@article{joo_sánchez-tapia_mortara_bellini_turner_hug_morandeira_bannert_almazrouq_hare_et al._2022, title={Ten simple rules to host an inclusive conference.}, volume={7}, url={http://europepmc.org/abstract/med/35862309}, DOI={10.1371/journal.pcbi.1010164}, abstractNote={Conferences are spaces to meet and network within and across academic and technical fields, learn about new advances, and share our work. They can help define career paths and create long-lasting collaborations and opportunities. However, these opportunities are not equal for all. This article introduces 10 simple rules to host an inclusive conference based on the authors’ recent experience organizing the 2021 edition of the useR! statistical computing conference, which attracted a broad range of participants from academia, industry, government, and the nonprofit sector. Coming from different backgrounds, career stages, and even continents, we embraced the challenge of organizing a high-quality virtual conference in the context of the Coronavirus Disease 2019 (COVID-19) pandemic and making it a kind, inclusive, and accessible experience for as many people as possible. The rules result from our lessons learned before, during, and after the organization of the conference. They have been written mainly for potential organizers and selection committees of conferences and contain multiple practical tips to help a variety of events become more accessible and inclusive. We see this as a starting point for conversations and efforts towards building more inclusive conferences across the world. * Translated versions of the English abstract and the list of rules are available in 10 languages in S1 Text: Arabic, French, German, Italian, Japanese, Korean, Portuguese, Spanish, Tamil, and Thai.}, journal={PLoS computational biology}, author={Joo, R and Sánchez-Tapia, A and Mortara, S and Bellini, Saibene Y and Turner, H and Hug, Peter D and Morandeira, NS and Bannert, M and Almazrouq, B and Hare, E and et al.}, year={2022}, month={Jul} }
 @article{bezuidenhout_drummond-curtis_walker_shanahan_alfaro-córdoba_2021, title={A School and a Network: CODATA-RDA Data Science Summer Schools Alumni Survey}, volume={20}, url={http://doi.org/10.5334/dsj-2021-010}, DOI={10.5334/dsj-2021-010}, abstractNote={The CODATA-RDA Schools for Research Data Science (SRDS) is a network of schools originating in the RDA in 2016. In 2019 it was recognized as an RDA output. To date, over 400 students from 40 countries have been trained in 10 schools. The majority of these students were postgraduates from low/middle-income countries (LMICs). In contrast to many other data science training approaches, the SRDS schools are designed to be 2-week, disciplinarily-agnostic, residential events where students are introduced to a broad range of tools requisite for efficient and responsible data-centric research. This paper presents the results of a survey carried out on alumni from schools held between 2016 and 2019 (45% response). The results of the survey strongly support the SRDS’s long-term goals of facilitating data science training/capacity building within LMICs, and to foster communities of early career researchers (ECRs) conducting responsible and open data science research. The survey results demonstrated that 90% of respondent alumni continued to conduct research and make use of the skills acquired at the SRDS. Modules on open and responsible research and research data management were rated as important for future research. 79% of respondents confirmed that they maintained contact with peers, and 31% had set up academic collaborations with peers and/or instructors. Many had gone on to present content from the schools in their home institutions. The survey results clearly demonstrate the impact of the SRDS, and the value of an expanding network of schools supported by the RDA and CODATA.}, note={DOI:}, number={1}, journal={Data Science Journal}, publisher={Ubiquity Press, Ltd.}, author={Bezuidenhout, Louise and Drummond-Curtis, Sara and Walker, Bridget and Shanahan, Hugh and Alfaro-Córdoba, Marcela}, year={2021}, month={Feb}, pages={10} }
