bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of cuproptosis-related subtypes, construction of a prognostic model, and characterization of the tumor immune microenvironment in gastric cancer
Authors: Xin Dao , Man Yuxin , Yang Yalan , Wang Feng 
Published: May 2022

Abstract
Background: Gastric cancer represents a significant global public health burden worldwide. Although treatment strategies are continuously improving, the overall prognosis remains poor. Cuproptosis is a newly discovered form of cell death, and the relationship between cuproptosis in tumor immune microenvironment (TIME) and prognosis in STAD has hitherto not been reported.Methods: Stomach adenocarcinoma (STAD) data were downloaded from TCGA and GEO databases. Bioinformatics analysis was performed to construct a cuproptosis-related risk model and identify cancer subtypes. The association between TIME and risk score was comprehensively explored.Results: STAD samples were stratified into three subtypes according to prognostic cuproptosis gene expression. A cuproptosis risk model was constructed and validated based on the expression of 5 genes (RPL39L, PEG10, SYNPO2, MMP11, and KRT17). The model was significantly associated with the prognosis of STAD patients and TIME, including immune cell infiltration, microsatellite instability (MSI) status, tumor mutational burden (TMB) score, immune checkpoint, and human leukocyte antigen (HLA) gene expression. A prognostic nomogram based on the cuproptosis risk score was additionally constructed.Conclusion: We identified a practical prognostic model based on cuproptosis-related genes in STAD and comprehensively established the relationship between cuproptosis and tumor immunity. Further research is warranted on the predictive value of the cuproptosis risk score during immunotherapy in gastric cancer patients in clinical practice and the molecular mechanisms by which cuproptosis influences the TIME.
Understanding 2D MoSe2 grown by CVD
Authors: Fernandes João , Grzonka Justyna , Rodrigues João , Santos João , Bondarchuk Oleksandr , Ferreira Paulo , Alpuim Pedro , Capasso Andrea 
Published: May 2022

Abstract
Extended research on 2D transition metal dichalcogenides (TMDC) revealed viable routes to apply these materials in the semiconductor and (opto)electronic industry. However, fully reproducible methods for the wafer-scale production of crystalline and uniform 2D TMDCs have yet to be established. In this work, atomically thin MoSe2 films were grown on a Si/SiO2 substrate by a standard atmospheric-pressure chemical vapor deposition (CVD) using Se and MoO3 powder precursors. The samples were transferred from the original substrate by using water-soluble polymers as supporting materials, which allowed a clean and efficient transfer process. Extensive characterization was performed via Raman and photoluminescence spectroscopy, atomic force microscopy, transmission electron microscopy and X-ray photoelectron spectroscopy. The CVD growth led to cm-sized, few-layer polycrystalline MoSe2 films made of sub-µm crystalline grains, which are randomly orientated grains and different in lateral size, forming overall fragmented structures. The grains present varying thickness, from bilayer (weakly photoluminescent) to multilayer. Additionally, the different multilayer stacking orientations found on the grown samples give rise to different material phases, as confirmed by TEM. These features need to be taken into consideration for the fabrication of MoSe2-based devices.
FAT4 Overexpression in Peripheral Blood Mononuclear Cells and Tumor Tissues is Associated With a Favorable Prognosis and Promotes Immune Cell Infiltration in Hepatocellular Carcinoma
Authors: Li Jing , Huang Qi , Lv Minling , Zhang Renjie , Ma MengQing , Hu Rui , Zhong Xin , Sun Xinfeng , Feng Wenxing , Han Zhiyi , Ma Wenfeng , Zhang Wei , Zhou Xiaozhou 
Published: May 2022

