Mora: abundance aware metagenomic read re-assignment for disentangling similar strains

BACKGROUND

Taxonomic classification of reads obtained by metagenomic sequencing is often a first step for understanding a microbial community, but correctly assigning sequencing reads to the strain or sub-species level has remained a challenging computational problem.

RESULTS

We introduce Mora, a MetagenOmic read Re-Assignment algorithm capable of assigning short and long metagenomic reads with high precision, even at the strain level. Mora is able to accurately re-assign reads by first estimating abundances through an expectation-maximization algorithm and then utilizing abundance information to re-assign query reads. The key idea behind Mora is to maximize read re-assignment qualities while simultaneously minimizing the difference from estimated abundance levels, allowing Mora to avoid over assigning reads to the same genomes. On simulated diverse reads, this allows Mora to achieve F1 scores comparable to other algorithms while having less runtime. However, Mora significantly outshines other algorithms on very similar reads. We show that the high penalty of over assigning reads to a common reference genome allows Mora to accurately infer correct strains for real data in the form of E. coli reads.

CONCLUSIONS

Mora is a fast and accurate read re-assignment algorithm that is modularized, allowing it to be incorporated into general metagenomics and genomics workflows. It is freely available at https://github.com/AfZheng126/MORA .

Role of β3 subunit of the GABA type A receptor in triple negative breast cancer proliferation, migration, and cell cycle progression

Triple negative breast cancer (TNBC) is known for its heterogeneous nature and aggressive onset. The unresponsiveness to hormone therapies and immunotherapy and the toxicity of chemotherapeutics account for the limited treatment options for TNBC. Ion channels have emerged as possible therapeutic candidates for cancer therapy, but little is known about how ligand gated ion channels, specifically, GABA type A ligand-gated ion channel receptors (GABAAR), affect cancer pathogenesis. Our results show that the GABAA β3 subunit is expressed at higher levels in TNBC cell lines than non-tumorigenic cells, therefore contributing to the idea that limiting the GABAAR via knockdown of the GABAA β3 subunit is a potential strategy for decreasing the proliferation and migration of TNBC cells. We employed pharmacological and genetic approaches to investigate the role of the GABAA β3 subunit in TNBC proliferation, migration, and cell cycle progression. The results suggest that pharmacological antagonism or genetic knockdown of GABAA β3 subunit decreases TNBC proliferation and migration. In addition, GABAA β3 subunit knockdown causes cell cycle arrest in TNBC cell lines via decreased cyclin D1 and increased p21 expression. Our findings suggest that membrane bound GABAA receptors containing the β3 subunit can be further developed as a potential novel target for the treatment of TNBC.

Measuring quality of care in autologous breast reconstruction: a Delphi consensus

Measuring and benchmarking quality of care in surgical oncology has been gaining popularity. In autologous breast reconstruction (ABR), a standardized set of indicators to assess quality of care is lacking. In this study, we defined a set of evidence-based quality indicators for autologous breast reconstruction. First, we performed a systematic review to identify factors related to quality of care in ABR. Variables were categorized depending on their function: indicators related to outcome, indicators related to process and case-mix variables. The review was followed by a 3-round Delphi Consensus to determine which indicators and case-mix-variables were considered relevant and feasible for inclusion in an ABR standard set of indicators. 932 unique articles were identified, of which 110 papers were included in the study. Indicators were categorized by function: outcome, process and case-mix variables. In total, 8 process indicators and 41 outcome indicators were extracted. 30 case-mix-variables were included. Following 3 rounds of questioning in the Delphi Consensus, all respondents agreed on type of ABR, oncological outcomes and patient satisfaction for the standard set. Indicators related to complications were consistently ranked highly. Most process indicators were not chosen after 3 rounds of questioning. 11 case-mix-variables were included in the final set. Following the Delphi Consensus, it was possible to identify 33 process and outcome indicators and 11 case-mix-variables for inclusion for a standard set of quality indicators. With the inclusion of both objective and patient-reported outcome measures, this set of indicators provides a multidimensional measurement tool for quality assessment for ABR.

Fast and robust metagenomic sequence comparison through sparse chaining with skani

Sequence comparison tools for metagenome-assembled genomes (MAGs) struggle with high-volume or low-quality data. We present skani ( https://github.com/bluenote-1577/skani ), a method for determining average nucleotide identity (ANI) via sparse approximate alignments. skani outperforms FastANI in accuracy and speed (>20× faster) for fragmented, incomplete MAGs. skani can query genomes against >65,000 prokaryotic genomes in seconds and 6 GB memory. skani unlocks higher-resolution insights for extensive, noisy metagenomic datasets.

Perspectives on Patient-Reported Outcome Data After Treatment Discontinuation in Cancer Clinical Trials

OBJECTIVES

Patient-reported outcome (PRO) data are critical in understanding treatments from the patient perspective in cancer clinical trials. The potential benefits and methodological approaches to the collection of PRO data after treatment discontinuation (eg, because of progressive disease or unacceptable drug toxicity) are less clear. The purpose of this article is to describe the Food and Drug Administration's Oncology Center of Excellence and the Critical Path Institute cosponsored 2-hour virtual roundtable, held in 2020, to discuss this specific issue.

METHODS

We summarize key points from this discussion with 16 stakeholders representing academia, clinical practice, patients, international regulatory agencies, health technology assessment bodies/payers, industry, and PRO instrument development.

RESULTS

Stakeholders recognized that any PRO data collection after treatment discontinuation should have clearly defined objectives to ensure that data can be analyzed and reported.

CONCLUSIONS

Data collection after discontinuation without a justification for its use wastes patients' time and effort and is unethical.

Silos and rigid processes: Barriers to the successful implementation of the Older prisoner Health and Social Care Assessment and Plan

Older adults are the fastest growing sub-group in prisons. They have complex health, social care and custodial needs and often the support they receive is sub-optimal. The Older prisoner Health and Social Care Assessment and Plan (OHSCAP) aimed to better meet these inter-related needs. As part of a wider study, a randomised controlled trial was conducted to evaluate the OHSCAPs effectiveness in meeting older prisoners' health, social care and custodial needs in comparison to treatment as usual. This article describes the nested qualitative study which aimed to explore the barriers and facilitators to the effective implementation of the OHSCAP. Semi-structured interviews were conducted with older adults (n = 14) and staff members t (n = 12). Data was analysed using the framework method. Three overarching key themes were identified. These were: (1) balancing care and custodial requirements; (2) prison, health and social care silos; and (3) rigid prison processes. Prison is an important opportunity to engage residents and improve public health. Cultural and strategic change is required for health, social care and custodial interventions, such as the OHSCAP, to be successfully implemented into prison settings.

