bluuebunny/crossref_metadata_2025_split huggingface dataset:
Opportunities and challenges for ChatGPT and large language models in biomedicine and health
Authors: Tian Shubo , Jin Qiao , Yeganova Lana , Lai Po-Ting , Zhu Qingqing , Chen Xiuying , Yang Yifan , Chen Qingyu , Kim Won , Comeau Donald C , Islamaj Rezarta , Kapoor Aadit , Gao Xin , Lu Zhiyong 
Published: January 2024

Abstract
ChatGPT has drawn considerable attention from both the general public and domain experts with its remarkable text generation capabilities. This has subsequently led to the emergence of diverse applications in the field of biomedicine and health. In this work, we examine the diverse applications of large language models (LLMs), such as ChatGPT, in biomedicine and health. Specifically, we explore the areas of biomedical information retrieval, question answering, medical text summarization, information extraction and medical education and investigate whether LLMs possess the transformative power to revolutionize these tasks or whether the distinct complexities of biomedical domain presents unique challenges. Following an extensive literature survey, we find that significant advances have been made in the field of text generation tasks, surpassing the previous state-of-the-art methods. For other applications, the advances have been modest. Overall, LLMs have not yet revolutionized biomedicine, but recent rapid progress indicates that such methods hold great potential to provide valuable means for accelerating discovery and improving health. We also find that the use of LLMs, like ChatGPT, in the fields of biomedicine and health entails various risks and challenges, including fabricated information in its generated responses, as well as legal and privacy concerns associated with sensitive patient data. We believe this survey can provide a comprehensive and timely overview to biomedical researchers and healthcare practitioners on the opportunities and challenges associated with using ChatGPT and other LLMs for transforming biomedicine and health.
A critical assessment of clustering algorithms to improve cell clustering and identification in single-cell transcriptome study
Authors: Liang Xiao , Cao Lijie , Chen Hao , Wang Lidan , Wang Yangyun , Fu Lijuan , Tan Xiaqin , Chen Enxiang , Ding Yubin , Tang Jing 
Published: January 2024

Abstract
Cell clustering is typically the initial step in single-cell RNA sequencing (scRNA-seq) analyses. The performance of clustering considerably impacts the validity and reproducibility of cell identification. A variety of clustering algorithms have been developed for scRNA-seq data. These algorithms generate cell label sets that assign each cell to a cluster. However, different algorithms usually yield different label sets, which can introduce variations in cell-type identification based on the generated label sets. Currently, the performance of these algorithms has not been systematically evaluated in single-cell transcriptome studies. Herein, we performed a critical assessment of seven state-of-the-art clustering algorithms including four deep learning-based clustering algorithms and commonly used methods Seurat, Cosine-based Tanimoto similarity-refined graph for community detection using Leiden’s algorithm (CosTaL) and Single-cell consensus clustering (SC3). We used diverse evaluation indices based on 10 different scRNA-seq benchmarks to systematically evaluate their clustering performance. Our results show that CosTaL, Seurat, Deep Embedding for Single-cell Clustering (DESC) and SC3 consistently outperformed Single-Cell Clustering Assessment Framework and scDeepCluster based on nine effectiveness scores. Notably, CosTaL and DESC demonstrated superior performance in clustering specific cell types. The performance of the single-cell Variational Inference tools varied across different datasets, suggesting its sensitivity to certain dataset characteristics. Notably, DESC exhibited promising results for cell subtype identification and capturing cellular heterogeneity. In addition, SC3 requires more memory and exhibits slower computation speed compared to other algorithms for the same dataset. In sum, this study provides useful guidance for selecting appropriate clustering methods in scRNA-seq data analysis.
Contrasting patterns of genetic structure and population demography in two Dicraeus species feeding on bamboo flowers in Japan
Authors: Sakata Yuzu , Hirota Shun K , Matsuo Ayumi , Kobayashi Keito , Nakahama Naoyuki , Suyama Yoshihisa 
Published: January 2024

