Automated reanalysis application to assist in detecting novel gene-disease associations after genome sequencing.

PURPOSE: This study aimed to investigate whether a bioinformatics application can streamline genome reanalysis and yield new diagnoses for patients with rare diseases. METHODS: We developed TierUp to identify variants in new disease genes for unresolved rare disease cases recruited to the 100,000 Genomes Project, all of whom underwent genome sequencing. TierUp uses the NHS Genomic Medicine Service bioinformatics infrastructure by securely accessing case details from the Clinical Interpretation Portal application programming interface and by querying the curated PanelApp database for novel gene-disease associations. We applied TierUp to 948 cases, and a subset of variants were reclassified according to the American College of Medical Genetics and Genomics/Association of Molecular Pathology guidelines. RESULTS: A rare form of spondylometaphyseal dysplasia was diagnosed through TierUp reanalysis, and an additional 4 variants have been reported to date. From a total of 564,441 variants across patients, TierUp highlighted 410 variants present in novel disease genes in under 77 minutes, successfully expediting an important reanalysis strategy. CONCLUSION: TierUp supports claims that automation can reduce the time taken to reanalyze variants and increase the diagnostic yield from molecular testing. Clinical services should leverage bioinformatics expertise to develop tools that enable routine reanalysis. In addition, services must also explore the ethical, legal, and health economic considerations raised by automation.

Estimating uncertainty for the instrument transfer function measurement of 3D scanners.

Spatial resolution is an important aspect of many optical instruments. It is defined as the ability of surface-topography measuring instruments to distinguish closely spaced surface features. Following convention, spatial resolution can be defined as the spatial frequency response of the instrument, known as the instrument transfer function (ITF). In this paper, we describe the step-artifact approach for estimating the ITF for 3D scanners, discuss step artifact characterization and validation approaches, and present a method to estimate the combined uncertainty of the ITF measurement. The approach is demonstrated using the EinScan-Pro 3D scanner. A step artifact is used for the measurement that takes advantage of the cleaving properties of a single-side polished silicon wafer. The uncertainty analysis includes simulations to estimate the contribution due to influencing factors such as the alignment of the step artifact to the measurement axis, the diffuse versus specular scattering properties of the step edge, and various processing parameter choices.

A global perspective on evolving bioinformatics and data science training needs.

Bioinformatics is now intrinsic to life science research, but the past decade has witnessed a continuing deficiency in this essential expertise. Basic data stewardship is still taught relatively rarely in life science education programmes, creating a chasm between theory and practice, and fuelling demand for bioinformatics training across all educational levels and career roles. Concerned by this, surveys have been conducted in recent years to monitor bioinformatics and computational training needs worldwide. This article briefly reviews the principal findings of a number of these studies. We see that there is still a strong appetite for short courses to improve expertise and confidence in data analysis and interpretation; strikingly, however, the most urgent appeal is for bioinformatics to be woven into the fabric of life science degree programmes. Satisfying the relentless training needs of current and future generations of life scientists will require a concerted response from stakeholders across the globe, who need to deliver sustainable solutions capable of both transforming education curricula and cultivating a new cadre of trainer scientists.

Problem-based learning in clinical bioinformatics education: Does it help to create communities of practice?

