bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effect of omega-3 fatty acid diet on prostate cancer progression and cholesterol efflux in tumor-associated macrophages—dependence on GPR120
Authors: Liang Pei , Henning Susanne M. , Grogan Tristan , Elashoff David , Said Jonathan , Cohen Pinchas , Aronson William J. 
Published: October 2023

Abstract
Background
Preclinical and clinical translational research supports the role of an ω-3 fatty acid diet for prostate cancer prevention and treatment. The anti-prostate cancer effects of an ω-3 diet require a functional host g-protein coupled receptor 120 (GPR120) but the underlying effects on the tumor microenvironment and host immune system are yet to be elucidated.

Methods
Friend leukemia virus B (FVB) mice received bone marrow from green fluorescent protein (GFP) labeled GPR120 wild-type (WT) or knockout (KO) mice followed by implanting Myc-driven mouse prostate cancer (MycCap) allografts and feeding an ω-3 or ω-6 diet. Tumor associated immune cells were characterized by flow cytometry, and CD206+ tumor infiltrating M2-like macrophages were isolated for gene expression studies. MycCap prostate cancer cell conditioned medium (CM) was used to stimulate murine macrophage cells (RAW264.7) and bone marrow-derived (BMD) macrophages to study the effects of docosahexanoic acid (DHA, fish-derived ω-3 fatty acid) on M2 macrophage function and cholesterol metabolism.

Results
The bone marrow transplantation study showed that an ω-3 as compared to an ω-6 diet inhibited MycCaP allograft tumor growth only in mice receiving GPR120 WT but not GPR120 KO bone marrow. In the ω-3 group, GPR120 WT BMD M2-like macrophages infiltrating the tumor were significantly reduced in number and gene expression of cholesterol transporters Abca1, Abca6, and Abcg1. RAW264.7 murine macrophages and BMDMs exposed to MycCaP cell CM had increased gene expression of cholesterol transporters, depleted cholesterol levels, and were converted to the M2 phenotype. These effects were inhibited by DHA through the GPR120 receptor.

Conclusion
Host bone marrow cells with functional GPR120 are essential for the anticancer effects of dietary ω-3 fatty acids, and a key target of the ω-3 diet are the M2-like CD206+ macrophages. Our preclinical findings provide rationale for clinical trials evaluating ω-3 fatty acids as a potential therapy for prostate cancer through inhibition of GPR120 functional M2-like macrophages.
The E3 ligase TRIM26 suppresses ferroptosis through catalyzing K63-linked ubiquitination of GPX4 in glioma
Authors: Wang Zhangjie , Xia Yuan , Wang Yang , Zhu Ruiqiu , Li Hongbo , Liu Yu , Shen Na 
Published: October 2023

AbstractThe selenium-containing enzyme GPX4 moonlights as a central regulator of ferroptosis, an iron-dependent, nonapoptotic form of regulated cell death caused by lipid peroxidation. Yet, little is known about the mechanisms underlying the regulation of its post-transcriptional modifications. Here, we identify the tripartite motif-containing protein TRIM26 as an E3 ubiquitin ligase of GPX4. TRIM26 directly interacts with GPX4 through its Ring domain and catalyzes the ubiquitination of GPX4 at K107 and K117, which promotes the switch in polyubiquitination of GPX4 from K48 to K63, thus enhancing GPX4 protein stability. Moreover, PLK1-mediated S127 phosphorylation of TRIM26 enhances the interaction between TRIM26 and GPX4. Inhibition of TRIM26 phosphorylation causes a reduction in GPX4 K63-linked polyubiquitination and diminishes GPX4 protein levels in tumor cells. Further investigation revealed that TRIM26 is overexpressed in glioma cells. TRIM26 silencing dramatically impedes ferroptosis resistance and tumorigenesis in glioma in vivo and in vitro. Clinically, TRIM26 expression shows a direct correlation with GPX4 and PLK1 levels in glioma samples and is associated with poor outcome in patients with glioma. Collectively, these findings define the role of GPX4 K63-linked polyubiquitination in ferroptosis and suggest a potential strategy for glioma treatment.
The role of SARS-CoV-2-mediated NF-κB activation in COVID-19 patients
Authors: Zhou Qiaoqiao , Zhang Lei , Dong Yanming , Wang Yuan , Zhang Bin , Zhou Shiyi , Huang Qing , Wu Tian , Chen Gongxuan 
Published: October 2023

