bluuebunny/crossref_metadata_2025_split huggingface dataset:
FAT4 expression in peripheral blood mononuclear cells is associated with prognosis and immune cell infiltration in hepatocellular carcinoma
Authors: Li Jing , Lv Minling , Huang Qi , Hu Rui , Zhong Xin , Sun Xinfeng , Feng Wenxing , Han Zhiyi , Ma MengQing , Zhang Wei , Zhou Xiaozhou 
Published: September 2023

AbstractPeripheral blood mononuclear cell (PBMC) genes reflect the host immune status and could be suitable for evaluating the prognosis of patients with hepatocellular carcinoma (HCC), for which a reliable biomarker is unavailable and the host immune responses to cancer cells. This study aimed to investigate prognostically relevant genes in HCC PBMCs and assessed whether their expression represents tumor immune infiltration. Gene expression in PBMCs from patients with advanced or terminal HCC who had survived or died was examined. Correlations among FAT atypical cadherin 4 (FAT4) expression, cancer immune characteristics, and infiltrated immune cell gene marker sets were analyzed. FAT4 expression was lower in the PBMCs of patients with advanced or terminal HCC who had died than that in patients who survived. Kaplan–Meier analysis indicated that FAT4 downregulation was associated with a relatively poor prognosis while overexpression was positively correlated with immune cell infiltration, several immune cell markers, and immune checkpoint expression. Hsa-miR-93-5p represented the most probable upstream microRNA of FAT4. Thus, upregulated FAT4 in PBMCs and HCC tissues might indicate a favorable prognosis and increased immune cell infiltration, while miRNA-93-5p could be a modulator of FAT4 expression. Collectively, these findings suggest novel immunotherapy targets for HCC.
Flow phenomena in laminar flow through streamlined and sharp-edged short monolithic structures
Authors: Korpyś Mateusz , Iwaniszyn Marzena , Sindera Katarzyna , Suwak Mikołaj , Gancarczyk Anna , Kołodziej Andrzej 
Published: September 2023

AbstractMonolithic structures of catalytic reactors offer low flow resistance, but their drawback is weak heat and mass transport. For transport intensification, innovative streamlined structures were designed, the walls of which are shaped like an airplane wing. Extensive CFD (Computer Fluid Dynamics) studies were performed for the streamlined and—for comparison—classic (sharp-edged) structures, covered flow phenomena, and heat transfer to channel walls. The streamlined structures were made using the SLM (Selective Laser Melting) method to perform heat transfer experiments that gave a satisfactory agreement with the CFD. Heat transfer for streamlined structures was, by CFD, more intensive than for the classical ones. CFD simulations showed a significant reduction of vortices in streamlined structures. The lack of an inlet vortex was demonstrated, for classic structures strongly limiting transfer properties. For the streamlined structures the outlet vortex even intensifies heat transport near the outlet of the channel. The CFD showed the flow patterns for the structures as well as the distribution of transport coefficients within the millimetre-sized channels.
The transfer of 137Cs and heavy metals to tissues within the organs of snails
Authors: Baigazinov Zhanat , Lukashenko Sergey , Silybayeva Batiyash , Zharykbasova Klara , Bukabayeva Zhanylkhan , Muhamediarov Nurlan , Kantbayeva Bagdat , Kozhakhmetova Balzhan , Ganbaatar Tuvshinsaikhan , Toth-Bodrogi Edit , Hegedus Miklos , Kovacs Tibor 
Published: September 2023

AbstractThis paper describes the dynamics of 137Cs accumulation and its concentration ratio as well as that of some stable elements in the body, shell, gastrointestinal tract and albumin gland of a particular species of snail (terrestrial gastropod), namely the Giant African snail (Lissachatina fulica), after the long-term ingestion of contaminated forage and/or soil. The activity concentration of 137Cs in the their bodies increased over the first 40 days of the experiment, after which the increase in the activity of this radionuclide significantly reduced. The distribution of 137Cs in the body of a snail decreases as follows: gastrointestinal tract ˃ body = albumin gland ˃ shell. It was found that the contribution of soil towards the contamination of their bodies by 137Cs is far less than that of forage. Although the biological availability of Pb and U in forage is one order of magnitude higher than in soil, the main contribution to the contamination of snails originates from soil.
Effects of bone-conducted vibration stimulation of various frequencies on the vertical vection
Authors: Kondo Tetsuta , Hirao Yutaro , Narumi Takuji , Amemiya Tomohiro 
Published: September 2023

