TorchMD-Net 2.0: Fast Neural Network Potentials for Molecular Simulations

Achieving a balance between computational speed, prediction accuracy, and universal applicability in molecular simulations has been a persistent challenge. This paper presents substantial advancements in TorchMD-Net software, a pivotal step forward in the shift from conventional force fields to neural network-based potentials. The evolution of TorchMD-Net into a more comprehensive and versatile framework is highlighted, incorporating cutting-edge architectures such as TensorNet. This transformation is achieved through a modular design approach, encouraging customized applications within the scientific community. The most notable enhancement is a significant improvement in computational efficiency, achieving a very remarkable acceleration in the computation of energy and forces for TensorNet models, with performance gains ranging from 2× to 10× over previous, nonoptimized, iterations. Other enhancements include highly optimized neighbor search algorithms that support periodic boundary conditions and smooth integration with existing molecular dynamics frameworks. Additionally, the updated version introduces the capability to integrate physical priors, further enriching its application spectrum and utility in research. The software is available at https://github.com/torchmd/torchmd-net.

TorchMD-Net 2.0: Fast Neural Network Potentials for Molecular Simulations

Achieving a balance between computational speed, prediction accuracy, and universal applicability in molecular simulations has been a persistent challenge. This paper presents substantial advancements in the TorchMD-Net software, a pivotal step forward in the shift from conventional force fields to neural network-based potentials. The evolution of TorchMD-Net into a more comprehensive and versatile framework is highlighted, incorporating cutting-edge architectures such as TensorNet. This transformation is achieved through a modular design approach, encouraging customized applications within the scientific community. The most notable enhancement is a significant improvement in computational efficiency, achieving a very remarkable acceleration in the computation of energy and forces for TensorNet models, with performance gains ranging from 2-fold to 10-fold over previous iterations. Other enhancements include highly optimized neighbor search algorithms that support periodic boundary conditions and the smooth integration with existing molecular dynamics frameworks. Additionally, the updated version introduces the capability to integrate physical priors, further enriching its application spectrum and utility in research. The software is available at https://github.com/torchmd/torchmd-net.

OpenMM 8: Molecular Dynamics Simulation with Machine Learning Potentials

Machine learning plays an important and growing role in molecular simulation. The newest version of the OpenMM molecular dynamics toolkit introduces new features to support the use of machine learning potentials. Arbitrary PyTorch models can be added to a simulation and used to compute forces and energy. A higher-level interface allows users to easily model their molecules of interest with general purpose, pretrained potential functions. A collection of optimized CUDA kernels and custom PyTorch operations greatly improves the speed of simulations. We demonstrate these features in simulations of cyclin-dependent kinase 8 (CDK8) and the green fluorescent protein chromophore in water. Taken together, these features make it practical to use machine learning to improve the accuracy of simulations with only a modest increase in cost.

OpenMM 8: Molecular Dynamics Simulation with Machine Learning Potentials

Machine learning plays an important and growing role in molecular simulation. The newest version of the OpenMM molecular dynamics toolkit introduces new features to support the use of machine learning potentials. Arbitrary PyTorch models can be added to a simulation and used to compute forces and energy. A higher-level interface allows users to easily model their molecules of interest with general purpose, pretrained potential functions. A collection of optimized CUDA kernels and custom PyTorch operations greatly improves the speed of simulations. We demonstrate these features on simulations of cyclin-dependent kinase 8 (CDK8) and the green fluorescent protein (GFP) chromophore in water. Taken together, these features make it practical to use machine learning to improve the accuracy of simulations at only a modest increase in cost.

NNP/MM: Accelerating Molecular Dynamics Simulations with Machine Learning Potentials and Molecular Mechanics

Machine learning potentials have emerged as a means to enhance the accuracy of biomolecular simulations. However, their application is constrained by the significant computational cost arising from the vast number of parameters compared with traditional molecular mechanics. To tackle this issue, we introduce an optimized implementation of the hybrid method (NNP/MM), which combines a neural network potential (NNP) and molecular mechanics (MM). This approach models a portion of the system, such as a small molecule, using NNP while employing MM for the remaining system to boost efficiency. By conducting molecular dynamics (MD) simulations on various protein-ligand complexes and metadynamics (MTD) simulations on a ligand, we showcase the capabilities of our implementation of NNP/MM. It has enabled us to increase the simulation speed by ∼5 times and achieve a combined sampling of 1 μs for each complex, marking the longest simulations ever reported for this class of simulations.

Dying at home: enablers and barriers

BACKGROUND

According to the Grattan institute in 2014, 70% of Australians indicated a preference to die at home, however, only 14% of all deaths were at home.

AIMS

To identify how patients can be supported to die at home if that is their preference.

METHODS

A retrospective medical record audit of eligible Community Palliative Care (CPC) patients who indicated a wish to die at home was undertaken.

FINDINGS

Out of a total of 114 patients, 74% indicated a preference to die at home. Of these, 66% achieved a home death, and most lived with a carer. Enablers for home death included family support, regular nursing visits and equipment. People who attended an emergency department in their last month of life, lived alone or were undergoing oncological treatment were more likely to die elsewhere.

