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opencc-by-4.0Oct 2024View details →

Dataset for "Predicting the Strength of Composites with Computer Vision Using Small Experimental Datasets"

Composite_Strength_Prediction_by_CNN_v1.0

opencc-by-4.0Dec 2023View details →

Error Analysis of Kernel EDMD for Prediction and Control in the Koopman Framework

This repository contains code and data to re-create the numerical results shown in "Error analysis of kernel EDMD for prediction and control in the Koopman framework"  <a href="http://arxiv.org/abs/2312.10460">http://arxiv.org/abs/2312.10460</a> Please see the README file for detailed description of the codes in this repository.

restrictedcc-by-4.0Sep 2024View details →

Online water quality monitoring data from full scale CS#3 DWDN for the DBP prediction model

Online water quality data though the drinking water distribution network. More than 1 year of data. SCADA data source. Provide water quality of the whole system at selected locations.

opencc-by-4.0Jul 2021View details →

Predicting the crossmodal correspondences of odors using an electronic nose

Odour Recordings There are 100 recordings in total of 10 different essential oils; five were from Mystic Moments™ (caramel, cherry, coffee, freshly cut grass, and pine) and five from Miaroma™ (black pepper, lavender, lemon, orange, and peppermint). Each recording is 10 minutes in duration (600 seconds). Columns in each of the .csv files are in the following order: time, air quality, pollution level, temperature, pressure, humidity, gas, MQ3, MQ5, MQ9, and HCHO. The file's name denotes the odour being recorded and the record number (1 - 10). For more information, please view the publication - R.J. Ward, S. Rahman, S.M. Wuerger, A. Marshall, Predicting the crossmodal correspondences of odors using an electronic nose, Heliyon. Perceptual Data  The underlying perceptual data used from R.J. Ward, S.M. Wuerger, A. Marshall, Smelling Sensations: Olfactory Crossmodal Correspondences, J. Percept. Imaging. 4 (2021) 1–12. https://doi.org/10.2352/j.percept.imaging.2021.4.2.020402. The data used from the later paper is the (angularity of shapes, smoothness of texture, perceived pleasantness, pitch, and the colour ratings in L*a*b* space). Each file contains the raw perceptual ratings for the ten different odours (columns) from sixty-eight different participants (rows) in the following order: black pepper, caramel, cherry, coffee, freshly cut grass, lavender, lemon, orange, peppermint, and pine. NOTE: the pitch ratings only contain data from sixy participants due to it being added to the experiment at a later date. The folder regression models contains the required MATLAB code to train and test the regression models for predicting the crossmodal correspondences of odors using physicochemical data. The folder raw perceptual data contains the raw unprocessed perceptual data in .csv format. The folder e-nose code contains the code to drive the Arduino circuit and additional libraries required by the sensors. The folder e-nose recorder contains a Unity project and code to receive the UDP packets from the e-nose and log them. If you use this data please cite the following papers; Perceptual Data R.J. Ward, S.M. Wuerger, A. Marshall, Smelling Sensations: Olfactory Crossmodal Correspondences, J. Percept. Imaging. 4 (2021) 1–12. https://doi.org/10.2352/j.percept.imaging.2021.4.2.020402 Chemical Data R. Ward, S. Rahman, S. Wuerger, A. Marshall, Predicting the colour associated with odours using an electronic nose, in: 1st Work. Multisensory Exp. - SensoryX’21, 2021: pp. 1–6. https://doi.org/10.5753/sensoryx.2021.15683. R.J. Ward, S. Rahman, S.M. Wuerger, A. Marshall, Predicting the crossmodal correspondences of odors using an electronic nose, Heliyon, (under review as of file upload).

Figure 4 in Calling phenology of anurans in a tropical rainforest in South Mexico: testing predictive models

Figure 4. Best models of each general structure. Model 6 (M6) for linear and 13 (M13) for sinusoidal structure. I = relative calling intensity, t = time. The solid lines represent the predictions of the models; the points represent the data acquired from the ARS.

Figure 3 in Calling phenology of anurans in a tropical rainforest in South Mexico: testing predictive models

Figure 3. Rose-diagram of anuran assemblage relative calling intensity. The length and colour (light = low, dark = high) of the bars from the centre indicate the intensity of vocalisation for the temporal section. A Rayleigh z test for unimodal orientation was performed, resulting in significant evidence of non-uniform distribution of vocalisations across the year (P = 0.0303).