AbstractIllusory self-motion (“vection”) has been used to present a sense of movement in virtual reality (VR) and other similar applications. It is crucial in vection research to present a stronger sense of movement. Bone-conducted vibration (BCV) is a small and generally acceptable method for enhancing the sense of movement in VR. However, its effects on vection have not been extensively studied. Here, we conducted two experiments to investigate the effect of BCV on the vection, which generates an upward sensation under the hypothesis that BCV stimulation to the mastoid processes causes noise in the vestibular system and enhances visually-induced self-motion perception. The experiments focused on the effects of BCV stimuli of different frequencies on the vection experience. The results suggested that 500 Hz BCV was more effective as noise to the vestibular system than other frequency BCVs and improved self-motion sensation. This study examines the effects of BCV with different frequencies on the vection experience and designs a theory for using BCV in VR.
Homeology of sex chromosomes in Amazonian Harttia armored catfishes supports the X-fission hypothesis for the X1X2Y sex chromosome system origin
Authors: de Menezes Cavalcante Sassi Francisco , Sember Alexandr , Deon Geize Aparecida , Liehr Thomas , Padutsch Niklas , Oyakawa Osvaldo Takeshi , Vicari Marcelo Ricardo , Bertollo Luiz Antonio Carlos , Moreira-Filho Orlando , de Bello Cioffi Marcelo 
Published: September 2023

AbstractThe Neotropical monophyletic catfish genus Harttia represents an excellent model to study karyotype and sex chromosome evolution in teleosts. Its species split into three phylogenetic clades distributed along the Brazilian territory and they differ widely in karyotype traits, including the presence of standard or multiple sex chromosome systems in some members. Here, we investigate the chromosomal rearrangements and associated synteny blocks involved in the origin of a multiple X1X2Y sex chromosome system present in three out of six sampled Amazonian-clade species. Using 5S and 18S ribosomal DNA fluorescence in situ hybridization and whole chromosome painting with probes corresponding to X1 and X2 chromosomes of X1X2Y system from H. punctata, we confirm previous assumptions that X1X2Y sex chromosome systems of H. punctata, H. duriventris and H. villasboas represent the same linkage groups which also form the putative XY sex chromosomes of H. rondoni. The shared homeology between X1X2Y sex chromosomes suggests they might have originated once in the common ancestor of these closely related species. A joint arrangement of mapped H. punctata X1 and X2 sex chromosomes in early diverging species of different Harttia clades suggests that the X1X2Y sex chromosome system may have formed through an X chromosome fission rather than previously proposed Y-autosome fusion.
Plasticity of cone photoreceptors in adult zebrafish revealed by thyroid hormone exposure
Authors: Farre Ashley A. , Thomas Preston , Huang Johnson , Poulsen Rachel A. , Owusu Poku Emmanuel , Stenkamp Deborah L. 
Published: September 2023

AbstractVertebrate color vision is predominantly mediated by the presence of multiple cone photoreceptor subtypes that are each maximally sensitive to different wavelengths of light. Thyroid hormone (TH) has been shown to be essential in the spatiotemporal patterning of cone subtypes in many species, including cone subtypes that express opsins that are encoded by tandemly replicated genes. TH has been shown to differentially regulate the tandemly replicated lws opsin genes in zebrafish, and exogenous treatments alter the expression levels of these genes in larvae and juveniles. In this study, we sought to determine whether gene expression in cone photoreceptors remains plastic to TH treatment in adults. We used a transgenic lws reporter line, multiplexed fluorescence hybridization chain reaction in situ hybridization, and qPCR to examine the extent to which cone gene expression can be altered by TH in adults. Our studies revealed that opsin gene expression, and the expression of other photoreceptor genes, remains plastic to TH treatment in adult zebrafish. In addition to retinal plasticity, exogenous TH treatment alters skin pigmentation patterns in adult zebrafish after 5 days. Taken together, our results show a remarkable level of TH-sensitive plasticity in the adult zebrafish.
Binary code similarity analysis based on naming function and common vector space
Authors: Xia Bing , Pang Jianmin , Zhou Xin , Shan Zheng , Wang Junchao , Yue Feng 
Published: September 2023

