bluuebunny/crossref_metadata_2025_split huggingface dataset:
Surgical Outcomes of Amniotic Membrane Transplantation in Impending or Full-Thickness Corneal Perforation
Authors: Zatarain-Barrón Naomi C. , Vera-Duarte Guillermo Raul , Velasco-Sepulveda Braulio , Ramirez-Miranda Arturo , Navas Alejandro , Garfias Yonathan , Graue-Hernandez Enrique O. 
Published: January 2025

Purpose:
The aim of this study was to determine the efficacy and surgical outcomes of cryopreserved amniotic membrane transplantation in impending (ie, descemetocele) or full-thickness corneal perforation.

Methods:
A retrospective chart review that included patients who underwent AMT because of impending or full-thickness corneal perforation. Data collected were preoperative diagnosis, surgical indication, pre- and postoperative uncorrected (UCVA) and best-corrected visual acuity (LogMAR), intraocular pressure (IOP) (mm Hg), postoperative complications, and their resolutions. The primary outcome was defined as a complete closure of the corneal wound.

Results:
A total of 33 eyes from 31 patients were included, of which 29 were in the full-thickness perforation group, and 4 in the descemetocele group. Mean follow-up period was 15.84 ± 13.43 months. Preoperative UCVA and best-corrected visual acuity improved slightly postoperative, and IOP levels were maintained. There were no intraoperative complications. Postoperative complications were found in 11 eyes, with recurrent perforation the most common, predominantly in patients with autoimmune disease diagnosis versus nonautoimmune etiologies (P < 0.002). Eleven patients from the full-thickness corneal perforation group required surgical reintervention. Complete closure of the corneal wound was achieved in 25 eyes overall.

Conclusions:
AMT is a safe procedure that can be performed to manage corneal imminent or full-thickness perforation, with successful surgical outcomes, and stability in visual acuity and IOP levels. Patients with autoimmune diagnoses have a worse prognosis compared with those with nonautoimmune etiologies. Further research is needed to help predict surgical failure and prevent unfavorable results.
Prevalence of some cardiovascular risk factors: obesity, hypertension, and smoking among medical students
Authors: Alrasheed Asayil A. , Alabdullatif Norah I. , AlOmair Aljawhara W. , Almutairi Atheer K. , Moria Abdulaziz H. , Amjad Zainab , Elsheikh Eman 
Published: January 2025

Introduction:
Cardiovascular diseases (CVDs) are the principal cause of worldwide mortality, with 17.9 million deaths reported in 2019. In Saudi Arabia, CVDs account for 42% of all deaths, occurring on average 10 years earlier than in Western populations. Medical students are particularly susceptible to Cardiovascular disease CVD risk factors due to demanding academic schedules and lifestyle changes. This study aims to identify cardiovascular risk factors (CVRF) among medical students at King Faisal University, highlighting the need for preventive measures and curriculum modifications.

Methods:
This prospective cross-sectional study was conducted from February to April 2024 at King Faisal University, focusing on undergraduate medical students. Participants not enrolled in the College of Medicine, those who declined to complete the survey, or those who submitted incomplete responses were excluded. A total of 313 students participated in the study. Data collection involved physical evaluations and a validated questionnaire covering demographics, medical history, lifestyle, and diet. Measurements included waist circumference, weight, height, blood pressure, and pulse. Data was analyzed using IBM SPSS Statistics version 19.

Results:
Among participants, 52.4% had a normal body mass index BMI, while 19.5% were overweight and 11.2% obese. Blood pressure measurements showed 45.7% had normal BP, but 44.4% were prehypertensive. A family history of CVDs was reported by 55.6% of students, with hypertension (HTN) and diabetes being the most common. Smoking was infrequent, with only 5.1% reporting regular habits. Dietary analysis showed moderate consumption of unhealthy foods, with 80% maintaining a moderately healthy diet. Physical activity assessment indicated significant portions engaged in light or moderate activities, but only a minority met recommended levels for vigorous activities. Significant associations were found between physical activity levels and academic year, personal history of diseases, and smoking behavior.