Proving sequence aligners can guarantee accuracy in almost O(m log n) time through an average-case analysis of the seed-chain-extend heuristic

Seed-chain-extend with k-mer seeds is a powerful heuristic technique for sequence alignment used by modern sequence aligners. Although effective in practice for both runtime and accuracy, theoretical guarantees on the resulting alignment do not exist for seed-chain-extend. In this work, we give the first rigorous bounds for the efficacy of seed-chain-extend with k-mers in expectation Assume we are given a random nucleotide sequence of length ∼n that is indexed (or seeded) and a mutated substring of length ∼m ≤ n with mutation rate θ < 0.206. We prove that we can find a k = Θ(log n) for the k-mer size such that the expected runtime of seed-chain-extend under optimal linear-gap cost chaining and quadratic time gap extension is O(mn f (θ) log n), where f(θ) < 2.43 · θ holds as a loose bound. The alignment also turns out to be good; we prove that more than [Formula: see text] fraction of the homologous bases is recoverable under an optimal chain. We also show that our bounds work when k-mers are sketched, that is, only a subset of all k-mers is selected, and that sketching reduces chaining time without increasing alignment time or decreasing accuracy too much, justifying the effectiveness of sketching as a practical speedup in sequence alignment. We verify our results in simulation and on real noisy long-read data and show that our theoretical runtimes can predict real runtimes accurately. We conjecture that our bounds can be improved further, and in particular, f(θ) can be further reduced.

Vaccine hesitancy in cancer patients: A rapid review

INTRODUCTION

Vaccination is a key strategy to limit the impact of the COVID-19 pandemic, among vulnerable groups such as cancer patients. However, COVID-19 vaccine hesitancy is limiting vaccination uptake in this population as in others. This study aimed to synthesise the emerging literature on vaccine hesitancy in this population and in Oncology health professionals, reasons for and factors associated with hesitancy, and interventions that address hesitancy.

METHODS

A rapid review was undertaken PubMed, Ovid and Google across all years up to October 2021 for articles in English, from any country or region, addressing the above issues. Individual case studies, opinion pieces, commentary articles and conference abstracts were excluded. Article screening, data extraction and bias assessment were conducted by two authors. A narrative synthesis of the data was undertaken.

RESULTS

Eighteen eligible articles were identified. Reported COVID-19 vaccine hesitancy rates varied from 76.7 % to 3.9 %, with a mean of 38.4 %. A large international study (n > 20,000) reported a more conservative hesitancy rate of 19 %. Six broad, common reasons for hesitancy were identified. Oncologist advice was valued by patients.

DISCUSSION

Vaccine hesitancy remains a significant concern in the oncology context. Oncologists are key to addressing hesitancy and providing tailored advice to cancer patients.

PRACTICE IMPLICATIONS

Where possible, patients appreciate personalised, tailored information about vaccination which addresses its interaction with cancer and its treatment. Education programmes for oncologists to support effective communication in this context are needed. Webinars and peer-to-peer counselling may be useful but remain to be proven.

A balancing act: sex selection after pre-implantation genetic testing for aneuploidy for first versus second baby

STUDY QUESTION

How often do patients undergoing frozen embryo transfer (FET) after preimplantation genetic testing for aneuploidy (PGT-A) choose to select for sex and do sex selection rates differ before and after successful delivery of a first baby?

SUMMARY ANSWER

When a choice was available between male and female embryos, patients selected the sex more frequently when trying to conceive the second child (62%) as compared to the first child (32.4%) and most commonly selected for the opposite sex of the first child.

WHAT IS KNOWN ALREADY

Sex selection is widely available in US fertility clinics. However, the rate of sex selection for patients undergoing FET after PGT-A is unknown.

STUDY DESIGN, SIZE, DURATION

This is a retrospective cohort study of 585 patients that took place between January 2013 and February 2021.

PARTICIPANTS/MATERIALS, SETTING, METHODS

The study took place at a single, urban academic fertility center in the USA. Patients were included if they had a live birth after single euploid FET and returned for at least one subsequent euploid FET. The primary outcomes were the rates of sex selection for first versus second baby. Secondary outcomes were rate of selection for same versus opposite sex as first live birth and overall rate of selection for males versus females.

MAIN RESULTS AND THE ROLE OF CHANCE

Five hundred and eighty-five patients underwent a total of 1560 single euploid FETs resulting in either one or two live births. A choice between male and female euploid embryos was available for 919 FETs (first child: 67.5% (519/769) versus second child: 50.6% (400/791), P < 0.01). When a choice was available, patients selected the sex more frequently when trying to conceive the second child (first child: 32.4% (168/519) versus second child: 62.0% (248/400), P < 0.01). When sex was selected after first live birth, the opposite sex of the first child was selected 81.8% (203/248 FETs) of the time. Of transfers that involved sex selection, rates of male and female selection were similar for the first child, but selection for females was greater for the second child (first child: 51.2% (86/168) male versus 48.9% (82/168) female, second child: 41.1% (102/248) male versus 58.9% (146/248) female, P < 0.04).

LIMITATIONS, REASONS FOR CAUTION

The study was performed at one urban academic medical center in the Northeastern US, which may limit generalizability to other settings where PGT-A may be performed less frequently, or sex selection may be limited or not permitted. In addition, we could not reliably account for whether patients or their partners had prior children and if so, of what sex.

WIDER IMPLICATIONS OF THE FINDINGS

Patients undergoing PGT-A with both male and female euploid embryos were more likely to select for sex when attempting a second child and usually selected for the opposite sex of their first child. These findings highlight the potential for family balancing for patients who undergo PGT-A in settings where sex selection is permitted.

STUDY FUNDING/COMPETING INTEREST(S)

This study received no funding. The authors have no conflicts of interest to declare.

