bluuebunny/crossref_metadata_2025_split huggingface dataset:
PQSDC: a parallel lossless compressor for quality scores data via sequences partition and run-length prediction mapping
Authors: Sun Hui , Zheng Yingfeng , Xie Haonan , Ma Huidong , Zhong Cheng , Yan Meng , Liu Xiaoguang , Wang Gang 
Published: May 2024

Abstract

Motivation
The quality scores data (QSD) account for 70% in compressed FastQ files obtained from the short and long reads sequencing technologies. Designing effective compressors for QSD that counterbalance compression ratio, time cost, and memory consumption is essential in scenarios such as large-scale genomics data sharing and long-term data backup. This study presents a novel parallel lossless QSD-dedicated compression algorithm named PQSDC, which fulfills the above requirements well. PQSDC is based on two core components: a parallel sequences-partition model designed to reduce peak memory consumption and time cost during compression and decompression processes, as well as a parallel four-level run-length prediction mapping model to enhance compression ratio. Besides, the PQSDC algorithm is also designed to be highly concurrent using multicore CPU clusters.

Results
We evaluate PQSDC and four state-of-the-art compression algorithms on 27 real-world datasets, including 61.857 billion QSD characters and 632.908 million QSD sequences. (1) For short reads, compared to baselines, the maximum improvement of PQSDC reaches 7.06% in average compression ratio, and 8.01% in weighted average compression ratio. During compression and decompression, the maximum total time savings of PQSDC are 79.96% and 84.56%, respectively; the maximum average memory savings are 68.34% and 77.63%, respectively. (2) For long reads, the maximum improvement of PQSDC reaches 12.51% and 13.42% in average and weighted average compression ratio, respectively. The maximum total time savings during compression and decompression are 53.51% and 72.53%, respectively; the maximum average memory savings are 19.44% and 17.42%, respectively. (3) Furthermore, PQSDC ranks second in compression robustness among the tested algorithms, indicating that it is less affected by the probability distribution of the QSD collections. Overall, our work provides a promising solution for QSD parallel compression, which balances storage cost, time consumption, and memory occupation primely.

Availability and implementation
The proposed PQSDC compressor can be downloaded from https://github.com/fahaihi/PQSDC.
Meaning and prediction of ‘excess mortality’: a comparison of Covid-19 and pre-Covid-19 mortality data in 31 Eurostat countries from 1965 to 2021
Authors: Gill Bernhard , Kehler Theresa , Schneider Michael 
Published: May 2024

Abstract
Determining ‘excess mortality’ makes it possible to compare the burden of disasters between countries and over time, and thus also to evaluate the success of mitigation measures. However, the debate on coronavirus disease 2019 (Covid-19) has exposed that calculations of excess mortalities vary considerably depending on the method and its specification. Moreover, it is often unclear what exactly is meant by ‘excess mortality’. We define excess mortality as the excess over the number of deaths that would have been expected counter-factually, that is without the catastrophic event in question. Based on this definition, we use a very parsimonious calculation method, namely the linear extrapolation of death figures from previous years to determine the excess mortality during the Covid-19 pandemic. But unlike most other literature on this topic, we first evaluated and optimized the specification of our method using a larger historical data set in order to identify and minimize estimation errors and biases. The result shows that excess mortality rates in the literature are often inflated. Moreover, they would have exhibited considerable excess mortalities in the period before Covid-19, if this value had already been of public interest at that time. Three conclusions can be drawn from this study and its findings: (i) All calculation methods for current figures should first be evaluated against past figures. (ii) To avoid alarm fatigue, thresholds should be introduced which would differentiate between ‘usual fluctuations’ and ‘remarkable excess’. (iii) Statistical offices could provide more realistic estimates.
O05 Single-cell transcriptomic signature of paradoxical eczema in patients with psoriasis treated with biologics
Authors: Al-Janabi Ali , Martin Paul , Simpson Catherine , Rhys Hefin , Khan Adnan , Eyre Steve , Christofi Maria , Foulkes Amy , Skelton Andrew , Viatte Sebastien , Barton Anne , Morris Andrew , Smith Catherine , Griffiths Christopher , Warren Richard 
Published: May 2024

Abstract

Introduction and aims
Biologics targeting the tumour necrosis factor (TNF) and the interleukin (IL)-17/23 axis are highly effective treatments for psoriasis but can result in cutaneous adverse events. The pathogenesis of paradoxical eczema, an atopic dermatitis (AD) phenotype occurring after biologic initiation in people with psoriasis, is unknown. This study explored the systemic disease signature of paradoxical eczema.

