bluuebunny/crossref_metadata_2025 huggingface dataset:
Towards more accurate microbial source tracking via non-negative matrix factorization (NMF)
Authors: Huang Ziyi , Cai Dehan , Sun Yanni
Published: June 2024

Motivation

The microbiome of a sampled habitat often consists of microbial communities from various sources, including potential contaminants. Microbial source tracking (MST) can be used to discern the contribution of each source to the observed microbiome data, thus enabling the identification and tracking of microbial communities within a sample. Therefore, MST has various applications, from monitoring microbial contamination in clinical labs to tracing the source of pollution in environmental samples. Despite promising results in MST development, there is still room for improvement, particularly for applications where precise quantification of each source’s contribution is critical.

Results

In this study, we introduce a novel tool called SourceID-NMF towards more precise microbial source tracking. SourceID-NMF utilizes a non-negative matrix factorization (NMF) algorithm to trace the microbial sources contributing to a target sample. By leveraging the taxa abundance in both available sources and the target sample, SourceID-NMF estimates the proportion of available sources present in the target sample. To evaluate the performance of SourceID-NMF, we conducted a series of benchmarking experiments using simulated and real data. The simulated experiments mimic realistic yet challenging scenarios for identifying highly similar sources, irrelevant sources, unknown sources, low abundance sources, and noise sources. The results demonstrate the superior accuracy of SourceID-NMF over existing methods. Particularly, SourceID-NMF accurately estimated the proportion of irrelevant and unknown sources while other tools either over- or under-estimated them. In addition, the noise sources experiment also demonstrated the robustness of SourceID-NMF for MST.

Availability and implementation

SourceID-NMF is available online at https://github.com/ZiyiHuang0708/SourceID-NMF.
Approximating facial expression effects on diagnostic accuracy via generative AI in medical genetics
Authors: Patel Tanviben , Othman Amna A , Sümer Ömer , Hellman Fabio , Krawitz Peter , André Elisabeth , Ripper Molly E , Fortney Chris , Persky Susan , Hu Ping , Tekendo-Ngongang Cedrik , Hanchard Suzanna Ledgister , Flaharty Kendall A , Waikel Rebekah L , Duong Dat , Solomon Benjamin D
Published: June 2024

Summary

Artificial intelligence (AI) is increasingly used in genomics research and practice, and generative AI has garnered significant recent attention. In clinical applications of generative AI, aspects of the underlying datasets can impact results, and confounders should be studied and mitigated. One example involves the facial expressions of people with genetic conditions. Stereotypically, Williams (WS) and Angelman (AS) syndromes are associated with a “happy” demeanor, including a smiling expression. Clinical geneticists may be more likely to identify these conditions in images of smiling individuals. To study the impact of facial expression, we analyzed publicly available facial images of approximately 3500 individuals with genetic conditions. Using a deep learning (DL) image classifier, we found that WS and AS images with non-smiling expressions had significantly lower prediction probabilities for the correct syndrome labels than those with smiling expressions. This was not seen for 22q11.2 deletion and Noonan syndromes, which are not associated with a smiling expression. To further explore the effect of facial expressions, we computationally altered the facial expressions for these images. We trained HyperStyle, a GAN-inversion technique compatible with StyleGAN2, to determine the vector representations of our images. Then, following the concept of InterfaceGAN, we edited these vectors to recreate the original images in a phenotypically accurate way but with a different facial expression. Through online surveys and an eye-tracking experiment, we examined how altered facial expressions affect the performance of human experts. We overall found that facial expression is associated with diagnostic accuracy variably in different genetic conditions.
Deciphering high-order structures in spatial transcriptomes with graph-guided Tucker decomposition
Authors: Broadbent Charles , Song Tianci , Kuang Rui
Published: June 2024

Spatial transcripome (ST) profiling can reveal cells’ structural organizations and functional roles in tissues. However, deciphering the spatial context of gene expressions in ST data is a challenge—the high-order structure hiding in whole transcriptome space over 2D/3D spatial coordinates requires modeling and detection of interpretable high-order elements and components for further functional analysis and interpretation. This paper presents a new method GraphTucker—graph-regularized Tucker tensor decomposition for learning high-order factorization in ST data. GraphTucker is based on a nonnegative Tucker decomposition algorithm regularized by a high-order graph that captures spatial relation among spots and functional relation among genes. In the experiments on several Visium and Stereo-seq datasets, the novelty and advantage of modeling multiway multilinear relationships among the components in Tucker decomposition are demonstrated as opposed to the Canonical Polyadic Decomposition and conventional matrix factorization models by evaluation of detecting spatial components of gene modules, clustering spatial coefficients for tissue segmentation and imputing complete spatial transcriptomes. The results of visualization show strong evidence that GraphTucker detect more interpretable spatial components in the context of the spatial domains in the tissues.

