Combining Multi-Fidelity Modelling and Asynchronous Batch Bayesian Optimization

Bayesian Optimization is a useful tool for experiment design. Unfortunately, the classical, sequential setting of Bayesian Optimization does not translate well into laboratory experiments, for instance battery design, where measurements may come from different sources and their evaluations may require significant waiting times. Multi-fidelity Bayesian Optimization addresses the setting with measurements from different sources. Asynchronous batch Bayesian Optimization provides a framework to select new experiments before the results of the prior experiments are revealed. This paper proposes an algorithm combining multi-fidelity and asynchronous batch methods. We empirically study the algorithm behavior, and show it can outperform single-fidelity batch methods and multi-fidelity sequential methods. As an application, we consider designing electrode materials for optimal performance in pouch cells using experiments with coin cells to approximate battery performance

Observational signatures of disk and jet misalignment in images of accreting black holes

Black hole accretion is one of nature's most efficient energy extraction processes. When gas falls in, a significant fraction of its gravitational binding energy is either converted into radiation or flows outwards in the form of black hole-driven jets and disk-driven winds. Recently, the Event Horizon Telescope (EHT), an Earth-size sub-millimetre radio interferometer, captured the first images of M87's black hole. These images were analysed and interpreted using general-relativistic magnetohydrodynamics (GRMHD) models of accretion disks with rotation axes aligned with the black hole spin axis. However, since infalling gas is often insensitive to the black hole spin direction, misalignment between accretion disk and black hole spin may be a common occurrence in nature. In this work, we use the general-relativistic radiative transfer (GRRT) code \texttt{BHOSS} to calculate the first synthetic radio images of (highly) tilted disk/jet models generated by our GPU-accelerated GRMHD code \texttt{HAMR}. While the tilt does not have a noticeable effect on the system dynamics beyond a few tens of gravitational radii from the black hole, the warping of the disk and jet can imprint observable signatures in EHT images on smaller scales. Comparing the images from our GRMHD models to the 43 GHz and 230 GHz EHT images of M87, we find that M87 may feature a tilted disk/jet system. Further, tilted disks and jets display significant time variability in the 230 GHz flux that can be further tested by longer-duration EHT observations of M87

Co-designing Indices for Tailored Seasonal Climate Forecasts in Malawi

In central and southern Malawi, climate variability significantly impacts agricultural production and food availability owing to a high dependence on rain-fed maize production. Seasonal climate forecast information has the potential to inform farmers' agricultural planning, thereby improving preparedness to extreme events. In this paper we describe and evaluate an approach to co-designing and testing agro-climatic indices for use in seasonal forecasts that are tailored to farmer-defined decision-making needs in three districts of central and southern Malawi. Specifically, we aim to (a) identify critical maize specific agro-climatic indices by engaging key stakeholders and farmers; (b) compare and triangulate these indices with the historical climate record in study districts; and (c) analyze empirical relationships between seasonal total rainfall and maize specific indices in order to assess the potential for forecasting them at appropriate seasonal timescales. The identified agro-climatic indices include critical temperature/rainfall thresholds that are directly associated with phenological stages of maize growth with direct implications for maize yield and quality. While there are statistically significant relationships between observed wet season rainfall totals and several agro-climatic indices (e.g., heavy rainfall days and dry spell), the forecast skill of the UK Met Office's coupled initialized global seasonal forecasting system (GloSea5) over Malawi is currently low to provide confident predictions of total wet season rainfall and the agro-climatic indices correlated with it. We reflect on some of the opportunities and challenges associated with integrating farmers' information needs into a seasonal forecast process, through the use of agro-climatic indices

Multi-component assessment of chronic obstructive pulmonary disease: an evaluation of the ADO and DOSE indices and the global obstructive lung disease categories in international primary care data sets

Acknowledgements We thank Sian Williams of the International Primary Care Respiratory Group for her help and encouragement with the project. The OPCRD database was made available courtesy of the Respiratory Effectiveness Group and RIRL and the data were kindly prepared for analysis by Julie von Ziegenweidt. Funding The International Primary Care Respiratory Group (IPCRG) provided funding for this research project as an UNLOCK group study for which the funding was obtained through an unrestricted grant by Novartis AG, Basel, Switzerland. The latter funders had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript. Database access for the OPCRD was provided by the Respiratory Effectiveness Group (REG) and Research in Real Life; the OPCRD statistical analysis was funded by REG. The Bocholtz Study was funded by PICASSO for COPD, an initiative of Boehringer Ingelheim, Pfizer and the Caphri Research Institute, Maastricht University, The Netherlands.Peer reviewedPublisher PD

A data mining approach for classifying DNA repair genes into ageing-related or non-ageing-related

