A systems biology approach to defining regulatory mechanisms for cartilage and tendon cell phenotypes

Phenotypic plasticity of adult somatic cells has provided emerging avenues for the development of regenerative therapeutics. In musculoskeletal biology the mechanistic regulatory networks of genes governing the phenotypic plasticity of cartilage and tendon cells has not been considered systematically. Additionally, a lack of strategies to effectively reproduce in vitro functional models of cartilage and tendon is retarding progress in this field. De- and redifferentiation represent phenotypic transitions that may contribute to loss of function in ageing musculoskeletal tissues. Applying a systems biology network analysis approach to global gene expression profiles derived from common in vitro culture systems (monolayer and three-dimensional cultures) this study demonstrates common regulatory mechanisms governing de- and redifferentiation transitions in cartilage and tendon cells. Furthermore, evidence of convergence of gene expression profiles during monolayer expansion of cartilage and tendon cells, and the expression of key developmental markers, challenges the physiological relevance of this culture system. The study also suggests that oxidative stress and PI3K signalling pathways are key modulators of in vitro phenotypes for cells of musculoskeletal origin

Deformation of lamellar γ-TiAl below the general yield stress

The occurrence of plasticity below the macroscopic yield stress during tensile monotonic loading of nearly lamellar Ti-45Al-2Nb-2Mn(at%)-0.8vol% TiB2 at both 25 °C and 700 °C, and in two conditions of lamellar thickness, was measured by digital image correlation strain mapping of a remodelled Au surface speckle pattern. Such initial plasticity, not necessarily related to the presence of common stress concentrators such as hard particles or cracks, could occur at applied stresses as low as 64 % of the general yield stress. For a same applied strain it was more prominent at room temperature, and located as slip and twinning parallel to, and near to or at (respect.) lamellar interfaces of all types in soft modeoriented colonies. These stretched the full colony width and the shear strain was most intense in the centre of the colonies. Further, the most highly operative microbands of plasticity at specimen fracture were not those most active prior to yielding. The strain mapping results from polycrystalline tensile loading were further compared to those from microcompression testing of soft-mode stacks of lamellae milled from single colonies performed at the same temperatures. Combined with post-mortem transmission electron microscopy of the pillars, the initial plasticity by longitudinal dislocation glide was found to locate within 30 – 50 nm of the lamellar interfaces, and not at the interfaces themselves. The highly localised plasticity that precedes high cycle fatigue failure is therefore inherently related to the lamellar structure, which predetermines the locations of plastic strain accumulation, even in a single loading cycle.The work was supported by the EPSRC / Rolls-Royce Strategic Partnership (EP/M005607/1). T.E.J.E. also acknowledges the kind support of the Worshipful Company of Armourers and Brasiers’ Gauntlet Trust

Finding the "Dark Matter'' in Human and Yeast Protein Network Prediction and Modelling

Accurate modelling of biological systems requires a deeper and more complete knowledge about the molecular components and their functional associations than we currently have. Traditionally, new knowledge on protein associations generated by experiments has played a central role in systems modelling, in contrast to generally less trusted bio-computational predictions. However, we will not achieve realistic modelling of complex molecular systems if the current experimental designs lead to biased screenings of real protein networks and leave large, functionally important areas poorly characterised. To assess the likelihood of this, we have built comprehensive network models of the yeast and human proteomes by using a meta-statistical integration of diverse computationally predicted protein association datasets. We have compared these predicted networks against combined experimental datasets from seven biological resources at different level of statistical significance. These eukaryotic predicted networks resemble all the topological and noise features of the experimentally inferred networks in both species, and we also show that this observation is not due to random behaviour. In addition, the topology of the predicted networks contains information on true protein associations, beyond the constitutive first order binary predictions. We also observe that most of the reliable predicted protein associations are experimentally uncharacterised in our models, constituting the hidden or "dark matter'' of networks by analogy to astronomical systems. Some of this dark matter shows enrichment of particular functions and contains key functional elements of protein networks, such as hubs associated with important functional areas like the regulation of Ras protein signal transduction in human cells. Thus, characterising this large and functionally important dark matter, elusive to established experimental designs, may be crucial for modelling biological systems. In any case, these predictions provide a valuable guide to these experimentally elusive regions

