Online and offline heuristics for inferring hierarchies of repetitions in sequences

Hierarchical dictionary-based compression schemes form a grammar for a text by replacing each repeated string with a production rule. While such schemes usually operate online, making a replacement as soon as repetition is detected, offline operation permits greater freedom in choosing the order of replacement. In this paper, we compare the online method with three offline heuristics for selecting the next substring to replace: longest string first, most common string first, and the string that minimized the size of the grammar locally. Surprisingly, two of the offline techniques, like the online method, run in time linear in the size of the input. We evaluate each technique on artificial and natural sequences. In general, the locally-most-compressive heuristic performs best, followed by most frequent, the online technique, and, lagging by some distance, the longest-first technique

Hybrid solid state qubits: the powerful role of electron spins

We review progress on the use of electron spins to store and process quantum information, with particular focus on the ability of the electron spin to interact with multiple quantum degrees of freedom. We examine the benefits of hybrid quantum bits (qubits) in the solid state that are based on coupling electron spins to nuclear spin, electron charge, optical photons, and superconducting qubits. These benefits include the coherent storage of qubits for times exceeding seconds, fast qubit manipulation, single qubit measurement, and scalable methods for entangling spatially separated matter-based qubits. In this way, the key strengths of different physical qubit implementations are brought together, laying the foundation for practical solid-state quantum technologies.Comment: 54 pages, 7 figure

Mass Drug Administration and beyond: how can we strengthen health systems to deliver complex interventions to eliminate neglected tropical diseases?

Achieving the 2020 goals for Neglected Tropical Diseases (NTDs) requires scale-up of Mass Drug Administration (MDA) which will require long-term commitment of national and global financing partners, strengthening national capacity and, at the community level, systems to monitor and evaluate activities and impact. For some settings and diseases, MDA is not appropriate and alternative interventions are required. Operational research is necessary to identify how existing MDA networks can deliver this more complex range of interventions equitably. The final stages of the different global programmes to eliminate NTDs require eliminating foci of transmission which are likely to persist in complex and remote rural settings. Operational research is required to identify how current tools and practices might be adapted to locate and eliminate these hard-to-reach foci. Chronic disabilities caused by NTDs will persist after transmission of pathogens ceases. Development and delivery of sustainable services to reduce the NTD-related disability is an urgent public health priority. LSTM and its partners are world leaders in developing and delivering interventions to control vector-borne NTDs and malaria, particularly in hard-to-reach settings in Africa. Our experience, partnerships and research capacity allows us to serve as a hub for developing, supporting, monitoring and evaluating global programmes to eliminate NTDs

The combined molecular adjuvant CASAC enhances the CD8+ T cell response to a tumor-associated self-antigen in aged, immunosenescent mice

BACKGROUND: Ineffective induction of T cell mediated immunity in older individuals remains a persistent challenge for vaccine development. Thus, there is a need for more efficient and sophisticated adjuvants that will complement novel vaccine strategies for the elderly. To this end, we have investigated a previously optimized, combined molecular adjuvant, CASAC (Combined Adjuvant for Synergistic Activation of Cellular immunity), incorporating two complementary Toll-like receptor agonists, CpG and polyI:C, a class-II epitope, and interferon (IFN)-γ in aged mice. FINDINGS: In aged mice with typical features of immunosenescence, antigen specific CD8+ T cell responses were stimulated after serial vaccinations with CASAC or Complete/Incomplete Freund's Adjuvant (CFA/IFA) and a class I epitope, deriving either from ovalbumin (SIINFEKL, SIL) or the melanoma-associated self-antigen, tyrosinase-related protein-2 (SVYDFFVWL, SVL). Pentamer analysis revealed that aged, CASAC/SIL-vaccinated animals had substantially higher frequencies of H-2K(b)/SIL-specific CD8+ T cells compared to the CFA/IFA-vaccinated groups. Similarly, higher frequencies of H-2K(b)/SVL-pentamer+ and IFN-γ+ CD8+ T cells were detected in the aged, CASAC + SVL-vaccinated mice than in their CFA/IFA-vaccinated counterparts. In both antigen settings, CASAC promoted significantly better functional CD8+ T cell activity. CONCLUSION: These studies demonstrate that functional CD8+ T cells, specific for both foreign and tumour-associated self-antigens, can be effectively induced in aged immunosenescent mice using the novel multi-factorial adjuvant CASAC

