cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.2065884.v1
title: Influence of medical nutrition therapy on borderline glucose intolerance in pregnant Taiwanese women

description: <i>Objective</i>: To investigate the influence of medical nutrition therapy (MNT) on borderline glucose intolerance (BGI) in pregnant Taiwanese women. <i>Methods</i>: A total of 5194 singleton pregnant women were enrolled in this prospective, non-randomized study. The participants were subjected to the 50 g 1-h glucose challenge test (GCT) and 100 g 3-h oral glucose tolerance test (OGTT) to screening gestational diabetes mellitus (GDM). BGI was defined as a positive GCT and normal OGTT results. GDM was defined as a positive GCT and abnormal OGTT results. The women were categorized into the following groups: (1) GCT-negative, <i>n</i> = 3881; (2) BGI with MNT, <i>n</i> = 273; (3) BGI without MNT, <i>n</i> = 712; and (4) GDM, <i>n</i> = 328. Multiple logistic analyses were used to estimate the risks of pregnancy outcomes. <i>Results</i>: The odds ratios (95% confidence interval) for total cesareans, third- or fourth-degree perineal lacerations, gestational hypertension or preeclampsia and macrosomia were 1.24 (1.04–1.49), 1.55 (1.06–1.28), 1.78 (1.21–2.61) and 2.50 (1.28–4.91) in the BGI without MNT group compared to the GCT-negative group. There was no difference between BGI with MNT and GCT-negative groups. <i>Conclusions</i>: Women with BGI who did not receive MNT had increased risks of adverse pregnancy outcomes, whereas who received MNT had no different risk with GCT-negative women.
DOI: 10.6084/m9.figshare.2066037.v7
title: MNI space average T1-weighted MRI of the brain with anatomical labels.

description: MNI space average brain with associated labels. Many of these labels are lifted from Chris Rorden's micron.<br>parc268 is derived from: http://www.nature.com/neuro/journal/v18/n11/abs/nn.4135.html
DOI: 10.6084/m9.figshare.2066037.v8
title: MNI space average T1-weighted MRI of the brain with anatomical labels.

description: MNI space average brain with associated labels. Many of these labels are lifted from Chris Rorden's micron.<br>parc268 is derived from: http://www.nature.com/neuro/journal/v18/n11/abs/nn.4135.html
DOI: 10.6084/m9.figshare.2065845
title: Volatiles of larval frass deter oviposition in the invasive box tree moth (Cydalima perspectalis)

description: Data used in the applied statistical tests in the manuscript written by Molnár et al.
DOI: 10.6084/m9.figshare.2066037.v9
title: MNI space average T1-weighted MRI of the brain with anatomical labels.

description: MNI space average brain with associated labels. Many of these labels are lifted from Chris Rorden's micron.<br>parc268 is derived from: http://www.nature.com/neuro/journal/v18/n11/abs/nn.4135.html
DOI: 10.6084/m9.figshare.2065809
title: Experiment: Stimulus

description: Stimulus Materials for QJE Paper: How social and non-social information influence classification decisions: A computational modeling approach
DOI: 10.6084/m9.figshare.2065845.v1
title: Volatiles of larval frass deter oviposition in the invasive box tree moth (Cydalima perspectalis)

description: Data used in the applied statistical tests in the manuscript written by Molnár et al.
DOI: 10.6084/m9.figshare.2066037.v10
title: MNI space average T1-weighted MRI of the brain with anatomical labels.

description: MNI space average brain with associated labels. Many of these labels are lifted from Chris Rorden's micron.<br>parc268 is derived from: http://www.nature.com/neuro/journal/v18/n11/abs/nn.4135.html
DOI: 10.6084/m9.figshare.2066037.v12
title: MNI space average T1-weighted MRI of the brain with anatomical labels.