Methods
We used single-cell RNA-Seq on peripheral blood mononuclear cells (PBMCs) from three patients with psoriasis with paradoxical eczema, and three matched, biologic-treated controls who had psoriasis. Differential gene expression, gene network expression and cell–cell interaction (using MultiNicheNet) analyses allowed comparison of cases and controls. We assessed overlap between paradoxical eczema and AD using six AD transcriptome datasets.

Results
Overall, 32 827 PBMCs (14 521 from cases, 18 306 from controls) were included and categorized into 27 clusters. Between cases and controls, there were 727 differentially expressed genes (DEGs) (log fold-change &gt; 0.25, adjusted P &lt; 0.05). A total of 94 of the top 100 DEGs were from monocytes. Significant DEG networks (P &lt; 0.05) mostly mapped to T-cell and monocyte clusters, with commonly enriched pathways in cases including interferon (IFN)-γ, IFN-α, TNF, IL-2/signal transducer and activator of transcription 5 and T-cell differentiation pathways. Cell–cell interaction analysis revealed that the most prioritized interactions in controls, based on differential expression data and known ligand-receptor interactions, included immune regulatory interactions (including ligands such as transforming growth factor β1 and lymphocyte-activation gene 3). In cases, functions of prioritized interactions included chemotaxis, leucocyte activation, T-cell priming and IFN-γ signalling. There was significant enrichment of concordance in the direction of effect of DEGs (65%, P = 5.39 × 10−6) and enriched pathways (85%, P = 3.62 × 10−13) between AD and paradoxical eczema.

Conclusions
Patients with paradoxical eczema have reduced immune regulatory mechanisms and evidence of monocyte and T-cell activation systemically, with increased production IFN-γ, IFN-α and TNF. There is a significant overlap with the AD transcriptome.
O06 Naïve human keratinocytes initiate a chromatin-protective mechanism in response to ultraviolet radiation through the upregulation of histone deacetylase 5
Authors: Tsai Yu-Hsuan , Watson Rachel , Langton Abigail 
Published: May 2024

Abstract

Introduction and aims
During normal development and throughout life, epigenetic changes arise in response to an individuals’ behaviour and environmental exposures. Histone deacetylases (HDACs) are chromatin-modifying enzymes that regulate gene expression and their activity and expression in primary human keratinocytes alters with increasing age. Solar ultraviolet radiation (UVR) is a major causative factor of skin ageing, but how this factor affects HDAC expression and activity is largely unknown. We aimed to determine how UVR exposure affects HDAC expression and activity in primary human keratinocytes.

Methods
Normal human epidermal keratinocytes (NHEKs) from juvenile (aged 1–6 years; n = 3), middle-aged (56–61 years; n = 3) and aged (83–85 years; n = 3) donors were exposed to solar-simulated radiation (SSR) and HDAC abundance and activity were assayed.

Results
Exposure to SSR significantly increased HDAC activity in primary NHEKs irrespective of donor age (P &lt; 0.05). However, Western blotting for HDAC abundance revealed that there was a differential response to SSR exposure across age groups; juvenile NHEKs expressed significantly more HDAC5 in response to SSR (P &lt; 0.05) than cells from middle-aged or aged donors. Furthermore, following SSR exposure of juvenile NHEKs, the cellular localization of HDAC5 was redistributed to the nucleus from the cytoplasm. Dual immunofluorescence staining revealed that those NHEKs with nuclear HDAC5 expression were also positive for p16INK4a, a robust marker of cellular senescence (P &lt; 0.01).