Conclusion:
Most students had normal body weight, but many were overweight or pre-hypertensive. Family histories of CVDs, particularly (HTN) and diabetes, were common. Smoking was rare, but diets included frequent unhealthy foods. These findings underscore the need for targeted health programs to reduce cardiovascular risks in this population.
Scleral Tattooing Complications: Surgical Management of Granulomas in a Cosmetic Procedure
Authors: Ortiz-Morales Gustavo , Haro-Morlett Luis , Eskenazi-Betech Ruth , Navas Alejandro , Ramirez-Miranda Arturo , Perezpeña-Diazconti Mario , Graue-Hernandez Enrique O. 
Published: January 2025

Purpose:
To report the surgical management and outcomes of a patient with granulomatous inflammation following scleral tattooing, emphasizing the associated risks and clinical implications.

Methods:
A 26-year-old woman with a history of multiple body modifications, including scleral tattooing, presented with bilateral ocular pain and discomfort. Clinical examination revealed corneal dellen and subconjunctival granulomas. The patient underwent surgical excision of the granulomas, with efforts to preserve the black conjunctival pigmentation. Histopathological analysis was performed on the excised tissue. The patient's visual acuity and ocular condition were monitored for 12 months postoperatively.

Results:
Preoperative best-corrected visual acuity was 20/50 in the right eye and 20/60 in the left. Surgical excision of the granulomas was successfully performed, resulting in symptomatic relief and preservation of the black scleral coloration. Histopathological analysis confirmed the presence of exogenous pigment without hemosiderin or melanin deposits. Twelve months after surgery, the patient maintained a best-corrected visual acuity of 20/20 in both eyes, with no recurrence of granulomas or additional complications.

Conclusions:
This case highlights the serious risks associated with scleral tattooing, including granulomatous reactions and corneal complications. Surgical intervention effectively addressed the ocular issues while preserving the desired cosmetic outcome. Greater public awareness and stronger regulations are critical to prevent such complications, and to prepare ophthalmologists for managing cases of scleral tattooing–related injuries.
The utility of 8-Hydroxydeoxyguanosine and 8-Oxoguanine DNA glycosylase as a novel diagnostic marker for autistic children
Authors: Ismael Hawnaz Mohammad , Ismail Parween Abdulsamad 
Published: January 2025

AbstractAutism spectrum disorder (ASD) is a neurodevelopmental condition that develops in childhood. Although genetics are a key factor in its development, neurological, environmental, and immunological influences also play significant roles. This study investigated the oxidative DNA damage (ODD) biomarker 8-hydroxy-2-deoxyguanosine (8OHdG) in children with autism, exploring its connection to disease severity and the DNA repair enzyme oxoguanine glycosylase 1 (OGG1). This study investigated the oxidative DNA damage (ODD) biomarker, 8-hydroxy-2-deoxyguanosine (8OHdG), in children with autism, examining its relationship with disease severity and the DNA repair enzyme oxoguanine glycosylase 1 (OGG1). The study included 89 children with ASD and 29 typically developing children in an observational controlled cross-sectional design. Autism severity was assessed using the Diagnostic and Statistical Manual of Mental Disorders (DSM-5). ELISA was used to measure serum levels of 8-OHdG and OGG1.The results showed that children with autism had significantly higher serum 8-OHdG levels compared to healthy children (P=0.04), with a significant positive correlation with autism severity (P=0.02). Additionally, serum OGG1 levels were significantly lower in children with autism than in their healthy counterparts (P=0.0004), with a notable positive association with disease severity (P=0.0001). These findings indicate that elevated serum 8-OHdG levels may play a key role in oxidative DNA damage in ASD. Higher levels of 8-OHdG in children with severe ASD symptoms could serve as a potential biomarker for diagnosis. Furthermore, the reduced levels of the repair enzyme OGG1, associated with increased 8-OHdG levels, contribute to the observed DNA damage in ASD.
Frequent lncRNA-derived fusions in pediatric neuroblastoma identified byLncFusion: potential biomarker and therapeutic implications
Authors: Li Zixiu , Wu Joae , Zhou Peng , Zhou Chan 
Published: January 2025