CONCLUSION

A range of enablers and barriers to home death were found, with many of the enablers being factors that prevented hospital presentations.

Does cancer type and adjuvant analgesic prescribing influence opioid dose?-a retrospective cross-sectional study

Opioids are the backbone of cancer pain management. Minimal evidence exists examining the relationship between cancer type and opioid dose. Similarly, the use of adjuvant analgesics and its impact within an inpatient cancer setting is understudied. This study examined the influence of cancer type upon opioid dose, measured by oral morphine equivalent daily dose (oMEDD). The effect of adjuvant analgesics on patient oMEDD was also examined. This retrospective cross-sectional study examined records of 520 patients admitted to Royal Melbourne Hospital or Peter MacCallum Cancer Centre between 2016 and 2018 with advanced cancer. Number and dose of both opioid and adjuvant analgesics were collected along with demographic and cancer data. Comparisons of median oMEDD by cancer type [analysis of variance (ANOVA), non-parametric t-tests] and adjuvant analgesics (Kruskal-Wallis test) were performed. There were no statistically significant differences in oMEDD between the 12 cancer types (P=0.83; n=215). Patients co-prescribed pregabalin (n=102) and paracetamol (n=73) as adjuvant analgesics were on significantly higher daily oMEDD [60 mg (P=0.015), 90 mg (P<0.001), respectively]. Opioid dose did not differ significantly between cancer types. The observed use of adjuvant analgesics coincided with significantly higher oMEDD prescription which may relate to complex pain seen in this cohort of inpatients in a quarternary cancer centre. Future research should focus on pain type and aetiology, and pain scores in different cancer pain syndromes to determine the net effect of opioids and adjuvants in cancer pain prescribing.

SPICE, A Dataset of Drug-like Molecules and Peptides for Training Machine Learning Potentials

Machine learning potentials are an important tool for molecular simulation, but their development is held back by a shortage of high quality datasets to train them on. We describe the SPICE dataset, a new quantum chemistry dataset for training potentials relevant to simulating drug-like small molecules interacting with proteins. It contains over 1.1 million conformations for a diverse set of small molecules, dimers, dipeptides, and solvated amino acids. It includes 15 elements, charged and uncharged molecules, and a wide range of covalent and non-covalent interactions. It provides both forces and energies calculated at the ωB97M-D3(BJ)/def2-TZVPPD level of theory, along with other useful quantities such as multipole moments and bond orders. We train a set of machine learning potentials on it and demonstrate that they can achieve chemical accuracy across a broad region of chemical space. It can serve as a valuable resource for the creation of transferable, ready to use potential functions for use in molecular simulations.

Telehealth: rapid adoption in community palliative care due to COVID-19: patient and professional evaluation

BACKGROUND/OBJECTIVE

The COVID-19 pandemic has brought the use of telehealth to the fore, as many people have been unable to interact directly with healthcare professionals (HCP). For community palliative care (CPC) services, this has meant a sudden change from a predominantly face-to-face model of care to one that incorporates telehealth. Understanding patient and HCP experiences with telehealth and how telehealth compares to 'usual' care will be crucial in planning future CPC services.

METHODOLOGY

All patients of the Barwon Health CPC service between 1 April and 31 May 2020 were invited to complete a questionnaire evaluating their interactions with the palliative care service and specifically their involvement with telehealth consultations. Palliative care HCP who provided clinical services during the same time period were also surveyed.

RESULTS/CONCLUSION

Seventy-four patients (response rate 36%) and 22 HCP returned surveys. Both groups felt comfortable using telehealth, however, also encountered a range of issues when undertaking telehealth consultations. Despite reporting issues, the preference of both groups was for a CPC service model, which combined face-to-face and telehealth consultations. This study is one of the first to directly ask this question and as such provides useful guidance for health services when planning future CPC service models.

Population-based analysis of radiotherapy and chemotherapy treatment in the last month of life within regional Australia

BACKGROUND

Cancer treatment near end of life is not likely to add meaningful benefit and minimising intervention rates has been promoted as an indicator of quality of care. Population-based analysis of treatment allows comparative analysis of treatment rates and provides insight into patterns of care.

AIMS

To report a population-based analysis of both radiotherapy and active systemic therapy (AST) delivery rates along with patterns of treatment within the last 14 and 30 days of life.

METHODS

The Evaluation of Cancer Outcomes Registry records clinical information on all newly diagnosed cancer patients for the Barwon South West Region of Victoria, Australia. Diagnosis details, tumour type and stage as well as core treatment details and date of death were extracted for all patients diagnosed from 2009 to 2015 inclusive.

RESULTS

A total of 12 760 cases cancers were recorded. The median age of all cases was 68.8, and 53% were male. AST was received by 3699 (29%) of patients and radiotherapy by 3811 (30%). Patient deaths within 14 and 30 days of treatment for AST were 4.3 and 8.7%, respectively, and deaths within 14 and 30 days of treatment for radiotherapy 3.8 and 8.0% respectively. Factors associated with death within 30 days of AST and/or radiotherapy were male gender, age greater than 70 years and higher disease stage (all P < 0.01). Treatment rates within 30 days of death were highest for lung cancer (23% of cases) and lowest for breast cancer (2% of cases).

