Simulating structurally variable nuclear pore complexes for microscopy.

MOTIVATION: The nuclear pore complex (NPC) is the only passageway for macromolecules between nucleus and cytoplasm, and an important reference standard in microscopy: it is massive and stereotypically arranged. The average architecture of NPC proteins has been resolved with pseudoatomic precision, however observed NPC heterogeneities evidence a high degree of divergence from this average. Single-molecule localization microscopy (SMLM) images NPCs at protein-level resolution, whereupon image analysis software studies NPC variability. However, the true picture of this variability is unknown. In quantitative image analysis experiments, it is thus difficult to distinguish intrinsically high SMLM noise from variability of the underlying structure. RESULTS: We introduce CIR4MICS ('ceramics', Configurable, Irregular Rings FOR MICroscopy Simulations), a pipeline that synthesizes ground truth datasets of structurally variable NPCs based on architectural models of the true NPC. Users can select one or more N- or C-terminally tagged NPC proteins, and simulate a wide range of geometric variations. We also represent the NPC as a spring-model such that arbitrary deforming forces, of user-defined magnitudes, simulate irregularly shaped variations. Further, we provide annotated reference datasets of simulated human NPCs, which facilitate a side-by-side comparison with real data. To demonstrate, we synthetically replicate a geometric analysis of real NPC radii and reveal that a range of simulated variability parameters can lead to observed results. Our simulator is therefore valuable to test the capabilities of image analysis methods, as well as to inform experimentalists about the requirements of hypothesis-driven imaging studies. AVAILABILITY AND IMPLEMENTATION: Code: https://github.com/uhlmanngroup/cir4mics. Simulated data: BioStudies S-BSST1058.

Idiopathic Fistula in an Unrepaired Submucous Cleft Palate.

Palatal fistulae are a recognised complication in individuals who have undergone surgical repair of a cleft palate, however, congenital or idiopathic palatal fistulae are rare. This report discusses the presentation and treatment of a 16-year-old female with a submucous cleft palate, who presented with a recent onset change in speech and evidence of a new palatal fistula. There was no history of recent infection or known trauma, and the patient had not undergone any previous palatal surgery. This report discusses the clinical presentation, recommended management and relevant literature for this rare phenomenon.

Cleft lip Sidedness and the Association with Additional Congenital Malformations.

OBJECTIVE: To investigate the association between the sidedness of orofacial clefts and additional congenital malformations. DESIGN: Linkage of a national registry of cleft births to national administrative data of hospital admissions. SETTING: National Health Service, England. PARTICIPANTS: 2007 children born with cleft lip ± alveolus (CL ± A) and 2724 with cleft lip and palate (CLP) born between 2000 and 2012. MAIN OUTCOME MEASURE: The proportion of children with ICD-10 codes for additional congenital malformations by the sidedness (left, right or bilateral) of orofacial clefts. RESULTS: For CL ± A phenotypes, there was no evidence for a difference in the prevalence of additional anomalies between left (22%, reference), right (22%, aOR 1.02, 95% CI 0.80 to 1.28; P = .90) and bilateral clefts (23%, aOR 1.09, 95% CI 0.75 to 1.57; P = .66). For CLP phenotypes, there was evidence of a lower prevalence of additional malformations in left (23%, reference) compared to right (32%, aOR 1.54, 95% CI 1.25 to 1.91; P < .001) and bilateral clefts (33%, aOR 1.64, 95% CI 1.35 to 1.99; P < .001). CONCLUSIONS: The prevalence of additional congenital malformations was similar across sidedness subtypes with CL ± A phenotypes but was different for sidedness subtypes within CLP cases. These data support the hypothesis that CL ± A has a different underlying aetiology from CLP and that within the CLP phenotype, right sided CLP may lie closer in aetiology to bilateral CLP than it does to left sided CLP.

Pictures at an exhibition: How to share your imaging data.

Open access to data underpinning published results is a key pillar of scientific reproducibility. Making data available at scale also provides opportunities for data reuse, encouraging the development of new analysis approaches. In this poster article, accompanying a recorded talk, we will explain the benefits of publicly archiving your image data alongside your published manuscripts, as well as highlight what resources are available to do this. This will include the BioImage Archive, EMBL-EBI's new resource for biological image data, https://www.ebi.ac.uk/bioimage-archive/. We will look at how image data submission works, how to prepare in advance for archiving your data and upcoming developments.

The COVID-19 Data Portal: accelerating SARS-CoV-2 and COVID-19 research through rapid open access data sharing.

