Characterization of Integrase and Excisionase Activity in a Cell-Free Protein Expression System Using a Modeling and Analysis Pipeline

We present a full-stack modeling, analysis, and parameter identification pipeline to guide the modeling and design of biological systems starting from specifications to circuit implementations and parametrizations. We demonstrate this pipeline by characterizing the integrase and excisionase activity in a cell-free protein expression system. We build on existing Python tools─BioCRNpyler, AutoReduce, and Bioscrape─to create this pipeline. For enzyme-mediated DNA recombination in a cell-free system, we create detailed chemical reaction network models from simple high-level descriptions of the biological circuits and their context using BioCRNpyler. We use Bioscrape to show that the output of the detailed model is sensitive to many parameters. However, parameter identification is infeasible for this high-dimensional model; hence, we use AutoReduce to automatically obtain reduced models that have fewer parameters. This results in a hierarchy of reduced models under different assumptions to finally arrive at a minimal ODE model for each circuit. Then, we run sensitivity analysis-guided Bayesian inference using Bioscrape for each circuit to identify the model parameters. This process allows us to quantify integrase and excisionase activity in cell extracts enabling complex-circuit designs that depend on accurate control over protein expression levels through DNA recombination. The automated pipeline presented in this paper opens up a new approach to complex circuit design, modeling, reduction, and parametrization.

Telehealth in cancer care during the COVID-19 pandemic

INTRODUCTION

The Victorian COVID-19 Cancer Network (VCCN) Telehealth Expert Working Group aimed to evaluate the telehealth (TH) experience for cancer patients, carers and clinicians with the rapid uptake of TH in early 2020 during the COVID-19 pandemic.

METHODS

We conducted a prospective multi-centre cross-sectional survey involving eight Victorian regional and metropolitan cancer services and three consumer advocacy groups. Patients or their carers and clinicians who had TH consultations between 1 July 2020 and 31 December 2020 were invited to participate in patient and clinician surveys, respectively. These surveys were opened from September to December 2020.

RESULTS

The acceptability of TH via both video (82.9%) and phone (70.4%) were high though acceptability appeared to decrease in older phone TH users. Video was associated with higher satisfaction compared to phone (87.1% vs 79.7%) even though phone was more commonly used. Various themes from the qualitative surveys highlighted barriers and enablers to rapid TH implementation.

DISCUSSION

The high TH acceptability supports this as a safe and effective strategy for continued care and should persist beyond the pandemic environment, where patient preferences are considered and clinically appropriate. Ongoing support to health services for infrastructure and resources, as well as expansion of reimbursement eligibility criteria for patients and health professionals, including allied health and nursing, are crucial for sustainability.

Identifying and understanding the factors that influence the functioning of integrated healthcare systems in the NHS: a systematic literature review

OBJECTIVES

The National Health Service has been moving towards integrated care for the best part of two decades to address the growing financial and service pressures created by an ageing population. Integrated healthcare systems (IHSs) join up health and social care services and have been established to manage the care of individuals with complex chronic conditions but with varied success. It is therefore imperative to conduct a Systematic Literature Review (SLR) to identify and understand the factors that influence their successful functioning, and ascertain the factor with the greatest influence, in order to ensure positive outcomes when establishing future IHSs.

METHODS

Articles published between 1 January 1997 and 8 March 2020 were analysed from the following six databases: Healthcare Management Information Consortium, Nuffield Trust, Cumulative Index to Nursing and Allied Health Literature, PubMed, National Institute for Health and Care Excellence Evidence and Health Systems Evidence. Those deemed relevant after title and abstract screening were procured for subsequent review of the full-text article.

RESULTS

Thirty-three finalised articles were analysed in this SLR to provide a comprehensive overview of the factors that influence the functioning of IHSs. Factors were stratified into six key categories: organisational culture, workforce management, interorganisational collaboration, leadership ability of staff, economic factors and political factors. Leadership was deemed to be the most influential factor due to its intrinsic and instrumental role in influencing the other key factors.