TRIAL REGISTRATION NUMBER

N/A.

Extended pilot test of a cross-injection in situ denitrification system for pre-emptive treatment of municipal well water

Elevated groundwater nitrate concentrations have been linked to deleterious health and environmental effects. A significant source of the nitrate is nitrogen fertilizers applied to agricultural landscapes. Beneficial Management Practices (BMPs), including the optimization of fertilizer use and selective crop rotations, have proven to be effective in some cases. The city of Woodstock in southern Ontario relies on public wells for all of its municipal supply. Several of the wells have experienced chronic increases in nitrate concentrations exceeding the maximum allowable limit of 10 mg/L N-NO₃^-. While BMPs are established, an interim reduction plan based on enhanced in situ denitrification (Cross Injection System, CIS) in a 15 m thick zone of high nitrate mass flux within the aquifer zone was evaluated. Based in the results of preliminary acetate injection experiments, a C:N ratio of 2.35, (approximately 260 mg acetate/L), was selected to optimize the denitrification reaction. Injections were performed for six hours a day every day for a period of approximately two months. Dissolved oxygen (DO) and nitrate concentrations recorded over time indicated that reduction of both commenced within a few days of the beginning of the acetate injections and reduced levels were maintained for the remainder of the two-month injection period. Denitrification occurred throughout the profile although nitrate reduction was the highest in the lower groundwater velocity zones. An overall reduction of nitrate of 50% was achieved through the treated section of the aquifer. It is estimated that an upscaled treatment system utilizing a treatment width of only 70 m would be sufficient to reduce the nitrate concentrations to below the drinking water limit demonstrating the potential for the CIS method to functions as an interim groundwater nitrate reduction strategy.

How to optimally sample a sequence for rapid analysis

MOTIVATION

We face an increasing flood of genetic sequence data, from diverse sources, requiring rapid computational analysis. Rapid analysis can be achieved by sampling a subset of positions in each sequence. Previous sequence-sampling methods, such as minimizers, syncmers and minimally overlapping words, were developed by heuristic intuition, and are not optimal.

RESULTS

We present a sequence-sampling approach that provably optimizes sensitivity for a whole class of sequence comparison methods, for randomly evolving sequences. It is likely near-optimal for a wide range of alignment-based and alignment-free analyses. For real biological DNA, it increases specificity by avoiding simple repeats. Our approach generalizes universal hitting sets (which guarantee to sample a sequence at least once) and polar sets (which guarantee to sample a sequence at most once). This helps us understand how to do rapid sequence analysis as accurately as possible.

AVAILABILITY AND IMPLEMENTATION

Source code is freely available at https://gitlab.com/mcfrith/noverlap.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Absolute risks of self-harm and interpersonal violence by diagnostic category following first discharge from inpatient psychiatric care

BACKGROUND

Persons discharged from inpatient psychiatric services are at greatly elevated risk of harming themselves or inflicting violence on others, but no studies have reported gender-specific absolute risks for these two outcomes across the spectrum of psychiatric diagnoses. We aimed to estimate absolute risks for self-harm and interpersonal violence post-discharge according to gender and diagnostic category.

METHODS

Danish national registry data were utilized to investigate 62,922 discharged inpatients, born 1967-2000. An age and gender matched cohort study was conducted to examine risks for self-harm and interpersonal violence at 1 year and at 10 years post-discharge. Absolute risks were estimated as cumulative incidence percentage values.

RESULTS

Patients diagnosed with substance misuse disorders were at especially elevated risk, with the absolute risks for either self-harm or interpersonal violence being 15.6% (95% CI 14.9, 16.3%) of males and 16.8% (15.6, 18.1%) of females at 1 year post-discharge, rising to 45.7% (44.5, 46.8%) and 39.0% (37.1, 40.8%), respectively, within 10 years. Diagnoses of personality disorders and early onset behavioral and emotional disorders were also associated with particularly high absolute risks, whilst risks linked with schizophrenia and related disorders, mood disorders, and anxiety/somatoform disorders, were considerably lower.

CONCLUSIONS

Patients diagnosed with substance misuse disorders, personality disorders and early onset behavioral and emotional disorders are at especially high risk for internally and externally directed violence. It is crucial, however, that these already marginalized individuals are not further stigmatized. Enhanced care at discharge and during the challenging transition back to life in the community is needed.

O007 Pancreas and islet transplantation in the United Kingdom during the COVID-19 era

Introduction

Methods

Results

Conclusion

Take-home message

The impact of COVID-19 on cancer patients, their carers and oncology health professionals: A qualitative study

OBJECTIVE

Cancer patients, carers and oncology health professionals have been impacted by the COVID-19 pandemic in many ways, but their experiences and psychosocial responses to the pandemic are still being explored. This study aimed to document the experience of Australians living with cancer, family carers, and Oncology health professionals (HPs) when COVID-19 first emerged.

METHODS

In this qualitative study, participants (cancer patients currently receiving treatment, family carers and HPs) completed a semi-structured interview exploring their experiences of COVID-19 and the impact it had on cancer care. Participants also completed the Hospital Anxiety and Depression Scale (patients) and the Depression, Anxiety and Stress Scale (carers and HPs) to assess emotional morbidity. Thematic analysis was undertaken on qualitative data.

RESULTS

32 patients, 16 carers and 29 HPs participated. Qualitative analysis yielded three shared themes: fear and death anxiety, isolation, and uncertainty. For HPs, uncertainty incorporated the potential for moral distress and work-stress. Patients and carers scoring high on anxiety/depression measures were more likely to have advanced disease, expressed greater death anxiety, talked about taking more extreme precautionary measures, and felt more impacted by isolation.

CONCLUSION

Cancer and COVID-19 can have compounding psychological impacts on all those receiving or giving care.

PRACTICE IMPLICATIONS

Screening for distress in patients, and burnout in HPs, is recommended. Increased compassionate access and provision of creative alternatives to face-to-face support are warrented.