CONCLUSIONS

This population-based analysis of AST and radiotherapy treatment within the last 30 days of life within a region of Australia has shown overall treatment rates below 10%. Treatment rates appear influenced by both patient and tumour characteristics. Future focus on subgroups with high rates of late intervention may help minimise treatment unlikely to add benefit.

Evaluation of a Multidisciplinary Cachexia and Nutrition Support Service- The Patient and Carers Perspective

The Barwon Health Cachexia & Nutrition Support Service (CNSS) is an outpatient service focused on improving clinical outcomes and quality of life for patients with or at high risk of cancer cachexia. Patients see a multidisciplinary team, comprising a palliative medicine physician, physiotherapist, dietitian, and nurse practitioner. This study evaluated the service from patient and carer perspectives. In 2016/17, semistructured interviews were conducted with 12 patients and 9 carers attending the service, focusing on: (1) reflection on experience of the CNSS, and (2) describing how a cachexia-specific service can meet their needs and concerns. Analysis generated 4 superordinate themes: evolving perception of service value, empowerment through person-centered care, communication to patients and carers regarding health/disease information, and the importance of the multidisciplinary team-based approach. Generally, patients and carers reported overall positive experiences with the service, particularly with regard to improved communication and management of the patient. Findings confirmed the patient-centered and individualized approaches were particularly valued. These insights are a critical step in the development of recommendations for future clinical management of cancer cachexia.

Mapping non-malignant respiratory palliative care services in Australia and New Zealand

Objective Despite needs, people with advanced non-malignant respiratory disease are infrequently referred to palliative care services. Integrated models of palliative care and respiratory service delivery have been advocated to address this inequity of access. This study mapped current ambulatory palliative care service provision for patients with advanced non-malignant respiratory disease in Australia and New Zealand. Methods An online survey was distributed to the palliative care physician membership of the Australian and New Zealand Society of Palliative Medicine. Information was sought regarding access to specific breathlessness and integrated respiratory and palliative care services, and their operation. Data were described using descriptive statistics. Results In all, 133 respondents (93 from Australia, 40 from New Zealand; representing 55 Australian and 26 New Zealand discrete sites) with complete data were available for analysis. More than half the respondents reported seeing patients with advanced non-malignant respiratory disease frequently (56/97; 58%), and 18 of 81 services (22%) reported having breathlessness or integrated respiratory and palliative care services caring for this patient group. Such services were mostly staffed by respiratory and palliative care doctors and nurses and based in the clinic environment, with limited support available outside this setting. Of the 63 respondents without existing breathlessness or integrated services, 49 (78%) expressed interest in their establishment, with limited resources cited as the most common barrier. Conclusions There is limited availability of integrated respiratory and palliative care or specialised breathlessness services in Australia and New Zealand despite widespread support by palliative care physicians. This study provides a snapshot to inform strategic service development. What is known about the topic? People with advanced respiratory disease have very significant morbidity with complex needs equivalent to, and in many cases more intense than, people with end-stage lung cancer; they also have significant mortality. Yet, these people frequently do not access palliative care services. The establishment of integrated respiratory and palliative care services has been advocated as an effective means to overcome the barriers to palliative care access. Such services have demonstrated improved patient and family-reported outcomes, as well as service-level improvements. What does this paper add? This paper maps the availability of integrated respiratory palliative care services in Australia and New Zealand. We reveal that although most palliative care physicians report seeing patients with advanced respiratory disease in practice, just one-fifth of services report having an integrated service approach. There was high interest and enthusiasm for such services (78%), but resources limited their establishment. What are the implications for practitioners? Palliative care services recognise the needs of patients with advanced respiratory disease and the benefits of integrated respiratory and palliative care services to address these needs, but scarcity of resources limits the ability to respond accordingly. This study provides a snapshot of current service level to inform strategic development.

Managing Severe Chronic Breathlessness in Chronic Obstructive Pulmonary Disease Is Challenging for General Practitioners

CONTEXT

Patients with advanced chronic obstructive pulmonary disease (COPD) can develop increasing breathlessness, which can persist despite optimal medical management-refractory breathlessness. Management can be challenging for all clinicians and requires a broad approach that includes optimization of disease directed therapies, non-pharmacological strategies to manage breathlessness and for some patients opioids.

OBJECTIVES

To explore the approaches to breathlessness management and palliative care undertaken by Australian General Practitioners (GP) for patients with severe COPD and refractory breathlessness.

METHODS

A case-vignette based survey was conducted with Australian GPs to determine their approaches to breathlessness management and palliative care in COPD.

RESULTS

Of the 137 GPs, 66% recommended commencing an additional medication to manage refractory breathlessness. Thirty-eight GPs (28%) recommended opioids and 26 (19%) recommended guideline discordant treatments. Two-thirds of GPs had concerns regarding the use of opioids in COPD. Half (55%) of GPs were comfortable providing general palliative care to patients with COPD and 62 (45%) had referred patients with COPD to specialist palliative care services. Most respondents wanted further training to manage severe COPD and severe chronic breathlessness.

