bluuebunny/crossref_metadata_2025_split huggingface dataset:
BCLAF1 is expressed as an oncogene in Bile Duct Cancer
Authors: Zhou Yutong , Ran Xun , Han Min 
Published: August 2023

Abstract
OBJECTIVE:
Validating the role of BCLAF1 in the development of bile duct cancer.
METHODS:
Differential expression of BCLAF1 in cholangiocarcinoma and normal tissues was analysed bioinformatically and immuno-infiltration analysis was performed by R. We also derived the correlation between the expression of BCLAF1 and HIF-1α by bioinformatics analysis and validated by Western Bloting, qRT- PCR and scratch assay before and after hypoxia.
RESULTS:
Through bioinformatics analysis, we found that BCLAF1 mRNA was significantly higher in tumour tissues of cholangiocarcinoma. And the high expression of BCLAF1 implied a more advanced stage but a lower mortality rate. KEGG and GO enrichment analysis showed that BCLAF1 overexpression in cholangiocarcinoma was mainly associated with histone modification, peptidyl lysine modification and macromolecular methylation. We used the TIMER algorithm to show that BCLAF1 expression in cholangiocarcinoma is associated with immune cell infiltration, which affects tumour progression and patient prognosis. We confirmed by normoxia and hypoxia qRT-PCR, Western bloting and scratch assays that BCLAF1 and HIF-1α expression are positively correlated and that BCLAF1 may be expressed as an oncogene in cholangiocarcinoma.
CONCLUSION:
These findings demonstrate that BCLAF1 may act as an oncogene in cholangiocarcinoma and may be involved in immune cell infiltration in cholangiocarcinoma, suppressing the expression of HIF-1α.
Validation of the Predictive Model for Operative Intervention after Blunt Abdominal Trauma in Children with Equivocal Computed Tomography Findings: A Multi-institutional Study
Authors: Lamoshi Abdulraouf , Lay Raymond , Wakeman Derek , Edwards Mary , Wallenstein Kim , Fabiano Tiffany , Singh Zorawar , Zipkin Jacob , Park Soyun , Yu Jihnhee , Chess Mitchell , Vali Kaveh 
Published: August 2023

Abstract
Background: We recently developed a preliminary predictive model identifying clinical and radiologic factors associated with the need for surgery following blunt abdominal trauma (BAT) in children. Our aim in this study was to further validate the factors in this predictive model in a multi-institutional study.
Methods: A retrospective chart review of pediatric patients from five pediatric trauma centers who experienced BAT between 2011 to 2020 was performed. Patients under 18 years of age who had BAT and Computed Tomography(CT) abdomen imaging we included. Children with evidence of pneumoperitoneum, and hemodynamicinstability were excluded. Fisher's exact test was used for statistical analysis of the association between the following risk factors and need for laparotomy: Abdominal wall bruising (AWB), abdominal pain/tenderness (APT), thoracolumbar fracture (TLF), presence of free fluid (FF), presence of solid organ injury (SOI). A predictive logistic regression model was then estimated employing these factors.
Findings: 734 patients were identified in this multi-institutional dataset with BAT and abdominal CT imaging, and 726 were included. Of those, 59 underwent surgical intervention (8.8%). Univariate analysis of association between the studied factors and need for surgical management showed that the presence of TLF (p < 0.01), APT (p < 0.01), FF (p < 0.01), and SOI (p < 0.01) were significantly associated. A predictive model was created using the 5 factors resulting in an Area Under the Curve (AUC) of 0.80. For the MVC group, only FF, SOI, and TLF are significantly associated with the need for surgical intervention. The AUC for the MVC group was 0.87.
Conclusions: A clinical and radiologic prediction rule was validated using a large multi-institutional dataset of pediatric BAT patients, demonstrating a high degree of accuracy in identifying children who underwent surgery. FF, SOI, and TLF are the most important factors associated with the need for surgical intervention.
Type of the study: Original research article, Retrospective multi-institutional study Level of Evidence: Level III
Neuronal perception of aversive odor shortens life span in Caenorhabditis elegans
Authors: Sarkar Joyobrata , Vashishth Kshitij , Dixit Anubhuti 
Published: August 2023