CONCLUSIONS

The findings of this SLR may serve as a guide to developing tailor-made recommendations and policies that address the identified key factors and thereby improve the functioning of present and future IHSs. Furthermore, due to both its overarching influence and the inadequacy of literature in this field, there is a strong case for further research exploring leadership development specifically for IHSs.

BioCRNpyler: Compiling chemical reaction networks from biomolecular parts in diverse contexts

Biochemical interactions in systems and synthetic biology are often modeled with chemical reaction networks (CRNs). CRNs provide a principled modeling environment capable of expressing a huge range of biochemical processes. In this paper, we present a software toolbox, written in Python, that compiles high-level design specifications represented using a modular library of biochemical parts, mechanisms, and contexts to CRN implementations. This compilation process offers four advantages. First, the building of the actual CRN representation is automatic and outputs Systems Biology Markup Language (SBML) models compatible with numerous simulators. Second, a library of modular biochemical components allows for different architectures and implementations of biochemical circuits to be represented succinctly with design choices propagated throughout the underlying CRN automatically. This prevents the often occurring mismatch between high-level designs and model dynamics. Third, high-level design specification can be embedded into diverse biomolecular environments, such as cell-free extracts and in vivo milieus. Finally, our software toolbox has a parameter database, which allows users to rapidly prototype large models using very few parameters which can be customized later. By using BioCRNpyler, users ranging from expert modelers to novice script-writers can easily build, manage, and explore sophisticated biochemical models using diverse biochemical implementations, environments, and modeling assumptions.

This paper describes a new software package BioCRNpyler (pronounced “Biocompiler”) designed to support rapid development and exploration of mathematical models of biochemical networks and circuits by computational biologists, systems biologists, and synthetic biologists. BioCRNpyler allows its users to generate large complex models using very few lines of code in a way that is modular. To do this, BioCRNpyler uses a powerful new representation of biochemical circuits which defines their parts, underlying biochemical mechanisms, and chemical context independently. BioCRNpyler was developed as a Python scripting language designed to be accessible to beginning users as well as easily extendable and customizable for advanced users. Ultimately, we see Biocrnpyler being used to accelerate computer automated design of biochemical circuits and model driven hypothesis generation in biology.

Vivarium: an interface and engine for integrative multiscale modeling in computational biology

MOTIVATION

This article introduces Vivarium-software born of the idea that it should be as easy as possible for computational biologists to define any imaginable mechanistic model, combine it with existing models and execute them together as an integrated multiscale model. Integrative multiscale modeling confronts the complexity of biology by combining heterogeneous datasets and diverse modeling strategies into unified representations. These integrated models are then run to simulate how the hypothesized mechanisms operate as a whole. But building such models has been a labor-intensive process that requires many contributors, and they are still primarily developed on a case-by-case basis with each project starting anew. New software tools that streamline the integrative modeling effort and facilitate collaboration are therefore essential for future computational biologists.

RESULTS

Vivarium is a software tool for building integrative multiscale models. It provides an interface that makes individual models into modules that can be wired together in large composite models, parallelized across multiple CPUs and run with Vivarium's discrete-event simulation engine. Vivarium's utility is demonstrated by building composite models that combine several modeling frameworks: agent-based models, ordinary differential equations, stochastic reaction systems, constraint-based models, solid-body physics and spatial diffusion. This demonstrates just the beginning of what is possible-Vivarium will be able to support future efforts that integrate many more types of models and at many more biological scales.

AVAILABILITY AND IMPLEMENTATION

The specific models, simulation pipelines and notebooks developed for this article are all available at the vivarium-notebooks repository: https://github.com/vivarium-collective/vivarium-notebooks. Vivarium-core is available at https://github.com/vivarium-collective/vivarium-core, and has been released on Python Package Index. The Vivarium Collective (https://vivarium-collective.github.io) is a repository of freely available Vivarium processes and composites, including the processes used in Section 3. Supplementary Materials provide with an extensive methodology section, with several code listings that demonstrate the basic interfaces.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Release of individual surgeon data to the public: patients' and surgeons' views

BACKGROUND

Limited surgeon-specific outcomes data are currently released to the public. Existing schemes generally result from the recommendations of public enquiries, addressing breaches to patient safety and malpractice. We found limited evidence in the literature about patients' or orthopaedic surgeons' wishes regarding the release of such data to the public.