CONCLUSION

Most GPs recognized and were willing to add specific treatments for severe chronic breathlessness. However, experience prescribing opioids for severe chronic breathlessness was low, with many practitioners holding significant concerns regarding adverse effects. Many GPs are uncomfortable offering a palliative approach to their COPD patients, yet these patients are not routinely referred to specialist palliative care services despite their immense needs. GPs therefore desire education and support to overcome these barriers.

Palliative care for the patient without cancer

BACKGROUND

Palliative care aims to improve quality of life for patients with life-limiting illnesses. It is often linked to the care of people with cancer; however, patients with non-cancer end-stage conditions also have significant needs.

OBJECTIVES

The aims of this paper are to discuss common trajectories of deterioration in non-malignant conditions, consider possible barriers to palliative care referral, review the principles of the palliative care approach and illustrate specific factors relevant for common non-cancer conditions.

DISCUSSION

The symptom burden and care needs for patients with end-stage, nonmalignant illnesses are similar to those of patients with advanced cancer. These patients benefit from a palliative approach, comprising management of the underlying condition and attention to symptoms, psychosocial needs and carer support. Advance care planning provides an opportunity to prepare for future illness episodes, including provision of end-of-life care. General practitioners are well placed to provide palliative care for patients with advanced non-cancer illnesses.

Symptom burden in malignant and non-malignant disease on admission to a palliative care unit

BACKGROUND

There is increasing recognition that patients with non-malignant diseases have comparable physical and psychosocial symptom burden to patients with cancer. There is currently limited data directly comparing symptom burden between these patient groups.

OBJECTIVE

To investigate differences in symptom burden between patients with malignant and non-malignant conditions admitted to a palliative care unit (PCU).

METHOD

A cross-sectional study involving 186 patients admitted to a PCU was undertaken. Patients were dichotomised into malignant or non-malignant disease categories. Symptom burden at admission was assessed using the Symptom Assessment Scale and Palliative Care Problem Severity Score. Group differences in symptoms were analysed using univariate and multivariate approaches.

RESULTS

One hundred patients (53.8%) had cancer, with upper gastrointestinal the most common type (18.0%). Among the 86 patients with non-malignant disease, neurological conditions were most prevalent (40.7%). Patients admitted with non-malignant diseases were older, more functionally impaired and more likely to be deteriorating or terminal. A malignant diagnosis was associated with a higher likelihood of clinician-assessed pain, patient-assessed pain, fatigue, psychological/spiritual symptoms and other symptoms. However, when adjusted for confounders, disease category ceased to be a significant predictor of symptom burden. Younger patients experienced worse pain and patients in terminal phase experienced less symptom burden.

CONCLUSION

Symptom burden was similar between patients with malignant and non-malignant disease after adjustment for confounders. Further research is needed to understand the palliative care needs of patients with non-malignant disease.

Integrated respiratory and palliative care leads to high levels of satisfaction: a survey of patients and carers

BACKGROUND

The Advanced Lung Disease Service is a unique, new model of integrated respiratory and palliative care, which aims to address the unmet needs of patients with advanced, non-malignant, respiratory diseases. This study aimed to explore patients' and carers' experiences of integrated palliative care and identify valued aspects of care.

METHODS

All current patients of the integrated service and their carers were invited to complete a confidential questionnaire by post or with an independent researcher.

RESULTS

Eighty-eight responses were received from 64 (80.0%) eligible patients and from 24 (60%) eligible carers. Most participants (84, 95.5%) believed the integrated service helped them to manage breathlessness and nearly all participants (87, 98.9%) reported increased confidence managing symptoms. One third of patients (34.4%) had received a nurse-led domiciliary visit, with nearly all regarding this as helpful. Most participants believed the integrated respiratory and palliative care team listened to them carefully (87, 98.9%) with opportunities to express their views (88, 100%). Highly valued aspects of the service were continuity of care (82, 93.2%) and long-term care (77, 87.5%). Three quarters of participants (66, 75.0%) rated their care as excellent, with 20.5% rating it as very good. Nearly all (87, 98.9%) participants reported that they would recommend the service to others.

CONCLUSIONS

Patients and carers expressed high levels of satisfaction with this model of integrated respiratory and palliative care. Continuity of care, high quality communication and feeling cared for were greatly valued and highlight simple but important aspects of care for all patients.

Medication management for community palliative care patients and the role of a specialist palliative care pharmacist: A qualitative exploration of consumer and health care professional perspectives

BACKGROUND

Pharmacists have a key role to play in optimisation of medication regimens and promotion of medication safety. The role of specialist pharmacists as part of the multidisciplinary palliative care team, especially in the primary care setting, is not widely recognised.

AIM

To explore the perspectives of stakeholders about the gaps in the current model of community palliative care services in relation to medication management and to assess their opinions pertaining to the role of a specialist palliative care pharmacist in addressing some of those gaps.

DESIGN

Qualitative study utilising three focus groups involving 20 stakeholders. Thematic analysis was carried out using a framework approach and interpreted in the context of the Chronic Care Model for improving primary care for patients with chronic illness.