Abstract
Population outbreaks of insects provide an excellent opportunity to elucidate their evolutionary history. In this study, we uncovered the phylogenetic relationships of Dicraeus spp. in Japan and compared the population genetic structure of two bamboo-feeding Dicraeus spp., Dicraeus phyllostachyus and Dicraeus nartshukae, by leveraging a recent nationwide mass flowering event of several bamboo species in Japan. We performed analysis using mitochondrial COI gene sequencing and genome-wide single-nucleotide polymorphisms detected by multiplexed inter-simple sequence repeat genotyping by sequencing (MIG-seq). We found genetic similarity in COI haplotypes over a large geographical range in the two Dicraeus spp., but, for both species, no concordance was detected between the collected host plants and genetic structures. In the genome-wide single-nucleotide polymorphism data, no clear genetic clusters were detected for D. phyllostachyus populations, whereas D. nartshukae populations were divided into two groups, in the north and south of Japan. Demographic analysis indicated that D. phyllostachyus had greatly expanded its population recently compared with D. nartshukae. These contrasting patterns between the two species might reflect the differences in the demographic history between the species. Our study suggested that the mass flowering event might cascade to the genetic structure of the florivorous insects through trophic interactions.
Biological characteristics of pregnancy in captive Yangtze finless porpoises revealed by urinary metabolomics
Authors: Tang Bin , Hao Yujiang , Wang Chaoqun , Deng Zhengyu , Kou Zhangbing , Zhou Haojie , Zhang Haobo , Fan Fei , Wang Kexiong , Wang Ding 
Published: January 2024

Abstract
The Yangtze finless porpoises (Neophocaena asiaeorientalis a.) are an endemic and critically endangered species in China. Intensive captive breeding is essential for understanding the biology of critically endangered species, especially their pregnancy characteristics, knowledge of which is crucial for effective breeding management. Urine metabolomics can reveal metabolic differences, arising from physiological changes across pregnancy stages. Therefore, we used the urinary metabolomic technology, to explore urinary metabolite changes in pregnant Yangtze finless porpoises. A total of 2281 metabolites were identified in all samples, which including organic acids and derivatives (24.45%), organoheterocyclic compounds (20.23%), benzenoids (18.05%), organic oxygen compounds (7.73%), and phenylpropanoids and polyketides (6.48%). There were 164, 387, and 522 metabolites demonstrating differential abundance during early pregnancy, mid pregnancy, and late pregnancy, respectively, from the levels observed in nonpregnancy. The levels of pregnenolone, 17α-hydroxyprogesterone, and tetrahydrocortisone were significantly higher during all pregnancy stages, indicating their important roles in fetal development. The differential metabolites between nonpregnancy and pregnancy were mainly associated with amino acid and carbohydrate metabolism. Moreover, metabolic activity varied across pregnancy stages; steroid hormone biosynthesis was predominant in early pregnancy, and amino acid biosynthesis and carbohydrate metabolism were predominant in mid pregnancy and late pregnancy, respectively. Our results provide new insights into metabolic characteristics in the Yangtze finless porpoises’ urine during pregnancy, and indicate that the differential levels of urine metabolites can determine pregnancy in Yangtze finless porpoises, providing valuable information for the husbandry and management of pregnant Yangtze finless porpoises in captivity.
O01 Inborn errors of metabolism - Solving the puzzle of prolidase deficiency
Authors: Byth Lachlan , McPherson Tess 
Published: January 2024

Abstract
Inborn errors of metabolism (IEM) may present with ­distinctive cutaneous manifestations as part of a multisystem phenotype. Diagnosis is a multidisciplinary affair, made difficult by their rarity and complex genetic architectures. Knowledge of molecular mechanisms provides hope for targeted therapies, but unmet needs remain in the treatment of skin disease.
Prolidase deficiency (OMIM #170100) is a rare IEM characterised by impaired collagen recycling, recalcitrant lower limb ulceration and massive imidodipeptiduria. The cases of two siblings born to related parents are reported, presenting initially in childhood with hydroa vacciniforme-like photosensitivity. Following a decade-long journey, the diagnosis of prolidase deficiency was eventually made. Pitfalls including the limitations of conventional diagnostic modalities and whole genome sequencing are examined, as well as the effects of chronic skin changes and associated disability on quality of life in childhood and adolescence. Therapeutic options, possible connections to hydroa vacciniforme, and prospects for translational research are reviewed. A rational approach to the clinical and genetic diagnosis of IEM in the paediatric dermatology clinic is proposed.
P05 Pre-visit online paediatric atopic dermatitis questionnaire – a feasibility study
Authors: Gan Alex , Vaughan Emily , Heysa Nataliya , Mann Nina , Ravenscroft Jane , Williams Hywel , Tang Ting Seng 
Published: January 2024

Abstract

Introduction
The use of structured questionnaires is common in patients with atopic dermatitis. Traditionally, this is done by paper-based questionnaires in clinics. Since the SARS-CoV-2 pandemic, many regard the shift from paper to digital forms as inevitable in order to improve efficiency, sustainability and reduce the risk of transmission.