We have now reached the genomics era within medicine; genomics is being used to personalise treatment, make diagnoses, prognoses, and predict adverse outcomes resulting from treatment with certain drugs. Genomic data is now abundant in healthcare, and the newly created profession of clinical bioinformaticians are responsible for its analysis. In the United Kingdom, clinical bioinformaticians are trained within a 3-year programme, integrating a work-based placement with a part-time Master's degree. As this profession is still developing, trainees can feel isolated from their peers whom are located in other hospitals and can find it difficult to gain the mentorship that they require to complete their training. Building strong networks or communities of practice (CoPs) and allowing sharing of knowledge and experiences is one solution to addressing this isolation. Within the Master's delivered at the University of Manchester, we have integrated group-centred problem-based learning (PBL) using real clinical case studies worked on during each course unit. This approach is combined with a flipped style of teaching providing access to online content in our Virtual Learning Environment before the course. The face-to-face teaching is used to focus on the application of the students' knowledge to clinical case studies. In this study, we conducted semistructured interviews with 8 students, spanning 3 cohorts of students. We evaluated the effectiveness of this style of teaching and whether it had contributed to the formation of CoPs between our students. Our findings demonstrated that this style of teaching was preferred by our students to a more traditional lecture-based format and that the problem-based learning approach enabled the formation of CoPs within these cohorts. These CoPs are valuable in the development of this new profession and assist with the production of new guidelines and policies that are helping to professionalise this new group of healthcare scientists.

A multi-modal relative spatial access assessment approach to measure spatial accessibility to primary care providers.

Two-step floating catchment area (2SFCA) methods that account for multiple transportation modes provide more realistic accessibility representation than single-mode methods. However, the use of the impedance coefficient in an impedance function (e.g., Gaussian function) introduces uncertainty to 2SFCA results. This paper proposes an enhancement to the multi-modal 2SFCA methods through incorporating the concept of a spatial access ratio (SPAR) for spatial access measurement. SPAR is the ratio of a given place's access score to the mean of all access scores in the study area. An empirical study on spatial access to primary care physicians (PCPs) in the city of Albuquerque, NM, USA was conducted to evaluate the effectiveness of SPAR in addressing uncertainty introduced by the choice of the impedance coefficient in the classic Gaussian impedance function. We used ESRI StreetMap Premium and General Transit Specification Feed (GTFS) data to calculate the travel time to PCPs by car and bus. We first generated two spatial access scores-using different catchment sizes for car and bus, respectively-for each demanding population location: an accessibility score for car drivers and an accessibility score for bus riders. We then computed three corresponding spatial access ratios of the above scores for each population location. Sensitivity analysis results suggest that the spatial access scores vary significantly when using different impedance coefficients (p < 0.05); while SPAR remains stable (p = 1). Results from this paper suggest that a spatial access ratio can significantly reduce impedance coefficient-related uncertainties in multi-modal 2SFCA methods.

Validity of the instrument transfer function for fringe projection metrology.

When fringe projection profilometry is used for measuring texture on rough surfaces, the measurement resolution is subject to the spatial frequency response of the instrument. The instrument transfer function (ITF) is a good metric to quantify this property. A valid ITF analysis requires the system to be linear. In this paper, we investigate the validity of using ITF to characterize the spatial resolution of a fringe projection system. Approximate linearity is shown through a mathematical analysis and simulation. We also demonstrate a practical method for measuring ITF using a stepped surface. The measured ITF is compared with an ITF prediction, which is simulated with a theoretical model.

Life cycle of Hepatozoon affluomaloti sp. n. (Apicomplexa: Haemogregarinidae) in crag lizards (Sauria: Cordylidae) and in culicine mosquitoes from South Africa.

A new haemogregarine species Hepatozoon affluomaloti sp. n. is described from erythrocytes in the peripheral blood of crag lizards Pseudocordylus melanotus (Smith) and Pseudocordylus subviridis (Smith) (Sauria: Cordylidae) from mountainous regions in the Eastern Free State, South Africa. This species can be distinguished from all other congeners based on its large size, staining properties and life cycle development in its vector, Culex (Afroculex) lineata (Theobald) (Diptera: Culicidae). Mature gamonts stain mostly uniformly pinkish-purple with Giemsa, sometimes containing darker azurophilic granules anterior and posterior to the nucleus. The reflexed posterior extremity of the gamont stage sometimes stains slightly deeper purple and the nucleus is dense and placed in the posterior third of the parasite body. Merogonic stages of this haemogregarine occur in the liver tissues of P. melanotus with dizoic meronts. Macromeronts contains 2-7 macromerozoites and micromeronts contains 9-24 micromerozoites. Sporogonic developmental stages found in the proposed final host and vector, C. lineata, include large oocysts, measuring 54 × 48 µm on average. Sporulating oocysts with 8 nuclei are present in mosquitoes 6-7 days post-feeding on infected lizards. Sporocysts with mature sporozoites measure 31.0 × 21.8 µm on average and each contains 2-8 large sporozoites. It is suggested that transmission of infective sporozoites is achieved through predation of lizards on mosquitoes.

