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The Oxford MinION, the first commercial nanopore sequencer, is also the first to implement molecule-by-molecule real-time selective sequencing or “Read Until”. As DNA transits a MinION nanopore, real-time pore current data can be accessed and analyzed to provide active feedback to that pore. Fragments of interest are sequenced by default, while DNA deemed non-informative is rejected by reversing the pore bias to eject the strand, providing a novel means of background depletion and/or target enrichment. In contrast to the previously published pattern-matching Read Until approach, our RUBRIC method is the first example of real-time selective sequencing where on-line basecalling enables alignment against conventional nucleic acid references to provide the basis for sequence/reject decisions. We evaluate RUBRIC performance across a range of optimizable parameters, apply it to mixed human/bacteria and CRISPR/Cas9-cut samples, and present a generalized model for estimating real-time selection performance as a function of sample composition and computing configuration.

Objectives Literature on dermatology outpatient demographic and clinical data is limited, and the few studies on this topic are mainly conducted overseas, with medical systems and case mix different to Australia. This study presents demographic data relating to dermatology public outpatient referrals to a tertiary hospital in Brisbane, Australia, and determines what additional structured data should be collected to formulate and evaluate initiatives to address service issues such as referral quality, triage process and wait times. Methods A four-year retrospective audit was undertaken, summarising all referrals (n = 7140) and clinical dermatology encounters (n = 53 844) between January 2016 and December 2019 at Princess Alexandra Hospital (PAH), the largest hospital in Metro South Health (MSH), serving a population of one million. PAH has one of the two largest public dermatology clinics in Queensland and is the only dermatology service within MSH. Results Patient demographic data, wait time by triage category, referral rates over time and encounter durations were collected. Structured diagnostic data (e.g. ICD-10 coding) of the provisional diagnosis, comorbidities, medications and the final diagnosis are not collected in a structured format and would be a valuable addition. Conclusions The clinical burden of public dermatology is increasing. Both collection and analysis of structured data pertaining to the referrals and encounters are important to help formulate, implement and evaluate initiatives that aim to improve health service provision in this area.

Background Scabies is a neglected tropical disease of the skin, causing severe itching, stigmatizing skin lesions and systemic complications. Since 2015, the DerMalawi project provide an integrated skin diseases clinics and Tele-dermatology care in Malawi. Clinic based data suggested a progressive increase in scabies cases observed. To better identify and treat individuals with scabies in the region, we shifted from a clinic-based model to a community based outreach programme. Methodology/Principal findings From May 2015, DerMalawi project provide integrated skin diseases and Tele-dermatological care in the Nkhotakota and Salima health districts in Malawi. Demographic and clinical data of all patients personally attended are recorded. Due to a progressive increase in the number of cases of scabies the project shifted to a community-based outreach programme. For the community outreach activities, we conducted three visits between 2018 to 2019 and undertook screening in schools and villages of Alinafe Hospital catchment area. Treatment was offered for all the cases and school or household contacts. Scabies increased from 2.9% to 39.2% of all cases seen by the DerMalawi project at clinics between 2015 to 2018. During the community-based activities approximately 50% of the population was assessed in each of three visits. The prevalence of scabies was similar in the first two rounds, 15.4% (2392) at the first visit and 17.2% at the second visit. The prevalence of scabies appeared to be lower (2.4%) at the third visit. The prevalence of impetigo appeared unchanged and was 6.7% at the first visit and 5.2% at the final visit. Conclusions/Significance Prevalence of scabies in our setting was very high suggesting that scabies is a major public health problem in parts of Malawi. Further work is required to more accurately assess the burden of disease and develop appropriate public health strategies for its control., Author summary Scabies is an infestation of the skin caused by a mite. There is limited data on how common scabies is in sub-Saharan Africa, including Malawi. The DerMalawi project has been providing care for dermatological conditions in rural Malawi since 2015. Between 2015 and 2018 we observed an increase in patients with scabies attending for treatment. In response the project shifted from providing care at clinics to an approach using community-based outreach. Between 2018 and 2019 we conducted community-based activities on three occasions in an area of approximately 30,000 individuals. The DerMalawi team visited schools and villages to identify and treat cases of scabies and their contacts. We were able to examine about 50% of the population on each visit. Initially a large proportion of the population had scabies (15%) and this was similar during our second community survey. At our third survey this appeared to have decreased to 2% but it is difficult for us to know if this is because of treatment given in the previous rounds. Scabies is a major problem in rural populations in Malawi and public health strategies are needed to reduce the disease burden.

The COVID-19 pandemic has required health services worldwide to adapt to dramatically changing healthcare needs and risks across all medical specialties. In the dermatology department at Princess Alexandra Hospital, Brisbane, Australia, we developed and implemented a teledermatology system with 1 week's notice to help reduce infection risk bidirectionally, while saving patients many hours of travel and waiting time with acceptable technological substitutes for the clinical encounters. In this study, we report the efficacy and tolerability of our telephone consultation and store and forward imaging system, including patient experience from validated survey data. Our design, implementation and usage of a remote-default system provides experience and lessons to draw upon in developing future telemedicine systems to address dermatology service maldistribution – an issue affecting large areas of Australia – as well as preparedness for future infection mitigation requirements.

