bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Impact of Language-Discordant Care Upon the Patient Family Experience in Pediatric Plastic Surgery
Authors: Yau Alice , Lentskevich Marina A. , Figueroa Ariel E. , Gutowski Kristof S. , Bajaj Anitesh , Donaldson Rachel , Herbener Cara E. , Gosain Arun K. 
Published: November 2024

Background:
Patient satisfaction surveys usually overlook differences in patient family experience (PFE) for families whose spoken language is different from that of the treating physician. This study examines the relationship between language-discordant care and patient experience.

Methods:
A retrospective review of deidentified pediatric plastic surgery PFE survey responses from 2018 to 2021 was performed with permission from Lurie Children’s Hospital’s PFE Team.

Results:
A total of 443 pediatric plastic surgery patients were included. The race breakdown was White (49%), Other (23.9%), Black (8.8%), and Asian (5.9%). Ethnic distribution included “Not Hispanic/Latino” (58.2%) and “Hispanic/Latino” (31.4%). Languages spoken were English (80.4%), Spanish (18.1%), and Other (2.3%). Eighty-seven (19.64%) patients were language-discordant with their providers; out of this group, 68 (78.2%) preferred interpreter services. Methods of interpreter services included in-person (54.4%), over-the-phone (27.9%), video (1.5%), and no services (16.2%). The language-discordant group was less likely to give the highest ranking to “provider courtesy and respect” [odds ratio (OR)=0.200, P<0.001], “provider listened carefully” (OR=0.202, P<0.001), and “knowing what to do with subsequent questions following visit” (OR=0.435, P<0.01). No differences in PFE ratings existed for: “enough information provided,” overall provider rating, and whether they would recommend the facility. There were no significant differences in provider ratings by interpreter service method.

Conclusions:
Patient/provider language discordance results in significantly lower PFE ratings in areas involving patient teaching and perceptions of provider respect, courtesy, and careful listening. This underscores the importance of providers better accommodating families with limited English proficiency.
Development and validation of novel proliferation-related gene signature for MSS colorectal cancer prognosis
Authors: Wang Sen , Yu Zhiyu , Xu Peng , Zhang Cheng 
Published: November 2024

AbstractColorectal cancer (CRC) is classified into microsatellite instability (MSI) and microsatellite stabilized (MSS) based on the differences in DNA repair mechanisms. In recent years, many studies have proved that some emerging therapeutic approaches have good therapeutic effects on MSI as a subtype but are ineffective for MSS as a subtype. This paper aims to start with the molecular mechanism of MSS and try to find the characteristic target genes of MSS as a subtype. We used bioinformatics techniques and machine learning to find GTF2IRD1. The gene GTF2IRD1 is highly expressed in MSS-type CRC but is stable in MSI. Subsequently, we verified its expression and function with relevant experiments. We demonstrated that GTF2IRD1 can promote the proliferation of MSS-type colorectal cancer and correlate with the poor prognosis of MSS-type colorectal cancer patients, which may provide a potential target gene for the clinical treatment of MSS-type colorectal cancer.
Prey movement shapes the acquisition of predator expertise in a virtual bi-trophic system
Authors: Fraser Franco Maxime , Santostefano Francesca , Martin Julien G. A. , Kelly Clint D. , Montiglio Pierre-Olivier 
Published: November 2024

ABSTRACTThe acquisition of expertise is crucial for predators to be successful hunters. To achieve this, predators must hone their skills and gain knowledge through repeated and extensive practice. On the other hand, prey may hinder the acquisition of predator expertise by employing antipredator tactics to evade detection and pursuit. However, empirical evidence on how predators acquire expertise through repeated encounters with their prey remains limited, largely due to the challenges of monitoring direct interactions in the wild. Here, we use a virtual predator-prey system (the gameDead by Daylight) to investigate how experience shapes individual and population hunting success in human predators across repeated interactions with their prey. We show that predators optimized prey consumption as they gained experience, indicating that they acquired expertise through extensive practice. At the population-level, we found that faster prey impaired the acquisition of expertise by reducing hunting success. Prey speed was also an important mediator of this relationship at the individual level, driving differences among predators in the acquisition of expertise. Our study outlines how prey antipredator behaviour can mediate the acquisition of expertise in predator populations.
Oncogene-induced senescence and senescence-associated secretory phenotype (SASP) determine the efficacy of palbociclib in PIK3CA mutated colorectal cancer
Authors: Cao Pingping , Zhou Xiaohui , Yang Suisui , Shen Tianqi , Wang Shuai , Yu Hanyang , Liu Xiaorong , Gong Yeqing , Wang WenHong , Wang Haiyang , Zhou Tingting , Wang Jing , Fan Zhining , Huang Mingde , Qian Xu , Wang Xiuxing , Wang Qianghu , Yang Liu , Zhang Yingjian , Lin Fan 
Published: November 2024