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic will be remembered as one of the defining events of the 21st century. The rapid global outbreak has had significant impacts on human society and is already responsible for millions of deaths. Understanding and tackling the impact of the virus has required a worldwide mobilisation and coordination of scientific research. The COVID-19 Data Portal (https://www.covid19dataportal.org/) was first released as part of the European COVID-19 Data Platform, on April 20th 2020 to facilitate rapid and open data sharing and analysis, to accelerate global SARS-CoV-2 and COVID-19 research. The COVID-19 Data Portal has fortnightly feature releases to continue to add new data types, search options, visualisations and improvements based on user feedback and research. The open datasets and intuitive suite of search, identification and download services, represent a truly FAIR (Findable, Accessible, Interoperable and Reusable) resource that enables researchers to easily identify and quickly obtain the key datasets needed for their COVID-19 research.

The Cleft Lip Education with Augmented Reality (CLEAR) VR Phase 2 Trial: A Pilot Randomized Crossover Trial of a Novel Patient Information Leaflet.

BACKGROUND: The Cleft Lip Education with Augmented Reality (CLEAR) project centers around the use of augmented reality (AR) in patient leaflets, as a visual means to overcome the "health literacy" gap. This trial followed Virtual Reality (VR CORE) guidelines for VR Phase 2 (Pilot) trials. METHODS: Participants included families of children treated for Cleft Lip and Palate at the Royal Hospital for Children, Glasgow. Interventions were AR leaflet or Traditional Leaflet. Objectives were to calculate sample sizes, assess outcome instruments, trial design, and acceptability to patients. Primary outcome measure was Mental Effort Rating Scale, and secondary outcomes were Patient Satisfaction (Visual Analogue Scale), Usefulness Scale for Patient Information Material (USE) scale, and Instructional Materials Motivation Survey (IMMS). Randomization was by block randomization. The trial was single blinded with assessors blinded to group assignment. RESULTS: 12 Participants were randomized, with crossover design permitting analysis of 12 per group. Primary outcome with Mental Effort Rating Scale indicated higher mental effort with Traditional compared to AR Leaflet (4.75 vs 2.00, P = .0003). Secondary outcomes for Satisfaction were Traditional 54.50 versus AR 93.50 (P = .0001); USE scale 49.42 versus 74.08 (P = .0011); and IMMS 112.50 versus 161.75 (P = .0003). Subjective interviews noted overwhelmingly positive patient comments regarding the AR leaflet. Outcome instruments and trial design were acceptable to participants. No harms were recorded. CONCLUSIONS: The CLEAR pilot trial provides early evidence of clinical efficacy of AR leaflets in patient education. It is hoped that this will provide a future paradigm shift in the way patient education is delivered.

Sidedness in Unilateral Orofacial Clefts: A Systematic Scoping Review.

OBJECTIVE: An overview of the literature relating to the sidedness of unilateral cleft lip with or without cleft palate to map current knowledge on the cause and impact of directional asymmetry. DESIGN: Scoping review with a systematic search of Medline and Embase from inception to May 2023. PATIENTS, PARTICIPANTS: Humans born with a left or right unilateral cleft lip with or without a cleft palate. MAIN OUTCOME MEASURES: Cleft sidedness as a co-occurrence, an outcome or an exposure. RESULTS: Forty studies were eligible for inclusion and confirmed the predilection for the occurrence of left sided cleft lips; 12 studies reported cleft sidedness co-occurring with another phenotype, 11 studies report sidedness as an outcome and 17 studies as an exposure. Phenotypes which were reported to co-occur with either left or right sided clefts included congenital dental anomalies, handedness and additional congenital anomalies. Variables investigated as a potential cause of left or right sided clefts as an outcome included chromosomal anomalies, genetic variants and environmental factors. Outcomes investigated in relation to cleft sidedness as an exposure included facial anatomical features, facial growth, educational attainment, functional and psychological characteristics. More studies showed worse outcomes in right sided clefts versus left sided clefts than vice versa, although studies were inconsistent, and a quality assessment was not performed. CONCLUSIONS: The field of cleft sidedness research is expanding and there are promising early findings to differentiate cause and outcome by sidedness of the cleft.

Investigating the Impact of Patient-Related Factors on Speech Outcomes at 5 Years of Age in Children With a Cleft Palate.

