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opencc-by-4.0Oct 2024View details →

MATLAB Code for "Joint Image Processing with Learning-Driven Data Representation and Model Behavior for Non-Intrusive Anemia Diagnosis in Pediatric Patients"

This MATLAB code is part of the study titled "Joint Image Processing with Learning-Driven Data Representation and Model Behavior for Non-Intrusive Anemia Diagnosis in Pediatric Patients", which has been accepted for publication in the Journal of Imaging (MDPI). The code supports image processing, feature extraction, and deep learning model training (including LSTM and RexNet) to classify pediatric patients as anemic or non-anemic based on palm, conjunctival, and fingernail images. Full study details are available in this paper: Berghout T. Joint Image Processing with Learning-Driven Data Representation and Model Behavior for Non-Intrusive Anemia Diagnosis in Pediatric Patients. Journal of Imaging. 2024; 10(10):245. <a href="https://doi.org/10.3390/jimaging10100245">https://doi.org/10.3390/jimaging10100245 </a> The datsets use in this work are: Asare, J. W., Appiahene, P. & Donkoh, E. (2022). Anemia Detection using Palpable Palm Image Datasets from Ghana. Mendeley Data. https://doi.org/10.17632/ccr8cm22vz.1 Asare, J. W., Appiahene, P. & Donkoh, E. (2023). CP-AnemiC (A Conjunctival Pallor) Dataset from Ghana. Mendeley Data. https://doi.org/10.17632/m53vz6b7fx.1 Asare, J. W., Appiahene, P. & Donkoh, E. (2020). Detection of Anemia using Colour of the Fingernails Image Datasets from Ghana. Mendeley Data. https://doi.org/10.17632/2xx4j3kjg2.1

opencc-by-4.0Oct 2024View details →

Modeling and Elucidating the Behavior of a Thermoresponsive LCST Ionic-Liquid

Input files for RESP calculation of TMBS necessary to reproduce results presented in the paper: "Modeling and Elucidating the Behavior of a Thermoresponsive LCST Ionic-Liquid"  by: Hussen O. Mohammed, Abel de Cozar, and Ronen Zangi Gromacs version 2023.1, used for all simulations in this work, is available to the public via the link https://manual.gromacs.org

opencc-by-nc-nd-4.0Aug 2021View details →

Predicting readers' prototypical eye-movement behavior using MASC, a model of Attention in the Superior Colliculus: Stimulus materials, model code, data, and statistical analyses.

The goal of the present research was to determine the role of rudimentary visuo-motor pathways, from the retina and the primary visual cortex to the superior colliculus (SC), in the guidance of human eye movement during reading. To this end, we used MASC, our model of Attention in the Superior Colliculus (Adeli et al., Journal of Neuroscience 2017), a model that relies on well-established saccade-programming principles in the SC. MASC predicts sequences of fixations over an input image by spatially integrating incoming signals in the space of the SC. Here, MASC computed the distribution of luminance contrast over sentences' images (visual-saliency map), after blurring it proportional to retinal eccentricity (retina transformation). It then projected the visual-saliency map into SC space, using a logarithmic afferent-mapping function (magnification factor). Input signals were averaged over retinotopically organized populations of neurons (point images) of constant size, first in the visual map and then in a spatially-registered motor map. The most active population was identified through a winner-take-all process. After jitter applied to the winning population, the next fixation location was determined using inverse efferent mapping. This sequence of events was then repeated to predict following fixation locations, but inserting after each saccade an inhibitory spatial tag (Inhibition of Saccade Return; ISR -referred to as IOR in the uploaded files). All MASC's parameters, but one, were biologically determined, using electrophysiological data in macaque; the ISR window was the one fit parameter. MASC was tested by comparing its predicted sequences of fixations over sentences from the French-Sentence Corpus (FSC) to the eye-movement behavior of 40 French-native speakers reading the same sentences for comprehension (Albrengues et al., Plos One 2019). Then, MASC was dissected to determine the crucial processing steps enabling prediction of human behavior (10 comparison models -see the general README file). Finally, to address crucial issues in the reading literature, i.e., the role of inter-word spacing and character print size in eye-movement guidance, MASC was additionally tested in four additional display conditions: the same sentences from the FSC, but with blank spaces between words being either filled or removed, or with the screen width angle being multiplied by 2 or 4, such that characters were larger in angular size (0.5° and 1°) than in the original experiment (0.25°). MASC's predicted effects of inter-word spacing and print size were compared to previously published data. All material relevant to the project is reported here, including the FSC materials (bitmap and information text files), the Matlab code for our MASC model, raw simulation data for MASC and all our comparison models, as well as MASC's simulations in the different display conditions, the scripts we developed in R to transform raw simulation data into data matrices for statistical analyses of (word-based) eye-movement behavior, the resulting data matrices for all models as well as the data matrix for FSC readers, the R-scripts for statistical comparison of oculomotor behavior between data sets and conditions, literature-review tables of previously published data (for comparison with MASC's predictions), and the R-scripts generating the figures summarizing our results. Further information can be found in the general README file as well as in the README files attached to each folder. The authors' respective contributions to the project, the licence attached to the included materials and their condition of use are listed in the general README file. A manuscript reporting and discussing these modeling data is in preparation (Vitu, F., Adeli, H. & Zelinsky, G. J.); A reference will be provided here when the manuscript appears in a journal. Other references to be cited: - For the model code: Adeli, H., Vitu, F., & Zelinsky, G. J. (2017). A model of the superior colliculus predicts fixation locations during scene viewing and visual search. Journal of Neuroscience, 37(6), 1453-1467. http://www.jneurosci.org/content/37/6/1453 - For FSC materials and data: Albrengues, C., Lavigne, F., Aguilar, C., Castet, E., & Vitu, F. (2019). Linguistic processes do not beat visuo-motor constraints, but they modulate where the eyes move regardless of word boundaries: Evidence against top-down word-based eye-movement control during reading. PLoS ONE 14(7): e0219666. https://doi.org/10.1371/journal.pone.0219666

