bluuebunny/crossref_metadata_2025_split huggingface dataset:
Generalization of beneficial exposure effects to untreated stimuli from another fear category
Authors: Kodzaga Iris , Dere Ekrem , Zlomuzica Armin 
Published: December 2023

AbstractPrevious research has shown that fear associated with one stimulus often spreads to other stimuli with similar perceptual features as well as across different stimulus categories. Exposure is considered as the most effective intervention to attenuate exaggerated fear. The extent to which exposure treatment effects can generalize to fears not targeted during treatment remains elusive. Previous studies on possible generalization of beneficial effects of exposure used stimuli sharing the same stimulus category and/or stimuli having high perceptual similarity. The current study examined whether exposure treatment generalization can be achieved for untreated stimuli which do not share any perceptual resemblance and belong to a different fear category. An analogue sample of fifty participants with fear of spiders (animal-related fears) and heights (natural environment-related fears) was tested. Participants have been randomly assigned to either an exposure treatment (n = 24) or a control condition (n = 26). Exposure treatment was designed to only target participants’ fear of spiders, leaving their fear of heights untreated. Results demonstrated that the effects of exposure treatment generalized to fear of heights, as indicated by a reduction in behavioral avoidance, as well as self-reported acrophobia symptoms. The present study confutes the assumption that generalization of exposure effects to untreated fears is based on perceptual similarity. Clearly, further research is required to determine the decisive factors, in order to expand the generalization effect permanently to any given type of fear.
Mutual communication between radiosensitive and radioresistant esophageal cancer cells modulates their radiosensitivity
Authors: Xie Congying , Chen Xiao , Chen Yueming , Wang Xingyue , Zuo Jiwei , Zheng Anqi , Luo Zhicheng , Cheng Xiaoxiao , Zhong Shouhui , Jiang Jiayu , Du Jizao , Zhao Yuemei , Jiang Peipei , Zhang Wei , Chen Didi , Pan Huanle , Shen Lanxiao , Zhu Baoling , Zhou Qingyu , Xu Yunsheng , Tang Kai-Fu 
Published: December 2023

AbstractRadiotherapy is an important treatment modality for patients with esophageal cancer; however, the response to radiation varies among different tumor subpopulations due to tumor heterogeneity. Cancer cells that survive radiotherapy (i.e., radioresistant) may proliferate, ultimately resulting in cancer relapse. However, the interaction between radiosensitive and radioresistant cancer cells remains to be elucidated. In this study, we found that the mutual communication between radiosensitive and radioresistant esophageal cancer cells modulated their radiosensitivity. Radiosensitive cells secreted more exosomal let-7a and less interleukin-6 (IL-6) than radioresistant cells. Exosomal let-7a secreted by radiosensitive cells increased the radiosensitivity of radioresistant cells, whereas IL-6 secreted by radioresistant cells decreased the radiosensitivity of radiosensitive cells. Although the serum levels of let-7a and IL-6 before radiotherapy did not vary significantly between patients with radioresistant and radiosensitive diseases, radiotherapy induced a more pronounced decrease in serum let-7a levels and a greater increase in serum IL-6 levels in patients with radioresistant cancer compared to those with radiosensitive cancer. The percentage decrease in serum let-7a and the percentage increase in serum IL-6 levels at the early stage of radiotherapy were inversely associated with tumor regression after radiotherapy. Our findings suggest that early changes in serum let-7a and IL-6 levels may be used as a biomarker to predict the response to radiotherapy in patients with esophageal cancer and provide new insights into subsequent treatments.
Plasma cell-free DNA 5-hydroxymethylcytosine and whole-genome sequencing signatures for early detection of esophageal cancer
Authors: Lu Di , Wu Xuanzhen , Wu Wendy , Wu Shuangxiu , Li Hui , Zhang Yuhong , Yan Xuebin , Zhai Jianxue , Dong Xiaoying , Feng Siyang , Zhang Xueying , Sun Fuming , Wang Shaobo , Cai Kaican 
Published: December 2023