To investigate the relationship between patient-related factors (sex, cleft type, cleft extent, and Robin Sequence [RS]) and speech outcome at 5 years of age for children born with a cleft palate ± lip (CP ± L).3157 Children (1426 female:1731 male) with a nonsyndromic CP ± L, born between 2006 and 2014 in England, Wales, and Northern Ireland.Perceptual speech analysis utilized the Cleft Audit Protocol for Speech-Augmented (CAPS-A) rating and UK National Speech Outcome Standards: Speech Standard 1 (SS1)-speech within the normal range, SS2a-no structurally related speech difficulties or history of speech surgery, and SS3-speech without significant cleft-related articulation difficulties.Odds of achieving SS1 were lower among boys (aOR 0.771 [CI 0.660-0.901]), those with clefts involving the lip and palate (vs palate only) (UCLP-aOR 0.719 [CI 0.591-0.875]; BCLP-aOR 0.360 [CI 0.279-0.463]), and clefts involving the hard palate (incomplete-aOR 0.701 [CI 0.540-0.909]; complete-aOR 0.393 [CI 0.308-0.501]). Similar relationships with these patient factors were observed for SS3. SS2 was affected by the extent of hard palate involvement (complete; aOR 0.449 [CI 0.348-0.580]). Although those with CP and RS were less likely to meet all 3 standards than those without RS, odds ratios were not significant when adjusting for sex and cleft extent.Sex, cleft type, and extent of hard palate involvement have a significant impact on speech outcome at 5 years of age. Incorporating these factors into risk-adjustment models for service-level outcome reporting is recommended.

The Relationship Between Maxillary Growth and Speech in Children With a Unilateral Cleft Lip and Palate at 5 Years of Age.

OBJECTIVE: This study sought to investigate the association between maxillary growth and speech outcomes for children with a repaired unilateral cleft lip and palate (UCLP) at 5 years of age. PARTICIPANTS: In all, 521 children (180 females and 341 males) with a nonsyndromic complete UCLP, born between 2007 and 2012 in England, Wales, and Northern Ireland were included in this study. OUTCOME MEASURES: Maxillary growth was analyzed using dental models scored by the 5-Year-Olds' index, and perceptual speech analyses were scored by the Cleft Audit Protocol for Speech - Augmented rating. RESULTS: Forty-one percent of the children achieved good maxillary growth (scores 1 and 2 on 5-Year-Old' index). Fifty percent of the children achieved normal speech (achieving UK speech standard 1). Maxillary growth was not found to have an impact on speech outcome when described by the 3 UK National Cleft Lip and Palate Speech Audit Outcome Standards. Analysis according to individual speech parameters showed dentalizations to be less prevalent in children with good maxillary growth compared to fair and poor growth (P = .001). The remaining speech parameters within resonance, nasal airflow, and articulation categories were not significantly associated with maxillary growth. CONCLUSION: The findings from this study suggest that children with a history of complete UCLP, who have poor maxillary growth, are not at a higher risk of having major speech errors compared to children with good or fair maxillary growth at 5 years of age.

mmSIM: an open toolbox for accessible structured illumination microscopy.

Since the first practical super-resolution structured illumination fluorescence microscopes (SIM) were demonstrated more than two decades ago, the method has become increasingly popular for a wide range of bioimaging applications. The high cost and relative inflexibility of commercial systems, coupled with the conceptual simplicity of the approach and the desire to exploit and customize existing hardware, have led to the development of a large number of home-built systems. Several detailed hardware designs are available in the scientific literature, complemented by open-source software tools for SIM image validation and reconstruction. However, there remains a lack of simple open-source software to control these systems and manage the synchronization between hardware components, which is critical for effective SIM imaging. This article describes a new suite of software tools based on the popular Micro-Manager package, which enable the keen microscopist to develop and run a SIM system. We use the software to control two custom-built, high-speed, spatial light modulator-based SIM systems, evaluating their performance by imaging a range of fluorescent samples. By simplifying the process of SIM hardware development, we aim to support wider adoption of the technique. This article is part of the Theo Murphy meeting issue 'Super-resolution structured illumination microscopy (part 1)'.

Profiling gene expression dynamics underpinning conventional testing approaches to better inform pre-clinical evaluation of an age appropriate spironolactone formulation.

