cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1597648.v1
title: The percentage of males that attempt to mate is higher when they are exposed to females than to hermaphrodites

description: The male response efficiency assay measures the percentage of males that attempt to mate with the opposite sex. One day before the experiment, NGM plates were spotted with 13 µL of E. coli OP50-1 culture. Before the experiment, 5 males were placed for 10 min in the center of the ~ 5 mm diameter bacterial spot to let them acclimatize. 15 animals of the opposite sex (hermaphrodites or females) were added to the bacterial spot and observed for 4 min. If a male attempted to mate, as determined by the male tail scanning the body of the other sex, the male response was scored with the number 1. In case there was no attempt, the response was scored as 0. The behavior of each male was recorded only once. For each type of mating (male/hermaphrodite or male/female), 5 replicates were performed.
DOI: 10.6084/m9.figshare.1597645.v1
title: Elevational variation in body-temperature response to immune challenge in a lizard

description: _
DOI: 10.6084/m9.figshare.1597646.v1
title: Sexes of SB347 F1 from selfing or outcrossing parents.

description: Data from Figure 2a. To determine the sex of the F1 from selfing hermaphrodites, the self-progeny of 20 SB347 animals was collected throughout their lifespan. The hermaphrodite mothers were selected by first isolating dauers, which in SB347 always develop into hermaphrodites. Dauers were placed into single 6 cm agar plates seeded with E. coli OP50-1 and left to mature into adults. Every 8 h of their reproductive life, the hermaphrodite mothers were transferred to a new plate until they stopped laying eggs. To control more precisely for worms that may escape the plate before being scored, we sexed the progeny while they were at larval stages (two days after hatching). We scored the three sexes using several traits, including developmental rates and morphologies. Dauer larvae (destined to become hermaphrodites) are thin with darkly-pigmented guts. Larger larvae with long thin tails develop into females. Male larvae have a characteristically blunt tail.
DOI: 10.6084/m9.figshare.1597647.v5
title: Rhabditis sp. SB347 virgin females, mated females and hermaphrodites attraction to supernatant of males

description: Data from Figure 3a. To quantify the degree of attraction of worms to conditioned medium produced by different sexes, we used chemotaxis assays. Conditioned medium (henceforth referred to as ‘supernatant’) was generated by placing 5-10 worms in 100 µL of M9 buffer for 12 h at room temperature. The supernatant was stored in 10 µL aliquots at -20 °C until required. The assay was performed either on a microscope slide with a layer of 1.5% agar placed on top of an empty plate, or on a 6 cm NGM plate. 3 µL of supernatant was added on one side of the slide and 3 cm apart from the control drop that just contained M9. 15 young-adults were placed on the midline between the spots. After 30 min, worms were scored on the basis of their location. The values for the chemotaxis index (CI) were calculated with at least ten replicates for each condition. To calculate the CI, the number of worms attracted to the test spot were subtracted by the number of worms in the control spot, and divided by the total number of males assayed. A CI of one indicates that all worms are attracted to the chemical in the test spot, whereas a CI close to zero indicates no attraction. ‘Mated females’ were generated by placing single virgin females in contact with 4-5 males for 6 h.
DOI: 10.6084/m9.figshare.1597647.v4
title: Rhabditis sp. SB347 virgin females, but not mated females or hermaphrodites (H), are attracted to supernatant of males

description: Data from Figure 3a. To quantify the degree of attraction of worms to conditioned medium produced by different sexes, we used chemotaxis assays. Conditioned medium (henceforth referred to as ‘supernatant’) was generated by placing 5-10 worms in 100 µL of M9 buffer for 12 h at room temperature. The supernatant was stored in 10 µL aliquots at -20 °C until required. The assay was performed either on a microscope slide with a layer of 1.5% agar placed on top of an empty plate, or on a 6 cm NGM plate. 3 µL of supernatant was added on one side of the slide and 3 cm apart from the control drop that just contained M9. 15 young-adults were placed on the midline between the spots. After 30 min, worms were scored on the basis of their location. The values for the chemotaxis index (CI) were calculated with at least ten replicates for each condition. To calculate the CI, the number of worms attracted to the test spot were subtracted by the number of worms in the control spot, and divided by the total number of males assayed. A CI of one indicates that all worms are attracted to the chemical in the test spot, whereas a CI close to zero indicates no attraction. ‘Mated females’ were generated by placing single virgin females in contact with 4-5 males for 6 h.
DOI: 10.6084/m9.figshare.1597612
title: Best Practices in Environmental Communication - Appendices