POS1268 PHASE II TRIAL OF ENPATORAN IN PATIENTS HOSPITALIZED WITH COVID-19 PNEUMONIA

Background

Enpatoran is a selective and potent dual toll-like receptor (TLR) 7/8 inhibitor in development for the treatment of cutaneous and systemic lupus erythematosus (CLE/SLE). Enpatoran inhibits TLR7/8 activation in vitro and suppresses disease activity in lupus mouse models.1 Enpatoran was well tolerated and had linear pharmacokinetic (PK) parameters in healthy volunteers.2 As TLR7/8 mediate immune responses to single-stranded RNA viruses, including SARS-CoV-2, it was postulated that enpatoran may prevent hyperinflammation and cytokine storm in COVID-19.

Objectives

In response to the COVID-19 pandemic, we conducted an exploratory Phase II trial to assess safety and determine whether enpatoran prevents clinical deterioration in patients (pts) hospitalized with COVID-19 pneumonia. PK and pharmacodynamics (PD) of enpatoran were also evaluated.

Methods

ANEMONE was a randomized, double-blind, placebo (PBO)-controlled study conducted in Brazil, the Philippines, and the USA (NCT04448756). Pts aged 18–75 years, hospitalized with COVID-19 pneumonia (WHO 9-point scale score =4) but not mechanically ventilated, with SpO2 <94% and PaO2/FiO2 ≥150 (FiO2 maximum 0.4) were eligible. Those with a history of uncontrolled illness, active/unstable cardiovascular disease and SARS-CoV-2 vaccination were excluded. Pts received PBO or enpatoran (50 or 100 mg twice daily [BID]) for 14 days, with monitoring to Day 28 and safety follow-up to Day 60. Primary outcomes were safety and time to recovery (WHO 9-point scale ≤3). Clinical deterioration (time to clinical status >4, WHO 9-point scale) was a secondary outcome. Exploratory endpoints were enpatoran and biomarker concentrations (cytokines, C-reactive protein [CRP], D-dimer and interferon gene signature [IFN-GS] scores) assessed over time.

Results

149 pts received either PBO (n=49), or enpatoran 50 mg (n=54) or 100 mg (n=46) BID; 88% completed treatment and 86% received concomitant steroids. Median age was 50 years (77% <60 years old), 66% were male, and 50% had ≥1 comorbidity (40% hypertension, 24% diabetes). Overall, 59% pts reported a treatment-emergent adverse event (TEAE) with three non-treatment-related deaths; 11% reported a treatment-related TEAE. The proportion of pts in the enpatoran group reporting serious TEAEs was low (50 mg BID 9%; 100 mg BID 2%) vs PBO (18%). Gastrointestinal disorders were most common (PBO 8%; 50 mg BID 28%; 100 mg BID 9%). The primary outcome of time to recovery with enpatoran vs PBO was not met; medians were 3.4–3.9 days. A positive signal in time to clinical deterioration from Day 1 through Day 28 was observed; hazard ratios [95% CI] for enpatoran vs PBO were 0.39 [0.13, 1.15] (50 mg BID) and 0.30 [0.08, 1.08] (100 mg BID). Mean enpatoran exposure was dose-proportional, and PK properties were within expectations. The median (quartile [Q]1– Q3) interleukin 6 (IL-6), CRP and D-dimer baseline concentration across the groups were 5.7 (4.0–13.5) pg/mL, 30.04 (11.40–98.02) and 0.62 (0.39–1.01) mg/L, respectively. Baseline IFN-GS scores were similar across groups.

Conclusion

The ANEMONE trial was the first to evaluate the safety and efficacy of a TLR7/8 inhibitor in an infectious disease for preventing cytokine storm. Enpatoran up to 100 mg BID for 14 days was well tolerated by patients acutely ill with COVID-19 pneumonia. Time to recovery was not improved with enpatoran, perhaps due to the younger age of patients who had fewer comorbidities compared to those in similar COVID-19 trials. However, there was less likelihood for clinical deterioration with enpatoran than placebo. This trial provides important safety, tolerability, PK and PD data supporting continued development of enpatoran in SLE and CLE (NCT04647708, NCT05162586).

References

[1]Vlach, et al. J Pharmacol Exp Ther 2021;376:397–409;

[2]Port, et al. Pharmacol Res Perspect 2021;9:e00842.

Acknowledgements

We would like to thank those who took part in the the ANEMONE trial. This study was sponsored by the healthcare business of Merck KGaA, Darmstadt, Germany (CrossRef Funder ID: 10.13039/100009945), who funded medical writing support by Bioscript Stirling Ltd.

Disclosure of Interests

John E. McKinnon Consultant of: EMD Serono Research & Development Institute, Inc., Billerica, MA, USA, an affiliate of Merck KGaA, Joel Santiaguel Speakers bureau: Merck Healthcare KGaA, Claudia Murta Speakers bureau: Pfizer/Wyeth, Dongzi Yu Employee of: EMD Serono Research & Development institute (an affiliate of Merck KGaA), Mukhy Khursheed Employee of: Merck Serono Ltd (an affiliate of Merck KGaA), Flavie Moreau Employee of: EMD Serono Research & Development institute (an affiliate of Merck KGaA), Lena Klopp-Schulze Employee of: Merck Healthcare KGaA, Jamie Shaw Employee of: EMD Serono Research & Development institute (an affiliate of Merck KGaA), Sanjeev Roy Employee of: Ares Trading SA (an affiliate of Merck KGaA), Amy Kao Employee of: EMD Serono Research & Development institute (an affiliate of Merck KGaA)

Using Satellite Observations to Evaluate Model Microphysical Representation of Arctic Mixed-Phase Clouds

Mixed-phase clouds play an important role in determining Arctic warming, but are parametrized in models and difficult to constrain with observations. We use two satellite-derived cloud phase metrics to investigate the vertical structure of Arctic clouds in two global climate models that use the Community Atmosphere Model version 6 (CAM6) atmospheric component. We report a model error limiting ice nucleation, produce a set of Arctic-constrained model runs by adjusting model microphysical variables to match the cloud phase metrics, and evaluate cloud feedbacks for all simulations. Models in this small ensemble uniformly overestimate total cloud fraction in the summer, but have variable representation of cloud fraction and phase in the winter and spring. By relating modeled cloud phase metrics and changes in low-level liquid cloud amount under warming to longwave cloud feedback, we show that mixed-phase processes mediate the Arctic climate by modifying how wintertime and springtime clouds respond to warming.

