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- Creator:
- Moore, Talia Y., Danforth, Shannon M., Larson, Joanna G., and Davis Rabosky, Alison R.
- Description:
- Warning signals in chemically defended organisms are critical components of predator-prey interactions, often requiring multiple coordinated display components for a signal to be effective. When threatened by a predator, venomous coral snakes (genus Micrurus) display a vigorous, non-locomotory thrashing behaviour that has been only qualitatively described. Given the high-contrast and often colourful banding patterns of these snakes, this thrashing display is hypothesized to be a key component of a complex aposematic signal under strong stabilizing selection across species in a mimicry system. By experimentally testing snake response across simulated predator cues, we analysed variation in the presence and expression of a thrashing display across five species of South American coral snakes. Although the major features of the thrash display were conserved across species, we found significant variation in the propensity to perform a display at all, the duration of thrashing, and the curvature of snake bodies that was mediated by predator cue type, snake body size, and species identity. We also found an interaction between curve magnitude and body location that clearly shows which parts of the display vary most across individuals and species. Our results suggest that contrary to the assumption in the literature that all species and individuals perform the same display, a high degree of variation persists in thrashing behaviour exhibited by Micrurus coral snakes despite presumably strong selection to converge on a common signal. This quantitative behavioural characterization presents a new framework for analysing the non-locomotory motions displayed by snakes in a broader ecological context, especially for signalling systems with complex interaction across multiple modalities.
- Keyword:
- aposematism, biomechanics, coral snake mimicry, curvature, Elapidae, non-locomotory motion, Peruvian Amazon, and snake behaviour
- Citation to related publication:
- Moore, T. Y., Danforth, S. M., Larson, J. G., & Davis Rabosky, A. R. (2020). A Quantitative Analysis of Micrurus Coral Snakes Reveals Unexpected Variation in Stereotyped Anti-Predator Displays Within a Mimicry System. Integrative Organismal Biology, 2(1). https://doi.org/10.1093/iob/obaa006
- Discipline:
- Science
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- Creator:
- Burgin, Tucker and Mayes, Heather B.
- Description:
- This project aimed to discover and analyze the molecular mechanism of synthesis of two particular fucosylated oligosaccharide products in a mutant enzyme, Thermatoga maratima Alpha-L-Fucosidase D224G, whose wild type performs the opposite reaction (cleavage of fucosyl glycosidic bonds). Discovery of the mechanism was performed using an unbiased simulations method known as aimless shooting, whereas analysis of the mechanism in terms of the energy profile was performed using a separate method known as equilibrium path sampling. The data here concerns the latter method. and The contents of the atesa_master.zip are the ATESA GitHub project. A Python program for automating transition path sampling with aimless shooting using Amber. https://github.com/team-mayes/atesa
- Keyword:
- Equilibrium Path Sampling, Transition Path Sampling, Enzymatic Mechanism, and GH29
- Citation to related publication:
- Burgin, T., & Mayes, H. B. (2019). Mechanism of oligosaccharide synthesis via a mutant GH29 fucosidase. Reaction Chemistry & Engineering, 4(2), 402–409. https://doi.org/10.1039/C8RE00240A
- Discipline:
- Engineering
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- Creator:
- Ruas, Terry, Ferreira, Charles H. P., Grosky, William, França, Fabrício O., and Medeiros, Débora M. R,
- Description:
- The relationship between words in a sentence often tell us more about the underlying semantic content of a document than its actual words, individually. Recent publications in the natural language processing arena, more specifically using word embeddings, try to incorporate semantic aspects into their word vector representation by considering the context of words and how they are distributed in a document collection. In this work, we propose two novel algorithms, called Flexible Lexical Chain II and Fixed Lexical Chain II that combine the semantic relations derived from lexical chains, prior knowledge from lexical databases, and the robustness of the distributional hypothesis in word embeddings into a single decoupled system. In short, our approach has three main contributions: (i) unsupervised techniques that fully integrate word embeddings and lexical chains; (ii) a more solid semantic representation that considers the latent relation between words in a document; and (iii) lightweight word embeddings models that can be extended to any natural language task. Knowledge-based systems that use natural language text can benefit from our approach to mitigate ambiguous semantic representations provided by traditional statistical approaches. The proposed techniques are tested against seven word embeddings algorithms using five different machine learning classifiers over six scenarios in the document classification task. Our results show that the integration between lexical chains and word embeddings representations sustain state-of-the-art results, even against more complex systems. Github: https://github.com/truas/LexicalChain_Builder
- Keyword:
- document classification, lexical chains, word embeddings, synset embeddings, chain2vec, and natural language processing
- Citation to related publication:
- Terry Ruas, Charles Henrique Porto Ferreira, William Grosky, Fabrício Olivetti de França, Débora Maria Rossi de Medeiros, "Enhanced word embeddings using multi-semantic representation through lexical chains", Information Sciences, 2020, https://doi.org/10.1016/j.ins.2020.04.048
- Discipline:
- Other, Science, and Engineering
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- Creator:
- Ruas, Terry, Grosky, William, and Aizawa, Akiko
- Description:
- This data set is a collection of word similarity benchmarks (RG65, MEN3K, Wordsim 353, simlex999, SCWS, yp130, simverb3500) in their original format and converted into a cosine similarity scale. In addition, we have two Wikpedia Dumps from 2010 (April) and 2018 (January) in which we provide the original format (raw words), converted using the techniques described in the paper (MSSA, MSSA-D and MSSA-NR) (title in this repository), and also the word embeddings models for 300d and 1000d using a word2vec implementation. A readme.txt is provided with more details for each file.