description: MNI space average brain with associated labels. Many of these labels are lifted from Chris Rorden's micron.<br>parc268 is derived from: http://www.nature.com/neuro/journal/v18/n11/abs/nn.4135.html<br>yeo is from: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3174820/
DOI: 10.6084/m9.figshare.2065839
title: R code for Brewer, Butler and Cooksley in MEE (2016)

description: This code reproduces the results in the paper "The relative performance of AIC, AICC and BIC in the presence of unobserved heterogeneity", in the journal Methods in Ecology and Evolution [doi: 10.1111/2041-210X.12541]. There are also a number of data files included, which include the simulation data; note that if rerunning the simulations, the plots produced may look different from those in the paper.<br>
DOI: 10.6084/m9.figshare.2065779
title: Bayesian Inference for Assessing Effects of Email Marketing Campaigns

description: Email marketing has been an increasingly important tool for today’s businesses. In this article, we propose a counting-process-based Bayesian method for quantifying the effectiveness of email marketing campaigns in conjunction with customer characteristics. Our model explicitly addresses the seasonality of data, accounts for the impact of customer characteristics on their purchasing behavior, and evaluates effects of email offers as well as their interactions with customer characteristics. Using the proposed method, together with a propensity-score-based unit-matching technique for alleviating potential confounding, we analyze a large email marketing dataset of an online ticket marketplace to evaluate the short- and long-term effectiveness of their email campaigns. It is shown that email offers can increase customer purchase rate both immediately and during a longer term. Customers’ characteristics such as length of shopping history, purchase recency, average ticket price, average ticket count, and number of genres purchased also affect customers’ purchase rate. A strong positive interaction is uncovered between email offer and purchase recency, suggesting that customers who have been inactive recently are more likely to take advantage of promotional offers. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.2066037.v13
title: MNI space average T1-weighted MRI of the brain with anatomical labels.

description: MNI space average brain with associated labels. Many of these labels are lifted from Chris Rorden's micron.<br>parc268 is derived from: http://www.nature.com/neuro/journal/v18/n11/abs/nn.4135.html<br>yeo is from: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3174820/
DOI: 10.6084/m9.figshare.2065782
title: Efficient synthesis of β-lactam containing α-hydroxy phosphonates using tartaric acid and fumaric acid as mild catalysts

description: A short and efficient protocol for the synthesis of β-lactam containing α-hydroxy phosphonate esters using inexpensive catalysts such as tartaric acid and fumaric acid is described.
DOI: 10.6084/m9.figshare.2065776
title: Max-Linear Competing Factor Models

description: Models incorporating “latent” variables have been commonplace in financial, social, and behavioral sciences. Factor model, the most popular latent model, explains the continuous observed variables in a smaller set of latent variables (factors) in a matter of linear relationship. However, complex data often simultaneously display asymmetric dependence, asymptotic dependence, and positive (negative) dependence between random variables, which linearity and Gaussian distributions and many other extant distributions are not capable of modeling. This article proposes a nonlinear factor model that can model the above-mentioned variable dependence features but still possesses a simple form of factor structure. The random variables, marginally distributed as unit Fréchet distributions, are decomposed into max linear functions of underlying Fréchet idiosyncratic risks, transformed from Gaussian copula, and independent shared external Fréchet risks. By allowing the random variables to share underlying (latent) pervasive risks with random impact parameters, various dependence structures are created. This innovates a new promising technique to generate families of distributions with simple interpretations. We dive in the multivariate extreme value properties of the proposed model and investigate maximum composite likelihood methods for the impact parameters of the latent risks. The estimates are shown to be consistent. The estimation schemes are illustrated on several sets of simulated data, where comparisons of performance are addressed. Bootstrap method is employed to obtain standard errors in real data analysis. Real application to financial data reveals inherent dependencies that previous work has not disclosed and demonstrates the model’s interpretability to real data. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.2065782.v2
title: Efficient synthesis of β-lactam containing α-hydroxy phosphonates using tartaric acid and fumaric acid as mild catalysts

description: A short and efficient protocol for the synthesis of β-lactam containing α-hydroxy phosphonate esters using inexpensive catalysts such as tartaric acid and fumaric acid is described.
DOI: 10.6084/m9.figshare.2066037.v14
title: MNI space average T1-weighted MRI of the brain with anatomical labels.

