Improving reporting standards for phenotyping algorithm in biomedical research: 5 fundamental dimensions

INTRODUCTION

Phenotyping algorithms enable the interpretation of complex health data and definition of clinically relevant phenotypes; they have become crucial in biomedical research. However, the lack of standardization and transparency inhibits the cross-comparison of findings among different studies, limits large scale meta-analyses, confuses the research community, and prevents the reuse of algorithms, which results in duplication of efforts and the waste of valuable resources.

RECOMMENDATIONS

Here, we propose five independent fundamental dimensions of phenotyping algorithms-complexity, performance, efficiency, implementability, and maintenance-through which researchers can describe, measure, and deploy any algorithms efficiently and effectively. These dimensions must be considered in the context of explicit use cases and transparent methods to ensure that they do not reflect unexpected biases or exacerbate inequities.

Use of diamond sensors for a high-flux, high-rate X-ray pass-through diagnostic

X-ray free-electron lasers (XFELs) deliver pulses of coherent X-rays on the femtosecond time scale, with potentially high repetition rates. While XFELs provide high peak intensities, both the intensity and the centroid of the beam fluctuate strongly on a pulse-to-pulse basis, motivating high-rate beam diagnostics that operate over a large dynamic range. The fast drift velocity, low X-ray absorption and high radiation tolerance properties of chemical vapour deposition diamonds make these crystals a promising candidate material for developing a fast (multi-GHz) pass-through diagnostic for the next generation of XFELs. A new approach to the design of a diamond sensor signal path is presented, along with associated characterization studies performed in the XPP endstation of the LINAC Coherent Light Source (LCLS) at SLAC. Qualitative charge collection profiles (collected charge versus time) are presented and compared with those from a commercially available detector. Quantitative results on the charge collection efficiency and signal collection times are presented over a range of approximately four orders of magnitude in the generated electron-hole plasma density.

The new NHGRI-EBI Catalog of published genome-wide association studies (GWAS Catalog)

The NHGRI-EBI GWAS Catalog has provided data from published genome-wide association studies since 2008. In 2015, the database was redesigned and relocated to EMBL-EBI. The new infrastructure includes a new graphical user interface (www.ebi.ac.uk/gwas/), ontology supported search functionality and an improved curation interface. These developments have improved the data release frequency by increasing automation of curation and providing scaling improvements. The range of available Catalog data has also been extended with structured ancestry and recruitment information added for all studies. The infrastructure improvements also support scaling for larger arrays, exome and sequencing studies, allowing the Catalog to adapt to the needs of evolving study design, genotyping technologies and user needs in the future.

X-ray power and yield measurements at the refurbished Z machine

Advancements have been made in the diagnostic techniques to measure accurately the total radiated x-ray yield and power from z-pinch implosion experiments at the Z machine with high accuracy. The Z machine is capable of outputting 2 MJ and 330 TW of x-ray yield and power, and accurately measuring these quantities is imperative. We will describe work over the past several years which include the development of new diagnostics, improvements to existing diagnostics, and implementation of automated data analysis routines. A set of experiments on the Z machine were conducted in which the load and machine configuration were held constant. During this shot series, it was observed that the total z-pinch x-ray emission power determined from the two common techniques for inferring the x-ray power, a Kimfol filtered x-ray diode diagnostic and the total power and energy diagnostic, gave 449 TW and 323 TW, respectively. Our analysis shows the latter to be the more accurate interpretation. More broadly, the comparison demonstrates the necessity to consider spectral response and field of view when inferring x-ray powers from z-pinch sources.

The NHGRI GWAS Catalog, a curated resource of SNP-trait associations

The National Human Genome Research Institute (NHGRI) Catalog of Published Genome-Wide Association Studies (GWAS) Catalog provides a publicly available manually curated collection of published GWAS assaying at least 100,000 single-nucleotide polymorphisms (SNPs) and all SNP-trait associations with P <1 × 10(-5). The Catalog includes 1751 curated publications of 11 912 SNPs. In addition to the SNP-trait association data, the Catalog also publishes a quarterly diagram of all SNP-trait associations mapped to the SNPs' chromosomal locations. The Catalog can be accessed via a tabular web interface, via a dynamic visualization on the human karyotype, as a downloadable tab-delimited file and as an OWL knowledge base. This article presents a number of recent improvements to the Catalog, including novel ways for users to interact with the Catalog and changes to the curation infrastructure.

