bluuebunny/crossref_metadata_2025_split huggingface dataset:
‘And now I feel I don’t have a clear future’: Hauntings and temporal uncertainty in refugee narratives
Authors: Brøndum Tine 
Published: February 2025

Abstract
As a consequence of the so-called ‘paradigm shift’, that defines all refugee protection as temporary, the last decade has seen the focus for refugee administration in Denmark move from ‘integration’ towards ‘repatriation and self-provision’. Through analysis of life stories from people arriving to Denmark as refugees before and after this shift, this article examines how people seeking protection experience and make meaning of their new reality as refugees within the Danish welfare state. Drawing on the perspectives of narrativity and hauntology, that acknowledges the workings of past injustices in the present, the analysis shows that people living in temporary protection experience being kept waiting in a never-ending present. Uncertain waiting destroys people’s sense of agency and belonging and counteracts their ability to reorient themselves towards a meaningful future. The article suggests that this ongoing uncertainty conjures up ghosts from the past that reappear and continue to haunt and ruin their present lives.
Population genetic structure and human adaptation of Kaposi Sarcoma-associated Herpesvirus
Authors: Mozzi Alessandra , Forni Diego , Cagliani Rachele , Molteni Cristian , Clerici Mario , Sironi Manuela 
Published: February 2025

Abstract

Background
Kaposi Sarcoma-associated Herpesvirus (KSHV), the etiologic agent of Kaposi’s sarcoma, is human-specific and it is thought to have emerged from primate-infecting gammaherpesviruses. KSHV seroprevalence shows geographic variation, being highest in Sub-Saharan Africa, intermediate in the Mediterranean area, and low in most other locations. However, KSHV prevalence is also particularly high in specific regions such as the Miyako Islands (Japan).

Methods
We retrieved KSHV genomes from public repositories and we analyzed geographic patterns using principal component analysis and STRUCTURE. Adaptation to the human host was investigated by likelihood ratio tests for positive selection. Protein structures were derived from HerpesFolds.

Results
Most non-African genomes are genetically separated by the African ones and the latter are divided into two main lineages. The African genomes received most of their ancestry from two populations showing limited drift, suggesting an African origin for circulating KSHV strains. Several non-African genomes have instead most of their ancestry covered by a highly drifted ancestral population. However, some non-African genomes show similar ancestry proportions to the African ones, including those from Miyako Islands and the variant F subtype sampled in France. Molecular analysis of adaptation to the human host identified core genes as the major selection targets, including two viral enzymes that counteract human immune defenses.

Conclusions
We suggest that the genetic diversity of extant strains reflects relatively recent demographic events associated with viral lineage extinctions, which may have influenced KSHV epidemiology. Adaptation to the human host involved changes in core genes, possibly a strategy to optimize protein-protein interactions.
Meeting evaluation criteria based on authorship positions by gender, academic age, and research field: the Spanish case
Authors: Chinchilla-Rodríguez Zaida , Escabias Manuel , Morillo Fernanda 
Published: February 2025

Abstract
This study aims to provide an overview of the distribution of the Spanish scientific workforce focusing on differences in authorship position by gender, academic age, number of authors, and research field. The results show some degree of parity in younger age cohorts and areas such as biomedicine, but little participation of females in the oldest age cohort and areas such as mathematics. In addition, the presence of women undergoes significant changes in certain areas and decreases in oldest age cohorts. This circumstance leads to a low probability of finding women or junior researchers in relevant authorship positions. Policymakers should know that inequalities in the scientific workforce must be considered when addressing/proposing scientific evaluation criteria.
Recently reported SARS-CoV-2 genomes suggested to be intermediate between the two early main lineages are instead likely derived
Authors: Pekar Jonathan E , Moshiri Niema , Lemey Philippe , Crits-Christoph Alexander , Débarre Florence , Goldstein Stephen A , Hensel Zach , Rambaut Andrew , Worobey Michael , Holmes Edward C , Wertheim Joel O 
Published: February 2025