Reducing broad-spectrum antibiotic use in intensive care unit between first and second waves of COVID-19 did not adversely affect mortality

Background: The COVID-19 pandemic increased the use of broad-spectrum antibiotics due to diagnostic uncertainty, particularly in critical care. Multi-professional communication became more difficult, weakening stewardship activities. Aim: To determine changes in bacterial co-/secondary infections and antibiotics used in COVID-19 patients in critical care, and mortality rates, between the first and second waves. Methods: Prospective audit comparing bacterial co-/secondary infections and their treatment during the first two waves of the pandemic in a single-centre teaching hospital intensive care unit. Data on demographics, daily antibiotic use, clinical outcomes, and culture results in patients diagnosed with COVID-19 infection were collected over 11 months. Findings: From March 9th, 2020 to September 2nd, 2020 (Wave 1), there were 156 patients and between September 3rd, 2020 and February 1st, 2021 (Wave 2) there were 235 patients with COVID-19 infection admitted to intensive care. No significant difference was seen in mortality or positive blood culture rates between the two waves. The proportion of patients receiving antimicrobial therapy (93.0% vs 81.7%; P < 0.01) and the duration of meropenem use (median (interquartile range): 5 (2–7) vs 3 (2–5) days; P = 0.01) was lower in Wave 2. However, the number of patients with respiratory isolates of Pseudomonas aeruginosa (4/156 vs 21/235; P < 0.01) and bacteraemia from a respiratory source (3/156 vs 20/235; P < 0.01) increased in Wave 2, associated with an outbreak of infection. There was no significant difference between waves with respect to isolation of other pathogens. Conclusion: Reduced broad-spectrum antimicrobial use in the second wave of COVID-19 compared with the first wave was not associated with significant change in mortality

The sugar content of children’s and lunchbox beverages sold in the UK before and after the soft drink industry levy

Background: Childhood obesity is associated with an increased intake of sugary soft drinks and juice drinks. The aims of this study were (1) to report the sugar and energy content in commercial fruit juice (FJ), juice drinks (JD) and smoothies (S) specifically targeted at children in the UK, (2) to identify beverages liable for the Soft Drinks Industry Levy (SDIL) and (3) to compare the amount of sugar in these beverages before and after the levy. Methods: The beverages were retrieved using the online shopping tool my Supermarket, websites of nine major supermarket in the UK and manufacturers webpages. Comparisons of sugar content were taken before and after the introduction of the SDIL. Results: 131 FJJDS fulfilled the inclusion criteria. The mean sugar content of all the beverages was 6.3g±4.5/100mL. There was large variation in the sugar content from 0.1g/100mL to 15.2g/100mL, with smoothies found to contain the most sugar (11.55±1.62 g/mL). The beverages were reanalysed in September 2018 to determine their eligibility for the SDIL. Of the 131 products only 7 JD were eligible for the levy. Four of these beverages had reformulated their ingredients since the initial analysis resulting in a sugar content of <5g/100mL. Conclusions: The majority of the beverages targeted at children and children’s lunch boxes were not eligible for the SDIL. This study suggests the necessity to adapt the SDIL to include all FJJDS aimed at children as the total sugar content of these beverages are still above the recommended quantities for this age group

CODA: Accurate Detection of Functional Associations between Proteins in Eukaryotic Genomes Using Domain Fusion

