bluuebunny/crossref_metadata_2025_split huggingface dataset:
Investigating New Particle Formation and Growth Over an Urban Location in the Eastern Mediterranean
Authors: Ajith T. C. , Windwer Eli , Li Chunlin , Fang Zheng , Kompalli Sobhan Kumar , Nursanto Farhan R. , Olayemi Temitope E. , Ese Julius I. , Sharpe Steven A. L. , Fraund Matthew , Moffet Ryan C. , Laskin Alexander , Fry Juliane L. , Rudich Yinon 
Published: December 2024

AbstractThis study investigates the new particle formation (NPF) events at an urban location in the Eastern Mediterranean. Particle size distribution, particulate chemical composition, and gaseous pollutants were monitored in Rehovot, Israel (31°53″N 34°48″E) during two campaigns: from April 29 to 3 May 2021 (Campaign 1) and from May 3 to 11 May 2023 (Campaign 2), coinciding with an intensive bonfire burning festival. The organic aerosols (OA) source apportionment identified two major factors—Hydrocarbon‐like OA and Biomass‐burning OA—as well as two secondary factors—MO‐OOA (more oxidized‐oxygenated OA) and LO‐OOA (low oxidized oxygenated OA). NPF events were frequently observed during the day (mostly well‐defined nucleation events) and at night (burst of ultrafine mode particles without any discernible growth). A condensation sink value of (9.4 ± 4.0) × 10−3 s−1 during Campaign 1 and (14.2 ± 6.0) × 10−3 s−1 during Campaign 2 was obtained. The daytime events were associated with enhanced sulfuric acid proxy concentrations of (2–12) × 106 molecules cm−3, suggesting the role of gas‐phase photochemistry in promoting NPF. A novel approach of hybrid positive matrix factorization analysis was used to deconvolve the chemical species responsible for the observed events. The results suggest the involvement of multiple components, including ammonium sulfate and MO‐OOA, in the nucleation; Nitrate, HOA and LO‐OOA participate in the subsequent particle growth for the daytime events. Nighttime events involve only semi‐volatile species (LO‐OOA, HOA and nitrate) along with ammonium sulfate.
Expression of p53 in human adipose tissue correlates positively with FAS and BMI
Authors: Wueest Stephan , Scaffidi Chiara , van Krieken Pim P. , Konrad Nils K. , Koch Christian , Lempesis Ioannis G. , Fullin Jonas , Manolopoulos Konstantinos N. , Böttcher Steffen , Goossens Gijs H. , Blüher Matthias , Konrad Daniel 
Published: December 2024

AbstractActivation of Fas (CD95) in adipocytes inhibits browning and may contribute to body weight gain in mice. Moreover, Fas expression in white adipose tissue (WAT) correlates positively with body mass index (BMI) in humans. However, molecular pathways involved in the inhibitory effect of Fas on energy metabolism remain incompletely understood. Herein, we report that protein levels of the tumor suppressor p53 were reduced in primary white adipocytes of adipocyte-specific Fas-knockout mice. Moreover, Fas ligand (FasL) treatment increased p53 concentrations in cultured adipocytes and decreased mitochondrial oxygen consumption in control but not in p53-depleted cells, indicating that Fas activation reduces energy expenditure in a p53-dependent manner. In line, in differentiated human mesenchymal stem cells and WAT derived from different anatomical depots, FAS expression was positively associated with p53. Furthermore, p53 expression in human subcutaneous and visceral WAT correlated positively with BMI, whereas its expression in visceral WAT was inversely associated with insulin sensitivity (as assessed by hyperinsulinemic-euglycemic clamp). Taken together, our data suggest that Fas regulates p53 expression in adipocytes, and may thereby affect body weight gain and insulin sensitivity.
Liquid biopsy in cancer: current status, challenges and future prospects
Authors: Ma Liwei , Guo Huiling , Zhao Yunxiang , Liu Zhibo , Wang Chenran , Bu Jiahao , Sun Ting , Wei Jianwei 
Published: December 2024