description: MNI space average brain with associated labels. Many of these labels are lifted from Chris Rorden's micron.<br>parc268 is derived from: http://www.nature.com/neuro/journal/v18/n11/abs/nn.4135.html<br>yeo is from: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3174820/
DOI: 10.6084/m9.figshare.2065776.v1
title: Max-Linear Competing Factor Models

description: Models incorporating “latent” variables have been commonplace in financial, social, and behavioral sciences. Factor model, the most popular latent model, explains the continuous observed variables in a smaller set of latent variables (factors) in a matter of linear relationship. However, complex data often simultaneously display asymmetric dependence, asymptotic dependence, and positive (negative) dependence between random variables, which linearity and Gaussian distributions and many other extant distributions are not capable of modeling. This article proposes a nonlinear factor model that can model the above-mentioned variable dependence features but still possesses a simple form of factor structure. The random variables, marginally distributed as unit Fréchet distributions, are decomposed into max linear functions of underlying Fréchet idiosyncratic risks, transformed from Gaussian copula, and independent shared external Fréchet risks. By allowing the random variables to share underlying (latent) pervasive risks with random impact parameters, various dependence structures are created. This innovates a new promising technique to generate families of distributions with simple interpretations. We dive in the multivariate extreme value properties of the proposed model and investigate maximum composite likelihood methods for the impact parameters of the latent risks. The estimates are shown to be consistent. The estimation schemes are illustrated on several sets of simulated data, where comparisons of performance are addressed. Bootstrap method is employed to obtain standard errors in real data analysis. Real application to financial data reveals inherent dependencies that previous work has not disclosed and demonstrates the model’s interpretability to real data. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.2065782.v1
title: Efficient Synthesis of β-Lactam Containing α-Hydroxy Phosphonates Using Tartaric Acid and Fumaric Acid as Mild Catalysts

description: A short and efficient protocol for the synthesis of β-lactam containing α-hydroxy phosphonate esters using inexpensive catalysts such as tartaric acid and fumaric acid is described.
DOI: 10.6084/m9.figshare.2066037.v15
title: MNI space average T1-weighted MRI of the brain with anatomical labels.

description: MNI space average brain with associated labels. Many of these labels are lifted from Chris Rorden's micron.<br>parc268 is derived from: http://www.nature.com/neuro/journal/v18/n11/abs/nn.4135.html<br>yeo is from: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3174820/
DOI: 10.6084/m9.figshare.2065722
title: Censored Quantile Instrumental Variable Estimates of the Price Elasticity of Expenditure on Medical Care

description: Efforts to control medical care costs depend critically on how individuals respond to prices. I estimate the price elasticity of expenditure on medical care using a censored quantile instrumental variable (CQIV) estimator. CQIV allows estimates to vary across the conditional expenditure distribution, relaxes traditional censored model assumptions, and addresses endogeneity with an instrumental variable. My instrumental variable strategy uses a family member’s injury to induce variation in an individual’s own price. Across the conditional deciles of the expenditure distribution, I find elasticities that vary from −0.76 to −1.49, which are an order of magnitude larger than previous estimates. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.2065722.v1
title: Censored Quantile Instrumental Variable Estimates of the Price Elasticity of Expenditure on Medical Care

description: Efforts to control medical care costs depend critically on how individuals respond to prices. I estimate the price elasticity of expenditure on medical care using a censored quantile instrumental variable (CQIV) estimator. CQIV allows estimates to vary across the conditional expenditure distribution, relaxes traditional censored model assumptions, and addresses endogeneity with an instrumental variable. My instrumental variable strategy uses a family member’s injury to induce variation in an individual’s own price. Across the conditional deciles of the expenditure distribution, I find elasticities that vary from −0.76 to −1.49, which are an order of magnitude larger than previous estimates. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.2065608
title: Tissue-specific patterns of allelically-skewed DNA methylation