3D surface mapping of freeform optics using wavelength scanning lateral shearing interferometry.

Freeform optics have emerged as promising components in diverse applications due to the potential for superior optical performance. There are many research fields in the area ranging from fabrication to measurement, with metrology being one of the most challenging tasks. In this paper, we describe a new variant of lateral shearing interferometer with a tunable laser source that enables 3D surface profile measurements of freeform optics with high speed, high vertical resolution, large departure, and large field-of-view. We have verified the proposed technique by comparing our measurement result with that of an existing technique and measuring a representative freeform optic.

Reassignment of the land tortoise haemogregarine Haemogregarina fitzsimonsi Dias 1953 (Adeleorina: Haemogregarinidae) to the genus Hepatozoon Miller 1908 (Adeleorina: Hepatozoidae) based on parasite morphology, life cycle and phylogenetic analysis of 18S rDNA sequence fragments.

SUMMARY Research was undertaken to clarify the true taxonomic position of the terrestrial tortoise apicomplexan, Haemogregarina fitzsimonsi (Dias, 1953). Thin blood films were screened from 275 wild and captive South African tortoises of 6 genera and 10 species between 2009-2011. Apicomplexan parasites within films were identified, with a focus on H. fitzsimonsi. Ticks from wild tortoises, especially Amblyomma sylvaticum and Amblyomma marmoreum were also screened, and sporogonic stages were identified on dissection of adult ticks of both species taken from H. fitzsimonsi infected and apparently non-infected tortoises. Parasite DNA was extracted from fixed, Giemsa-stained tortoise blood films and from both fresh and fixed ticks, and PCR was undertaken with two primer sets, HEMO1/HEMO2, and HepF300/HepR900, to amplify parasite 18S rDNA. Results indicated that apicomplexan DNA extracted from tortoise blood films and both species of tick had been amplified by one or both primer sets. Haemogregarina  fitzsimonsi 18S rDNA sequences from tortoise blood aligned with those of species of Hepatozoon, rather than those of species of Haemogregarina or Hemolivia. It is recommended therefore that this haemogregarine be re-assigned to the genus Hepatozoon, making Hepatozoon fitzsimonsi (Dias, 1953) the only Hepatozoon known currently from any terrestrial chelonian. Ticks are its likely vectors.

جِین(Gene): A Co-Designed Smartphone App for Genetics Education and Empowerment in the Pakistani Community.

In the Pakistani/British Pakistani community in England it is quite common for people to marry close cousin relatives, which can increase the chances of certain genetic problems in their children. Families in these situations often have little knowledge of genetics and encounter difficulties accessing genetic counselling services and culturally appropriate genetics information is needed to support these families. We describe the co-design of a prototype culturally sensitive smart phone app with the British Pakistani community, to improve understanding of genetics and genetic services.

Phase I/II trial of pemetrexed plus nab-paclitaxel in advanced solid tumor patients with emphasis on non-small cell lung cancer.