AbstractEsophageal cancer is a highly incidence and deadly disease with a poor prognosis, especially in developing countries. Owing to the lack of specific symptoms and early diagnostic biomarkers, most patients are diagnosed with advanced disease, leading to a 5-year survival rate of less than 15%. Early (n = 50) and middle-advanced (n = 50) esophageal squamous cell carcinoma (ESCC) patients, as well as 71 healthy individuals, underwent 5-hydroxymethylcytosine (5hmC) sequencing on their plasma cell-free DNA (cfDNA). A Northern Chinese cohort of cfDNA 5hmC dataset of 150 ESCC patients and 183 healthy individuals were downloaded for validation. A diagnostic model was developed using cfDNA 5hmC signatures and then improved by low-pass whole genome sequencing (WGS) features of cfDNA. Conserved cfDNA 5hmC modification motifs were observed in the two independent ESCC cohorts. The diagnostic model with 5hmC features achieved an AUC of 0.810 and 0.862 in the Southern and Northern cohorts, respectively, with sensitivities of 69.3–74.3% and specificities of 82.4–90.7%. The performance was well maintained in Stage I to Stage IV, with accuracy of 70–100%, but low in Stage 0, 33.3%. Low-pass WGS of cfDNA improved the AUC to 0.934 with a sensitivity of 82.4%, a specificity of 88.2%, and an accuracy of 84.3%, particularly significantly in Stage 0, with an accuracy up to 80%. 5hmC and WGS could efficiently differentiate very early ESCC from healthy individuals. These findings imply a non-invasive and convenient method for ESCC detection when clinical treatments are available and may eventually prolong survival.
Ultra-wide field and new wide field composite retinal image registration with AI-enabled pipeline and 3D distortion correction algorithm
Authors: Kalaw Fritz Gerald P. , Cavichini Melina , Zhang Junkang , Wen Bo , Lin Andrew C. , Heinke Anna , Nguyen Truong , An Cheolhong , Bartsch Dirk-Uwe G. , Cheng Lingyun , Freeman William R. 
Published: December 2023

Abstract
Purpose
This study aimed to compare a new Artificial Intelligence (AI) method to conventional mathematical warping in accurately overlaying peripheral retinal vessels from two different imaging devices: confocal scanning laser ophthalmoscope (cSLO) wide-field images and SLO ultra-wide field images.

Methods
Images were captured using the Heidelberg Spectralis 55-degree field-of-view and Optos ultra-wide field. The conventional mathematical warping was performed using Random Sample Consensus—Sample and Consensus sets (RANSAC-SC). This was compared to an AI alignment algorithm based on a one-way forward registration procedure consisting of full Convolutional Neural Networks (CNNs) with Outlier Rejection (OR CNN), as well as an iterative 3D camera pose optimization process (OR CNN + Distortion Correction [DC]). Images were provided in a checkerboard pattern, and peripheral vessels were graded in four quadrants based on alignment to the adjacent box.

Results
A total of 660 boxes were analysed from 55 eyes. Dice scores were compared between the three methods (RANSAC-SC/OR CNN/OR CNN + DC): 0.3341/0.4665/4784 for fold 1-2 and 0.3315/0.4494/4596 for fold 2-1 in composite images. The images composed using the OR CNN + DC have a median rating of 4 (out of 5) versus 2 using RANSAC-SC. The odds of getting a higher grading level are 4.8 times higher using our OR CNN + DC than RANSAC-SC (p < 0.0001).

Conclusion
Peripheral retinal vessel alignment performed better using our AI algorithm than RANSAC-SC. This may help improve co-localizing retinal anatomy and pathology with our algorithm.
Undiscovered bird extinctions obscure the true magnitude of human-driven extinction waves
Authors: Cooke Rob , Sayol Ferran , Andermann Tobias , Blackburn Tim M. , Steinbauer Manuel J. , Antonelli Alexandre , Faurby Søren 
Published: December 2023

AbstractBirds are among the best-studied animal groups, but their prehistoric diversity is poorly known due to low fossilization potential. Hence, while many human-driven bird extinctions (i.e., extinctions caused directly by human activities such as hunting, as well as indirectly through human-associated impacts such as land use change, fire, and the introduction of invasive species) have been recorded, the true number is likely much larger. Here, by combining recorded extinctions with model estimates based on the completeness of the fossil record, we suggest that at least ~1300–1500 bird species (~12% of the total) have gone extinct since the Late Pleistocene, with 55% of these extinctions undiscovered (not yet discovered or left no trace). We estimate that the Pacific accounts for 61% of total bird extinctions. Bird extinction rate varied through time with an intense episode ~1300 CE, which likely represents the largest human-driven vertebrate extinction wave ever, and a rate 80 (60–95) times the background extinction rate. Thus, humans have already driven more than one in nine bird species to extinction, with likely severe, and potentially irreversible, ecological and evolutionary consequences.
High resolution mapping of the tumor microenvironment using integrated single-cell, spatial and in situ analysis
Authors: Janesick Amanda , Shelansky Robert , Gottscho Andrew D. , Wagner Florian , Williams Stephen R. , Rouault Morgane , Beliakoff Ghezal , Morrison Carolyn A. , Oliveira Michelli F. , Sicherman Jordan T. , Kohlway Andrew , Abousoud Jawad , Drennon Tingsheng Yu , Mohabbat Seayar H. ,   10x Development Teams, Taylor Sarah E. B. 
Published: December 2023