Figure 1 in Calling phenology of anurans in a tropical rainforest in South Mexico: testing predictive models

Figure 1. Study site location and land use, natural protected area of Nahá, Ocosingo, Chiapas, México.

Figure 2. a in Calling phenology of anurans in a tropical rainforest in South Mexico: testing predictive models

Figure 2. a) Calling anuran species recorded at temporary sections (7 months). The horizontal axis corresponds to temporary sections and the vertical to species. b) Average temperature T � (° C) (continuous line) and accumulated rainfall Ra (dashed line) by temporary section (32 in 7 months). Both graphs share the horizontal axis, where breaks indicate recording gaps, and the numbers are the days of the months covered.

opencc-zeroOct 2021View details →

Predictability and parallelism in the contemporary evolution of hybrid genomes

Hybridization between species is widespread across the tree of life. As a result, many species, including our own, harbor regions of their genome derived from hybridization. Despite the recognition that this process is widespread, we understand little about how the genome stabilizes following hybridization, and whether the mechanisms driving this stabilization tend to be shared across species. Here, we dissect the drivers of variation in local ancestry across the genome in replicated hybridization events between two species pairs of swordtail fish: Xiphophorus birchmanni × X. cortezi and X. birchmanni × X. malinche . We find surprisingly high levels of repeatability in local ancestry across the two types of hybrid populations. This repeatability is attributable in part to the fact that the recombination landscape and locations of functionally important elements play a major role in driving variation in local ancestry in both types of hybrid populations. Beyond these broad scale patterns, we identify dozens of regions of the genome where minor parent ancestry is unusually low or high across species pairs. Analysis of these regions points to shared sites under selection across species pairs, and in some cases, shared mechanisms of selection. We show that one such region is a previously unknown hybrid incompatibility that is shared across X. birchmanni × X. cortezi and X. birchmanni × X. malinche hybrid populations.

Supplementary code for: "Historical glacier change on Svalbard predicts doubling of mass loss by 2100"

Code to perform the analysis in: Geyman, E.C., van Pelt, W., Maloof, A.C., Faste Aas, H., and Kohler, J., 2021. "Historical glacier change on Svalbard predicts doubling of mass loss by 2100." Nature. Abstract: The melting of glaciers and ice caps accounts for about one third of current sea level rise, exceeding the mass loss from the more voluminous Greenland or Antarctic Ice Sheets. The Arctic archipelago of Svalbard, which hosts spatial climate gradients that are larger than the expected temporal shifts over the next century, is a natural laboratory to constrain the climate sensitivity of glaciers and predict their response to future warming. Leveraging an archive of historical aerial images from 1936 and 1938, we use structure-from-motion (SfM) photogrammetry to reconstruct the 3D geometry of 1,594 glaciers across Svalbard. We compare these reconstructions to modern ice elevation data to derive the spatial pattern of mass balance over a >70-year timespan, allowing us to see through the noise of annual and decadal variability to quantify how variables such as temperature and precipitation control ice loss. We find a robust temperature dependence of melt rates, whereby a 1°C rise in mean summer temperature corresponds to a decrease in area-normalized mass balance of -0.27 m yr-1 of water equivalent. Finally, we design a space-for-time substitution to make first-order predictions of 21st century glacier change across Svalbard. Even in the most modest scenario (a ~1.4°C rise in mean summer temperature by 2100), we predict average glacier thinning rates in 2010-2100 of -0.67 m yr-1, approximately twice the 1936-2010 rates.

Data from: Resource predictability drives inter-annual variation in migratory behaviour in a long-lived bird

There is a growing awareness that experience may play a major role in migratory decisions, especially in long-lived species. However, empirical support remains to date scarce. Here, we use multi-year GPS-tracking data on 28 adult Lesser Black-backed Gulls (Larus fuscus), a long-lived species for which migratory strategies typically consist of a series of long stopovers, to assess how experience affects interannual variation in stopover selection. We expect that food source reliability should play a pivotal role, as it both reduces the uncertainty on food availability across years, and enables for more efficient foraging during stopovers by reducing searching efforts. We found that during stopovers gulls indeed developed high fidelity to particular foraging locations, which strongly reduced the daily distance travelled for foraging. When revisiting stopovers in consecutive years, birds used over 80% of foraging locations from the previous year. Although the average fidelity to stopovers across years was a high as 85%, stopovers where birds showed high foraging site fidelity were up to 60% more likely to be revisited compared to stopover with low foraging site fidelity. Accordingly, birds using more stopovers with reliable foraging opportunities showed significantly less interannual variation in their stopover use than birds using stopovers with less reliable foraging opportunities. Our results thus highlight the need to further deepen our understanding of the role of cognitive processes in individual variation in migratory behaviour.

