Weak-form inference for hybrid dynamical systems in ecology.

Species subject to predation and environmental threats commonly exhibit variable periods of population boom and bust over long timescales. Understanding and predicting such behaviour, especially given the inherent heterogeneity and stochasticity of exogenous driving factors over short timescales, is an ongoing challenge. A modelling paradigm gaining popularity in the ecological sciences for such multi-scale effects is to couple short-term continuous dynamics to long-term discrete updates.

CLosure of Abdominal MidlineS Survey (CLAMSS): A national survey investigating current practice in the closure of abdominal midline incisions in UK surgical practice.

Aim: Incisional herniation (IH) is a frequent complication following midline abdominal closure with significant associated morbidity. Randomized controlled trials have demonstrated that the small bites technique (SBT) and prophylactic mesh augmentation (PMA) may reduce IH compared to mass closure techniques, but data are lacking on their implementation in contemporary surgical practice. This survey aimed to evaluate the use of the SBT and PMA and to identify factors associated with their adoption.

Coarse-graining Hamiltonian systems using WSINDy.

Weak form equation learning and surrogate modeling has proven to be computationally efficient and robust to measurement noise in a wide range of applications including ODE, PDE, and SDE discovery, as well as in coarse-graining applications, such as homogenization and mean-field descriptions of interacting particle systems. In this work we extend this coarse-graining capability to the setting of Hamiltonian dynamics which possess approximate symmetries associated with timescale separation. A smooth -dependent Hamiltonian vector field possesses an approximate symmetry if the limiting vector field possesses an exact symmetry.

An adaptable ensemble model of the arachidonic acid cascade.

Eicosanoids are a family of bioactive lipids, including derivatives of the ubiquitous fatty acid arachidonic acid (AA). The intimate involvement of eicosanoids in inflammation motivates the development of predictive models for a systems-level exploration of disease mechanisms, drug development and replacement of animal models. Using an ensemble modelling strategy, we developed a computational model of the AA cascade.

SARS-CoV-2 infection among physicians over time in Ontario, Canada: a population-based retrospective cohort study.

Aim: To assess this risk of SARS-CoV-2 infection among Ontario physicians by specialty and in comparison with non-physician controls during the COVID-19 pandemic.

Methods: In this retrospective cohort study, the primary outcome was incident SARS-CoV-2 infection confirmed by polymerase chain reaction (PCR). Secondary outcomes were hospitalization, use of critical care, and mortality.

Direct Estimation of Parameters in ODE Models Using WENDy: Weak-Form Estimation of Nonlinear Dynamics.

We introduce the Weak-form Estimation of Nonlinear Dynamics (WENDy) method for estimating model parameters for non-linear systems of ODEs. Without relying on any numerical differential equation solvers, WENDy computes accurate estimates and is robust to large (biologically relevant) levels of measurement noise. For low dimensional systems with modest amounts of data, WENDy is competitive with conventional forward solver-based nonlinear least squares methods in terms of speed and accuracy.

Colorectal cancer incidence trends by tumour location among adults of screening-age in England: a population-based study.

Aim: Proximal and distal colorectal cancers (CRCs) exhibit different clinical, molecular and biological patterns. The aim of this study was to determine temporal trends in the age-standardized incidence rates (ASIRs) of proximal and distal CRC following the introduction of the English Bowel Cancer Screening Programme (BCSP) in 2006.

Method: The National Cancer Registration and Analysis Service database was used to identify incident cases of CRC among adults of screening age (60-74 years) between 2001 and 2017.

Learning mean-field equations from particle data using WSINDy.

We develop a weak-form sparse identification method for interacting particle systems (IPS) with the primary goals of reducing computational complexity for large particle number and offering robustness to either intrinsic or extrinsic noise. In particular, we use concepts from mean-field theory of IPS in combination with the weak-form sparse identification of nonlinear dynamics algorithm (WSINDy) to provide a fast and reliable system identification scheme for recovering the governing stochastic differential equations for an IPS when the number of particles per experiment is on the order of several thousands and the number of experiments is less than 100. This is in contrast to existing work showing that system identification for less than 100 and on the order of several thousand is feasible using strong-form methods.

Direct Estimation of Parameters in ODE Models Using WENDy: Weak-form Estimation of Nonlinear Dynamics.

We introduce the Weak-form Estimation of Nonlinear Dynamics (WENDy) method for estimating model parameters for non-linear systems of ODEs. Without relying on any numerical differential equation solvers, WENDy computes accurate estimates and is robust to large (biologically relevant) levels of measurement noise. For low dimensional systems with modest amounts of data, WENDy is competitive with conventional forward solver-based nonlinear least squares methods in terms of speed and accuracy.

Making and breaking of boron bridges in the pectic domain rhamnogalacturonan-II at apoplastic pH in vivo and in vitro.

Cross-linking of the cell-wall pectin domain rhamnogalacturonan-II (RG-II) via boron bridges between apiose residues is essential for normal plant growth and development, but little is known about its mechanism or reversibility. We characterized the making and breaking of boron bridges in vivo and in vitro at 'apoplastic' pH. RG-II (13-26 μm) was incubated in living Rosa cell cultures and cell-free media with and without 1.

Managing surgical demand when needs outstrip resource: qualitative investigation of colorectal cancer surgery provision in the first wave of the COVID-19 pandemic.