Background: In order to understand how biological systems function it is necessary to determine the interactions and associations between proteins. Gene fusion prediction is one approach to detection of such functional relationships. Its use is however known to be problematic in higher eukaryotic genomes due to the presence of large homologous domain families. Here we introduce CODA (Co-Occurrence of Domains Analysis), a method to predict functional associations based on the gene fusion idiom.Methodology/Principal Findings: We apply a novel scoring scheme which takes account of the genome-specific size of homologous domain families involved in fusion to improve accuracy in predicting functional associations. We show that CODA is able to accurately predict functional similarities in human with comparison to state-of-the-art methods and show that different methods can be complementary. CODA is used to produce evidence that a currently uncharacterised human protein may be involved in pathways related to depression and that another is involved in DNA replication.Conclusions/Significance: The relative performance of different gene fusion methodologies has not previously been explored. We find that they are largely complementary, with different methods being more or less appropriate in different genomes. Our method is the only one currently available for download and can be run on an arbitrary dataset by the user. The CODA software and datasets are freely available from ftp://ftp.biochem.ucl.ac.uk/pub/gene3d_data/v6.1.0/CODA/. Predictions are also available via web services from http://funcnet.eu/

Persistent anthrax as a major driver of wildlife mortality in a tropical rainforest

Anthrax is a globally important animal disease and zoonosis. Despite this, our current knowledge of anthrax ecology is largely limited to arid ecosystems, where outbreaks are most commonly reported. Here we show that the dynamics of an anthrax-causing agent, Bacillus cereus biovar anthracis, in a tropical rainforest have severe consequences for local wildlife communities. Using data and samples collected over three decades, we show that rainforest anthrax is a persistent and widespread cause of death for a broad range of mammalian hosts. We predict that this pathogen will accelerate the decline and possibly result in the extirpation of local chimpanzee (Pan troglodytes verus) populations. We present the epidemiology of a cryptic pathogen and show that its presence has important implications for conservation

Home-based Extended Rehabilitation for Older people (HERO): study protocol for an individually randomised controlled multi-centre trial to determine the clinical and cost-effectiveness of a home-based exercise intervention for older people with frailty as extended rehabilitation following acute illness or injury, including embedded process evaluation

Background: The majority of older people (> 65 years) in hospital have frailty and are at increased risk of readmission or death following discharge home. In the UK, following acute hospitalisation, around one third of older people with frailty are referred on for rehabilitation, termed ‘intermediate care’ services. Although this rehabilitation can reduce early readmission to hospital (< 30 days), recipients often do not feel ready to leave the service on discharge, suggesting possible incomplete recovery. Limited evidence suggests extended rehabilitation is of benefit in several conditions and there is preliminary evidence that progressive physical exercise can improve mobility and function for older people with frailty, and slow progression to disability. Our aim is to evaluate the effectiveness of the Home-based Older People’s Exercise (HOPE) programme as extended rehabilitation for older people with frailty discharged home from hospital or intermediate care services after acute illness or injury. Methods: A multi-centre individually randomised controlled trial, to evaluate the clinical and cost-effectiveness of the HOPE programme. This individualised, graded and progressive 24-week exercise programme is delivered by NHS physiotherapy teams to people aged 65 and older with frailty, identified using the Clinical Frailty Scale, following discharge from acute hospitalisation and linked intermediate care rehabilitation pathways. The primary outcome is physical health-related quality of life, measured using the physical component summary score of the modified Short Form 36- item health questionnaire (SF36) at 12 months. Secondary outcomes include self-reported physical and mental health, functional independence, death, hospitalisations, care home admissions. Plans include health economic analyses and an embedded process evaluation. Discussion: This trial seeks to determine if extended rehabilitation, via the HOPE programme, can improve physical health-related quality of life for older people with frailty following acute hospitalisation. Results will improve awareness of the rehabilitation needs of older people with frailty, and provide evidence on the clinical and cost-effectiveness of the targeted exercise intervention. There is potential for considerable benefit for health and social care services through widespread implementation of trial findings if clinical and cost-effectiveness is demonstrated

STAT-HI: A Socio-Technical Assessment Tool for Health Informatics Implementations

This paper proposes a socio-technical assessment tool (STAT-HI) for health informatics implementations. We explore why even projects allegedly using sound methodologies repeatedly fail to give adequate attention to socio-technical issues, and we present an initial draft of a structured assessment tool for health informatics implementation that encapsulates socio-technical good practice. Further work is proposed to enrich and validate the proposed instrument. This proposal was presented for discussion at a meeting of the UK Faculty of Health Informatics in December 2009