AbstractCancer has a high mortality rate across the globe, and tissue biopsy remains the gold standard for tumor diagnosis due to its high level of laboratory standardization, good consistency of results, relatively stable samples, and high accuracy of results. However, there are still many limitations and drawbacks in the application of tissue biopsy in tumor. The emergence of liquid biopsy provides new ideas for early diagnosis and prognosis of tumor. Compared with tissue biopsy, liquid biopsy has many advantages in the diagnosis and treatment of various types of cancer, including non-invasive, quickly and so on. Currently, the application of liquid biopsy in tumor detection has received widely attention. It is now undergoing rapid progress, and it holds significant potential for future applications. Around now, liquid biopsies encompass several components such as circulating tumor cells, circulating tumor DNA, exosomes, microRNA, circulating RNA, tumor platelets, and tumor endothelial cells. In addition, advances in the identification of liquid biopsy indicators have significantly enhanced the possibility of utilizing liquid biopsies in clinical settings. In this review, we will discuss the application, advantages and challenges of liquid biopsy in some common tumors from the perspective of diverse systems of tumors, and look forward to its future development prospects in the field of cancer diagnosis and treatment.
Phosphorylation determines the glucose metabolism reprogramming and tumor-promoting activity of sine oculis homeobox 1
Authors: Lin Yanni , Li Ling , Yuan Bin , Luo Fei , Zhang Xiujuan , Yang Yuanjun , Luo Shaliu , Lin Jing , Ye Tianxing , Zhang Youzhi , Gao Shan , Ye Qinong 
Published: December 2024

AbstractAerobic glycolysis is a hallmark of cancer and is regulated by growth factors, protein kinases and transcription factors. However, it remains poorly understood how these components interact to regulate aerobic glycolysis coordinately. Here, we show that sine oculis homeobox 1 (SIX1) phosphorylation integrates growth factors (e.g. TGFβ, EGF) to control aerobic glycolysis and determines its tumor-promoting activity. SIX1 is phosphorylated at serine 225 (S225) by growth factors-activated protein kinases ERK1/2 and its phosphorylation is responsible for glycolysis stimulated by some growth factors. SIX1 is dephosphorylated by the atypical protein phosphatase eyes absent 4 (EYA4). Phosphorylation blocks non-canonical ubiquitination and degradation of SIX1 through the E3 ubiquitin ligase FZR1. Unexpectedly, the non-canonical phosphorylation mimic SIX1 (S225K), but not the canonical phosphorylation mimic SIX1 (S225D/E), phenocopies the effects of SIX1 phosphorylation on glycolysis and cancer cell growth and metastasis in vitro and in mice. Compared to normal liver tissues, SIX1 phosphorylation at S225 (pS225) is upregulated in human liver cancer tissues. ERK1/2 expression is positively correlated with pS225 and EYA4 expression is negatively associated with pS225 in liver cancer specimens. Moreover, low expression of pS225 had longer disease-free survival and overall survival in patients with liver cancer. Thus, we identify a common mechanism underlying growth factors-mediated glycolysis, and provide a previously unidentified mode for non-classical phosphorylation mimics of a protein. Targeting growth factors/SIX1 signaling pathway may be beneficial to cancer treatment.
Innovation and application of Large Language Models (LLMs) in dentistry – a scoping review
Authors: Umer Fahad , Batool Itrat , Naved Nighat 
Published: December 2024

Abstract
Objective
Large Language Models (LLMs) have revolutionized healthcare, yet their integration in dentistry remains underexplored. Therefore, this scoping review aims to systematically evaluate current literature on LLMs in dentistry.

Data sources
The search covered PubMed, Scopus, IEEE Xplore, and Google Scholar, with studies selected based on predefined criteria. Data were extracted to identify applications, evaluation metrics, prompting strategies, and deployment levels of LLMs in dental practice.

Results
From 4079 records, 17 studies met the inclusion criteria. ChatGPT was the predominant model, mainly used for post-operative patient queries. Likert scale was the most reported evaluation metric, and only two studies employed advanced prompting strategies. Most studies were at level 3 of deployment, indicating practical application but requiring refinement.

