Chinese family care partners of older adults in Canada have grit: A qualitative study

AIM

To explain the process taken by Chinese family care partners of older adults in the Greater Toronto Area, Canada, to access health and social services in their communities. The research question was: What mechanisms and structures impact the agency of Chinese family care partners of older adults, in the process of assisting them to access health and social services?

DESIGN

This qualitative study was informed by critical realism.

METHODS

Chinese family care partners of older adults in the Greater Toronto Area, Canada, were interviewed from August 2020 to June 2021. Transcripts underwent thematic analysis.

FINDINGS

Twenty-eight Chinese family care partners expressed a firm commitment to maintain caregiving conditions and to judiciously access health and social services. Their commitment was made up of three parts: (a) legislative and cultural norms of family, work, and society; (b) their perseverance to fill gaps with limited social and financial resources; (c) the quality of their relationship to, and illness trajectory of the older adults. The social structures created tension in how Chinese family care partners made decisions, negotiated resources, and ultimately monitored and coordinated timely access with older adults.

CONCLUSION

Participants' commitment and perseverance were conceptualized as "grit," central to their agency to conform to legislative and cultural norms. Moreover, findings support grit's power to motivate and sustain family caregiving, in order for older adults to age in place as long as possible with finite resources.

IMPLICATIONS FOR THE PROFESSION

This study highlights the importance of cultural awareness education for nurses, enabling continuity of care at a systems level and for a more resilient healthcare system.

IMPACT

Family care partners' grit may be crucial for nurses to harness when together, they face limited access to culturally appropriate health and social services in a system grounded in values of equity and inclusion, as in Canada.

REPORTING METHOD

When writing this manuscript, we adhered to relevant EQUATOR guidelines of the Consolidated Criteria for Reporting Qualitative Research (COREQ).

PATIENT OR PUBLIC INVOLVEMENT AND ENGAGEMENT

No patient or public involvement.

A peptide derived from TID1S rescues frataxin deficiency and mitochondrial defects in FRDA cellular models

Friedreich's ataxia (FRDA), the most common recessive inherited ataxia, results from homozygous guanine-adenine-adenine (GAA) repeat expansions in intron 1 of the FXN gene, which leads to the deficiency of frataxin, a mitochondrial protein essential for iron-sulphur cluster synthesis. The study of frataxin protein regulation might yield new approaches for FRDA treatment. Here, we report tumorous imaginal disc 1 (TID1), a mitochondrial J-protein cochaperone, as a binding partner of frataxin that negatively controls frataxin protein levels. TID1 interacts with frataxin both in vivo in mouse cortex and in vitro in cortical neurons. Acute and subacute depletion of frataxin using RNA interference markedly increases TID1 protein levels in multiple cell types. In addition, TID1 overexpression significantly increases frataxin precursor but decreases intermediate and mature frataxin levels in HEK293 cells. In primary cultured human skin fibroblasts, overexpression of TID1S results in decreased levels of mature frataxin and increased fragmentation of mitochondria. This effect is mediated by the last 6 amino acids of TID1S as a peptide made from this sequence rescues frataxin deficiency and mitochondrial defects in FRDA patient-derived cells. Our findings show that TID1 negatively modulates frataxin levels, and thereby suggests a novel therapeutic target for treating FRDA.

Quantum gate algorithm for reference-guided DNA sequence alignment

Reference-guided DNA sequencing and alignment is an important process in computational molecular biology. The amount of DNA data grows very fast, and many new genomes are waiting to be sequenced while millions of private genomes need to be re-sequenced. Each human genome has 3.2B base pairs, and each one could be stored with 2 bits of information, so one human genome would take 6.4B bits or ∼760MB of storage (National Institute of General Medical Sciences, n.d.). Today's most powerful tensor processing units cannot handle the volume of DNA data necessitating a major leap in computing power. It is, therefore, important to investigate the usefulness of quantum computers in genomic data analysis, especially in DNA sequence alignment. Quantum computers are expected to be involved in DNA sequencing, initially as parts of classical systems, acting as quantum accelerators. The number of available qubits is increasing annually, and future quantum computers could conduct DNA sequencing, taking the place of classical computing systems. We present a novel quantum algorithm for reference-guided DNA sequence alignment modeled with gate-based quantum computing. The algorithm is scalable, can be integrated into existing classical DNA sequencing systems and is intentionally structured to limit computational errors. The quantum algorithm has been tested using the quantum processing units and simulators provided by IBM Quantum, and its correctness has been confirmed.

aaHash: recursive amino acid sequence hashing

Motivation

K-mer hashing is a common operation in many foundational bioinformatics problems. However, generic string hashing algorithms are not optimized for this application. Strings in bioinformatics use specific alphabets, a trait leveraged for nucleic acid sequences in earlier work. We note that amino acid sequences, with complexities and context that cannot be captured by generic hashing algorithms, can also benefit from a domain-specific hashing algorithm. Such a hashing algorithm can accelerate and improve the sensitivity of bioinformatics applications developed for protein sequences.