Body mass and hibernation microclimate may predict bat susceptibility to white-nose syndrome

In multi-host disease systems, differences in mortality between species may reflect variation in host physiology, morphology, and behavior. In systems where the pathogen can persist in the environment, microclimate conditions, and the adaptation of the host to these conditions, may also impact mortality. White-nose syndrome is an emerging disease of hibernating bats caused by an environmentally persistent fungus, Pseudogymnoascus destructans. We assessed the effects of body mass, torpid metabolic rate, evaporative water loss, and hibernaculum temperature and water vapor deficit on predicted overwinter survival of bats infected by P. destructans. We used a hibernation energetics model in an individual-based model framework to predict the probability of survival of nine bat species at eight sampling sites across North America. The model predicts time until fat exhaustion as a function of species-specific host characteristics, hibernaculum microclimate, and fungal growth. We fit a linear model to determine relationships with each variable and predicted survival and semi-partial correlation coefficients to determine the major drivers in variation in bat survival. We found host body mass and hibernaculum water vapor deficit explained over half of the variation in survival with white-nose syndrome across species. As previous work on the interplay between host and pathogen physiology and the environment has focused on species with narrow microclimate preferences, our view on this relationship is limited. Our results highlight some key predictors of interspecific survival among western bat species and provide a framework to assess impacts of white-nose syndrome as the fungus continues to spread into western North America.

Screening of 6000 compounds for uncoupling activity: input parameters, the predicted uncoupling activity, as well as the results in respect to structural alerts

Protonophoric uncoupling of phosphorylation is an important factor when assessing chemicals for their toxicity, and has recently moved into focus in pharmaceutical research with respect to the treatment of diseases such as cancer, diabetes or obesity. Reliably identifying uncoupling activity is thus a valuable goal. To that end, we screened more than 6000 anionic compounds for in-vitro uncoupling activity, using a biophysical model based on ab-initio COSMO-RS input parameters with the molecular structure as the only external input. We combined these results with a model for baseline toxicity (narcosis). Our model identified more than 1250 possible uncouplers in the screening dataset, and identified possible new uncoupler classes such as thiophosphoric acids. When tested against 423 known uncouplers and 612 known inactive compounds in the dataset, the model reached a sensitivity of 83% and a specificity of 96%. In a direct comparison, it showed a similar specificity than the structural alert profiler Mitotox (97%), but much higher sensitivity than Mitotox (47%). The biophysical model thus allows for a more accurate screening for uncoupling activity than existing structural alert profilers. We propose to use our model as a complementary tool to screen large datasets for protonophoric uncoupling activity in drug development and toxicity assessment.

Validation of the predictive accuracy of health-state utility values based on the Lloyd model for metastatic or recurrent breast cancer in Japan

Although there is a lack of data on health-state utility values (HSUVs) for calculating quality-adjusted life years in Japan, Cost-utility analysis has been introduced by the Japanese government to inform decision-making in the medical field since 2016. This study aimed to determine whether the Lloyd model which was a predictive model of HSUVs for metastatic breast cancer (MBC) patients in the United Kingdom can accurately predict actual HSUVs for Japanese patients with MBC. The prospective observational study, followed by the validation study of the clinical predictive model. Forty-four Japanese patients with MBC were studied at 336 survey points. This study consisted of two phases. In the first phase, we constructed a database of clinical data prospectively and HSUVs for Japanese patients with MBC to evaluate the predictive accuracy of HSUVs calculated using the Lloyd model. In the second phase, Bland-Altman analysis was used to determine how accurately predicted HSUVs (based on the Lloyd model) correlated with actual HSUVs obtained using the EuroQol 5-Dimension 5-Level questionnaire, a preference-based measure of HSUVs in patients with MBC. In the Bland-Altman analysis, the mean difference between HSUVs estimated by the Lloyd model and actual HSUVs, or systematic error, was -0.106. The precision was 0.165. The 95% limits of agreement ranged from -0.436 to 0.225. The t value was 4.6972, which was greater than the t value with 2 degrees of freedom at the 5% significance level (p=0.425). There were acceptable degrees of fixed and proportional errors associated with the prediction of HSUVs based on the Lloyd model for Japanese patients with MBC. We recommend that sensitivity analysis be performed when conducting cost-effectiveness analyses with HSUVs calculated using the Lloyd model.

Strong perceptual consequences of low-level visual predictions: a new illusion

Experimental data.