Abstract
Purpose: To identify prognostically relevant genes in hepatocellular carcinoma, and to investigate whether gene expression in peripheral blood mononuclear cells (PBMCs) and hepatocellular carcinoma tissues can be used as a diagnostic and prognostic marker. Methods: Using RNA-sequencing, gene expression was examined in PBMCs from patients with advanced hepatocellular carcinoma who survived or died. The expression of the top 10 genes in the survival group was validated.Results: The Gene Expression Omnibus and The Cancer Genome Atlas databases were used to analyze FAT atypical cadherin 4 (FAT4) transcript levels in PBMCs and in hepatocellular carcinoma and normal tissues. FAT4 expression was lower in hepatocellular carcinoma than in normal PBMCs and tissues. Kaplan–Meier analysis suggested that downregulated FAT4 was associated with a relatively poor prognosis. The correlation between FAT4 expression and immune cell infiltration was also explored using Tumor Immune Estimation Resource, Gene Expression Profiling Interactive Analysis 2, and the Tumor and Immune System Interaction Database. FAT4 overexpression was positively correlated with immune cell infiltration, several immune cell markers, and immune checkpoint expression. MicroRNAs regulating FAT4 expression were identified using correlation, expression, and survival analyses. Hsa-miR-93-5p was the most likely upstream microRNA of FAT4 in hepatocellular carcinoma.Conclusion: FAT4 is highly expressed in PBMCs and hepatocellular carcinoma tissues, indicating a favorable prognosis and immune cell infiltration in hepatocellular carcinoma, and revealing the potential role of miRNA-93-5p-mediated downregulation of FAT4 in hepatocellular carcinoma immunology. Our findings provide a new direction for the development of novel immunotherapy targets for hepatocellular carcinoma.
High body temperature increases microbiota-dependent host resistance to influenza A virus and SARS-CoV-2 infection
Authors: Ichinohe Takeshi , Nagai Minami , Moriyama Miyu , Ishii Chiharu , Mori Hirotake , Watanabe Hikaru , Nitta Yuuka , Arimitsu Noriko , Nishimoto Moe , Nakahara Taku , Yamada Takuji , Ishikawa Dai , Ishikawa Takamasa , Hirayama Akiyoshi , Kimura Ikuo , Nagahara Akihito , Naito Toshio , Fukuda Shinji 
Published: May 2022

Abstract
While a common symptom of influenza and coronavirus disease 2019 (COVID-19) is fever, its physiological role on host resistance to viral infection remains less clear. Here, we demonstrate that exposure of mice to the high ambient temperature of 36 °C increase host resistance to viral pathogens including influenza virus and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). High heat-exposed mice increase basal body temperature over 38 °C to enable more bile acids production in a gut microbiota-dependent manner. The microbiota-derived deoxycholic acid (DCA) and its plasma membrane-bound receptor Takeda G-protein-coupled receptor 5 (TGR5) signaling increase host resistance to influenza virus infection by suppressing virus replication and neutrophil-dependent tissue damage. Furthermore, the DCA and its nuclear farnesoid X receptor (FXR) agonist protect Syrian hamster from lethal SARS-CoV-2 infection. Moreover, we demonstrate that certain bile acids are reduced in the plasma of COVID-19 patients who developed moderate I/II disease compared with minor illness group. These findings uncover an unexpected mechanism by which virus-induced high fever increases host resistance to influenza virus and SARS-CoV-2 in a microbiota-dependent manner.
Predicting Probabilistic Causes of Colorectal and Gastric Cancers using Bayesian Networks
Authors: Zarei Masoud , Naghibzadeh-Tahami Ahmad , Haghdoost Ali Akbar , Karamoozian Ali 
Published: May 2022

Abstract
Introduction: Being aware of the relationships between risk and protective factors could be helpful to control and prevent diseases. The disease system analysis will be more complex with increasing risk and protective factors. Therefore, in this article, we use Bayesian Networks (BNs) to investigate the relationship between variables and predict the probabilistic causes of colorectal and gastric cancers.Methods: In this study, structure learning algorithms were score-based (hill-climbing) and hypothetical. Parameter learning was estimated by Bayesian method. Network scores (AIC, BIC and BDe), cross-validation methods, and Bayes factor were used to compare both structure learning algorithms and indicate the optimal structure. Data were analyzed by bnlearn R package (ver. 3.0.4). Results: The variables age, gender, smoking, hookah, alcohol, opium, diet, and family history were involved in colorectal and gastric cancers. In both Hill-Climbing and hypothetical algorithms, the odds of developing colorectal and gastric cancers in opium users were (OR = 4.31, OR = 4.35) and (OR = 5.85, OR = 6.06), respectively. Comparing the hypothetical algorithm with network scores and cross-validation showed the hypothetical algorithm was appropriate for colorectal and gastric cancer data. Conclusion: BNs are probabilistic graphical models that demonstrate the cause-and-effect relationship between variables as graphical networks. This method could be beneficial and effective in the fields of biology, medicine, and epidemiology for predicting uncertainty and supporting expert opinions.
WITHDRAWN: The Study on Angiotensin II Induced-Ferroptosis in Vascular Endothelial Cells
Authors: fang hong , liu Chi , Cavdar Omer , Shen Yi 
Published: May 2022