Availability and implementation

https://github.com/kuanglab/GraphTucker.
Closing the computational biology ‘knowledge gap’: Spanish Wikipedia as a case study
Authors: Sélem-Mojica Nelly , Karakulak Tülay , Anjum Audra , Pashkov Antón , Pérez-Estrada Rafael , Enriquez-Guillén Karina , DeBlasio Dan , Ferreira-Gonzalez Sofia , Medina-Rivera Alejandra , Rodrigo-Torres Daniel , Kilpatrick Alastair M , Welch Lonnie R , Rahman Farzana
Published: June 2024

Motivation

Wikipedia is a vital open educational resource in computational biology. The quality of computational biology coverage in English-language Wikipedia has improved steadily in recent years. However, there is an increasingly large ‘knowledge gap’ between computational biology resources in English-language Wikipedia, and Wikipedias in non-English languages. Reducing this knowledge gap by providing educational resources in non-English languages would reduce language barriers which disadvantage non-native English speaking learners across multiple dimensions in computational biology.

Results

Here, we provide a comprehensive assessment of computational biology coverage in Spanish-language Wikipedia, the second most accessed Wikipedia worldwide. Using Spanish-language Wikipedia as a case study, we generate quantitative and qualitative data before and after a targeted educational event, specifically, a Spanish-focused student editing competition. Our data demonstrates how such events and activities can narrow the knowledge gap between English and non-English educational resources, by improving existing articles and creating new articles. Finally, based on our analysis, we suggest ways to prioritize future initiatives to improve open educational resources in other languages.

Availability and Implementation

Scripts for data analysis are available at: https://github.com/ISCBWikiTeam/spanish.
Modeling metastatic progression from cross-sectional cancer genomics data
Authors: Rupp Kevin , Lösch Andreas , Hu Yanren Linda , Nie Chenxi , Schill Rudolf , Klever Maren , Pfahler Simon , Grasedyck Lars , Wettig Tilo , Beerenwinkel Niko , Spang Rainer
Published: June 2024

Motivation

Metastasis formation is a hallmark of cancer lethality. Yet, metastases are generally unobservable during their early stages of dissemination and spread to distant organs. Genomic datasets of matched primary tumors and metastases may offer insights into the underpinnings and the dynamics of metastasis formation.

Results

We present metMHN, a cancer progression model designed to deduce the joint progression of primary tumors and metastases using cross-sectional cancer genomics data. The model elucidates the statistical dependencies among genomic events, the formation of metastasis, and the clinical emergence of both primary tumors and their metastatic counterparts. metMHN enables the chronological reconstruction of mutational sequences and facilitates estimation of the timing of metastatic seeding. In a study of nearly 5000 lung adenocarcinomas, metMHN pinpointed TP53 and EGFR as mediators of metastasis formation. Furthermore, the study revealed that post-seeding adaptation is predominantly influenced by frequent copy number alterations.

Availability and implementation

All datasets and code are available on GitHub at https://github.com/cbg-ethz/metMHN.
Floria: fast and accurate strain haplotyping in metagenomes
Authors: Shaw Jim , Gounot Jean-Sebastien , Chen Hanrong , Nagarajan Niranjan , Yu Yun William
Published: June 2024

Shotgun metagenomics allows for direct analysis of microbial community genetics, but scalable computational methods for the recovery of bacterial strain genomes from microbiomes remains a key challenge. We introduce Floria, a novel method designed for rapid and accurate recovery of strain haplotypes from short and long-read metagenome sequencing data, based on minimum error correction (MEC) read clustering and a strain-preserving network flow model. Floria can function as a standalone haplotyping method, outputting alleles and reads that co-occur on the same strain, as well as an end-to-end read-to-assembly pipeline (Floria-PL) for strain-level assembly. Benchmarking evaluations on synthetic metagenomes show that Floria is  > 3× faster and recovers 21% more strain content than base-level assembly methods (Strainberry) while being over an order of magnitude faster when only phasing is required. Applying Floria to a set of 109 deeply sequenced nanopore metagenomes took <20 min on average per sample and identified several species that have consistent strain heterogeneity. Applying Floria’s short-read haplotyping to a longitudinal gut metagenomics dataset revealed a dynamic multi-strain Anaerostipes hadrus community with frequent strain loss and emergence events over 636 days. With Floria, accurate haplotyping of metagenomic datasets takes mere minutes on standard workstations, paving the way for extensive strain-level metagenomic analyses.

Availability and implementation

Floria is available at https://github.com/bluenote-1577/floria, and the Floria-PL pipeline is available at https://github.com/jsgounot/Floria_analysis_workflow along with code for reproducing the benchmarks.
SPRITE: improving spatial gene expression imputation with gene and cell networks
Authors: Sun Eric D , Ma Rong , Zou James
Published: June 2024

Motivation

Spatially resolved single-cell transcriptomics have provided unprecedented insights into gene expression in situ, particularly in the context of cell interactions or organization of tissues. However, current technologies for profiling spatial gene expression at single-cell resolution are generally limited to the measurement of a small number of genes. To address this limitation, several algorithms have been developed to impute or predict the expression of additional genes that were not present in the measured gene panel. Current algorithms do not leverage the rich spatial and gene relational information in spatial transcriptomics. To improve spatial gene expression predictions, we introduce Spatial Propagation and Reinforcement of Imputed Transcript Expression (SPRITE) as a meta-algorithm that processes predictions obtained from existing methods by propagating information across gene correlation networks and spatial neighborhood graphs.