<p>Abstract</p> <p>Background</p> <p>The ageing of the worldwide population means there is a growing need for research on the biology of ageing. DNA damage is likely a key contributor to the ageing process and elucidating the role of different DNA repair systems in ageing is of great interest. In this paper we propose a data mining approach, based on classification methods (decision trees and Naive Bayes), for analysing data about human DNA repair genes. The goal is to build classification models that allow us to discriminate between ageing-related and non-ageing-related DNA repair genes, in order to better understand their different properties.</p> <p>Results</p> <p>The main patterns discovered by the classification methods are as follows: (a) the number of protein-protein interactions was a predictor of DNA repair proteins being ageing-related; (b) the use of predictor attributes based on protein-protein interactions considerably increased predictive accuracy of attributes based on Gene Ontology (GO) annotations; (c) GO terms related to "response to stimulus" seem reasonably good predictors of ageing-relatedness for DNA repair genes; (d) interaction with the XRCC5 (Ku80) protein is a strong predictor of ageing-relatedness for DNA repair genes; and (e) DNA repair genes with a high expression in T lymphocytes are more likely to be ageing-related.</p> <p>Conclusions</p> <p>The above patterns are broadly integrated in an analysis discussing relations between Ku, the non-homologous end joining DNA repair pathway, ageing and lymphocyte development. These patterns and their analysis support non-homologous end joining double strand break repair as central to the ageing-relatedness of DNA repair genes. Our work also showcases the use of protein interaction partners to improve accuracy in data mining methods and our approach could be applied to other ageing-related pathways.</p

The T cell differentiation landscape is shaped by tumour mutations in lung cancer

Tumour mutational burden (TMB) predicts immunotherapy outcome in non-small cell lung cancer (NSCLC), consistent with immune recognition of tumour neoantigens. However, persistent antigen exposure is detrimental for T cell function. How TMB affects CD4 and CD8 T cell differentiation in untreated tumours and whether this affects patient outcomes is unknown. Here, we paired high-dimensional flow cytometry, exome, single-cell and bulk RNA sequencing from patients with resected, untreated NSCLC to examine these relationships. TMB was associated with compartment-wide T cell differentiation skewing, characterized by loss of TCF7-expressing progenitor-like CD4 T cells, and an increased abundance of dysfunctional CD8 and CD4 T cell subsets with strong phenotypic and transcriptional similarity to neoantigen-reactive CD8 T cells. A gene signature of redistribution from progenitor-like to dysfunctional states was associated with poor survival in lung and other cancer cohorts. Single-cell characterization of these populations informs potential strategies for therapeutic manipulation in NSCLC

Changes in Invasive Pneumococcal Disease Caused by Streptococcus pneumoniae Serotype 1 Following Introduction of PCV10 and PCV13: Findings from the PSERENADE Project.

Streptococcus pneumoniae serotype 1 (ST1) was an important cause of invasive pneumococcal disease (IPD) globally before the introduction of pneumococcal conjugate vaccines (PCVs) containing ST1 antigen. The Pneumococcal Serotype Replacement and Distribution Estimation (PSERENADE) project gathered ST1 IPD surveillance data from sites globally and aimed to estimate PCV10/13 impact on ST1 IPD incidence. We estimated ST1 IPD incidence rate ratios (IRRs) comparing the pre-PCV10/13 period to each post-PCV10/13 year by site using a Bayesian multi-level, mixed-effects Poisson regression and all-site IRRs using a linear mixed-effects regression (N = 45 sites). Following PCV10/13 introduction, the incidence rate (IR) of ST1 IPD declined among all ages. After six years of PCV10/13 use, the all-site IRR was 0.05 (95% credibility interval 0.04–0.06) for all ages, 0.05 (0.04–0.05) for <5 years of age, 0.08 (0.06–0.09) for 5–17 years, 0.06 (0.05–0.08) for 18–49 years, 0.06 (0.05–0.07) for 50–64 years, and 0.05 (0.04–0.06) for ≥65 years. PCV10/13 use in infant immunization programs was followed by a 95% reduction in ST1 IPD in all ages after approximately 6 years. Limited data availability from the highest ST1 disease burden countries using a 3+0 schedule constrains generalizability and data from these settings are needed

From Sensor Data to Animal Behaviour: An Oystercatcher Example

Animal-borne sensors enable researchers to remotely track animals, their physiological state and body movements. Accelerometers, for example, have been used in several studies to measure body movement, posture, and energy expenditure, although predominantly in marine animals. In many studies, behaviour is often inferred from expert interpretation of sensor data and not validated with direct observations of the animal. The aim of this study was to derive models that could be used to classify oystercatcher (Haematopus ostralegus) behaviour based on sensor data. We measured the location, speed, and tri-axial acceleration of three oystercatchers using a flexible GPS tracking system and conducted simultaneous visual observations of the behaviour of these birds in their natural environment. We then used these data to develop three supervised classification trees of behaviour and finally applied one of the models to calculate time-activity budgets. The model based on accelerometer data developed to classify three behaviours (fly, terrestrial locomotion, and no movement) was much more accurate (cross-validation error = 0.14) than the model based on GPS-speed alone (cross-validation error = 0.35). The most parsimonious acceleration model designed to classify eight behaviours could distinguish five: fly, forage, body care, stand, and sit (cross-validation error = 0.28); other behaviours that were observed, such as aggression or handling of prey, could not be distinguished. Model limitations and potential improvements are discussed. The workflow design presented in this study can facilitate model development, be adapted to a wide range of species, and together with the appropriate measurements, can foster the study of behaviour and habitat use of free living animals throughout their annual routine