The Bioperl toolkit: Perl modules for the life sciences

The Bioperl project is an international open-source collaboration of biologists, bioinformaticians, and computer scientists that has evolved over the past 7 yr into the most comprehensive library of Perl modules available for managing and manipulating life-science information. Bioperl provides an easy-to-use, stable, and consistent programming interface for bioinformatics application programmers. The Bioperl modules have been successfully and repeatedly used to reduce otherwise complex tasks to only a few lines of code. The Bioperl object model has been proven to be flexible enough to support enterprise-level applications such as EnsEMBL, while maintaining an easy learning curve for novice Perl programmers. Bioperl is capable of executing analyses and processing results from programs such as BLAST, ClustalW, or the EMBOSS suite. Interoperation with modules written in Python and Java is supported through the evolving BioCORBA bridge. Bioperl provides access to data stores such as GenBank and SwissProt via a flexible series of sequence input/output modules, and to the emerging common sequence data storage format of the Open Bioinformatics Database Access project. This study describes the overall architecture of the toolkit, the problem domains that it addresses, and gives specific examples of how the toolkit can be used to solve common life-sciences problems. We conclude with a discussion of how the open-source nature of the project has contributed to the development effort.     

Improving health care for disabled people in COVID-19 and beyond: Lessons from Australia and England

COVID-19 has exacerbated pre-existing difficulties children and adults with disability face accessing quality health care. Some people with disability are at greater risk of contracting COVID-19 because they require support for personal care and are unable to physically distance, e.g. those living in congregate settings. Additionally, some people with disability have health conditions that put them at higher risk of poor outcomes if they become infected. Despite this, governments have been slow to recognise, and respond to, the unique and diverse health care needs of people with disability during COVID-19. While some countries, including Australia, have improved access to high-quality health care for people with disability others, like England, have failed to support their citizens with disability. In this Commentary we describe the health care responses of England and Australia and make recommendations for rapidly improving health care for people with disability in the pandemic and beyond.     

Assessing Diet Quality of Indigenous Food Systems in Three Geographically Distinct Solomon Islands Sites (Melanesia,Pacific Islands)

Indigenous Solomon Islanders, like many living in Pacific Small Island Developing States (PSIDS), are currently experiencing the global syndemic—the combined threat of obesity, undernutrition, and climate change. This mixed-method study aimed to assess nutrition transitions and diet quality by comparing three geographically unique rural and urban indigenous Solomon Islands populations. Participants in rural areas sourced more energy from wild and cultivated foods; consumed a wider diversity of foods; were more likely to meet WHO recommendations of >400 g of non-starchy fruits and vegetables daily; were more physically active; and had significantly lower body fat, waist circumference, and body mass index (BMI) when compared to urban populations. Urban populations were found to have a reduced ability to self-cultivate agri-food products or collect wild foods, and therefore consumed more ultra-processed foods (classified as NOVA 4) and takeout foods, and overall had less diverse diets compared to rural populations. Clear opportunities to leverage traditional knowledge and improve the cultivation and consumption of underutilized species can assist in building more sustainable and resilient food systems while ensuring that indigenous knowledge and cultural preferences are respected.     

Giving a voice to patient experiences through the insights of pragmatism

As a philosophical position, pragmatism can be critiqued to distinguish truth only with methods that bring about desired results, predominantly with scientific enquiry. The article hopes to dismiss this oversimplification and propose that within mental health nursing, enquiry enlightened by pragmatism can be anchored to methods helping to tackle genuine human problems. Whilst pragmatists suggest one reality exists, fluctuating experiences and shifting beliefs about the world can inhabit within; hence, pragmatists propose reality has the potential to change. Moreover, pragmatism includes being cognisant of what works to whom reality concerns, making reality context-driven, with a view to understand how actions shape experiences so what is generated has usefulness. Hence, it somewhat follows pragmatism can inform mental health nursing, after all, nursing is a discipline of action, and awareness is needed in how actions produce experiences that patients find helpful. Given the principles of recovery are preferably adopted in mental health care, the paper will explore how pragmatism can help nurses move towards that goal; specifically, with patients voicing their experiences. This is because like pragmatism, recovery subscribes to hope that reality can progress, and through meaningful experiences and beliefs, patients have expertise about personal difficulties alongside how life may flourish, despite mental illness.     