Results

SPRITE improves spatial gene expression predictions across multiple spatial transcriptomics datasets. Furthermore, SPRITE predicted spatial gene expression leads to improved clustering, visualization, and classification of cells. SPRITE can be used in spatial transcriptomics data analysis to improve inferences based on predicted gene expression.

Availability and implementation

The SPRITE software package is available at https://github.com/sunericd/SPRITE. Code for generating experiments and analyses in the manuscript is available at https://github.com/sunericd/sprite-figures-and-analyses.
A machine-learning-based alternative to phylogenetic bootstrap
Authors: Ecker Noa , Huchon Dorothée , Mansour Yishay , Mayrose Itay , Pupko Tal
Published: June 2024

Motivation

Currently used methods for estimating branch support in phylogenetic analyses often rely on the classic Felsenstein’s bootstrap, parametric tests, or their approximations. As these branch support scores are widely used in phylogenetic analyses, having accurate, fast, and interpretable scores is of high importance.

Results

Here, we employed a data-driven approach to estimate branch support values with a probabilistic interpretation. To this end, we simulated thousands of realistic phylogenetic trees and the corresponding multiple sequence alignments. Each of the obtained alignments was used to infer the phylogeny using state-of-the-art phylogenetic inference software, which was then compared to the true tree. Using these extensive data, we trained machine-learning algorithms to estimate branch support values for each bipartition within the maximum-likelihood trees obtained by each software. Our results demonstrate that our model provides fast and more accurate probability-based branch support values than commonly used procedures. We demonstrate the applicability of our approach on empirical datasets.

Availability and implementation

The data supporting this work are available in the Figshare repository at https://doi.org/10.6084/m9.figshare.25050554.v1, and the underlying code is accessible via GitHub at https://github.com/noaeker/bootstrap_repo.
MolPLA: a molecular pretraining framework for learning cores, R-groups and their linker joints
Authors: Gim Mogan , Park Jueon , Park Soyon , Lee Sanghoon , Baek Seungheun , Lee Junhyun , Nguyen Ngoc-Quang , Kang Jaewoo
Published: June 2024

Motivation

Molecular core structures and R-groups are essential concepts in drug development. Integration of these concepts with conventional graph pre-training approaches can promote deeper understanding in molecules. We propose MolPLA, a novel pre-training framework that employs masked graph contrastive learning in understanding the underlying decomposable parts in molecules that implicate their core structure and peripheral R-groups. Furthermore, we formulate an additional framework that grants MolPLA the ability to help chemists find replaceable R-groups in lead optimization scenarios.

Results

Experimental results on molecular property prediction show that MolPLA exhibits predictability comparable to current state-of-the-art models. Qualitative analysis implicate that MolPLA is capable of distinguishing core and R-group sub-structures, identifying decomposable regions in molecules and contributing to lead optimization scenarios by rationally suggesting R-group replacements given various query core templates.

Availability and implementation

The code implementation for MolPLA and its pre-trained model checkpoint is available at https://github.com/dmis-lab/MolPLA.
Optimal sequencing budget allocation for trajectory reconstruction of single cells
Authors: Moriel Noa , Memet Edvin , Nitzan Mor
Published: June 2024

Background

Charting cellular trajectories over gene expression is key to understanding dynamic cellular processes and their underlying mechanisms. While advances in single-cell RNA-sequencing technologies and computational methods have pushed forward the recovery of such trajectories, trajectory inference remains a challenge due to the noisy, sparse, and high-dimensional nature of single-cell data. This challenge can be alleviated by increasing either the number of cells sampled along the trajectory (breadth) or the sequencing depth, i.e. the number of reads captured per cell (depth). Generally, these two factors are coupled due to an inherent breadth-depth tradeoff that arises when the sequencing budget is constrained due to financial or technical limitations.

Results

Here we study the optimal allocation of a fixed sequencing budget to optimize the recovery of trajectory attributes. Empirical results reveal that reconstruction accuracy of internal cell structure in expression space scales with the logarithm of either the breadth or depth of sequencing. We additionally observe a power law relationship between the optimal number of sampled cells and the corresponding sequencing budget. For linear trajectories, non-monotonicity in trajectory reconstruction across the breadth-depth tradeoff can impact downstream inference, such as expression pattern analysis along the trajectory. We demonstrate these results for five single-cell RNA-sequencing datasets encompassing differentiation of embryonic stem cells, pancreatic beta cells, hepatoblast and multipotent hematopoietic cells, as well as induced reprogramming of embryonic fibroblasts into neurons. By addressing the challenges of single-cell data, our study offers insights into maximizing the efficiency of cellular trajectory analysis through strategic allocation of sequencing resources.
MolLM: a unified language model for integrating biomedical text with 2D and 3D molecular representations
Authors: Tang Xiangru , Tran Andrew , Tan Jeffrey , Gerstein Mark B
Published: June 2024

Motivation

The current paradigm of deep learning models for the joint representation of molecules and text primarily relies on 1D or 2D molecular formats, neglecting significant 3D structural information that offers valuable physical insight. This narrow focus inhibits the models’ versatility and adaptability across a wide range of modalities. Conversely, the limited research focusing on explicit 3D representation tends to overlook textual data within the biomedical domain.

