analysis code: https://github.com/jflournoy/gender-in-medical-authorship- Gender-guessing code: https://bitbucket.org/jlev_uo/ucla-pubmed-gender-bias<br>
DOI: 10.6084/m9.figshare.7889729.v1
title: gVCF_HG01284

description: 1000 Genomes gVCF mapped to hs37d5 for HG01284. Complete collection: https://doi.org/10.6084/m9.figshare.c.4414307
DOI: 10.6084/m9.figshare.7888178
title: The burden of pertussis in older adults: what is the role of vaccination? A systematic literature review

description: <b>Introduction</b>: Pertussis (whooping cough) is a vaccine-preventable disease; however, neither natural- nor vaccine-induced protection is life-long. Although generally not severe in adults, pertussis can be associated with complications in patients with chronic conditions such as asthma or chronic obstructive pulmonary disease, and can be readily transmitted to more vulnerable populations, including neonates before they complete their primary vaccination. Furthermore, as the global population ages, the health and economic burden of the disease is expected to rise. <b>Areas covered</b>: A systematic literature review was conducted to ascertain the current epidemiological and financial burden of pertussis in older adults and to discuss the potential value of a booster vaccination in this population. <b>Expert commentary</b>: Our review indicates a considerable underestimation of the pertussis burden amongst older adults. Seroprevalence studies consistently demonstrate that the reported incidence may be much lower than the actual incidence. Tetanus toxoid-reduced diphtheria toxoid and acellular pertussis vaccines are immunogenic in older adults, induce high booster responses and are well-tolerated. There is therefore a good rationale for the advocacy of booster pertussis vaccination throughout life to prevent pertussis infection and its transmission, especially in adults aged ≥50 years. Read the transcript Watch the video on Vimeo
DOI: 10.6084/m9.figshare.7889648.v1
title: Gender parity in medical authorship

description: Author lists from published papers for the years 2002-2014 across a large range of medical subspecialties collected from PubMed. Each name is assigned gender automatically.<br>- Analysis and writeup: https://jflournoy.github.io/gender-in-medical-authorship/gender_parity.html- Analysis code: https://github.com/jflournoy/gender-in-medical-authorship- Gender-guessing code: https://bitbucket.org/jlev_uo/ucla-pubmed-gender-bias<br>
DOI: 10.6084/m9.figshare.7888028
title: Analysis-of-Marginal-Tail-Means (ATM): A Robust Method for Discrete Black-Box Optimization

description: We present a new method, called analysis-of-marginal-tail-means (ATM), for effective robust optimization of discrete black-box problems. ATM has important applications in many real-world engineering problems (e.g., manufacturing optimization, product design, and molecular engineering), where the objective to optimize is black-box and expensive, and the design space is inherently discrete. One weakness of existing methods is that they are not robust: these methods perform well under certain assumptions, but yield poor results when such assumptions (which are difficult to verify in black-box problems) are violated. ATM addresses this by combining both rank- and model-based optimization, via the use of marginal tail means. The trade-off between rank- and model-based optimization is tuned by first identifying important main effects and interactions from data, then finding a good compromise which best exploits additive structure. ATM provides improved robust optimization over existing methods, particularly in problems with (i) a large number of factors, (ii) unordered factors, or (iii) experimental noise. We demonstrate the effectiveness of ATM in simulations and in two real-world engineering problems: the first on robust parameter design of a circular piston, and the second on product family design of a thermistor network.
DOI: 10.6084/m9.figshare.7888178.v2
title: The burden of pertussis in older adults: what is the role of vaccination? A systematic literature review

description: <b>Introduction</b>: Pertussis (whooping cough) is a vaccine-preventable disease; however, neither natural- nor vaccine-induced protection is life-long. Although generally not severe in adults, pertussis can be associated with complications in patients with chronic conditions such as asthma or chronic obstructive pulmonary disease, and can be readily transmitted to more vulnerable populations, including neonates before they complete their primary vaccination. Furthermore, as the global population ages, the health and economic burden of the disease is expected to rise. <b>Areas covered</b>: A systematic literature review was conducted to ascertain the current epidemiological and financial burden of pertussis in older adults and to discuss the potential value of a booster vaccination in this population. <b>Expert commentary</b>: Our review indicates a considerable underestimation of the pertussis burden amongst older adults. Seroprevalence studies consistently demonstrate that the reported incidence may be much lower than the actual incidence. Tetanus toxoid-reduced diphtheria toxoid and acellular pertussis vaccines are immunogenic in older adults, induce high booster responses and are well-tolerated. There is therefore a good rationale for the advocacy of booster pertussis vaccination throughout life to prevent pertussis infection and its transmission, especially in adults aged ≥50 years. Read the transcript Watch the video on Vimeo
DOI: 10.6084/m9.figshare.7887980
title: Multivariate Design of Experiments for Engineering Dimensional Analysis

