bluuebunny/crossref_metadata_2025 huggingface dataset:
Development and application of ultrafast circular dichroism
spectroscopy techniques
Authors: Cui Tong , Jia Menghui , Wu Peicong , Hu Ke , Wang Xueli , Zhang Sanjun , Pan Haifeng , Chen Jinquan
Published: June 2024

Chirality hold broad applications in life sciences, quantum devices, and various other areas. Traditionally, molecular chirality can be characterized by using steady-state circular dichroism spectroscopy. However, the techniques that can characterize excited state chirality are progressively capturing the public interest as it can provide the dynamic information for chirality generation and transfer. In this review, we focus on the theoretical background and the developmental history of femtosecond time-resolved circular dichroism spectroscopy (TR-CD) techniques around the world. Additionally, we provide examples to showcase the utility of these techniques in the analysis of the dynamical molecular chemical structures, the investigation of molecular chirality generation, and the detection of electron spin dynamics in semiconductor quantum dots.
Ultra-soft desorption assisted mass spectrometry using picosecond
infrared laser for the detection of ions in the liquid surface
Authors: Li Ziyuan , Wang Yue , Tong Tiantian , Chen Ziwei , Tian Shan Xi
Published: June 2024

To identify the species in liquid surface using mass spectrometry, we must eliminate or reduce interferences during the vaporization or desorption of the species from the liquid surface. It is much more challenging to isolate the ionic, larger species from the liquid surfaces because of the frangible structures and the higher solvation energies of those species. Here we demonstrate a new mass spectrometry in which the ionic species at the liquid surface can be desorbed with ultrasoft infrared picosecond laser pulses while the liquid surface is not breached. This laser desorption assisted mass spectrometry is not only a powerful tool to detect the fragile species but also promising to investigate vibrational energy transfer dynamics in the liquid surface.
Māori loanwords in New Zealand English
Authors: Calude Andreea S. , Zenner Eline , Rosseel Laura , Whaanga Hēmi
Published: June 2024

The Indigenous language of ANZ, Māori is undergoing significant revitalisation, following severe loss of vitality
caused by English colonialism. One dimension to this revitalisation is the normalising of borrowings from Māori into New Zealand
English (NZE). However, there are currently no empirical studies of adults’ naming patterns for concepts that can be lexicalised
by Māori words in NZE. We report on a picture-naming experiment in which 48 participants are asked to name a set of target and
control pictures depicting everyday concepts from three semantic categories which involve Māori borrowings: flora/fauna,
people/places, material culture. Following a background questionnaire, we group participants into three categories, depending on
their orientation towards Māori language and culture. Results suggest a clear association between participant orientation and
their use of Māori loanwords. Alternative interpretations are discussed, including questions for future research on the
relationship between NZE lexical variation and language planning.
Comparison of the density and composition of bacteria and fungi in the air of anoxic and aeration tanks in the wastewater treatment plant
Authors: Nga Dang Diep Yen , Gam Nguyen Thi Hong , Minh Tran Hoang , Hien To Thi
Published: June 2024

The bioaerosols from the wastewater treatment plant can be propagated into the air, affecting the health of residents, animals, and plants around the area. This study was conducted to evaluate the density and composition of bioaerosols (bacteria and fungi) in anoxic and aeration tanks of a domestic wastewater treatment plant. Bioaerosol samples were taken by the active method with SKC Biostage. The agar dishes were placed at a height of 1.5 m above the ground. After sample collection, the dishes were incubated at 37 ±1 °C for 24h-48h for bacteria and at 25 ±1 °C for 72h-120h for fungi. Then, these microorganisms were identified by 16S rRNA (16S Metabarcoding) method for bacteria and taxonomy method for fungi. The results showed that the density of bacteria and mold in the anoxic tank ranged from 233.2 ±7.8 to 339.2 ±13.9 CFU/m3 and 91.8 ±3.2 to 197.9 ±10.1 CFU/m3, respectively. Meanwhile, bacterial and mold densities of aeration tank ranged from 275.6 ±10.4 to 424.0 ±17.3 CFU/m3 and 176.7 ±5.8 to 254.4 ±12.1 CFU/m3, respectively. The density of bacteria and mold in the aeration tank is higher than in the anoxic tank. On the other hand, the 16S Metabarcoding analysis for the microbial diversity detects more than 100 species in two tanks, the predominant bacterial species are: Bacillus megaterium (B. megaterium), Bacillus cereus (B. cereus), Staphylococcus sciuri (S. sciuri) and two common fungi Aspergillus tamarii (A. tamarii), and Penicillium rubers (P. rubers). This preliminary survey in Viet Nam reveals the existence and diversity of bioaerosols in the air from the biological treatment tanks of the wastewater treatment plant.
Assessing the invasive potential of Hydrocharis dubia (Blume) Backer in U Minh Thuong National Park, Vietnam
Authors: Tran Q D , Le B T , Pham Q H , Nguyen T L T
Published: June 2024