METHODS

We surveyed 80 joint replacement patients and 41 orthopaedic surgeons regarding their wishes concerning collection and release of individual surgeon data to the public.

RESULTS

Of 80 patients, 30% (24/80) were aware of data on the NHS-My Choices website, 16% (13/80) had reviewed data prior to operation and 95% (76/80) wanted data concerning surgeons' experience, length of stay and complications including revisions. Patients expected more current monitoring of data than occurs. Of 41 surgeons, 20% (8/41) thought national joint registry (NJR) derived data accurately reflected their NHS work. Surgeons did not think this data improved patient outcomes (34%, 14/41), and that it reduced innovation (61%, 25/41) and training (75%, 31/41) and increased risk of adverse behaviour (61%, 25/41). Surgeons wanted a minimal data set accurately presented and risk adjusted.

CONCLUSION

In the future, it is likely that more individual surgeon data will be released to the public. There needs to be an agreed, accurate minimum dataset collected, reviewed in local clinical governance meetings and published with explanatory notes regarding the interfering variables and what conclusions can be drawn regarding the ability of the surgeon. This process needs to be overseen by an independent body trusted by the public.

Interprosthetic femoral fractures managed with modern distal femoral locking plates: 10 years' experience at a UK major trauma centre

INTRODUCTION

Interprosthetic femoral fractures (IFF) are rare but increasing with an ageing population. Operative management is challenging and there is currently a paucity of outcome data in literature. The purpose of this study was to evaluate outcomes of IFFs managed with modern distal femoral locking plates, in a larger sample size than previously published.

METHOD

This retrospective study reviewed 49 closed IFFs in 48 patients at a major trauma center from 2009 to 2019 occurring between previous total hip arthroplasty (n=38), hemi hip arthroplasty (n=3), dynamic hip screw (n=6) or cephalomedullary nail (n=2) and total knee arthroplasty. They were managed with Minimally Invasive Plate Osteosynthesis (MIPO) employing modern biological fixation techniques and stabilised with VA-LCP Condylar (Synthes; n=28) or Peri-Loc (S&N; n=21) plate. Clinical and radiographic outcomes were measured.

RESULTS

The majority of fractures were in female patients (80%), who were elderly (average 83 years), and comorbid (55% ASA grade 3 or 4). Most fractures were Pires type IIA and OTA/AO type 33A. Average plate spanning femur was 16 holes, with average working length of 6 holes. 86% had unrestricted weight bearing immediately post operatively. 31 fractures reached radiological (n=25) or clinical (n=6) union. 13 patients died with 2 lost to follow up. There were 3 non-unions, with implant failure occurring before 4 months in all 3. We present a union rate of 91% (n=31/34).

CONCLUSION

IFFs are occurring with increasing frequency in a frail elderly population. In patients with IFFs, MIPO and biological fixation techniques using modern distal femoral locking plates can achieve high rate of union when combined with immediate unrestricted weight bearing postoperatively.

A Cost Utility Analysis of Minimally Invasive Surgery with Thrombolysis Compared to Standard Medical Treatment in Spontaneous Intracerebral Haemorrhagic Stroke

OBJECTIVES

Standard medical management of spontaneous intracerebral haemorrhage (ICH) and surgical hematoma evacuation starkly differ, and whilst landmark randomised control trials report no clinical benefit of early surgical evacuation compared with medical treatment in supratentorial ICH, minimally invasive surgery (MIS) with thrombolysis has been neglected within these studies. However, recent technological advancements in MIS have renewed interest in the surgical treatment of ICH. Several economic evaluations have focused on the benefits of MIS in ischaemic stroke management, but no economic evaluations have yet been performed comparing MIS to standard medical treatment for ICH.

MATERIALS AND METHOD

All costs were sourced from the UK in GBP. Where possible, the 2019/2020 NHS reference costs were used. The MISTIE III study was used to analyse the outcomes of patients undergoing either MIS or standard medical treatment in this economic evaluation.