 @article{mora-castro r_2021, title={First evidence for an aposematic function of a very common color pattern in small insects}, volume={16}, url={https://doi.org/10.1371/journal.pone.0237288}, DOI={doi:10.1371/journal.pone.0237288}, abstractNote={Many small parasitoid wasps have a black head, an orange mesosoma and a black metasoma (BOB color pattern), which is usually present in both sexes. A likely function of this widespread pattern is aposematic (warning) coloration, but this has never been investigated. To test this hypothesis, we presented spider predators (Lyssomanes jemineus), both field-captured and bred in captivity from eggs, to four wasp genera (Baryconus, Chromoteleia, Macroteleia and Scelio), each genus being represented by a BOB morphospecies and black morphospecies. We also used false prey, consisting of lures made of painted rice grains. Behavioral responses were analyzed with respect to presence or absence of the BOB pattern. In order to better understand the results obtained, two additional studies were performed. First, the reflection spectrum of the cuticle of the wasp and a theoretical visual sensibility of the spider were used to calculate a parameter we called “absorption contrast” that allows comparing the perception contrast between black and orange in each wasp genus as viewed by the spider. Second, acute toxicity trials with the water flea, Daphnia magna, were performed to determine toxicity differences between BOB and non-BOB wasps. At least some of the results suggest that the BOB color pattern may possibly play an aposematic role.}, number={2}, journal={Plos one}, author={Mora-Castro R, Alfaro-Córdoba M}, year={2021}, month={Jan}, pages={0237288} }
 @article{eger_martens_sauma chacon_alfaro cordoba_hidalgo-cespedes_2021, title={Operationalizing Intentionality to Play Hanabi With Human Players}, volume={13}, ISSN={["2475-1510"]}, DOI={10.1109/TG.2020.3009359}, abstractNote={The cooperative card game Hanabi has become of increasing interest in the community, since it combines partially hidden information with information exchange using restricted communication channels. In this article, we describe artificial intelligence agents that are designed to play the game with human players. Our agents make use of the fact that human players expect other players to act intentionally by formulating goals of their own and planning how to achieve them. They then use the available actions available to communicate their plan to the human player. On the flip side, our agents also interpret the actions performed by the human player as containing information about their plans. We present two different variants of our agent that perform this interpretation in different ways. Additionally, since part of human communication happens in subtle indirect ways, we also demonstrate that our agent can use the timing of the human player’s actions as additional information. In order to validate our agents, we have performed two separate experiments: one was done to validate the intentional component of the agents, while the other focused on the interpretation of received information. In this article, we also present the results obtained from these two experiments.}, number={4}, journal={IEEE TRANSACTIONS ON GAMES}, author={Eger, Markus and Martens, Chris and Sauma Chacon, Pablo and Alfaro Cordoba, Marcela and Hidalgo-Cespedes, Jeisson}, year={2021}, month={Dec}, pages={388–397} }
 @article{córdoba_hidalgo_alfaro_2020, title={Aridity Trends in Central America: A Spatial Correlation Analysis}, url={http://dx.doi.org/10.3390/atmos11040427}, DOI={10.3390/atmos11040427}, abstractNote={Trend analyses are common in several types of climate change studies. In many cases, finding evidence that the trends are different from zero in hydroclimate variables is of particular interest. However, when estimating the confidence interval of a set of hydroclimate stations or gridded data the spatial correlation between can affect the significance assessment using for example traditional non-parametric and parametric methods. For this reason, Monte Carlo simulations are needed in order to generate maps of corrected trend significance. In this article, we determined the significance of trends in aridity, modeled runoff using the Variable Infiltration Capacity Macroscale Hydrological model, Hagreaves potential evapotranspiration (PET) and near-surface temperature in Central America. Linear-regression models were fitted considering that the predictor variable is the time variable (years from 1970 to 1999) and predictand variable corresponds to each of the previously mentioned hydroclimate variables. In order to establish if the temporal trends were significantly different from zero, a Mann Kendall and a Monte Carlo test were used. The spatial correlation was calculated first to correct the variance of each trend. It was assumed in this case that the trends form a spatial stochastic process that can be modeled as such. Results show that the analysis considering the spatial correlation proposed here can be used for identifying those extreme trends. However, a set of variables with strong spatial correlation such as temperature can have robust and widespread significant trends assuming independence, but the vast majority of the stations can still fail the Monte Carlo test. We must be vigilant of the statistically robust changes in key primary parameters such as temperature and precipitation, which are the driving sources of hydrological alterations that may affect social and environmental systems in the future.}, journal={Atmosphere}, author={Córdoba, Marcela Alfaro and Hidalgo, Hugo and Alfaro, Eric}, year={2020}, month={Apr} }