ABSTRACTDespite growing interest in the onco-fusion proteins and long noncoding RNAs (lncRNAs) in cancers, lncRNA-derived fusion transcripts in pediatric cancers remain understudied. To address this gap, we first developedLncFusion, a novel computational pipeline that systematically detects lncRNA-derived fusion transcripts from RNA-seq data. Leveraging our previously publishedFlnc(for comprehensive lncRNA identification) as a foundation and applyingLncFusion, we identified over 900 high-confidence lncRNA-derived fusions (lnc-fusions) in pediatric neuroblastoma by analyzing the transcriptomics datasets from three major pediatric cancer cohorts—TARGET, Gabriella Miller Kids First, and St. Jude Cloud. The number of lnc-fusions exceeds the number of mRNA-derived fusions (mRNA-fusions) in neuroblastoma. Whole genome sequencing analyses revealed that approximately 40% of these lnc-fusions result from chromosomal rearrangements, while over 60% may arise from aberrant splicing events. Among these high-confidence lnc-fusions, 61 are enriched in pediatric neuroblastoma compared to healthy controls; and 20s exhibit subtype-specific expressions in pediatric neuroblastoma patients, which would be categorized into three groups: MYCN-amplified patients, c-MYC-highly expressed patients and the remaining (MYCN-unamplified and c-MYC not high expression). Subtype-specific enrichment of certain lnc-fusions, particularly in MYCN-amplified and c-MYC-high subgroups, underscores distinct oncogenic roles. Further functional studies implicated lnc-fusions in key pathways related to neuron development, translation, and energy metabolism, suggesting potential contributions to neuroblastoma pathogenesis. Additionally, We found several novel fusions might serve as potential diagnostic or prognostic biomarkers in neuroblastoma. A few candidates correlate with either favorable histology and lower-risk patient subsets, or poorer survival outcomes, indicating strong prognostic biomarker potential. Experiments in cell line further confirmed the presence of a few key lnc-fusions discovered from patient samples. Our findings provide the first comprehensive insight into lncRNA-derived fusions in pediatric neuroblastoma, providing the promise of lnc-fusions as novel biomarkers and therapeutic targets. TheLncFusiontool developed can also be applied to explore lnc-fusions in other pediatric and adult cancers.
Embryonic macrophages in brown adipose tissue are spatially associated with developing nerves
Authors: Félix Inês , Ollikainen Janni , Haque Afra , Karhula Joonas , Salmi Marko , Jokela Heli , Rantakari Pia 
Published: January 2025

AbstractBrown adipose tissue (BAT) is a specialized adipose tissue that produces heat through sympathetic nerve-dependent thermogenesis and influences glucose and triglyceride metabolism, making it a potential target for obesity-related diseases. In mice, interscapular BAT (iBAT) emerges on embryonic days (E)14.5-15.5, with extensive vessel and nerve networks still maturing postnatally. These developmental stages are critical for BAT, impacting long-term BAT function. In adult mice, macrophages regulate sympathetic innervation and thermogenesis. However, research on BAT macrophage characters, ontogeny, and functions in early life is lacking. Using single-cell genomics and proteomics, fate-mapping techniques, and 3D imaging, we analyzed iBAT macrophages during early development. We discovered the presence of fetal liver-derived macrophages as early as E15.5, which are later fully replaced by bone marrow-derived macrophages. Transcriptomics data highlight mononuclear phagocyte subpopulations, from which most express macrophage-associated genes (Adgre1, Fcgr1, Csf1r) and monocytic markers (Ccr2,Ly6c2) together. Embryonic macrophages interact closely with developing neural networks, while postnatal bone marrow-derived macrophages associate with blood vessels. Lack of fetal liver-derived macrophages disrupts nerve and vessel development and causes downregulation of genes related to neuronal diseases and protein digestion pathways. Our data suggest that fetal liver-derived macrophages, interacting with BAT’s developing sympathetic neural network, guide the development of tissue morphology. Understanding further the mechanism behind these events can unravel novel targets for BAT immunomodulation.
Crop genotype modulates root rot resistance-associated microbial community composition and abundance of key taxa
Authors: Gfeller Valentin , Schneider Michael , Bodenhausen Natacha , Horton Matthew W. , Wille Lukas , Oldach Klaus H. , Studer Bruno , Hartmann Martin , Messmer Monika M. , Hohmann Pierre 
Published: January 2025