SETTING/PARTICIPANTS

Setting was a large regional Australian palliative care service. Participants included palliative care consumers and clinicians specifically patients, caregivers, physicians, nurses and pharmacists.

RESULTS

Five major themes emerged from the focus groups: access to resources, medicines and information; shared care; challenges of polypharmacy; informal caregiver needs and potential roles of a palliative care pharmacist. Gaps in access to medicines/resources, training for generalist practitioners, communication between treating teams and lack of support for patients and carers were cited as factors adversely impacting medication management in community-based palliative care.

CONCLUSION

While community-based palliative care is an essential aspect of meeting the health care demands of an ageing society, the current model has several gaps and limitations. An appropriately qualified and skilled pharmacist within the palliative care team may help to address some of the gaps in relation to medication access and appropriateness.

Solving the RNA design problem with reinforcement learning

We use reinforcement learning to train an agent for computational RNA design: given a target secondary structure, design a sequence that folds to that structure in silico. Our agent uses a novel graph convolutional architecture allowing a single model to be applied to arbitrary target structures of any length. After training it on randomly generated targets, we test it on the Eterna100 benchmark and find it outperforms all previous algorithms. Analysis of its solutions shows it has successfully learned some advanced strategies identified by players of the game Eterna, allowing it to solve some very difficult structures. On the other hand, it has failed to learn other strategies, possibly because they were not required for the targets in the training set. This suggests the possibility that future improvements to the training protocol may yield further gains in performance.

Designing RNA sequences that fold to desired structures is an important problem in bioengineering. We have applied recent advances in machine learning to address this problem. The computer learns without any human input, using only trial and error to figure out how to design RNA. It quickly discovers powerful strategies that let it solve many difficult design problems. When tested on a challenging benchmark, it outperforms all previous algorithms. We analyze its solutions and identify some of the strategies it has learned, as well as other important strategies it has failed to learn. This suggests possible approaches to further improving its performance. This work reflects a paradigm shift taking place in computer science, which has the potential to transform computational biology. Instead of relying on experts to design algorithms by hand, computers can use artificial intelligence to learn their own algorithms directly. The resulting methods often work better than the ones designed by humans.

Advanced Potential Energy Surfaces for Molecular Simulation

Advanced potential energy surfaces are defined as theoretical models that explicitly include many-body effects that transcend the standard fixed-charge, pairwise-additive paradigm typically used in molecular simulation. However, several factors relating to their software implementation have precluded their widespread use in condensed-phase simulations: the computational cost of the theoretical models, a paucity of approximate models and algorithmic improvements that can ameliorate their cost, underdeveloped interfaces and limited dissemination in computational code bases that are widely used in the computational chemistry community, and software implementations that have not kept pace with modern high-performance computing (HPC) architectures, such as multicore CPUs and modern graphics processing units (GPUs). In this Feature Article we review recent progress made in these areas, including well-defined polarization approximations and new multipole electrostatic formulations, novel methods for solving the mutual polarization equations and increasing the MD time step, combining linear-scaling electronic structure methods with new QM/MM methods that account for mutual polarization between the two regions, and the greatly improved software deployment of these models and methods onto GPU and CPU hardware platforms. We have now approached an era where multipole-based polarizable force fields can be routinely used to obtain computational results comparable to state-of-the-art density functional theory while reaching sampling statistics that are acceptable when compared to that obtained from simpler fixed partial charge force fields.

Integrated respiratory and palliative care may improve outcomes in advanced lung disease

The unaddressed palliative care needs of patients with advanced, nonmalignant, lung disease highlight the urgent requirement for new models of care. This study describes a new integrated respiratory and palliative care service and examines outcomes from this service. The Advanced Lung Disease Service (ALDS) is a long-term, multidisciplinary, integrated service. In this single-group cohort study, demographic and prospective outcome data were collected over 4 years, with retrospective evaluation of unscheduled healthcare usage. Of 171 patients included, 97 (56.7%) were male with mean age 75.9 years and 142 (83.0%) had chronic obstructive pulmonary disease. ALDS patients had severely reduced pulmonary function (median (interquartile range (IQR)) forced expiratory volume in 1 s 0.8 (0.6-1.1) L and diffusing capacity of the lung for carbon monoxide 37.5 (29.0-48.0) % pred) and severe breathlessness. All patients received nonpharmacological breathlessness management education and 74 (43.3%) were prescribed morphine for breathlessness (median dose 9 mg·day-1). There was a 52.4% reduction in the mean number of emergency department respiratory presentations in the year after ALDS care commenced (p=0.007). 145 patients (84.8%) discussed and/or completed an advance care plan. 61 patients died, of whom only 15 (24.6%) died in an acute hospital bed. While this was a single-group cohort study, integrated respiratory and palliative care was associated with improved end-of-life care and reduced unscheduled healthcare usage.

OpenMM 7: Rapid development of high performance algorithms for molecular dynamics

OpenMM is a molecular dynamics simulation toolkit with a unique focus on extensibility. It allows users to easily add new features, including forces with novel functional forms, new integration algorithms, and new simulation protocols. Those features automatically work on all supported hardware types (including both CPUs and GPUs) and perform well on all of them. In many cases they require minimal coding, just a mathematical description of the desired function. They also require no modification to OpenMM itself and can be distributed independently of OpenMM. This makes it an ideal tool for researchers developing new simulation methods, and also allows those new methods to be immediately available to the larger community.