 @article{zuleta-correa_chinn_alfaro-córdoba_truong_yencho_bruno-bárcena_2020, place={George Craig Yencho}, title={Use of unconventional mixed Acetone-Butanol-Ethanol solvents for anthocyanin extraction from Purple-Fleshed sweetpotatoes}, volume={314}, ISSN={0308-8146}, url={http://dx.doi.org/10.1016/j.foodchem.2019.125959}, DOI={10.1016/j.foodchem.2019.125959}, abstractNote={Anthocyanins from purple-fleshed sweetpotatoes constitute highly valued natural colorants and functional ingredients. In the past, anthocyanin extraction conditions and efficiencies using a single acidified solvent have been assessed. However, the potential of solvent mixes that can be generated by fermentation of biomass-derived sugars have not been explored. In this study, the effects of single and mixed solvent, time, temperature, sweetpotato genotype and preparation, on anthocyanin and phenolic extraction were evaluated. Results indicated that unconventional diluted solvent mixes containing acetone, butanol, and ethanol were superior or equally efficient for extracting anthocyanins when compared to commonly used concentrated extractants. In addition, analysis of anthocyanidins concentrations including cyanidin (cy), peonidin (pe), and pelargonidin (pl), indicated that different ratios of pn/cy were obtained depending on the solvent used. These results could be useful when selecting processing conditions that better suit particular end-use applications and more environmentally friendly process development for purple sweetpotatoes.}, journal={Food Chemistry}, publisher={Elsevier BV}, author={Zuleta-Correa, Ana and Chinn, Mari Sum and Alfaro-Córdoba, Marcela and Truong, Van-Den and Yencho, George Craig and Bruno-Bárcena, José Manuel}, year={2020}, month={Jun}, pages={125959} }
 @book{shanahan_2019, title={A curriculum for foundational Research Data Science skills for Early Career Researchers}, url={https://www.rd-alliance.org/group/rdacodata-summer-schools-data-science-and-cloud-computing-developing-world-wg/outcomes-0}, DOI={10.15497/RDA00038}, journal={Research Data Alliance}, author={Shanahan, H.}, year={2019}, month={Dec} }
 @article{spectral measure of color variation of black-orange-black (bob) pattern in small parasitoid wasps (hymenoptera: scelionidae), a statistical approach_2019, volume={14}, url={http://dx.doi.org/10.1371/journal.pone.0218061}, DOI={10.1371/journal.pone.0218061}, abstractNote={Small parasitoid wasps are abundant and extremely diverse, yet their colors have not been analyzed. One of the more common color patterns observed in these wasps is a black-orange-black pattern, which is especially common among neotropical species of Scelionidae ranging in size from 2 to 10 mm. Due to the methodological challenges involved in extracting and analyzing pigments from small-sized insects, other methods for examining colors need to be explored. In this work, we propose the use of microspectrophotometry in combination with statistical analysis methods in order to 8 study the spectral properties in such cases. We examined 8 scelionid genera and 1 genus from a distantly related family (Evaniidae), all showing the black-orange-black pattern. Functional Data Analysis and statistical analysis of Euclidean distances for color components were applied to study color differences both between and within genera. The Functional Data Analysis proved to be a better method for treating the reflectance data because it gave a better representation of the physical information. Also, the reflectance spectra were separated into spectral color component contributions and each component was labeled according to its own dominant wavelength at the maximum of the spectrum: Red, Green and Blue. When comparing spectral components curves, the spectral blue components of the orange and black colors, independent of the genera being compared, result almost identical, suggesting that there is a common compound for the pigments. The results also suggest that cuticle from different genera, but with the same color might have a similar chemical composition. This is the first time that the black and orange colors in small parasitoid wasps has been analyzed and our results provide a basis for future research on the color patterns of an abundant but neglected group of insects.}, number={10}, journal={PLOS ONE}, year={2019}, month={Oct} }