Eco-physiological characteristics of Hydrocharis dubia (Blume) Backer in the U Minh Thuong National Park (UMTNP) were surveyed from April 2022 to May 2023 to assess its invasive potential risk. Thirty-six four-square-meter plots (4m x 1m) were established along the canals in the core zone to determine the coverage of H. dubia and other hydrophytes, which were used to calculate the Importance Value Index (IVI%) and Shannon-Wiener index (H’). PSII Maximum quantum efficiency (Fv/Fm), Performance Index (PIabs), and Chlorophyll concentration (Chl) in leaves were measured to assess photosynthetic efficiency. The IVI indices showed that Pistia stratiotes L. and H. dubia were the most and second dominant species in the hydrophytic plant community, respectively. However, the photosynthetic activity of H. dubia was significantly higher than that of P. stratiotes. The Fv/Fm (0.830-0.842) of H. dubia were stable during the study period. The higher value of PIabs in the wet season (2.293 ± 0.191) compared to the dry season (1.402 ± 0.105) indicated that H. dubia’s growth was favored in this period. The eco-physiological characteristics of H. dubia claim its high photosynthetic activity, which can be considered an early warning of the species’ spread in the UMTNP, although it is currently suppressed by P. stratiotes.
Assessing impact of sluice gate operation on salinity intrusion in Ho Chi Minh City
Authors: Danh Vo Thanh , Linh Do Quang , Thuy Nguyen Thi Diem
Published: June 2024

This study aims to evaluate salinity intrusion propagation in Ho Chi Minh City under the operation of six tidal sluice gates, namely, Ben Nghe, Tan Thuan, Phu Xuan, Muong Chuoi, Cay Kho, and Phu Dinh by utilizing the HEC-RAS model. The outcomes during calibration and validation procedures underscore the high performance of the HEC-RAS model in simulating salinity intrusion over the study area. In particular, R2 and NSE values were higher than satisfactory thresholds of 0.80 for water level and discharge simulations and 0.50 for salinity concentration simulations. Based on the calibrated HEC-RAS model, this study examined the potential influences of sluice gate operations on salinity distribution under different scenarios. Results indicate that salinity concentration would exhibit increasing trends when operating Ben Nghe and Tan Thuan sluices, while the closure of the Phu Xuan and Muong Chuoi sluices would cause a reduction in the salinity concentration within the areas enclosed by these sluices. In addition, the operations of the Cay Kho and Phu Dinh sluices would lead to decreases and increases in salinity concentration in the upstream and downstream areas of each corresponding sluice gate, respectively. Moreover, when closing six sluice gates simultaneously, the salinity concentration inside and outside the sluice gates would decrease and increase, respectively. In general, these findings indicate that salinity concentration and spatial distribution are significantly influenced by the location and structure of each tidal sluice gate.
Evaluating and predicting coastal shoreline changes in the Doi Duong - Phan Thiet beach area by remote sensing and GIS technology
Authors: Thi My Diem Phung , Thi Kim Tran , Thuy Linh Phan , Nguyen Ky Phung , Thi Bay Nguyen
Published: June 2024

Assessing the shoreline variability is paramount in understanding the erosion and coastal accretion processes. The potential impact of erosion on coastal communities, particularly in coastal regions, amplifies the vulnerability to coastal disasters. In this study, Landsat satellite imagery captured from 1990 to 2022 was utilized, in conjunction with Geographic Information System (GIS), to scrutinize alterations in the shoreline of Doi Duong Beach - Phan Thiet. The satellite images were independently processed using aspect-ratio methods and thresholding techniques to determine the prevailing condition of the coastline. The rate of shoreline change was quantified using the DSAS tool. The investigation’s findings reveal a dynamic interplay between erosion and accretion, with accretion dominance explicitly evident within the areas surrounding the Ca Ty - Phu Hai river mouth. The average annual shoreline change rate is 27.1 m/yr for the Ca Ty River mouth and 16.5 m/yr for the Phu Hai River mouth. The most significant disparity between the recorded coastline in 1990 and 2022 measures 868 m. Additionally, the projections for the coastline until 2032 indicate that accretion remains the dominant process. This research shows that combining geospatial techniques and numerical models is a reliable way to study shoreline change trends.
Proposed solutions for grapes development in Ninh Thuan by Fuzzy-ANP-SWOT
Authors: Tuan Nguyen Hoang , Canh Truong Thanh
Published: June 2024

Ninh Thuan is one of the extremely dry regions in Vietnam, and choosing farming solutions in the agricultural sector is one of the top priorities. Research chooses grapes to propose solutions for development in drought because this is considered one of the local staple crops. The study used a multi-criteria decision-making method (MCDM) with a combination of Fuzzy Analytic Network Processes (Fuzzy - ANP). Through the study of published documents and surveys, the study has identified 24 factors belonging to four groups: natural, economic, social and policy and total as a SWOT matrix. Through the Fuzzy ANP model and expert assessment, the research has proposed eight strategies, and the study identified priority strategies for the sustainable development of vines in Ninh Thuan. The results are ranked as follows: WO2 (0.162), ST1 (0.148), WO1 (0.137), SO2(0.124), WT2(0.128), ST2 (0.122), WT1(0.119) and SO1 (0.059). Research results are the basis for helping local governments have more quantitative decision-making tools, thereby helping proposed solutions to be more objective and suitable to the actual situation.
FRESH-based 3D bioprinting of complex biological geometries using chitosan bioink
Authors: Chaurasia Parul , Singh Richa , Mahto Sanjeev Kumar
Published: June 2024