Results

Here, we present aaHash, a recursive hashing algorithm tailored for amino acid sequences. This algorithm utilizes multiple hash levels to represent biochemical similarities between amino acids. aaHash performs ∼10× faster than generic string hashing algorithms in hashing adjacent k-mers.

Availability and implementation

aaHash is available online at https://github.com/bcgsc/btllib and is free for academic use.

Quantum algorithm for de novo DNA sequence assembly based on quantum walks on graphs

De novo DNA sequence assembly is based on finding paths in overlap graphs, which is a NP-hard problem. We developed a quantum algorithm for de novo assembly based on quantum walks in graphs. The overlap graph is partitioned repeatedly to smaller graphs that form a hierarchical structure. We use quantum walks to find paths in low rank graphs and a quantum algorithm that finds Hamiltonian paths in high hierarchical rank. We tested the partitioning quantum algorithm, as well as the quantum algorithm that finds Hamiltonian paths in high hierarchical rank and confirmed its correct operation using Qiskit. We developed a custom simulation for quantum walks to search for paths in low rank graphs. The approach described in this paper may serve as a basis for the development of efficient quantum algorithms that solve the de novo DNA assembly problem.

Initial Experience with the Commercial Electron FLASH Research Extension

PURPOSE/OBJECTIVE(S)

The purpose of this study was to introduce a new commercial electron FLASH system that has the potential to become widely available for FLASH researchers globally. In this study, we first present the initial acceptance and commissioning tests for the FLASH system, and second, we highlight preliminary FLASH effect results from our cell studies.

MATERIALS/METHODS

A linear accelerator was converted into a commercial research platform with the FLASH Research Extension, enabling the generation of a powerful 16 MeV electron FLASH beam. The dosimetric and stability tests were conducted using various dosimeters (i.e., radiochromic film, optically stimulated luminescent dosimeters (OSLDs), and a plane-parallel ionization chamber). To evaluate the FLASH effect, normal and cancer cell lines were FLASH irradiated using different pulse repetition frequencies (PRF) of 18 pulses/s and 180 pulses/s.

RESULTS

The electron FLASH mode was able to generate over 1 Gy per pulse at the isocenter and a dose rate of up to 690 Gy/s near the accessory mount of the Linac gantry head. The charge collected by the plane-parallel ionization chamber at the highest PRF (i.e., 180 pulses/s) showed a linear relationship with the delivered number of pulses (i.e., 1 to 99 pulses) with a coefficient of determination (R2) of 0.9996. The absorbed dose measured using radiochromic film and OSLDs agreed within 3%, on average, and followed an inverse square law as the source-to-axis distance (SAD) varied for which the R2 values were 0.9972 and 0.9955 for radiochromic film and OSLDs, respectively. The profile of the FLASH beam was symmetrical but was not as flat as the conventional 16 MeV electron beam due to the use of a thinner custom scattering foil to reduce the degradation of the ultra-high dose rate. The depth-dose curve beyond the build-up region for the FLASH beam was similar to the conventional 16 MeV electron beam for which the range at 50% the maximum dose (R50) agreed within 0.5 mm. The FLASH beam output remained consistent over a 4-month period with a variation of 2.5%, on average. The FLASH sparing effect was observed in vitro for healthy human pancreatic cells. Furthermore, we observed that the highest PRF beam (180 pulses/s) was more effective at destroying pancreatic cancerous cells while minimizing damage to healthy cells compared to the lowest PRF beam (18 pulses/s).

CONCLUSION

The novel commercial FLASH Research Extension system was dosimetrically characterized for pre-clinical FLASH research, and preliminary in vitro results demonstrated the FLASH effect. Given the prevalence of linear accelerators, this new commercial system has the potential to greatly increase the access to FLASH research.

Linear time complexity de novo long read genome assembly with GoldRush

Current state-of-the-art de novo long read genome assemblers follow the Overlap-Layout-Consensus paradigm. While read-to-read overlap - its most costly step - was improved in modern long read genome assemblers, these tools still often require excessive RAM when assembling a typical human dataset. Our work departs from this paradigm, foregoing all-vs-all sequence alignments in favor of a dynamic data structure implemented in GoldRush, a de novo long read genome assembly algorithm with linear time complexity. We tested GoldRush on Oxford Nanopore Technologies long sequencing read datasets with different base error profiles sourced from three human cell lines, rice, and tomato. Here, we show that GoldRush achieves assembly scaffold NGA50 lengths of 18.3-22.2, 0.3 and 2.6 Mbp, for the genomes of human, rice, and tomato, respectively, and assembles each genome within a day, using at most 54.5 GB of random-access memory, demonstrating the scalability of our genome assembly paradigm and its implementation.