opencc-by-4.0Nov 2022View details →

Modeling of Creep Behavior of Particulate Composites with Focus on Interfacial Adhesion Effect

Evaluation of creep compliance of particulate composites using empirical models always provides parameters depending on initial stress and material composition. The effort spent to connect model parameters with physical properties has not resulted in success yet. Further, during the creep, delamination between matrix and filler may occur depending on time and initial stress, reducing an interface adhesion and load transfer to filler particles. In this paper, the creep compliance curves of glass beads reinforced poly(butylene terephthalate) composites were fitted with Burgers and Findley models providing different sets of time-dependent model parameters for each initial stress. Despite the finding that the Findley model performs well in a primary creep, the Burgers model is more suitable if secondary creep comes into play; they allow only for a qualitative prediction of creep behavior because the interface adhesion and its time dependency is an implicit, hidden parameter. As Young’s modulus is a parameter of these models (and the majority of other creep models), it was selected to be introduced as a filler content-dependent parameter with the help of the cube in cube elementary volume approach of Paul. The analysis led to the time-dependent creep compliance that depends only on the time-dependent creep of the matrix and the normalized particle distance (or the filler volume content), and it allowed accounting for the adhesion effect. Comparison with the experimental data confirmed that the elementary volume-based creep compliance function can be used to predict the realistic creep behavior of particulate composites.

dryad32/100

Data for: Temperature and hygrometry of amphibian agar models in behavioral simulation and operational temperature of two forested areas

