Publisher Correction: Real-Time Selective Sequencing with RUBRIC: Read Until with Basecall and Reference-Informed Criteria.

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

Real-Time Selective Sequencing with RUBRIC: Read Until with Basecall and Reference-Informed Criteria.

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.

A novel sequencing-based vaginal health assay combining self-sampling, HPV detection and genotyping, STI detection, and vaginal microbiome analysis.

The composition of the vaginal microbiome, including both the presence of pathogens involved in sexually transmitted infections (STI) as well as commensal microbiota, has been shown to have important associations for a woman's reproductive and general health. Currently, healthcare providers cannot offer comprehensive vaginal microbiome screening, but are limited to the detection of individual pathogens, such as high-risk human papillomavirus (hrHPV), the predominant cause of cervical cancer. There is no single test on the market that combines HPV, STI, and microbiome screening.

Differential and convergent utilization of autophagy components by positive-strand RNA viruses.

Many viruses interface with the autophagy pathway, a highly conserved process for recycling cellular components. For three viral infections in which autophagy constituents are proviral (poliovirus, dengue, and Zika), we developed a panel of knockouts (KOs) of autophagy-related genes to test which components of the canonical pathway are utilized. We discovered that each virus uses a distinct set of initiation components; however, all three viruses utilize autophagy-related gene 9 (ATG9), a lipid scavenging protein, and LC3 (light-chain 3), which is involved in membrane curvature.

Self-Sampling for Human Papillomavirus Testing: Increased Cervical Cancer Screening Participation and Incorporation in International Screening Programs.

In most industrialized countries, screening programs for cervical cancer have shifted from cytology (Pap smear or ThinPrep) alone on clinician-obtained samples to the addition of screening for human papillomavirus (HPV), its main causative agent. For HPV testing, self-sampling instead of clinician-sampling has proven to be equally accurate, in particular for assays that use nucleic acid amplification techniques. In addition, HPV testing of self-collected samples in combination with a follow-up Pap smear in case of a positive result is more effective in detecting precancerous lesions than a Pap smear alone.

Systematic and stochastic influences on the performance of the MinION nanopore sequencer across a range of nucleotide bias.

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.

A smartphone-based diagnostic platform for rapid detection of Zika, chikungunya, and dengue viruses.

Current multiplexed diagnostics for Zika, dengue, and chikungunya viruses are situated outside the intersection of affordability, high performance, and suitability for use at the point-of-care in resource-limited settings. Consequently, insufficient diagnostic capabilities are a key limitation facing current Zika outbreak management strategies. Here we demonstrate highly sensitive and specific detection of Zika, chikungunya, and dengue viruses by coupling reverse-transcription loop-mediated isothermal amplification (RT-LAMP) with our recently developed quenching of unincorporated amplification signal reporters (QUASR) technique.

A Genome-Wide RNA Interference Screen Identifies a Role for Wnt/β-Catenin Signaling during Rift Valley Fever Virus Infection.

Unlabelled: Rift Valley fever virus (RVFV) is an arbovirus within the Bunyaviridae family capable of causing serious morbidity and mortality in humans and livestock. To identify host factors involved in bunyavirus replication, we employed genome-wide RNA interference (RNAi) screening and identified 381 genes whose knockdown reduced infection. The Wnt pathway was the most represented pathway when gene hits were functionally clustered.

The pitfalls of prescribing for family and friends.

In most of Australia there is no legislation prohibiting medical practitioners from prescribing for family and friends. In South Australia it is prohibited to prescribe Schedule 8 drugs for family members unless it is a verifiable emergency. The Medical Board of Australia states medical practitioners should avoid providing medical care to anyone with whom they have a close personal relationship.

Escape of non-enveloped virus from intact cells.

How do viruses spread from cell to cell? Enveloped viruses acquire their surrounding membranes by budding. If a newly enveloped virus has budded through the plasma membrane, it finds itself outside the cell immediately. If it has budded through the bounding membrane of an internal compartment such as the ER, the virus finds itself in the lumen, from which it can exit the cell via the conventional secretion pathway.

Patients' use of social media: e-rating of doctors.

Background: Patients are increasingly posting online reviews about their medical care, including rating their doctors.

Objective: This article discusses patients' use of social media to comment on and 'rate' their medical care, with a particular focus on what a general practitioner (GP) can do about a negative online review.

Discussion: The vast majority of online reviews about doctors are positive.

Nonlytic spread of naked viruses.