Abstract
Understanding the genomic diversity of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) at the outset of the coronavirus disease 2019 (COVID-19) pandemic can provide insight into the circumstances leading to its emergence. Early SARS-CoV-2 genomic diversity has been classified into two distinct viral lineages, denoted “A” and “B”, which we hypothesized were separately introduced into humans. Recently published data contain two genomes with a haplotype suggested to be an evolutionary intermediate to these two lineages, known as “T/T”. We used a phylodynamic approach to analyze SARS-CoV-2 genomes from early 2020 to determine whether these two T/T genomes represent an evolutionarily intermediate haplotype between lineages A and B, or if they are a later descendent of either of these two lineages. We find that these two recently published T/T genomes do not represent an evolutionarily intermediate haplotype and were, instead, derived from either lineage A or B. However, we cannot conclusively determine from which lineage they were derived. After including additional data from the start of the pandemic, including these two T/T genomes, we again find a discrepancy in the molecular clock when inferring the ancestral haplotype of SARS-CoV-2, corroborating existing evidence for the separate introductions of SARS-CoV-2 lineages A and B into the human population in late 2019.
A Rare Case of Combined Merkel Cell Cancer and Squamous Cell Carcinoma of the Face in an Older Woman of Southern Italy
Authors: Mariniello Domenico , D’Antonio Santolo , Castellaneta Francesco , Grieco Michele , Fabrizio Tommaso 
Published: February 2025

Summary:
Merkel cell carcinoma (MCC) is a rare, aggressive neuroendocrine skin tumor, whereas squamous cell carcinoma (SCC) is a more common form of skin cancer. Both tumors share similar risk factors, including advanced age, sun exposure, and fair skin. Cases of synchronous MCC and SCC are rare, and there are no established guidelines for their combined management. We report the case of an 85-year-old White woman from Southern Italy, presenting with a nodular lesion on her right forehead and a flat keratotic lesion on her right zygomatic region. The patient was treated with surgical excision and close postoperative follow-up. Histopathological analysis confirmed 2 distinct tumor populations in the forehead lesion: poorly differentiated neuroendocrine cells, consistent with MCC, and squamous cells with invasive characteristics. The zygomatic lesion contained only squamous cells. Despite surgical intervention and multidisciplinary postoperative care, the patient experienced recurrence within 4 months and died. This case illustrates a rare occurrence of combined MCC and SCC, presenting challenges in diagnosis and treatment. Given the lack of guidelines for managing dual diagnoses, this case highlights the need for further studies to establish standardized treatment protocols. The aggressive nature of these tumors underscores the importance of early detection and ongoing research to improve outcomes.
Acute abdominal pain as the initial presenting symptom of pediatric Burkitt lymphoma: A case report and literature review
Authors: Tan Qing-Lin , Tang Qing , Chen Xiu-Qi , Huang Li , Yun Xiang , Shan Qing-Wen 
Published: February 2025

Rationale:
Acute abdominal pain is a prevalent clinical symptom in pediatric patients, primarily attributed to pediatric acute abdomen. However, there are rare exceptional instances where neoplastic diseases may cause acute abdominal pain.

Patient concerns:
The present study encompasses a case of pediatric Burkitt lymphoma wherein acute abdominal pain manifested as the initial symptom, erroneously diagnosed as acute appendicitis.

Diagnoses:
The immunohistochemistry results of laparoscopic biopsy revealed Burkitt lymphoma, characterized by positive expression of CD20, CD79a, CD10, BCL-6, MUM1, and strong positive expression of CD38, c-myc, cyclinD1, and Ki-67 positive index >90%+.

Interventions:
The child underwent regular chemotherapy according to the SCCCG-BL/DLBCL-2017 regimen.

Outcomes:
During the 13-month follow-up period, the patient’s obtained complete remission by Positron emission tomography–computed tomography scan.

Lessons:
The objective of this study is to enhance the awareness of clinical pediatricians regarding cases of acute abdominal pain caused by lymphoma.
Intracranial phosphaturic mesenchymal tumor: A rare case report and systematic review
Authors: Song Shuyue , Zhao Yuyang , Wang Yiquan , Zhao Yujing , Liu Wenqiang , Wang Zhe 
Published: February 2025

Rationale:
Phosphaturic mesenchymal tumors (PMTs) are rare soft-tissue and bone tumors that can occur intracranially. Low incidence, nonspecific symptoms, and diverse histomorphology of PMTs contribute to a high rate of misdiagnosis.