There is a need to accelerate paediatric formulation evaluation and enhance quality of early stage data in drug development to alleviate the information pinch point present between formulation development and clinical evaluation. This present work reports application of DNA microarrays as a high throughput screening tool identifying markers for prediction of bioavailability and formulation driven physiological responses. With a focus on enhancing paediatric medicine provision, an oral liquid spironolactone suspension was formulated addressing a paediatric target product profile. Caco-2 cells cultured on transwell inserts were implemented in transport assays in vitro and DNA microarrays were used to examine gene expression modulation. Wistar rats were used to derive in vivo bioavailability data. In vitro, genomic, and in vivo data sets were concurrently evaluated linking drug transport and the genomic fingerprint generated by spironolactone formulation exposure. Significant changes in gene expression are reported as a result of formulation exposure. These include genes coding for ATP-binding cassette (ABC) transporters, solute carrier (SLC) transporters, cytochrome P450 (CYP) enzymes, and carboxylesterase enzymes. Genomic findings better inform pre-clinical understanding of pharmacokinetic and pharmacodynamic responses to spironolactone and its active metabolites than current in vitro drug transport assays alone.

Homographically generated light sheets for the microscopy of large specimens.

We compare the performance of linear and nonlinear methods for aligning the excitation and detection planes throughout volumes of large specimens in digitally scanned light sheet microscopy. An effective nonlinear method involves the registration of four corner extrema of the imaging volume via a projective transform. We show that this improves the light collection efficiency of the commonly used three-point affine registration by an average of 42% over a typical specimen volume. Accurate illumination/detection registration methods are now pertinent to biological research in view of current trends towards imaging large or expanded samples, at depth, with diffraction limited resolution.

Multichannel electrocardiogram diagnostics for the diagnosis of arrhythmogenic right ventricular dysplasia.

Aims: The identification of arrhythmogenic right ventricular dysplasia (ARVD) from 12-channel standard electrocardiogram (ECG) is challenging. High density ECG data may identify lead locations and criteria with a higher sensitivity. Methods and results: Eighty-channel ECG recording from patients diagnosed with ARVD and controls were quantified by magnitude and integral measures of QRS and T waves and by a measure (the average silhouette width) of differences in the shapes of the normalized ECG cycles. The channels with the best separability between ARVD patients and controls were near the right ventricular wall, at the third intercostal space. These channels showed pronounced differences in P waves compared to controls as well as the expected differences in QRS and T waves. Conclusion: Multichannel recordings, as in body surface mapping, add little to the reliability of diagnosing ARVD from ECGs. However, repositioning ECG electrodes to a high anterior position can improve the identification of ECG variations in ARVD. Additionally, increased P wave amplitude appears to be associated with ARVD.

Systematic screening of photopolymer resins for stereolithography (SLA) 3D printing of solid oral dosage forms: Investigation of formulation factors on printability outcomes.

Pharmaceutical three-dimensional printing (3DP) is now in its golden age. Recent years have seen a dramatic increase in the research in 3D printed pharmaceuticals due to their potential to deliver highly personalised medicines, thus revolutionising the way medicines are designed, manufactured, and dispensed. A particularly attractive 3DP technology used to manufacture medicines is stereolithography (SLA), which features key advantages in terms of printing resolution and compatibility with thermolabile drugs. Nevertheless, the enthusiasm for pharmaceutical SLA has not been followed by the introduction of novel excipients specifically designed for the fabrication of medicines; hence, the choice of biocompatible polymers and photoinitiators available is limited. This work provides an insight on how to maximise the usefulness of the limited materials available by evaluating how different formulation factors affect printability outcomes of SLA 3D printed medicines. 156 photopolymer formulations were systematically screened to evaluate the influence of factors including photoinitiator amount, photopolymer molecular size, and type and amount of liquid filler on the printability outcomes. Collectively, these factors were found highly influential in modulating the print quality of the final dosage forms. Findings provide enhanced understanding of formulation parameters informing the future of SLA 3D printed medicines and the personalised medicines revolution.

Hyperspectral Mapping of Human Primary and Stem Cells at Cell-Matrix Interfaces.

Extracellular matrices interface with cells to promote cell growth and tissue development. Given this critical role, matrix mimetics are introduced to enable biomedical materials ranging from tissue engineering scaffolds and tumor models to organoids for drug screening and implant surface coatings. Traditional microscopy methods are used to evaluate such materials in their ability to support exploitable cell responses, which are expressed in changes in cell proliferation rates and morphology. However, the physical imaging methods do not capture the chemistry of cells at cell-matrix interfaces. Herein, we report hyperspectral imaging to map the chemistry of human primary and embryonic stem cells grown on matrix materials, both native and artificial. We provide the statistical analysis of changes in lipid and protein content of the cells obtained from infrared spectral maps to conclude matrix morphologies as a major determinant of biochemical cell responses. The study demonstrates an effective methodology for evaluating bespoke matrix materials directly at cell-matrix interfaces.