Abstract
Sensory perception of a variety of environmental cues is crucial for animal’s survival. However, role of odor perception in longevity and health is incompletely defined. Here, we show that olfactory neuron AWB is essential for inducing the harmful effects of an aversive odor in C. elegans. We found that exposure to 2-nonanone odor reduces life span, brood size and feeding rate, and increases lipid storage in worms. These effects were restored up to wild type levels in mutant worms lacking a functional olfactory AWB neuron. The study substantiates the role of olfaction in regulating life span and health span.
MiR-328-5p functions as a critical negative regulator in early endothelial inflammation and advanced atherosclerosis
Authors: Li Han , Ji Longkai , Han Zhisheng , Li Yingke , Wang Beilei , Liu Xuejia , Zhu Xinxing , Lin Juntang 
Published: August 2023

Abstract
Early proatherogenic inflammation is a major risk factor for the development of atherogenesis. However, the molecular mechanisms underlying this pathological process remain largely unknown. In this study, we have discovered that the microRNA miR-328-5p negatively regulates endothelial inflammation by controlling the stability of JUNB. Disruption of miR-328-5p markedly augments monocyte adhesion to endothelial cells and their transendothelial migration. Consistently, enforced overexpression of miR-328-5p mimics shows a strong resistance to endothelial inflammation characterized by reduced monocyte adhesion with endothelial cells, monocyte transendothelial migration to the endothelium and production of key pro-inflammatory factors. Moreover, miR-328-5p significantly dampens the conversion of macrophages to M1-type polarization. An in vivo study illustrates that miR-328-5p negatively modulates atherosclerotic plaque formation. Interestingly, JUNB, a crucial regulator to trigger inflammatory response, is found to be a direct target for miR-328-5p. Reintroduction of JUNB was able to rescue the significant inhibition of atherosclerosis caused by miR-328-5p. Overall, these findings suggest an inhibitory role of miR-328-5p in proatherogenic process, at least in part, by controlling the abundance of JUNB. Thus, pharmacological targeting of miR-328-5p might be a beneficial strategy for the clinical treatment of inflammatory atherosclerosis.
The global container-shipping network’s survivability evolution based on big data statistics: A computational approach and its empirical evidence
Authors: Yu Anqi , Wang Nuo 
Published: August 2023

Abstract
How to precisely estimate the survivability of the container maritime system is a crucial but unsolved problem. In this paper, we propose an improved container liner network model based on data from global container liner routes and ports of call for several years. Afterward, we applied kernel principal component analysis to reconstruct commonly-used network metrics. As a measure of survivability, we took the critical points of their variance during errors and attacks. We further analysed the evolution of container-shipping network survivability in recent years. Our research revealed that as the ports and density of routes increased over the past few years, the node strength distribution of the container-shipping network became more and more heterogeneous. The robustness increased while the vulnerability aggravated, and both indicators are slowing down. The paper examines how the container-shipping network has evolved in recent years using a model more consistent with container transportation scenarios. By analysing the characteristics and evolutionary trend of the container-shipping network, this paper provides insight into how to take advantage of the changing situation.
Interactive Constituents and Related Analysis of Dynamical Systems in Different Dimensions: Cosmic Evolution Stories
Authors: DEOGHARIA GIRIDHARI 
Published: August 2023

Abstract
A coupled model of variable modified Chaplygin gas (as a candidate of dark energy) and dark matter is assumed in the background of Friedmann-Lemaître-Robertson-Walker universe. $B(a)=B_0a^{-n}$ is assigned in the equation of state for variable modified Chaplygin gas. Since we do not know the actual nature of dark matter and dark energy, it is plausible to assign an interaction between them and for phenomenological requirement, the interaction term is chosen as $Q=3Hc\rho$, $c$ being the coupling parameter and $\rho$ is the total density. Firstly, a two-dimensional autonomous dynamical system is considered for flat universe after considering some suitable dimensionless parameters. Evolutions of those parameters along with the deceleration parameter are observed. Next, evolvements of matter and energy density parameters are studied for variational coupling parameter. Phase portrait analysis is performed to explain present as well as future expansion of universe. Secondly, both three- and four-dimensional dynamical systems are constructed when the evolution of spatially homogeneous and isotropic model of universe is considered, which includes cosmological constant and three-curvature symmetry surfaces. For the three-dimensional system, updatations of dimensionless parameters along with deceleration parameter are analysed for variational coupling parameter with respect to progression of universe. Again, evolutions of deceleration parameter are studied for different values of $n$. Stability analysis for the concerned dynamical system with the help of eigen values is done. The four-dimensional dynamical system is remarkable as it helps to study the evolution of $\Lambda$ density along with other parameters. Lastly, for the concerned dynamical system, evolvements of matter and energy density parameters are analysed for different values of $c$ to study whether coupling parameter affect the ultimate evolution of universe or not. Some constraints of the coupling parameters and n for accelerating universe are discovered. An attractor solution is analysed in the phase portraits, which indicates the present time scenario. Interestingly, for our three-dimensional dynamical system, a super-exponentially accelerated universe is predicted in the near future. Surprisingly, when a four-dimensional dynamical system with the evolution of cosmological constant is considered for a homogeneous and isotropic universe, cosmological constant will dominate variable Chaplygin gas in future.
PACS NO: 95.36.+x, 95.35.+d, 98.80.Cq.
The Significance of INSM1 in the Pathological Diagnosis of Small-Cell Lung Cancer on Biopsy Specimens
Authors: Yan Limin , Zhao Xueli , Chang Liming , Jiang Haixian , Zhang Zhiyong 
Published: August 2023