Objective
This study aims to examine the feasibility and acceptability of pre-visit digital questionnaires in paediatric dermatology clinics.
Methods Text message invitations to complete online questionnaires were sent to all patients who are due to attend a paediatric dermatology clinic at Nottingham University Hospitals.

Results
1,218 responses were received between Sept 2021 and Mar 2022. 338 patients were reported to have eczema as their main skin complaint (71 new patients, 267 follow-ups). Amongst these, 113 patients were under 4 years old, 136 were between 4-12 years old and 89 were aged 13 or above. The average patient reported eczema severity was recorded as 12.6 +/– 7.8 SD using the Patient Oriented Eczema Measure (POEM) questionnaire.
The majority of the questionnaires were filled in by the parents and required less than 5min to complete. 97.5% reported that they found the online questionnaire easier to use when compared to the paper format. Most participants and clinicians also reported they feel the online questionnaire enhanced their experience and consultation in the clinic.

Conclusions
Digital pre-visit online questionnaires are an acceptable method to gather information from parents of children with atopic dermatitis. Further work is required to assess the accuracy and clinical usefulness of the data.
P11 A Rare and Serious Cause of “Blueberry Muffin Syndrome”
Authors: Oldham Jaimie , Dunnigan Anna , Barbosa Elsa , Huang Sylvia , Dhoat Sasha , McDonald Bryan , O’Toole Edel , Atkar Ravinder 
Published: January 2024

Abstract
Urgent dermatology review was sought for a neonate born at term via emergency caesarean section for reduced movements. The pregnancy was complicated by gestational diabetes and infection with suspected coxsackie virus in the second trimester.
There were 15 purple/blue nodules consistent with “blueberry muffin syndrome” and associated anaemia (118 g/L). Due to hypoxia, she was given antibiotics for suspected sepsis. TORCH screen was negative and USS abdomen and cranium were normal. A blood film showed B cell aplasia and LDH was raised (710 unit/L). CXR showed a mediastinal mass, left pleural effusion and left lung opacity. A skin biopsy was taken, chest drain placed and the baby transferred to Great Ormond Street.
She was subsequently diagnosed with acute myeloid leukaemia following bone marrow and lumbar puncture. All three skin biopsies showed a malignant infiltrate with one displaying positivity for CD12 and CD33. CT and MRI scans have shown widespread nodules in the lungs, liver, kidneys, bones and intra-cranially.
She is being treated with chemotherapy which has been complicated by a cardiac arrest and severe mucositis leading to colostomy. She is also NG fed and has sensorineural hearing loss.
The nodules seen in “blueberry muffin syndrome” are most commonly extramedullary erythropoiesis but can also represent purpura or metastases. The causes are congenital infections, blood disorders or tumours. There is frequently associated anaemia (as in our case) and hepatosplenomegaly. This case demonstrates a rare and concerning cause of the syndrome and highlights the role dermatologists can play in diagnosis.
P15 A Case of Juvenile Dermatomyositis in a 15-year old African-descent Girl
Authors: Vetsiou Evangelia , Armon Kate , Gass Julia 
Published: January 2024

Abstract
A 15-year-old female with skin of colour (SOC), was diagnosed with Juvenile dermatomyositis (JDM) following a presentation with muscle weakness, swallowing difficulties and rash. Investigations showed CK&gt;1300, positive Mi-2 alpha, beta antibodies and bilateral myositis on MRI pelvis. Her skin features commenced 2 months prior to her rheumatological presentation. They included erythematous pruritic patches on the limbs, generalised hyperpigmentation of the face and trunk, hyperpigmentation of palmar creases and nail folds, flagellate hyperpigmentation of the hands & arms, and hypopigmented macules with follicular sparing across the face. She also presented skin thickening over the interphalangeal joints and nail fold capillary dilatation and infarctions. Skin biopsy showed interface dermatitis, in keeping with dermatomyositis.
She was managed with weaning prednisolone, methotrexate, topical tacrolimus and sunscreen.
JDM is a small-vessel autoimmune vasculopathy leading to muscle inflammation and skin changes. Unlike adult-onset disease, JDM is not associated with malignancy. The typically described violaceous skin features of JDM including photosensitive rash periorbitally, and over the knees and knuckles (Gottron’s sign) may be hyperpigmented rather than erythematous in skin of colour. Additional skin features described in SOC are generalised hyperpigmentation and pigmentation in skin creases. A flagellate dermatitis is uncommon, but recognised in association with Mi-2 antibodies in JDM. TIF1 antibodies have been reported in association with hypopigmented patches which may mimic vitiligo postulated possibly secondary to interface inflammation perhaps leading to dyspigmnentation. Notably our patient was negative for TIF1.
This presentation highlights some of the less commonly described skin features of dyspigmentation in JDM in SOC.
P24 Improving the patient pathway for timely referral and management of infantile haemangioma
Authors: Scott-Bazaldua Jacqueline , Dubois Anna 
Published: January 2024