AbstractBinary code similarity analysis is widely used in the field of vulnerability search where source code may not be available to detect whether two binary functions are similar or not. Based on deep learning and natural processing techniques, several approaches have been proposed to perform cross-platform binary code similarity analysis using control flow graphs. However, existing schemes suffer from the shortcomings of large differences in instruction syntaxes across different target platforms, inability to align control flow graph nodes, and less introduction of high-level semantics of stability, which pose challenges for identifying similar computations between binary functions of different platforms generated from the same source code. We argue that extracting stable, platform-independent semantics can improve model accuracy, and a cross-platform binary function similarity comparison model N_Match is proposed. The model elevates different platform instructions to the same semantic space to shield their underlying platform instruction differences, uses graph embedding technology to learn the stability semantics of neighbors, extracts high-level knowledge of naming function to alleviate the differences brought about by cross-platform and cross-optimization levels, and combines the stable graph structure as well as the stable, platform-independent API knowledge of naming function to represent the final semantics of functions. The experimental results show that the model accuracy of N_Match outperforms the baseline model in terms of cross-platform, cross-optimization level, and industrial scenarios. In the vulnerability search experiment, N_Match significantly improves hit@N, the mAP exceeds the current graph embedding model by 66%. In addition, we also give several interesting observations from the experiments. The code and model are publicly available at https://www.github.com/CSecurityZhongYuan/Binary-Name_Match.
Wnt activation as a potential therapeutic approach to treat partial limbal stem cell deficiency
Authors: Bonnet Clémence , González Sheyla , Deng Sophie X. , Zheng Jie J. 
Published: September 2023

AbstractLimbal epithelial stem/progenitor cells (LSCs) are adult stem cells located at the limbus, tightly regulated by their niche involving numerous signaling pathways, such as Wnt. Wnt proteins are secreted morphogens that play critical roles in embryonic development, stem cell proliferation, self-renewal, tissue regeneration, and remodeling in adults. It has been shown that a small molecule Wnt mimic could improve LSCs expansion ex vivo. Damage to the LSCs and/or their niche can lead to limbal stem cell deficiency (LSCD), a condition that can cause corneal blindness and is difficult to treat. This study explored if repopulating residual LSCs in partial LSCD through Wnt activation could be a novel therapeutic approach. To mimic LSCD due to a chemical injury, single cultured LSCs were exposed to various concentrations of sodium hydroxide. A progressive loss of the LSCs phenotype was observed: the percentage of p63bright cells and cytokeratin (K)14+ cells decreased while the percentage of K12+ increased. Wnt activation was attained by treating the LSCs with lithium chloride (LiCl) and a small-molecule Wnt mimic, respectively. After 18 h of treatment, LSCs proliferation was increased, and the LSCs phenotype was recovered, while the untreated cells did not proliferate and lost their phenotype. The percentage of p63bright cells was significantly higher in the Wnt mimic-treated cells compared with untreated cells, while the percentage of K12+ cells was significantly lower. These findings suggest that local Wnt activation may rescue LSCs upon alkaline injury.
Distinct patterns of copy number alterations may predict poor outcome in central nervous system germ cell tumors
Authors: Takami Hirokazu , Satomi Kaishi , Fukuoka Kohei , Nakamura Taishi , Tanaka Shota , Mukasa Akitake , Saito Nobuhito , Suzuki Tomonari , Yanagisawa Takaaki , Sugiyama Kazuhiko , Kanamori Masayuki , Kumabe Toshihiro , Tominaga Teiji , Tamura Kaoru , Maehara Taketoshi , Nonaka Masahiro , Asai Akio , Yokogami Kiyotaka , Takeshima Hideo , Iuchi Toshihiko , Kobayashi Keiichi , Yoshimoto Koji , Sakai Keiichi , Nakazato Yoichi , Matsutani Masao , Nagane Motoo , Nishikawa Ryo , Ichimura Koichi 
Published: September 2023