Abstract
PurposeTo verify the effect of Angiotensin II on ferroptosis in vascular endothelial cells and clarify the related mechanism. MethodsHUVECs were evaluated for p53, P21,ALOX12, VEGF, MDA,GSH. Molecular marker impact upon AngII-induced ferroptosis was evaluated with students’ t-test，one-way analysis of variance (ANOVA).ResultsAs the concentration of Ang II increased，the level of ALOX12, P53,GSH and MDA increased in HUVECs. The expression of VEGFA in HUVECs is negatively correlated with dose of Ang II. Incubation of HUVECs in AngII and valsartan for 48hr reduces ALOX12, P21, GSH and MDA. Compared with the single AngII group, ALOX12, P21, GSH and MDA in valsartan group was decreased significantly（p=0.000）.In pifithrin-α hydrobromide-treated, ALOX12, P21, GSH and MDA was reduced significantly, as compared to valsartan group（p=0.000）. The most larger reduction in ALOX12, P21,GSH and MDA was pifithrin - α hydrobromide combined with valsartan group. In contrast, the expression of VEGFA increased significantly after HUVECs were treated with pifithrin - α hydrobromide and valsartan（p=0.000）.ConclusionsAngII can induce ferroptosis of vascular endothelial cells in a dose-dependent manner. The mechanism of AngII-induced ferroptosis may be regulated through the signal axis of ATR1,2-p53-ALOX12.
Determination of salt concentration in water using decision trees and electromagnetic waves
Authors: Efeoglu Ebru , Tuna Gurkan 
Published: May 2022

Abstract
Salt water adversely affects human health and plant growth. In parallel with the increasing interest in non-contact determination of salt concentration in water, a novel approach is proposed in this study. In the proposed approach, S parameter measurements, which show the scattering properties of electromagnetic waves, are used. First, the relationship between salt concentration in water and permittivity values, a distinguishing feature for liquids, is shown. Then, based on the derived correlations from a set of S parameter measurements, it is shown that the salt concentration in water can be predicted. Finally, after exactly determining the relations of permittivity, salt concentration and S parameter, a system that allows non-contact determination of salt concentration is proposed. Since the proposed system makes its prediction using a classifier, decision tree algorithms are employed for this purpose. In order to evaluate the appropriateness and success of the algorithms, a set of classification experiments were held using various water samples with different levels of salt concentration. The results of the classification experiments show that the Hoeffding tree algorithm achieved the best results and is the most suitable decision tree algorithm for determining the salt concentration of liquids. For this reason, the proposed non-contact approach can be used to determine the salt concentration in water reliably and quickly if its hardware and software components can be embedded into a prototype system.
HIGHLIGHTS Showing the relationship between salt concentration in water and permittivity values. Predicting salt concentration. Proposing a system that allows non-contact determination of salt concentration.
Trace elements, anions, and carbohydrates in the recirculating aquaculture system using woodchip denitrification, constructed wetland, and sand infiltration
Authors: Lindholm-Lehto Petra Camilla , Lindroos Antti-Jussi , Pulkkinen Jani Tapio , Kiuru Tapio , Vielma Jouni 
Published: May 2022

Abstract
A recirculating aquaculture system (RAS) aims to achieve fish production with negligible discharge into the environment. RASs have been applied for fish production in several countries, but nitrate removal is often a limiting factor for production increases. In this study, a pilot-scale RAS (10 tons of fish/year) was connected to a water treatment field which consisted of a denitrifying woodchip bioreactor (9 m × 14 m) filled with birch woodchips (Betula pendula), a constructed wetland (7.5 m × 6 m), and sand infiltration (16 m × 31 m) to achieve high water quality with low-maintenance treatment units. In the constructed wetland, a perennial common reed (Phragmites australis) was used in a well-drained soil for nutrient re-use. Concentrations of different elements, diluted anions, and selected hydrocarbons were monitored and quantified. Some Mn leaching occurred during the sand infiltration stage. However, Mn concentrations decreased towards the end of the experiment. Concentrations of total-Fe increased up to 2.75 mg L−1 and Mn up to 5 mg L−1 in the sand infiltration stage of the water treatment field, probably due to anoxic conditions and leaching of fine particles. This type of process design offers effective but low-maintenance treatment of circulating water.
Isolation of napin from Brassica nigra seeds and coagulation activity to turbid pond water
Authors: Khaliq Binish , Sarwar Hamsa , Akrem Ahmed , Azam Mehvish , Ali Naila 
Published: May 2022