BACKGROUND: Despite advances in targeted therapies, there is an ongoing need to develop new and effective cytotoxic drug combinations in non-small cell lung cancer (NSCLC). Based on preclinical demonstration of additive cytotoxicity, we evaluated the safety and efficacy of combining pemetrexed and nanoparticle albumin bound (nab) paclitaxel with a focus on NSCLC for phase II expansion. METHODS: A 3 + 3 dose-escalation design was used to determine the maximum tolerated dose (MTD) and the recommended phase II dose (RP2D). Three dose levels were tested: pemetrexed 500 mg/m(2) day 1 and nab-paclitaxel day 1 at 180, 220, & 260 mg/m(2) every 21 days. Phase II eligibility included advanced NSCLC, ≤2 line prior therapy, PS 0-1, adequate organ function. Primary endpoint for further study was response rate (RR) ≥ 25%. RESULTS: Planned dose escalation was completed without reaching the MTD. The RP2D was pemetrexed 500 mg/m(2) and nab-paclitaxel 260 mg/m(2). The phase II portion accrued 37 pts before early closure due to increasing first-line pemetrexed/platinum doublet use in non-squamous NSCLC. In 31 assessable phase II patients there were 5 partial responses, 12 stable disease, 14 progressive disease. The median overall survival was 8.8 months; progressive disease 4.4 months and disease control 15.6 months. CONCLUSIONS: Pemetrexed 500 mg/m(2) day 1 with nab-paclitaxel 260 mg/m(2) was feasible and well tolerated. The phase II component demonstrated activity in second/third-line therapy of advanced NSCLC; response rate 14% and disease control rate 46%. Treatment practice patterns of advanced NSCLC have evolved; further trials of this regimen are not planned.

Application of the random ball test for calibrating slope-dependent errors in profilometry measurements.

Optical profilometers such as scanning white light interferometers and confocal microscopes provide high-resolution measurements and are widely utilized in many fields for measuring surface topography. Slope-dependent systematic errors can be present in the measurement and can be the same order of magnitude as features on the surface to be measured. We propose a self-calibration technique, the random ball test (RBT), for calibrating slope-dependent errors of such instruments. The calibration result can be used to compensate future measurements of similar spherical geometries such as profiles of refractive microlenses. A simulation study validates the approach and shows that the RBT is effective in practical limits. We demonstrate the calibration on a 50× confocal microscope and find a surface slope-dependent bias that increases monotonically with the magnitude of the surface slope and is as large as ∼800 nm at a surface slope of 12°. The uncertainty of the calibration is smaller than the observed measurement bias and is dominated by residual random noise. Effects such as drift and ball radius uncertainty were investigated to understand their contribution to the calibration uncertainty.

Hepatozoon langii n. sp. and Hepatozoon vacuolatus n. sp. (Apicomplexa: Adele-orina: Hepatozoidae) from the crag lizard (Sauria: Cordylidae) Pseudocordylus langi from the North Eastern Drakensberg escarpment, Eastern Free State, South Africa.

Two new haemogregarine species, Hepatozoon langii n. sp. and Hepatozoon vacuolatus n. sp., are described from the pe-ripheral blood of the high altitude crag lizard, Pseudocordylus langi, collected between October 2006 and April 2009 from the North Eastern Drakensberg, Eastern Free State. Hepatozoon langii n. sp. has maturing and mature gamonts that appear encapsulated and have narrow, curved tails. Their cytoplasm stains pinkish-purple with Giemsa, while their nuclei are pur-ple stained with stranded chromatin. Mature gamonts measure 19.1 ± 1.0 (15.4-28.1) µm long by 6.2 ± 1.1 (3.5-7.9) µm wide. Hepatozoon vacuolatus n. sp. gamonts are mostly broader at one pole than the other, have bluish-pink cytoplasm characterised by distinctive rounded and oval vacuoles, and demonstrate pink granules with Giemsa staining. Nuclei stain purple and are mainly coarsely granular. Mature gamonts measure 16.5 ± 1.0 (14.7 - 17.6) µm long by 5.9 ± 1.2 (4.0 - 7.7) µm wide. Both species parasitize erythroblasts, as well as erythrocytes and can dehaemoglobinize the cytoplasm of their host cells. Hepatozoon langii n. sp occurred in the absence of H. vacuolatus n. sp., but the latter haemogregarine always formed mixed infections with the former; no stages intermediate between the two haemogregarine types were observed.