Conclusion
LLMs showed extensive applicability in dental specialties; however, reliance on ChatGPT necessitates diversified assessments across multiple LLMs. Standardizing reporting practices and employing advanced prompting techniques are crucial for transparency and reproducibility, necessitating continuous efforts to optimize LLM utility and address existing challenges.
DOCK8 gene mutation alters cell subsets, BCR signaling, and cell metabolism in B cells
Authors: Gu Heng , Xie Miaomiao , Zhao Siyu , Luo Xi , Huang Yanmei , Yang Lu , Guan Fei , Lei Jiahui , Liu Chaohong 
Published: December 2024

AbstractDOCK8 deficiency has been shown to affect the migration, function, and survival of immune cells in innate and adaptive immune responses. The immunological mechanisms underlying autosomal recessive (AR) hyper-IgE syndrome (AR-HIES) caused by DOCK8 mutations remain unclear, leading to a lack of specific therapeutic options. In this study, we used CRISPR/Cas9 technology to develop a mouse model with a specific DOCK8 point mutation in exon 45 (c.5846C>A), which is observed in patients with AR-HIES. We then investigated the effect of this mutation on B cell development, cell metabolism, and function in a mouse model with Dock8 gene mutation. The results demonstrated that Dock8 gene mutation inhibited splenic MZ and GC B cell development and crippled BCR signaling. In addition, it resulted in enhanced glycolysis in B cells. Mechanistically, the reduced BCR signaling was related to decreased B cell spreading, BCR clustering, and signalosomes, mediated by inhibited activation of WASP. Furthermore, the DOCK8 mutation led to increased expression of c-Myc in B cells, which plays an important role in glycolysis. As such, GC B cells’ formation and immune responses were disturbed in LCMV-infected mice. These findings will provide new insights into the immunological pathogenesis of primary immunodeficiency disorder caused by DOCK8 mutation.
The USP11/Nrf2 positive feedback loop promotes colorectal cancer progression by inhibiting mitochondrial apoptosis
Authors: Lu Yuanyuan , wei Wanhui , Li Mengting , Chen Danyang , Li Wenjie , Hu Qian , Dong Shouquan , Liu Lan , Zhao Qiu 
Published: December 2024

AbstractAbnormal antioxidant capacity of cancer is closely related to tumor malignancy. Modulation of oxidative stress status is a novel anticancer therapeutic target. Nrf2 is a key regulator of various antioxidant enzymes, but the mechanism of its deubiquitination remains largely unclear. This study unveiled that Nrf2 received post-transcriptional regulation from a proteasome-associated deubiquitinating enzyme, USP11, in colorectal cancer (CRC). It was found that USP11 was overexpressed in CRC tissues acting as an oncogene by inhibiting mitochondrial apoptosis, and USP11 managed to maintain balance in the production and elimination of reactive oxygen species (ROS). Mechanistically, we identified a feedback loop between USP11 and Nrf2 maintaining the redox homeostasis. USP11 stabilized Nrf2 by deubiquitinating and protecting it from proteasome-mediated degradation. Interestingly, we also map that Nrf2 could bind to the antioxidant reaction element (ARE) in the USP11 promoter to promote its transcription. Hence, USP11/Nrf2 positive feedback loop inhibited mitochondrial apoptosis of CRC cells by activating Nrf2/ARE signaling pathway, thus promoting CRC progression.
Organizing space through saccades and fixations between primate posterior parietal cortex and hippocampus
Authors: Vericel Marie E. , Baraduc Pierre , Duhamel Jean-René , Wirth Sylvia 
Published: December 2024

AbstractThe primate posterior parietal cortex (PPC) withholds a unified representation of the visual space supporting visual exploration, while the hippocampus (HPC) provides a memory-based cognitive place map of the environment. To probe the interactions between these two representations, i.e. between view and place, we compared neural activity in the two regions of macaques navigating a virtual maze. We show that a large proportion of PPC neurons displayed spatial selectivity, along with the HPC. We hypothesized that such modulation by self-position might stem from visual cues processing through saccades and fixations. Accordingly, we found saccade-modulated neurons and cells driven by direct fixations on maze paths or landmarks in both brain regions. These populations of “path” and “landmark cells” gave rise to task-relevant maze segmentation, specific to each region. Finally, both regions anticipated landmarks before they appeared in the field of view, suggesting a shared knowledge of the spatial layout. Altogether, these findings highlight the neural processes that make up place, combining visual exploration of objects in space with memory-driven actions.
SAM-DNMT3A, a strategy for induction of genome-wide DNA methylation, identifies DNA methylation as a vulnerability in ER-positive breast cancers
Authors: Hosseinpour Mahnaz , Xi Xinqi , Liu Ling , Malaver-Ortega Luis , Perlaza-Jimenez Laura , Joo Jihoon E. , York Harrison M. , Beesley Jonathan , Caldon C. Elizabeth , Dugué Pierre-Antoine , Dowty James G. , Arumugam Senthil , Southey Melissa C. , Rosenbluh Joseph 
Published: December 2024

