On the importance of nonlinear modeling in computer performance prediction

Computers are nonlinear dynamical systems that exhibit complex and sometimes even chaotic behavior. The models used in the computer systems community, however, are linear. This paper is an exploration of that disconnect: when linear models are adequate for predicting computer performance and when they are not. Specifically, we build linear and nonlinear models of the processor load of an Intel i7-based computer as it executes a range of different programs. We then use those models to predict the processor loads forward in time and compare those forecasts to the true continuations of the time seriesComment: Appeared in "Proceedings of the 12th International Symposium on Intelligent Data Analysis

Large-scale phenotyping of patients with long COVID post-hospitalization reveals mechanistic subtypes of disease

One in ten severe acute respiratory syndrome coronavirus 2 infections result in prolonged symptoms termed long coronavirus disease (COVID), yet disease phenotypes and mechanisms are poorly understood1. Here we profiled 368 plasma proteins in 657 participants ≥3 months following hospitalization. Of these, 426 had at least one long COVID symptom and 233 had fully recovered. Elevated markers of myeloid inflammation and complement activation were associated with long COVID. IL-1R2, MATN2 and COLEC12 were associated with cardiorespiratory symptoms, fatigue and anxiety/depression; MATN2, CSF3 and C1QA were elevated in gastrointestinal symptoms and C1QA was elevated in cognitive impairment. Additional markers of alterations in nerve tissue repair (SPON-1 and NFASC) were elevated in those with cognitive impairment and SCG3, suggestive of brain–gut axis disturbance, was elevated in gastrointestinal symptoms. Severe acute respiratory syndrome coronavirus 2-specific immunoglobulin G (IgG) was persistently elevated in some individuals with long COVID, but virus was not detected in sputum. Analysis of inflammatory markers in nasal fluids showed no association with symptoms. Our study aimed to understand inflammatory processes that underlie long COVID and was not designed for biomarker discovery. Our findings suggest that specific inflammatory pathways related to tissue damage are implicated in subtypes of long COVID, which might be targeted in future therapeutic trials

SARS-CoV-2-specific nasal IgA wanes 9 months after hospitalisation with COVID-19 and is not induced by subsequent vaccination

BACKGROUND: Most studies of immunity to SARS-CoV-2 focus on circulating antibody, giving limited insights into mucosal defences that prevent viral replication and onward transmission. We studied nasal and plasma antibody responses one year after hospitalisation for COVID-19, including a period when SARS-CoV-2 vaccination was introduced. METHODS: In this follow up study, plasma and nasosorption samples were prospectively collected from 446 adults hospitalised for COVID-19 between February 2020 and March 2021 via the ISARIC4C and PHOSP-COVID consortia. IgA and IgG responses to NP and S of ancestral SARS-CoV-2, Delta and Omicron (BA.1) variants were measured by electrochemiluminescence and compared with plasma neutralisation data. FINDINGS: Strong and consistent nasal anti-NP and anti-S IgA responses were demonstrated, which remained elevated for nine months (p < 0.0001). Nasal and plasma anti-S IgG remained elevated for at least 12 months (p < 0.0001) with plasma neutralising titres that were raised against all variants compared to controls (p < 0.0001). Of 323 with complete data, 307 were vaccinated between 6 and 12 months; coinciding with rises in nasal and plasma IgA and IgG anti-S titres for all SARS-CoV-2 variants, although the change in nasal IgA was minimal (1.46-fold change after 10 months, p = 0.011) and the median remained below the positive threshold determined by pre-pandemic controls. Samples 12 months after admission showed no association between nasal IgA and plasma IgG anti-S responses (R = 0.05, p = 0.18), indicating that nasal IgA responses are distinct from those in plasma and minimally boosted by vaccination. INTERPRETATION: The decline in nasal IgA responses 9 months after infection and minimal impact of subsequent vaccination may explain the lack of long-lasting nasal defence against reinfection and the limited effects of vaccination on transmission. These findings highlight the need to develop vaccines that enhance nasal immunity. FUNDING: This study has been supported by ISARIC4C and PHOSP-COVID consortia. ISARIC4C is supported by grants from the National Institute for Health and Care Research and the Medical Research Council. Liverpool Experimental Cancer Medicine Centre provided infrastructure support for this research. The PHOSP-COVD study is jointly funded by UK Research and Innovation and National Institute of Health and Care Research. The funders were not involved in the study design, interpretation of data or the writing of this manuscript

More Flexible Radial Layout

We describe an algorithm for radial layout of undirected graphs, in which nodes are constrained to concentric circles centered at the origin. Such constraints are typical, e.g., in the layout of social networks, when structural centrality is mapped to geometric centrality or when the primary intention of the layout is the display of the vicinity of a distinguished node. Our approach is based on an extension of stress minimization with a weighting scheme that gradually imposes radial constraints on the intermediate layout during the majorization process, and thus is an attempt to preserve as much information about the graph structure as possible.

An experimental study on distance-based graph drawing

Abstract. In numerous application areas, general undirected graphs need to be drawn, and force-directed layout appears to be the most frequent choice. We present an extensive experimental study showing that, if the goal is to represent the distances in a graph well, a combination of two simple algorithms based on variants of multi-dimensional scaling is to be preferred because of their efficiency, reliability, and even simplicity. We also hope that details in the design of our study help advance experimental methodology in algorithm engineering and graph drawing, independent of the case at hand.

User-centric time-distance representation of road networks

This paper presents a new algorithm for computing timedistance transformations of a road network based on modified multidimensional scaling. The algorithm is designed to perform on a realworld road network, and provides alternative visualisations for travel time cognition and route planning. Several extensions are explored, including user-centric and route-centric road map transformations. Our implementation of the algorithm can be applied to any locality where travel time road network data is available. Here, it is illustrated on road network data for a rural region in Ireland. Limitations of the proposed algorithm are examined, and potential solutions are discussed