Patient concerns:
This report presents a rare case of an intracranial PMT located in the posterior cranial fossa. In addition, a systematic review of previously reported intracranial PMT cases was conducted and summarized.

Diagnoses:
Incorporating clinical symptoms, laboratory findings, and imaging features, the definitive diagnosis of PMT was based on pathological examination.

Interventions:
The patient underwent consultations in endocrinology, orthopedics, and neurosurgery, and ultimately had a surgical procedure to remove the intracranial tumor.

Outcomes:
After tumor resection, the patient’s laboratory values returned to normal, his symptoms improved, and he could walk again.

Lessons:
Due to the rarity and high misdiagnosis rate of PMTs, no unified diagnosis and treatment standards have been established. Early identification, accurate diagnosis, and timely treatment are essential for optimal management. Surgical resection remains the preferred treatment for PMTs, with total tumor resection strongly recommended. In case of incomplete resection, tumor recurrence and persistent symptoms may necessitate adjunctive drug therapy and radiation therapy.
Association Between Vascular Calcifications on Joint Radiographs and Calcium Pyrophosphate Crystal Arthritis
Authors: Brikman Shay , Tannous Hani , Novofastovski Irina , Abuhasira Ran , Mader Reuven , Bieber Amir 
Published: February 2025

Objective
Previous studies have shown an association between chondrocalcinosis (CC) and vascular calcifications (VCs). This study aimed to investigate the association of VCs detected on joint radiographs (XRs) of older patients diagnosed with calcium pyrophosphate (CPP) arthritis compared with a control group with osteoarthritis (OA).

Methods
A medical records review study of joint radiographs (knee and wrist) was conducted. CPP crystal arthritis was diagnosed based on at least 1 documented episode of arthritis with synovial fluid analysis positive for CPP crystals or imaging showing CC at 1 or more sites, with no alternative inflammatory arthritis diagnosis. The control group comprised patients with OA and no CC, matched 1:1 for age and sex. All participants were over 60 years of age. XRs were reviewed for CC, OA, and VCs at the affected joint by 2 independent observers.

Results
A total of 98 patients were enrolled in both the CPP arthritis group and the OA group. VCs adjacent to the affected joint were detected in 69 patients of the CPP group and 19 patients of the control group (70.4% vs 19.4%, p < 0.001). Among patients aged 60 to 80 years, the presence of VCs on XRs was highly indicative of CPP, demonstrating a specificity of 89.2% (95% confidence interval: 79.1%–95.6%). In the CPP group, patients with VCs had a significantly higher prevalence of cardiovascular (CV) comorbidities.

Conclusions
The detection of VCs on XRs was strongly associated with CPP crystal arthritis. The presence of VCs may further serve as a biomarker for an increased burden of CV comorbidities.
Diagnostic investigations in adults with suspected stroke—improvement of door-to-imaging time: a best practice implementation project
Authors: Licenik Radim , Sedova Petra , Ismail Tahir , Khaled Hasan Muhammad , Klugar Miloslav , Riad Abanoub , Klugarová Jitka 
Published: February 2025

ABSTRACT

Objectives:
This evidence implementation project aimed to assess and improve compliance with evidence-based neuroimaging criteria for adult patients with suspected stroke.

Introduction:
Stroke is the second leading cause of mortality and severe disability, requiring timely and accurate diagnosis. Clinical guidelines recommend brain imaging within 60 minutes of hospital arrival for suspected stroke patients. This project involved hospitals in North West Anglia NHS Foundation Trust, UK, serving 850,000 people with over 800 admissions annually.

Methods:
The JBI Evidence Implementation Framework was used to guide this project. JBI software, the Practical Application of Clinical Evidence System (PACES), as well as JBI's Getting Research into Practice (GRiP) approach, were used to conduct the audit and implementation phases. The project followed three stages: (1) implementation planning, (2) baseline assessment and implementation, and (3) impact evaluation. Three audit criteria were used to represent best practices for diagnosing suspected stroke patients.