Traditional three-dimensional (3D) bioprinting has always been associated with the challenge of print fidelity of complex geometries due to the gel-like nature of the bioinks. Embedded 3D bioprinting has emerged as a potential solution to print complex geometries using proteins and polysaccharides-based bioinks. This study demonstrated the Freeform Reversible Embedding of Suspended Hydrogels (FRESH) 3D bioprinting method of chitosan bioink to 3D bioprint complex geometries. 4.5% chitosan was dissolved in an alkali solvent to prepare the bioink. Rheological evaluation of the bioink described its shear-thinning nature. The power law equation was fitted to the shear rate-viscosity plot. The flow index value was found to be less than 1, categorizing the material as pseudo-plastic. The chitosan bioink was extruded into another medium, a thermo-responsive 4.5% gelatin hydrogel. This hydrogel supports the growing print structures while printing. After this, the 3D bioprinted structure was crosslinked with hot water to stabilize the structure. Using this method, we have 3D bioprinted complex biological structures like the human tri-leaflet heart valve, a section of a human right coronary arterial tree, a scale-down outer structure of the human kidney, and a human ear. Additionally, we have shown the mechanical tunability and suturability of the 3D bioprinted structures. This study demonstrates the capability of the chitosan bioink and FRESH method for 3D bioprinting of complex biological models for biomedical applications.
A biopsy-sized 3D skin model with a perifollicular vascular plexus enables studying immune cell trafficking in the skin
Authors: Shah Krutav Rakesh , Garriga-Cerda Laura , Pappalardo Alberto , Sorrells Leila , Jeong Hun Jin , Lee Chang H , Abaci Hasan Erbil
Published: June 2024

Human skin vasculature features a unique anatomy in close proximity to the skin appendages and acts as a gatekeeper for constitutive lymphocyte trafficking to the skin. Approximating such structural complexity and functionality in 3D skin models is an outstanding tissue engineering challenge. In this study, we leverage the capabilities of the digital-light-processing bioprinting to generate an anatomically-relevant and miniaturized 3D skin-on-a-chip (3D-SoC) model in the size of a 6 mm punch biopsy. The 3D-SoC contains a perfusable vascular network resembling the superficial vascular plexus of the skin and closely surrounding bioengineered hair follicles. The perfusion capabilities of the 3D-SoC enables the circulation of immune cells, and high-resolution imaging of the immune cell-endothelial cell interactions, namely tethering, rolling, and extravasation in real-time. Moreover, the vascular pattern in 3D-SoC captures the physiological range of shear rates found in cutaneous blood vessels and allows for studying the effect of shear rate on T cell trafficking. In 3D-SoC, as expected,in vitro-polarized T helper 1 (Th1) cells show a stronger attachment on the vasculature compared to naïve T cells. Both naïve and T cells exhibit higher retention in the low-shear zones in the early stages (<5 min) of T cell attachment. Interestingly, at later stages T cell retention rate becomes independent of the shear rate. The attached Th1 cells further transmigrate from the vessel walls to the extracellular space and migrate toward the bioengineered hair follicles and interfollicular epidermis. When the epidermis is not present, Th1 cell migration toward the epidermis is significantly hindered, underscoring the role of epidermal signals on T cell infiltration. Our data validates the capabilities of 3D-SoC model to study the interactions between immune cells and skin vasculature in the context of epidermal signals. The biopsy-sized 3D-SoC model in this study represents a new level of anatomical and cellular complexity, and brings us a step closer to generating a truly functional human skin with its tissue-specific vasculature and appendages in the presence of circulating immune cells.
Quantum physics: the tranquillity of the Euclidean time circle
Authors: Zaanen Jan
Published: June 2024

It is argued that the standard expositions of quantum weirdness, resting on small atomic physics-inspired systems, is rather pathological since nature is nearly invariably based on the collective behaviour of infinities of microscopic quantum degrees of freedom. A concise and original descriptive explanation of the way that thermal field theory works that governs this physics is presented, culminating in the Euclidean path integral formalism. This exposes in turn the deeply acausal nature of time when this microscopic reality is ‘left alone’, subjected to the principle of unitary time evolution. Upon connecting this to the macroscopic world with its causal time, probability itself emerges through the mystery of the collapse of the wavefunction. Finally, combining this with the Euclidean signature black hole geometry of Chapter 2, the Hawking temperature is very easy to understand. This may be the most challenging chapter of the book for the non-professional physics reader.
ifDEEPre: large protein language-based deep learning enables interpretable and fast predictions of enzyme commission numbers
Authors: Tan Qingxiong , Xiao Jin , Chen Jiayang , Wang Yixuan , Zhang Zeliang , Zhao Tiancheng , Li Yu
Published: June 2024