AbstractSingle-cell and spatial technologies that profile gene expression across a whole tissue are revolutionizing the resolution of molecular states in clinical samples. Current commercially available technologies provide whole transcriptome single-cell, whole transcriptome spatial, or targeted in situ gene expression analysis. Here, we combine these technologies to explore tissue heterogeneity in large, FFPE human breast cancer sections. This integrative approach allowed us to explore molecular differences that exist between distinct tumor regions and to identify biomarkers involved in the progression towards invasive carcinoma. Further, we study cell neighborhoods and identify rare boundary cells that sit at the critical myoepithelial border confining the spread of malignant cells. Here, we demonstrate that each technology alone provides information about molecular signatures relevant to understanding cancer heterogeneity; however, it is the integration of these technologies that leads to deeper insights, ushering in discoveries that will progress oncology research and the development of diagnostics and therapeutics.
Magmatic immiscibility and the origin of magnetite-(apatite) iron deposits
Authors: Pietruszka Dorota K. , Hanchar John M. , Tornos Fernando , Wirth Richard , Graham Nathan A. , Severin Kenneth P. , Velasco Francisco , Steele-MacInnis Matthew , Bain Wyatt M. 
Published: December 2023

AbstractThe origin of magnetite-(apatite) iron deposits (MtAp) is one of the most contentious issues in ore geology with competing models that range from hydrothermal to magmatic processes. Here we report melt inclusions trapped in plagioclase phenocrysts in andesite hosting the MtAp mineralization at El Laco, Chile. The results of our study reveal that individual melt inclusions preserve evidence of complex processes involved in melt immiscibility, including separation of Si- and Fe-rich melts, the latter hosting Cu sulfide-rich, phosphate-rich, and residual C-O-HFSE-rich melts, with their melting temperature at 1145 °C. This association is consistent with the assemblages observed in the ore, and provides a link between silicate and Fe-P-rich melts that subsequently produced the magnetite-rich magmas that extruded on the flanks of the volcano. These results strongly suggest that the El Laco mineralization was derived from crystallization of Fe-P-rich melts, thus providing insight into the formation of similar deposits elsewhere.
Strongly interacting matter exhibits deconfined behavior in massive neutron stars
Authors: Annala Eemeli , Gorda Tyler , Hirvonen Joonas , Komoltsev Oleg , Kurkela Aleksi , Nättilä Joonas , Vuorinen Aleksi 
Published: December 2023

AbstractNeutron-star cores contain matter at the highest densities in our Universe. This highly compressed matter may undergo a phase transition where nuclear matter melts into deconfined quark matter, liberating its constituent quarks and gluons. Quark matter exhibits an approximate conformal symmetry, predicting a specific form for its equation of state (EoS), but it is currently unknown whether the transition takes place inside at least some physical neutron stars. Here, we quantify this likelihood by combining information from astrophysical observations and theoretical calculations. Using Bayesian inference, we demonstrate that in the cores of maximally massive stars, the EoS is consistent with quark matter. We do this by establishing approximate conformal symmetry restoration with high credence at the highest densities probed and demonstrating that the number of active degrees of freedom is consistent with deconfined matter. The remaining likelihood is observed to correspond to EoSs exhibiting phase-transition-like behavior, treated as arbitrarily rapid crossovers in our framework.
Blue-shift photoconversion of near-infrared fluorescent proteins for labeling and tracking in living cells and organisms
Authors: Pennacchietti Francesca , Alvelid Jonatan , Morales Rodrigo A. , Damenti Martina , Ollech Dirk , Oliinyk Olena S. , Shcherbakova Daria M. , Villablanca Eduardo J. , Verkhusha Vladislav V. , Testa Ilaria 
Published: December 2023