aaHash: recursive amino acid sequence hashing

Motivation

K-mer hashing is a common operation in many foundational bioinformatics problems. However, generic string hashing algorithms are not optimized for this application. Strings in bioinformatics use specific alphabets, a trait leveraged for nucleic acid sequences in earlier work. We note that amino acid sequences, with complexities and context that cannot be captured by generic hashing algorithms, can also benefit from a domain-specific hashing algorithm. Such a hashing algorithm can accelerate and improve the sensitivity of bioinformatics applications developed for protein sequences.

Results

Here, we present aaHash, a recursive hashing algorithm tailored for amino acid sequences. This algorithm utilizes multiple hash levels to represent biochemical similarities between amino acids. aaHash performs ~10X faster than generic string hashing algorithms in hashing adjacent k-mers.

Availability and implementation

aaHash is available online at https://github.com/bcgsc/btllib and is free for academic use.

ntLink: A Toolkit for De Novo Genome Assembly Scaffolding and Mapping Using Long Reads

With the increasing affordability and accessibility of genome sequencing data, de novo genome assembly is an important first step to a wide variety of downstream studies and analyses. Therefore, bioinformatics tools that enable the generation of high-quality genome assemblies in a computationally efficient manner are essential. Recent developments in long-read sequencing technologies have greatly benefited genome assembly work, including scaffolding, by providing long-range evidence that can aid in resolving the challenging repetitive regions of complex genomes. ntLink is a flexible and resource-efficient genome scaffolding tool that utilizes long-read sequencing data to improve upon draft genome assemblies built from any sequencing technologies, including the same long reads. Instead of using read alignments to identify candidate joins, ntLink utilizes minimizer-based mappings to infer how input sequences should be ordered and oriented into scaffolds. Recent improvements to ntLink have added important features such as overlap detection, gap-filling, and in-code scaffolding iterations. Here, we present three basic protocols demonstrating how to use each of these new features to yield highly contiguous genome assemblies, while still maintaining ntLink's proven computational efficiency. Further, as we illustrate in the alternate protocols, the lightweight minimizer-based mappings that enable ntLink scaffolding can also be utilized for other downstream applications, such as misassembly detection. With its modularity and multiple modes of execution, ntLink has broad benefit to the genomics community, from genome scaffolding and beyond. ntLink is an open-source project and is freely available from https://github.com/bcgsc/ntLink. © 2023 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: ntLink scaffolding using overlap detection Basic Protocol 2: ntLink scaffolding with gap-filling Basic Protocol 3: Running in-code iterations of ntLink scaffolding Alternate Protocol 1: Generating long-read to contig mappings with ntLink Alternate Protocol 2: Using ntLink mappings for genome assembly correction with Tigmint-long Support Protocol: Installing ntLink.

Interdisciplinary management of an adult patient with significant tooth wear

Adult patients may present with compromised dentitions which require extensive oral rehabilitation. This case report shows the fulfilment of both functional and aesthetic treatment objectives for a patient with significant tooth wear through carefully planned interdisciplinary management. © 2022 Australian Dental Association.

1301 OUTCOMES FROM A PILOT PROJECT OFFERING FRAIL OLDER ADULTS LIVING WITH HIV A VIRTUAL MDT COMPREHENSIVE GERIATRIC ASSESSMENT

Introduction

Advancements in HIV treatment has resulted in an ageing population in people living with HIV (PLWH). Increasing prevalence of frailty in older PLWH has been demonstrated, giving rise to multi-morbidities, polypharmacy and consequently, complex medical and social needs. Approximately 5650 people are living with HIV across Greater Manchester. With increasing patient complexity, a pathway was developed to help provide holistic care and improve quality of life for older adults living with HIV.

Methods

A pilot involving multi-disciplinary professionals from the hospital frailty, HIV and community teams was established. Patients were screened using the Clinical Frailty Scale and patients with a CFS ≥ 4 were referred for completion of a comprehensive geriatric assessment (CGA). Patients would then be discussed at the Frailty MDT meeting, where action plans were devised.

Results

47 patients were assessed between October 2020 to December 2021, with 30 eligible for review in the frailty clinic. Commonly reported issues were mobility n=26 (86.6%), pain n=23 (76.6%), low mood n= 14 (46.6%), memory issues n=3 (43.3%) and falls n=12 (40%). Following MDT recommendations, 8 (26.6%) referrals were completed for social care, 1 (3%) referral for safeguarding and 9 (30%) referrals for active case management community teams for co-ordination of care in the community. Deprescribing recommendations were suggested for 16 (53.3%) patients and new medicine recommendations made for 24 (80%) patients.