AbstractThe SARS-CoV-2 pandemic, now in its third year, has had a profound impact on public health and economics all over the world. Different populations showed varied susceptibility to this virus and mortality after infection. Clinical and laboratory data revealed that the uncontrolled inflammatory response plays an important role in their poor outcome. Herein, we summarized the role of NF-κB activation during SARS-CoV-2 invasion and replication, particularly the angiotensin-converting enzyme 2 (ACE2)-mediated NF-κB activation. Then we summarized the COVID-19 drugs’ impact on NF-κB activation and their problems. A favorable prognosis is linked with timely treatment with NF-κB activation inhibitors, such as TNFα, IL-1β, and IL-6 monoclonal antibodies. However, further clinical researches are still required to clarify the time window, dosage of administration, contraindication, and potential side effects of these drugs, particularly for COVID-19 patients with hypertension, hyperglycemia, diabetes, or other chronic diseases.
Scalable genetic screening for regulatory circuits using compressed Perturb-seq
Authors: Yao Douglas , Binan Loic , Bezney Jon , Simonton Brooke , Freedman Jahanara , Frangieh Chris J. , Dey Kushal , Geiger-Schuller Kathryn , Eraslan Basak , Gusev Alexander , Regev Aviv , Cleary Brian 
Published: October 2023

AbstractPooled CRISPR screens with single-cell RNA sequencing readout (Perturb-seq) have emerged as a key technique in functional genomics, but they are limited in scale by cost and combinatorial complexity. In this study, we modified the design of Perturb-seq by incorporating algorithms applied to random, low-dimensional observations. Compressed Perturb-seq measures multiple random perturbations per cell or multiple cells per droplet and computationally decompresses these measurements by leveraging the sparse structure of regulatory circuits. Applied to 598 genes in the immune response to bacterial lipopolysaccharide, compressed Perturb-seq achieves the same accuracy as conventional Perturb-seq with an order of magnitude cost reduction and greater power to learn genetic interactions. We identified known and novel regulators of immune responses and uncovered evolutionarily constrained genes with downstream targets enriched for immune disease heritability, including many missed by existing genome-wide association studies. Our framework enables new scales of interrogation for a foundational method in functional genomics.
A comparative study of freeze-drying heat transfer in polymeric vials and glass vials
Authors: Sarmadi Morteza , Holmes Spencer , Agha Royal , Davenport Brandon , Weikart Christopher , Thompson T. N. 
Published: October 2023

AbstractImplementation of polymeric vials for freeze-dried drug products has been practically non-existent because of unique moisture barrier and thermodynamic technical challenges. Hybrid vials, which combine the benefits of polymer and glass, have been shown to address the challenges of ordinary polymeric vials. Tackling thermodynamic challenges starts with a clear understanding of the heat transfer mechanism. To this end, multi-physics simulations and experimentation were used to compare the heat transfer between hybrid cyclic olefin polymer (COP) vials and borosilicate glass vials during freeze-drying. Parametric models were developed for hybrid COP and glass vials to systematically study the effect of five design parameters based on the arrangement of the vials on a tray inside a lyophilization chamber. Heat transfer in glass vials were dominated by heat conduction with the surrounding vapor, while hybrid COP vials were governed by conduction with the bottom shelf. Furthermore, hybrid COP vials exhibited more consistent heat flow rate and total heat transfer coefficient compared to glass vials, suggesting higher product quality as a result. The distance between adjacent vials and the drug product height were the most important parameters affecting heat transfer irrespective of vial type. Results indicated that hybrid COP vials can be filled to higher fill volumes with higher heat transfer and without the risk of breakage. Results of this study can help design innovative primary packaging systems for freeze drying or optimizing heat transfer for existing glass or hybrid COP vial systems regarding product consistency and drying time.
Establishment of the microstructure of porous materials and its relationship with effective mechanical properties
Authors: Chen Kangni , Qin Hongling , Ren Zhiying 
Published: October 2023