We investigated how thermoregulatory behaviors affect hydro-thermoregulation in anurans, using agar models as a sampling unit, simulating four behaviors related to behavioral fever and sickness behavior. We collected data in two forest environments (Wet forest and transitional forest) in the Parque Estadual Intervales (PEI), an Integral Conservation Unit of the Atlantic Forest (24°12' - 24°25' S; 48°03 - 48°30' W). The Wet forest is a mature Atlantic Forest, and the Transitional forest is a young secondary forest adjacent to open areas. We measured operational temperatures (temperatures of inanimate objects comparable to real frog species in size and shape) of agar models across 8 replicates in the two forest environments. We also measured agar models' temperature and water loss in different behavior simulations. In each transect, we used eight sampling unit (called tetrad) that was composed of two sets of four sensor-fit agar models. One of the sets was used to collect the operational temperature of the forest areas. These agar models were fitted with a 170 cm HOBO® Data Logger (U12-008) sensor programmed to record the temperature every 15 min. The second set of tetrads was used to collect the agar models' body temperature and water loss in different behavior simulations. The behavioral simulations were defined as: (a) strong behavioral fever (SBF); (b) apathy behavior (AB); (c) single thermoregulatory event (STE); and (d) control model (CO). After the temperature data were collected at 0600 h, three of the agar models (SBF, AB, and STE) were moved immediately, each one according to their corresponding protocol (SBF: Warmest Neighboring Site, AB: closest shelter, mainly small burrows, or accumulations of leaf litter; STE: Alternative Warmest Neighboring site). The selection of the places was made by using a FLIR TG165 Thermal Imaging Thermometer. One hour later, at about 0700 h, and hereafter hourly, a similar procedure was repeated, but only the SBF model required movement. We placed each model within 5 cm of another in this set to ensure similar initial thermal conditions. These tetrads were left undisturbed overnight, and no manipulation occurred after 2000 h. On the next day, at 0600 h, we measured the surface temperatures of the models and immediately applied the corresponding behavioral rule. This procedure was performed hourly until 2000 h. To analyze water loss, we recorded the mass of each model at 0600 h just after measuring temperature and repeated this every two hours. We used a portable balance (A&D Newton EJ-123, 0.01g accuracy) and calculated water loss rates from the difference between the initial model mass and mass measured at each subsequent 2-hour period. We express water loss as a percentage of maximum hydration.

opencc-zeroNov 2022View details →

FIGURE 8 in Two new species of the ant-like spider genus Fluda Peckham & Peckham, 1892 from Bolivia with first reports of potential ant models for the genus and a novel ant-resembling behavior (Araneae: Salticidae, Simonellini)

FIGURE 8. Living habitus of Fluda spp. and potential ant models. Fluda thuruampara sp. nov.: A–C. Males; D. Female; E. Camponotus sanctaefidei Dalla Torre, 1892, minor worker, Villa Teresa, La Paz Dept.; F. Camponotus latangulus Roger, 1863, minor worker, Buena Vista, Santa Cruz Dept.; G. Odontomachus sp., Villa Teresa, La Paz Dept.; H. Crematogaster pusillus Klug, 1824, minor worker, Villa Tunari, Cochabamba Dept.; F. dauca sp. nov.: I–K. Males; L. Female, dark form.

FIGURE 7 in Two new species of the ant-like spider genus Fluda Peckham & Peckham, 1892 from Bolivia with first reports of potential ant models for the genus and a novel ant-resembling behavior (Araneae: Salticidae, Simonellini)

FIGURE 7. Genitalia of Fluda thuruampara sp. nov. Palp of holotype (IBSI-Ar0958): A. Retrolateral view; B. Ventral view; C. Dorsal view, expanded; D. Retrolateral view, expanded; E. Course of spermatophore in D. Epigyne of paratype (IBSI-Ar0956): F. Ventral; G. Dorsal, cleared; H. Ventral, cleared.

FIGURE 5 in Two new species of the ant-like spider genus Fluda Peckham & Peckham, 1892 from Bolivia with first reports of potential ant models for the genus and a novel ant-resembling behavior (Araneae: Salticidae, Simonellini)

FIGURE 5. Genitalia of Fluda dauca sp. nov. Palp of holotype (IBSI-Ar1758): A. Ventral view; B. Retrolateral view. Epigyne of paratype (IBSI-Ar1027): C. Ventral view; D. Dorsal view, cleared; E. Ventral view, cleared.

FIGURE 4 in Two new species of the ant-like spider genus Fluda Peckham & Peckham, 1892 from Bolivia with first reports of potential ant models for the genus and a novel ant-resembling behavior (Araneae: Salticidae, Simonellini)

FIGURE 4. Habitus of Fluda dauca sp. nov. A. Holotype male (IBSI-Ar1758), dorsal; B. Idem, lateral; C. Female paratype, dark form (IBSI-Ar1027), dorsal; D. Idem, lateral; E. Female paratype, orange form (IBSI-Ar1027), dorsal; F. Idem, lateral.