Conclusion

A collaborative MDT approach to managing older PLWH can facilitate formulation of action plans to address patients physical, psychological and social needs.

Short-term risk prediction after major lower limb amputation: PERCEIVE study

BACKGROUND

The accuracy with which healthcare professionals (HCPs) and risk prediction tools predict outcomes after major lower limb amputation (MLLA) is uncertain. The aim of this study was to evaluate the accuracy of predicting short-term (30 days after MLLA) mortality, morbidity, and revisional surgery.

METHODS

The PERCEIVE (PrEdiction of Risk and Communication of outcomE following major lower limb amputation: a collaboratIVE) study was launched on 1 October 2020. It was an international multicentre study, including adults undergoing MLLA for complications of peripheral arterial disease and/or diabetes. Preoperative predictions of 30-day mortality, morbidity, and MLLA revision by surgeons and anaesthetists were recorded. Probabilities from relevant risk prediction tools were calculated. Evaluation of accuracy included measures of discrimination, calibration, and overall performance.

RESULTS

Some 537 patients were included. HCPs had acceptable discrimination in predicting mortality (931 predictions; C-statistic 0.758) and MLLA revision (565 predictions; C-statistic 0.756), but were poor at predicting morbidity (980 predictions; C-statistic 0.616). They overpredicted the risk of all outcomes. All except three risk prediction tools had worse discrimination than HCPs for predicting mortality (C-statistics 0.789, 0.774, and 0.773); two of these significantly overestimated the risk compared with HCPs. SORT version 2 (the only tool incorporating HCP predictions) demonstrated better calibration and overall performance (Brier score 0.082) than HCPs. Tools predicting morbidity and MLLA revision had poor discrimination (C-statistics 0.520 and 0.679).

CONCLUSION

Clinicians predicted mortality and MLLA revision well, but predicted morbidity poorly. They overestimated the risk of mortality, morbidity, and MLLA revision. Most short-term risk prediction tools had poorer discrimination or calibration than HCPs. The best method of predicting mortality was a statistical tool that incorporated HCP estimation.

Spruce giga-genomes: structurally similar yet distinctive with differentially expanding gene families and rapidly evolving genes

Spruces (Picea spp.) are coniferous trees widespread in boreal and mountainous forests of the northern hemisphere, with large economic significance and enormous contributions to global carbon sequestration. Spruces harbor very large genomes with high repetitiveness, hampering their comparative analysis. Here, we present and compare the genomes of four different North American spruces: the genome assemblies for Engelmann spruce (Picea engelmannii) and Sitka spruce (Picea sitchensis) together with improved and more contiguous genome assemblies for white spruce (Picea glauca) and for a naturally occurring introgress of these three species known as interior spruce (P. engelmannii × glauca × sitchensis). The genomes were structurally similar, and a large part of scaffolds could be anchored to a genetic map. The composition of the interior spruce genome indicated asymmetric contributions from the three ancestral genomes. Phylogenetic analysis of the nuclear and organelle genomes revealed a topology indicative of ancient reticulation. Different patterns of expansion of gene families among genomes were observed and related with presumed diversifying ecological adaptations. We identified rapidly evolving genes that harbored high rates of non-synonymous polymorphisms relative to synonymous ones, indicative of positive selection and its hitchhiking effects. These gene sets were mostly distinct between the genomes of ecologically contrasted species, and signatures of convergent balancing selection were detected. Stress and stimulus response was identified as the most frequent function assigned to expanding gene families and rapidly evolving genes. These two aspects of genomic evolution were complementary in their contribution to divergent evolution of presumed adaptive nature. These more contiguous spruce giga-genome sequences should strengthen our understanding of conifer genome structure and evolution, as their comparison offers clues into the genetic basis of adaptation and ecology of conifers at the genomic level. They will also provide tools to better monitor natural genetic diversity and improve the management of conifer forests. The genomes of four closely related North American spruces indicate that their high similarity at the morphological level is paralleled by the high conservation of their physical genome structure. Yet, the evidence of divergent evolution is apparent in their rapidly evolving genomes, supported by differential expansion of key gene families and large sets of genes under positive selection, largely in relation to stimulus and environmental stress response.

ntHash2: recursive spaced seed hashing for nucleotide sequences

Motivation

Spaced seeds are robust alternatives to k-mers in analyzing nucleotide sequences with high base mismatch rates. Hashing is also crucial for efficiently storing abundant sequence data. Here, we introduce ntHash2, a fast algorithm for spaced seed hashing that can be integrated into various bioinformatics tools for efficient sequence analysis with applications in genome research.