AbstractIn this study, a porous structure for a porous liquid storage medium is generated, and the homogenization theory based on displacement boundary conditions is used to predict the effective mechanical properties. The relationship between the porous material’s macroscopic mechanical properties and microstructure is next analyzed. In order to establish the relationship between the microstructure of porous materials and their macroscopic mechanical properties, assuming that the pores grow along the z direction, a method is proposed to generate 3D open-cell porous materials based on six design parameters (i.e., the number of pores, porosity, irregularity of pore distribution, the randomness of pore growth in the x and y directions, and randomness of pore size). Since the porosity of oil-bearing materials ranges from 20 to 30%, the porosity of the RVE (Representative Volume Element) was kept under control at about 25%, and the effect of the six design factors on the mechanical properties of the RVE was investigated. Utilizing SLA 3D printing technology, specimens were produced, and compression tests were used to show how useful the results of the numerical analysis were. The results demonstrated that after the number of RVE pores reaches 9, the numerical results have good repeatability. The irregularity of the initial pore distribution has little effect on the effective mechanical properties of the RVE. At the same time, the increase in the randomness of pore growth and the randomness of pore size increases the degree of weakening of the mechanical properties in the z-direction, while reducing the degree of weakening in the x and y directions, but the latter has a smaller impact. Furthermore, there is a superimposition effect of design parameters on the RVE.
The enhanced cytotoxicity on breast cancer cells by Tanshinone I-induced photodynamic effect
Authors: Fengchao Chen , Siya Zhang , Tongtong Yan , Hongquan Wang , Jie Li , Qiang Wang , Danish Subhan , Kun Li 
Published: October 2023

AbstractRecently, natural photosensitizers, such as berberine, curcumin, riboflavin, and emodin, have received more and more attention in photodynamic therapy. Tanshinone I (TanI) is extracted from a traditional Chinese herb Danshen, and exhibits many physiological functions including antitumor. TanI is a photoactive phytocompounds, but no work was tried to investigate its potential photodynamic effect. This study evaluated the cytotoxicity induced by the photodynamic effect of TanI. The photochemical reactions of TanI were firstly investigated by laser flash photolysis. Then breast cancer cell line MDA-MB-231 was chosen as a model and the photodynamic effect of TanI on cancer cell was evaluated by MTT assay and flow cytometry. The results showed that TanI could be photoexcited by its UV–Vis absorption light to produce 3TanI* which was quickly quenched by O2. MTT assay showed that the photodynamic effect of TanI resulted in more obvious inhibitive effect on cell survival and cell migration. Besides, the photodynamic effect of TanI could induce cell apoptosis and necrosis, lead to cell cycle arrest in G2, increase intracellular ROS, and decrease the cellular Δψm. It can be concluded that the photodynamic effect of TanI can obviously enhance the cytotoxicity of TanI on MDA-MB-231 cells in vitro, which indicated that TanI might serve as a natural photosensitizer.
RNA modification regulator DDC in endometrial cancer affects the tumor microenvironment and patient prognosis
Authors: Zhao Huai , Shi Chuang , Zhao Guoguang , Liu Jiamin , Wang Xi , Liang Jie , Li Fangmei 
Published: October 2023

AbstractUterine corpus endometrial carcinoma (UCEC) is infiltrated by immune cells, which are involved in the growth and proliferation of malignant tumors and resistance to immunotherapy. This study suggested that RNA modification regulators played an important role in the development and prognosis of UCEC. Many studies confirmed that RNA modification played an essential role in tumor immune regulation, and abnormal RNA modification contributed to tumorigenesis and cancer progression. Based on the RNA modification regulatory factors, the UCEC samples from TCGA (The Cancer Genome Atlas) were classified into two clusters, namely Cluster A and Cluster B, using unsupervised consensus clustering. We obtained DEG (differentially expressed genes) between the two clusters, and constructed a risk model of RNA modification-related genes using DEGs. Cluster A had lower RNA modification regulatory factors, richer immune cell infiltration, and better prognosis. The differentially expressed genes between the two clusters were obtained, and these genes were used for modeling. This model divided patients with UCEC into two groups. The low-risk group had better immune infiltration, and the ROC (receiver operating characteristic) curve showed that this model had good predictive efficacy. The low-risk group had a better response to immunotherapy by immune checkpoint prediction. We obtained the key gene l-dopa decarboxylase (DDC) through the intersection of LASSO model genes and GEO dataset GSE17025. We evaluated the potential biological functions of DDC. The differences in the expression of DDC were verified by immunohistochemistry. We evaluated the relationship between DDC and immune cell infiltration and verified this difference using immunofluorescence. Cluster A with low expression of RNA modification regulators has better prognosis and richer immune cell infiltration, therefore, we believed that RNA modification regulators in UCEC were closely related to the tumor microenvironment. Also, the risk score could well predict the prognosis of patients and guide immunotherapy, which might benefit patients with UCEC.
Challenges of AI driven diagnosis of chest X-rays transmitted through smart phones: a case study in COVID-19
Authors: Antony Mariamma , Kakileti Siva Teja , Shah Rachit , Sahoo Sabyasachi , Bhattacharyya Chiranjib , Manjunath Geetha 
Published: October 2023