 @article{tekbudak_alfaro-córdoba_maity_staicu_2018, title={A comparison of testing methods in scalar-on-function regression}, volume={103}, ISSN={1863-8171 1863-818X}, url={http://dx.doi.org/10.1007/S10182-018-00337-X}, DOI={10.1007/s10182-018-00337-x}, abstractNote={A scalar-response functional model describes the association between a scalar response and a set of functional covariates. An important problem in the functional data literature is to test nullity or linearity of the effect of the functional covariate in the context of scalar-on-function regression. This article provides an overview of the existing methods for testing both the null hypotheses that there is no relationship and that there is a linear relationship between the functional covariate and scalar response, and a comprehensive numerical comparison of their performance. The methods are compared for a variety of realistic scenarios: when the functional covariate is observed at dense or sparse grids and measurements include noise or not. Finally, the methods are illustrated on the Tecator data set.}, number={3}, journal={AStA Advances in Statistical Analysis}, publisher={Springer Science and Business Media LLC}, author={Tekbudak, Merve Yasemin and Alfaro-Córdoba, Marcela and Maity, Arnab and Staicu, Ana-Maria}, year={2018}, month={Oct}, pages={411–436} }
 @article{zhang_roell_truong_tanguay_reif_2017, title={A data-driven weighting scheme for multivariate phenotypic endpoints recapitulates zebrafish developmental cascades}, volume={314}, ISSN={["1096-0333"]}, url={https://dx.doi.org/10.1016/j.taap.2016.11.010}, DOI={10.1016/j.taap.2016.11.010}, abstractNote={Zebrafish have become a key alternative model for studying health effects of environmental stressors, partly due to their genetic similarity to humans, fast generation time, and the efficiency of generating high-dimensional systematic data. Studies aiming to characterize adverse health effects in zebrafish typically include several phenotypic measurements (endpoints). While there is a solid biomedical basis for capturing a comprehensive set of endpoints, making summary judgments regarding health effects requires thoughtful integration across endpoints. Here, we introduce a Bayesian method to quantify the informativeness of 17 distinct zebrafish endpoints as a data-driven weighting scheme for a multi-endpoint summary measure, called weighted Aggregate Entropy (wAggE). We implement wAggE using high-throughput screening (HTS) data from zebrafish exposed to five concentrations of all 1060 ToxCast chemicals. Our results show that our empirical weighting scheme provides better performance in terms of the Receiver Operating Characteristic (ROC) curve for identifying significant morphological effects and improves robustness over traditional curve-fitting approaches. From a biological perspective, our results suggest that developmental cascade effects triggered by chemical exposure can be recapitulated by analyzing the relationships among endpoints. Thus, wAggE offers a powerful approach for analysis of multivariate phenotypes that can reveal underlying etiological processes.}, journal={TOXICOLOGY AND APPLIED PHARMACOLOGY}, publisher={Elsevier BV}, author={Zhang, Guozhu and Roell, Kyle R. and Truong, Lisa and Tanguay, Robert L. and Reif, David M.}, year={2017}, month={Jan}, pages={109–117} }
 @misc{data from: the use of functional data analysis to evaluate activity in a spontaneous model of degenerative joint disease associated pain in cats_2017, url={http://datadryad.org/resource/doi:10.5061/dryad.v1c16}, DOI={10.5061/dryad.v1c16}, year={2017}, month={Jan} }
 @article{gruen_alfaro-córdoba_thomson_worth_staicu_lascelles_2017, title={The Use of Functional Data Analysis to Evaluate Activity in a Spontaneous Model of Degenerative Joint Disease Associated Pain in Cats}, volume={12}, ISSN={1932-6203}, url={http://dx.doi.org/10.1371/journal.pone.0169576}, DOI={10.1371/journal.pone.0169576}, abstractNote={Introduction and objectives Accelerometry is used as an objective measure of physical activity in humans and veterinary species. In cats, one important use of accelerometry is in the study of therapeutics designed to treat degenerative joint disease (DJD) associated pain, where it serves as the most widely applied objective outcome measure. These analyses have commonly used summary measures, calculating the mean activity per-minute over days and comparing between treatment periods. While this