Challenging stigma and attitudes towards ECT via an educational video.

While electroconvulsive therapy (ECT) is an effective therapeutic modality for the treatment of mental illness, negative attitudes and stigma exist about ECT in the general community and even within health services. Investigating interventions that improve the attitudes of health professionals towards ECT is beneficial as this reduces stigma and increases the acceptability of ECT for consumers. The primary aim of this study was to evaluate the change in attitude of nursing graduates and medical students towards ECT by watching an educational video. The secondary aim was to compare health professional attitudes to those of the general community. An educational video was co-designed with consumers and members of the mental health Lived Experience (Peer) Workforce Team about ECT outlining the procedure, side effects, treatment considerations and lived experiences. Nursing graduates and medical students completed the ECT Attitude Questionnaire (EAQ) prior to and after watching the video. Descriptive statistics, paired samples t-tests and one sample t-tests were completed. One hundred and twenty-four participants completed pre- and post- questionnaires. Attitudes towards ECT significantly improved after watching the video. Positive responses towards ECT increased from 67.09% to 75.72%. Participants in this study reported higher positive attitudes towards ECT than members of the general public before and after watching the intervention. Results indicated that the video educational intervention was effective in improving attitudes towards ECT for nursing graduates and medical students. While the video is promising as an educational tool, further research is required to explore the use of the video in reducing stigma for consumers and carers.

Digital interventions for genomics and genetics education, empowerment, and service engagement: A systematic review.

BACKGROUND: Patient-facing digital technologies may reduce barriers to and alleviate the burden on genetics services. However, no work has synthesised the evidence for patient-facing digital interventions for genomics/genetics education and empowerment, or to facilitate service engagement more broadly. It is also unclear which groups have been engaged by digital interventions. AIM: This systematic review explores which existing patient-facing digital technologies have been used for genomics/genetics education and empowerment, or to facilitate service engagement, and for whom and for which purposes the interventions have been developed. METHODS: The review adhered to the Preferred Reporting Items for Systematic reviews and Meta-Analyses guidelines. Eight databases were searched for literature. Information was extracted into an Excel sheet and analysed in a narrative manner. Quality assessments were conducted using the Mixed Methods Appraisal Tool. RESULTS: Twenty-four studies were included, of which 21 were moderate or high quality. The majority (88%) were conducted in the United States of America or within a clinical setting (79%). More than half (63%) of the interventions were web-based tools, and almost all focussed on educating users (92%). There were promising results regarding educating patients and their families and facilitating engagement with genetics services. Few of the studies focussed on empowering patients or were community-based. CONCLUSION: Digital interventions may be used to deliver information about genetics concepts and conditions, and positively impact service engagement. However, there is insufficient evidence related to empowering patients and engaging underserved communities or consanguineous couples. Future work should focus on co-developing content with end users and incorporating interactive features.

Characterising meaningful patient and public involvement in the pharmaceutical industry research setting: a retrospective quality assessment.

OBJECTIVES: Patient and public involvement (PPI) in clinical research has a well-established infrastructure in the UK, and while there has been good progress within pharmaceutical-industry-sponsored research, further improvements are still needed. This review aims to share learnings from quality assessments of historical PPI projects within Pfizer UK to inform future projects and drive PPI progress in the pharmaceutical industry. DESIGN AND SETTING: Internal assessments of Pfizer UK PPI projects were conducted to identify all relevant projects across the medicines development continuum between 2017 and 2021. Five sample projects were developed into case studies. OUTCOME MEASURE: Retrospective quality assessments were performed using the Patient Focused Medicines Development (PFMD) Patient Engagement Quality Guidance (PEQG) tool. Recommendations for improvement were developed. RESULTS: Retrospective case study analysis and quality framework assessment revealed benefits of PPI to both Pfizer UK and to external partners, as well as challenges and learnings to improve future practice. Recommendations for improvement based on these findings focused on processes and procedures for PPI, group dynamics and diversity for PPI activities, sharing of expertise, the importance of bidirectional and timely feedback, and the use of understandable language in materials. CONCLUSIONS: PPI in medicines development is impactful and beneficial but is still being optimised in the pharmaceutical industry. Using the PFMD PEQG tool to define gaps, share learnings and devise recommendations for improvement helps to ensure that PPI is genuine and empowering, rather than tokenistic. Ultimately, these recommendations should be acted on to further embed PPI as an integral part of medicines development and health research within the pharmaceutical industry. This article includes a plain language summary in the supplement.