Accurate understanding of the biological functions of enzymes is vital for various tasks in both pathologies and industrial biotechnology. However, the existing methods are usually not fast enough and lack explanations on the prediction results, which severely limits their real-world applications. Following our previous work, DEEPre, we propose a new interpretable and fast version (ifDEEPre) by designing novel self-guided attention and incorporating biological knowledge learned via large protein language models to accurately predict the commission numbers of enzymes and confirm their functions. Novel self-guided attention is designed to optimize the unique contributions of representations, automatically detecting key protein motifs to provide meaningful interpretations. Representations learned from raw protein sequences are strictly screened to improve the running speed of the framework, 50 times faster than DEEPre while requiring 12.89 times smaller storage space. Large language modules are incorporated to learn physical properties from hundreds of millions of proteins, extending biological knowledge of the whole network. Extensive experiments indicate that ifDEEPre outperforms all the current methods, achieving more than 14.22% larger F1-score on the NEW dataset. Furthermore, the trained ifDEEPre models accurately capture multi-level protein biological patterns and infer evolutionary trends of enzymes by taking only raw sequences without label information. Meanwhile, ifDEEPre predicts the evolutionary relationships between different yeast sub-species, which are highly consistent with the ground truth. Case studies indicate that ifDEEPre can detect key amino acid motifs, which have important implications for designing novel enzymes. A web server running ifDEEPre is available at https://proj.cse.cuhk.edu.hk/aihlab/ifdeepre/ to provide convenient services to the public. Meanwhile, ifDEEPre is freely available on GitHub at https://github.com/ml4bio/ifDEEPre/.
Conway–Bromage–Lyndon (CBL): an exact, dynamic representation of k-mer sets
Authors: Martayan Igor , Cazaux Bastien , Limasset Antoine , Marchet Camille
Published: June 2024

In this article, we introduce the Conway–Bromage–Lyndon (CBL) structure, a compressed, dynamic and exact method for representing k-mer sets. Originating from Conway and Bromage’s concept, CBL innovatively employs the smallest cyclic rotations of k-mers, akin to Lyndon words, to leverage lexicographic redundancies. In order to support dynamic operations and set operations, we propose a dynamic bit vector structure that draws a parallel with Elias-Fano’s scheme. This structure is encapsulated in a Rust library, demonstrating a balanced blend of construction efficiency, cache locality, and compression. Our findings suggest that CBL outperforms existing dynamic k-mer set methods. Unique to this work, CBL stands out as the only known exact k-mer structure offering in-place set operations. Its different combined abilities position it as a flexible Swiss knife structure for k-mer set management.

Availability and implementation

https://github.com/imartayan/CBL.
Learning locality-sensitive bucketing functions
Authors: Yuan Xin , Chen Ke , Li Xiang , Shi Qian , Shao Mingfu
Published: June 2024

Motivation

Many tasks in sequence analysis ask to identify biologically related sequences in a large set. The edit distance, being a sensible model for both evolution and sequencing error, is widely used in these tasks as a measure. The resulting computational problem—to recognize all pairs of sequences within a small edit distance—turns out to be exceedingly difficult, since the edit distance is known to be notoriously expensive to compute and that all-versus-all comparison is simply not acceptable with millions or billions of sequences. Among many attempts, we recently proposed the locality-sensitive bucketing (LSB) functions to meet this challenge. Formally, a (d1,d2)-LSB function sends sequences into multiple buckets with the guarantee that pairs of sequences of edit distance at most d1 can be found within a same bucket while those of edit distance at least d2 do not share any. LSB functions generalize the locality-sensitive hashing (LSH) functions and admit favorable properties, with a notable highlight being that optimal LSB functions for certain (d1,d2) exist. LSB functions hold the potential of solving above problems optimally, but the existence of LSB functions for more general (d1,d2) remains unclear, let alone constructing them for practical use.

Results

In this work, we aim to utilize machine learning techniques to train LSB functions. With the development of a novel loss function and insights in the neural network structures that can potentially extend beyond this specific task, we obtained LSB functions that exhibit nearly perfect accuracy for certain (d1,d2), matching our theoretical results, and high accuracy for many others. Comparing to the state-of-the-art LSH method Order Min Hash, the trained LSB functions achieve a 2- to 5-fold improvement on the sensitivity of recognizing similar sequences. An experiment on analyzing erroneous cell barcode data is also included to demonstrate the application of the trained LSB functions.

Availability and implementation

The code for the training process and the structure of trained models are freely available at https://github.com/Shao-Group/lsb-learn.
An algorithm for decoy-free false discovery rate estimation in XL-MS/MS proteomics
Authors: Peng Yisu , Jain Shantanu , Radivojac Predrag
Published: June 2024

Motivation

Cross-linking tandem mass spectrometry (XL-MS/MS) is an established analytical platform used to determine distance constraints between residues within a protein or from physically interacting proteins, thus improving our understanding of protein structure and function. To aid biological discovery with XL-MS/MS, it is essential that pairs of chemically linked peptides be accurately identified, a process that requires: (i) database search, that creates a ranked list of candidate peptide pairs for each experimental spectrum and (ii) false discovery rate (FDR) estimation, that determines the probability of a false match in a group of top-ranked peptide pairs with scores above a given threshold. Currently, the only available FDR estimation mechanism in XL-MS/MS is the target-decoy approach (TDA). However, despite its simplicity, TDA has both theoretical and practical limitations that impact the estimation accuracy and increase run time over potential decoy-free approaches (DFAs).

