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opencc-zeroDec 2022View details →

On the predictability of phenotypic divergence in geographic isolation

Do related populations that are separated by barriers predictably evolve differences from one another over time, or is such divergence idiosyncratic and unpredictable? We test these alternatives by investigating patterns of trait evolution for 54 sister pairs of Andean forest birds that live in similar environments on either side of the arid Marañón Gap, a strong dispersal barrier for humid montane species. We measured divergence in both sexual (song and plumage) and ecological (beak size and beak shape) traits. Sexual traits evolve in a clock-like fashion, with trait divergence positively correlated with genetic distance (r = 0.6 to 0.7). In contrast, divergence in ecological traits is uncorrelated or only loosely correlated with genetic distance (r = 0.0 to 0.3). Thus, for geographically isolated Andean montane forest birds that live in similar environments, divergence is predictable in sexual traits, but not for ecological traits. This means that sexual trait divergence occurs independently of adaptive ecological divergence within the mega-diverse tropical Andean avifauna. Last, we show that variation in genetic divergence across a biogeographic barrier is associated with traits that are proxies for species' opportunities for dispersal (low elevation limit and elevational niche breadth), but not with traits that are proxies for species' dispersal abilities (hand-wing index and foraging strata).

opencc-zeroJan 2023View details →

Predictive modeling reveals that higher-order cooperativity drives transcriptional repression in a synthetic developmental enhancer

A challenge in quantitative biology is to predict output patterns of gene expression from knowledge of input transcription factor patterns and from the arrangement of binding sites for these transcription factors on regulatory DNA. We tested whether widespread thermodynamic models could be used to infer parameters describing simple regulatory architectures that inform parameter-free predictions of more complex enhancers in the context of transcriptional repression by Runt in the early fruit fly embryo. By modulating the number and placement of Runt binding sites within an enhancer, and quantifying the resulting transcriptional activity using live imaging, we discovered that thermodynamic models call for higher-order cooperativity between multiple molecular players. This higher-order cooperativity capture the combinatorial complexity underlying eukaryotic transcriptional regulation and cannot be determined from simpler regulatory architectures, highlighting the challenges in reaching a predictive understanding of transcriptional regulation in eukaryotes and calling for approaches that quantitatively dissect their molecular nature.

A Predictive Coding Approach to Modelling Perceived Drum Pattern Complexity

Commented R script and matrices to carry out drum pattern complexity prediction.

Youngs Modulus Prediction tfrecord Training Data

Tfrecords containing a microstructure and its youngs modulus simulated along the y-axis. The data_definition.json that explicitly describes the content of the tfrecords is also contained within the zip file.

Pairwise Learning to Rank for Hit Song Prediction: Dataset

Dataset for the paper "Pairwise Learning to Rank for Hit Song Prediction", to be published at BTW 2023.

Data for Structural Features of Interfacial Water Predict the Hydrophobicity of Chemically Heterogeneous Surfaces

Scripts, raw and processed data, Jupyter notebooks, and force field files for the simulations performed in: B. C. Dallin, A. S. Kelkar, and R. C. Van Lehn. “Structural Features of Interfacial Water Predict the Hydrophobicity of Chemically Heterogeneous Surfaces.” Chemical Science 2023.

Key sulphur species predicted by photochemical models and their employed chemical networks

The volume mixing ratio output of the key sulphur species computed by photochemical models for producing Fig. 1 in Tsai et al. 2023 and the chemical networks used in each model.

Improved National-Scale Flood Prediction for Gauged and Ungauged Basins using a Spatio-temporal Hierarchical Model

Composite data with NWM 2.0 streamflow, basin PET, drainage area and stoage. SAR data used in this study are downloaded from <a href="https://scihub.copernicus.eu/">https://scihub.copernicus.eu/</a>

Data for Sleep cycle-dependent vascular dynamics and the predicted effects on perivascular cerebrospinal fluid flow and solute transport

Datasets containing derived data and results used by code in: https://github.com/AlexandraVallet/PVSflow for "Sleep cycle-dependent vascular dynamics and the predicted effects on perivascular cerebrospinal fluid flow and solute transport", Bojarskaite et al. 2023. Please see github for instructions.

opencc-zeroJan 2023View details →

Relevant Datasets and Software Used for Paper "KGML-xDTD: A Knowledge Graph-based Machine Learning Framework for Drug Treatment Prediction and Mechanism Description"

