bluuebunny/crossref_metadata_2025_split huggingface dataset:
A pan-cancer analysis of DDR1 in prognostic signature and tumor immunity, drug resistance
Authors: Yang Longfei , Zhang Yuwei , Tang Yifan , Wang Yang , Jiang Peng , Liu Fengping , Feng Ninghan 
Published: April 2023

AbstractDisk-like domain receptor 1 (DDR1) is a crucial regulator of pro-inflammatory mediators and matrix-degrading enzymes. Although mounting evidence supports a vital role for DDR1 in the tumorigenesis of some cancers, no pan-cancer analysis of DDR1 has been reported. Therefore, we aimed to explore the prognostic value of DDR1 in 33 cancer types and investigate its potential immune function. We used a range of bioinformatics approaches to explore the potential carcinogenic role of DDR1 in multiple cancers. We found that DDR1 was expressed at high levels in most cancers. DDR1 expression was positively or negatively associated with prognosis in different cancers. DDR1 expression was significantly associated with DNA methylation in 8 cancers, while there was a correlation between DDR1 expression and RNA methylation-related genes and mismatch repair gene in most cancers. Furthermore, DDR1 expression was significantly associated with microsatellite instability in 6 cancers and tumor mutation burden in 11 cancers. In addition, DDR1 expression was also significantly correlated with immune cell infiltration, tumor microenvironment, immune-related genes, and drug resistance in various cancers. In conclusion, DDR1 can serve as a potential therapeutic target and prognostic marker for various malignancies due to its vital role in tumorigenesis and tumor immunity.
Machine learning based prediction for oncologic outcomes of renal cell carcinoma after surgery using Korean Renal Cell Carcinoma (KORCC) database
Authors: Kim Jung Kwon , Lee Sangchul , Hong Sung Kyu , Kwak Cheol , Jeong Chang Wook , Kang Seok Ho , Hong Sung-Hoo , Kim Yong-June , Chung Jinsoo , Hwang Eu Chang , Kwon Tae Gyun , Byun Seok-Soo , Jung Yu Jin , Lim Junghyun , Kim Jiyeon , Oh Hyeju 
Published: April 2023

AbstractWe developed a novel prediction model for recurrence and survival in patients with localized renal cell carcinoma (RCC) after surgery and a novel statistical method of machine learning (ML) to improve accuracy in predicting outcomes using a large Asian nationwide dataset, updated KOrean Renal Cell Carcinoma (KORCC) database that covered data for a total of 10,068 patients who had received surgery for RCC. After data pre-processing, feature selection was performed with an elastic net. Nine variables for recurrence and 13 variables for survival were extracted from 206 variables. Synthetic minority oversampling technique (SMOTE) was used for the training data set to solve the imbalance problem. We applied the most of existing ML algorithms introduced so far to evaluate the performance. We also performed subgroup analysis according to the histologic type. Diagnostic performances of all prediction models achieved high accuracy (range, 0.77–0.94) and F1-score (range, 0.77–0.97) in all tested metrics. In an external validation set, high accuracy and F1-score were well maintained in both recurrence and survival. In subgroup analysis of both clear and non-clear cell type RCC group, we also found a good prediction performance.
Impact of porous microsponges in minimizing myotoxic side effects of simvastatin
Authors: Ali Ahmed U. , Abd-Elkareem Mahmoud , Kamel Amira A. , Abou Khalil Nasser S. , Hamad D. , Nasr Nasr Eldin Hussein , Hassan Maha A. , El Faham Tahani H. 
Published: April 2023

AbstractSimvastatin (SV) is a poorly soluble drug; its oral administration is associated with a significant problem: Myopathy. The present study aims to formulate SV microsponges that have the potential to minimize the myotoxicity accompanying the oral administration of the drug. SV microsponges were prepared by exploiting the emulsion solvent evaporation technique. The % entrapment efficiency (%EE) of the drug approached 82.54 ± 1.27%, the mean particle size of SV microsponges ranged from 53.80 ± 6.35 to 86.03 ± 4.79 µm in diameter, and the % cumulative drug release (%CDR) of SV from microsponges was significantly higher than that from free drug dispersion much more, the specific surface area of the optimized microsponges formulation was found to be 16.6 m2/g revealed the porosity of prepared microsponges. Histological and glycogen histochemical studies in the skeletal muscles of male albino rats revealed that microsponges were safer than free SV in minimizing myotoxicity. These findings were proven by Gene expression of Mitochondrial fusion and fission (Mfn1) & (Fis1) and (Peroxisome proliferator-activated receptor gamma co-activator 1α) PGC-1α. Finally, our study ascertained that SV microsponges significantly decreased the myotoxicity of SV.
Sex-specific differences in the genetic and environmental effects on cardiac phenotypic variation assessed by echocardiography
Authors: Lin Honghuang , Kwan Alan C. , Castro-Diehl Cecilia , Short Meghan I. , Xanthakis Vanessa , Yola Ibrahim M. , Salto Gerran , Mitchell Gary F. , Larson Martin G. , Vasan Ramachandran S. , Cheng Susan 
Published: April 2023