AbstractDNA methylation is an epigenetic mark that plays a critical role in regulating gene expression. DNA methyltransferase (DNMT) inhibitors, inhibit global DNA methylation and have been a key tool in studies of DNA methylation. A major bottleneck is the lack of tools to induce global DNA methylation. Here, we engineered a CRISPR based approach, that we initially designed, to enable site-specific DNA methylation. Using the synergistic activation mediator (SAM) system, we unexpectedly find that regardless of the targeted sequence any sgRNA induces global genome-wide DNA methylation. We term this method SAM-DNMT3A and show that induction of global DNA methylation is a unique vulnerability in ER-positive breast cancer suggesting a therapeutic approach. Our findings highlight the need of caution when using CRISPR based approaches for inducing DNA methylation and demonstrate a method for global induction of DNA methylation.
Probabilistic photonic computing with chaotic light
Authors: Brückerhoff-Plückelmann Frank , Borras Hendrik , Klein Bernhard , Varri Akhil , Becker Marlon , Dijkstra Jelle , Brückerhoff Martin , Wright C. David , Salinga Martin , Bhaskaran Harish , Risse Benjamin , Fröning Holger , Pernice Wolfram 
Published: December 2024

AbstractBiological neural networks effortlessly tackle complex computational problems and excel at predicting outcomes from noisy, incomplete data. Artificial neural networks (ANNs), inspired by these biological counterparts, have emerged as powerful tools for deciphering intricate data patterns and making predictions. However, conventional ANNs can be viewed as “point estimates” that do not capture the uncertainty of prediction, which is an inherently probabilistic process. In contrast, treating an ANN as a probabilistic model derived via Bayesian inference poses significant challenges for conventional deterministic computing architectures. Here, we use chaotic light in combination with incoherent photonic data processing to enable high-speed probabilistic computation and uncertainty quantification. We exploit the photonic probabilistic architecture to simultaneously perform image classification and uncertainty prediction via a Bayesian neural network. Our prototype demonstrates the seamless cointegration of a physical entropy source and a computational architecture that enables ultrafast probabilistic computation by parallel sampling.
Resolving Duodenal Gastric Outlet Obstruction: A Case Report of Successful Management of Phytobezoar Impaction in a Duodenal Diverticulum
Authors: Jhajharia Ashok , Bishnoi Narendra Kumar , Ashdhir Prachis , Nijhawan Sandeep 
Published: December 2024

AbstractGastric outlet obstruction (GOO) is a clinical syndrome characterized by hindrance in the passage of gastric contents into the duodenum, with various etiologies including bezoars. Phytobezoars, composed of undigested food fibers, represent a rare but significant cause of GOO. Herein, we present a case of a 34-year-old female with recurrent vomiting and early satiety, diagnosed with GOO caused by an impacted phytobezoar in the duodenum. Despite initial unsuccessful attempts at endoscopic removal, alternative techniques led to successful extraction. Postprocedure evaluation revealed a large duodenal diverticulum. Our experience underscores the complexity of managing duodenal phytobezoars and highlights the efficacy of combined therapeutic approaches. Heightened awareness among gastroenterologists regarding this condition is essential to optimize patient outcomes. Recurrence prevention strategies include dietary modifications and periodic endoscopic interventions for challenging cases.
Follow the LINE: A novel case of dilated cardiomyopathy caused by a LINE-1 insertion in the TTN gene
Authors: Ding Qiliang , Fine Jenna , Hoffman Frank T , Kluge Michelle L , Kuennen Rhonda K , Thieke Sarah M , Hoppman Nicole L , Marcou Cherisse A , Rowsey Ross A , Thorland Erik C , Baudhuin Linnea M , Moyer Ann M , Buglioni Alessia 
Published: December 2024

Abstract

Objectives
Protein-truncating variants in the TTN gene are a well-established cause of dilated cardiomyopathy (DCM). We report a novel case of DCM caused by a mobile element insertion (MEI) in TTN, through which we highlight the key features of MEIs in next-generation sequencing data. Because of the rarity of MEIs, the next-generation sequencing data features associated with these events may be mistaken as noise, potentially leading to missed diagnoses.