Mathematical model of volume kinetics and renal function after burn injury and resuscitation

This paper presents a mathematical model of blood volume kinetics and renal function in response to burn injury and resuscitation, which is applicable to the development and non-clinical testing of burn resuscitation protocols and algorithms. Prior mathematical models of burn injury and resuscitation are not ideally suited to such applications due to their limited credibility in predicting blood volume and urinary output observed in wide-ranging burn patients as well as in incorporating contemporary knowledge of burn pathophysiology. Our mathematical model consists of an established multi-compartmental model of blood volume kinetics, a hybrid mechanistic-phenomenological model of renal function, and novel lumped-parameter models of burn-induced perturbations in volume kinetics and renal function equipped with contemporary knowledge on burn-related physiology and pathophysiology. Using the dataset collected from 16 sheep, we showed that our mathematical model can be characterized with physiologically plausible parameter values to accurately predict blood volume kinetic and renal function responses to burn injury and resuscitation on an individual basis against a wide range of pathophysiological variability. Pending validation in humans, our mathematical model may serve as an effective basis for in-depth understanding of complex burn-induced volume kinetic and renal function responses as well as development and non-clinical testing of burn resuscitation protocols and algorithms.     

Total Hip Arthroplasty in Patients With Osteoarthritis Associated With Legg-Calve-Perthes Disease: Perioperative Complications and Patient-Reported Outcomes

BackgroundComplications and patient-reported outcomes (PROs) of total hip arthroplasty (THA) in patients with Legg-Calve-Perthes disease (LCPD) have demonstrated variable results. The purpose of this study was to use a validated grading scheme to analyze complications associated with THA in patients with residual LCPD deformities. Second, we report PROs and intermediate-term survivorship in this patient population.MethodsA retrospective, single-center review was performed on 61 hips in 61 patients who underwent THA for residual Perthes disease. Average patient age was 42 years and 26% of hips had previous surgery. Complications were determined and categorized using a validated grading scheme that included five grades based on the treatment required to manage the complication and on persistent disability. PROs were compared from preoperative to most recent follow-up time points.ResultsMajor complications (grade III) occurred in three patients (5%) which each required a second surgical intervention. The most common minor grade I or II complications (11.5%) were asymptomatic heterotopic ossification (3.3%). Patients were lengthened on the surgical side an average of 1.4 cm with no nerve palsies. All patient PROs improved from preoperative to postoperative time points with the modified Harris Hip Score improving from 46.9 preoperatively to 85.4 postoperatively (P < .01). Patients free from revision for any reason at final follow-up (5.6 years; range 2-13 years) was 98.4% with one patient needing a revision of their femoral component.ConclusionsTHA for the sequelae of the LCPD has an acceptable complication rate and provides excellent patient reported outcomes at mid-term follow-up.     

Risk factors for Epstein–Barr virus reactivation after renal transplantation: Results of a large,multi-centre study

Epstein–Barr virus (EBV) reactivation is a very common and potentially lethal complication of renal transplantation. However, its risk factors and effects on transplant outcome are not well known. Here, we have analysed a large, multi-centre cohort (N = 512) in which 18.4% of the patients experienced EBV reactivation during the first post-transplant year. The patients were characterized pre-transplant and two weeks post-transplant by a multi-level biomarker panel. EBV reactivation was episodic for most patients, only 12 patients showed prolonged viraemia for over four months. Pre-transplant EBV shedding and male sex were associated with significantly increased incidence of post-transplant EBV reactivation. Importantly, we also identified a significant association of post-transplant EBV with acute rejection and with decreased haemoglobin levels. No further severe complications associated with EBV, either episodic or chronic, could be detected. Our data suggest that despite relatively frequent EBV reactivation, it had no association with serious complications during the first post-transplantation year. EBV shedding prior to transplantation could be employed as biomarkers for personalized immunosuppressive therapy. In summary, our results support the employed immunosuppressive regimes as relatively safe with regard to EBV. However, long-term studies are paramount to support these conclusions.     

Variable effects of obesity on access to total hip and knee arthroplasty

BackgroundObesity is an important comorbidity affecting outcomes after total joint arthroplasty. Consequently, surgeons may delay care of obese patients to first address obesity through different care pathways. The effect of obesity on patient wait times for total joint arthroplasty has not been explored. The purpose of this study was to evaluate the effect of obesity on access to total hip (THA) and knee (TKA) arthroplasty.MethodsThe study data set was constructed from the Nova Scotia Health Authority’s Horizon Patient Folder system and the Patient Access Registry Nova Scotia. Wait time was measured as days between the decision to treat and date of surgery. Body mass index (BMI) was calculated from a preoperative assessment, and patients were grouped into BMI categories. Multivariate log-linear regression was used to test for statistical differences, controlling for confounding factors.ResultsWe observed longer wait times for TKA with increasing BMI weight class. Patients with BMIs greater than 50 had 34% longer waits than reference weight patients. However, THA recipients showed no statistical difference in wait times across weight categories. Furthermore, there was variability among surgeons in the wait times experienced by patients.ConclusionThe finding of longer wait times for TKAs, but not THAs, among patients who were obese was unexpected. This shows the variable wait times for THA and TKA that patients who are obese can experience with different surgeons. It is important to understand the variability in wait times so that efforts to standardize the patient experience can be accomplished.