Results

We present a unified pre-trained language model, MolLM, that concurrently captures 2D and 3D molecular information alongside biomedical text. MolLM consists of a text Transformer encoder and a molecular Transformer encoder, designed to encode both 2D and 3D molecular structures. To support MolLM’s self-supervised pre-training, we constructed 160K molecule-text pairings. Employing contrastive learning as a supervisory signal for learning, MolLM demonstrates robust molecular representation capabilities across four downstream tasks, including cross-modal molecule and text matching, property prediction, captioning, and text-prompted molecular editing. Through ablation, we demonstrate that the inclusion of explicit 3D representations improves performance in these downstream tasks.

Availability and implementation

Our code, data, pre-trained model weights, and examples of using our model are all available at https://github.com/gersteinlab/MolLM. In particular, we provide Jupyter Notebooks offering step-by-step guidance on how to use MolLM to extract embeddings for both molecules and text.
Adaptive digital tissue deconvolution
Authors: Görtler Franziska , Mensching-Buhr Malte , Skaar Ørjan , Schrod Stefan , Sterr Thomas , Schäfer Andreas , Beißbarth Tim , Joshi Anagha , Zacharias Helena U , Grellscheid Sushma Nagaraja , Altenbuchinger Michael
Published: June 2024

Motivation

The inference of cellular compositions from bulk and spatial transcriptomics data increasingly complements data analyses. Multiple computational approaches were suggested and recently, machine learning techniques were developed to systematically improve estimates. Such approaches allow to infer additional, less abundant cell types. However, they rely on training data which do not capture the full biological diversity encountered in transcriptomics analyses; data can contain cellular contributions not seen in the training data and as such, analyses can be biased or blurred. Thus, computational approaches have to deal with unknown, hidden contributions. Moreover, most methods are based on cellular archetypes which serve as a reference; e.g. a generic T-cell profile is used to infer the proportion of T-cells. It is well known that cells adapt their molecular phenotype to the environment and that pre-specified cell archetypes can distort the inference of cellular compositions.

Results

We propose Adaptive Digital Tissue Deconvolution (ADTD) to estimate cellular proportions of pre-selected cell types together with possibly unknown and hidden background contributions. Moreover, ADTD adapts prototypic reference profiles to the molecular environment of the cells, which further resolves cell-type specific gene regulation from bulk transcriptomics data. We verify this in simulation studies and demonstrate that ADTD improves existing approaches in estimating cellular compositions. In an application to bulk transcriptomics data from breast cancer patients, we demonstrate that ADTD provides insights into cell-type specific molecular differences between breast cancer subtypes.

Availability and implementation

A python implementation of ADTD and a tutorial are available at Gitlab and zenodo (doi:10.5281/zenodo.7548362).
CPC07 Occupational cutaneous larva migrans presenting as diffuse folliculitis with concurrent helminthiasis
Authors: Beck-Sander Kellen , Coulton Alice , Cooke Joanna , Cooper Hywel
Published: June 2024

Cutaneous larva migrans (CLM) occurs following human skin contact with the larvae of animal hookworms, including the dog hookworm Ancylostoma caninum. To date, these hookworms cannot complete their life cycle in humans. The condition is mostly seen in the tropics or subtropics or in returning travellers; however, cases following local exposure to animal hookworms have been identified. Less than 5% of cases of CLM reported in the literature present as folliculitis. Strongyloidiasis is caused by infection with the soil-transmitted roundworm Strongyloides stercoralis and is seen in areas of poor sanitation. It can complete its life cycle within the human host, and infection can persist asymptomatically for decades. Toxocariasis is infection caused by the larvae of the dog or cat Toxocara spp. roundworm. Human infection occurs through ingestion of eggs, but these roundworms do not complete their life cycle in humans. Infection can be subclinical or present as visceral or ocular larva migrans. A 62-year-old man was admitted to hospital with an un­usual rash and significant metabolic derangement. He had a 4-week history of a diffuse, pruritic, erythematous, papulonodular rash extending from his flanks to his thighs with florid pustular areas on examination. He had no pre-existing medical conditions and denied sexual contact or foreign travel for over a decade. He worked as a cleaner in a large governmental organization with regular exposure to human and animal excrement, although he reported adequate personal protective equipment. Laboratory results revealed a new diagnosis of type 2 diabetes and eosinophils of 0.1 × 109 L−1, and blood culture grew multiple gastrointestinal bacteria. A skin biopsy demonstrated purulent folliculitis, abundant eosinophil infiltration, and multiple rhabditiform larvae within dilated and ruptured follicles. Slides were sent for specialist opinion, and filiform larvae with the characteristic double lateral alae of Ancylostoma spp. were identified. Given the patient’s occupational exposure, the findings were deemed to be compatible with CLM caused by the dog hookworm, A. caninum. Serology also revealed weak-positive Strongyloides, and positive Toxocara antibodies, although two faecal samples were negative for helminths. The patient was treated with a one-off dose of ivermectin and a 7-day course of albendazole. This is a highly unusual case of CLM presenting as fulminant folliculitis secondary to A. caninum, in the absence of foreign travel, and likely contracted through occupational exposure. The possible coinfection with S. stercoralis and Toxocara canis prompts discussion of the transmission, life cycle, diagnostic testing and management of all three helminths.
P010 Eosinophilic dermatosis of haematological malignancy mimicking insect bite-like reaction in a patient with chronic lymphocytic leukaemia: a case report
Authors: Nallathamby Kasthuri , Moss Kat , Azurdia Richard , Khirwadkar Nitin
Published: June 2024