FIGURE 1 in Two new species of the ant-like spider genus Fluda Peckham & Peckham, 1892 from Bolivia with first reports of potential ant models for the genus and a novel ant-resembling behavior (Araneae: Salticidae, Simonellini)

FIGURE 1. Sampled locations and ecoregions according to the regionalization by Navarro & Ferreira (2007), map produced with QGIS (version 2.14.3, http://www.qgis.org/en/site/). 1. Riberalta, Beni Dept.; 2. Villa Teresa, La Paz Dept.; 3. Villa Tunari, Cochabamba Dept.; 4. Santa Rosa de la Mina, Santa Cruz Dept.; 5. Santa Maria la Antigua, Santa Cruz Dept.; 6. Cafetal, Buena Vista, Santa Cruz Dept.; 7. Cotoca, Santa Cruz Dept.; 8. La Guardia, Santa Cruz Dept.; 9. Bermejo, Santa Cruz Dept.; 10. Santiago de Chiquitos, Santa Cruz Dept.; 11. Teja Huasi, Chuquisaca Dept.; 12. Arambulo, Tarija Dept.

FIGURE 6 in Two new species of the ant-like spider genus Fluda Peckham & Peckham, 1892 from Bolivia with first reports of potential ant models for the genus and a novel ant-resembling behavior (Araneae: Salticidae, Simonellini)

FIGURE 6. Habitus of Fluda thuruampara sp. nov. A. Holotype male (IBSI-Ar0958), dorsal; B. Idem, lateral; C. Paratype female (IBSI-Ar0956), lateral; D. Idem, dorsal.

FIGURE 3 in Two new species of the ant-like spider genus Fluda Peckham & Peckham, 1892 from Bolivia with first reports of potential ant models for the genus and a novel ant-resembling behavior (Araneae: Salticidae, Simonellini)

FIGURE 3. Habitus of Fluda spp. A. Fluda dauca sp. nov., male holotype (IBSI-Ar1758), dorsal; Fluda thuruampara sp. nov.: B. Holotype male (IBSI-Ar0958), dorsal; C. Idem, lateral.

opencc-by-4.0Apr 2023View details →

Thermodynamic modelling of the nature of speciation and phase behavior of binary and ternary mixtures of formaldehyde, water and methanol

Data underlying the journal article titled "Thermodynamic modelling of the nature of speciation and phase behavior of binary and ternary mixtures of formaldehyde, water and methanol" published in the Journal of Molecular Physics

opencc-by-4.0May 2023View details →

Data associated with Cell Reports publication: Dura-Bernal et al. 2023, "Multiscale model of primary motor cortex circuits predicts in vivo cell type-specific, behavioral state-dependent dynamics"

This dataset includes experimental data used to constrain and validate the model, and model simulation output data. The source code for the associated M1 model and data analysis can be found here: https://github.com/suny-downstate-medical-center/M1_NetPyNE_CellReports_2023 Please download the data_v2.zip file, which contains the most updated and complete version of the data. For more information please contact: salvador.dura-bernal@downstate.edu

opencc-by-4.0Jul 2023View details →

Anonymized data for paper "Automatic Bug Fixing in the Era of Large Language Models: Interactive Simulation of Programmer Behavior" submitted to ICSE 2024

The project includes the BFP benchmark used in the submitted ICSE 2024 paper titled "Automatic Bug Fixing in the Era of Large Language Models: Interactive Simulation of Programmer Behavior"

Fig. 3 in Modeling the peroxyl radical scavenging behavior of Carnosic acid: Mechanism, kinetics, and effects of physiological environments

Fig. 3. Deprotonated forms of CA under the physiological aqueous environment. The proton affinity (PA) values are in kcal/mol.

Fig. 6 in Modeling the peroxyl radical scavenging behavior of Carnosic acid: Mechanism, kinetics, and effects of physiological environments

Fig. 6. Optimized structures of the TSs of CA + HOO• reaction in physiological environments (W = water and PE = pentyl ethanoate). Distances are in Aand angles in ◦.

Fig. 2 in Modeling the peroxyl radical scavenging behavior of Carnosic acid: Mechanism, kinetics, and effects of physiological environments

Fig. 2. The stable conformation, HOMO, LUMO, and ESP of CA calculated at M06–2X/6–311++ G(d,p) level.

Fig. 4 in Modeling the peroxyl radical scavenging behavior of Carnosic acid: Mechanism, kinetics, and effects of physiological environments

Fig. 4. Computed BDE values in kcal/mol of CA in the gas phase (G) and pentyl ethanoate (PE) as well as of CA– in water (W).