Results

We introduce a novel decoy-free framework for FDR estimation in XL-MS/MS. Our approach relies on multi-sample mixtures of skew normal distributions, where the latent components correspond to the scores of correct peptide pairs (both peptides identified correctly), partially incorrect peptide pairs (one peptide identified correctly, the other incorrectly), and incorrect peptide pairs (both peptides identified incorrectly). To learn these components, we exploit the score distributions of first- and second-ranked peptide-spectrum matches for each experimental spectrum and subsequently estimate FDR using a novel expectation-maximization algorithm with constraints. We evaluate the method on ten datasets and provide evidence that the proposed DFA is theoretically sound and a viable alternative to TDA owing to its good performance in terms of accuracy, variance of estimation, and run time.

Availability and implementation

https://github.com/shawn-peng/xlms
Scalable de novo classification of antibiotic resistance of Mycobacterium tuberculosis
Authors: Serajian Mohammadali , Marini Simone , Alanko Jarno N , Noyes Noelle R , Prosperi Mattia , Boucher Christina
Published: June 2024

Motivation

World Health Organization estimates that there were over 10 million cases of tuberculosis (TB) worldwide in 2019, resulting in over 1.4 million deaths, with a worrisome increasing trend yearly. The disease is caused by Mycobacterium tuberculosis (MTB) through airborne transmission. Treatment of TB is estimated to be 85% successful, however, this drops to 57% if MTB exhibits multiple antimicrobial resistance (AMR), for which fewer treatment options are available.

Results

We develop a robust machine-learning classifier using both linear and nonlinear models (i.e. LASSO logistic regression (LR) and random forests (RF)) to predict the phenotypic resistance of Mycobacterium tuberculosis (MTB) for a broad range of antibiotic drugs. We use data from the CRyPTIC consortium to train our classifier, which consists of whole genome sequencing and antibiotic susceptibility testing (AST) phenotypic data for 13 different antibiotics. To train our model, we assemble the sequence data into genomic contigs, identify all unique 31-mers in the set of contigs, and build a feature matrix M, where M[i, j] is equal to the number of times the ith 31-mer occurs in the jth genome. Due to the size of this feature matrix (over 350 million unique 31-mers), we build and use a sparse matrix representation. Our method, which we refer to as MTB++, leverages compact data structures and iterative methods to allow for the screening of all the 31-mers in the development of both LASSO LR and RF. MTB++ is able to achieve high discrimination (F-1 >80%) for the first-line antibiotics. Moreover, MTB++ had the highest F-1 score in all but three classes and was the most comprehensive since it had an F-1 score >75% in all but four (rare) antibiotic drugs. We use our feature selection to contextualize the 31-mers that are used for the prediction of phenotypic resistance, leading to some insights about sequence similarity to genes in MEGARes. Lastly, we give an estimate of the amount of data that is needed in order to provide accurate predictions.

Availability

The models and source code are publicly available on Github at https://github.com/M-Serajian/MTB-Pipeline.
CODEX: COunterfactual Deep learning for the in silico EXploration of cancer cell line perturbations
Authors: Schrod Stefan , Zacharias Helena U , Beißbarth Tim , Hauschild Anne-Christin , Altenbuchinger Michael
Published: June 2024

Motivation

High-throughput screens (HTS) provide a powerful tool to decipher the causal effects of chemical and genetic perturbations on cancer cell lines. Their ability to evaluate a wide spectrum of interventions, from single drugs to intricate drug combinations and CRISPR-interference, has established them as an invaluable resource for the development of novel therapeutic approaches. Nevertheless, the combinatorial complexity of potential interventions makes a comprehensive exploration intractable. Hence, prioritizing interventions for further experimental investigation becomes of utmost importance.

Results

We propose CODEX (COunterfactual Deep learning for the in silico EXploration of cancer cell line perturbations) as a general framework for the causal modeling of HTS data, linking perturbations to their downstream consequences. CODEX relies on a stringent causal modeling strategy based on counterfactual reasoning. As such, CODEX predicts drug-specific cellular responses, comprising cell survival and molecular alterations, and facilitates the in silico exploration of drug combinations. This is achieved for both bulk and single-cell HTS. We further show that CODEX provides a rationale to explore complex genetic modifications from CRISPR-interference in silico in single cells.

Availability and implementation

Our implementation of CODEX is publicly available at https://github.com/sschrod/CODEX. All data used in this article are publicly available.
Hide and seek: chemical cues drive site preference among potential mates and intraguild competitors
Authors: Dionisio-da-Silva Welton , Araujo Rocha-da-Silva Katarina Luisa , Veloso Helena Maria Gonçalves , DaSilva Marcio Bernardino
Published: June 2024