We present a case of a patient presenting with severe insect bite-like reactions in her skin with underlying chronic lymphocytic leukaemia (CLL). A 71-year-old woman was diagnosed with CLL in 2017 after presenting with a low-level lymphocytosis. She has never required treatment for CLL and remains under active observation in the haematology clinic. She was initially referred to dermatology 5 years ago with a nonresolving insect bite-like rash on her chest. The biopsy of the lesion was thought to be reactive with CLL infiltration. Over the years she has had a number of flare-ups of differing severity; the rash has always been itchy, and she has often presented with tense vesiculobullous lesions, occasionally haemorrhagic in appearance. Multiple biopsies were taken over a period of 5 years due to the diagnostic challenge, with the main differentials being urticarial vasculitis, insect bite-like reactions, Wells syndrome/dermal hypersensitivity reaction and Churg–Strauss syndrome. One of the common trends with the patient’s rash and blistering lesions is that they have often flared up during the summer, during gardening or travelling, and she has also reported them after receiving the COVID-19 vaccine. There was no reaction following the flu vaccine. Biopsies were always negative for direct immunofluorescence, ruling out immunobullous reactions. There was often the presence of a heavy neutrophilic infiltrate, vascular inflammation, and vague granulomata with absence of frank vasculitis. Following multidisciplinary team discussion and close clinicopathological correlation, we have concluded that this could be eosinophilic dermatosis of haematological malignancy mimicking insect bites, of which only a few reported cases have been documented. This case report reviews the association between CLL and insect bite-like reaction and highlights the challenges associated with diagnosing and managing such dermatological manifestations. Previous literature showed no clear association with regards to treatment of CLL causing regression of the dermatological manifestation. The treatment is difficult and recurrences are common (Rodríguez-Lojo R, Almagro M, Piñeyro F et al. Eosinophilic panniculitis and insect bite-like eruption in a patient with chronic lymphocytic leukaemia: a spectrum of the same entity. Dermatol Res Pract 2010; 2010: 263827). In our case, the plan is to actively treat the underlying haematological malignancy and to assess the possibility of bringing the cutaneous manifestation under control. This case also highlights the lack of tailored therapeutic strategies for patients with CLL, in the context of its diverse and complex dermatological presentation.
P043 Readability assessment of British Journal of Dermatology plain language summaries
Authors: Barry Rory , O’Gorman Susan
Published: June 2024

Plain language summaries (PLSs) are being increasingly implemented and required by regulatory bodies to improve accessibility of scientific research for the general population. In 2014, the British Journal of Dermatology (BJD) introduced freely available PLSs to improve patient access to high-quality dermatology research. Over 40% of adults in England do not have adequate literacy skills for health information. As such, when developing PLSs, the NHS recommend targeting a reading age of 9–11 years, up to 14 years in particularly complex medical information. While social media may remain more accessible, the misinformation risk underlines the important role of scientific journals in engaging the lay community in high-quality published research. Based on NHS guidelines, we assessed the readability level of published PLSs in the last 12 issues of the BJD, from 1 December 2022 to 16 November 2023. Multiple established readability metrics were used, including Flesch–Kincaid (FK), Simple Measure of Gobbledygook (SMOG), Gunning Fog Index (GFI), FORCAST, and Flesch Reading Ease (FRE). Only English-language PLSs were included for analysis. Ninety-nine English-language PLSs were published in those 12 BJD issues. According to FK, the mean readability US grade level was 13.0 [95% confidence interval (CI) 12.7–13.4]. A US grade level is one integer less than the UK year system (e.g. US grade 6 = UK year 7). As such, a US grade level of 13 corresponds to an age range of 18–20 years, or a college-level student. SMOG, an NHS-recommended readability instrument, evaluates text for 100% comprehensibility. Evaluating BJD PLSs using SMOG, the mean US grade level was 11.9 (95% CI 11.5–12.2), indicative of a 17–18-year reading age in the UK. The GFI analysis gave a mean US grade level of 16.2 (95% CI 15.7–16.6) for the PLSs, equating to a reading age of 22 years. The average grade level from FORCAST assessment was 11.5 (95% CI 11.4–11.7), giving a reading age of 17 years. Finally, using FRE testing, the mean output was 41.5 (95% CI 39.4–43.6), corresponding to the ‘difficult’ category in the Flesch read­ability chart, a reading age of 18 years or above. This research suggests that the BJD PLSs are not appropriately written for dermatology patients, according to the England population literacy level and NHS guidelines. Readability formulas, while potentially limited through lack of comprehension and reading ease assessment, provide authors guidance of appropriate literacy level PLS. By encouraging authors to use readability resources and PLS guidelines the BJD may improve patient engagement with the journal.
P084 The prevalence of inflammatory back pain in a secondary care psoriasis cohort
Authors: Phillips Alexandra , Eddison Joe , Sinha Aparna , Reilly Elizabeth
Published: June 2024