Results

ntHash2 is up to 2.1× faster at hashing various spaced seeds than the previous version and 3.8× faster than conventional hashing algorithms with naïve adaptation. Additionally, we reduced the collision rate of ntHash for longer k-mer lengths and improved the uniformity of the hash distribution by modifying the canonical hashing mechanism.

Availability and implementation

ntHash2 is freely available online at github.com/bcgsc/ntHash under an MIT license.

Supplementary information

Supplementary data are available at Bioinformatics online.

RResolver: efficient short-read repeat resolution within ABySS

BACKGROUND

De novo genome assembly is essential to modern genomics studies. As it is not biased by a reference, it is also a useful method for studying genomes with high variation, such as cancer genomes. De novo short-read assemblers commonly use de Bruijn graphs, where nodes are sequences of equal length k, also known as k-mers. Edges in this graph are established between nodes that overlap by [Formula: see text] bases, and nodes along unambiguous walks in the graph are subsequently merged. The selection of k is influenced by multiple factors, and optimizing this value results in a trade-off between graph connectivity and sequence contiguity. Ideally, multiple k sizes should be used, so lower values can provide good connectivity in lesser covered regions and higher values can increase contiguity in well-covered regions. However, current approaches that use multiple k values do not address the scalability issues inherent to the assembly of large genomes.

RESULTS

Here we present RResolver, a scalable algorithm that takes a short-read de Bruijn graph assembly with a starting k as input and uses a k value closer to that of the read length to resolve repeats. RResolver builds a Bloom filter of sequencing reads which is used to evaluate the assembly graph path support at branching points and removes paths with insufficient support. RResolver runs efficiently, taking only 26 min on average for an ABySS human assembly with 48 threads and 60 GiB memory. Across all experiments, compared to a baseline assembly, RResolver improves scaffold contiguity (NGA50) by up to 15% and reduces misassemblies by up to 12%.

CONCLUSIONS

RResolver adds a missing component to scalable de Bruijn graph genome assembly. By improving the initial and fundamental graph traversal outcome, all downstream ABySS algorithms greatly benefit by working with a more accurate and less complex representation of the genome. The RResolver code is integrated into ABySS and is available at https://github.com/bcgsc/abyss/tree/master/RResolver .

AB0979 Recommendations for weight management in osteoarthritis: a systematic review of clinical practice guidelines

Background

Weight loss interventions are often recommended to target overweight and obesity in the clinical practice guidelines (CPGs) for the management of osteoarthritis. This is despite evidence from meta-analyses of clinical trials that significant weight loss results in modest improvements in symptoms and minimal effects on disease progression1,2. There is evidence that weight gain is associated with increase in knee pain3,4. In countries such as USA, adults gain on average 0.5 to 1 kilogram per year from early to middle adulthood Preventing weight gain is easier to achieve and sustain than losing weight.

Objectives

Given that weight loss is accepted as fundamental to osteoarthritis management, we systematically reviewed the recommendations and approaches for weight management in all current osteoarthritis CPGs.

Methods

Nine databases were searched (1st January 2010 to 30th September 2021) to identify guidelines informing the non-pharmacological management of osteoarthritis. Three reviewers appraised guidelines according to the AGREE II instrument, and independently extracted data on their characteristics. One author extracted and summarised guideline recommendations on weight management. This systematic review is registered on PROSPERO (CRD42021274195).

Results

Fifteen CPGs from developed and developing countries were included. Weight loss was recommended for knee (12 of 13 guidelines) and hip (10 of 11 guidelines) but not hand osteoarthritis (0 of 4 guidelines). Combination approaches of diet and/or exercise were recommended for overweight or obese individuals (knee: 8 of 12; hip: 4 of 10), with 2 guidelines specifying ≥5% weight loss for knee and hip osteoarthritis. One of 15 guidelines specified strategies for weight loss and maintenance of lost weight. Two of 15 guidelines recommended controlling body weight for osteoarthritis, regardless of obesity status.

Conclusion

Most CPGs for knee and hip osteoarthritis include recommendations for weight loss in those with overweight or obesity as key to managing osteoarthritis, despite evidence of modest at best effect of weight loss on symptoms and no effect on joint structure1,2. Given obesity is a major risk factors for osteoarthritis, the prevention of weight gain may be more effective and practical in improving clinical outcomes for osteoarthritis, and hence should be considered as part of the key management in osteoarthritis.

References

[1]Chu IJH, Lim AYT, Ng CLW. Effects of meaningful weight loss beyond symptomatic relief in adults with knee osteoarthritis and obesity: a systematic review and meta-analysis. Obes Rev. 2018;19(11):1597-1607.