How do viruses spread from cell to cell? Enveloped viruses acquire their surrounding membranes by budding: either through the plasma membrane or an internal membrane of infected cells. Thus, a newly budded enveloped virus finds itself either in the extracellular milieu or in a lumenal compartment from which it can exit the cell by conventional secretion. On the other hand, naked viruses such as poliovirus, nodavirus, adenovirus, and SV40 lack an external membrane.

How to write a medico-legal report.

Background: The preparation and provision of medico-legal reports by the treating doctor is an inevitable but sometimes unwelcome part of general practice.

Objective: This article outlines the steps involved in preparing a 'good' medico-legal report, including some of the common pitfalls to avoid.

Discussion: General practitioners play an important role in providing medico-legal reports about their patients for a wide variety of purposes.

The ins and outs of viral infection: keystone meeting review.

Newly observed mechanisms for viral entry, assembly, and exit are challenging our current understanding of the replication cycle of different viruses. To address and better understand these mechanisms, a Keystone Symposium was organized in the snowy mountains of Colorado ("The Ins and Outs of Viral Infection: Entry, Assembly, Exit, and Spread"; 30 March-4 April 2014, Beaver Run Resort, Breckenridge, Colorado, organized by Karla Kirkegaard, Mavis Agbandje-McKenna, and Eric O. Freed).

Nonlytic viral spread enhanced by autophagy components.

The cell-to-cell spread of cytoplasmic constituents such as nonenveloped viruses and aggregated proteins is usually thought to require cell lysis. However, mechanisms of unconventional secretion have been described that bypass the secretory pathway for the extracellular delivery of cytoplasmic molecules. Components of the autophagy pathway, an intracellular recycling process, have been shown to play a role in the unconventional secretion of cytoplasmic signaling proteins.

Advance care planning.

Background: Good Medical Practice: A Code of Conduct for Doctors in Australia states that in caring for patients towards the end of their life, good medical practice involves facilitating advance care planning.

Objective: This article discusses the role of advance care planning in end-of-life care, with an emphasis on the ethical and legal framework for advance care directives.

Discussion: There has been an increased focus on advanced care planning and advance care directives in Australia, partly driven by the ageing population and technological advances, as well as the principle of patient-centred care.

Genetic testing: medico-legal issues.

Background: The availability and frequency of genetic testing is increasing. Genetic testing poses some unique ethical and legal issues for medical practitioners because of the potential to identify genetic variants that carry implications for the risk of disease in the future for the patient and their relatives. The regulatory framework within which genetic testing is provided in Australia is also changing.

Managing professional boundaries.

The maintenance of boundaries in the doctor-patient relationship is central to good medical practice and the appropriate care of patients. This article examines the nature of boundaries in medical practice and outlines some strategies to minimise the risk of a boundary violation.

The duty of GPs to follow up patients.

A recent Supreme Court of Victoria judgement examined the legal obligations of a general practitioner to recall a patient who does not undergo a test that has been recommended by the GP or to return for a consultation, despite being asked to do so.

An intellectual property sharing initiative in agricultural biotechnology: development of broadly accessible technologies for plant transformation.

The Public Intellectual Property Resource for Agriculture (PIPRA) was founded in 2004 by the Rockefeller Foundation in response to concerns that public investments in agricultural biotechnology benefiting developing countries were facing delays, high transaction costs and lack of access to important technologies due to intellectual property right (IPR) issues. From its inception, PIPRA has worked broadly to support a wide range of research in the public sector, in specialty and minor acreage crops as well as crops important to food security in developing countries. In this paper, we review PIPRA's work, discussing the failures, successes, and lessons learned during its years of operation.

Child abuse - mandatory reporting requirements.

All Australian states and territories have legislation that requires medical practitioners to report cases of child abuse to the appropriate child protection service. This article outlines the obligations of medical practitioners to report child abuse and highlights the differences that exist in the legislative requirements in each state and territory.

How to complete a death certificate - a guide for GPs.

This article discusses some questions that frequently arise in general practice with regard to the completion of death certificates.

Capacity to consent to treatment.

A competent adult patient has an ethical and legal right to give, or withhold, consent to an examination, investigation or treatment. Depending on the nature and complexity of an intervention, a patient with an intellectual disability may be capable of consenting to their own medical treatment. In circumstances in which an adult patient does not have the capacity to consent, there is specific guardianship legislation enacted in each state and territory which provides for valid consent by a substitute decision maker.