technique has been effective, information about the pattern of activity in cats is lost. In this study, functional data analysis was applied to activity data from client-owned cats with (n = 83) and without (n = 15) DJD. Functional data analysis retains information about the pattern of activity over the 24-hour day, providing insight into activity over time. We hypothesized that 1) cats without DJD would have higher activity counts and intensity of activity than cats with DJD; 2) that activity counts and intensity of activity in cats with DJD would be inversely correlated with total radiographic DJD burden and total orthopedic pain score; and 3) that activity counts and intensity would have a different pattern on weekends versus weekdays. Results and conclusions Results showed marked inter-cat variability in activity. Cats exhibited a bimodal pattern of activity with a sharp peak in the morning and broader peak in the evening. Results further showed that this pattern was different on weekends than weekdays, with the morning peak being shifted to the right (later). Cats with DJD showed different patterns of activity from cats without DJD, though activity and intensity were not always lower; instead both the peaks and troughs of activity were less extreme than those of the cats without DJD. Functional data analysis provides insight into the pattern of activity in cats, and an alternative method for analyzing accelerometry data that incorporates fluctuations in activity across the day.}, number={1}, journal={PLOS ONE}, publisher={Public Library of Science (PLoS)}, author={Gruen, Margaret E. and Alfaro-Córdoba, Marcela and Thomson, Andrea E. and Worth, Alicia C. and Staicu, Ana-Maria and Lascelles, B. Duncan X.}, editor={Harezlak, JaroslawEditor}, year={2017}, month={Jan}, pages={e0169576} }
 @article{variable selection methods with applications to atmospheric sciences_2017, url={https://repository.lib.ncsu.edu/handle/1840.20/34318?show=full}, journal={North Carolina State University}, year={2017}, month={May} }
 @article{mileto_marin_alfaro-cordoba_ramirez-giraldo_eusemann_scribano_blandino_mazziotti_ascenti_2014, title={Iodine Quantification to Distinguish Clear Cell from Papillary Renal Cell Carcinoma at Dual-Energy Multidetector CT: A Multireader Diagnostic Performance Study}, volume={273}, ISSN={["0033-8419"]}, url={https://doi.org/10.1148%2Fradiol.14140171}, DOI={10.1148/radiol.14140171}, abstractNote={PURPOSE
To investigate whether dual-energy multidetector row computed tomographic (CT) imaging with iodine quantification is able to distinguish between clear cell and papillary renal cell carcinoma ( RCC renal cell carcinoma ) subtypes.


MATERIALS AND METHODS
In this retrospective, HIPAA-compliant, institutional review board-approved study, 88 patients (57 men, 31 women) with diagnosis of either clear cell or papillary RCC renal cell carcinoma at pathologic analysis, who underwent contrast material-enhanced dual-energy nephrographic phase study between December 2007 and June 2013, were included. Five readers, blinded to pathologic diagnosis, independently evaluated all cases by determining the lesion iodine concentration on color-coded iodine maps. The receiving operating characteristic curve analysis was adopted to estimate the optimal threshold for discriminating between clear cell and papillary RCC renal cell carcinoma , and results were validated by using a leave-one-out cross-validation. Interobserver agreement was assessed by using an intraclass correlation coefficient. The correlation between tumor iodine concentration and tumor grade was investigated.


RESULTS
A tumor iodine concentration of 0.9 mg/mL represented the optimal threshold to discriminate between clear cell and papillary RCC renal cell carcinoma , and it yielded the following: sensitivity, 98.2% (987 of 1005 [95% confidence interval: 97.7%, 98.7%]); specificity, 86.3% (272 of 315 [95% confidence interval: 85.0%, 87.7%]); positive predictive value, 95.8% (987 of 1030 [95% confidence interval: 95.0%, 96.6%]); negative predictive value, 93.7% (272 of 290 [95% confidence interval: 92.8%, 94.7%]); overall accuracy of 95.3% (1259 of 1320 [95% confidence interval: 94.6%, 96.2%]), with an area under the curve of 0.923 (95% confidence interval: 0.913, 0.933). An excellent agreement was found among the five readers in measured tumor iodine concentration (intraclass correlation coefficient, 0.9990 [95% confidence interval: 0. 9987, 0.9993). A significant correlation was found between tumor iodine concentration and tumor grade for both clear cell (τ = 0.85; P < .001) and papillary RCC renal cell carcinoma (τ = 0.53; P < .001).