[2]Daugaard CL, Hangaard S, Bartels EM, Gudbergsen H, Christensen R, Bliddal H, et al. The effects of weight loss on imaging outcomes in osteoarthritis of the hip or knee in people who are overweight or obese: a systematic review. Osteoarthritis Cartilage. 2020;28(1):10-21.

[3]Tanamas SK, Wluka AE, Davies-Tuck M, Wang Y, Strauss BJ, Proietto J, et al. Association of weight gain with incident knee pain, stiffness, and functional difficulties: a longitudinal study. Arthritis Care Res (Hoboken). 2013;65(1):34-43.

[4]Teichtahl AJ, Wluka AE, Tanamas SK, Wang Y, Strauss BJ, Proietto J, et al. Weight change and change in tibial cartilage volume and symptoms in obese adults. Annals of the rheumatic diseases. 2015;74(6):1024-1029.

[5]Zheng Y, Manson JE, Yuan C, Liang MH, Grodstein F, Stampfer MJ, et al. Associations of Weight Gain From Early to Middle Adulthood With Major Health Outcomes Later in Life. JAMA. 2017;318(3):255-269.

Disclosure of Interests

None declared

ntEdit+Sealer: Efficient Targeted Error Resolution and Automated Finishing of Long-Read Genome Assemblies

High‐quality genome assemblies are crucial to many biological studies, and utilizing long sequencing reads can help achieve higher assembly contiguity. While long reads can resolve complex and repetitive regions of a genome, their relatively high associated error rates are still a major limitation. Long reads generally produce draft genome assemblies with lower base quality, which must be corrected with a genome polishing step. Hybrid genome polishing solutions can greatly improve the quality of long‐read genome assemblies by utilizing more accurate short reads to validate bases and correct errors. Currently available hybrid polishing methods rely on read alignments, and are therefore memory‐intensive and do not scale well to large genomes. Here we describe ntEdit+Sealer, an alignment‐free, k‐mer‐based genome finishing protocol that employs memory‐efficient Bloom filters. The protocol includes ntEdit for correcting base errors and small indels, and for marking potentially problematic regions, then Sealer for filling both assembly gaps and problematic regions flagged by ntEdit. ntEdit+Sealer produces highly accurate, error‐corrected genome assemblies, and is available as a Makefile pipeline from https://github.com/bcgsc/ntedit_sealer_protocol. © 2022 The Authors. Current Protocols published by Wiley Periodicals LLC.

Basic Protocol: Automated long‐read genome finishing with short reads

Support Protocol: Selecting optimal values for k‐mer lengths (k) and Bloom filter size (b)

Long term non-invasive endothelial function assessment in patients with paediatric inflammatory multisystem syndrome temporarily associated with Covid 19 (PIMS TS)

Funding Acknowledgements

Type of funding sources: None.

Introduction

Patients with PIMS-TS present with features of vasculitis (bright coronary arteries and diffuse coronary ectasia on transthoracic echocardiography) and prothrombotic features (e.g. elevated D Dimers) indicating involvement of the endothelial layer in the inflammatory process. Impairment in endothelial function may contribute to the acute but also to possible long-term consequences in patients with PIMS-TS. The aim of this pilot study is to assess non-invasively the endothelial (dys)function using reactive hyperemic peripheral arterial tonometry (RH-PAT) 6 months after the acute inflammatory phase. 

Methods

Ten patients with previous diagnosis of PIMS-TS were compared to  age-matched controls. The endothelial function was assessed using the EndoPAT device which provides the reactive hyperemic index (RHI) of endothelial function in a 15-min test. Cardiac function indices by means of LV fractional shortening (FS) was also assessed.

Results

There were no significant differences regarding age (11.2 ± 3.0 vs 13.6 ± 2.4, p = 0.063), height, weight and body surface area, (BSA: 1.49 ± 0.36 vs 1.52 ± 0.25, p = 0.856) in patients with previous diagnosis of PIMS-TS and controls respectively. The two groups also had similar LV systolic function assessed by FS (36.3 ± 9.1% vs 36.7 ± 7.1%, p = 0.922). The RHI in the PIMS TS group was similar to the control group (1.65 ± 0.43 vs 1.81 ± 0.60, p = 0.533 respectively).

Conclusions.  Patients with PIMS-TS who may present with features of vasculitis during the acute phase, do not show evidence of endothelial dysfunction during the long term follow-up, suggesting resolution. Further studies are required to accurately determine the endothelial (dys)function during the acute phase of the inflammatory syndrome and course.

LongStitch: high-quality genome assembly correction and scaffolding using long reads

BACKGROUND

Generating high-quality de novo genome assemblies is foundational to the genomics study of model and non-model organisms. In recent years, long-read sequencing has greatly benefited genome assembly and scaffolding, a process by which assembled sequences are ordered and oriented through the use of long-range information. Long reads are better able to span repetitive genomic regions compared to short reads, and thus have tremendous utility for resolving problematic regions and helping generate more complete draft assemblies. Here, we present LongStitch, a scalable pipeline that corrects and scaffolds draft genome assemblies exclusively using long reads.