Treating and managing atrial fibrillation.

The management of atrial fibrillation is complex and is influenced by the type of AF, the severity of symptoms, underlying disease and patient choice. The aim of treatment is to alleviate symptoms, prevent strokes and reduce other complications, such as heart failure. The incidence of AF is increasing due to an ageing population and most health professionals will encounter patients with AF during their career. A widespread knowledge of AF management among the nursing profession is important to ensure that appropriate treatment and patient support are provided. This article is the second in a two-part series on AF. Part one discussed the importance of detecting and treating AF and screening strategies. This second part discusses the management of AF and treatment options, using recent guidelines.

Opportunistic screening for atrial fibrillation.

Atrial fibrillation is the most common arrhythmia and the likelihood of having it increases with age. If left untreated it can lead to heart failure and is a significant risk factor for stroke but risk can be greatly reduced with oral anticoagulation. Many people with AF remain asymptomatic, but the risk of stroke remains the same. Simple screening methods will help detect those at risk. Many of those with a diagnosis and at high risk of stroke remain untreated. This two-part series aims to raise awareness of the importance of early detection and appropriate treatment. Part one discusses the complications linked to AF and explores the nurse's role in screening; part two will look at management.

Longitudinal educational attainment among children with isolated oral cleft: a cohort study.

OBJECTIVES: (1) To explore differences in educational attainment between children born with isolated clefts and the general population at ages 5, 7 and 11 years; (2) to describe longitudinal changes in attainment among children with cleft through primary education. DESIGN: Analysis of Cleft Registry and Audit Network data linked to national educational outcomes. SETTING: English state schools. PATIENTS: 832 children born with isolated cleft, aged 5 years in 2006-2008. MAIN OUTCOME MEASURES: Difference in teacher-assessed attainment between children with a cleft and general population at each age, for all children and by cleft type. Percentage of children with low attainment at age 5 years who had low attainment at age 11 years, for all children and by cleft type. RESULTS: Children with a cleft had lower attainment than the general population in all subject areas (Z-score range: -0.29 (95% CI -0.36 to -0.22) to -0.22 (95% CI -0.29 to -0.14)). This difference remained consistent in size at all ages, and was larger among children with a cleft affecting the palate (cleft palate/cleft lip and palate (CP/CLP)) than those with a cleft lip (CL). Of 216 children with low attainment in any subject at age 5 years, 54.2% had low attainment in at least one subject at age 11 years. Compared with children with CL, those with CP/CLP were more likely to have persistent low attainment. CONCLUSIONS: An educational attainment gap for children born with isolated clefts is evident throughout primary education. Almost half of children with low attainment at age 5 years achieve normal attainment at age 11 years.

Number and timing of primary cleft lip and palate repair surgeries in England: whole nation study of electronic health records before and during the COVID-19 pandemic.

OBJECTIVE: To quantify differences in number and timing of first primary cleft lip and palate (CLP) repair procedures during the first year of the COVID-19 pandemic (1 April 2020 to 31 March 2021; 2020/2021) compared with the preceding year (1 April 2019 to 31 March 2020; 2019/2021). DESIGN: National observational study of administrative hospital data. SETTING: National Health Service hospitals in England. STUDY POPULATION: Children <5 years undergoing primary repair for an orofacial cleft Population Consensus and Surveys Classification of Interventions and Procedures-fourth revisions (OPCS-4) codes F031, F291). MAIN EXPOSURE: Procedure date (2020/2021 vs 2019/2020). MAIN OUTCOMES: Numbers and timing (age in months) of first primary CLP procedures. RESULTS: 1716 CLP primary repair procedures were included in the analysis. In 2020/2021, 774 CLP procedures were carried out compared with 942 in 2019/2020, a reduction of 17.8% (95% CI 9.5% to 25.4%). The reduction varied over time in 2020/2021, with no surgeries at all during the first 2 months (April and May 2020). Compared with 2019/2020, first primary lip repair procedures performed in 2020/2021 were delayed by 1.6 months on average (95% CI 0.9 to 2.2 months). Delays in primary palate repairs were smaller on average but varied across the nine geographical regions. CONCLUSION: There were significant reductions in the number and delays in timing of first primary CLP repair procedures in England during the first year of the pandemic, which may affect long-term outcomes.