Abstract
Infantile haemangiomas (IH) are vascular tumours which typically present soon after birth and grow rapidly at a young age. Complications can arise depending on location and rapidity of growth of the lesion1. Timely treatment with an oral beta-blocker can limit growth and speed up resolution of IH.
Not infrequently, we noted babies were being referred at a stage when most of the growth of the IH had already taken place. These patients often had skin breakdown, or a large haemangioma, making successful treatment harder to achieve. We aimed to educate GPs and health-visitors regarding the need for timely referral and to speed up the triage process for these patients.
Information was sent to regional GP practices, with instructions on referral criteria according to the BSPAD guidelines for treatment of IH. A photograph of the IH was requested at the time of referral. Submitted referrals were triaged promptly and where appropriate, booked directly into a telephone clinic.
After telephone consult, IH meeting the criteria for propranolol were booked directly for commencement of the beta-blocker with a paediatric review. If there was diagnostic doubt or other complications, a timely face to face review was arranged. Patients not requiring oral treatment were discharged back to GP.
A patient satisfaction questionnaire revealed that parents appreciated the speed of assessment and reduced hospital visits.
We describe an educational intervention and triage strategy resulting in improvement in the timing of referral and management of infantile haemangioma.
Metabolic reprogramming in skin wound healing
Authors: Wang Zitong , Zhao Feng , Xu Chengcheng , Zhang Qiqi , Ren Haiyue , Huang Xing , He Cai , Ma Jiajie , Wang Zhe 
Published: January 2024

Abstract
Metabolic reprogramming refers to the ability of a cell to alter its metabolism in response to different stimuli and forms of pressure. It helps cells resist external stress and provides them with new functions. Skin wound healing involves the metabolic reprogramming of nutrients, such as glucose, lipids, and amino acids, which play vital roles in the proliferation, differentiation, and migration of multiple cell types. During the glucose metabolic process in wounds, glucose transporters and key enzymes cause elevated metabolite levels. Glucose-mediated oxidative stress drives the proinflammatory response and promotes wound healing. Reprogramming lipid metabolism increases the number of fibroblasts and decreases the number of macrophages. It enhances local neovascularization and improves fibrin stability to promote extracellular matrix remodelling, accelerates wound healing, and reduces scar formation. Reprogramming amino acid metabolism affects wound re-epithelialization, collagen deposition, and angiogenesis. However, comprehensive reviews on the role of metabolic reprogramming in skin wound healing are lacking. Therefore, we have systematically reviewed the metabolic reprogramming of glucose, lipids, and amino acids during skin wound healing. Notably, we identified their targets with potential therapeutic value and elucidated their mechanisms of action.
Neurological prognosis in surgically treated acute aortic dissection with brain computed tomography perfusion
Authors: Zhao Hongliang , Li Chengxiang , Duan Weixun , Wei Dong , Xue Ruijia , Wei Mengqi , Chang Yingjuan , Shang Lei , Lin Shushen , Xu Jian , Zheng Minwen 
Published: January 2024

Abstract

OBJECTIVES
The aim of this study was to explore the prognostic value of brain computed tomography perfusion (CTP) for postoperative new stroke in acute type A aortic dissection (ATAAD) patients.

METHODS
Patients with ATAAD and suspected cerebral malperfusion who underwent brain CTP and surgical repair were retrospectively analysed. Brain perfusion was quantified mainly with the averaged cerebral blood flow. Significant clinical and imaging findings were identified through univariable and multivariable regression analysis. Furthermore, the added prognostic benefit of perfusion parameters was confirmed with the receiver operating characteristic curves in the entire cohort and subgroup analysis.