Conclusions
Our Results suggest that naïve human keratinocytes are responsive to UVR exposure and appear to initiate a chromatin-protective mechanism through the upregulation of HDAC5 to prevent gene expression of damaged DNA.
O08 Exploring the effect of skin ageing-related basement membrane collagen loss on nuclear mechanics
Authors: Summan Simranpreet , Mayes Andrew , Gunn David , Madapura Pradeepa , Gautrot Julien , Caley Matthew , O’Toole Edel 
Published: May 2024

Abstract

Introduction and aims
Skin ageing is a universal process that can increase susceptibility to inflammation and disease. Basement membrane collagens (BMCs) are reduced during ageing and the consequences are poorly understood. BMC sensing of mechanical stress, vital for skin homeostasis, elicits signalling sensed via cytoskeletal actin filaments to the linker of nucleoskeleton and cytoskeleton (LINC) complex (composed of nesprin and sun proteins), nuclear lamina and lamina-associated chromatin. Our hypothesis is that BMC loss during ageing leads to a deformation of the nucleocytoskeleton and disrupts chromatin organization in keratinocytes, leading to impairment of epidermal differentiation and inability to withstand mechanical stress.

Methods
To explore the role of BMC in mechanical stress response, stable lentiviral short hairpin (sh)RNA knockdowns of Col7 (shCol7) and Col17 (shCol17) were generated in immortalized N/TERT keratinocytes. Western blot (WB) validated knockdowns were compared with shC nontargeting control. IncuCyte assays showed shCol17 had a hyperproliferative phenotype compared with shC. Sun2 was reduced in shCol17 (P &lt; 0.001) compared with shC (n = 5 experimental replicates). The mechanical stretch effect on cells on a flexible membrane was studied using immunofluorescence and WB analysis. Images taken from the IN Cell Analyzer confocal microscope were analysed to detect changes in protein expression and localization. Nuclear and cytoplasmic fractions made before and after stretch were analysed by WB.

Results
We observed collagen-specific responses to stretch-induced stress with changes to actin, components of the nuclear membrane, and LINC complex proteins. Additionally, work on investigating chromatin changes with BMC knockdown using Cleavage Under Targets & Tagmentation and Cleavage Under Targeted Accessible Chromatin assays is ongoing.

Conclusions
Our data show an altered nucleocytoskeleton in the context of BMC loss and mechanotransduction in skin. These data could provide novel insights into epidermal regulation by BMC in ageing.
O13 Benchmarking a human pluripotent stem cell-derived hair-bearing skin organoid model to prenatal skin
Authors: Gambardella Laure , Torabi Feri , Foster April , Admane Chloe , Winheim Elena , Gopee Nusayhah Hudaa , Olabi Bayanne , Rowe Vicky , Sumanaweera Dinithi , Le Phuong Ahn , Serdy Sara , Kim Jin , Deakin CiCi , Lee Jiyoon , Stephenson Emily , Botting Rachel , Koehler Karl , Teichmann Sarah , Haniffa Muzlifah 
Published: May 2024

Abstract

Introduction and aims
Molecular regulation of mammalian skin development has been largely derived from murine studies. The lack of human studies stems primarily from the difficulties in prenatal human skin access. There is an important need to study human prenatal skin owing to the notable differences between human and mouse skin and the paucity of mechanistic understanding of congenital skin disorders.

Methods
We assembled the first comprehensive multiomic reference atlas of prenatal human skin (21 samples from 7 to 16 postconception weeks), combining single-cell (235 201 cells) and spatial transcriptomic data. We followed 84 skin organoids (SkOs) using single-cell analysis over a 5-month culture period and characterized the spatial organization of the skin in mature SkOs. Prenatal skin, SkO and any relevant pre-existing single-cell RNA-Seq datasets were integrated into the analysis. Cell–cell interactions and cell-lineage determination were explored using CellPhoneDB and trajectory inferences. We evaluated the differentiation trajectory alignment between prenatal skin and SkO using the Genes2Genes analysis.

Results
Our findings reveal predicted factors regulating the epithelial–mesenchymal crosstalk during human hair follicle formation; progressive expression of scar-promoting genes in later gestation, potentially contributing to scarless healing properties of human prenatal skin observed during the early stages of gestation and expression of genes causing genetic skin disorders in the same cell types in prenatal human skin and SkO. We also found that SkOs morphologically recapitulate human skin development from early (periderm formation and shedding) to late (cornification and hair follicle formation) stages. We also demonstrated that SkO and prenatal skin mesenchyme differentiation into hair follicle dermal condensate and dermal papilla is highly conserved at the cellular and molecular level.