AbstractPlants are constantly challenged by pathogens, which can cause substantial yield losses. The aggressiveness of and damage by pathogens depends on the host-associated microbiome, which might be shaped by plant genetics to improve resistance. How different crop genotypes modulate their microbiota when challenged by a complex of pathogens is largely unknown. Here, we investigate if and how pea (Pisum sativum L.) genotypes shape their root microbiota upon challenge by soil-borne pathogens and how this relates to a genotype’s resistance. Building on the phenotyping efforts of 252 pea genotypes grown in naturally infested soil, we characterized root fungi and bacteria by ITS region and 16S rRNA gene amplicon sequencing, respectively. Pea genotype markedly affected both fungal and bacterial community composition, and these genotype-specific microbiota were associated with root rot resistance. For example, genotype resistance was correlated (R2= 19%) with root fungal community composition. Further, several key microbes, showing a high relative abundance, heritability, connectedness with other microbes, and correlation with plant resistance, were identified. Our findings highlight the importance of crop genotype-specific root microbiota under root rot stress and the potential of the plant to shape its associated microbiota as a second line of defense.
Reefal regions were biodiversity hotspots throughout the Phanerozoic
Authors: Close Roger A. , Benson Roger B.J. , Kiessling Wolfgang , Saupe Erin E. 
Published: January 2025

Reefs are important hotspots of marine biodiversity today, and acted as cradles of diversification in the geological past. However, we know little about how the diversity of reef-supporting regions varied through deep time, and how this differed from other regions. We quantified regional diversity patterns in reef-supporting and non-reef-supporting regions in the fossil record of Phanerozoic marine invertebrates. Diversity in reef-supporting regions is on average two- to three-fold higher than in non-reef-supporting regions, and has been remarkably stable over timescales of tens to hundreds of millions of years. This signal is present in both reefal and non-reefal facies within reef-supporting regions, suggesting that reefs enriched diversity in surrounding environments. Sepkoski’s ‘Modern Fauna’, an assemblage of higher taxa that includes gastropods, bivalves and echinoids, has been a key component of reef-supporting regions since the Paleozoic, contrasting with its later rise to dominance in non-reef-supporting regions during the later Mesozoic–Cenozoic.One-Sentence SummaryRegions of the globe that supported reefal environments have been key hotspots of marine animal diversity for over 400 million years.
Telomeric G-quadruplex Intermediates unveiled by Complex Markov Network Analysis
Authors: Sáinz-Agost A. , Falo F. , Fiasconaro A. 
Published: January 2025

AbstractG-quadruplexes are secondary, non-canonical RNA/DNA structures formed by guanine-rich sequences assembled into four-stranded helical structures by the progressive stacking of G-Tetrads, planar arrangements of guanines stabilised by monovalent ions such as K+or Na+. Their stability plays a very important role in the prevention of DNA degradation, leading to the promotion or inhibition of specific biological pathways upon formation. In this work we study the different conformations of these structures through their Free Energy Landscape at different temperatures. All-atom simulations are adopted according to a mesoscopic G-quadruplex model previously developed by our group. We use a small number of significant reaction coordinates to analyze the evolution of the system by applying two dimensionality reduction techniques: Principal Component Analysis (PCA) and time-Independent Component Analysis (tICA). The data of the trajectories of the system in this reduced space are encoded into a Complex Markov Network which, in conjunction with an Stochastic Steepest Descent, provides an hierarchical organization of the different nodes into basins of attraction, so revealing the main intermediate states and the most relevant transitions the system undergoes in its denaturation path.Author summaryG-quadruplexes are fascinating structures formed in guanine-rich regions of DNA and RNA, and they are key players in gene regulation and genome stability. Their ability to promote or block biological processes makes them potential targets for therapies.In this study, we explored how G-quadruplexes evolve and melt at different temperatures. Through different data analyses of our molecular simulations, we mapped out their observed denaturation pathways together with their occurrence of their intermediate states. Specifically, with the use of Complex Markov Networks we encoded the trajectories into networks able to clearly reveal the main intermediates and quantify the most relevant connections between them, providing detailed information about the structural denaturation pathway.
Mathematical Modeling and Simulation of Tumor-Induced Angiogenesis in Retinal Hemangioblastoma
Authors: Pradelli Franco , Minervini Giovanni , Venkatesh Pradeep , Azad Shorya , Gomez Hector , Tosatto Silvio C.E. 
Published: January 2025