description: We consider the design of dimensional analysis experiments when there is more than a single response. We first give a brief overview of dimensional analysis experiments and the dimensional analysis (DA) procedure. The validity of the DA method for univariate responses was established by the Buckingham Π-Theorem in the early 20th century. We extend the theorem to the multivariate case, develop basic criteria for multivariate design of DA and give guidelines for design construction. Finally, we illustrate the construction of designs for DA experiments for an example involving the design of a heat exchanger.
DOI: 10.6084/m9.figshare.7888025
title: Tensor Mixed Effects Model With Application to Nanomanufacturing Inspection

description: Raman mapping technique has been used to perform in-line quality inspections of nanomanufacturing processes. In such an application, massive high-dimensional Raman mapping data with mixed effects is generated. In general, fixed effects and random effects in the multi-array Raman data are associated with different quality characteristics such as fabrication consistency, uniformity, and defects. The existing tensor decomposition methods cannot separate mixed effects, and existing mixed effects model can only handle matrix data but not high-dimensional multi-array data. In this article, we propose a tensor mixed effects (TME) model to analyze massive high-dimensional Raman mapping data with complex structure. The proposed TME model can (i) separate fixed effects and random effects in a tensor domain; (ii) explore the correlations along different dimensions; and (iii) realize efficient parameter estimation by a proposed iterative double Flip-Flop algorithm. We also investigate the properties of the TME model, existence and identifiability of parameter estimation. The numerical analysis demonstrates the efficiency and accuracy of the parameter estimation in the TME model. Convergence and asymptotic properties are discussed in the simulation and surrogate data analysis. The case study shows an application of the TME model in quantifying the influence of alignment on carbon nanotubes buckypaper. Moreover, the TME model can be applied to provide potential solutions for a family of tensor data analytics problems with mixed effects.
DOI: 10.6084/m9.figshare.7888178.v1
title: The burden of pertussis in older adults: what is the role of vaccination? A systematic literature review

description: <b>Introduction</b>: Pertussis (whooping cough) is a vaccine-preventable disease; however, neither natural- nor vaccine-induced protection is life-long. Although generally not severe in adults, pertussis can be associated with complications in patients with chronic conditions such as asthma or chronic obstructive pulmonary disease, and can be readily transmitted to more vulnerable populations, including neonates before they complete their primary vaccination. Furthermore, as the global population ages, the health and economic burden of the disease is expected to rise. <b>Areas covered</b>: A systematic literature review was conducted to ascertain the current epidemiological and financial burden of pertussis in older adults and to discuss the potential value of a booster vaccination in this population. <b>Expert commentary</b>: Our review indicates a considerable underestimation of the pertussis burden amongst older adults. Seroprevalence studies consistently demonstrate that the reported incidence may be much lower than the actual incidence. Tetanus toxoid-reduced diphtheria toxoid and acellular pertussis vaccines are immunogenic in older adults, induce high booster responses and are well-tolerated. There is therefore a good rationale for the advocacy of booster pertussis vaccination throughout life to prevent pertussis infection and its transmission, especially in adults aged ≥50 years.
DOI: 10.6084/m9.figshare.7888025.v1
title: Tensor Mixed Effects Model with Application to Nanomanufacturing Inspection