The articular manifestations of psoriasis are well recognized. While peripheral psoriatic arthritis is the most common form, patients with psoriasis are also more likely to have axial disease either through axial psoriatic arthritis or axial spondyloarthritis. Isolated axial disease may be missed by screening tools such as the Psoriasis Epidemiology Screening Tool (PEST) but can cause significant morbidity. In addition, the average diagnostic delay for axial spondyloarthritis is 8.5 years (Zhao SS, Pittam B, Harrison NL et al. Diagnostic delay in axial spondyloarthritis: a systematic review and meta-analysis. Rheumatology 2021; 60: 1620–8), and its association with psoriasis therefore presents an important screening opportunity within the dermatology clinic. This exploratory survey aimed to establish the prevalence of symptoms of inflammatory back pain (IBP) among a cohort of patients with psoriasis in secondary care to determine the unmet service need. Patients with a diagnosis of psoriasis seen in the dermatology department of a UK secondary care hospital between 1 March 2021 and 12 October 2023 (n = 1529) were identified through electronic clinical noting. Patients who had a mobile phone number recorded (n = 1516) received a text message inviting them to complete the National Axial Spondyloarthritis Society screening survey for IBP. The link remained open for 3 weeks and written consent was embedded within the questionnaire. Patients were then identified through their email address or by email contact to facilitate referral to rheumatology and the collection of additional clinical information. In total 355 responses were received, of which six patients did not provide consent, two patients entered duplicate responses and two patients did not have psoriasis. Overall, 30% (n = 103) reported having chronic back pain; 22% (n = 77) screened positively for possible IBP, of whom 47 were not known to rheumatology. Twenty-five patients provided identifying details allowing further analysis. The average Psoriasis Area and Severity Index score of those with possible IBP was 13.3 and the average Dermatology Life Quality Index was 16.4. The PEST score was recorded for seven patients and was positive for two of these. There is a high prevalence of possible IBP among our cohort of patients with psoriasis in secondary care. The majority of cases are not known to rheumatology, indicating a high potential unmet need. The PEST score was infrequently recorded and correlated poorly with the score for possible IBP, supporting the understanding that it is not an effective screening tool for axial disease. Use of a more sensitive screening tool for IBP may aid in identifying patients with psoriasis who also have axial PsA or spondyloarthritis and help facilitate earlier diagnosis and treatment.
P107 Updating the Assessment of the Psychological and Social Effects of Acne (APSEA) through factor analysis: developing the novel APSEA-3
Authors: Jones Georgina , Morgan Jim , Lau Eva , Latt Moe , Lee Natasha , El-Mansori Ibtessam , Layton Alison
Published: June 2024

Health-related quality of life is now recognized as an essential outcome to assess in acne trials and practice. Many patient-reported outcomes exist, including the Assessment of the Psychological and Social Effects of Acne (APSEA), which is an acne-specific measure (Layton AM, Seukeran D, Cunliffe WJ. Scarred for life? Dermatology 1997; 195: 15–21). APSEA was developed in 1990s and subsequently psychometric standards and methods have progressed. The purpose of this study is to conduct an updated psychometric analysis of the APSEA among a cohort of patients being treated for acne in routine clinical practice. Exploratory factor analysis (EFA), a method of classical test construction, was carried out (n = 993). To test the adequacy of the sample size for undertaking factor analysis, values for the Kaiser–Meyer–Olkin test and Bartlett’s test of sphericity were calculated, as well as Cronbach’s alpha. Following the EFA and generation of the proposed scales, the individual domains were calculated and transformed onto a scale of 0–100 by summing the items within the scale, dividing by the total possible score within that domain. A confirmatory factor analysis (CFA) was then undertaken using a new second dataset (n = 501) to test the factor conceptual framework, using MPlus 8.6 software (http://www.statmodel.com). Descriptive statistics and tests of internal consistency reliability and construct validity (concurrent) were also undertaken using a priori hypotheses and comparisons with the Dermatology Life Quality Index (DLQI) and Patient Health Questionniare-9 (PHQ-9). The EFA suggested a three-domain model (anxiety and depression, body image and self-esteem, and social functioning), which was confirmed in the CFA analysis whereby the goodness of fit indices all indicated good model fit (RMSEA = 0.038, CFI = 0.96, TLI = 0.96, SMR = 0.048). Cronbach’s alpha values exceeded 0.70, and item-total correlations exceeded 0.40 for all three domains, indicating good internal consistency reliability. All three APSEA domains were also positively correlated with the DLQI and the PHQ-9, indicating good construct validity of the tool. This EFA study has demonstrated the validity and reliability of a novel version of APSEA, which we have termed APSEA-3 to reflect the three unique domains it captures. Preliminary results show that the tool is responsive to change and useful for measuring the psychosocial impact of acne.
BH05 (P049) Best foot forward: awareness of melanoma of the foot among podiatrists
Authors: Nolan Brian , O’Connor Cathal , Murphy Michelle
Published: June 2024