AbstractPhotolabeling of intracellular molecules is an invaluable approach to studying various dynamic processes in living cells with high spatiotemporal precision. Among fluorescent proteins, photoconvertible mechanisms and their products are in the visible spectrum (400–650 nm), limiting their in vivo and multiplexed applications. Here we report the phenomenon of near-infrared to far-red photoconversion in the miRFP family of near infrared fluorescent proteins engineered from bacterial phytochromes. This photoconversion is induced by near-infrared light through a non-linear process, further allowing optical sectioning. Photoconverted miRFP species emit fluorescence at 650 nm enabling photolabeling entirely performed in the near-infrared range. We use miRFPs as photoconvertible fluorescent probes to track organelles in live cells and in vivo, both with conventional and super-resolution microscopy. The spectral properties of miRFPs complement those of GFP-like photoconvertible proteins, allowing strategies for photoconversion and spectral multiplexed applications.
High-throughput deconvolution of 3D organoid dynamics at cellular resolution for cancer pharmacology with Cellos
Authors: Mukashyaka Patience , Kumar Pooja , Mellert David J. , Nicholas Shadae , Noorbakhsh Javad , Brugiolo Mattia , Courtois Elise T. , Anczukow Olga , Liu Edison T. , Chuang Jeffrey H. 
Published: December 2023

AbstractThree-dimensional (3D) organoid cultures are flexible systems to interrogate cellular growth, morphology, multicellular spatial architecture, and cellular interactions in response to treatment. However, computational methods for analysis of 3D organoids with sufficiently high-throughput and cellular resolution are needed. Here we report Cellos, an accurate, high-throughput pipeline for 3D organoid segmentation using classical algorithms and nuclear segmentation using a trained Stardist-3D convolutional neural network. To evaluate Cellos, we analyze ~100,000 organoids with ~2.35 million cells from multiple treatment experiments. Cellos segments dye-stained or fluorescently-labeled nuclei and accurately distinguishes distinct labeled cell populations within organoids. Cellos can recapitulate traditional luminescence-based drug response of cells with complex drug sensitivities, while also quantifying changes in organoid and nuclear morphologies caused by treatment as well as cell-cell spatial relationships that reflect ecological affinity. Cellos provides powerful tools to perform high-throughput analysis for pharmacological testing and biological investigation of organoids based on 3D imaging.
Antigen recognition reinforces regulatory T cell mediated Leishmania major persistence
Authors: Zayats Romaniya , Mou Zhirong , Yazdanpanah Atta , Gupta Gaurav , Lopez Paul , Nayar Deesha , Koh Wan H. , Uzonna Jude E. , Murooka Thomas T. 
Published: December 2023

AbstractCutaneous Leishmania major infection elicits a rapid T cell response that is insufficient to clear residually infected cells, possibly due to the accumulation of regulatory T cells in healed skin. Here, we used Leishmania-specific TCR transgenic mice as a sensitive tool to characterize parasite-specific effector and immunosuppressive responses in vivo using two-photon microscopy. We show that Leishmania-specific Tregs displayed higher suppressive activity compared to polyclonal Tregs, that was mediated through IL-10 and not through disrupting cell-cell contacts or antigen presentation. In vivo expansion of endogenous Leishmania-specific Tregs resulted in disease reactivation that was also IL-10 dependent. Interestingly, lack of Treg expansion that recognized the immunodominant Leishmania peptide PEPCK was sufficient to restore robust effector Th1 responses and resulted in parasite control exclusively in male hosts. Our data suggest a stochastic model of Leishmania major persistence in skin, where cellular factors that control parasite numbers are counterbalanced by Leishmania-specific Tregs that facilitate parasite persistence.
Polycyclic aromatic hydrocarbon (PAH) source identification and a maternal transfer case study in threatened killer whales (Orcinus orca) of British Columbia, Canada
Authors: Lee Kiah , Raverty Stephen , Cottrell Paul , Zoveidadianpour Zeinab , Cottrell Brendan , Price Dana , Alava Juan José 
Published: December 2023