Chemical perception is essential among arthropods for mate recognition, prey search, and predator avoidance, especially for solitary predators which are often aggressive. Such mechanisms may be intensified in environments like the Caatinga, a seasonally dry tropical forest in Brazil, characterized by low habitat complexity and high seasonal variation. Thus, we investigated chemical perception between two scorpion species from this environment, involved in intraguild competition. Experiments assessed their response to chemical cues from prey, predators, and potential mates. We use Y-mazes to test the time spent by the scorpions between Y-arms with or without a given substrate-borne chemical cue (site preference) and the number of active individuals during trials (presence of activity). Scorpions’ activity was not influenced by chemical stimuli, although they clearly exhibit site preferences. The smaller predators avoided sites with the larger species’ chemical cues, while the larger predators preferred sites with the smaller species’ cues. Additionally, both species trailed female chemical cues. These findings suggest a dual-oriented arms race where prey and predator modulate their behaviour to avoid and hunt heterospecifics, respectively. This study provides the first evidence of a scorpion using chemical cues to detect a heterospecific scorpion and highlights the importance of this trait in arachnids.
CPC03 Notch your average dermatitis
Authors: Long Amy , Murphy Lisa , Quigley Claire , Leonard Niamh , Clowry Julieanne
Published: June 2024

We present the case of triangular nasal notch sign in a White woman with previous exposure to tumour necrosis factor (TNF) inhibition for Crohn disease, which persisted throughout a biologic-free period. The 33-year-old woman presented with symptoms of nasal rash, itch and cosmetic concern for bilateral indentations in the nasal soft triangle, ongoing for 6 years. Medical history was notable for childhood atopic dermatitis, herpes labialis and Crohn disease. Her Crohn disease was well controlled on ustekinumab, commenced in the last year. She commenced adalimumab 6 years before the rash first appeared, but had discontinued this agent 4 years prior to her presentation to dermatology. On examination she had patchy erythema with scale and crust affecting her nasal tip, septum, alar sidewalls and columella, with loss of the normal nostril contour and cicatricial indentation at the apex of the nasal soft triangle bilaterally. She had evidence of acute herpes simplex virus (HSV)-1 infection of the upper lip. A punch biopsy from the left nasal tip showed acanthosis and spongiosis with a dermal mixed inflammatory infiltrate including lymphocytes, histiocytes and neutrophils. There was focal ulceration and intraepithelial small abscesses, without features of granulomatous inflammation. Triangular nasal notch sign is a clinical sign that was first described in 2019 (Mesnard C, Aubert H, Bourreille A et al. The triangular nasal notch sign in patients with Crohn disease treated with tumour necrosis factor inhibitors. Br J Dermatol 2019; 181: 1103–4). This group reported eight patients with Crohn disease exposed to TNF inhibitors, presenting with a cicatricial triangular nasal notch, and hypothesized that TNF inhibition specifically was implicated in the development of the phenomenon. Similarly to these patients, our case had exposure to anti-TNF; however, the persistence of nasal dermatitis throughout a ‘biologic-free’ period is novel. The pathophysiology of TNF inhibitor-induced nasal dermatitis and triangular nasal notch sign is not fully understood. It has been hypothesized that it is within the scope of paradoxical reactions seen with TNF inhibitors and persistent Staphylococcal aureus infection. An association with HSV-1 has not been previously reported in the context of this condition. Nasal swabs in this case showed commensals only; however, clinical improvement of nasal inflammation was achieved with topical mupirocin, prophylactic valaciclovir and a short course of oral azithromycin. The singular association with Crohn disease and limited involvement of the nose is also as yet unexplained and requires further research. We encourage greater reporting of this phenomenon, to increase awareness among clinicians and to help identify the exact pathomechanism and optimal treatment.
CPC14 Winning streak: a case of congenital ichthyosiform erythroderma
Authors: O’Connor Cathal , Bussmann Neidín , Heffron Cynthia , Mhaolcatha Sarah Ní , O’Shea Sally
Published: June 2024

A first-born female infant was delivered at term with widespread redness and scale. There was no family history of genodermatoses or inflammatory dermatoses. There was no parental consanguinity and no history of miscarriages. On examination there was erythroderma, generalized thick adherent scale in a feathery pattern following lines of Blaschko, and shiny red whorls on the dorsolateral feet. There was no skin peeling or skin fragility. Several fingernails were hypoplastic. The nasal bridge was flat and the neck was short. Red reflex was present bilaterally but both eyes were noted to be small. The head and trunk were large relative to the limbs and the proximal limb segments were proportionately short. Given the constellation of signs, a specific syndromic ichthyosis was suspected. Skin biopsies from linear scaly streaks showed orthohyperkeratosis and numerous dilated follicular ostia with keratin plugs. Foci of calcification were seen in the corneocytes of the stratum corneum and hair follicles, highlighted with a von Kossa stain. Skeletal survey showed symmetric punctate calcification and stippling of the proximal femoral epiphysis and ankle bilaterally, and of the right humeral epiphysis and right carpus. These findings were in keeping with chondrodysplasia punctata, although no gross rhizomelia was appreciated radiologically. Ophthalmology review did not identify congenital cataracts. Bloods tests showed normal haematological, renal and bone parameters, and a hyperbilirubinaemia meeting the phototherapy threshold. The erythema was noted to improve markedly following 12 h of phototherapy. Urea 10% cream was helpful in reducing the ichthyosis. Genetic testing revealed a pathogenic variant in the ­emopamil-binding protein (EBP) gene (c.184C>T; p.Arg62Trp), confirming the diagnosis of Conradi–Hünermann–Happle syndrome. Conradi–Hünermann–Happle syndrome is a rare type of chondrodysplasia punctata associated with X-linked dominant mutations in the EBP gene, which impair cholesterol biosynthesis. Affected unborn males are not expected to survive to birth. Conradi–Hünermann–Happle syndrome is characterized by the triad of congenital ichthyosiform erythroderma, skeletal dysplasia and congenital cataracts. The cutaneous phenotype is variable, due to the effects of X-inactivation in female infants. Dystrophic calcifications within keratotic infundibular follicular plugs, especially in the stratum corneum, are a unique but under-recognized histopathological feature of newborns with Conradi–Hünermann–Happle syndrome. It is important to perform the skin biopsy early, as the dystrophic calcifications typically resolve spontaneously after the first few weeks of life. This case highlights a typical dramatic presentation of Conradi–Hünermann–Happle syndrome, and emphasizes the importance of early skin biopsy for diagnostic clues.
P009 Cylindrocarcinoma: a rare entity
Authors: Barry Rory , Boggs Jennifer , McMenamin Máirín , Barry Rupert
Published: June 2024