This repository contains relevant datasets and software used in a paper "KGML-xDTD: A Knowledge Graph-based Machine Learning Framework for Drug Treatment Prediction and Mechanism Description". They are used to run the code of KGML-xDTD stored on <a href="https://github.com/chunyuma/KGML-xDTD">Github</a> and support the results of this paper. About the datasets 1. bkg_rtxkg2c_v2.7.3.tar.gz This tar.gz file contains three sub-folders: tsv_files, scripts, and relevant_dbs. The "tsv_files" sub-folder has the input files that the neo4j software uses. The "scripts" sub-folder contains a shell script with a relevant python script to construct the biomedical knowledge graph. The "relevant_dbs" sub-folder stores two auxiliary databases that KGML-xDTD needs to use.  2. indication_paths.yaml This file contains the <a href="https://sulab.github.io/DrugMechDB">DrugMechDB</a> MOA paths that we used to evaluate the predicted MOA paths by KGML-xDTD. It is downloaded from the official <a href="https://github.com/SuLab/DrugMechDB">GitHub repository</a> of DrugMechDB. 3. training_data.tar.gz This tar.gz file contains the processed training data of four data sources (e.g., <a href="https://mychem.info">MyChem</a>, <a href="https://lhncbc.nlm.nih.gov/ii/tools/SemRep_SemMedDB_SKR/SemMedDB_download.html">SemMedDB</a>, <a href="https://bioportal.bioontology.org/ontologies/NDFRT">NDF-RT</a>, <a href="https://unmtid-shinyapps.net/shiny/repodb/">RepoDB</a>) mentioned in the paper. These processed drug-disease pairs have been matched to the identifiers of biological entities used in our biomedical knowledge graph and respectively split into true positive (tp) sets and true negative (tn) sets. We also provide the names of these drug identifiers and disease identifiers under a sub-folder "translated _to_name". About the software neo4j-community-3.5.26.tar.gz This tar.gz is the Neo4j community version 3.5.26 downloaded from <a href="https://neo4j.com/download-center/#community">Neo4j Download Center</a>. Although the newer versions are available, due to their big changes in the Neo4j setting that are not compatible with our scripts on Github, we provide the version that we used in our research. If you would like to use the newer version, modifications to our script will be required to import the biomedical knowledge graph into your local Neo4j database with the new setting.

openmit-licenseJul 2022View details →

Skillful decadal flood prediction

Data and scripts required to reproduce the analysis described in the Geophysical Research Letters journal article Skillful decadal flood prediction (<a href="https://doi.org/10.1029/2022GL100650">https://doi.org/10.1029/2022GL100650</a>).

Dataset from "Predicting final results of brace treatment of adolescents with idiopathic scoliosis: first out-of-brace radiograph is better than in-brace radiograph-SOSORT 2020 award winner"

Dataset from the paper published in the European Spine Journal titled "Predicting final results of brace treatment of adolescents with idiopathic scoliosis: first out-of-brace radiograph is better than in-brace radiograph-SOSORT 2020 award winner"

ActTemp+sMSA dataset of "Biasing AlphaFold2 to predict GPCRs and Kinases with user-defined functional or structural properties"

PDB models generated with the protocol described in "Biasing AlphaFold2 to predict GPCRs and Kinases with user-defined functional or structural properties"

Upper thermal limits predict herpetofauna responses to forest edge and cover

Amphibians and reptiles are sensitive to changes in the thermal environment, which varies considerably in human-modified landscapes. Although it is known that thermal traits of species influence their distribution in modified landscapes, how herpetofauna respond specifically to shifts in ambient temperature along forest edges remains unclear. This may be because most studies focus on local-scale metrics of edge exposure, which only account for a single edge or habitat patch. We predicted that accounting for the combined effect of multiple habitat edges in a landscape would best explain herpetofaunal response to thermally-mediated edge effects. We (1) surveyed herpetofauna at two lowland, fragmented forest sites in central Colombia, (2) measured the critical thermal maximum (CTmax) of the species sampled, (3) measured their edge exposure at both local and landscape scales, and (4) created a thermal profile of the landscape itself. We found that species with low CTmax occurred both further from forest edges and in areas of denser vegetation, but were unaffected by the landscape-scale configuration of habitat edges. Variation in the thermal landscape was driven primarily by changes in vegetation density. Our results suggest that amphibians and reptiles with low CTmax are limited by both canopy gaps and proximity to edge, making them especially vulnerable to human modification of tropical forest.

Data from: Can body mass and skull morphology predict seed and fruit ingestion potential for mammal species? A test using extant species and its application to extinct species