RESULTS

The incremental cost-effectiveness ratio (ICER) for MIS was £485,240.26 for every quality-adjusted life year (QALY) gained. Although MIS resulted in a higher QALY compared to medical treatment, the gain was insignificant at 0.011 QALY. Four sensitivity analyses based on combinations of alternative EQ-5D values and categorisation of MIS outcomes, alongside alterations to the cost of significant adverse events, were performed to check the robustness of the ICER calculation. The most realistic sensitivity analysis showed a potential increase in cost effectiveness when clot size is reduced to <15ml, with the ICER falling to £74,335.57.

DISCUSSION

From the perspective of the NHS, MIS with thrombolysis is not cost-effective compared to optimal medical treatment. ICER shows that intention-to-treat MIS would require a cost of £485,240.26 to gain one extra QALY, which is significantly above the NHS threshold of £30,000. Further UK studies with ICH survivor utilities, more replicable surgical technique, and the reporting of clot size reduction are indicated as the present sensitivity analysis suggests that MIS is promising. Greater detail about outcomes and complications would ensure improved cost-benefit analyses and support valid and efficient allocation of resources by the NHS.

292 Publication of Individual Surgeon Outcomes Data: The Wishes of Orthopaedic Patients and Their Surgeons

Background

The Paterson report recommended increased release of individual surgeon data to the public. There is limited evidence in the literature about patients’ or orthopaedic surgeons’ wishes regarding release of such data to the public.

Method

We surveyed 80 joint replacement patients and 41 orthopaedic surgeons to determine their wishes regarding collection and release of individual surgeon data to the public.

Results

Patients expected more current monitoring of data than actually occurs. Of the patients, 95% wanted data to be available describing surgeon experience, length of stay and complications. Regarding currently available data, 50% of patients who were aware of it were likely to view it on the internet.

Surgeons were aware of the data available, but 80% did not think it was accurate. Surgeons did not think this data improved standards, that it negatively affected innovation (61%) and training (76%) and led to risk averse behaviour (61%). Surgeons wanted a minimal data set accurately presented and risk adjusted.

Conclusions

We recommend an agreed minimum dataset of good quality data is collected and discussed in clinical governance sessions. It can then be released to the public with explanatory notes.

WHOLE CORE COUPLING METHODOLOGIES WITHIN WIMS

The ANSWERS® WIMS reactor physics code is being developed for whole core multiphysics modelling. The established neutronics capability for lattice calculations has recently been extended to be suitable for whole core modelling of Small Modular Reactors (SMRs). A whole core transport, SP3 or diffusion flux solution is combined with fuel assembly resonance shielding and pin-by-pin differential depletion. An integrated thermal hydraulic solver permits differential temperature and density variations to feedback to the neutronics calculation.

This paper presents new methodology developed in WIMS to couple the core neutronics to the integrated core thermal hydraulics solver. Two coupling routes are presented and compared using a challenging PWR SMR benchmark. The first route, called GEOM, dynamically calculates the resonance shielding and homogenisation with the whole core flux solution. The second coupling route, called CAMELOT, separates the resonance shielding and pincell homogenisation from the whole core solution via generating tabulated cross sections. Both routes can use the MERLIN homogenised pin-by-pin whole core flux solver and couple to the same integrated thermal hydraulic solver, called ARTHUR. Heterogeneous differences between the neutronics and thermal hydraulics are mapped via thermal identifiers for neutronics materials and thermal regions.

The ability for the integrated thermal hydraulic solver to call an external code via a Fortran-C-Python (FCP) interface is also summarised. This flexible external coupling permits one way coupling to an external fuel performance code or two way coupling to an external thermal hydraulic code.

Seventeenth-Century 'double writing' schemes, and a 1676 letter in the phonetic script and real character of John Wilkins

Royal Society Classified Papers XVI contains a letter written in not one but two seemingly mysterious scripts. As a result, this letter has remained until now effectively illegible, and has been miscatalogued. These scripts are rare examples of the written forms devised by John Wilkins to accompany his proposals for an artificial language, published under the auspices of the Royal Society in 1668. This article therefore first correctly identifies and decodes this letter, which is shown to be from the Somersetshire clergyman Andrew Paschall to Robert Hooke in London in 1676, and then surveys other surviving texts written in Wilkins's scripts or language. Finally the article addresses the contents of the letter, namely its author's attempt to build a workable double writing device, in effect an early 'pantograph'. Designs for such instruments had been much touted in the 1650s, and the complex history of such proposals is unravelled properly for the first time.