Background: At the onset of the COVID-19 pandemic, elective surgical provision was severely affected by the need for hospital reorganization to care for critically ill patients. In response, National Health Service (NHS) England issued national guidance proposing acceptable time intervals for postponing different types of surgical procedure. This study reports healthcare professionals' private accounts of the strategies adopted to manage the imbalance of demand and resource, using colorectal cancer surgery as a case study.

Airway injury from the presence of endotracheal tubes and the association with subglottic secretion drainage: a prospective observational study.

Purpose: Laryngeal and tracheal injuries are known complications of endotracheal intubation. Endotracheal tubes (ETTs) with subglottic suction devices (SSDs) are commonly used in the critical care setting. There is concern that herniation of tissue into the suction port of these devices may lead to tracheal injury resulting in serious clinical consequences such as tracheal stenosis.

A combined spatial score of granzyme B and CD68 surpasses CD8 as an independent prognostic factor in TNM stage II colorectal cancer.

Background: Previous assessments of peritumoral inflammatory infiltrate in colorectal cancer (CRC) have focused on the role of CD8 T lymphocytes. We sought to compare the prognostic value of CD8 with downstream indicators of active immune cell function, specifically granzyme B (GZMB) and CD68 in the tumour microenvironment.

Methods: Immunohistochemical (IHC) staining was performed for CD8, GZMB, CD68 and CD163 on next-generation tissue microarrays (ngTMAs) in a primary cohort (n = 107) and a TNM stage II validation cohort (n = 151).

Demographic trends in the incidence of malignant appendiceal tumours in England between 1995 and 2016: Population-based analysis.

Aims: Recent data suggest that the incidence of malignant appendiceal tumours is increasing. This study aimed to determine temporal trends in the incidence of malignant appendiceal tumours within England and a possible influence by demographic factors.

Methods: All incident cases of appendiceal tumours in patients aged 20 years and above were identified from the National Cancer Registration and Analysis Service database between 1995 and 2016 using ICD-9/10 codes.

Online Weak-form Sparse Identification of Partial Differential Equations.

This paper presents an online algorithm for identification of partial differential equations (PDEs) based on the weak-form sparse identification of nonlinear dynamics algorithm (WSINDy). The algorithm is online in the sense that if performs the identification task by processing solution snapshots that arrive sequentially. The core of the method combines a weak-form discretization of candidate PDEs with an online proximal gradient descent approach to the sparse regression problem.

Lower polyunsaturated fatty acid levels and FADS2 expression in adult compared to neonatal keratinocytes are associated with FADS2 promotor hypermethylation.

Keratinocytes produce lipids that are critical for the skin barrier, however, little is known about the impact of age on fatty acid (FA) biosynthesis in these cells. We have examined the relationship between keratinocyte FA composition, lipid biosynthetic gene expression, gene promoter methylation and age. Expression of elongase (ELOVL6 and 7) and desaturase (FADS1 and 2) genes was lower in adult versus neonatal keratinocytes, and was associated with lower concentrations of n-7, n-9 and n-10 polyunsaturated FA in adult cells.

Surgical site infection prevention bundle in elective colorectal surgery.

Objective: Surgical Site Infections (SSIs) are responsible for a significant economic burden as well as intangible costs suffered by the patient, with up to 60% deemed preventable. Colorectal patients are disproportionally affected by SSI due the risk of wound contamination with bowel content. We aimed to reduce the rate of superficial SSI after elective colorectal surgery using a bundle of evidence-based interventions.

WEAK SINDY FOR PARTIAL DIFFERENTIAL EQUATIONS.

Sparse Identification of Nonlinear Dynamics (SINDy) is a method of system discovery that has been shown to successfully recover governing dynamical systems from data [6, 39]. Recently, several groups have independently discovered that the weak formulation provides orders of magnitude better robustness to noise. Here we extend our Weak SINDy (WSINDy) framework introduced in [28] to the setting of partial differential equations (PDEs).

Routine Elastin Staining in Surgically Resected Colorectal Cancer: Impact on Venous Invasion Detection and its Association With Oncologic Outcomes.

Venous invasion (VI) is a powerful yet underreported prognostic factor in colorectal cancer (CRC). Its detection can be improved with an elastin stain. We evaluated the impact of routine elastin staining on VI detection in resected CRC and its relationship with oncologic outcomes.

Inhibition of the intestinal postprandial glucose transport by gallic acid and gallic acid derivatives.

Inhibition of glucose uptake in the intestine through sodium-dependent glucose transporter 1 (SGLT1) or glucose transporter 2 (GLUT2) may be beneficial in controlling postprandial blood glucose levels. Gallic acid and ten of its derivatives were identified in the active fractions of Terminalia chebula Retz. fructus immaturus, a popular edible plant fruit which has previously been associated with the inhibition of glucose uptake.

WEAK SINDy: GALERKIN-BASED DATA-DRIVEN MODEL SELECTION.

We present a novel weak formulation and discretization for discovering governing equations from noisy measurement data. This method of learning differential equations from data fits into a new class of algorithms that replace pointwise derivative approximations with linear transformations and variance reduction techniques. Compared to the standard SINDy algorithm presented in [S.

Outcomes following local excision of early anal squamous cell carcinomas of the anal canal and perianal margin.

Aim: There is a paucity of data on outcomes from local excision (LE) of early anal squamous cell carcinomas (ASCCs). This study aimed to assess survival outcomes according to tumour location, perianal (PAT) or anal canal (ACT), and to determine factors associated with R1 excision and outcomes according to T-category.

Methods: This was a retrospective cohort study of consecutive patients with early ASCC treated by LE from 2007 to 2019.