Exploration speed in captivity predicts foraging tactics and diet in free-living red knots

Variation in foraging tactics and diet are usually attributed to differences in morphology, experience, and prey availability. Recently, consistent individual differences in behaviour (personality) have been shown to be associated with foraging strategies. Bolder or more exploratory individuals are predicted to have a faster pace-of-life and offset the costs of moving more or in risky areas, with higher energetic gains by encountering profitable foraging opportunities and prey. However, the relationship between personality, foraging, and diet is poorly understood. We investigated how exploratory behaviour in red knots (Calidris canutus) is associated with foraging tactics and diet by combining laboratory experiments, field observations, and stable isotope analysis. First, we developed a mobile experimental arena to measure exploration speed in controlled settings. We validated the method by repeated testing of individuals over time and contexts. This setup allowed us to measure exploratory personality at the field site, eliminating the need to bring birds into captivity for long periods of time. After releasing birds within days of their capture, we asked whether exploration speed was associated with differences in foraging tactics and diet in the wild. We found that tactile foraging red knots mainly caught hard-shelled prey that are buried in the sediment, whereas visual foraging knots only captured soft preys located close to or on the surface. We also found that faster explorers showed a higher percentage of visual foraging than slower explorers. By contrast, morphology (bill length and gizzard size) had no significant effect on foraging tactics. Diet analysis based on δ15N and δ13C stable isotope values of plasma and red blood cells confirmed our field observations with slower explorers mainly consumed hard-shelled prey while faster explorers consumed more soft than hard-shelled prey. Our results show that foraging tactics and diet are associated with a personality trait, independent of morphological differences. We discuss how consistent behaviour might develop early in life through positive feedbacks between foraging tactics, prey type, and foraging efficiency.

Football is becoming more predictable: Network analysis of 88 thousand matches in 11 major leagues

In recent years excessive monetization of football and professionalism among the players has been argued to have affected the quality of the match in different ways. On the one hand, playing football has become a high-income profession and the players are highly motivated; on the other hand, stronger teams have higher incomes and therefore afford better players leading to an even stronger appearance in tournaments that can make the game more imbalanced and hence predictable. To quantify and document this observation, in this work we take a minimalist network science approach to measure the predictability of football over 26 years in major European leagues. We show that over time, the games in major leagues have indeed become more predictable. We provide further support for this observation by showing that inequality between teams has increased and the home-field advantage has been vanishing ubiquitously. We do not include any direct analysis on the effects of monetization on football's predictability or therefore, lack of excitement, however, we propose several hypotheses which could be tested in future analyses.

Molecular modelling of novel ADCY3 variant predicts a molecular target for tackling obesity

The present study aimed to identify ADCY3 genetic variants in severely obese young patients of Greek-Cypriot origin by genomic sequencing. Total genomic DNA samples were isolated from peripheral whole blood using the Gentra Puregene Blood kit (Qiagen GmbH). DNA sequencing was performed with 100 ng genomic DNA, which was amplified using primers designed by Primer3 software ver. 0.4.0 (http://frodo.wi.mit.edu/). PCR mixtures were prepared using the Taq DNA Polymerase Kit (Qiagen GmbH); they had a final volume of 20 μl and contained 2 μl PCR buffer (10X), 2 μl Q Solution (5X), 2 μl dNTPs (2mM), 0.3 μl of each primer (10μM), 0.2 μl Taq polymerase (5U/μl) and 100 ng genomic DNA. Amplification was performed with an initial denaturing temperature at 95˚C for 5 min, followed by 30 cycles of denaturation (95˚C, 45 sec), annealing (57˚C, 60 sec) and extension (72˚C, 45 sec), with a final extension at 72˚C for 5 min. The ADCY3 gene primers covered all exons. The PCR products were analysed on an Applied Biosystems 3130xl Genetic Analyzer and the results were analysed using Sequencing Analysis R 5.3 software (Applied Biosystems; Thermo Fisher Scientific, Inc.). The results revealed a total of five variants in patients, four of which were previously reported. A novel variant was identified in two patients (6%). The novel variant involves a heterozygous c.349T>A change in exon 1 of the gene locus, leading to a missense p.Leu117Met substitution.

Gut metabolites predict Clostridioides difficile recurrence

Additional datasets to reproduce figures and analyses that are not otherwise included in the publication's supplementary tables.

Gut metabolites predict Clostridioides difficile recurrence

Results of predictive analysis that can be used to reproduce figures and analyses without re-running predictive analysis.