Public Articles
Role of SARS-CoV-2 Virus in Brain Cells: A Brief Review
Technical Report: Team Emotional Coaching for IT Outsourcing improvement
Evaluating the impact of visual course outlines in the Faculty of Science at McMaster University (2 April 2022)
and 2 collaborators
Cyber Security Essentials
and 3 collaborators
Research data repositories chosen by researchers across broad range of disciplines, from an analysis of 145,000 data availability statements
and 3 collaborators
La valutazione di Impatto Sanitario (VIS)
and 1 collaborator
Is Authorea FAIR?
and 1 collaborator
Estimating water fluxes in the critical zone using water stable isotope approaches in the Groundnut and Ferlo basins of Senegal
and 5 collaborators
Monitoraggio di odori: modelli e dati
Apes in the Anthropocene: The impacts of global change on parochial cooperation and intergroup aggression in Pan troglodytes
Analisi comparativa delle performance ambientali dei materiali da costruzione mediante Life Cycle Assessment (LCA)
Unified Physics and Cosmology: the Theory of Everything
Roadway Crashes Prediction Model using: Different Analytical and Statistical Modeling Methods.
Fungi Database.
Genetic diversity Goals and Targets have improved, but remain insufficient
Linking human impacts to community processes in terrestrial and freshwater ecosystems
and 32 collaborators
A magnetorheological elastomer based proportional valve for soft pneumatic actuators
and 4 collaborators
Frequency patterns as the key to unlock the secrets of pulsations in \( \delta \) Scuti stars
and 5 collaborators
Delta Scuti (\( \delta \) Sct) stars are intermediate-mass pulsators whose intrinsic oscillations have been studied for decades. However, modelling their pulsations remains a real theoretical challenge, thereby even hampering the precise determination of global stellar parameters. Here we present a direct and precise measurement of the mean density of \( \delta \) Sct stars. This measurement is obtained from an observational relation that scales stellar mean density with an oscillation frequency pattern analogous to the solar-like large separation but in the low order regime. We also show that this relation is independent of the rotation rate of the star, thus allowing us to accurately determine the mass and the radius, constrain the evolutionary stage, and estimate the rotational velocity. This places tight constraints on stellar evolution theory and on the physical properties of planets orbiting A-type stars.
Automatic mpMRI-based Prostate Lesions Assessment with Unsupervised Domain Adaptation
and 9 collaborators
The Skeleton of the Milky Way
and 2 collaborators
Recently, \citet{Goodman_2014} argued that the very long, very thin infrared dark cloud “Nessie” lies directly in the Galactic midplane and runs along the Scutum-Centaurus arm in position-position-velocity (p-p-v) space as traced by lower density CO and higher density NH3 gas. Nessie was presented as the first “bone” of the Milky Way, an extraordinarily long, thin, high-contrast filament that can be used to map our Galaxy’s ”skeleton.“ Here, we present evidence for additional bones in the Milky Way Galaxy, arguing that Nessie is not a curiosity but one of several filaments that could potentially trace Galactic structure. Our ten bone candidates are all long, filamentary, mid-infrared extinction features which lie parallel to, and no more than twenty parsecs from, the physical Galactic mid-plane. We use CO, N2H+, HCO+ and NH3 radial velocity data to establish the three-dimensional location of the candidates in p-p-v space. Of the ten candidates, six also: have a projected aspect ratio of ≥50: 1; run along, or extremely close to, the Scutum-Centaurus arm in p-p-v space; and exhibit no abrupt shifts in velocity. Evidence suggests that these candidates are marking the locations of significant spiral features, with the bone called filament 5 (”BC_18.88-0.09") being a close analog to Nessie in the Northern Sky. As molecular spectral-line and extinction maps cover more of the sky at increasing resolution and sensitivity, we seek to find more bones in future studies, ultimately to create a global-fit to the Galaxy’s spiral arms by piecing together individual skeletal features.
Corrine Coakley, Mandy Munro-Stasiuk, Jim Tyner, Sokvisal Kimsroy, Chhunly Chhay
and 1 collaborator
KeywordsKhmer Rouge, Irrigation, Vegetation Index
Chemotherapy weakly contributes to predicted neoantigen expression in ovarian cancer
and 3 collaborators
Patients with highly mutated tumors, such as melanoma or smoking-related lung cancer, have higher rates of response to immune checkpoint blockade therapy, perhaps due to increased neoantigen expression. Many chemotherapies including platinum compounds are known to be mutagenic, but the impact of standard treatment protocols on mutational burden and resulting neoantigen expression in most human cancers is unknown.
We sought to quantify the effect of chemotherapy treatment on computationally predicted neoantigen expression for 12 high grade serous ovarian carcinoma (HGSC) patients with pre- and post-chemotherapy samples collected in the Australian Ovarian Cancer Study. We additionally analyzed 16 patients from the cohort with post-treatment samples only, including five primary surgical samples exposed to neoadjuvant chemotherapy. Our approach integrates tumor whole genome and RNA sequencing with class I MHC binding prediction and mutational signatures of chemotherapy exposure extracted from two preclinical studies.
The mutational signatures for cisplatin and cyclophosphamide identified in a preclinical model had significant but inexact associations with the relevant exposure in the clinical samples. In an analysis stratified by tissue type (solid tumor or ascites), relapse samples collected after chemotherapy harbored a median of 90% more expressed neoantigens than untreated primary samples, a figure that combines the effects of chemotherapy and other mutagenic processes operative during relapse. Neoadjuvant-treated primary samples showed no detectable increase over untreated samples. The contribution from chemotherapy-associated signatures was small, accounting for a mean of 5% (range 0–16) of the expressed neoantigen burden in relapse samples. In both treated and untreated samples, most neoantigens were attributed to COSMIC Signature (3), associated with BRCA disruption, Signature (1), associated with a slow mutagenic process active in healthy tissue, and Signature (8), of unknown etiology.
Relapsed HGSC tumors harbor nearly double the predicted expressed neoantigen burden of primary samples, but mutations associated with chemotherapy signatures account for only a small part of this increase. The mutagenic processes responsible for most neoantigens are similar between primary and relapse samples. Our analyses are based on mutations detectable from whole genome sequencing of bulk samples and do not account for neoantigens present in small populations of cells.
Predicting Peptide-MHC Binding Affinities With Imputed Training Data
and 3 collaborators
Predicting the binding affinity between MHC proteins and their peptide ligands is a key problem in computational immunology. State of the art performance is currently achieved by the allele-specific predictor NetMHC and the pan-allele predictor NetMHCpan, both of which are ensembles of shallow neural networks. We explore an intermediate between allele-specific and pan-allele prediction: training allele-specific predictors with synthetic samples generated by imputation of the peptide-MHC affinity matrix. We find that the imputation strategy is useful on alleles with very little training data. We have implemented our predictor as an open-source software package called MHCflurry and show that MHCflurry achieves competitive performance to NetMHC and NetMHCpan.
Review for: L'utilizzo delle bioplastiche può davvero ridurre l'inquinamento?
and 1 collaborator