Abstract
Objective: Our purpose was to investigate the clinicopathological diagnostic value of immunohistochemical antibody for Insulinoma-associated protein 1 (INSM1) in biopsy specimens of small-cell lung cancer.
Methods: Biopsy specimens of small-cell lung cancer diagnosed at the Pathology Department of Tangshan Gongren Hospital from January 2022 to June 2023 were selected. INSM1 expression was detected and compared with conventional neuroendocrine markers Syn, CgA, and CD56 regarding expression sensitivity and specificity.
Results: The sensitivity of INSM1 expression was significantly higher than that of CgA (94.64% vs. 50.00%, P=0.000), but there was no statistically significant difference in the specificity of INSM1, Syn, CgA and CD56 expression (100% vs. 94.00% vs. 98.00% vs. 92.00%, respectively, P=0.241, 1.000, 0.126).
Conclusions: INSM1 antibody shows high sensitivity and specificity in the expression of small-cell lung cancer and serves as a reliable immunohistochemical marker in the clinicopathological diagnosis of small-cell lung cancer in biopsy specimens.
Mechanism of Cr(VI) removal by efficient Cr(VI)-resistant Bacillus mobilis CR3
Authors: Ye Yubo , Hao Ruixia , Shan Bing , Zhang Junman , Li Jiani , Lu Anhuai 
Published: August 2023

Abstract
Cr(VI) is a hazardous environmental pollutant that poses significant risks to both ecosystems and human health. We successfully isolated a novel strain of Bacillus mobilis, strain CR3, from Cr(VI)-contaminated soil. The strain CR3 could show 86.70% removal capacity at 200 mg/L Cr(VI) and also good Cr(VI) removal capacity at different pH, temperature, coexisting ions and electron donor conditions. Different concentrations of Cr(VI) affected the activity of Bacillus mobilis CR3 cells and the removal rate of Cr(VI), and about 3.46% of total Cr was immobilized at the end of the reaction. The combination of SEM-EDS and TEM-EDS analysis showed that Cr accumulated both on the cell surface and inside the cells after treatment with Cr(VI). XPS analysis showed that both Cr(III) and Cr(VI) were present on the cell surface, and FTIR results indicated that the presence of Cr on the cell surface was mainly related to functional groups such as O-H, phosphate groups and -COOH. The removal of Cr(VI) was mainly bioreduction, which primarily occurred outside the cell. Metabolomics analysis revealed upregulation of five metabolites, including phenol and L-carnosine, closely associated with Cr(VI) reduction, heavy metal chelation, and detoxification mechanisms. Additionally, numerous other metabolites linked to cellular homeostasis exhibited differential expression. The presence of Cr(VI) exerted inhibitory effects on division rate and influenced critical pathways like energy metabolism, nucleotide metabolism, and amino acid synthesis and catabolism. These findings reveal the molecular mechanism of Cr(VI) removal by strain CR3 and provide valuable insights for guiding the remediation of Cr(VI)-contaminated sites.
Research on cost-optimal distribution route planning for fresh and live agricultural products from a low-carbon perspective
Authors: Pei Haijian 
Published: August 2023