description: While DNA methylation is usually thought to be symmetrical across both alleles, there are some notable exceptions. Genomic imprinting and X chromosome inactivation are two well-studied sources of allele-specific methylation (ASM), but recent research has indicated a more complex pattern in which genotypic variation can be associated with allelically-skewed DNA methylation in <i>cis</i>. Given the known heterogeneity of DNA methylation across tissues and cell types we explored inter- and intra-individual variation in ASM across several regions of the human brain and whole blood from multiple individuals. Consistent with previous studies, we find widespread ASM with &gt; 4% of the ∼220,000 loci interrogated showing evidence of allelically-skewed DNA methylation. We identify ASM flanking known imprinted regions, and show that ASM sites are enriched in DNase I hypersensitivity sites and often located in an extended genomic context of intermediate DNA methylation. We also detect examples of genotype-driven ASM, some of which are tissue-specific. These findings contribute to our understanding of the nature of differential DNA methylation across tissues and have important implications for genetic studies of complex disease. As a resource to the community, ASM patterns across each of the tissues studied are available in a searchable online database: http://epigenetics.essex.ac.uk/ASMBrainBlood.
DOI: 10.6084/m9.figshare.2065602
title: Research compendium for a report on archaeological excavations at Khao Toh Chong, Krabi, Thailand

description: Supplementary information for the publication on KTC. Development repository is at https://github.com/benmarwick/ktc11
DOI: 10.6084/m9.figshare.2065605
title: Gene promoter methylation signature predicts survival of head and neck squamous cell carcinoma patients

description: Infection with high-risk types of human papilloma virus (HPV) is currently the best-established prognostic marker for head and neck squamous cell carcinoma (HNSCC), one of the most common and lethal human malignancies worldwide. Clinical trials have been launched to address the concept of treatment de-escalation for HPV-positive HNSCC with the final aim to reduce treatment related toxicity and debilitating long-term impacts on the quality of life. However, HPV-related tumors are mainly restricted to oropharyngeal SCC (OPSCC) and there is an urgent need to establish reliable biomarkers for all patients at high risk for treatment failure. A patient cohort (n = 295) with mainly non-OPSCC (72.9%) and a low prevalence of HPV16-related tumors (8.8%) was analyzed by MassARRAY to determine a previously established prognostic methylation score (MS). Kaplan-Meier revealed a highly significant correlation between a high MS and a favorable survival for OPSCC (<i>P</i> = 0.0004) and for non-OPSCC (<i>P</i>&lt;0.0001), which was confirmed for all HNSCC by multivariate Cox regression models (HR: 9.67, 95% CI [4.61–20.30], <i>P</i>&lt;0.0001). Next, we established a minimal methylation signature score (MMSS), which consists of ten most informative of the originally 62 CpG units used for the MS. The prognostic value of the MMSS was confirmed by Kaplan-Meier analysis for all HNSCC (<i>P</i>&lt;0.0001) and non-OPSCC (<i>P</i> = 0.0002), and was supported by multivariate Cox regression models for all HNSCC (HR: 2.15, 95% CI [1.36–3.41], <i>P</i> = 0.001). In summary, the MS and the MMSS exhibit an excellent performance as prognosticators for survival, which is not limited by the anatomical site, and both could be implemented in future clinical trials.
DOI: 10.6084/m9.figshare.2065608.v1
title: Tissue-specific patterns of allelically-skewed DNA methylation

description: While DNA methylation is usually thought to be symmetrical across both alleles, there are some notable exceptions. Genomic imprinting and X chromosome inactivation are two well-studied sources of allele-specific methylation (ASM), but recent research has indicated a more complex pattern in which genotypic variation can be associated with allelically-skewed DNA methylation in <i>cis</i>. Given the known heterogeneity of DNA methylation across tissues and cell types we explored inter- and intra-individual variation in ASM across several regions of the human brain and whole blood from multiple individuals. Consistent with previous studies, we find widespread ASM with &gt; 4% of the ∼220,000 loci interrogated showing evidence of allelically-skewed DNA methylation. We identify ASM flanking known imprinted regions, and show that ASM sites are enriched in DNase I hypersensitivity sites and often located in an extended genomic context of intermediate DNA methylation. We also detect examples of genotype-driven ASM, some of which are tissue-specific. These findings contribute to our understanding of the nature of differential DNA methylation across tissues and have important implications for genetic studies of complex disease. As a resource to the community, ASM patterns across each of the tissues studied are available in a searchable online database: http://epigenetics.essex.ac.uk/ASMBrainBlood.
DOI: 10.6084/m9.figshare.2065614
title: Quantitative evaluation of first, second, and third generation hairpin systems reveals the limit of mammalian vector-based RNAi