A 73-year-old man was referred from a secondary hospital to the dermatology department with a 2-year history of a biopsy-reported recurrent basal cell carcinoma on the left nasal ala. Full-skin examination revealed a solitary 20 × 11-mm, slightly tender, pink-coloured nodule. His past medical history was significant for multiple nonmelanoma skin cancers and colon cancer. No regular medications were prescribed. Mohs micrographic surgery was performed, with two layers required for margin clearance. The Mohs debulk described a carcinoma with features suggestive of a cylindrocarcinoma with necrosis and a high mitotic rate. On immunohistochemical profiling, tumour cells were strongly positive for S0X10, p63 and p53; had multifocal moderate positive staining for S100; had membranous staining for BerEP4; and were focally positive for CD117. Tumour cells were negative for epithelial membrane antigen, calponin, smooth muscle actin, keratin 20, chromogranin, GATA3 and p16. A PET-CT scan was performed, which ruled out any metastatic disease. No clinical recurrence has been observed 8 months after excision. Cylindromas are benign adnexal neoplasms, usually arising on the head and neck. Malignant transformation of these tumours has been reported only rarely, with fewer than 50 cases in the literature. A female predominance has been noted in both benign and malignant cylindromas. Nineteen cases of metastatic disease have been described, typically in the high-grade form of this malignant tumour, with spread to local lymph nodes or distant viscera. Histopathologically, cylindrocarcinomas may show a salivary gland-type basal cell adenocarcinoma-like pattern. Depending on the grade of the tumour, basaloid cells vary in size and degree of nuclear pleomorphism, and are surrounded by a hyaline eosinophilic sheath. Loss of the hyaline sheath network in a jigsaw pattern can be recognized by partial or complete loss of periodic acid–Schiff positivity in malignant cases. Focal to extensive tumour necrosis is frequently seen. Lymphovascular or perineural invasion is not typically identified. The similar clinical characteristics of cylindrocarcinomas to basal cell carcinomas prompt an important differential diagnosis for dermatology clinicians to be aware of, given the metastatic potential. The rapid growth over 2 years in our case is atypical for basal cell carcinomas and more in keeping with cylindrocarcinomas, as documented in previous case reports of this rare tumour. This case also highlights the merits of reviewing histology slides from the original referring centre when performing Mohs micrographic surgery.
P028 The importance of clinical metadata when triaging patients for face-to-face assessment and possible biopsy in a teledermatology pathway
Authors: Islam Shafiqul , Walls Joseph , Hall Per , Raza Haider , Gan John , Garcia Alba , Wishart Gordon
Published: June 2024

The 7-point checklist (7PCL) is recommended by NICE to select patients with pigmented lesions and possible melanoma for urgent referral. This research investigates the potential of using machine learning (ML) models that utilize patient metadata from a teledermatology pathway including 7PCL for suspicious skin lesion detection, and compares the performance gain for each meta-feature added with the 7PCL. We analysed clinical metadata from 53 601 skin lesions in 25 105 patients who attended private skin cancer diagnosis clinics in the UK between 2015 and 2022. For each lesion, we included the following meta-features: 7PCL (change of lesion size, shape, colour, lesion > 7 mm, inflamed, oozing, itching), weighted 7PCL, Williams score characteristics (patient age, patient sex, natural hair colour, arm mole count, sunburn history, prior nonmelanoma skin cancer), the overall Williams score, prior melanoma, lesion location, lesion age, and whether this was a predominantly nonpigmented pink lesion. All lesions were categorized as suspicious (10%) or nonsuspicious (90%) by skin cancer specialists during telemedicine triage (cancer detection rate = 5%). All meta-features were used as ML model inputs to classify whether each input was associated with suspicious or nonsuspicious classes. This study integrates five ML models (naive Bayes, logistics regression, support vector machine, random forest, and multilayer perceptron) to detect suspicious skin lesions based on patient metadata. Firstly, we compared the ML model performance between the original 7PCL and weighted 7PCL in correctly identifying suspicious skin lesions. We then added each meta-feature with 7PCL and tabulated the performance gain. We utilized balanced accuracy, sensitivity, specificity and area under the curve as evaluation metrics. There were no significant differences observed in model performance between the 7PCL and weighted 7PCL (sensitivity 68.1%). However, the performance of the ML model was improved significantly for each added meta-feature, with the best performance gain (sensitivity 85.2%) observed when 11 meta-features (lesion pink, Williams score, lesion age, sunburn, patient age, Williams group, patient sex, hair colour, site of the lesion on the body, freckling tendency, and mole count) were added to the 7PCL. This research has identified the optimal subset of meta-features that improve ML model performance for categorizing suspicious skin lesions during telemedicine triage, compared with 7PCL alone. Fusing these high-performing meta-features with image modalities is likely to further boost the ML model performance for skin cancer detection, and they could also be used to modify current skin cancer referral guidelines. The study is funded and supported by Innovate UK and the private teledermatology pathway provider.
P029 Targeted skin examinations: a reasonable compromise?
Authors: Rabindranathnambi Aswatha , Ojelabi Modupe , Elston Georgina
Published: June 2024