Melanoma of the foot can masquerade as ulcerative conditions, congealed blood and trauma. Thus, even for experienced clinicians, diagnosis can prove challenging. There is a paucity of evidence about the role that podiatrists, who are routinely exposed to patients’ lower limbs, play in melanoma detection. The aim of this study was to assess the awareness and knowledge of melanoma among podiatrists, and to investigate whether podiatrists examine and assess suspicious pigmented lesions of the foot. An anonymous 18-question survey was designed assessing podiatrists’ knowledge of melanoma of the lower limb, and exposure to suspicious pigmented lesions. Ethical approval was granted by the local research ethics committee. This survey investigated the frequency of examination of suspicious pigmented lesions, insight into what constitutes a suspicious pigmented lesion, actions taken upon detection of such lesions, and suggestions for helping to improve early detection of melanoma. The survey was distributed anonymously by the national podiatrists’ association to 400 registered members over a 3-month period. The survey generated 247 responses (62% response rate, n = 400). Most podiatrists (81%) had over 20 years’ experience, and saw an average of 30 patients weekly. Over two-thirds (68%, n = 167) had been asked to examine suspicious pigmented lesions on the lower limb, of whom almost two-thirds (61%, n = 102) reported being frequently asked to examine suspicious pigmented lesions. Over two-thirds of podiatrists (71%, n = 175) reported identifying a lesion that they felt could represent melanoma, of whom 79% advised presentation to the general practitioner (GP), 8% advised dermatology review, 6% took photographs for skin-mapping, 6% contacted the patient’s GP directly, and one took a biopsy. Most (81.9%) did not receive subsequent feedback from the patients or GP. Just over a third (34.4%, n = 83) reported not feeling comfortable contacting a GP surgery directly to refer a patient, while 55.8% (n = 135) did not feel comfortable discussing sunscreen and photoprotection with patients. Most (81.7%, n = 196) did not feel they received satisfactory undergraduate education in melanoma. Suggestions for improving early detection of melanoma of the foot among podiatrists included enhanced undergraduate training, a clear referral pathway for podiatrists, and feedback from their referrals to GP or dermatologists. There is a concerning gap between the reported frequency of suspicious pigmented lesions in podiatry practice and the lack of formal training in melanoma detection and assessment. Improved training, clearer referral guidelines, and enhanced interprofessional communication strategies may improve early detection of melanoma of the foot among podiatrists.
BH11 A curious cause of ‘shrimp nail’
Authors: Kearney Nicola , Roche Muireann
Published: June 2024

A 25-year-old woman presented with a 7-year history of dystrophic great toenails, on a background of ulcerative colitis treated with the tumour necrosis factor (TNF)-α inhibitor, infliximab. The reported nail changes occurred after initiation of infliximab. Prior to review in the dermatology clinic, this patient had been treated with a year of oral antifungals without significant benefit. On examination, both great toenails were dystrophic with a stacked abnormal nail plate, particularly at the left great toenail, and had the appearance of ‘shrimp nail’. She was also noted to have a mild paronychia with some periungual ooze at the toenail of her right hallux. Her fingernails were normal. She was prescribed hydrocortisone plus miconazole to use for cuticular inflammation, and also had an avulsion of her left great toenail 8 months following the initial review, with very slow nail regrowth of approximately two-thirds over an 18-month period. A 32-year-old woman also attended our dermatology department with a history of psoriasis with associated psoriatic arthritis. She had been treated with apremilast for 2 years before being switched to the anti-TNF agent, certolizumab, as she was trying to conceive. Approximately 6 months following the initiation of this anti-TNF medication, the patient was noted to have dystrophic great toenails, most markedly at her left hallux, with a stacked abnormal nail plate. This patient’s nails also had the appearance of shrimp nails. She was referred for and is awaiting an avulsion of her left great toenail. These two clinical vignettes highlight cases of shrimp nail in patients who were newly commenced on anti-TNF medications. ‘Shrimp nail’, a rarely described entity, refers to a pronounced vertical curvature of the nail plate that resembles the back of a shrimp. It is caused by sequential onychomadesis that occurs before sufficient regeneration of the new nail is completed. Onychomadesis, related to spontaneous arrested growth of the nail matrix, has a multitude of causes including traumatic insults, systemic insults, local inflammation or infectious involvement of the nail matrix, and drug-induced arrest of nail matrix growth (Buttars B, Braswell MA, Huynh T et al. Congenital malalignment of the great toenail and onychomadesis in monozygotic twins. JAAD Case Rep 2021; 14: 1–3). To date, there are no cases in the literature that describe shrimp nail occurring in association with anti-TNF medication. Due to the development of shrimp nail within a number of months following the initiation of anti-TNF medication, coupled with an absence of traumatic insults to the nails, we contend that shrimp nail has occurred in these patients as an adverse effect of anti-TNF medication.
CD07 Let the games begin! Paediatric facial allergic contact dermatitis secondary to a gaming virtual reality headset
Authors: Akhtar Shaheen , Stone Natalie
Published: June 2024