RESULTS

LongStitch incorporates multiple tools developed by our group and runs in up to three stages, which includes initial assembly correction (Tigmint-long), followed by two incremental scaffolding stages (ntLink and ARKS-long). Tigmint-long and ARKS-long are misassembly correction and scaffolding utilities, respectively, previously developed for linked reads, that we adapted for long reads. Here, we describe the LongStitch pipeline and introduce our new long-read scaffolder, ntLink, which utilizes lightweight minimizer mappings to join contigs. LongStitch was tested on short and long-read assemblies of Caenorhabditis elegans, Oryza sativa, and three different human individuals using corresponding nanopore long-read data, and improves the contiguity of each assembly from 1.2-fold up to 304.6-fold (as measured by NGA50 length). Furthermore, LongStitch generates more contiguous and correct assemblies compared to state-of-the-art long-read scaffolder LRScaf in most tests, and consistently improves upon human assemblies in under five hours using less than 23 GB of RAM.

CONCLUSIONS

Due to its effectiveness and efficiency in improving draft assemblies using long reads, we expect LongStitch to benefit a wide variety of de novo genome assembly projects. The LongStitch pipeline is freely available at https://github.com/bcgsc/longstitch .

Does an empowerment-based self-care supportive intervention save cost for improving self-care and health service utilization among heart failure patients

Background

Heart failure (HF) evolves as a global pandemic and strains the over-stretched hospital service. Ineffective self-care remains the key factor to explain the avoidable hospital admission. Patient empowerment is as a theory-based strategy to optimize the patients' self-care changes for disease management [1]. Its cost-effectiveness to enhance self-care and health service utilization has yet to be determined.

Purpose

This was a double-blind randomized controlled trial to compare the effects and cost-effectiveness of a 12-week empowerment self-care program with a didactic education program on self-care maintenance and management as well as health service utilization among the community-dwelling HF patients.

Methods

A total of 236 HF patients were recruited from the specialist clinics of the Department of Cardiology in two regional hospitals. They were randomized to receive either the 12-week empowerment self-care program (Figure 1) or the 12-week didactic education. Outcome evaluation using the Self-care Heart Failure Index (SCHFI) at baseline, post-intervention (T1) and three months thereafter (T2), with record on the number of emergency room (ER) attendance and hospital admission. Cost effectiveness analyses were performed on total cost (medical, intervention and societal costs) incurred in both interventions as well as incremental cost-effectiveness ratios (ICER) expressed as incremental cost per 1) a reflected clinically meaningful improvement in self-care (i.e. a half standard deviation increase in SCHFI), 2) an ER attendance reduced, 3) a day of hospital stay reduced.

Results

As compared with the education group, the empowerment group reported significantly greater improvement in self-care management at T1 [B=13.77 (95% CI=6.07, 21.46), p<0.001] and T2 [B=10.98 (95% CI=3.21, 18.75), p=0.006]. For cost-effective analysis, The ICER (empowerment-education) was −USD220/0.5 SD increase in SCHFI, indicating the mean cost saved per patient for making a clinically significant improvement in self-care was USD 220. The cost-effectiveness acceptability curve showed patients were willing to pay at USD 207- 441 for a 80–90% chance of improved self-care, indicating that the empowerment approach was a cost saving strategy. Although the empowerment approach was associated with a lower risk of ER attendance [IRR=0.55, 95% CI=0.31–0.95)] and hospital admission [IRR=0.38 (95% CI=0.31–0.95)], it is not cost saving for reducing hospital service utilization.

Conclusions

The empowerment-based self-care program is a cost-saving strategy to produce a clinical significant change in HF-related self-care. Although it is associated with lower risk for hospital service utilization, its effect is not significant enough to be cost-saving. Future care model may explore the need to integrate dyadic science [2] and e-health [3] to strengthen the care continuity and effects of self-care intervention.

Funding Acknowledgement

Type of funding sources: Public grant(s) – National budget only. Main funding source(s): Health and Medical Research Fund, Food and Health Bureau, Hong Kong Special Administrative Region Figure 1

565 Predictors of Single Versus Multi-Level Lumbar Spinal Fusion: A Retrospective Cohort Study

Aim

Degenerative spine disease (DSD) of the lumbar spine is a common disorder among the aging population in the world, with a substantial humanistic and economic burden. Although lumbar spinal fusion is currently the mainstay surgical management of DSD, surgery is also associated with adjacent segment disease due to the modification of spinal biomechanics. Therefore, it is important to identify potential risk factors of DSD in order to prevent progressive deterioration and provide early intervention before the surgical option is absolutely necessary.