There has been a significant increase in referrals for suspected skin cancer since March 2021, resulting in busy urgent skin cancer clinics across the country. Gold-standard care would include a full-skin examination for all patients referred via this route to ensure other incidental lesions are not missed, but full-skin examinations are time-consuming and decrease the total number of patients who can be seen in clinic. There is only limited evidence regarding the benefits of full-skin examinations. We conducted a service evaluation: a retrospective review of all ‘new’ patients referred to a 2-week-wait skin cancer clinic in a district general hospital over a 12-month period (January to December 2022). All 205 patients were offered a full-skin examination, of whom 175 accepted full- or partial-skin examination. Overall, 21% (37 of 175) had incidental lesions identified that either warranted treatment or were concerning enough to need photography and further monitoring. Forty-four incidental lesions were picked up in total. The majority were actinic keratoses (n =  7) and basal cell cancers (n = 12). The other incidental lesions were atypical naevi (n = 8), intraepidermal carcinoma (n = 4), lentigo maligna (n = 1), vulval melanosis (n = 1) and malignant melanoma (n = 1). Importantly, most of the incidental lesions were seen in those > 50 years of age (92%) and were on the head and neck or upper body (89%). The majority of these patients (89% of those who had it documented) were found to have Fitzpatrick skin phototypes I or II. Our results suggest that examining the upper body in those > 50 years of age with skin type I and II has the highest yield of picking up further skin lesions that are either cancerous or could be precancerous. This upper-body, targeted skin examination has the potential to avoid further referrals, thus saving time and resources in the long run, for patients and primary and secondary care. Further research is needed to evaluate the impact on ‘hard’ outcomes such as morbidity and mortality rates, as well as potential cost benefits.
P032 Prevalence and severity of dermatological symptoms experienced after critical care admission: an observational study
Authors: Ali Zara , Kalsi Navneet
Published: June 2024

Recent medical advances mean that more people survive critical illnesses and intensive care unit (ICU) admissions. This has led to an uptick in reported physical, cognitive and mental health issues post-ICU (Hiser SL, Fatima A, Ali M et al. Post-intensive care syndrome (PICS): recent updates. J Intensive Care 2023; 11: 23). Despite existing research, dermatological symptoms post-ICU care have been overlooked. This study aims to assess the prevalence and extent of such symptoms in patients 1 month after ICU admission. Local approval was obtained for the study. We enrolled ICU patients admitted for 5 days or longer, or with advanced respiratory issues, from 1 August to 30 November 2023. Telephone interviews were conducted with patients 1 month after ICU admission to assess previous and new dermatological diagnoses or symptoms. If new disease was present, patients were asked about the impact on their quality of life, and if they had sought treatment. Of 148 ICU admissions in a 4-month period, 70 met the study’s criteria. Exclusions were made for patients with primary skin issues (n = 1), deceased or on an end-of-life pathway (n = 25), or still under specialist care (n = 10). Three patients could not be reached. In total, data from 31 patients were included; their ages ranged from 18 to 89 years (mean 61.8, SD 16.9) and 48% were female. Twenty-three patients (74%) experienced dermatological issues post-ICU, including xerosis (n = 8), nonspecific pruritic erythematous rash (n = 5), mouth ulcers (n = 3), hair loss (n = 3), brittle nails (n = 3), cellulitis (n = 2), seborrhoeic dermatitis (n = 2) and pruritus (n = 2). Six patients reported that these caused a significant impact on their daily life (causing low mood, or interrupting sleep or daily activities), while nine reported a moderate impact (causing irritation but not halting usual activities). Nine sought healthcare advice to treat their symptoms, while 10 self-managed with over-the-counter products. Among those with post-ICU dermatological issues, six had a formal chronic dermatology diagnosis, and a further nine reported previous skin problems. The eight patients without post-ICU dermatological symptoms had no formal skin disease diagnoses. Our findings indicate that a notable portion of ICU patients experience skin impairments, and a potential predictor is identified, as 65% of affected patients have a history of chronic skin disorders or symptoms. Dermatological symptoms post-ICU significantly or moderately affected daily life for most individuals, leading them to seek treatment following hospital discharge. Further research is warranted to explore the risk of cutaneous impairment post-ICU, and we propose preventive measures such as prescribing prophylactic emollients to mitigate this risk.