Abstract
With the continuous development of the domestic economy, the residents' demand for higher and higher quality of agricultural products has made the logistics distribution of fresh and live agricultural products face great challenges. In view of this, this study constructs a fresh and live agricultural products logistics distribution path model based on improved genetic algorithm. Firstly, a cold chain logistics distribution path model from a low carbon perspective is proposed, a local search algorithm (2-opt) is used to optimise two local elements, an initialisation counter count is set to 0 and a suitable maximum number of iterations Gen is set, and finally the route is simulated using improved genetic algorithm analysis, and the logistics distribution path was implemented. The results show that the improved GA algorithm can make the average population fitness closer to the maximum population fitness with fewer iterations, reflecting that the improved algorithm effectively improves the population fitness capability and has a stronger ability to search for optimal solutions; the improved GA obtains a total of $7989.47 for each cost, which is significantly better than the traditional GA algorithm. The improved GA algorithm proposed in this study can effectively optimize the objectives with the lowest total cost and the lowest carbon emission, which can take into account both economic and environmental benefits.
Prediction of methane emissions and electrical energy generation potential from MSW landfill in Khulna city of Bangladesh: A model-based approach
Authors: Setu Salahuddin , Pangkaj K. M. , Rafizul Islam M. , Kraft E. , Berner S. 
Published: August 2023

Abstract
Landfills and open dumps are associated with significant environmental problems, especially in developing countries. The decomposition of organic wastes generates methane (CH4) which is responsible for a significant increase in global warming potential (GWP). This study presents the methane emission from the Rajbandh landfill of Khulna city calculated by different prediction models (ZODM, FODM, MTM, LandGEM-V-3.03). The predicted average emissions from 2000 to 2036, as calculated by FODM, MTM, SP, CAAA, and IC simulations, demonstrate remarkably comparable emission estimates, with values around 2.14 to 2.97 Gg/year. This study compares the output and underlying assumptions of each model while attempting to identify an appropriate approach for estimating methane emissions under the specific conditions of Khulna. In addition, the seasonal variation of methane emission estimation according to SP reveals that the highest rate of methane generation occurs during the monsoon season, while the lowest rate is observed during winter. Moreover, the assessment of the economic feasibility of establishing an electricity generation facility using methane produced from landfilled MSW implies that the Rajbandh landfill site holds the economically viable potential to establish a 1 MW powerplant without subsidy. The total environmental lifetime benefits from this electricity generation project were found 0.563 MMTCO2-eq emissions will be reduced. The outcome of this study may apply to other landfills in Bangladesh and can contribute significantly to waste management planning and energy security.
Antiquity Validation by Amelogenin Peptidomics Profile: Sex Determination in an Ascetic Burial
Authors: Kotli Paula , Morgenstern David , Nagar Yossi , Katina Corine , 'Adawi Zubair , Arbiv Kfir , Boaretto Elisabetta 
Published: August 2023

Abstract

Analyzing human remains often confronts challenges due to poor preservation. Here we resolve a challenge in the characterization of a unique human dental element from a Byzantine ascetic at Khirbat el-Masani’, near Jerusalem. Unfortunately, traditional methods like osteological analysis and radiocarbon dating were unfeasible for sex determination and dating. Our innovation involves peptidomics-based antiquity validation using AmelX recovery spectra, including site specific post-translational modifications (PTMs) and hydrolysis patterns. Our result show that the ancient AmelX exhibited non-enzymatic hydrolysis reflected on significant shorter peptides than modern/control samples. Moreover, tryptophan oxidation emerged as an effective antiquity indicator, compensating for compromised deamidation due to etching process. Also, only one phosphorylated serine (Ser) was detected within AmelX, this last will be lost in a global phosphorylation calculation. Finally, the missing of unique AmelY spectra allow us to classify the remains as a female and, thus, as a Nun. Taken together, we show here that a simple peptidomics workflow is capable to validate antiquity based on physical properties of AmelX peptides in cases that deamidation values are corrupted and determinate sex. We believe our method provides a robust solution for the analysis of samples originating from sites with harsh environmental conditions or challenging collection scenarios for sample preservation.
Enhancement of targeted therapy in combination with metformin on humanbreast cancer models
Authors: Mahmoudi Ghazal , Ehteshaminia Yahya , Kokhaei Parviz , Jalali Seyedeh Farzaneh , Jadidi-Niaragh Farhad , Pagheh Abdol Sattar , Enderami Seyed Ehsan , Kenari Saeid Abedian , Hassannia Hadi 
Published: August 2023