Abstract
Approach to fresh water is limited due to the growing world population and supply of clean drinking water is a global challenge. Pond water is widely used for drinking in developing countries and it has higher turbidity during rainy seasons. This purpose requires a large number of chemical coagulants that lead to a high cost of treatment. Therefore there is a need to find an economical and natural coagulant to treat turbid water. Coagulation activity is an ability of a liquid, changing to a solid or semi-solid state after sometime period of time. This study focuses on the isolation of coagulant proteins from Brassica nigra seeds responsible for water clarification. The coagulant protein (napin) was purified, quantified and identified. Napin protein was precipitated with 70% saturation of ammonium sulfate solution combined with dialysis and size-exclusion chromatography. SDS-PAGE showed that isolated napin has a molecular weight of 16 kDa. Protein quantification was done by using a NanoDrop spectrophotometer. The coagulation activity of the napin protein was measured against synthetic clay solution and turbid pond water. The coagulation assay results showed that napin protein from Brassica nigra has 85% and Moringa seeds extract has 87% coagulation activity against the synthetic clay solution after 120 min. However, the coagulation activity of napin protein against the turbid pond water was higher 85% compared to Moringa seed extract of 80%. The active coagulant napin protein would be helpful in establishing cheaper methods in scaling up the coagulant protein from the Brassica nigra seeds acting as a potential agent for water treatment.
A Systematic Review of Nonclinical Studies on the Effect of Curcumin in Chemotherapy- induced Cardiotoxicity
Authors: Armandeh Maryam , Bameri Behnaz , Samadi Mahedeh , Heidari Shima , Foroumadi Roham , Abdollahi Mohammad 
Published: May 2022

Background:Various anticancer drugs are effective therapeutic agents for cancer treatment; however, they cause severe toxicity in body organs. Cardiotoxicity is one of the most critical side effects of these drugs. Based on various findings, turmeric extract has positive effects on cardiac cells.Objective:This study aims to evaluate how curcumin, as the main component of turmeric, may affect chemotherapy- induced cardiotoxicity.Method:A database search was performed up to April 2021 using “curcumin OR turmeric OR Curcuma longa” and “chemotherapy-induced cardiac disease”, including their equivalents and similar terms. After screening the total articles obtained from the electronic databases, 25 relevant articles were included in this systematic review.Results:The studies demonstrate lower body weight and increased mortality rates due to doxorubicin administration. Besides, cancer therapeutic agents induced various morphological and biochemical abnormalities compared to the non-treated groups. Based on most of the obtained results, curcumin at nontoxic doses can protect the cardiac cells mainly through modulating antioxidant capacity, regulation of cell death, and antiinflammatory effects. Nevertheless, according to a minority of findings, curcumin increases the susceptibility of the rat cardiomyoblast cell line (H9C2) to apoptosis triggered by doxorubicin.Conclusion:According to most nonclinical studies, curcumin could potentially have cardioprotective effects against chemotherapy-induced cardiotoxicity. However, based on limited, contradictory findings demonstrating the function of curcumin in potentiating doxorubicin-induced cardiotoxicity, well-designed studies are needed to evaluate the safety and effectiveness of treatment with new formulations of this compound during cancer therapy.
Nigella sativa Oil Alleviates Mouse Testis and Sperm Abnormalities Induced by BPA Potentially through Redox Homeostasis
Authors: Alghazeer Rabia O. , Al-Griw Mohamed A. , Shalabi Suliman M. , Elnfati Abdul H. , Treesh Soad A. , Benjama Ahmeda E. , Shamlan Ghalia , Habibullah Mahmmoud M. , Eskandrani Areej A. , Alnajeebi Afnan M. , Babteen Nouf A. , Alansari Wafa S. 
Published: May 2022