Larger animals are assumed to ingest larger seeds and consume larger fruits, but empirical studies reveal inconsistent trends between body mass and the average size of fruits and seeds ingested. Further, no studies have explored seed size relationships with morphological traits, such as skull dimensions. Such characteristics might provide more reliable estimates of ingestion ability and allow for accurate predictions of seed dispersal capacity in species for which we lack empirical data, especially extinct species. To determine whether (i) mammalian skull dimensions are better predictors of the maximum size of ingested seeds and fruits, compared to body mass and (ii) body mass are the better predictors of mean fruit and seed sizes, we studied these relationships across three mammalian orders: Chiroptera, Primates, and Carnivora. We collected novel data on skull dimensions and collated available data on body mass and maximum and mean sizes of ingested fruits and seeds for mammals (N=100) across the Neotropics, Asia, Africa, and Madagascar. We explored the relationships between anatomical traits and fruit and seed sizes of extant species and made predictions for five extinct species. Our results revealed that body mass and skull dimensions are essential determinants of ingested fruit and seed size in mammals. The latter traits can generate predictions for extinct species, especially coronoid height and maximum jaw gape. Nevertheless, body mass predicted larger ingested fruits and seeds than skull dimensions and explained a greater part of the variance for both maximum and mean sizes in our dataset. Our results show how body mass and cranial anatomy constrain seed size and reinforce the importance of maintaining functional diversity in seed dispersers to maintain tropical forest structure. We also show that scientists can use morphological characteristics to predict the seed dispersal potential of extinct mammals allowing better inferences on past and future consequences of frugivore extinctions within tropical forests.

Data for figures in manuscript "Aberrant splicing prediction across human tissues"

Minimal dataset to produce the figures in the publication "Aberrant splicing prediction across human tissues", using the plotting scripts in 'figures_R/' from the github repository https://github.com/gagneurlab/AbSplice_analysis. To run the plotting scripts unzip the data folder to the root directory of the git repository.

Predicting GPR40 Agonists with A Deep Learning-Based Ensemble Model

This dataset includes the calculation steps and optimization process of an ensemble model, along with various results and related intermediate files

Genome-wide association and genomic prediction for a reproductive index summarizing fertility outcomes in U.S. Holsteins

Subfertility represents one major challenge to enhancing dairy production and efficiency. Herein, we use a reproductive index (RI) expressing the predicted probability of pregnancy following artificial insemination with Illumina 778K genotypes to perform single and multi-locus genome-wide association analyses (GWAA) on 2,448 geographically diverse U.S. Holstein cows and produce genomic heritability estimates. Moreover, we use genomic best linear unbiased prediction (GBLUP) to investigate the potential utility of the RI by performing genomic predictions with cross-validation. Notably, genomic heritability estimates for the U.S. Holstein RI were moderate ( 0.1654± 0.0317 – 0.2550 ± 0.0348), while single and multi-locus GWAA revealed overlapping quantitative trait loci (QTL) on BTA6 and BTA29, including known QTL for daughter pregnancy rate (DPR) and cow conception rate (CCR). Multi-locus GWAA revealed seven additional QTL, including one on BTA7 (60 Mb) which is adjacent to a known heifer conception rate (HCR) QTL (59 Mb). Positional candidate genes for the detected QTL included male and female fertility loci (i.e., spermatogenesis, oogenesis), meiotic and mitotic regulators, and genes associated with immune response, milk yield, enhanced pregnancy rates, and the reproductive-longevity pathway. Based on the proportion of phenotypic variance explained (PVE), all detected QTL (n = 13; P ≤ 5e-05) were estimated to have moderate (1.0% < PVE ≤ 2.0%) or small effects (PVE ≤ 1.0%) on the predicted probability of pregnancy. Genomic prediction using GBLUP with cross-validation (k = 3) produced mean predictive abilities (0.1692–0.2301) and mean genomic prediction accuracies (0.4119–0.4557) that were similar to bovine health and production traits previously investigated.

Data for: When does early-life telomere length predict survival? A case study and meta-analysis

Suboptimal conditions during development can shorten telomeres, the protective DNA caps on the end of chromosomes. Shorter early-life telomere length (TL) can indicate reduced somatic maintenance, leading to lower survival and shorter lifespan. However, despite some clear evidence, not all studies show a relationship between early-life TL and survival or lifespan, which may be due to differences in biology or study design (e.g., survival period measured). In superb fairy-wrens (Malurus cyaneus), we assessed whether early-life TL predicts mortality across different life-history stages (fledgling, juvenile, adult). However, in contrast to a similar study on a congener, early-life TL did not predict mortality across any life stage in this species. We then performed a meta-analysis including 32 effect sizes from 23 studies (15 birds and 3 mammals) to quantify the effect of early-life TL on mortality whilst taking into consideration potential sources of biological and methodological variation. Overall, the effect of early-life TL on mortality was significant, corresponding to a 15% reduction in mortality risk with each standard deviation increase in TL. However, the effect became weaker when correcting for publication bias. Contrary to our predictions, there was no evidence that effects of early-life TL on mortality varied with species lifespan or the period over which survival was measured. However, negative effects of early-life TL on mortality risk were pervasive throughout life. These results imply that effects of early-life TL on mortality are more likely context-dependent rather than age-dependent, although substantial power and publication bias issues highlight the need for more research.

Predicted structures for comparison with IgFold

Predicted antibody structures used to compare the accuracy of IgFold to alternative methods, including RepertoireBuilder, DeepAb, ABlooper, NanoNet, and AlphaFold.