AbstractWe have previously reported that 12p gain may predict the presence of malignant components and poor prognosis for CNS germ cell tumor (GCT). Recently, 3p25.3 gain was identified as an independent predictor of poor prognosis for testicular GCT. Eighty-one CNS GCTs were analyzed. Copy number was calculated using methylation arrays. Five cases (6.2%) showed 3p25.3 gain, but only among the 40 non-germinomatous GCTs (NGGCTs) (5/40, 12.5%; p = 0.03). Among NGGCTs, those with a yolk sac tumor component showed a significantly higher frequency of 3p25.3 gain (18.2%) than those without (1.5%; p = 0.048). NGGCTs with gain showed significantly shorter progression-free survival (PFS) than those without (p = 0.047). The 3p25.3 gain and 12p gain were independent from each other. The combination of 3p25.3 gain and/or 12p gain was more frequent among NGGCTs with malignant components (69%) than among those without (29%; p = 0.02). Germinomas containing a higher number of copy number alterations showed shorter PFS than those with fewer (p = 0.03). Taken together, a finding of 3p25.3 gain may be a copy number alteration specific to NGGCTs and in combination with 12p gain could serve as a marker of negative prognosis or treatment resistance. Germinoma with frequent chromosomal instability may constitute an unfavorable subgroup.
Overcoming immune checkpoint blockade resistance in solid tumors with intermittent ITK inhibition
Authors: Zhao Manzhi , Li Ling , Kiernan Caoimhe H. , Castro Eiro Melisa D. , Dammeijer Floris , van Meurs Marjan , Brouwers-Haspels Inge , Wilmsen Merel E. P. , Grashof Dwin G. B. , van de Werken Harmen J. G. , Hendriks Rudi W. , Aerts Joachim G. , Mueller Yvonne M. , Katsikis Peter D. 
Published: September 2023

AbstractCytotoxic CD8 + T cell (CTL) exhaustion is driven by chronic antigen stimulation. Reversing CTL exhaustion with immune checkpoint blockade (ICB) has provided clinical benefits in different types of cancer. We, therefore, investigated whether modulating chronic antigen stimulation and T-cell receptor (TCR) signaling with an IL2-inducible T-cell kinase (ITK) inhibitor, could confer ICB responsiveness to ICB resistant solid tumors. In vivo intermittent treatment of 3 ICB-resistant solid tumor (melanoma, mesothelioma or pancreatic cancer) with ITK inhibitor significantly improved ICB therapy. ITK inhibition directly reinvigorate exhausted CTL in vitro as it enhanced cytokine production, decreased inhibitory receptor expression, and downregulated the transcription factor TOX. Our study demonstrates that intermittent ITK inhibition can be used to directly ameliorate CTL exhaustion and enhance immunotherapies even in solid tumors that are ICB resistant.
Defining and identifying cell sub-crosstalk pairs for characterizing cell–cell communication patterns
Authors: Zhang Chenxing , Hu Yuxuan , Gao Lin 
Published: September 2023

AbstractCurrent cell–cell communication analysis focuses on quantifying intercellular interactions at cell type level. In the tissue microenvironment, one type of cells could be divided into multiple cell subgroups that function differently and communicate with other cell types or subgroups via different ligand–receptor-mediated signaling pathways. Given two cell types, we define a cell sub-crosstalk pair (CSCP) as a combination of two cell subgroups with strong and similar intercellular crosstalk signals and identify CSCPs based on coupled non-negative matrix factorization. Using single-cell spatial transcriptomics data of mouse olfactory bulb and visual cortex, we find that cells of different types within CSCPs are significantly spatially closer with each other than those in the whole single-cell spatial map. To demonstrate the utility of CSCPs, we apply 13 cell–cell communication analysis methods to sampled single-cell transcriptomics datasets at CSCP level and reveal ligand–receptor interactions masked at cell type level. Furthermore, by analyzing single-cell transcriptomics data from 29 breast cancer patients with different immunotherapy responses, we find that CSCPs are useful predictive features to discriminate patients responding to anti-PD-1 therapy from non-responders. Taken together, partitioning a cell type pair into CSCPs enables fine-grained characterization of cell–cell communication in tissue and tumor microenvironments.
Effect of extracellular vesicles derived from induced pluripotent stem cells on mesangial cells underwent a model of fibrosis in vitro
Authors: dos Santos Bronel Bruno Aristides , Maquigussa Edgar , Boim Mirian Aparecida , da Silva Novaes Antônio 
Published: September 2023