Results:
The baseline audit revealed low compliance with the first criterion, with only 2.9% (1/35) of patients receiving a CT head scan within 1 hour of admission. In the follow-up audit, compliance improved to 45.2% (14/31). The other two criteria, diagnosis by a trained health care professional and baseline ECG assessment, had already achieved 100% compliance in the baseline audit.

Conclusions:
Compliance with evidence-based neuroimaging criteria improved after implementing targeted educational strategies and training. The rate of CT scans conducted within 1 hour increased, although door-to-imaging times remain suboptimal compared with achievable benchmarks of ≤ 20 minutes. Ongoing education and training are crucial for sustaining high compliance and improving stroke patient outcomes.

Spanish abstract:

http://links.lww.com/IJEBH/A324
Reconstructing the Huang Surname and Its Related Lineages: A Comprehensive Analysis of Molecular Genetics and Historical Genealogies
Authors: Huang Shi 
Published: February 2025

AbstractThe origin of the Huang surname is complex, but according to historical texts such asShiji, it can be traced back to the Yellow Emperor (Huang Di) and his descendant, Bo Yi, who played a key role in controlling the floods during the Xia Dynasty and was granted the surname Ying. Bo Yi had two sons who each established a state, one named Huang and the other Xu. After the fall of Huang, its people adopted Huang as their surname and migrated to Hubei. Similarly, after the fall of Xu, its people adopted Xu as their surname, spreading throughout Jiangsu. Further descendants of Bo Yi also gave rise to 12 other surnames, including the Liang surname. Given that the narratives of ancient texts are often regarded as legendary, we aim to independently verify the authenticity of the historical records by analyzing the paternal haplotypes of the Huang surname and its related surnames using scientific methods. We analyzed the surname genetic data of 207,333 Han Chinese males published by 23Mofang and combined it with independent sequencing research. In 189 Y chromosome haplotype branches, each containing at least five individuals with the surnames Huang, Xu, or Liang, and formed around 4,000 years ago, we analyzed the proportion of samples with the Huang surname from Hubei among all samples nationwide with the Huang surname. Branches with a high proportion in Hubei are likely to represent the Hubei-specific lineage of the Huang surname. We similarly analyzed the proportion of samples with the Xu surname in the Jiangsu area and of samples with the Liang surname in the Hebei area. We further applied two criteria to identify the ancestral genotype of a specific surname in a given region: first, the surname should appear at a high frequency among all surnames within that genotype; second, the proportion of samples of the region among nationwide samples should be high. The results showed that the Hubei-specific Huang surname likely carries the MF14296/MF15137 haplotype downstream of the supergrandfather O-M117-F8-F2137-A16635-A16636. Our independent sampling study found that A16636 is the dominant haplotype among the Huang surname population in nine neighboring Huang surname villages around Luohansi in Huangpi, Hubei. The Jiangsu-specific Xu surname likely carries the MF38096/SK1726 haplotype under the A16636 sister branch F15823, while the Hebei-specific Liang surname likely carries the F15823 related MF14287/MF15398/MF14963 haplotype. This conclusion aligns with the historical records, providing strong genetic evidence that supports the authenticity of these ancestral claims regarding the Huang and Xu states and the Xia dynasty.
BrAIn: A comprehensive artificial intelligence-based morphology analysis system for brain organoids and neuroscience
Authors: Kahveci Burak , Polatli Elifsu , Evranos Ali Eren , Güner Hüseyin , Bastanlar Yalin , Karakülah Gökhan , Güven Sinan 
Published: February 2025