Conclusions
SkOs faithfully recapitulate human prenatal skin development and are a valuable model for mechanistic studies on skin development including hair follicle biology and congenital skin disorders.
O18 Precision genome editing for targeted correction of pathogenic D50N mutation in keratitis–ichthyosis–deafness syndrome using CRISPR/Cas9 and homology-directed repair
Authors: Gobalakrishnan Krishshan , Jayarajan Vignesh , Kinsler Veronica , Di Wei-Li 
Published: May 2024

Abstract

Introduction and aims
Keratitis–ichthyosis–deafness (KID) syndrome is an ectodermal disorder that causes blindness, skin inflammation and deafness. It is caused by autosomal dominant mutations in the gap junction beta 2 (GJB2) gene with 86% being a hotspot mutation on c.148G&gt;A, resulting in the amino acid replacement (D50N) in its coding protein connexin 26 (Cx26). There is currently no curative treatment for KID syndrome. We aim to correct the hotspot mutation D50N using a genome-editing approach.

Methods
Keratinocytes generated from the patient with KID who had a D50N mutation (KID-KCs) were genetically corrected by homologous-directed repair/CRISPR-Cas9 using an electroporation approach. The correction efficiency was determined and analysed using Sanger sequencing and Synthego Inference of CRISPR Edits analysis. The off-target effects were confirmed by whole-exome sequencing [exome next-generation sequencing (NGS)]. Furthermore, the functional recovery following genome editing was assessed by GJB2 mRNA production, Cx26 protein expression, and trafficking and hemichannel activity.

Results
The correction efficiencies ranged from 95% to 100% with different doses of CRISPR-Cas9 and 8µg CRISPR-Cas9 was the most optimal concentration with the efficiency of 100% and approximately 0% insertion-deletion (INDEL). Fifty days after gene editing, the INDEL increased to only 2%, indicating a minimum residual CRISPR-Cas9 effect in edited cells. The exome-NGS analysis also showed no off-target effects in the outside target area. Functional studies showed that there was a significant increase in wildtype GJB2 mRNA expression and a reduction of mutant GJB2 expression (n = 5, P &lt; 0.01). Increased Cx26 membranous localization in KID-KCs was also observed (n = 3, P &lt; 0.01). Additionally, Cx26 hemichannel activity assessment using the neurobiotin assay showed a significant decrease in ‘leaky’ hemichannel in gene-edited KID-KCs compared with unedited cells (n = 3, P &lt; 0.05).

Conclusions
We can genome-correct KID keratinocytes harbouring the mutation D50N with 100% editing efficiency, 0–2% INDEL, and undetectable off-target effects. This result indicates a promising gene therapy for KID syndrome with the hotspot mutation D50N.
O21 Raman spectroscopy for detection of squamous cell carcinoma in recessive dystrophic epidermolysis bullosa skin
Authors: Dimitrievska Marija , Chiappini Ciro , McGrath John , Bergholt Mads S 
Published: May 2024

Abstract

Introduction and aims
Recessive dystrophic epidermolysis bullosa (RDEB) is a genetic skin disorder caused by biallelic pathogenic variants in COL7A1, which encodes type VII collagen (C7). Lack of C7 leads to blistering, chronic wounds, scarring and early onset of life-shortening squamous cell carcinomas (SCCs). Currently, the suspicion of SCC is mostly determined by clinical observation of visible changes in chronic wounds, and often requires multiple biopsies for histological diagnosis. This project aims to improve clinical care by developing a new noninvasive means of detecting SCC. To achieve this, we used Raman spectroscopy, a nondestructive analytical technique to study the changes occurring in RDEB skin when SCC is present, with the goal of creating a bedside test that can aid clinicians in the early diagnosis of SCC.

Methods
Raman spectroscopic imaging was performed on 7-µm frozen skin sections from RDEB (n = 3), RDEB SCC (n = 3) and normal skin (n = 3) to identify signalling changes between nonlesional and lesional states. An in-depth molecular composition analysis of the samples was performed using multivariate analysis with the goal of highlighting changes in abundance of specific molecules when SCC is present.

Results
For both nonmalignant and RDEB SCC skin sites we found specific Raman peaks associated with protein (1004 cm−1, 1650 cm−1) or lipids (1450 cm−1). RDEB SCC indicated a relative increase in DNA and protein. High-quality Raman spectroscopic images could be acquired that showed clear correlation with histological appearances. Current work is under way to determine which specific biological compounds contribute to the Raman spectra observed.