Abstract
Background
Breast cancer remains a primary global health concern due to its limited treatment options, frequent disease recurrence, and high rates of morbidity and mortality. Thereby, there is a need for more effective treatment approaches. The proposal suggests that the combination of targeted therapy with other antitumoral agents could potentially address drug resistance. In this study, we examined the antitumoral effect of combining metformin, an antidiabetic drug, with targeted therapies, including tamoxifen for estrogen receptor-positive (MCF-7), trastuzumab for HER2-positive (SKBR-3), and anti-ROR1 therapy against triple-negative breast cancer (MDA-MB-231).
Methods
Once the expression of relevant receptors on each cell line was confirmed and appropriate drug concentrations were selected through cytotoxicity assays, the antitumor effects of both monotherapy and combination therapy were assessed in in vitro and ex ovo models.
Results
The results exhibited the synergistic effects of metformin when combined with targeted therapy. This combination effectively inhibited cell growth, colony formation, migration, and invasion in vitro. Additionally, it significantly reduced tumor size and metastatic potential in an ex ovo model.
Conclusions
The findings indicate that a favorable strategy to enhance the efficacy of breast cancer treatment would be to combine metformin with targeted therapies.
Central MOTS-c Infusion Affects Reproductive Hormones in Obese and Non-Obese Rats
Authors: OZTURK Dilara ALTAY , ERDEN Yavuz , TEKIN Suat 
Published: August 2023

Abstract
MOTS-c, a mitochondrial-derived peptide, acts as a systemic hormone and MOTS-c level is inversely correlated with markers of obesity. Obesity is a risk factor for male reproductive physiology and is expressed as an important cause of infertility. In this study, we aimed to determine the effects of MOTS-c, which has been proven in the hypothalamus and testicles, on the actors involved in the reproductive axis. In the study, 80 male Wistar-Albino rats were divided into two main groups, obese and non-obese (n = 40). Rats in the first main group were fed with fatty diet feed and obesity was induced. The second main group was fed with normal diet feed. Each main group was divided into 4 small groups (Control, Sham, 10 and 100 µM MOTS-c). The lateral ventricles of the animals in the treatment groups were infused with 10 and 100 µM MOTS-c (solvent in Sham group) for 14 days. At the end of the experiment, hypothalamic Gonadotropin-Releasing Hormone (GnRH) gene expression level, serum testosterone, Luteinizing hormone (LH) and Follicle stimulating hormone (FSH) levels were determined. MOTS-c infusion caused an increase in GnRH mRNA, protein expression levels and serum testosterone, LH and FSH levels in obese and non-obese rats (p < 0.05). MOTS-c administration more significantly upregulated hormone levels in non-obese rats (p < 0.05). Our results reveal that MOTS-c plays a role in the central regulation of reproductive behavior, as well as causes increased LH, FSH and testosterone release. MOTS-c may emerge as a novel regulator for the prevention of obesity-induced infertility.
Hypoxia-inducible factor 3α1 increases epithelial-to-mesenchymal transition and iron uptake to drive colorectal cancer liver metastasis.
Authors: Villareal Luke B , Falcon Daniel M , Xie Liwei , Xue Xiang 
Published: August 2023

Abstract

In the tumor hypoxic environment, three isoforms of hypoxia-inducible factor (HIF)-α activates transcription of genes critical in the adaptive response to low oxygen levels in mammals. Most studies have focused on HIF-1α and HIF-2α, but not HIF-3α. Using RNA-seq, we found that overexpression of HIF-3α1 in colorectal cancer cells resulted in a gene signature of epithelial-mesenchymal transition (EMT) with especially highlyupregulated zinc finger E-box binding homeobox 2 (ZEB2) gene expression. Importantly, the expression of HIF-3α and ZEB2 are highly increased and are positively correlated with each other in human liver metastases. Standard dual luciferase reporter assay showed that ZEB2 is a direct target gene of HIF-3α1. Scratch assay showed that overexpression of HIF-3α1 promoted cancer cell migration whereas ZEB2 knockdown resulted in decreased protein levels of mesenchymal markers and reduced cell migration. As expected, HIF-3α1 overexpression increased colon tumor growth and liver metastasis. Interestingly, HIF-3α1 overexpression increased the master iron importer transferrin receptor (TFRC) and cellular iron levels. Iron chelation reduced HIF-3α overexpression-mediated mesenchymal phenotype, the survival of tumor cells and tumor growth. Together, HIF-3α1 increases the expression of ZEB2 and TFRC to promote iron accumulation, EMT and colon tumor liver metastasis.