A 13-year-old boy presented with an 8-year history of recurrent facial dermatitis. He had a history of atopic eczema and had developed intermittent swelling, redness and scaling of the face for several years, initially thought to be related to sunscreen exposure but more recently associated with prolonged time wearing his virtual reality (VR) headset. The distribution of the rash over the cheeks coincided with areas in contact with the headset rubber foam padding. Patch testing to the British Society for Cutaneous Allergy standard series, facial series, photoallergen series and a sample from the headset foam showed positive reactions to carba mix 3% (day 2+, day 4++), methylchloroisothiazolinone with methylisothiazolinone (MCI/MI) 0.02% (day 2+, day 4+), methylisothiazolinone (MI) 0.2% (day 2+, day 4+), 2-bromo-2-nitropropane 0.5% (day 2+, day 4+), methyldibromoglutaronitrile 0.3% (day 2−, day 4+), benzisothiazolinone 0.1% (day 2+, day 4+), propolis (day 2−, day 4+) and the patient’s own VR headset sample as is (day 2+, day 4+). Carba mix was felt to be relevant to the sponge rubber headset padding, which was also positive on testing. 2-Bromo-2-nitropropane was of current relevance to use of a facial ‘cooling spray’ containing this preservative. The other reactions were of unknown relevance. Avoidance of the headset led to complete resolution of symptoms. The VR company has since provided a cover for the padding, which has allowed our patient to wear the device without flaring his skin. The UK has one of Europe’s largest gaming markets, with projections indicating a surge in video game users from 51.2 million in 2023 to an estimated 57.6 million by 2027. Approximately 56% of the UK population engages in gaming, with most notably the demographic aged 16–24 years reporting 88% engagement in video games, and 68% of individuals aged 7–18 years owning gaming consoles. VR headsets are currently utilized by only 1% of children aged 3–15 years, hindered by the substantial price tag of £1420 for some VR headsets. However, the availability of more affordable alternatives will drive increased usage. Virtual meetings and working from home are becoming commonplace, widening potential exposure to VR headsets in the workplace. Gaming controllers are reported to cause ACD, as well as ‘PlayStation thumb’, with desquamation, lichenified hyperkeratotic papules and fissures on the lateral aspect of the thumbs. PlayStation palmar hidradenitis manifests with discrete, erythematous, tender nodules over the finger pulps and the palmar aspects of both hands, caused by repeated trauma while gaming. To our knowledge, ACD caused by a VR headset has not been previously reported. We would like to highlight this potential new source of ACD to the gaming and wider working population.
DS14 Not all dimples are simples
Authors: Sankey Sana , Ailenei Elena , Amarasena Chalani , Thomas Suraj , Preena Dhulsan , Gahir Daya , Paul Manju
Published: June 2024

We discuss four cases of orofacial fistulas presenting via the skin cancer pathway over 12 months. The predominant morphological presentation of the lesions was dimpling on the skin. The time to presentation ranged from 6 to 24 months. All patients required surgical input from the maxillofacial team. Case 1 is a 76-year-old man referred with a 2-year history of a lesion under the left submandibular area. Computed tomography (CT) of the neck revealed a dental apical cyst. The patient underwent a tooth extraction, leading to sinus resolution. Case 2 is a 58-year-old man who presented with a ruptured lesion on the left cheek, leading to recurrent discharges. The ultrasound scan (USS) revealed a sinus tract from a dental infection that had tracked to the skin. The sinus resolved after tooth extraction. Case 3 is a 54-year-old woman referred with a chronic, indented papule above the left nasolabial groove. USS examination revealed a heterogeneous lesion tracking deep into the subcutaneous tissue. An orthopantomogram identified a periapical infection of the upper-left third tooth. She underwent root canal treatment with resolution of the sinus. Case 4 is a 79-year-old woman with a 6-month history of a nonhealing discharging lesion in the left submental area. CT revealed soft-tissue thickening along the left mandible alveolar margin involving the buccal aspect, extending as a sinus to the skin surface and extensive osteoradionecrosis. Unfortunately, she succumbed to an unrelated illness and did not complete her treatment. An orofacial fistula, or sinus, is an abnormal connection between the oral cavity and the face’s surface. Despite its rarity, anyone can be affected regardless of age, sex or race. Dental issues cause most oral cutaneous fistulas and are often accompanied by inflammation. Chronic dental periapical infections and dentoalveolar abscesses are the most common culprits of intraoral and extraoral fistulas. The discharging points on the skin depend on the relationship between the muscle attachment and the site of the infection. These lesions may be mistaken for more severe conditions like squamous cell carcinoma or cysts, especially if ulcerated. Thus, careful examination of the oral cavity and dental history is crucial in diagnosis. Imaging tests like USS or CT can confirm the diagnosis. Treatment options involve antibiotics and dental treatment. Usually, fistulas present to dentists or surgeons, but occasionally they can be referred to the skin cancer clinics. A high level of suspicion is essential to achieve an early diagnosis and prompt treatment.