Novel, panzootic and hybrid genotypes of amphibian chytridiomycosis associated with the bullfrog trade.

Global amphibian declines are linked with the presence of specific, highly virulent genotypes of the emerging fungal disease chytridiomycosis caused by Batrachochytrium dendrobatidis (Bd) known as the global panzootic lineage (Bd-GPL). The global trade in amphibians for human consumption is suspected to have facilitated emergence of the disease, but evidence to support this is largely lacking. Here, we investigated the role the Lithobates catesbeianus (North American bullfrog) trade in spreading Bd genotypes by comparing strains associated with L. catesbeianus to a global panel using 36 sequenced loci from multiple chromosomal regions. Most bullfrogs were infected with Bd-GPL genotypes, but we also detected novel, highly divergent Bd genotypes (Bd-Brazil) from a live bullfrog in a US market and from native Brazilian anurans in the Atlantic Forest where bullfrogs are widely farmed. Sexual reproduction was also detected for the first time in Bd in the form of a hybrid genotype between the Bd-GPL and Bd-Brazil lineages in the Atlantic Forest. Despite the demonstration that ribosomal RNA types in Bd fail to undergo concerted evolution (over 20 sequence types may be found in a single strain), the Bd-GPL and Bd-Brazil lineages form largely separate clusters of related internal transcribed spacer (ITS) RNA sequences. Using ITS sequences, we then demonstrate the presence of Bd-Brazil in Japan, primarily on invasive L. catesbeianus. The finding that Bd is capable of sexual reproduction between panzootic and endemic genotypes emphasizes the risk of international wildlife trade as a source of additional Bd epizootics owing to hybridization.

Two-quadrant area structure function analysis for optical surface characterization.

This paper describes the use of the area structure function (SF) for the specification and characterization of optical surfaces. A two-quadrant area SF is introduced because the one-quadrant area SF does not completely describe surfaces with certain asymmetries. Area SF calculations of simulation data and of a diamond turned surface are shown and compared to area power spectral density (PSD) and area autocorrelation function (ACF) representations. The direct relationship between SF, PSD, and ACF for a stationary surface does not apply to non-stationary surfaces typical of optics with figure errors.

Image continuity at different levels of zoom for fringe patterns.

Fringe patterns are raw output data from many measurement systems including laser interferometers and moiré systems. For instruments with a range of zoom levels to measure the object at different scales, a technique (algorithm) is needed to combine and/or compare data to obtain information at different levels of details. A technique to keep the continuity of output images both at different levels of zoom and within the same level of zoom is developed and demonstrated. Image registration is used to correlate images, find relative zoom values, and obtain shift between images in the lateral plane. Fringe patterns from a moiré system and a laser interferometer are used as images to be stitched and demonstrate the technique. Interferomteric fringes are used to find the required parameters to inter-relate locations and scale of the fringe patterns at different levels of zoom. The calculated parameters are scale and translation in both directions; these parameters make it possible to locate the coordinates of the region that the measurement system is zoomed in on, related to the area with lower magnification and relative locations of images within the same level of zoom. Results show that this technique is capable of finding the scale and shift parameters within the resolution of one pixel and therefore can restore continuity between images at different levels of zoom.