AbstractHealthcare delivery during the initial days of outbreak of COVID-19 pandemic was badly impacted due to large number of severely infected patients posing an unprecedented global challenge. Although the importance of Chest X-rays (CXRs) in meeting this challenge has now been widely recognized, speedy diagnosis of CXRs remains an outstanding challenge because of fewer Radiologists. The exponential increase in Smart Phone ownership globally, including LMICs, provides an opportunity for exploring AI-driven diagnostic tools when provided with large volumes of CXRs transmitted through Smart Phones. However, the challenges associated with such systems have not been studied to the best of our knowledge. In this paper, we show that the predictions of AI-driven models on CXR images transmitted through Smart Phones via applications, such as , suffer both in terms of Predictability and Explainability, two key aspects of any automated Medical Diagnosis system. We find that several existing Deep learning based models exhibit prediction instability–disagreement between the prediction outcome of the original image and the transmitted image. Concomitantly we find that the explainability of the models deteriorate substantially, prediction on the transmitted CXR is often driven by features present outside the lung region, clearly a manifestation of Spurious Correlations. Our study reveals that there is significant compression of high-resolution CXR images, sometimes as high as 95%, and this could be the reason behind these two problems. Apart from demonstrating these problems, our main contribution is to show that Multi-Task learning (MTL) can serve as an effective bulwark against the aforementioned problems. We show that MTL models exhibit substantially more robustness, 40% over existing baselines. Explainability of such models, when measured by a saliency score dependent on out-of-lung features, also show a 35% improvement. The study is conducted on WaCXR dataset, a curated dataset of 6562 image pairs corresponding to original uncompressed and compressed CXR images. Keeping in mind that there are no previous datasets to study such problems, we open-source this data along with all implementations.
Plant mediated fabrication of silver nanoparticles, process optimization, and impact on tomato plant
Authors: Ansari Madeeha , Ahmed Shakil , Abbasi Asim , Khan Muhammad Tajammal , Subhan Mishal , Bukhari Najat A. , Hatamleh Ashraf Atef , Abdelsalam Nader R. 
Published: October 2023

AbstractNanotechnology is one of the fastest-growing markets, but developing eco-friendly products, their maximum production, stability, and higher yield is a challenge. In this study, silver nanoparticles were synthesized using an easily available resource, leaves extract of the Neem (Azadirachta indica) plant, as a reducing and capping agent, determined their effect on germination and growth of tomato plants. The maximum production of silver nanoparticles was noted at 70 °C after 3 h of reaction time while treating the 10 ml leaf extract of Neem plant with 10 ml of 1 mM silver nitrate. The impact of the extract preparation method and solvent type on the plant mediated fabrication of silver nanoparticles was also investigated. The UV-spectrophotometric analysis confirmed the synthesis of silver nanoparticles and showed an absorption spectrum within Δ420–440 nm range. The size of the fabricated silver nanoparticles was 22–30 nm. The functional groups such as ethylene, amide, carbonyl, methoxy, alcohol, and phenol attached to stabilize the nanoparticles were observed using the FTIR technique. SEM, EDX, and XRD analyses were performed to study the physiochemical characteristics of synthesized nanoparticles. Silver nanoparticles increased the germination rate of tomato seeds up to 70% while decreasing the mean germination time compared to the control. Silver nanoparticles applied at varying concentrations significantly increased the shoot length (25 to 80%), root length (10 to 60%), and fresh biomass (10 to 80%) biomass of the tomato plant. The production of total chlorophyll, carotenoid, flavonoids, soluble sugar, and protein was significantly increased in tomato plants treated with 5 and 10 ppm silver nanoparticles compared to the control. Green synthesized silver nanoparticles are cost-effective and nontoxic and can be applied in agriculture, biomedical, and other fields.
Hotspot movement of compound events on the Europe continent
Authors: Doshi Smit Chetan , Lohmann Gerrit , Ionita Monica 
Published: October 2023