The NHGRI GWAS Catalog, a curated resource of SNP-trait associations

The National Human Genome Research Institute (NHGRI) Catalog of Published Genome-Wide Association Studies (GWAS) Catalog provides a publicly available manually curated collection of published GWAS assaying at least 100,000 single-nucleotide polymorphisms (SNPs) and all SNP-trait associations with P <1 × 10(-5). The Catalog includes 1751 curated publications of 11 912 SNPs. In addition to the SNP-trait association data, the Catalog also publishes a quarterly diagram of all SNP-trait associations mapped to the SNPs' chromosomal locations. The Catalog can be accessed via a tabular web interface, via a dynamic visualization on the human karyotype, as a downloadable tab-delimited file and as an OWL knowledge base. This article presents a number of recent improvements to the Catalog, including novel ways for users to interact with the Catalog and changes to the curation infrastructure.

Learning Disability Liaison Nursing Services in south-east Scotland: a mixed-methods impact and outcome study

BACKGROUND

There have been significant concerns about the care and treatment of people with intellectual disabilities (ID) when attending general hospitals, which have led to inquiries that highlight service and systems failures. One response has been the development of Learning Disability Liaison Nursing (LDLN) Services across the UK that aim to ensure that additional, specialist support is available for patients, their carers and general healthcare professionals.

METHODS

A mixed-methods study to investigate the impact of LDLN Services across four Scottish NHS boards was undertaken. In total, 323 referrals made over 18 months were analysed along with qualitative data drawn from interviews and focus groups with a sample of 85 participants including patients with ID (n = 5), carers (n = 16), primary care healthcare professionals (n = 39) and general hospital professionals (n = 19) and learning disability liaison nurses (n = 6).

RESULTS

The referral patterns to the four liaison nursing services closely matched the known health needs of adults with ID, with common admissions being due to neurological, respiratory and gastrointestinal issues. The LDLN role was seen to be complex and impacted on three key areas: (i) clinical patient care; (ii) education and practice development; and (iii) strategic organisational developments. Specific patient outcomes were linked to issues relating to capacity and consent to treatment, fostering person-centred adjustments to care, augmenting communication and the liaison nurses acting as positive role models and ambassadors for people with ID.

CONCLUSIONS

The LDLN Services were valued by stakeholders by achieving person-centred outcomes. With their expert knowledge and skills, the liaison nurses had an important role in developing effective systems and processes within general hospital settings. The outcomes highlight the importance of supporting and promoting LDLN Services and the challenges in delivering the multifaceted elements of the role. There is a need to take account of the complex and multidimensional nature of the LDLN role and the possible tensions between achieving clinical outcomes, education and practice developments and organisational strategic initiatives.

Professional issues associated with the role of the research nurse

This article presents the findings of two studies undertaken during 2002 and 2003 that aimed to explore a range of professional issues facing research nurses. The results indicated that the position of research nurses is often complex because of a combination of contractual and accountability arrangements. This position can be intensified by feelings of isolation, a lack of professional support and limited specific educational opportunities. Experienced research nurses are often highly skilled in terms of their specialist clinical knowledge, and have a comprehensive understanding of all aspects of the research process, including methodological, ethical and practical issues.

Efficacy of mefloquine and sulfadoxine-pyrimethamine for the treatment of uncomplicated Plasmodium falciparum infection in Machinga District, Malawi, 1998

In response to the spread of chloroquine-resistant Plasmodium falciparum, Malaŵi changed its first-line antimalarial drug in 1993 from chloroquine to sulfadoxine-pyrimethamine (SP). Surveillance data has suggested that resistance to SP may be increasing. We compared the efficacy of SP with a potential successor, mefloquine (MQ). By use of a modified World Health Organization in vivo protocol, children infected with P. falciparum were randomized to receive SP (sulfadoxine 25 mg/kg) or MQ (15 mg/kg). We observed combined RII and RIII parasitologic failures of 20.0 and 22.0% in the SP and MQ arms, respectively. Among those in the MQ arm, the relative hazard of failing with a Day 2 drug level < 500 ng/mL was 10.6 times higher than those with levels > or = 500 ng/mL. Given the decreased efficacy of the first-line antimalarial drug and the high failure rates of MQ at this lower dosage, Malaŵi should consider assessing the efficacy and feasibility of alternative drugs to treat uncomplicated falciparum malaria.

A simple effective technique for performing intraoperative cholangiography

This simple, effective technique for performing intraoperative cholangiography uses a smooth-tipped side port cannula that is easily threaded into the cystic duct. Performance of intraoperative cholangiography is expedited by this method and artifacts commonly produced during cholangiography are avoided.