description: Appendices for: Jarreau, P. B., Altinay, Z., & Reynolds, A. (2015). Best Practices in Environmental Communication: A Case Study of Louisiana's Coastal Crisis.Environmental Communication, 1-23.
DOI: 10.6084/m9.figshare.1597608
title: Sildenafil: In depth case study

description: Vantage Group health economics report on antenatal sildenafil
DOI: 10.6084/m9.figshare.1597610
title: Best Practices in Environmental Communication_Appendix B

description: Best Practices in Environmental Communication - Appendix B
DOI: 10.6084/m9.figshare.1597612.v1
title: Best Practices in Environmental Communication - Appendices

description: Appendices for: Jarreau, P. B., Altinay, Z., & Reynolds, A. (2015). Best Practices in Environmental Communication: A Case Study of Louisiana's Coastal Crisis.Environmental Communication, 1-23.
DOI: 10.6084/m9.figshare.1597605
title: Networking for career development (in STEM) - Presentation - in 3 file formats

description: A presentation I gave at the Postdoc Retreat of the DKFZ (German Cancer Reseach Centre in Heidelberg, Germany) on November 5th 2015, with tips and description and activities for networking, with a focus on career development. Provided in PDF, PPTX, and Keynote formats (originally made in Keynote, so might be some funny formating in PPTX and PDF). Updated November 24th 2015 to spell Alaina's name correctly!
DOI: 10.6084/m9.figshare.1597607
title: Marked strain-to-strain diversity in light harvesting antenna complex gene composition and expression in photosynthetic bacteria affiliated with or closely related to Rhodopseudomonas palustris

description: Alignment of <em>pucA </em>or <em>pucB </em>genes from photosynthetic bacteria affiliated with or closely related to <em>Rhodopseudomonas palustris.</em> These alignments were used to construct the phylogenetic trees in Fig. 1 and Fig. 2.
DOI: 10.6084/m9.figshare.1597608.v1
title: Sildenafil: In depth case study

description: Vantage Group health economics report on antenatal sildenafil
DOI: 10.6084/m9.figshare.1597605.v2
title: Networking for career development (in STEM) - Presentation - in 3 file formats

description: A presentation I gave at the Postdoc Retreat of the DKFZ (German Cancer Reseach Centre in Heidelberg, Germany) on November 5th 2015, with tips and description and activities for networking, with a focus on career development. Provided in PDF, PPTX, and Keynote formats (originally made in Keynote, so might be some funny formating in PPTX and PDF). Updated November 24th 2015 to spell Alaina's name correctly!
DOI: 10.6084/m9.figshare.1597612.v2
title: Best Practices in Environmental Communication - Appendices

description: Appendices for: Jarreau, P. B., Altinay, Z., & Reynolds, A. (2015). Best Practices in Environmental Communication: A Case Study of Louisiana's Coastal Crisis.Environmental Communication, 1-23.
DOI: 10.6084/m9.figshare.1597605.v1
title: Networking for career development (in STEM) - Presentation - in 3 file formats

description: A presentation I gave at the Postdoc Retreat of the DKFZ (German Cancer Reseach Centre in Heidelberg, Germany) on November 5th 2015, with tips and description and activities for networking, with a focus on career development. Provided in PDF, PPTX, and Keynote formats (originally made in Keynote, so might be some funny formating in PPTX and PDF)
DOI: 10.6084/m9.figshare.1597595
title: Building scientific communities

description: Presentation on building scientiic communities that I gave at the BioRN lounge in Heidelberg,Germany, on 27th October 2015. Presentation is provided as PDF, PPTX, and keynote format (it was originally written in keynote, hence some of the formatting in the PPTX is different from in the other versions)
DOI: 10.6084/m9.figshare.1597595.v1
title: Building scientific communities

description: Presentation on building scientiic communities that I gave at the BioRN lounge in Heidelberg,Germany, on 27th October 2015. Presentation is provided as PDF, PPTX, and keynote format (it was originally written in keynote, hence some of the formatting in the PPTX is different from in the other versions)
DOI: 10.6084/m9.figshare.1597587
title: Eye Movement Evidence for Hierarchy Effects on Memory Representation of Discourses

description: data for Plos One paper
DOI: 10.6084/m9.figshare.1597477
title: Analysis of the Proportional Hazards Model With Sparse Longitudinal Covariates