RESULTS
The incidence of postoperative new stroke was 30.8% (44/143). The independent adjusted predictors of postoperative new stroke included an impaired averaged cerebral blood flow (ml/100 ml/min) (odds ratio: 0.889; P &lt; 0.001), severe stenosis (odds ratio: 5.218; P = 0.011) or occlusion (odds ratio: 14.697; P = 0.048) of the true lumen in common carotid artery (CCA), hypotension on admission (odds ratio: 9.644; P = 0.016) and a longer surgery time (odds ratio: 1.593; P = 0.021). The area under the receiver operating characteristic curves significantly improved after adding perfusion parameters to clinical and computed tomography angiography characteristics (P = 0.048). This benefit was more pronounced in patients with severe stenosis or occlusion in CCA true lumen (P = 0.004).

CONCLUSIONS
Brain CTP could be a useful prognostic tool for surgically treated ATAAD patients and especially beneficial in patients with severe stenosis or occlusion of the CCA true lumen.
Consumption of foods and beverages rich in added sugar associated with incident metabolic syndrome: the Coronary Artery Risk Development in Young Adults (CARDIA) study
Authors: Goins Rae K , Steffen Lyn M , Yi So-Yun , Zhou Xia , Van Horn Linda , Shikany James M , Terry James G , Jacobs David R 
Published: January 2024

Abstract

Aims
Numerous studies report positive associations between total carbohydrate (CHO) intake and incident metabolic syndrome (MetS), but few differentiate quality or type of CHO relative to MetS. We examined source of CHO intake, including added sugar (AS), AS-rich CHO foods, and sugar-sweetened beverages (SSBs) associated with incident MetS in adults enrolled in the Coronary Artery Risk Development in Young Adults (CARDIA) study.

Methods and results
Among 3154 Black American and White American women and men aged 18–30 years at baseline, dietary intake was assessed by diet history three times over 20 years. Sources of AS-rich CHO foods and beverages include sugar-rich refined grain products, candy, sugar products, and SSBs. Incident MetS was created according to standard criteria. Time-dependent Cox proportional hazards regression analysis evaluated the associations of incident MetS across quintiles of cumulative intakes of AS-rich CHO foods and beverages, AS, and SSBs adjusted for potential confounding factors over 30 years of follow-up. The associations of AS-rich CHO foods and beverages, AS, and SSB intakes with incident MetS were consistent. Compared with the lowest intake, the greatest intakes of AS-rich CHOs, AS, and SSBs were associated with 59% (Ptrend &lt; 0.001), 44% (Ptrend = 0.01), and 34% (Ptrend = 0.03) higher risk of developing MetS, respectively. As expected, diet quality was lower across increasing quintiles of AS-rich CHO foods and beverages, AS, and SSBs (all Ptrend &lt; 0.001).

Conclusion
Our study findings are consistent with an elevated risk of developing MetS with greater consumption of AS, AS-rich CHO foods, and SSBs, which support consuming fewer AS-rich CHO foods and SSBs.
Phylogenetic analysis of Nostocales (Cyanobacteria) based on two novel molecular markers, implicated in the nitrogenase biosynthesis
Authors: Giannakopoulos Christos , Panou Manthos , Gkelis Spyros 
Published: January 2024

Abstract
The characterization of cyanobacteria communities remains challenging, as taxonomy of several cyanobacterial genera is still unresolved, especially within Nostocales taxa. Nostocales cyanobacteria are capable of nitrogen fixation; nitrogenase genes are grouped into operons and are located in the same genetic locus. Structural nitrogenase genes (nifH, nifK and nifD) as well as 16S rRNA have been shown to be adequate genetic markers for distinguishing cyanobacterial genera. However, there is no available information regarding the phylogeny of regulatory genes of the nitrogenase cluster. Aiming to provide a more accurate overview of the evolution of nitrogen fixation, this study analyzed for the first time nifE and nifN genes, which regulate the production of nitrogenase, alongside nifH. Specific primers were designed to amplify nifE and nifN genes, previously not available in literature and phylogenetic analysis was carried out in 13 and 14 TAU-MAC culture collection strains, respectively, of ten Nostocales genera along with other sequences retrieved from cyanobacteria genomes. Phylogenetic analysis showed that these genes seem to follow a common evolutionary pattern with nitrogenase structural genes and 16S rRNA. The classification of cyanobacteria based on these molecular markers seems to distinguish Nostocales strains with common morphological, ecological, and physiological characteristics.