Fear of Progression in chronic illnesses other than cancer: A systematic review and meta-analysis of a transdiagnostic construct

Fear of cancer recurrence (FCR) is the most common psychosocial issue amongst cancer survivors. However, fear of progression (FoP) has been studied outside of the cancer context. This review aimed to: (1) meta-synthesize qualitative studies of FoP in illnesses other than cancer; and (2) quantify the relationship between FoP and anxiety, depression, and quality of life (QoL) in non-cancer chronic illnesses. We identified 25 qualitative and 11 quantitative studies in a range of chronic illnesses. Participants described fears of progression and recurrence of their illness, including fears of dying, and fears of becoming a burden to family. Fears were often triggered by downward comparison (i.e. seeing people worse off than themselves). Participants coped in different ways, including by accepting the illness or seeking knowledge. Those for whom these fears caused distress reported hypervigilance to physical symptoms and avoidance. Distress, and seeking information, were associated with adherence. In quantitative analyses, FoP was moderately associated with QoL, and strongly associated with anxiety and depression. These results suggest that FoP in illnesses other than cancer is similar to FCR. FoP appears to be an important transdiagnostic construct associated with distress. Evidence-based FCR interventions could be adapted to better manage FoP in other illnesses.

flopp: Extremely Fast Long-Read Polyploid Haplotype Phasing by Uniform Tree Partitioning

Resolving haplotypes in polyploid genomes using phase information from sequencing reads is an important and challenging problem. We introduce two new mathematical formulations of polyploid haplotype phasing: (1) the min-sum max tree partition problem, which is a more flexible graphical metric compared with the standard minimum error correction (MEC) model in the polyploid setting, and (2) the uniform probabilistic error minimization model, which is a probabilistic analogue of the MEC model. We incorporate both formulations into a long-read based polyploid haplotype phasing method called flopp. We show that flopp compares favorably with state-of-the-art algorithms-up to 30 times faster with 2 times fewer switch errors on 6 × ploidy simulated data. Further, we show using real nanopore data that flopp can quickly reveal reasonable haplotype structures from the autotetraploid Solanum tuberosum (potato).

Theory of local k-mer selection with applications to long-read alignment

Motivation

Selecting a subset of k-mers in a string in a local manner is a common task in bioinformatics tools for speeding up computation. Arguably the most well-known and common method is the minimizer technique, which selects the ‘lowest-ordered’ k-mer in a sliding window. Recently, it has been shown that minimizers may be a sub-optimal method for selecting subsets of k-mers when mutations are present. There is, however, a lack of understanding behind the theory of why certain methods perform well.

Results

We first theoretically investigate the conservation metric for k-mer selection methods. We derive an exact expression for calculating the conservation of a k-mer selection method. This turns out to be tractable enough for us to prove closed-form expressions for a variety of methods, including (open and closed) syncmers, (a, b, n)-words, and an upper bound for minimizers. As a demonstration of our results, we modified the minimap2 read aligner to use a more conserved k-mer selection method and demonstrate that there is up to an 8.2% relative increase in number of mapped reads. However, we found that the k-mers selected by more conserved methods are also more repetitive, leading to a runtime increase during alignment. We give new insight into how one might use new k-mer selection methods as a reparameterization to optimize for speed and alignment quality.

Availability and implementation

Simulations and supplementary methods are available at https://github.com/bluenote-1577/local-kmer-selection-results. os-minimap2 is a modified version of minimap2 and available at https://github.com/bluenote-1577/os-minimap2.

Supplementary information

Supplementary data are available at Bioinformatics online.

Outcomes after percutaneous coronary intervention (PCI) in patients with prior coronary artery bypass grafting (cabg)

Background

In patients with prior CABG requiring subsequent PCI there is uncertainty whether bypass grafts or native coronary arteries should be targeted.

Methods

We analysed data from 2,764 patients with prior CABG in the Melbourne Interventional Group registry (2005–2018), divided into two groups: those undergoing PCI to a native vessel (n=1,928) and those with PCI to a graft vessel (n=836).

Results

Patients with a graft vessel PCI were older, had more high-risk clinical characteristics (prior MI, heart failure, ejection fraction &lt;50%, renal impairment, peripheral and cerebrovascular disease), and high-risk procedural features (ACC/AHA types B2/C lesions). However, patients in the native vessel group were more likely to have PCI to a chronic total occlusion. The majority of graft PCI were to saphenous vein grafts (84%), with 10% to radial and 6% to LIMA/RIMA grafts. Distal embolic protection devices were used in 30% of graft PCI. Patients with graft PCI had higher rates of no reflow (6.3% vs. 1.5%; p&lt;0.001), coronary perforation (p=0.016) and inpatient stent thrombosis (p=0.028). However, 30-day mortality and major adverse cardiovascular and cerebrovascular events (MACCE) were similar. Unadjusted long-term mortality (median follow up 4.8 years) was higher in patients who had undergone a graft PCI (44% vs. 32%, p&lt;0.001), but following Cox proportional hazards modelling, PCI vessel type was not a predictor of long-term mortality (HR 1.13; 95% CI 0.96–1.33, p=0.14).

Conclusions

Early clinical outcomes and risk-adjusted long-term mortality are similar for patients with prior CABG undergoing PCI to a native vessel or a bypass graft.

Funding Acknowledgement

Type of funding sources: Public hospital(s). Main funding source(s): The Alfred Hospital

Sex differences in pre-hospital analgesia and outcomes in patients presenting with acute coronary syndromes

Background

Opioid analgesia remains the mainstay of pain management in acute coronary syndromes (ACS). Significant sex differences persist in ACS presentation, management and outcomes, but the impact of sex-differences on pre-hospital pain management of ACS with opioids is unknown. There is increasing awareness of the importance of pre-hospital factors in ACS, as well as emerging concerns with opioid use impairing the gastrointestinal absorption of oral P2Y12 inhibitors.

Purpose

This study examined if sex-differences in pre-hospital pain scores, opioid administration and clinical outcomes exist in ACS patients.