description: Regression analysis of censored failure observations via the proportional hazards model permits time-varying covariates that are observed at death times. In practice, such longitudinal covariates are typically sparse and only measured at infrequent and irregularly spaced follow-up times. Full likelihood analyses of joint models for longitudinal and survival data impose stringent modeling assumptions that are difficult to verify in practice and that are complicated both inferentially and computationally. In this article, a simple kernel weighted score function is proposed with minimal assumptions. Two scenarios are considered: half kernel estimation in which observation ceases at the time of the event and full kernel estimation for data where observation may continue after the event, as with recurrent events data. It is established that these estimators are consistent and asymptotically normal. However, they converge at rates that are slower than the parametric rates that may be achieved with fully observed covariates, with the full kernel method achieving an optimal convergence rate that is superior to that of the half kernel method. Simulation results demonstrate that the large sample approximations are adequate for practical use and may yield improved performance relative to last value carried forward approach and joint modeling method. The analysis of the data from a cardiac arrest study demonstrates the utility of the proposed methods. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.1597478
title: Geoquímica de Sinter Silíceo en el campo geotérmico de Puchuldiza

description: Resumen Charla XIV Congreso geológico chileno. Los depósitos de sínter silíceo son rocas sedimentarias químicas ricas en sílice formadas por precipitación a partir de fluidos hidrotermales. Se asocian comúnmente a actividad geotermal y a mineralización epitermal de oro. A pesar de su importancia como marcadores en superficies de sistemas de alta entalpía y como vectores de mineralización aurífera, el contenido y especiación de metales (ej. Au, Hg) y metaloides (ej. As, Sb) en estos depósitos no se ha constreñido adecuadamente. En particular, se desconoce la relación entre el grado de cristalinidad o “madurez” de la sílice y la presencia/concentración de determinadas especies de metales y metaloides. En este estudio, se reportan observaciones mineralógicas por difracción de rayos X y análisis de elementos traza (LA-ICP-MS) en depósitos de sínter silíceo del campo geotérmico de Puchuldiza, en el Altiplano (4200 m s.n.m.), Región de Tarapacá. Se identifica mayoritariamente ópalo A, al igual que en El Tatio. Además, se reconoce que el Au y el Hg se ligan a fases maduras, mientras que el As tiende a asociarse a las fases inmaduras. Se sugiere preliminarmente un importante impacto de la morfología y grado de cristalinidad de la sílice en la captura de metales y metaloides en sistemas geotermales.
DOI: 10.6084/m9.figshare.1597477.v1
title: Analysis of the Proportional Hazards Model With Sparse Longitudinal Covariates

description: Regression analysis of censored failure observations via the proportional hazards model permits time-varying covariates that are observed at death times. In practice, such longitudinal covariates are typically sparse and only measured at infrequent and irregularly spaced follow-up times. Full likelihood analyses of joint models for longitudinal and survival data impose stringent modeling assumptions that are difficult to verify in practice and that are complicated both inferentially and computationally. In this article, a simple kernel weighted score function is proposed with minimal assumptions. Two scenarios are considered: half kernel estimation in which observation ceases at the time of the event and full kernel estimation for data where observation may continue after the event, as with recurrent events data. It is established that these estimators are consistent and asymptotically normal. However, they converge at rates that are slower than the parametric rates that may be achieved with fully observed covariates, with the full kernel method achieving an optimal convergence rate that is superior to that of the half kernel method. Simulation results demonstrate that the large sample approximations are adequate for practical use and may yield improved performance relative to last value carried forward approach and joint modeling method. The analysis of the data from a cardiac arrest study demonstrates the utility of the proposed methods. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.1597472
title: Bias-Reduced Doubly Robust Estimation

description: Over the past decade, doubly robust estimators have been proposed for a variety of target parameters in causal inference and missing data models. These are asymptotically unbiased when at least one of two nuisance working models is correctly specified, regardless of which. While their asymptotic distribution is not affected by the choice of root-<i>n</i> consistent estimators of the nuisance parameters indexing these working models when all working models are correctly specified, this choice of estimators can have a dramatic impact under misspecification of at least one working model. In this article, we will therefore propose a simple and generic estimation principle for the nuisance parameters indexing each of the working models, which is designed to improve the performance of the doubly robust estimator of interest, relative to the default use of maximum likelihood estimators for the nuisance parameters. The proposed approach locally minimizes the squared first-order asymptotic bias of the doubly robust estimator under misspecification of both working models and results in doubly robust estimators with easy-to-calculate asymptotic variance. It moreover improves the stability of the weights in those doubly robust estimators which invoke inverse probability weighting. Simulation studies confirm the desirable finite-sample performance of the proposed estimators. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.1597472.v1
title: Bias-Reduced Doubly Robust Estimation