CONCLUSION
Dual-energy multidetector CT with iodine quantification can be used to distinguish between clear cell and papillary RCC renal cell carcinoma , and it provides insights regarding the tumor grade.}, number={3}, journal={RADIOLOGY}, publisher={Radiological Society of North America (RSNA)}, author={Mileto, Achille and Marin, Daniele and Alfaro-Cordoba, Marcela and Ramirez-Giraldo, Juan Carlos and Eusemann, Christian D. and Scribano, Emanuele and Blandino, Alfredo and Mazziotti, Silvio and Ascenti, Giorgio}, year={2014}, month={Dec}, pages={813–820} }
 @article{mileto_ramirez-giraldo_marin_alfaro-cordoba_eusemann_scribano_blandino_mazziotti_ascenti_2014, title={Nonlinear Image Blending for Dual-Energy MDCT of the Abdomen: Can Image Quality Be Preserved If the Contrast Medium Dose Is Reduced?}, volume={203}, ISSN={["1546-3141"]}, url={https://doi.org/10.2214%2Fajr.13.12179}, DOI={10.2214/ajr.13.12179}, abstractNote={OBJECTIVE
The objective of this study was to compare the image quality of a dual-energy nonlinear image blending technique at reduced load of contrast medium with a simulated 120-kVp linear blending technique at a full dose during portal venous phase MDCT of the abdomen.


SUBJECTS AND METHODS
Forty-five patients (25 men, 20 women; mean age, 65.6 ± 9.7 [SD] years; mean body weight, 74.9 ± 12.4 kg) underwent contrast-enhanced single-phase dual-energy CT of the abdomen by a random assignment to one of three different contrast medium (iomeprol 400) dose injection protocols: 1.3, 1.0, or 0.65 mL/kg of body weight. The contrast-to-noise ratio (CNR) and noise at the portal vein, liver, aorta, and kidney were compared among the different datasets using the ANOVA. Three readers qualitatively assessed all datasets in a blinded and independent fashion.


RESULTS
Nonlinear blended images at a 25% reduced dose allowed a significant improvement in CNR (p < 0.05 for all comparisons), compared with simulated 120-kVp linear blended images at a full dose. No statistically significant difference existed in CNR and noise between the nonlinear blended images at a 50% reduced dose and the simulated 120-kVp linear blended images at a full dose. Nonlinear blended images at a 50% reduced dose were considered in all cases to have acceptable image quality.


CONCLUSION
The dual-energy nonlinear image blending technique allows reducing the dose of contrast medium up to 50% during portal venous phase imaging of the abdomen while preserving image quality.}, number={4}, journal={AMERICAN JOURNAL OF ROENTGENOLOGY}, publisher={American Roentgen Ray Society}, author={Mileto, Achille and Ramirez-Giraldo, Juan Carlos and Marin, Daniele and Alfaro-Cordoba, Marcela and Eusemann, Christian D. and Scribano, Emanuele and Blandino, Alfredo and Mazziotti, Silvio and Ascenti, Giorgio}, year={2014}, month={Oct}, pages={838–845} }
 @article{comparación metodológica de encuestas vía telefonía fija y celular en costa rica_2010, url={https://revistas.ucr.ac.cr/index.php/economicas/article/view/7064/6749}, journal={Revista de Ciencias Económicas}, year={2010}, month={Jun} }
 @unpublished{ multivariate spatial-temporal variable selection with applications to seasonal tropical cyclone modeling, url={https://arxiv.org/abs/1805.03318}, journal={North Carolina State University} }
 @inproceedings{an intentional ai for hanabi, DOI={10.1109/CIG.2017.8080417}, abstractNote={Cooperative games with partial observability are a challenging domain for AI research, especially when the AI should cooperate with a human player. In this paper we investigate one such game, the award-winning card game Hanabi, which has been studied by other researchers before. We present an agent designed to play better with a human cooperator than these previous results by basing it on communication theory and psychology research. To demonstrate that our agent performs better with a human cooperator we ran an experiment in which 224 participants played one or more games of Hanabi with different AIs, and will show that our AI scores higher than previously published work in such a setting.} }
 @article{mora_hernandez-jimenez_alfaro-córdoba_avendaño-soto_hanson, title={Spectral measure of color variation of black - orange - black (BOB) pattern in small parasitic wasps (Hymenoptera: Scelionidae), a statistical approach}, DOI={10.1101/652594}, abstractNote={Abstract}, author={Mora, Rebeca and Hernandez-Jimenez, Marcela and Alfaro-Córdoba, Marcela and Avendaño-Soto, Esteban and Hanson, Paul} }