MSMBuilder: Statistical Models for Biomolecular Dynamics

MSMBuilder is a software package for building statistical models of high-dimensional time-series data. It is designed with a particular focus on the analysis of atomistic simulations of biomolecular dynamics such as protein folding and conformational change. MSMBuilder is named for its ability to construct Markov state models (MSMs), a class of models that has gained favor among computational biophysicists. In addition to both well-established and newer MSM methods, the package includes complementary algorithms for understanding time-series data such as hidden Markov models and time-structure based independent component analysis. MSMBuilder boasts an easy to use command-line interface, as well as clear and consistent abstractions through its Python application programming interface. MSMBuilder was developed with careful consideration for compatibility with the broader machine learning community by following the design of scikit-learn. The package is used primarily by practitioners of molecular dynamics, but is just as applicable to other computational or experimental time-series measurements.

Efficient gaussian density formulation of volume and surface areas of macromolecules on graphical processing units

We present an algorithm to efficiently compute accurate volumes and surface areas of macromolecules on graphical processing unit (GPU) devices using an analytic model which represents atomic volumes by continuous Gaussian densities. The volume of the molecule is expressed by means of the inclusion-exclusion formula, which is based on the summation of overlap integrals among multiple atomic densities. The surface area of the molecule is obtained by differentiation of the molecular volume with respect to atomic radii. The many-body nature of the model makes a port to GPU devices challenging. To our knowledge, this is the first reported full implementation of this model on GPU hardware. To accomplish this, we have used recursive strategies to construct the tree of overlaps and to accumulate volumes and their gradients on the tree data structures so as to minimize memory contention. The algorithm is used in the formulation of a surface area-based non-polar implicit solvent model implemented as an open source plug-in (named GaussVol) for the popular OpenMM library for molecular mechanics modeling. GaussVol is 50 to 100 times faster than our best optimized implementation for the CPUs, achieving speeds in excess of 100 ns/day with 1 fs time-step for protein-sized systems on commodity GPUs. © 2017 Wiley Periodicals, Inc.

Palliative care in general practice: GP integration in caring for patients with advanced cancer

BACKGROUND

Patients with advanced cancer often desire home-based care, placing general practitioners (GPs) at the centre of complex clinical situations. The objective of this article was to determine GPs' needs when providing home-based palliative care in collaboration with existing palliative care services.

METHODS

A survey of GPs was conducted to determine knowledge, skills and confidence in providing community-based palliative care.

RESULTS

Of the 56 respondents, 82% reported that they were involved in palliative management of at least one cancer patient in the previous year. A significant number of GPs (31%) lacked confidence in providing this care because of patient complexity, inadequate training and insufficient resources. Other barriers included poor communication from specialists and treating teams. Factors facilitating provision of home-based palliative care were community palliative care services and links to hospital-based palliative care teams.

DISCUSSION

This survey highlights the importance of support and resources to empower GPs to confidently provide home-based palliative care for patients with advanced cancer.

Examining Clinical Utility of Imaging for Inpatient Palliative Care

BACKGROUND

Medicine in the final months of life is increasingly interventional, both in the manner by which life may be prolonged and symptoms may be reduced. Radiology is frequently utilized to provide diagnostic clarity and improve symptom control. As with any intervention, examining the benefit and potential harms of a procedure is required to establish its role in ongoing clinical care.

METHODS

This retrospective cohort study involved patients admitted to an inpatient palliative care unit between October 2013 and September 2014. Data were collected using clinical databases manually searched by the researchers.

RESULTS

Of 388 admissions, there were a total of 154 imaging events completed in 85 patients. Patients who had imaging performed had longer mean length of stays, more likely to be discharged home, and male. Very few imaging events (4%) occurred in the 3 days prior to death and none on the day of death. In total, 43% of imaging confirmed the clinical suspicion and management changed 42% of times. Limbs X-rays and computed tomography brain had low rates of confirming clinical suspicion (21% and 17%) and changing management (21% and 33%). There were a total of 7 complications resulting from imaging, the majority due to interventional procedures.

CONCLUSION

The use of imaging in inpatient palliative care seems to be of substantive utility, prompting alterations in management in >40% of instances. The majority of imaging occurred prior to the terminal phase of the disease and with few complications.

Corticosteroids as co-analgesics with opioids for cancer pain: a survey of Australian and New Zealand palliative care clinicians

Corticosteroids are commonly used as co-analgesics with opioids for cancer pain; however limited quality data exist supporting their efficacy for this purpose. Further, little is known about individual prescribing practices. The current study surveyed members of the Australian New Zealand Society of Palliative Medicine about their use of corticosteroids as adjuvant analgesics in cancer pain. It confirmed high rates of utilisation and found variability in starting doses and associated decision-making. Further research is required to determine the efficacy and safety of corticosteroids as co-analgesics in cancer pain management.