description: Over the past decade, doubly robust estimators have been proposed for a variety of target parameters in causal inference and missing data models. These are asymptotically unbiased when at least one of two nuisance working models is correctly specified, regardless of which. While their asymptotic distribution is not affected by the choice of root-<i>n</i> consistent estimators of the nuisance parameters indexing these working models when all working models are correctly specified, this choice of estimators can have a dramatic impact under misspecification of at least one working model. In this article, we will therefore propose a simple and generic estimation principle for the nuisance parameters indexing each of the working models, which is designed to improve the performance of the doubly robust estimator of interest, relative to the default use of maximum likelihood estimators for the nuisance parameters. The proposed approach locally minimizes the squared first-order asymptotic bias of the doubly robust estimator under misspecification of both working models and results in doubly robust estimators with easy-to-calculate asymptotic variance. It moreover improves the stability of the weights in those doubly robust estimators which invoke inverse probability weighting. Simulation studies confirm the desirable finite-sample performance of the proposed estimators. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.1597468
title: Likelihood Inferences on Semiparametric Odds Ratio Model

description: A flexible semiparametric odds ratio model has been proposed to unify and to extend both the log-linear model and the joint normal model for data with a mix of discrete and continuous variables. The semiparametric odds ratio model is particularly useful for analyzing biased sampling designs. However, statistical inference of the model has not been systematically studied when more than one nonparametric component is involved in the model. In this article, we study the maximum semiparametric likelihood approach to estimation and inference of the semiparametric odds ratio model. We show that the maximum semiparametric likelihood estimator of the odds ratio parameter is consistent and asymptotically normally distributed. We also establish statistical inference under a misspecified semiparametric odds ratio model, which is important when handling weak identifiability in conditionally specified models under biased sampling designs. We use simulation studies to demonstrate that the proposed approaches have satisfactory finite sample performance. Finally, we illustrate the proposed approach by analyzing multiple traits in a genome-wide association study of high-density lipid protein. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.1597469
title: The E-MS Algorithm: Model Selection With Incomplete Data

description: We propose a procedure associated with the idea of the E-M algorithm for model selection in the presence of missing data. The idea extends the concept of parameters to include both the model and the parameters under the model, and thus allows the model to be part of the E-M iterations. We develop the procedure, known as the E-MS algorithm, under the assumption that the class of candidate models is finite. Some special cases of the procedure are considered, including E-MS with the generalized information criteria (GIC), and E-MS with the adaptive fence (AF; Jiang et al.). We prove numerical convergence of the E-MS algorithm as well as consistency in model selection of the limiting model of the E-MS convergence, for E-MS with GIC and E-MS with AF. We study the impact on model selection of different missing data mechanisms. Furthermore, we carry out extensive simulation studies on the finite-sample performance of the E-MS with comparisons to other procedures. The methodology is also illustrated on a real data analysis involving QTL mapping for an agricultural study on barley grains. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.1597468.v1
title: Likelihood Inferences on Semiparametric Odds Ratio Model

description: A flexible semiparametric odds ratio model has been proposed to unify and to extend both the log-linear model and the joint normal model for data with a mix of discrete and continuous variables. The semiparametric odds ratio model is particularly useful for analyzing biased sampling designs. However, statistical inference of the model has not been systematically studied when more than one nonparametric component is involved in the model. In this article, we study the maximum semiparametric likelihood approach to estimation and inference of the semiparametric odds ratio model. We show that the maximum semiparametric likelihood estimator of the odds ratio parameter is consistent and asymptotically normally distributed. We also establish statistical inference under a misspecified semiparametric odds ratio model, which is important when handling weak identifiability in conditionally specified models under biased sampling designs. We use simulation studies to demonstrate that the proposed approaches have satisfactory finite sample performance. Finally, we illustrate the proposed approach by analyzing multiple traits in a genome-wide association study of high-density lipid protein. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.1597469.v1
title: The E-MS Algorithm: Model Selection With Incomplete Data

description: We propose a procedure associated with the idea of the E-M algorithm for model selection in the presence of missing data. The idea extends the concept of parameters to include both the model and the parameters under the model, and thus allows the model to be part of the E-M iterations. We develop the procedure, known as the E-MS algorithm, under the assumption that the class of candidate models is finite. Some special cases of the procedure are considered, including E-MS with the generalized information criteria (GIC), and E-MS with the adaptive fence (AF; Jiang et al.). We prove numerical convergence of the E-MS algorithm as well as consistency in model selection of the limiting model of the E-MS convergence, for E-MS with GIC and E-MS with AF. We study the impact on model selection of different missing data mechanisms. Furthermore, we carry out extensive simulation studies on the finite-sample performance of the E-MS with comparisons to other procedures. The methodology is also illustrated on a real data analysis involving QTL mapping for an agricultural study on barley grains. Supplementary materials for this article are available online.