Method

Adult patients who underwent posterior lumbar spinal fusion from 2006-2016 were identified via OPCS-4codes. Smoking status, weight, age of operation, gender, diagnosis of ischaemic heart disease (IHD) were obtained via TrakCare®. The degree of deprivation was extrapolated using the Scottish Index of Multiple Deprivation (SIMD) 2020 quintile score. Data were analysed using logistic regression.

Results

In total, 313 met inclusion criteria and had data available, of which 205 and 108 patients underwent single and multi-level lumbar fusion respectively. Within the study population, 66.8% (206) and 33.2% (104) were female and male. Adjusted for all outcome measures, age of operation achieved statistical significance (p = 0.040). There was a 1.021-fold increase in risk of multi-level spinal fusion with each additional year of age. Weight was approaching statistical significance (p = 0.068).

Conclusions

Lumbar spinal health declines over time, but some patients experience more progressive deterioration. While some components of the spine are irreparable, early prescription of regimented exercise programs may strengthen spinal musculature to maintain a healthy sagittal balance, particularly in older, overweight, female patients.

ONTbarcoder and MinION barcodes aid biodiversity discovery and identification by everyone, for everyone

BACKGROUND

DNA barcodes are a useful tool for discovering, understanding, and monitoring biodiversity which are critical tasks at a time of rapid biodiversity loss. However, widespread adoption of barcodes requires cost-effective and simple barcoding methods. We here present a workflow that satisfies these conditions. It was developed via "innovation through subtraction" and thus requires minimal lab equipment, can be learned within days, reduces the barcode sequencing cost to < 10 cents, and allows fast turnaround from specimen to sequence by using the portable MinION sequencer.

RESULTS

We describe how tagged amplicons can be obtained and sequenced with the real-time MinION sequencer in many settings (field stations, biodiversity labs, citizen science labs, schools). We also provide amplicon coverage recommendations that are based on several runs of the latest generation of MinION flow cells ("R10.3") which suggest that each run can generate barcodes for > 10,000 specimens. Next, we present a novel software, ONTbarcoder, which overcomes the bioinformatics challenges posed by MinION reads. The software is compatible with Windows 10, Macintosh, and Linux, has a graphical user interface (GUI), and can generate thousands of barcodes on a standard laptop within hours based on only two input files (FASTQ, demultiplexing file). We document that MinION barcodes are virtually identical to Sanger and Illumina barcodes for the same specimens (> 99.99%) and provide evidence that MinION flow cells and reads have improved rapidly since 2018.

CONCLUSIONS

We propose that barcoding with MinION is the way forward for government agencies, universities, museums, and schools because it combines low consumable and capital cost with scalability. Small projects can use the flow cell dongle ("Flongle") while large projects can rely on MinION flow cells that can be stopped and re-used after collecting sufficient data for a given project.

Acute kidney injury following hepatectomy and its impact on long-term survival for patients with hepatocellular carcinoma

Background

Acute kidney injury (AKI) is increasingly being recognized after hepatectomy. This study aimed to identify factors predicting its occurrence and its impact on long-term outcome among patients with hepatocellular carcinoma (HCC).

Methods

This was a retrospective analysis of the incidence of AKI, factors predicting its occurrence, and its impact on patients undergoing hepatectomy between September 2007 and December 2018. A subgroup analysis included patients with histologically proven HCC.

Results

The incidence of AKI was 9.2 per cent in 930 patients. AKI was associated with increased mortality, morbidity, posthepatectomy liver failure (PHLF), and a longer hospital stay. On multivariable analysis, study period December 2013 to December 2018, diabetes mellitus, mean intraoperative BP below 72.1 mmHg, operative blood loss exceeding 377ml, high Model for End-Stage Liver Disease (MELD) score, and PHLF were predictive factors for AKI. Among 560 patients with HCC, hypertension, BP below 76.9 mmHg, blood loss greater than 378ml, MELD score, and PHLF were predictive factors. The 1-, 3-, and 5-year overall survival rates were 74.1, 59.2, and 51.6 per cent respectively for patients with AKI, and 91.8, 77.9, and 67.3 per cent for those without AKI. Corresponding 1-, 3-, and 5-year disease-free survival rates were 56.9, 42.3, and 35.4 per cent respectively in the AKI group, and 71.7, 54.5, and 46.2 per cent in the no-AKI group. AKI was an independent predictor of survival in multivariable analysis.

Conclusion

AKI is associated with longer hospital stay, and higher morbidity and mortality rates. It is also associated with shorter long-term survival among patients with HCC. To avoid AKI, control of blood loss and maintaining a reasonable BP (72–77 mmHg) during hepatectomy is important.