AbstractThe fibrogenic process plays a significant pathophysiological role in the progression of chronic kidney disease. Inhibition of the renin-angiotensin system (RAS) is one strategy to delay disease progression but does not reverse established fibrosis. In this context, induced pluripotent stem cells (iPSCs) have been considered an alternative due to their regenerative potential. iPSCs exert their effects through paracrine signaling, which releases specific biomolecules into the extracellular environment, either directly or within extracellular vesicle (EVs), that can reach target cells. This study aims to evaluate the potential beneficial effects of iPSC-derived EVs (EV-iPSCs) in an in vitro model of fibrosis using mouse mesangial cells (MMCs) stimulated with TGF-β. EV-iPSCs were obtained by differentially ultracentrifuging iPSCs culture medium. MMCs were stimulated with 5 ng/mL of TGF-β and simultaneously treated with or without EV-iPSCs for 24 h. Markers of inflammation, fibrosis, and RAS components were assessed using RT-PCR, western blotting, and immunofluorescence. Under TGF-β stimulus, MMCs exhibited increased expression of inflammation markers, RAS components, and fibrosis. However, these changes were mitigated in the presence of EV-iPSCs. EV-iPSCs effectively reduced inflammation, RAS activation, and fibrogenesis in this fibrosis model involving mesangial cells, suggesting their potential as a strategy to reduce glomerular sclerosis.
Survival prediction and prognostic factors in colorectal cancer after curative surgery: insights from cox regression and neural networks
Authors: Alinia Shayeste , Asghari-Jafarabadi Mohammad , Mahmoudi Leila , Norouzi Solmaz , Safari Maliheh , Roshanaei Ghodratollah 
Published: September 2023

AbstractMedical research frequently relies on Cox regression to analyze the survival distribution of cancer patients. Nonetheless, in specific scenarios, neural networks hold the potential to serve as a robust alternative. In this study, we aim to scrutinize the effectiveness of Cox regression and neural network models in assessing the survival outcomes of patients who have undergone treatment for colorectal cancer. We conducted a retrospective study on 284 colorectal cancer patients who underwent surgery at Imam Khomeini clinic in Hamadan between 2001 and 2017. The data was used to train both Cox regression and neural network models, and their predictive accuracy was compared using diagnostic measures such as sensitivity, specificity, positive predictive value, accuracy, negative predictive value, and area under the receiver operating characteristic curve. The analyses were performed using STATA 17 and R4.0.4 software. The study revealed that the best neural network model had a sensitivity of 74.5% (95% CI 61.0–85.0), specificity of 83.3% (65.3–94.4), positive predictive value of 89.1% (76.4–96.4), negative predictive value of 64.1% (47.2–78.8), AUC of 0.79 (0.70–0.88), and accuracy of 0.776 for death prediction. For recurrence, the best neural network model had a sensitivity of 88.1% (74.4–96.0%), specificity of 83.7% (69.3–93.2%), positive predictive value of 84.1% (69.9–93.4%), negative predictive value of 87.8% (73.8–95.9%), AUC of 0.86 (0.78–0.93), and accuracy of 0.859. The Cox model had comparable results, with a sensitivity of 73.6% (64.8–81.2) and 85.5% (78.3–91.0), specificity of 89.6% (83.8–93.8) and 98.0% (94.4–99.6), positive predictive value of 84.0% (75.6–90.4) and 97.4% (92.6–99.5), negative predictive value of 82.0% (75.6–90.4) and 88.8% (0.83–93.1), AUC of 0.82 (0.77–0.86) and 0.92 (0.89–0.95), and accuracy of 0.88 and 0.92 for death and recurrence prediction, respectively. In conclusion, the study found that both Cox regression and neural network models are effective in predicting early recurrence and death in patients with colorectal cancer after curative surgery. The neural network model showed slightly better sensitivity and negative predictive value for death, while the Cox model had better specificity and positive predictive value for recurrence. Overall, both models demonstrated high accuracy and AUC, indicating their usefulness in predicting these outcomes.