Methods
Next-generation sequencing gene panel testing for DCM was performed on a 17-year-old male patient presenting with severe left ventricular dilatation and systolic dysfunction. Manta was used for structural variant detection, followed by manual review of NGS data for potential structural variants.

Results
Manta detected a potential insertion in TTN. Manual review identified hallmark features consistent with a LINE-1 MEI. This finding was orthogonally confirmed by long-range polymerase chain reaction and gel electrophoresis, which indicated an insertion of approximately 4 to 5 kilobase pairs. The insertion disrupted the reading frame of TTN within an A-band exon, resulting in protein truncation that was classified as likely pathogenic.

Conclusions
This case expands the mutational spectrum of TTN protein-truncating variants. It also underscores the importance of recognizing rarer types of pathogenic variants (eg, MEIs) to produce accurate genetic diagnostics.
Migrants, Violence, and Discrimination in Early Modern Holland
Authors: van der Heijden Manon , Luk Karlijn , Sint Nicolaas Samantha 
Published: December 2024

Abstract
This study examines the experiences of migrants in early modern Dutch cities, focusing on violence and indications of social tensions in criminal cases from 1680 to 1810. Despite the prevailing notion of harmonious coexistence, migrants, comprising a significant portion of urban residents, faced stigmatization and bias. The research focuses on Amsterdam, Rotterdam, and Leiden, major economic centers witnessing high immigration rates. Whereas existing studies suggest migrants faced similar treatment in courts, this article challenges such notions. It explores tensions and conflicts in violence-related cases, revealing subtle forms of discrimination against immigrants. Through quantitative analysis and case studies, it uncovers differential treatment in the reporting of violence, court sentencing, and procedures. The findings reveal that while the overall patterns of violent crime were similar between local and immigrant offenders, immigrants were disproportionately accused of more serious offenses. Moreover, immigrants faced differential treatment in the judicial system, including harsher interrogation methods, limited opportunities for settlement, and a higher likelihood of expulsion and corporal punishment. The study highlights the complex interplay between immigration, social tensions, and discriminatory practices in early modern Dutch cities. It underscores the need for further research to fully understand the extent of discrimination against immigrants in historical criminal justice systems, advocating for a nuanced approach that combines quantitative analysis with qualitative examination of individual cases.
Pediatric Brain Injuries are Associated With Intimate Partner Violence-Related Brain Injuries Among Women in Adulthood
Authors: Macaranas Anjeli R. , Tanriverdi Aylin E. , Joseph Annie-Lori , Iverson Grant L. , Valera Eve M. 
Published: December 2024

Objective:
Prior studies have reported associations between childhood physical abuse and intimate partner violence (IPV). However, there has been limited literature examining the relationship between pediatric brain injuries and IPV-related brain injuries later in life. We examined the association between childhood brain injuries and brain injuries sustained from IPV in adulthood.

Setting:
Participants were recruited through Mass General Brigham’s “Rally,” social media, and information sheets distributed in locations likely to serve women in current or past abusive relationships (eg, domestic violence shelters, and IPV support programs).

Participants:
Women who have experienced IPV with and without brain injury (n = 129), ages 19 to 69.

Design:
Retrospective, cross-sectional study design.

Main Measures:
We administered the Ohio State University Traumatic Brain Injury Identification Method and the Brain Injury Severity Assessment to assess brain injury history, and the Childhood Trauma Questionnaire (CTQ). A logistic regression was used to examine the association between pediatric brain injuries and IPV-related brain injuries, adjusting for childhood trauma, years of education, and age.

Results:
A majority of participants (64.3%) reported experiencing at least 1 IPV-related brain injury, and 30.2% experienced at least 1 childhood brain injury. Child abuse-related brain injuries occurred in 10.9% of the sample, whereas childhood brain injuries from other causes occurred in 19.4% of participants. Participants who sustained at least 1 childhood BI were significantly more likely to sustain a future IPV-related brain injury as an adult (OR = 4.652, P = .004). For each additional childhood BI sustained, participants were more likely to sustain an IPV-related BI (OR = 3.198, P = .005).

Conclusion:
This study illustrates a high prevalence of childhood brain injuries among women who have experienced IPV and identifies an association between pediatric brain injuries and brain injuries due to partner violence in adulthood. Our findings speak to the urgency of increasing our understanding of childhood brain injuries and whether they or other related factors might confer an increased risk for brain injuries or possibly IPV later in life.