description: Incorporating miRNA-like features into vector-based hairpin scaffolds has been shown to augment small RNA processing and RNAi efficiency. Therefore, defining an optimal, native hairpin context may obviate a need for hairpin-specific targeting design schemes, which confound the movement of functional siRNAs into shRNA/artificial miRNA backbones, or large-scale screens to identify efficacious sequences. Thus, we used quantitative cell-based assays to compare separate third generation artificial miRNA systems, miR-E (based on miR-30a) and miR-3G (based on miR-16-2 and first described in this study) to widely-adopted, first and second generation formats in both Pol-II and Pol-III expression vector contexts. Despite their unique structures and strandedness, and in contrast to first and second-generation RNAi triggers, the third generation formats operated with remarkable similarity to one another, and strong silencing was observed with a significant fraction of the evaluated target sequences within either promoter context. By pairing an established siRNA design algorithm with the third generation vectors we could readily identify targeting sequences that matched or exceeded the potency of those discovered through large-scale sensor-based assays. We find that third generation hairpin systems enable the maximal level of siRNA function, likely through enhanced processing and accumulation of precisely-defined guide RNAs. Therefore, we predict future gains in RNAi potency will come from improved hairpin expression and identification of optimal siRNA-intrinsic silencing properties rather than further modification of these scaffolds. Consequently, third generation systems should be the primary format for vector-based RNAi studies; miR-3G is advantageous due to its small expression cassette and simplified, cost-efficient cloning scheme.
DOI: 10.6084/m9.figshare.2065605.v2
title: Gene promoter methylation signature predicts survival of head and neck squamous cell carcinoma patients

description: Infection with high-risk types of human papilloma virus (HPV) is currently the best-established prognostic marker for head and neck squamous cell carcinoma (HNSCC), one of the most common and lethal human malignancies worldwide. Clinical trials have been launched to address the concept of treatment de-escalation for HPV-positive HNSCC with the final aim to reduce treatment related toxicity and debilitating long-term impacts on the quality of life. However, HPV-related tumors are mainly restricted to oropharyngeal SCC (OPSCC) and there is an urgent need to establish reliable biomarkers for all patients at high risk for treatment failure. A patient cohort (n = 295) with mainly non-OPSCC (72.9%) and a low prevalence of HPV16-related tumors (8.8%) was analyzed by MassARRAY to determine a previously established prognostic methylation score (MS). Kaplan-Meier revealed a highly significant correlation between a high MS and a favorable survival for OPSCC (<i>P</i> = 0.0004) and for non-OPSCC (<i>P</i>&lt;0.0001), which was confirmed for all HNSCC by multivariate Cox regression models (HR: 9.67, 95% CI [4.61–20.30], <i>P</i>&lt;0.0001). Next, we established a minimal methylation signature score (MMSS), which consists of ten most informative of the originally 62 CpG units used for the MS. The prognostic value of the MMSS was confirmed by Kaplan-Meier analysis for all HNSCC (<i>P</i>&lt;0.0001) and non-OPSCC (<i>P</i> = 0.0002), and was supported by multivariate Cox regression models for all HNSCC (HR: 2.15, 95% CI [1.36–3.41], <i>P</i> = 0.001). In summary, the MS and the MMSS exhibit an excellent performance as prognosticators for survival, which is not limited by the anatomical site, and both could be implemented in future clinical trials.