Immunotherapies and targeted therapies have shown significant benefits for melanoma survival in the clinical trial setting. Much less is known about the characteristics and associated outcomes of those receiving such therapies in real-world settings. This study describes the characteristics of patients with advanced melanoma receiving immuno- and/or targeted therapies in a real-world setting. This prospective cohort study enrolled participants aged >18 years, diagnosed with advanced melanoma and currently undergoing immuno- and/or targeted therapies outside a clinical trial for follow-up with three-dimensional (3D) total-body imaging. Participants (n = 41) had a mean age of 62 years (range 29–86), 26 (63%) were male and the majority (n = 26, 63%) had ≥2 comorbidities. After a median of 39 months (range 1–52) follow-up, 59% (n = 24/41) of participants were alive. Despite multiple co-morbidities, the survival of participants with advanced melanoma treated using immuno- and/or targeted therapies was similar or better in our real-world setting compared to those treated in clinical trials using similar therapies. Larger studies powered to evaluate phenotypic and socio-economic characteristics, as well as specific comorbidities associated with survival in a real-world setting, are required to help determine those who will most benefit from immuno- and/or targeted therapies.

Background: Cherry angiomas are common benign vascular skin lesions of unknown aetiology, found largely on the trunk. However, their exact anatomic distribution besides their truncal predisposition, and how they manifest in the general population, has not been characterised. Methods: Three-dimensional (3D) total body imaging was obtained from 163 adult participants of a general population cohort study in Brisbane, Australia. Demographic, phenotypic, and sun behaviour characteristics were collected using a standard questionnaire along with history of melanoma and keratinocyte cancers. Cherry angiomas were identified using an automated classification algorithm with a sensitivity of 87% and a specificity of 99%, developed specifically for this study population. Results: The 3D total body images of 163 participants were analysed. Participants had a median age of 57 years and 61% were male. On average, males had more angiomas than females (median of 16 vs. 12) and the number and size of cherry angiomas increased with age. In addition to male sex and age, an increase in angiomas was associated with Caucasian ancestry other than British/Irish only, fair skin colour opposed to medium/olive, having green/hazel eyes compared to blue/grey, and personal history of melanoma. The most common site for cherry angiomas was the front trunk, followed by the back. Interestingly, although males had more angiomas overall, females had more angiomas on the legs. Conclusion: Describing the distribution of cherry angiomas by body site is an important step towards further understanding of the aetiology of angiomas. While personal history of melanoma is associated with an increased number of cherry angiomas, whether this association is prognostic, co-occurs with development of melanoma, or is merely fortuitous requires further investigation.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

In ultralow Pu analyses, the gold standard is thermal ionization mass spectrometry (TIMS), which requires pure sources to achieve its performance. This purity is achieved through step-wise purifications. In this work single, anion-exchange beads were trapped in the tubing to allow for dynamic solution cycling over the surface of the beads to improve the rates of metal complex uptake. Rates of Pu sorption on single ∼900 μm SIR-1200 and ∼620 μm Reillex-HPQ beads were determined for single beads trapped in a tube with syringe pump driven dynamic solution cycling over the bead, improving sorption and desorption rates. A static control was used as a comparison. Using 238Pu to enable facile activity-based measurements, rates were determined by measuring the residual Pu after contact with beads using liquid scintillation analysis (LSA) for fixed periods of time. Syringe pump driven dynamic solution cycling results in ∼5 and ∼15-fold improvements in the sorption rates for SIR-1200 and Reillex-HPQ. Impacts on desorption were also examined.

Emerging sequencing technologies are allowing us to characterize environmental, clinical and laboratory samples with increasing speed and detail, including real-time analysis and interpretation of data. One example of this is being able to rapidly and accurately detect a wide range of pathogenic organisms, both in the clinic and the field. Genomes can have radically different GC content however, such that accurate sequence analysis can be challenging depending upon the technology used. Here, we have characterized the performance of the Oxford MinION nanopore sequencer for detection and evaluation of organisms with a range of genomic nucleotide bias. We have diagnosed the quality of base-calling across individual reads and discovered that the position within the read affects base-calling and quality scores. Finally, we have evaluated the performance of the current state-of-the-art neural network-based MinION basecaller, characterizing its behavior with respect to systemic errors as well as context- and sequence-specific errors. Overall, we present a detailed characterization the capabilities of the MinION in terms of generating high-accuracy sequence data from genomes with a wide range of nucleotide content. This study provides a framework for designing the appropriate experiments that are the likely to lead to accurate and rapid field-forward diagnostics.

Advances in molecular biology, microfluidics, and laboratory automation continue to expand the accessibility and applicability of these methods beyond the confines of conventional, centralized laboratory facilities and into point of use roles in clinical, military, forensic, and field-deployed applications. As a result, there is a growing need to adapt the unit operations of molecular biology (e.g., aliquoting, centrifuging, mixing, and thermal cycling) to compact, portable, low-power, and automation-ready formats. Here we present one such adaptation, the rotary zone thermal cycler (RZTC), a novel wheel-based device capable of cycling up to four different fixed-temperature blocks into contact with a stationary 4-microliter capillary-bound sample to realize 1-3 second transitions with steady state heater power of less than 10 W. We demonstrate the utility of the RZTC for DNA amplification as part of a highly integrated rotary zone PCR (rzPCR) system that uses low-volume valves and syringe-based fluid handling to automate sample loading and unloading, thermal cycling, and between-run cleaning functionalities in a compact, modular form factor. In addition to characterizing the performance of the RZTC and the efficacy of different online cleaning protocols, we present preliminary results for rapid single-plex PCR, multiplex short tandem repeat (STR) amplification, and second strand cDNA synthesis.