AbstractHuman-induced pluripotent stem cells (iPSCs) offer transformative potential for biomedical research, with iPSC-derived organoids providing more physiologically relevant models than traditional 2D cell cultures. Among these, brain organoids are particularly valuable for drug screening, disease modeling, and investigations into molecular pathways. Accurate representation of brain morphology is critical, as more complex organoid structures better mimic the human brain. Deep learning (DL) and machine learning (ML) approaches have become integral to analyzing organoid morphology, yet tools for comprehensive, time-resolved assessments are scarce. Here, we introduceBrAIn, a DL-based application for analyzing the developmental progression of brain organoids. BrAIn tracks their evolution from embryoid bodies and quantifies parameters including area, Feret diameter, perimeter, roundness, and circularity. It also classifies budding and abnormal morphologies of 3D organoids and detects monolayer neural rosette structures, key features of neuronal differentiation. Designed with accessibility in mind, BrAIn provides a no-code interface, enabling researchers of all technical backgrounds to conduct advanced morphological analyses with ease. Our study demonstrates the application of BrAIn to evaluate the effects of different growth conditions - static, orbital shaker, and microfluidic chip-based - on brain organoid development. Orbital shaker cultures resulted in the largest organoids, while chip-based systems achieved more homogeneous growth. Both conditions produced organoids with greater morphological complexity compared to static culture. BrAIn emerges as a robust, user-friendly tool to quantify brain organoid development and explore how versatile growth conditions influence their morphology and maturation.
The novel SCN5A-P1891A mutation is associated with left ventricular hypertrabeculation and links Nav1.5 to cardiomyocyte proliferation and disrupted 3D cardiac tissue formation
Authors: Majid Qasim A. , Prajapati Chandra , Liu Xiaonan , Kari-Koskinen Julia , Pohjolainen Lotta , Karhu S. Tuuli , Ruskoaho Heikki , Varjosalo Markku , Aalto-Setälä Katriina , Talman Virpi 
Published: February 2025

AbstractBackgroundLeft ventricular hypertrabeculation (LVHT) is a heterogenous cardiac condition with a complex and poorly understood aetiology. We comprehensively characterised the effect of a novel P1891A mutation in theSCN5Agene, which encodes the voltage-gated sodium channel Nav1.5, identified in a Finnish family diagnosed with LVHT.MethodsWe generatedSCN5A-P1891A mutation-carrying human induced pluripotent stem cell-derived cardiomyocytes (P1891A-hiPSC-CMs) and performed electrophysiological assessments, including patch-clamp studies, and fluorescent calcium imaging, to determine the mutation’s effect on hiPSC-CM electrophysiology. We also evaluated the impact of the mutation on the proliferative capacity in response to mitogenic stimuli and on the hypertrophic response following cyclic mechanical stretch or endothelin-1 treatment. Further, we assessed the effect on contractile parameters in three-dimensional (3D) contractile hydrogels (engineered heart tissues, EHTs) and conducted advanced proteomics to understand the consequences of the mutation on Nav1.5 protein-protein interactions.ResultsTheSCN5A-P1891A mutation reduced the sodium current densities and increased both the sodium window current and arrhythmogenicity; however, action potential parameters were unaffected. Advanced proteomics characterised, for the first time, the complete Nav1.5 interactome and revealed that theSCN5A-P1891A mutation negated interactions with fibroblast growth factor 12 (FGF12) and FGF13, that are known to modulate sodium channel activity. Baseline proliferation was unchanged, although aged P1891A-hiPSC-CMs demonstrated enhanced proliferative capacity following mitogenic stimulation. Further, P1891A-hiPSC-CMs exhibited a heightened stress response upon mechanical stretch, resulting in the upregulation of heart failure-associated genes. Strikingly, EHTs derived from P1891A-hiPSC-CMs yielded disparate phenotypes. Whilst the majority condensed only partially and failed to beat synchronously, a small subset condensed fully yet exhibited weak contractile properties, alongside age-associated functional decline. In contrast, EHTs derived from healthy control hiPSC-CMs consistently condensed fully and demonstrated a positive correlation between post-fabrication age and contractile propertiesConclusionsOur study presents a unique aetiology of LVHT and reveals a novel association betweenSCN5Amutations and enhanced human cardiomyocyte proliferation. Further, the inability of P1891A-hiPSC-CMs to consistently form fully condensed 3D cardiac tissues may be linked to their abnormal response to mechanical stretch and provides a powerful 3D model for future mechanistic research and drug development studies to better understand and treat LVHT.