Methods

Patients presenting with ACS via ambulance (2014–2018) that underwent percutaneous coronary intervention (PCI) were prospectively collected via the Victorian Cardiac Outcomes Registry (VCOR), the Melbourne Interventional Group (MIG), and linked to the Ambulance Victoria database. The primary outcome was 30-day major adverse cardiac events (MACE). Secondary outcomes were descriptive analyses of pre-hospital pain score, intravenous morphine equivalent analgesic dosing, plus predictors of MACE and Thrombolysis In Myocardial Infarction (TIMI) 0–1 flow pre-PCI using logistic regression.

Results

10,547 patients were included (female: 2,775 [26.3%]). Opioids were administered to 1,585 (57%) females and 5,068 (65%) males (p&lt;0.001). Adjusted 30-day MACE was similar between opioid groups in both sexes (female: OR 1.21, CI 0.82–1.79, p=0.34; male: OR 0.89, 0.68–1.16, p=0.40). Median pain score at presentation was 6 (IQR 4,8) for both sexes. Median opioid dose was 2.5 mg (IQR 0,10) in females and 5 mg (IQR 0,10) in males (p&lt;0.001), with similar pain relief achieved. Adjusted rates of TIMI 0–1 pre-PCI were higher in patients administered opioids (female: OR 2.83, CI 2.14–3.56, p&lt;0.001; male: OR 2.95, CI 2.49–3.49, p&lt;0.001).

Conclusions

Female patients undergoing PCI received less opioid analgesia, but no sex-differences in pre-hospital pain scores were seen. Opioid administration was associated with impaired antegrade flow in the culprit artery in both sexes, but not short-term MACE. Randomised trials evaluating the clinical implications of opioid administration in ACS with sex subgroup analyses are needed to guide clinical practice.

Funding Acknowledgement

Type of funding sources: Public Institution(s). Main funding source(s): Melbourne Interventional GroupVictorian Cardiac Outcomes Registry

Trends in intra-aortic balloon pump use in cardiogenic shock in the post-SHOCK II trial era

Background

Myocardial infarction complicated by cardiogenic shock (MI-CS) has a poor prognosis, even with early revascularisation. Previously, intra-aortic balloon pump (IABP) use was thought to improve outcomes, but the SHOCK-II trial in 2012 found no survival benefit.

Purpose

This study aimed to determine the trends in IABP use in patients with MI-CS undergoing percutaneous intervention (PCI) over time and characteristics associated with use.

Methods

Between 2005–2018, patients presenting with MI-CS that underwent percutaneous coronary intervention (PCI) at a hospital participating in the Melbourne Interventional Group Registry were included. The primary outcome was the trend in IABP use over time. Secondary outcomes included mortality, 30-day MACCE (major adverse cardiovascular and cerebrovascular events) and predictors of outcome, determined via logistic regression.

Results

Of the 1,110 patients identified, IABP was used in 478 (43%). IABP was used more in patients with left main and left anterior descending culprit lesions (62% vs. 46%), lower ejection fraction (&lt;35%; 18% vs. 11%), and pre-procedural inotrope use (81% vs. 73%), all p&lt;0.05. IABP use was associated with higher inpatient bleeding (18% vs. 13%) and 30-day MACCE (58% vs. 51%), both p&lt;0.05. The rate of MI-CS increased over time, but after 2012 there was a decline in IABP use (Figure 1). IABP use was a predictor of 30-day MACCE (OR 1.6, 95% CI 1.18–2.29, p=0.003). However, IABP was not associated with in-hospital, 30-day or long-term mortality (45% vs. 47%, p=0.44; 46% vs. 50%, p=0.25; 60% vs. 62%, p=0.39).

Conclusions

Consistent with the SHOCK II trial, IABP use is not associated with reduced short- or long-term mortality, but in this study was associated with increased short-term adverse events. IABP use is declining, but is still used in sicker patients with greater myocardium at risk, given limited alternatives.

Funding Acknowledgement

Type of funding sources: Public Institution(s). Main funding source(s): Melbourne interventional group

Lignocaine versus opioids in coronary intervention: assessing antiplatelet activity and ticagrelor levels (LOCAL) study

Background

Opioid analgesia impairs the bioavailability and antiplatelet effect of oral P2Y12 inhibitors prompting investigation of mitigation strategies including identifying alternative analgesic agents.

Purpose

To assess the impact of intravenous fentanyl and lignocaine on the bioavailability and antiplatelet effect of ticagrelor in patients with unstable angina and non-ST elevation myocardial infarction, as well as their procedural analgesic efficacy and safety.

Methods

The LOCAL trial was a prospective, single centre, double-blind, randomized, controlled trial where intravenous lignocaine was the experimental analgesic agent assessed in this trial compared to intravenous fentanyl as procedural analgesia during coronary angiography and percutaneous coronary intervention. Patients with an indication for dual antiplatelet therapy and no contraindication were given 180mg of ticagrelor orally as integral tablets with 250 mL of tap water at the end of the case. Blood was sampled at time 0, 0.5, 1, 2 and 4 hours post administration of ticagrelor for pharmacokinetic and comprehensive pharmacodynamic analysis.

Results

Seventy patients undergoing coronary angiography with an indication for ticagrelor loading were included in the pharmacokinetic and pharmacodynamic analysis. Plasma ticagrelor levels at 2 h post loading dose were significantly lower in the fentanyl compared to lignocaine treatment arm (476 vs. 792 ng/mL, p=0.02, see figure 1). The area under the plasma-time curves for ticagrelor (987 vs. 2189 ng.h/mL, p=0.001) and its active metabolite (173 vs. 394 ng.h/mL, p&lt;0.001) were both significantly lower in the fentanyl arm. Platelet reactivity assessed by the VerifyNow assay was higher at all time points after baseline in the fentanyl compared to lignocaine arm. The VASP flow cytometry assay demonstrated higher platelet reactivity at 2 hours in the fentanyl group (40% vs. 22% platelet reactivity index, p=0.001). The Multiplate Analyzer demonstrated higher platelet reactivity in the fentanyl arm at 60 minutes (43 vs. 26 area under the curve units, p=0.001) as did expression of activated platelet GpIIb/IIIa receptor (2829 vs. 1426 geometric mean fluorescence intensity (GMFI), p=0.006) and P-selectin (439 vs. 211 GMFI, p=0.001). High on-treatment platelet reactivity (HPR) was significantly higher in the fentanyl arm at 60 min using the MPA (41% vs. 9%, p=0.002) and 120 min using the VFN (30% vs. 3%, p=0.003) and VASP (37% vs. 6%, p=0.002) assays (see figure 2). Both drugs were well tolerated with a high level of patient satisfaction (fentanyl 94% vs. lignocaine 97%, p=0.56).