AbstractClimate indices are often used as a climate monitoring tool, allowing us to understand how the frequency, intensity, and duration of extreme weather events are changing over time. Here, based on complex statistical analysis we identify highly correlated significant pairs of compound events at the highest spatial resolution, on a monthly temporal scale across Europe. Continental-scale monthly analysis unleashes information on compound events such as high-risk zones, hotspots, monthly shifts of hotspots and trends, risk exposure to land cover and population, and identification of maximum increasing trends. While there are many studies on single or compound climate extremes there are only a few studies that addresses the relationship between pairs of hazards, the incorporation of bioclimatic indices, the determination of a grid best-fit copula approach, and the outlining relevance of this work of compound event risks with exposures. In this respect, here, using 27-bivariate and 10-trivariate copula models, we show that the different hazard pairs have high combined risks of indices related to radiation, temperature, evapotranspiration, bioclimatic-based indices, such as the universal thermal climate index, wind chill index, and heat index, mainly over the northern and eastern European countries. Furthermore, we show that over the last 7 decades, agricultural and coastal areas are highly exposed to the risks of defined hotspots of compound events. In some of the hotspots of compound events-identified by clusters, there is no monthly shifts of hotspots, leading to higher impacts when compounded. Future work needs to integrate the framework and process to identify other compound pairs.
The effect of dynamic versus static visualizations on acquisition of basketball game actions: a diurnal study
Authors: Rekik Ghazi , Jouira Ghada , Belkhir Yosra , Jarraya Mohamed , Kuo Cheng-Deng , Chen Yung-Sheng 
Published: October 2023

AbstractThis study aimed to examine the effect of time of day (TOD) on the acquisition of basketball game actions from dynamic and static visualizations in physical education students (novice practitioners). Participants were quasi-randomly assigned to three treatments (static pictures, enriched static-pictures, or video). Morning and late-afternoon sessions were conducted, involving study phases and immediate-recall tests [game comprehension (GC) test and game performance (GP) test]. Oral temperature (OT) and mood states (MS) were also measured. Compared to the morning, the results revealed that afternoon resulted in higher OT, higher negative MS (e.g., anxiety and fatigue), and lower positive MS (i.e., vigor) in all experimental conditions. Moreover, the results showed that: (a) GC and GP decreased throughout the day (regardless of treatments), (b) GC and GP were better with enriched static-pictures (with arrows) than with static pictures, at both TOD, and (c) the video resulted in better GC and GP than the two static presentations, at both TOD. This study (a) highlights the morning's superiority in the acquisition of motor skills from dynamic and static visualizations, due to mood disturbances and lower arousal levels, and (b) encourages basketball teachers to use video modeling by experts, particularly in the morning, for explaining tactical skills.
Investigating the atomic behavior of carbon nanotubes as nanopumps
Authors: Shahryari Mehran , Nazari-Golshan Akbar , Nourazar S. Salman , Abedi Mohsen 
Published: October 2023

AbstractIn this study, we utilized molecular dynamics (MD) simulations to investigate the nano pumping process of Carbon Nanotube (CNT) in an aqueous environment. In this research, an attempt has been made to investigate and analyze the pumping process of fullerene C20 and water molecules through a carbon nanotube that is externally stimulated by two oscillators. It should be noted that this nano pump is completely immersed in an aqueous environment and the inside and outside of the carbon nanotube is filled with water molecules. To simulate the aqueous environment with NaCl impurities and carbon structures, we employed the Universal Force Field and Tersoff interatomic potentials, respectively. The stability of the simulated structures was demonstrated through an equilibrium process, which was a result of the appropriate settings in our MD simulations. To describe the CNT nano pumping process, we analyzed the velocity and translational/rotational components of C20 kinetic energy over time steps. By decreasing the water impurity concentration from 0.50 to 0.075 mol/l, the nano pumping time varied from 10.98 to 10.11 ps, respectively. Additionally, optimization of the atomic wave producing in the nano pumping process led to a further decrease in pumping time to 10.01 ps. Finally, a 2.86% variation in calculated results was observed by changing the water MD simulation model from SPC to TIP4P.