ABSTRACTPalbociclib is an excellent CDK4/6 inhibitor, but its clinical application is mainly limited to the treatment of advanced ER+/HR+and HER2−breast cancer. Its efficacy in colorectal cancer (CRC) is evaluated in multiple trials and so far remains undetermined. We found that the PIK3CA-mutant CRC cells were insensitive to palbociclib treatment compared with the PIK3CA wild-type counterparts, and they were in an OIS (oncogene-induced senescence) state which was predisposed to a strong senescence-associated secretory phenotype (SASP) upon treatment. These senescent cells excessively secreted various SASP factors LCN2, and ultimately caused palbociclib-resistance via upregulation of EGFR in the non-senescent CRC cells. Importantly, a drug combination screen identified that erlotinib could synergize with palbociclib to overcome the SASP-induced resistance. Overall, we found that PIK3CA mutation-induced senescence compromised the efficacy of palbociclib treatment in CRC but co-targeting EGFR could minimize the OIS-associated side effects while preserving the beneficial effects.
CellPatch: a Highly Efficient Foundation Model for Single-Cell Transcriptomics with Heuristic Patching
Authors: Zhu Hanwen , Yuan Yushun , Yang Jiyuan , Cai Kangwen , Wei Nana , Zhang Senxin , Wang Lu , Jiang Wen-Jie , Sun YuanChen , Liu An , Lai Futing , Wang Yu-Juan , Ma Zeyu , Zheng Xiaoqi , Wu Hua-Jun 
Published: November 2024

AbstractThe rapid advancement of foundation models has significantly enhanced the analysis of single-cell omics data, enabling researchers to gain deeper insights into the complex interactions between cells and genes across diverse tissues. However, existing foundation models often exhibit excessive complexity, hindering their practical utility for downstream tasks. Here, we present CellPatch, a lightweight foundation model that leverages the strengths of the cross-attention mechanism and patch tokenization to reduce model complexity while extracting efficient biological representations. Comprehensive evaluations conducted on single-cell RNA-sequencing datasets across multiple organs and tissue states demonstrate that CellPatch achieves state-of-the-art performance in downstream analytical tasks while maintaining ultra-low computational costs during both pretraining and finetuning phases. Moreover, the flexibility and scalability of CellPatch allow it to serve as a general framework that can be incorporated with other well established single-cell analysis software, thereby enhancing their performance through transfer learning on diverse downstream tasks.
MICROPLASTICS IN THE MOUNT TERMINILLO SNOW’S (RIETI, ITALY)
Authors: Pietrelli Loris , Menegoni Patrizia , Millesimi Ines , Sighicelli Maria , Baldi Marina , Schirone Bartolomeo 
Published: November 2024

AbstractMicroplastics (MPs) concentrations in atmospheric fallout is a growing environmental concern, this paper reports data regarding the MPs pollution determined using snow samples collected in wintertime and in 6 different areas on Mount Terminillo (2216 m a.s.l.) a typical Apennines massif located north of Rome. Assessment results show that the maximum average concentration found un snow is 74.69 MPsL-1of melted snow. The results of the characterization show that the most common MPs form was microfibers having dimensions <5mm. The largest MPs were characterized by Fourier Transformed IR (FTIR) analysis, among the polymer materials, the most abundant were polyamide (PA, 25.93%), polyethylene terephthalate (PET, 22,23%), polyester (PES, 17.28%) polypropylene (PP, 8.64%) and polyethylene (PE, 7.40%). The presence of PTFE fibers and a fragment of ABS, typical materials of technical clothing, shows that MPs contamination is also due to recreational activities as well as atmospheric deposits. The Carbonyl Index values indicated that some MPs (PE, PP) are degraded.
Nemo knows: clownfishes differentiate cryptic host species across fine and broad geographic scales and reveal a potential adaptive radiation in the clownfish-hosting sea anemones
Authors: Chiodo Tommaso , De Jode Aurélien , Quattrini Andrea , Gibson Miranda K. , Froehlich Catheline Y. M. , Huang Danwei , Fujii Takuma , Yanagi Kensuke , Reimer James D. , Scott Anna , Rodríguez Estefanía , Titus Benjamin M. 
Published: November 2024