Background & Aim:Significant evidence indicates that endocrine disrupted bisphenol A (BPA) seriously endangers human health. In males, BPA affects testis architecture and sperm quality, and ultimately reduces fertility. This study explored the therapeutic potential of Nigella sativa (NS) seed extract on testis and sperm abnormalities in BPA-exposed mice and characterized the underlying mechanism.Methods:Forty male Swiss albino mice (5.5 weeks old, N = 8 per group) were randomly divided into five groups: Group I, normal control, Group II, vehicle control (sterile corn oil); Group III, NS-exposed (oral 200 mg/kg); Group IV, BPA-exposed (oral 400 μg/kg body weight); Group V, BPA + NS-exposed mice. Animals were treated for 6 weeks and sacrificed for biochemical and histological examination.Results:The results indicated that BPA exposure results in significant testis and sperm abnormalities. Specifically, BPA promoted a marked reduction in the body and testis compared with the control group. Histopathological findings showed that BPA caused a widespread degeneration of spermatogenic cells of the seminiferous epithelium, decreased sperm counts and motility, and augmented sperm abnormalities, and whereas little alteration to sperm DNA was observed. In addition, BPA increased the levels of the lipid peroxidation marker, malondialdehyde (MDA), and reduced the levels of the antioxidant marker, reducing glutathione (GSH). Treatment with NS oil extract during BPA exposure significantly alleviated testis and sperm abnormalities, reduced MDA levels, and enhanced GSH levels.Conclusions:The results demonstrate that NS oil protects mice against BPA-induced sperm and testis abnormalities, likely by suppressing levels of the oxidative stress marker, MDA, and enhancing the levels of the antioxidant marker, GSH.
Accounting Conformational Dynamics into Structural Modeling Reflected
by Cryo-EM with Deep Learning
Authors: Yang Zhiwei , Ye Qiushi , Zhao Yizhen , Li Xuhua , Zhao Yimin , Fu Xinyue , Zhang Shengli , Zhang Lei 
Published: May 2022

Abstract:
With the continuous development of structural biology, the requirement for accurate
three-dimensional structures during functional modulation of biological macromolecules is increasing.
Therefore, determining the dynamic structures of bio-macromolecular at high resolution has
been a high-priority task. With the development of cryo-electron microscopy (cryo-EM) techniques,
the flexible structures of biomacromolecules at the atomic resolution level grow rapidly.
Nevertheless, it is difficult for cryo-EM to produce high-resolution dynamic structures without a
great deal of manpower and time. Fortunately, deep learning, belonging to the domain of artificial
intelligence, speeds up and simplifies this workflow for handling the high-throughput cryo-EM
data. Here, we generalized and summarized some software packages and referred algorithms of
deep learning with remarkable effects on cryo-EM data processing, including Warp, user-free preprocessing
routines, TranSPHIRE, PARSED, Topaz, crYOLO, and self-supervised workflow, and
pointed out the strategies to improve the resolution and efficiency of three-dimensional reconstruction.
We hope it will shed some light on the bio-macromolecular dynamic structure modeling with
the deep learning algorithms.
Emodin Reduces Inflammatory and Nociceptive Responses in Different
Pain-and Inflammation-Induced Mouse Models
Authors: Li Jing , Zhang Xiuli , Guan Lili 
Published: May 2022

Aim:
Different nociceptive models induced with heat and chemicals were used to assess
the potency of emodin in alleviating pain. The anti-inflammatory properties of emodin at different
doses were also assessed using different anti-inflammatory in vivo models.

Objective:
Pain management is a global problem nowadays, and nonsteroidal anti-inflammatory
drugs (NSAIDs) are commonly prescribed to assuage inflammation and alleviate pain. Prolonged
usage of these NSAIDs triggers various adverse drug reactions (ADRs). The dose-dependent effect
of emodin was assessed by treating mice with three different doses (5, 10, and 20 mg/kg bwt) of
emodin.

Methods:
The effects of emodin in various nociceptive and inflammatory models were assessed.
The anti-nociceptive potential of emodin was evaluated with the hot plate and tail immersion tests.
The effects of emodin on acetic acid-, glutamate-, capsaicin-, and formalin-stimulated pain models
were examined. The anti-inflammatory potency of emodin was examined in a carrageenan-induced
inflammatory model. The sedative effect of emodin was assessed by an open field test.

Results:
Emodin potentially prevented the nociception provoked by thermal stressors during the
hot plate and tail immersion methods and from chemical stressors such as acetic acid, formalin,
capsaicin, and glutamate. The anti-inflammatory action of emodin was evidenced by carrageenaninduced
paw edema and peritoneal leukocyte penetration. The open field results confirmed that
emodin induced a mild sedative effect on the treated mice.

Conclusion:
Our overall results obtained from this study confirmed that emodin exhibits potent anti-
nociceptive and anti-inflammatory effects.