Conclusions
Raman spectroscopic imaging can provide comprehensive and noninvasive molecular tissue mapping with resolution comparable to histological sections, enabling molecular-based detection of SCC. Future work will focus on characterization of the SCC molecular profile, in addition to determining whether fibre optic Raman spectroscopy can be used to guide the biopsy/resection of RDEB lesions.
P08 Exploring the role of cellular senescence in cutaneous repair
Authors: Johns Alexander , Wilkinson Holly 
Published: May 2024

Abstract

Introduction and aims
Chronic nonhealing wounds are a life-threatening skin disease in elderly patients and patients with diabetes that costs the National Health Service over £8 billion per year to treat. Unfortunately, current treatments are inadequate, thus there is an urgent need to develop effective therapies. Cellular senescence is emerging as a potential therapeutic target owing to its association with a wide range of age-related pathologies. Cells undergo senescence in response to ageing and stress, losing their ability to proliferate or perform normal tissue functions. Our previous work in mice provided the first mechanistic demonstration that senescent cell accumulation drives poor healing. Moreover, clinical trials currently assessing the efficacy of senescence-targeted drugs (senolytics) are providing repurposing opportunities for cutaneous pathologies. Therefore, the aim of this research is to (i) investigate the role of senescence in human chronic wounds and (ii) determine whether senolytics can be repurposed to promote pathological skin repair.

Methods
Skin and wounds were collected from healthy, aged and diabetic donors to quantify senescence levels (senescence-associated β-galactosidase), characterize senescent cell types (immunofluorescence) and determine key drivers of skin senescence (RNA sequencing). Additionally, we screened the wound healing potential of a panel of senolytics in healthy skin vs. skin from patients with chronic wounds.

Results
We found significant accumulation of senescence in pathological skin wounds, localized to stromal cells. Senescence levels also correlated substantially with clinical parameters, such as wound site, diabetic status and infection. RNA sequencing revealed key links between senescence and immunity, suggesting inflammation as a crucial driver of skin senescence. Finally, senolytic treatment significantly accelerated healing in skin from patients with chronic wounds.

Conclusions
Our data provide the first in-depth characterization of senescence in human chronic skin wounds, crucially identifying novel therapeutic targets of senescence, while simultaneously assessing the potential of drug repurposing for patient benefit.
P11 A role for keratinocyte arginase in skin wound healing and barrier function
Authors: Szondi Denis-Cristian , Cruickshank Sheena , Vardy Leah , Wong Jason 
Published: May 2024

Abstract

Introduction and aims
Delayed cutaneous wound healing is a major problem that can result in social isolation and significant morbidity including amputation. There are many changes in cellular function in a chronic wound. Notably, the enzyme arginase (ARG)1 is markedly changed in wound healing. We have identified a role for ARG1 in keratinocyte re-epithelialization during wound closure, but the underlying mechanism driving re-epithelialization was not known. We aimed to determine the role of ARG1 in keratinocyte migration, differentiation and barrier formation.

Methods
Two-dimensional scratch and differentiation assays using immortalized keratinocytes (NTERT cells) treated with the ARG1 inhibitor, nor-NOHA, and short hairpin RNA-based knockdown cells were assessed. Gene and protein expression changes were highlighted. Expression of proteins was further validated using immunohistochemical profiling of human skin equivalents and human wound lesions by spatial transcriptomics.

Results
ARG1 was strongly expressed both 2–4h postscratching and at late stages of keratinocyte differentiation. Dysregulation of ARG1 expression was spatially highlighted in chronic lesions, further suggesting an involvement in keratinocyte migration and differentiation. ARG1 inhibition led to a significant delay in postscratch keratinocyte migration. Furthermore, upon ARG1 inhibition, a significant decrease was seen in the expression of late differentiation markers involucrin and filaggrin. ARG1 inhibition significantly decreased the expression of host defence genes β-defensin 3, lipocalin 2 and kallikrein 6. ARG1 triggers production of multiple downstream products and we confirmed a role for the pathway involving production of putrescine and urea, as the addition of these metabolites led to the rescue of these phenotypes.

Conclusions
ARG1 and its downstream metabolites play a major role in keratinocyte migration, differentiation, and barrier formation, which are vital functions for re-epithelialization and wound closure. Therefore, manipulation of the ARG1 pathway may be crucial in the management of chronic lesions.