AbstractThe symbiosis between clownfishes (or anemonefishes) and their host sea anemones ranks among the most recognizable animal interactions on the planet. Found on coral reef habitats across the Indian and Pacific Oceans, 28 recognized species of clownfishes adaptively radiated from a common ancestor to live obligately with only 10 nominal species of host sea anemones. Are the host sea anemones truly less diverse than clownfishes? Did the symbiosis with clownfishes trigger a reciprocal adaptive radiation in sea anemones, or minimally, a co-evolutionary response to the mutualism? To address these questions, we combined fine- and broad-scale biogeographic sampling with multiple independent genomic datasets for the bubble-tip sea anemone,Entacmaea quadricolor—the most common clownfish host anemone throughout the Indo-West Pacific. Fine-scale sampling and restriction site associated DNA sequencing (RADseq) throughout the Japanese Archipelago revealed three highly divergent cryptic species: two of which co-occur throughout the Ryukyu Islands and can be differentiated by the clownfish species they host. Remarkably, broader biogeographic sampling and bait-capture sequencing reveals that this pattern is not simply the result of local ecological processes unique to Japan, but part of a deeper evolutionary signal where some species ofE. quadricolorserve as host to the generalist clownfish speciesAmphiprion clarkiiand others serve as host to the specialist clownfishA. frenatus. In total, we delimit at least five cryptic species inE. quadricolorthat have diversified within the last five million years. The rapid diversification ofE. quadricolorcombined with functional ecological and phenotypic differentiation supports the hypothesis that this may represent an adaptive radiation in response to mutualism with clownfishes. Our data indicate that clownfishes are not merely settling in locally available hosts but recruiting to specialized host lineages with which they have co-evolved. These findings have important implications for understanding how the clownfish-sea anemone symbiosis has evolved and will shape future research agendas on this iconic model system.
On the Mkv Model with Among-Character Rate Variation
Authors: Capobianco Alessio , Höhna Sebastian 
Published: November 2024

AbstractModels used in likelihood-based morphological phylogenetics often adapt molecular phylogenetics models to the specificities of morphological data. Such is the case for the widely used Mkv model— which introduces an acquisition bias correction for sampling only characters that are observed to be variable—and for models of among-character rate variation (ACRV), routinely applied by researchers to relax the equal-rates assumption of Mkv. However, the interaction between variable character acquisition bias and ACRV has never been explored before. We demonstrate that there are two distinct approaches to condition the likelihood on variable characters when there is ACRV, and we call them joint and marginal acquisition bias. Far from being just a trivial mathematical detail, we show that the way in which the variable character conditional likelihood is calculated results in different assumptions about how rate variation is distributed in morphological datasets. Simulations demonstrate that tree length and amount of ACRV in the data are systematically biased when conditioning on variable characters differently from how the data was simulated. Moreover, an empirical case study with extant and extinct taxa reveals a potential impact not only on the estimation of branch lengths, but also of phylogenetic relationships. We recommend the use of the marginal acquisition bias approach for morphological datasets modeled with ACRV. Finally, we urge developers of phylogenetic software to clarify which acquisition bias correction is implemented for both estimation and simulation, and we discuss the implications of our findings on modeling variable characters for the future of morphological phylogenetics.
Predicting Prognostic Bidirectional Molecular Signatures Associating Myocardial Infarction and Lung Cancer: AnIn-SilicoPerspective
Authors: Nandi Dhruva , Janardhanan Rajiv , Agrawal Piyush 
Published: November 2024