Conclusion(s)

Unlike fentanyl, lignocaine does not impair the bioavailability or delay the antiplatelet effect of ticagrelor. Both drugs were well tolerated and effective with a high level of patient satisfaction for procedural analgesia. Systemic pain medication during PCI should be reconsidered and if performed, lignocaine is a beneficial alternative to fentanyl.

Funding Acknowledgement

Type of funding sources: Public grant(s) – National budget only. Main funding source(s): TBA Figure 1. Ticagrelor and AM pharmacokineticsFigure 2. Ticagrelor pharmacodynamics

A mixed methods pilot and feasibility open trial of internet-delivered cognitive behaviour therapy (iCanADAPT Advanced) for people with advanced cancer with depression and/or anxiety

PURPOSE

Evaluate the feasibility, acceptability and potential efficacy of a form of online therapy for clinical depression and/or anxiety in people living with advanced cancer.

METHODS

A single-arm open trial of a six-lesson clinician-supervised, internet-delivered cognitive behavioural therapy (iCBT) transdiagnostic intervention (iCanADAPT Advanced) was undertaken. Qualitative (semi-structured telephone interview conducted at 3-months) and quantitative data (questionnaires collected at pre-, post-, and 3-month follow-up) were analysed.

RESULTS

27 participants partook (26 women, 56% breast cancer, mean age 56yo; average number of mental health diagnoses 1.8, with majority (81%) meeting criteria for generalised anxiety disorder). Feasibility - Unanticipated numbers (48%) of participants had physical health deterioration (cancer progression or death). iCBT had high adherence overall (completion rates: 37% did 6 lessons; 70% did 4 lessons) but adherence was higher for those whose cancer remained stable (completion rates: 43% did 6 lessons; 85% did 4 lessons). Acceptability - the intervention was acceptable to the majority of participants, with high treatment satisfaction. Advisory data was achieved regarding future versions. Potential efficacy - regardless of physical health status, participants who completed the iCBT showed a significant decrease over time in anxiety and depression symptoms.

CONCLUSIONS

Online therapies may be useful in assisting those living with advanced cancer dealing with clinical depression and anxiety disorders. The specific modality of clinician supervised iCBT has significant potential to be a suitable modality of online therapy.

PREIMPLANTATION GENETIC TESTING: Non-invasive prenatal testing for aneuploidy, copy-number variants and single-gene disorders

The discovery of cell-free fetal DNA (cffDNA) in maternal plasma has enabled a paradigm shift in prenatal testing, allowing for safer, earlier detection of genetic conditions of the fetus. Non-invasive prenatal testing (NIPT) for fetal aneuploidies has provided an alternative, highly efficient approach to first-trimester aneuploidy screening, and since its inception has been rapidly adopted worldwide. Due to the genome-wide nature of some NIPT protocols, the commercial sector has widened the scope of cell-free DNA (cfDNA) screening to include sex chromosome aneuploidies, rare autosomal trisomies and sub-microscopic copy-number variants. These developments may be marketed as 'expanded NIPT' or 'NIPT Plus' and bring with them a plethora of ethical and practical considerations. Concurrently, cfDNA tests for single-gene disorders, termed non-invasive prenatal diagnosis (NIPD), have been developed for an increasing array of conditions but are less widely available. Despite the fact that all these tests utilise the same biomarker, cfDNA, there is considerable variation in key parameters such as sensitivity, specificity and positive predictive value depending on what the test is for. The distinction between diagnostics and screening has become blurred, and there is a clear need for the education of physicians and patients regarding the technical capabilities and limitations of these different forms of testing. Furthermore, there is a requirement for consistent guidelines that apply across health sectors, both public and commercial, to ensure that tests are validated and robust and that careful and appropriate pre-test and post-test counselling is provided by professionals who understand the tests offered.

Efficacy and safety of a sodium-glucose co-transporter-2 inhibitor versus placebo as an add-on therapy for people with type 2 diabetes inadequately treated with metformin and a dipeptidyl peptidase-4 inhibitor: a systematic review and meta-analysis of randomised controlled trials

AIMS

To conduct a systematic review and meta-analysis to assess the efficacy, safety and tolerability of sodium-glucose co-transporter-2 inhibitors vs placebo as add-on therapy after metformin and dipeptidyl peptidase-4 inhibitor dual therapy in type 2 diabetes.

METHODS

This systematic review was performed according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines (PROSPERO registration number: CRD42018099398). A search was conducted via PubMed, www.clinicaltrials.gov and Cochrane Central Register of Controlled Trials of relevant randomised controlled trials up until 14 August 2020 that compared sodium-glucose co-transporter-2 inhibitors vs placebo as add-on therapy after metformin and dipeptidyl peptidase-4 inhibitor therapy. A random-effects model was used.

RESULTS

Six randomised controlled trials (1661 participants) met the inclusion criteria. Compared with placebo, sodium-glucose co-transporter-2 inhibitor treatment, as add-on to metformin and dipeptidyl peptidase-4 inhibitor therapy, was associated with a significant reduction in HbA_1c level [mean difference -8 mmol/mol, 95% CI -10, -6 (-0.7%, 95% CI -0.9, -0.6); P < 0.00001], in fasting plasma glucose level [mean difference -1.70 mmol/l, 95% CI -1.91, -1.49; P < 0.00001], in weight (mean difference -1.76 kg, 95% CI -2.04, -1.48; P < 0.00001) and in blood pressure (systolic blood pressure: mean difference -3.6 mmHg, 95% CI -4.8, -2.4; P < 0.00001; diastolic blood pressure: mean difference -1.5 mmHg; 95% CI -2.4, -0.6; P = 0.002). Genital mycotic infections (odds ratio 7.37, 95% CI 3.06, 17.76; P < 0.00001) were more common with sodium-glucose co-transporter-2 inhibitors, but there was no significant statistical difference in urinary tract infections (odds ratio 1.16, 95% CI 0.63, 2.13; P = 0.64), in hypoglycaemia (odds ratio 1.36, 95% CI 0.61, 3.04; P = 0.45), or in discontinuation rates due to adverse events (odds ratio 1.52, 95% CI 0.78, 2.97; P = 0.22) between the two groups.