Uptake of clinical trials in a palliative care setting: a retrospective cohort study

AIM

There has been growth in the number of clinical trials conducted in the palliative care setting. However, issues exist regarding patient acceptance and vulnerability as well as the appropriateness of conducting trials in the dying patient. This study aimed to investigate the uptake of palliative care clinical trials at the Royal Melbourne Hospital, evaluate patient demographics for those enrolled onto study and assess the proportion of patients who died within 28 days of enrolling on a palliative care clinical trial.

METHOD

A retrospective cohort study of all patients prescreened and enrolled onto palliative care clinical trials by the Palliative Care Clinical Trials Team (PCCTT) at the Royal Melbourne Hospital over a 27-month period was undertaken.

RESULTS

Of 515 patients referred to the PCCTT for consideration of trial enrollment, 64 (12.4%) were subsequently enrolled onto one of six clinical trials open during the study period. About 62.5% were non-cancer patients; 81.3% of all patients completed the trial intervention and 65.6% completed trial follow-up; 28.1% of patients enrolled died within 28 days of trial commencement.

CONCLUSION

More than 500 patients were referred for assessment of clinical trial participation perhaps reflecting clinician acceptance of palliative care clinical trials. A number of enrolled patients were involved in trials during their terminal phase, indicating a willingness of participants to be involved, despite poor prognosis.

Is opioid-induced hyperalgesia a genuine issue for palliative care patients and clinicans?

197

Background: Opioid-Induced Hyperalgesia (OIH) has been described as a paradoxical response whereby opioid administration induces an increase in pain sensitivity rather than an analgesic effect. It is proposed this results from increased pro-nociceptive sensitivity following changes in central and peripheral neural pathways. While there is basic science and pre-clinical evidence supporting OIH, debate remains about its clinical relevance or even existence. The existence or otherwise of OIH has relevance for palliative care as many patients are prescribed opioids and the standard management of unstable pain in palliative care may worsen symptoms in OIH. Therefore recognition of the concept would seem important for palliative care clinicians. Methods: An electronic survey of Australian and New Zealand palliative care clinicians was undertaken addressing awareness of OIH as well as approaches to recognising and managing it. The survey which contained single response, multiple-choice and open-ended questions was distributed through the Australian New Zealand Society of Palliative Medicine. Mixed-methods analysis was performed. Results: One hundred and twenty-three surveys were returned (response rate = 31%). The majority of respondents identified as palliative care specialists. More than 75% of respondents reported observing OIH in their clinical practice, often with malignant disease and with morphine, oxycodone and fentanyl identified as the commonest causal agents. The three features felt to be most suggestive of OIH were; escalating pain despite increasing opioids, demonstrable hyperalgesia or allodynia and a more diffuse pain distribution away from pre-existing pain sites. Most clinicians utilized more than one approach when OIH was encountered. The commonest of these were opioid reduction, opioid rotation and optimization of adjuvant analgesia. Conclusions: Our survey found a higher rate of reported observation of OIH amongst clinicians than might have been anticipated given debate about the existence of OIH in humans outside of a research environment. These results suggest that many palliative care clinicians perceive OIH to be a genuine issue for their patients.

Inpatient palliative care consultation for patients with glioblastoma in a tertiary hospital

Glioblastoma (GBM) is an uncommon disease with significant mortality and morbidity, but there is a lack of published evidence on palliative care involvement with this population. This audit highlights the heavy symptom burden, extensive allied health involvement and discharge outcomes of GBM inpatients referred to the palliative care service at The Royal Melbourne Hospital. This information can provide an important framework for further research and also supports the role of multidisciplinary palliative care in the care of patients with GBM.

What does state-level inpatient palliative care data tell us about service provision?

BACKGROUND

Palliative care is increasingly seen as an integral component of care for patients with advanced malignant and nonmalignant illness. Clinical audit data can provide important insights into patient care, but limited published data are available investigating statewide palliative care provision issues.

OBJECTIVES

Our aim was to provide a comprehensive perspective on inpatient palliative care within a populous Australian state, and highlight potential gaps in service provision.

METHODS

Descriptive analysis was conducted of the Victorian Admitted Episodes Dataset (VAED, a comprehensive database of inpatient activity from all hospitals in Victoria). Variables analyzed included overall number of separations, average length of stay, referral source, age profile, and indigenous status.

RESULTS

The mean length of stay for patients in Victorian inpatient palliative care settings was 12.8 days, and there were 6004 separations reported over an 11 month period from approximately 264 designated palliative care beds in the state. The mode of separation for the majority of admissions to inpatient palliative care was death (65%). Few patients resided outside metropolitan regions, and no patients admitted identified as Aboriginal and/or Torres Strait Islander (the indigenous communities of Australia).

CONCLUSION

The pooled epidemiological data reviewed identify a number of areas of interest including the lack of Aboriginal Australians identified and accessing inpatient palliative care, and variations in inpatient care across geographical areas. This highlights issues of access and equity of access to inpatient palliative care.