School-university partnerships: Lessons learned from 10 years of spectroscopy for teachers and post 16 students

Spectroscopy covers a wide range of analytical techniques, a small sub-set of which UK pre-university chemistry students are required to study. The expense of such equipment means that it is not available to the vast majority of schools whilst it is commonplace in university chemistry departments. This article discusses the evolution of the Bristol ChemLabS spectroscopy outreach activities. The advantages and disadvantages of this method of engagement for both the participants and the providers are discussed from 10 years of activity

The perceptions of undertaking a higher degree alongside orthodontic speciality training: a cross-sectional survey of British Orthodontic Society members

Introduction: In the UK, orthodontic speciality training takes place over three years full-time. In addition to the clinical training, there is an expectation that trainees undertake a higher degree. Currently, there is little evidence regarding the impact of undertaking a higher degree on specialist orthodontists. Aims: Investigate UK orthodontists' perceptions of undertaking a higher degree alongside speciality training. Materials and methods: A cross-sectional research study involving the distribution of an anonymous, descriptive, online, questionnaire-based survey between May and June 2021 via the British Orthodontic Society. Data were obtained in relation to the impact of undertaking a higher degree on the completion of speciality training, research skills, delivery of patient care and career opportunities. Results: In total, 166 questionnaires were completed (approximately 13.3% response rate). Most respondents 'agreed' or 'strongly agreed' that undertaking a higher degree had improved their scientific (77.1%) and critical appraisal skills (80.7%), job prospects (60.2%) and career opportunities (63.9%). Most respondents felt the benefits of the higher degree outweighed the associated costs (65.1%) and was a worthwhile component of training (69.3%). Conclusions: Specialist orthodontists place a high value on undertaking a higher degree. The results of this questionnaire should be of importance to stakeholders involved in the development of the orthodontic curriculum

Rethinking how external pressure can suppress dendrites in lithium metal batteries

We offer an explanation for how dendrite growth can be inhibited when Li metal pouch cells are subjected to external loads, even for cells using soft, thin separators. We develop a contact mechanics model for tracking Li surface and sub-surface stresses where electrodes have realistically (micron-scale) rough surfaces. Existing models examine a single, micron-scale Li metal protrusion under a fixed local current density that presses more or less conformally against a separator or stiff electrolyte. At the larger, sub-mm scales studied here, contact between the Li metal and the separator is heterogeneous and far from conformal for surfaces with realistic roughness: the load is carried at just the tallest asperities, where stresses reach tens of MPa, while most of the Li surface feels no force at all. Yet, dendrite growth is suppressed over the entire Li surface. To explain this dendrite suppression, our electrochemical/mechanics model suggests that Li avoids plating at the tips of growing Li dendrites if there is sufficient local stress; that local contact stresses there may be high enough to close separator pores so that incremental Li+ ions plate elsewhere; and that creep ensures that Li protrusions are gradually flattened. These mechanisms cannot be captured by single-dendrite-scale analyses

Genomic surveillance reveals low prevalence of livestock-associated methicillin-resistant Staphylococcus aureus in the East of England

Livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) is an emerging problem in many parts of the world. LA-MRSA has been isolated previously from animals and humans in the United Kingdom (UK), but the prevalence is unknown. The aim of this study was to determine the prevalence and to describe the molecular epidemiology of LA-MRSA isolated in the East of England (broadly Cambridge and the surrounding area). We accessed whole genome sequence data for 2,283 MRSA isolates from 1,465 people identified during a 12-month prospective study between 2012 and 2013 conducted in the East of England, United Kingdom. This laboratory serves four hospitals and 75 general practices. We screened the collection for multilocus sequence types (STs) and for host specific resistance and virulence factors previously associated with LA-MRSA. We identified 13 putative LA-MRSA isolates from 12 individuals, giving an estimated prevalence of 0.82% (95% CI 0.47% to 1.43%). Twelve isolates were mecC-MRSA (ten CC130, one ST425 and one ST1943) and single isolate was ST398. Our data demonstrate a low burden of LA-MRSA in the East of England, but the detection of mecC-MRSA and ST398 indicates the need for vigilance. Genomic surveillance provides a mechanism to detect and track the emergence and spread of MRSA clones of human importance.Supported by grants from the UKCRC Translational Infection Research (TIR) Initiative, and the Medical Research Council (Grant Number G1000803) with contributions to the Grant from the Biotechnology and Biological Sciences Research Council, the National Institute for Health Research on behalf of the Department of Health, and the Chief Scientist Ofce of the Scottish Government Health Directorate (to Prof. Peacock); a Hospital Infection Society Major Research Grant, and by Wellcome Trust grant number 098051 awarded to the Wellcome Trust Sanger Institute. Tis work was supported by the Wellcome Trust 201344/Z/16/Z. M.E.T. is a Clinician Scientist Fellow, supported by the Academy of Medical Sciences and the Health Foundation, and by the NIHR Cambridge Biomedical Research Centre

The Filter Detection Task for measurement of breathing-related interoception and metacognition

The study of the brain’s processing of sensory inputs from within the body (‘interoception’) has been gaining rapid popularity in neuroscience, where interoceptive disturbances are thought to exist across a wide range of chronic physiological and psychological conditions. Here we present a task and analysis procedure to quantify specific dimensions of breathing-related interoception, including interoceptive sensitivity, decision bias, metacognitive bias, and metacognitive performance. Two major developments address some of the challenges presented by low trial numbers in interoceptive experiments: (i) a novel adaptive algorithm to maintain task performance at 70–75% accuracy; (ii) an extended hierarchical metacognitive model to estimate regression parameters linking metacognitive performance to relevant (e.g. clinical) variables. We demonstrate the utility of the task and analysis developments, using both simulated data and three empirical datasets. This methodology represents an important step towards accurately quantifying interoceptive dimensions from a simple experimental procedure that is compatible with clinical settings

Longitudinal genomic surveillance of MRSA in the UK reveals transmission patterns in hospitals and the community

Genome sequencing has provided snapshots of the transmission of methicillin-resistant Staphylococcus aureus (MRSA) during suspected outbreaks in isolated hospital wards. Scale-up to populations is now required to establish the full potential of this technology for surveillance. We prospectively identified all individuals over a 12-month period who had at least one MRSA-positive sample processed by a routine diagnostic microbiology laboratory in the East of England, which received samples from three hospitals and 75 general practitioner (GP) practices. We sequenced at least 1 MRSA isolate from 1465 individuals (2282 MRSA isolates) and recorded epidemiological data. An integrated epidemiological and phylogenetic analysis revealed 173 transmission clusters containing between 2 and 44 cases and involving 598 people (40.8%). Of these, 118 clusters (371 people) involved hospital contacts alone, 27 clusters (72 people) involved community contacts alone, and 28 clusters (157 people) had both types of contact. Community- and hospital-associated MRSA lineages were equally capable of transmission in the community, with instances of spread in households, long-term care facilities, and GP practices. Our study provides a comprehensive picture of MRSA transmission in a sampled population of 1465 people and suggests the need to review existing infection control policy and practice.This work was supported by grants from the UK Clinical Research Collaboration Translational Infection Research Initiative and the Medical Research Council (grant no. G1000803) with contributions to the grant from the Biotechnology and Biological Sciences Research Council, the National Institute for Health Research (NIHR) on behalf of the Department of Health, and the Chief Scientist Office of the Scottish Government Health Directorate (to S.J.P.); by a Hospital Infection Society Major Research Grant; by Wellcome Trust grant no. 098051 awarded to the Wellcome Trust Sanger Institute; and by Wellcome Trust 201344/Z/16/Z awarded to F.C. M.S.T. is a Wellcome Trust Clinical PhD fellow. M.E.T. is a Clinician Scientist Fellow, supported by the Academy of Medical Sciences and the Health Foundation and by the NIHR Cambridge Biomedical Research Centr