AbstractMyocardial Infarction (MI) and lung cancers substantially contributors to morbidity and mortality. They share common risk factors such as smoking, and hypertension. There is a pressing need to identify bidirectional molecular signatures linking MI and lung cancer relationship to create a unique triage to improve the clinical outcomes of the patient. In the current work, we extracted the common differentially expressed genes (DEGs) between MI and lung cancer and identified 2339 upregulated and 2973 downregulated genes in MI datasets; 952 upregulated and 653 downregulated genes in LUAD; 1466 upregulated and 2816 downregulated genes in LUSC. Among these, 27 genes (11 upregulated and 16 downregulated) were common across MI, LUAD, and LUSC. Functional enrichment analysis revealed shared biological processes, such as inflammatory response, and cell differentiation. KEGG pathway analysis highlighted common pathways such as B cell receptor signaling, TNF signaling. A protein-protein interaction study with STRING revealed a variety of interaction partners; miRNA-mRNA network analysis characterizes conserved binding sites for 6 genes while overall survival analysis for lung cancer patients shows a significant association with prognosis. In addition, machine learning models built using the Support Vector Machine and Random Forest algorithms demonstrated high AUROC values of 0.79 and 0.81 respectively on balanced dataset in the classifying MI patients from non-MI patients. Lastly, based on drug repurposing analysis, we proposed FDA-approved drugs such as Venetoclax, Lomitapide, Regorafenib that could potentially target these genes, indicating novel therapeutic options for the co-occurring conditions of MI and lung cancer. Our findings highlight the similarities in molecular makeup between lung cancer and MI, providing information for future investigations and therapeutic approaches.
Mutagenic impact and evolutionary influence of radiotherapy in hematologic malignancies
Authors: Diamond Benjamin , Chahar Dhanvantri , Jain Michael D. , Poos Alexandra M. , Durante Michael , Ziccheddu Bachisio , Kaddoura Marcella , Papadimitriou Marios , Maclachlan Kylee , Jelinek Tomas , Davies Faith , Figura Nicholas B , Morgan Gareth , Mai Elias , Weisel Katja C. , Fenk Roland , Raab Marc S. , Usmani Saad , Landgren Ola , Locke Frederick L. , Goldschmidt Hartmut , Schatz Jonathan H. , Weinhold Niels , Maura Francesco 
Published: November 2024

ABSTRACTIonizing radiotherapy (RT) is a widely used palliative and curative treatment strategy for malignancies. In solid tumors, RT-induced double strand breaks lead to the accumulation of indels, and their repair by non-homologous end-joining has been linked to the ID8 mutational signature in resistant cells. However, the extent of RT-induced DNA damage in hematologic malignancies and its impact on their evolution and interplay with commonly used chemotherapies has not yet been explored. Here, we interrogated 580 whole genome sequencing (WGS) from patients with large B-cell lymphoma, multiple myeloma, and myeloid neoplasms and identified ID8 only in relapsed disease. Yet, it was detected after exposure to both RT and mutagenic chemotherapy (i.e., platinum). Using WGS of single-cell colonies derived from treated lymphoma cells, we revealed a dose-response relationship between RT and platinum and ID8. Finally, using ID8 as a genomic barcode we demonstrate that a single RT-resistant cell may seed systemic relapse.
Single-cell epigenetic profiling reveals an interferon response-high program associated withBAP1deficiency in kidney cancer
Authors: Camp Sabrina Y. , He Meng Xiao , Cuoco Michael S. , Saad Eddy , Pimenta Erica , Meli Kevin , Bakouny Ziad , Labaki Chris , Titchen Breanna M. , Kang Yun Jee , Horst Jack , Trowbridge Rachel , Shannon Erin , Helvie Karla , Thorner Aaron R. , Vigneau Sébastien , Mayorga Angie , Kodali Jahnavi , Lachmayr Hannah , Bemus Meredith , Park Jihye , Choueiri Toni , Bi Kevin , Van Allen Eliezer M. 
Published: November 2024