description: Raman mapping technique has been used to perform in-line quality inspections of nanomanufacturing processes. In such an application, massive high-dimensional Raman mapping data with mixed effects is generated. In general, fixed effects and random effects in the multi-array Raman data are associated with different quality characteristics such as fabrication consistency, uniformity, defects, et al. The existing tensor decomposition methods cannot separate mixed effects, and existing mixed effects model can only handle matrix data but not high-dimensional multi-array data. In this paper, we propose a tensor mixed effects (TME) model to analyze massive high-dimensional Raman mapping data with complex structure. The proposed TME model can (i) separate fixed effects and random effects in a tensor domain; (ii) explore the correlations along different dimensions; and (iii) realize efficient parameter estimation by a proposed iterative double Flip-Flop algorithm. We also investigate the properties of the TME model, existence and identifiability of parameter estimation. The numerical analysis demonstrates the efficiency and accuracy of the parameter estimation in the TME model. Convergence and asymptotic properties are discussed in the simulation and surrogate data analysis. The case study shows an application of the TME model in quantifying the influence of alignment on carbon nanotubes buckypaper. Moreover, the TME model can be applied to provide potential solutions for a family of tensor data analytics problems with mixed effects.
DOI: 10.6084/m9.figshare.7888025.v2
title: Tensor Mixed Effects Model With Application to Nanomanufacturing Inspection

description: Raman mapping technique has been used to perform in-line quality inspections of nanomanufacturing processes. In such an application, massive high-dimensional Raman mapping data with mixed effects is generated. In general, fixed effects and random effects in the multi-array Raman data are associated with different quality characteristics such as fabrication consistency, uniformity, and defects. The existing tensor decomposition methods cannot separate mixed effects, and existing mixed effects model can only handle matrix data but not high-dimensional multi-array data. In this article, we propose a tensor mixed effects (TME) model to analyze massive high-dimensional Raman mapping data with complex structure. The proposed TME model can (i) separate fixed effects and random effects in a tensor domain; (ii) explore the correlations along different dimensions; and (iii) realize efficient parameter estimation by a proposed iterative double Flip-Flop algorithm. We also investigate the properties of the TME model, existence and identifiability of parameter estimation. The numerical analysis demonstrates the efficiency and accuracy of the parameter estimation in the TME model. Convergence and asymptotic properties are discussed in the simulation and surrogate data analysis. The case study shows an application of the TME model in quantifying the influence of alignment on carbon nanotubes buckypaper. Moreover, the TME model can be applied to provide potential solutions for a family of tensor data analytics problems with mixed effects.
DOI: 10.6084/m9.figshare.7888028.v1
title: Analysis-of-marginal-Tail-Means (ATM): a robust method for discrete black-box optimization

description: We present a new method, called Analysis-of-marginal-Tail-Means (ATM), for effective robust optimization of discrete black-box problems. ATM has important applications in many real-world engineering problems (e.g., manufacturing optimization, product design, molecular engineering), where the objective to optimize is black-box and expensive, and the design space is inherently discrete. One weakness of existing methods is that they are not robust: these methods perform well under certain assumptions, but yield poor results when such assumptions (which are difficult to verify in black-box problems) are violated. ATM addresses this by combining both rank- and model-based optimization, via the use of marginal tail means. The trade-off between rank- and model-based optimization is tuned by first identifying important main effects and interactions from data, then finding a good compromise which best exploits additive structure. ATM provides improved robust optimization over existing methods, particularly in problems with (i) a large number of factors, (ii) unordered factors, or (iii) experimental noise. We demonstrate the effectiveness of ATM in simulations and in two real-world engineering problems: the first on robust parameter design of a circular piston, and the second on product family design of a thermistor network.
DOI: 10.6084/m9.figshare.7887980.v2
title: Multivariate Design of Experiments for Engineering Dimensional Analysis

description: We consider the design of dimensional analysis experiments when there is more than a single response. We first give a brief overview of dimensional analysis experiments and the dimensional analysis (DA) procedure. The validity of the DA method for univariate responses was established by the Buckingham Π-Theorem in the early 20th century. We extend the theorem to the multivariate case, develop basic criteria for multivariate design of DA and give guidelines for design construction. Finally, we illustrate the construction of designs for DA experiments for an example involving the design of a heat exchanger.
DOI: 10.6084/m9.figshare.7887980.v1
title: Multivariate Design of Experiments for Engineering Dimensional Analysis

description: We consider the design of dimensional analysis experiments when there is more than a single response. We first give a brief overview of dimensional analysis experiments and the dimensional analysis (DA) procedure. The validity of the DA method for univariate responses was established by the Buckingham Π-Theorem in the early 20th century. We extend the theorem to the multivariate case, develop basic criteria for multivariate design of DA and give guidelines for design construction. Finally, we illustrate the construction of designs for DA experiments for an example involving the design of a heat exchanger.
DOI: 10.6084/m9.figshare.7888028.v3
title: Analysis-of-Marginal-Tail-Means (ATM): A Robust Method for Discrete Black-Box Optimization