Accelerated Molecular Dynamics Simulations with the AMOEBA Polarizable Force Field on Graphics Processing Units

The accelerated molecular dynamics (aMD) method has recently been shown to enhance the sampling of biomolecules in molecular dynamics (MD) simulations, often by several orders of magnitude. Here, we describe an implementation of the aMD method for the OpenMM application layer that takes full advantage of graphics processing units (GPUs) computing. The aMD method is shown to work in combination with the AMOEBA polarizable force field (AMOEBA-aMD), allowing the simulation of long time-scale events with a polarizable force field. Benchmarks are provided to show that the AMOEBA-aMD method is efficiently implemented and produces accurate results in its standard parametrization. For the BPTI protein, we demonstrate that the protein structure described with AMOEBA remains stable even on the extended time scales accessed at high levels of accelerations. For the DNA repair metalloenzyme endonuclease IV, we show that the use of the AMOEBA force field is a significant improvement over fixed charged models for describing the enzyme active-site. The new AMOEBA-aMD method is publicly available (http://wiki.simtk.org/openmm/VirtualRepository) and promises to be interesting for studying complex systems that can benefit from both the use of a polarizable force field and enhanced sampling.

Palliative care after attempted suicide in the absence of premorbid terminal disease: a case series and review of the literature

Palliative care involvement in the management of incomplete suicide in patients without terminal illness is rare. This paper documents two such cases and explores some of the clinical and ethical issues raised.

OpenMM 4: A Reusable, Extensible, Hardware Independent Library for High Performance Molecular Simulation

OpenMM is a software toolkit for performing molecular simulations on a range of high performance computing architectures. It is based on a layered architecture: the lower layers function as a reusable library that can be invoked by any application, while the upper layers form a complete environment for running molecular simulations. The library API hides all hardware-specific dependencies and optimizations from the users and developers of simulation programs: they can be run without modification on any hardware on which the API has been implemented. The current implementations of OpenMM include support for graphics processing units using the OpenCL and CUDA frameworks. In addition, OpenMM was designed to be extensible, so new hardware architectures can be accommodated and new functionality (e.g., energy terms and integrators) can be easily added.

Who, why and when: stroke care unit patients seen by a palliative care service within a large metropolitan teaching hospital

OBJECTIVES

To investigate factors associated with referral of patients from an Australian stroke care unit (SCU) to an inpatient palliative care service (PCS).

METHODS

This retrospective observational cohort study included patients who were referred to the PCS after SCU admission between 1 January and 31 December 2008. Variables measured included patient demographics, premorbid functional status, premorbid living situation, stroke type, history of previous stroke and discharge outcomes. Group differences between all SCU patients seen and not seen by the PCS were compared using univariate analyses. Multivariate logistic regression analysis was undertaken to identify factors associated with PCS involvement. Group differences were also compared between deceased stroke patients seen and not seen by the PCS.

RESULTS

544 patients were admitted to the SCU during the study period with 62 (11.4%) referred to the PCS. Assistance with end-of-life care was the commonest reason for referral. From univariate analyses, factors significantly associated with PCS involvement included age, gender, premorbid modified Rankin score, living situation prior to stroke and stroke type. Factors predicting PCS involvement for SCU patients from logistic regression were: increasing age, higher premorbid modified Rankin score and haemorrhagic stroke. 87 (16.0%) SCU patients died during their admission, with 49 (56.3%) seen by PCS. Deceased patients seen were significantly older, more disabled premorbidly and lived significantly longer.

CONCLUSIONS

This study indicates there are patient and condition-level factors associated with referral of stroke patients to PCS. It highlights factors that might better stratify hospitalised stroke patients to timely palliative care involvement, and adds an Australian perspective to limited data addressing this patient population.

Factors influencing survival after discharge from an Australian palliative care unit to residential aged care facilities: a retrospective audit

BACKGROUND

Increasing demand for palliative care unit (PCU) beds has led to shorter inpatient stays and a requirement to transfer some patients from a PCU to a residential aged care facility (RACF). Concerns have been raised regarding this move with suggestion that patients often die shortly after transfer. Published data investigating this patient group are limited. The aim of the current study was to audit discharges from a PCU to RACFs specifically looking at predictive factors for survival following discharge.

METHODS

A retrospective audit was undertaken of all discharges from the Barwon Health PCU to RACFs between July 2007 and July 2010. Data on patient demographics, clinical and functional status, admission and discharge details, and survival times were examined. Factors influencing survival were evaluated by Cox proportional-hazards regression analysis.

RESULTS

Sixty-two discharges from a PCU to an RACF were included in the analysis. The mean age at discharge was 76 and the majority of patients had malignant disease. Mean and median survival times post-transfer were 106 and 42.5 days, respectively, and 16% of subjects survived more than 100 days. From univariate analyses age, PCU length of stay, admission Resource Utilization Groups-Activities of Daily Living (RUG-ADL) score, dependent mobility, having lung cancer or cancer of unknown primary, and living alone or in an RACF pre PCU admission affected survival. Multivariate analyses showed age, PCU length of stay, RUG-ADL score, and living situation prior to PCU admission together were associated with postdischarge survival times.

CONCLUSIONS

This study is one of the largest investigating this cohort and suggests a number of factors that may predict survival for patients after discharge from a PCU to an RACF.