ABSTRACTRenal cell carcinoma (RCC) is characterized by recurrent somatic mutations in epigenetic regulators, which stratify patients into clinically significant subgroups with distinct prognoses and treatment responses. However, the cell type-specific epigenetic landscape of RCC—broadly and in the context of these mutations—is incompletely understood. To investigate these open questions, we integrated single nucleus ATAC sequencing data from RCC tumors across four independent cohorts. In clear cell RCC tumors, we identified four shared malignant epigenetic programs related to angiogenesis, proximal tubule-like features, interferon (IFN) signaling, and one that lacked distinct genomic regions with increased accessibility. Among the mutated epigenetic regulators,BAP1mutation exhibited the most significant impact on chromatin accessibility in tumor cells, and the associated epigenetic changes were linked to IFN response. We identify multiple potential sources of elevated IFN signaling in these lesions, such as increased immune infiltration and increased accessibility and expression of an IFN-associated ERV, ERV3-16A3_LTR. We find that the expression of ERV3-16A3_LTR may itself be a negative prognostic biomarker in ccRCC. Our findings highlight the convergence of malignant epigenetic programs across ccRCC tumors and suggest thatBAP1loss, potentially through ERV3-16A3_LTR dysregulation, is associated with an IFN response-high epigenetic program.
Comparison of Gene Expression between Chronic Rhinosinusitis with Nasal Polyposis and without Nasal Polyposis
Authors: Kasem Mahmoud Fawzy , Helal Mohamed Lotfy , Elsfafey Ola Hamdy 
Published: November 2024

AbstractObjectivesWe aimed to compare the gene expression between chronic sinusitis with nasal polyposis and chronic rhinosinusitis without nasal polyposis either eosinophilic or not.BackgroundChronic rhinosinusitis (CRS) is a disease characterized by chronic inflammation of the nasal cavity and sinus mucosa. CRS mainly presents as phenotypes, namely, CRS without nasal polyps (CRSsNP) and CRS with nasal polyps (CRSwNP), based on whether it is accompanied by polyps or not. Micro-array analyses investigating the immune endo-types and pathogenesis of CRSwNP typically rely on invasive nasal biopsies.MethodsThis prospective randomized study was conducted on 150 patients with chronic nasal obstruction (more than 3 months). These group of patients consisted of four groups as CRSwNP patients (including eosinophilic CRSwNP [ECRSwNP] and non-eosinophilic CRSwNP [NECRSwNP]) and CRSsNP patients including eosinophilic CRSwNP [ECRSwNP] and non-eosinophilic CRSwNP [NECRSwNP]) for protein quantification by COLOC platform and gene expression evaluation by RNA-sequencing. Spearman’s analysis was performed to detect correlations between protein expression levels and clinical assessment variables.ResultsThere were female predominance in eosinophilic CRS plus higher CT score in ECRSwNP than NECRSwNP. There was also higher SNOT-22 score in ECRSwNP than NECRSwNP. There were significant differences in all items of SNOT-22 scale after nasal polypectomy. The prevalence of the condition/disease is assumed to be 0.1. The sensitivity of 0.1 with 90% power, the specificity was 85%.ConclusionOur study revealed that there are higher recurrence, rate of manifestations for the patients with genetic predisposition of CCL18 and CCL13 more than others.
Long-term balancing selection maintains cryptic color polymorphism in frogs
Authors: Goutte Sandra , Boissinot Stéphane 
Published: November 2024

AbstractColor polymorphism can influence the evolutionary fate of cryptic species because it increases populations’ chances of survival in heterogenous or variable environments. Yet, little is known about the molecular and evolutionary mechanisms underlying the persistence of cryptic color polymorphisms, or the impact these polymorphisms have on the macro-evolutionary dynamics of lineages. Here, we examine the evolutionary history of the most widespread cryptic color polymorphism in anurans, involving green and brown morphs. Using an order-scale comparative analysis, we show that these morphs can co-exist within species over long periods of evolutionary time and that polymorphic lineages switch habitat more frequently and have greater diversification rates than other groups. We then identify the locus responsible for the green/brown polymorphism in a group of African grass frogs, and demonstrate that this genomic region is evolving under long-term balancing selection, resulting in trans-specific polymorphism. These results provide a micro-evolutionary mechanism for the long-term persistence of color polymorphism observed at a macro-evolutionary scale. This study highlights the importance of cryptic color polymorphism in the ecology and evolution of anurans, and provides a framework for future research on the genetic architecture and selective forces underlying cryptic traits.