description: We present a new method, called analysis-of-marginal-tail-means (ATM), for effective robust optimization of discrete black-box problems. ATM has important applications in many real-world engineering problems (e.g., manufacturing optimization, product design, and molecular engineering), where the objective to optimize is black-box and expensive, and the design space is inherently discrete. One weakness of existing methods is that they are not robust: these methods perform well under certain assumptions, but yield poor results when such assumptions (which are difficult to verify in black-box problems) are violated. ATM addresses this by combining both rank- and model-based optimization, via the use of marginal tail means. The trade-off between rank- and model-based optimization is tuned by first identifying important main effects and interactions from data, then finding a good compromise which best exploits additive structure. ATM provides improved robust optimization over existing methods, particularly in problems with (i) a large number of factors, (ii) unordered factors, or (iii) experimental noise. We demonstrate the effectiveness of ATM in simulations and in two real-world engineering problems: the first on robust parameter design of a circular piston, and the second on product family design of a thermistor network.
DOI: 10.6084/m9.figshare.7888028.v2
title: Analysis-of-Marginal-Tail-Means (ATM): A Robust Method for Discrete Black-Box Optimization

description: We present a new method, called analysis-of-marginal-tail-means (ATM), for effective robust optimization of discrete black-box problems. ATM has important applications in many real-world engineering problems (e.g., manufacturing optimization, product design, and molecular engineering), where the objective to optimize is black-box and expensive, and the design space is inherently discrete. One weakness of existing methods is that they are not robust: these methods perform well under certain assumptions, but yield poor results when such assumptions (which are difficult to verify in black-box problems) are violated. ATM addresses this by combining both rank- and model-based optimization, via the use of marginal tail means. The trade-off between rank- and model-based optimization is tuned by first identifying important main effects and interactions from data, then finding a good compromise which best exploits additive structure. ATM provides improved robust optimization over existing methods, particularly in problems with (i) a large number of factors, (ii) unordered factors, or (iii) experimental noise. We demonstrate the effectiveness of ATM in simulations and in two real-world engineering problems: the first on robust parameter design of a circular piston, and the second on product family design of a thermistor network.
DOI: 10.6084/m9.figshare.7887857
title: <i>Fomitopsis mounceae</i> and <i>F. schrenkii</i>—two new species from North America in the <i>F. pinicola</i> complex

description: Two new species, <i>Fomitopsis mounceae</i> and <i>F. schrenkii</i> (Polyporales, Basidiomycota) in the <i>F. pinicola</i> species complex in North America, are described and illustrated. Previous molecular phylogenetic analyses identified three well-delimited lineages that represent <i>F. mounceae</i> and <i>F. ochracea</i> from Canada, the Appalachian Mountains, and the northern United States and <i>F. schrenkii</i> from western and southwestern regions of the United States. <i>Fomitopsis pinicola</i> sensu stricto is restricted to Eurasia and does not occur in North America. Morphological descriptions of basidiocarps and cultures for <i>F. mounceae, F. schrenkii</i>, and <i>F. ochracea</i> are presented. The three species are readily differentiated by nuc rDNA internal transcribed spacer (ITS1-5.8S-ITS2 = ITS) sequence, geographic distribution, and basidiospore size. <i>Polyporus ponderosus</i> H. Schrenk is an earlier illegitimate synonym of <i>F. schrenkii</i>. Both <i>F. mounceae</i> and <i>F. schrenkii</i> have a heterothallic multiallelic incompatibility system.
DOI: 10.6084/m9.figshare.7887845
title: New species and records of bioluminescent <i>Mycena</i> from Mexico

description: Seven species of bioluminescent fungi are recorded from the cloud forests in Mexico. Six represent new species belonging to the genus <i>Mycena</i>, whereas <i>Mycena globulispora</i> is a new distribution record for the country. Descriptions, illustrations, photographs, and an identification key to bioluminescent fungi species from Mexico are provided. Sequences of nuc rDNA internal transcribed spacer (ITS1-5.8S-ITS2 = ITS) region were generated for barcoding purposes and comparisons with similar species.