AbstractThe northeastern Pacific (NEP) Ocean spans the coast of British Columbia (Canada) and is impacted by anthropogenic activities including oil pipeline developments, maritime fossil fuel tanker traffic, industrial chemical effluents, agricultural and urban emissions in tandem with stormwater and wastewater discharges, and forest wildfires. Such events may expose surrounding marine environments to toxic polycyclic aromatic hydrocarbons (PAHs) and impact critical habitats of threatened killer whales (Orcinus orca). We analyzed skeletal muscle and liver samples from stranded Bigg’s killer whales and endangered Southern Resident killer whales (SRKWs) for PAH contamination using LRMS. C3-phenanthrenes/anthracenes (mean: 632 ng/g lw), C4-dibenzothiophenes (mean: 334 ng/g lw), and C4-phenanthrenes/anthracenes (mean: 248 ng/g lw) presented the highest concentrations across all tissue samples. Diagnostic ratios indicated petrogenic-sourced contamination for SRKWs and pyrogenic-sourced burdens for Bigg’s killer whales; differences between ecotypes may be attributed to habitat range, prey selection, and metabolism. A mother-fetus skeletal muscle pair provided evidence of PAH maternal transfer; low molecular weight compounds C3-fluorenes, dibenzothiophene, and naphthalene showed efficient and preferential exposure to the fetus. This indicates in-utero exposure of PAH-contamination to the fetus. Our results show that hydrocarbon-related anthropogenic activities are negatively impacting these top predators; preliminary data found here can be used to improve oil spill and other PAH pollution management and regulation efforts, and inform policy to conserve killer whale habitats in the NEP.
Integration of multiomics analysis to reveal the major pathways of vitamin A deficiency aggravates acute respiratory distress syndrome in neonatal rats
Authors: Tang Jia , Yuan Jiaqin , Sun Jinghao , Yan Mi , Li Mengchun , Liu Yanfei , Xu Shaohua , Li Jing , Fu Hong , Li Wanwei , Hu Zhangxue 
Published: December 2023

AbstractAcute respiratory distress syndrome (ARDS) is a major disease that threatens the life and health of neonates. Vitamin A (VA) can participate in early fetal lung development and affect lung immune function. Researches revealed that the serum VA level in premature infants with ARDS was lower than that in premature infants without ARDS of the same gestational age, and premature infants with VA deficiency (VAD) were more likely to develop ARDS. Moreover, the VA levels can be used as a predictor of the development and severity of neonatal ARDS. However, the critical question here is; Does ARDS develop due to VAD in these systemic diseases? Or does ARDS develop because these diseases cause VAD? We hypothesize that VAD may aggravate neonatal ARDS by affecting immunity, metabolism, barriers and other pathways. In this article, we used multiomics analysis to find that VAD may aggravate ARDS mainly through the Fc epsilon RI signaling pathway, the HIF-1 signaling pathway, glutathione metabolism, and valine, leucine and isoleucine degradation signaling pathways, which may provide the molecular pathogenic mechanism behind the pathology of VAD-aggravated ARDS and can also provide potential molecular targets for subsequent research on ARDS.
4D evolutions of cracks, voids, and corrosion products in reinforced concrete materials
Authors: Taheri-Shakib Jaber , Al-Mayah Adil 
Published: December 2023

AbstractThis research paper presents a comprehensive investigation into the corrosion process in reinforced concrete structures using advanced analytical techniques, namely non-destructive X-ray computed tomography (CT) imaging, scanning electron microscopy (SEM) images, energy dispersive x-ray spectrometry (EDS), and Raman spectroscopy. The CT image analysis allowed for the identification and quantification of pore structures, crack propagation, and corrosion progression at different stages of corrosion. CT scanning and data analysis offer valuable 4D (3D spatial + time) insights into corrosion in reinforced concrete, revealing changes in pore sizes, with smaller pores increasing and larger pores decreasing as corrosion progresses. Our investigation reveals dynamic changes in reinforced concrete pores during the accelerated corrosion test leading to new pore formation and cracking. The research identifies two distinct types of cracks: one filled with corrosion products and the other, zipper-like cracks, resulting from the connection of deformed pores without corrosion products. The SEM images and EDS analysis confirmed the absence of corrosion products within these unique zipper cracks, suggesting a different mechanism of crack formation compared to the first type of cracks. The results revealed two distinct categories of corrosion products: iron oxides and iron hydroxides, with their distribution correlated to the duration of accelerated corrosion testing. The integration and verification of results from X-ray CT imaging and Raman spectroscopy established a comprehensive understanding of corrosion-induced damage in the reinforced concrete specimen, shedding light on complex interactions among different corrosion products during the corrosion process. These findings offer crucial insights for better understanding of the corrosion process in reinforced concrete paving the way for future development of effective treatments and strategies to mitigate corrosion impact.