ABSTRACTRetinal Hemangioblastoma (RH) is the most frequent manifestation of the von Hippel-Lindau syndrome (VHL), a rare disease associated with the germline mutation of the von Hippel-Lindau protein (pVHL). An emblematic feature of RH is the high vascularity, which is explained by the overexpression of angiogenic factors (AFs) arising from the pVHL impairment. The introduction of Optical Coherence Tomography Angiography (OCTA) allowed observing this feature with exceptional detail. Here, we combine OCTA images and a mechanistic model to investigate tumor growth and vascular development in a patient-specific way. We derived our model from the agreed pathology for RH and focused on the earliest stages of tumor-induced angiogenesis. Our simulations closely resemble the medical images, proving the capability of our model to recapitulate vascular patterning in actual patients. Our results also suggest that angiogenesis in RH occurs upon reaching a critical dimension (around 200 μm), followed by the rapid formation of stable vascular networks. These findings open a new perspective on the crucial role of time in antiangiogenic therapy in RH, which has resulted in ineffective control. Indeed, it might be that when RH is diagnosed, angiogenesis is already too advanced to be effectively targeted with any effective means. Moreover, our simulations suggest that vascularization in RH is not a continuous process but an inconstant development with long, stable phases and rapid episodes of vascular sprouting.AUTHOR SUMMARYTumor-induced angiogenesis is a survival strategy commonly exploited by solid tumors to access further nutrients and sustain their growth. The recent introduction of Optical Coherence Tomography Angiography (OCTA) enables scientists and physicians to observe vascular patterning in the retina, non-invasively and with unprecedented detail. Here, we exploit direct observations on a vascular retinal tumor, Retinal Hemangioblastoma (RH), and a mathematical model to investigate the earliest stages of tumor-induced angiogenesis. Our simulations closely match reality and provide critical insights into the role of time in anti-angiogenic therapy for this neoplasm.
Metabolic shifts in the heart of hypothyroid mice — insights from untargeted metabolomics
Authors: Guan Heng , Yang Yujie , Xiao Wenping , Wan Sha , Liu Fang 
Published: January 2025

ABSTRACTSIntroductionHypothyroidism is a prevalent disorder that affect all systems of body, including the cardiovascular system and control of cardiac function. However, much remains unknown about the metabolic pathways and disorders in the heart induced by hypothyroidism, as well as the metabolic mechanisms involved.ObjectivesThis work aims to investigate the impacts of hypothyroidism on the heart and explore its underlying mechanisms through untargeted metabolomics analysis.MethodsAn experimental model of hypothyroidism was established by giving water containing 0.1% methimazole and 1% potassium perchlorate to 12-week-old C57BL/6J mice for six consecutive weeks.ResultsAfter treatment, hypothyroidism significantly reduced mice’s heart weight and heart rate. Metabolomics analysis revealed that the different metabolites (DEMs) primarily concentrated in Phospholipids, Lipids or Lipids-like, Carbohydrates and Carbohydrate conjugates. These specific metabolites were mainly enriched in pathways related to lipid metabolism. The hearts of hypothyroid mice exhibited significantly lower levels of lipoyl-carnitine compared to controls, along with markedly higher levels of glycolysis and pentose phosphate pathway (PPP) intermediates. Furthermore, carnitine palmitoyltransferase 1B (CPT1B) and carnitine palmitoyltransferase 2 (CPT2) expressions were significantly decreased in the hypothyroid mouse heart, while lactate dehydrogenase A (LDHA) expressions was significantly increased, according to the immunoblotting assay.ConclusionsResearch indicates that hypothyroidism triggers disruptions in both cardiac energy metabolism and phospholipid metabolism in adult mice, which in turn results in myocardial atrophy. These findings could pave the way for novel therapeutic strategies aimed at treating hypothyroidism-induced myocardial atrophy.