- Keyword:
- multi-sense embeddings, MSSA, word2vec, wikipedia dump, synset, and natural language processing
- Citation to related publication:
- https://doi.org/10.1016/j.eswa.2019.06.026
- Discipline:
- Other
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- Creator:
- Pedde, Meredith
- Description:
- In this study, we took advantage of the randomized allocation of the US EPA's funding for school bus replacements and retrofits to causally assess the impacts of upgrading buses through the EPA’s national School Bus Rebate Program on attendance, educational performance, and community air quality (PM2.5). Specifically, we used classical intent-to-treat analyses for randomized controlled trials to compare the changes in school district average attendance, test scorers (reading language arts and math), and PM2.5 levels after vs before the 2012 through 2017 lotteries by funding selection status.
- Keyword:
- School Bus Emissions, Diesel Air Pollution, Attendance, Test scores, Educational performance, PM2.5, Air pollution, and Air quality
- Citation to related publication:
- Adar SD, Pedde M, Hirth R, Szpiro A. 2024. Assessing the National Health, Education, and Air Quality Benefits of the United States Environmental Protection Agency’s School Bus Rebate Program: A Randomized Controlled Trial Design. Research Report 221. Boston, MA: Health Effects Institute.
- Discipline:
- Health Sciences
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- Creator:
- Pedde, Meredith
- Description:
- In this study, we took advantage of the randomized allocation of the US EPA's funding for school bus replacements and retrofits to causally assess the impacts of upgrading buses on students' educational performance through the EPA’s national School Bus Rebate Program. Specifically, we used classical intent-to-treat analyses for randomized controlled trials to compare the change in school district level reading and language arts and math standardized test scores after vs before the 2012 through 2016 lotteries by funding selection status . We used overall district average standardized test scores since rates were not available for only school-bus riders.
- Keyword:
- School Bus Emissions, Diesel Air Pollution, and Student standardized testing
- Citation to related publication:
- Pedde, M., Szpiro, A., Hirth, R., Adar, S. School Bus Rebate Program and Student Educational Performance Test Scores. JAMA Network Open (2024). https://doi.org/10.1001/jamanetworkopen.2024.3121
- Discipline:
- Health Sciences
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- Creator:
- A. Abeid, Bachir , L. Fabiilli, Mario , Aliabouzar, Mitra, and Estrada, Jon B.
- Description:
- Images of droplet dynamics during and after optical excitation experiments were recorded in the ultra-fast regime at 1 million frames per second (fps) while the low-speed, quasi-static evolution was carried at 1 fps. During both the inertial and quasi-static phases, we record 1–3 frames in the reference configuration prior to the arrival of the laser-pulse to distinguish the bubble from the background. Lastly, due to the complex physics of plasma formation and chemistry, forward simulations begin at the time when the bubble reaches its maximum expansion
- Keyword:
- optical droplet vaporization, cavitation, viscoelasticity, ultra-high-speed imaging, hydrogel, numerical modeling.
- Citation to related publication:
- Abeid, Bachir A, et al. (2024). Experimental and numerical investigations of ultra-high-speed dynamics of optically induced droplet cavitation in soft materials
- Discipline:
- Science and Engineering
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- Creator:
- Hawes, Jason K
- Description:
- Most of this deposit is composed of a step-by-step explanation of how to replicate the work conducted in Chapters 2 and 5 of my dissertation (available in DeepBlue Documents under the title Urban Agriculture: Good for People, Places, and Planet?). Very little actual data is catalogued here, instead largely relying on links to the secondary datasets online. In fact, this is an intentional choice, since any replication would likely want updated data to produce more real-time results. This deposit is intended to accompany the dissertation and may not be the final version of these two manuscripts or their associated methods. For more up-to-date methods and analysis, please search Google Scholar or your affiliated library for Jason Hawes and some combination of keywords including urban agriculture, scaling-up, tradeoffs, or the names of the cities in question.
- Keyword:
- urban agriculture, tradeoffs, remote sensing, and multi-criteria analysis
- Discipline:
- Social Sciences
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- Creator:
- Wu, Wenbing, Kadar, Alain, Lee, Sang Hyun, Jung, Hong Ju, Park, Bum Chul, Raymond, Jeffery, Tsotsis, Thomas, Cesnik, Carlos, Glotzer, Sharon, Goss, Valerie, and Kotov, Nicholas
- Description:
- The goal of this project is to relate properties of nanowire networks to their structure. The structure of these networks was determined from electron and atomic force microscopy, which were used as the basis for property predictions. Properties include sheet resistance, conductive anisotropy, absorption spectra, and current capacity.
- Keyword:
- structural complexity, nanowires, graph theory (GT), complex particle systems, complex composites, correlated disorder
- Citation to related publication:
- Preprint: https://arxiv.org/pdf/2310.15369
- Discipline:
- Engineering
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- Creator:
- Ye, Zhengwei and Mi, Zetian
- Description:
- Generation of C2+ compounds using sunlight, carbon dioxide, and water provides a promising path for carbon neutrality. The exploration of a catalyst to break the bottleneck of C-C coupling, for constructing a rational artificial photosynthesis integrated device, is at the core. Herein, based on operando spectroscopy measurements, theoretical calculations, and feedstock experiments, it is discovered that gold, in conjunction with iridium, can catalyze the reduction of CO2, achieving C-C coupling by insertion of CO2 into -CH3. Owing to a combination of optoelectronic and catalytic properties, the assembly of AuIr with InGaN nanowires on silicon (AuIr@InGaN NWs/Si) enables the achievement of a C2H6 activity of 58.8 mmol‧g-1‧h-1 with a turnover number of 54,595 over 60 hours. A light-to-fuels efficiency of ~0.59% for solar fuels production from CO2 and H2O is achieved without any other energy inputs. This work provides a carbon-negative path for producing higher order C compounds.
- Keyword:
- Carbon dioxide reduction and Photocatalysis
- Discipline:
- Science