CONCLUSIONS

In comparison with placebo, add-on therapy with a sodium-glucose co-transporter-2 inhibitor is significantly more efficacious in lowering HbA_1c , fasting plasma glucose and weight in people with type 2 diabetes following inadequate glycaemic control with metformin and a dipeptidyl peptidase-4 inhibitor. The rate of discontinuation due to adverse events was similar despite higher risk of genital mycotic infections.

What factors influence organisational readiness for change? Implementation of the Australian clinical pathway for the screening, assessment and management of anxiety and depression in adult cancer patients (ADAPT CP)

AIMS

Translation of evidence-based psycho-oncology interventions into routine care can significantly improve patient outcomes, yet effective implementation remains challenging due to numerous real-world barriers. A key factor that may influence implementation is organisational readiness for change. This mixed method study sought to identify factors associated with organisational readiness for implementing the Australian clinical pathway for the screening, assessment and management of anxiety and depression in adult cancer patients (ADAPT CP).

METHODS

We collected data from multidisciplinary staff across six Australian cancer services who were preparing to implement the ADAPT CP. Services were categorised as having 'high' versus 'mid-range' organisational readiness based on a median split on the Organizational Readiness for Implementing Change (ORIC) questionnaire (score range = 12-60). Qualitative data from the semi-structured interviews based on the Promoting Action Research in Health Services (PARiHS) framework were analysed thematically and compared for services with high- versus mid-range organisational readiness.

RESULTS

Three services with high- (mean ORIC range, 52.25-56.88), and three with mid-range (range, 38.75-46.39) organisational readiness scores were identified. Staff at services reporting higher readiness described a more collaborative and proactive service culture, strong communication processes and greater role flexibility. They also reported greater confidence in overcoming anticipated barriers and clearer strategies for addressing issues.

CONCLUSIONS

Levels of organisational readiness were related to distinct qualitative themes. Targeting these issues in services where readiness is mid-range or low prior to full-scale roll-out may improve staff levels of confidence and efficacy in implementing psycho-oncology-focused interventions.

Post-tuberculosis lung health: perspectives from the First International Symposium

ALTHOUGH CURABLE, TB frequently leaves the individual with chronic physical and psycho-social impairment, but these consequences have been largely neglected. The 1^st International Post-Tuberculosis Symposium (Stellenbosch, South Africa) was held to discuss priorities and gaps in addressing this issue. A barrier to progress has been the varied terminology and nomenclature, so the Delphi process was used to achieve consensus on definitions. Lack of sufficient evidence hampered definitive recommendations in most domains, including prevention and treatment of post-TB lung disease (PTLD), but the discussions clarified the research needed. A consensus was reached on a toolkit for future PTLD measurement and on PTLD patterns to be considered. The importance of extra-pulmonary consequences and progressive impairment throughout the life-course was identified, including TB recurrence and increased mortality. Patient advocates emphasised the need to address the psychological and social impacts post TB and called for clinical guidance. More generally, there is an urgent need for increased awareness and research into post-TB complications.

The Mortality After Release from Incarceration Consortium (MARIC): Protocol for a multi-national, individual participant data meta-analysis

INTRODUCTION

More than 30 million adults are released from incarceration globally each year. Many experience complex physical and mental health problems, and are at markedly increased risk of preventable mortality. Despite this, evidence regarding the global epidemiology of mortality following release from incarceration is insufficient to inform the development of targeted, evidence-based responses. Many previous studies have suffered from inadequate power and poor precision, and even large studies have limited capacity to disaggregate data by specific causes of death, sub-populations or time since release to answer questions of clinical and public health relevance.

OBJECTIVES

To comprehensively document the incidence, timing, causes and risk factors for mortality in adults released from prison.

METHODS

We created the Mortality After Release from Incarceration Consortium (MARIC), a multi-disciplinary collaboration representing 29 cohorts of adults who have experienced incarceration from 11 countries. Findings across cohorts will be analysed using a two-step, individual participant data meta-analysis methodology.

RESULTS

The combined sample includes 1,337,993 individuals (89% male), with 75,795 deaths recorded over 9,191,393 person-years of follow-up.

CONCLUSIONS

The consortium represents an important advancement in the field, bringing international attention to this problem. It will provide internationally relevant evidence to guide policymakers and clinicians in reducing preventable deaths in this marginalized population.

KEY WORDS

Mortality; incarceration; prison; release; individual participant data meta-analysis; consortium; cohort.

Randomised controlled trial of internet-delivered cognitive behaviour therapy for clinical depression and/or anxiety in cancer survivors (iCanADAPT Early)

PURPOSE

To evaluate internet-delivered cognitive behavioural therapy (iCBT) on clinical depression and/or anxiety, distress, fear of cancer recurrence, and quality of life in cancer survivors.

METHODS

Random assignation of 114 participants to iCBT or treatment-as-usual (TAU). The clinician-supervised iCBT program (iCanADAPT Early) consisted of eight lessons over 16 weeks. Self-report questionnaires occurred at baseline, midpoint, and posttreatment for both groups with 3-month follow-up for iCBT participants. A mixed modelling approach to compare groups occurred.

RESULTS

iCBT was superior to TAU on all outcome measures at posttreatment. Compared with TAU, the iCBT group showed a significant decrease over time in anxiety and depression symptoms (primary outcome, Hospital Anxiety and Depression Scale, Hedges g = 1.51). Additionally the iCBT group had significantly lower general distress (Kessler-10, g = 1.56), fear of cancer recurrence (Fear of Cancer Recurrence Inventory, g = 0.39), and significantly higher quality of life (Functional Assessment of Cancer Therapy-General, g = 0.74) at posttreatment compared with the TAU group. High adherence and satisfaction were found for iCBT with low clinician time.

CONCLUSION

Clinician-supervised iCBT has significant benefits for cancer survivors with clinical depression and anxiety disorders.