Combining dependent P-values with an empirical adaptation of Brown's method

MOTIVATION

Combining P-values from multiple statistical tests is a common exercise in bioinformatics. However, this procedure is non-trivial for dependent P-values. Here, we discuss an empirical adaptation of Brown's method (an extension of Fisher's method) for combining dependent P-values which is appropriate for the large and correlated datasets found in high-throughput biology.

RESULTS

We show that the Empirical Brown's method (EBM) outperforms Fisher's method as well as alternative approaches for combining dependent P-values using both noisy simulated data and gene expression data from The Cancer Genome Atlas.

AVAILABILITY AND IMPLEMENTATION

The Empirical Brown's method is available in Python, R, and MATLAB and can be obtained from https://github.com/IlyaLab/CombiningDependentPvalues UsingEBM The R code is also available as a Bioconductor package from https://www.bioconductor.org/packages/devel/bioc/html/EmpiricalBrownsMethod.html

CONTACT

Theo.Knijnenburg@systemsbiology.org

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Delay to surgery does not affect survival following osteoporotic femoral fractures

AIMS

Fragility femoral fractures occur in a similar group of patients to hip fractures but they are not routinely managed along standardised guidelines. This study looked specifically at whether delay to surgery has an impact on mortality and morbidity.

PATIENTS AND METHODS

An international, multi-centre retrospective review was carried including all patients over 60 years with fragility femoral fractures, including most periprosthetic fractures, between December 2008-2014.

RESULTS

243 patients met the inclusion criteria with mean follow-up 25 months. 197 (81%) were female with mean age 81 years. Median time to surgery was 2 days; 39% were operated on <24h, 23% 24-48h, and 37% at >48h. 3- and 12-month mortality were 14% (95% CI: 9-18%) and 26% (20-31%) respectively. On Kaplan-Meier plotting, relationships were apparent between survival and sex, and ASA grade, but not delay to surgery or fracture type.

CONCLUSION

Fragility femoral fractures have equivalent mortality to hip fractures but we found no link between delay to surgery and mortality. We believe it is safe to delay surgery, within reason, whilst their acute and chronic medical problems are optimised. We believe this information will help develop guidelines similar to hip fracture pathways.

The first intravenous anaesthetic: how well was it managed and its potential realized?

Our speciality commonly traces its origin to a demonstration of the inhalation of ether by a patient undergoing surgery in Boston in 1846. Less well known is the demonstration of the i.v. injection of opium with alcohol into a dog in Oxford in 1656, leading to anaesthesia followed by full long-term recovery. After gaining i.v. access, a mixture of opium and alcohol was injected, resulting in a brief period of anaesthesia. After a period during which the dog was kept moving to assist recovery, a full recovery was made. Details from this momentous experiment allow us to compare the technique used with modern management. It is important to consider why there was a failure to translate the results into clinical practice and nearly 200 yr of potentially pain-free surgery. Possible factors include lack of equipment for i.v. access, lack of understanding of dose-response effects, and a climate of scientific discovery rather than clinical application. Given the current interest in total i.v. anaesthesia, it seems appropriate to identify its origins well before those of inhalation anaesthesia.

Theodoricus Gravius (fl. 1600-1661): some biographical notes on a German chymist and scribe working in seventeenth-century England

This article establishes the career of Theodoricus Gravius (fl. 1600-1661), a German refugee who worked in Great Linford as a laboratory assistant and scribe to the cleric and practitioner of astrological medicine, Richard Napier (1559-1634). Gravius was the first transmitter to England of the texts of the mystic Jacob Böhme, and although he settled in England, he undertook subsequent foreign visits to attempt the recovery of his property and to learn more about chymical matters. He also visited the Oxonian George Hakewill (1578-1649), and is responsible for scribing one of the manuscripts of the revisions to Hakewill's celebrated Apologie or Declaration Concerning the Power and Providence of God (1635).