AbstractThe drivers of sexual dimorphism in heart failure phenotypes are currently poorly understood. Divergent phenotypes may result from differences in heritability and genetic versus environmental influences on the interplay of cardiac structure and function. To assess sex-specific heritability and genetic versus environmental contributions to variation and inter-relations between echocardiography traits in a large community-based cohort. We studied Framingham Heart Study participants of Offspring Cohort examination 8 (2005–2008) and Third Generation Cohort examination 1 (2002–2005). Five cardiac traits and six functional traits were measured using standardized echocardiography. Sequential Oligogenic Linkage Analysis Routines (SOLAR) software was used to perform singular and bivariate quantitative trait linkage analysis. In our study of 5674 participants (age 49 ± 15 years; 54% women), heritability for all traits was significant for both men and women. There were no significant differences in traits between men and women. Within inter-trait correlations, there were two genetic, and four environmental trait pairs with sex-based differences. Within both significant genetic trait pairs, men had a positive relation, and women had no significant relation. We observed significant sex-based differences in inter-trait genetic and environmental correlations between cardiac structure and function. These findings highlight potential pathways of sex-based divergent heart failure phenotypes.
Expression and localisation of MUC1 modified with sialylated core-2 O-glycans in mucoepidermoid carcinoma
Authors: Sugiura Takanori , Hashimoto Kazuhiko , Kikuta Kazutaka , Anazawa Ukei , Nomura Takeshi , Kameyama Akihiko 
Published: April 2023

AbstractMucoepidermoid carcinoma (MEC) is the most frequent of the rare salivary gland malignancies. We previously reported high expression of Mucin 1 (MUC1) modified with sialylated core-2 O-glycans in MEC by using tissue homogenates. In this study, we characterised glycan structures of MEC and identified the localisation of cells expressing these distinctive glycans on MUC1. Mucins were extracted from the frozen tissues of three patients with MEC, and normal salivary glands (NSGs) extracted from seven patients, separated by supported molecular matrix electrophoresis (SMME) and the membranes stained with various lectins. In addition, formalin-fixed, paraffin-embedded sections from three patients with MEC were subjected to immunohistochemistry (IHC) with various monoclonal antibodies and analysed for C2GnT-1 expression by in situ hybridisation (ISH). Lectin blotting of the SMME membranes revealed that glycans on MUC1 from MEC samples contained α2,3-linked sialic acid. In IHC, MUC1 was diffusely detected at MEC-affected regions but was specifically detected at apical membranes in NSGs. ISH showed that C2GnT-1 was expressed at the MUC1-positive in MEC-affected regions but not in the NSG. MEC cells produced MUC1 modified with α2,3-linked sialic acid-containing core-2 O-glycans. MUC1 containing these glycans deserves further study as a new potential diagnostic marker of MEC.
Value of thyroid cancer history in the prognosis of pancreatic cancer: a SEER population-based study
Authors: He Jun , Wang Yu , Chen Xiangmei , Chen Wenxiang , Zhou Jianyin 
Published: April 2023

AbstractThyroid cancer patients have a good prognosis, and their long survival increases the likelihood of developing a second primary tumor. Meanwhile, pancreatic cancer (PC) has a poor prognosis and therapeutic efficacy. However, the association between prior thyroid cancer and the subsequent PC prognosis is unknown. Herein, we selected pathologically diagnosed PC patients older than 17 between 2010 and 2015 from the SEER database. We used propensity score matching (PSM) to reduce confounding factors between groups and matched each PC patient with a history of thyroid cancer with 10 PC patients without a history of thyroid cancer. Finally, we selected 103 PC patients with prior thyroid cancer and 1030 PC patients without prior thyroid cancer. Then, we analyzed the factors influencing the overall survival (OS) and the cancer-specific survival (CSS) of PC patients. The median overall survival of PC patients with and without a history of thyroid cancer was 12 and 9 months, respectively. The history of thyroid cancer in PC patients reduced the PC-specific mortality (p < 0.05). Prior thyroid cancer might be a favorable prognostic factor for PC-specific mortality in PC patients.
Giant localized electromagnetic field of highly doped silicon plasmonic nanoantennas
Authors: Alsayed Ahmad E. , Ghanim AbdelRahman M. , Yahia Ashraf , Swillam Mohamed A. 
Published: April 2023

AbstractIn this work, we present the analysis and design of an efficient nanoantenna sensor based on localized surface plasmon resonance (LSPR). A high refractive index dielectric nanostructure can exhibit strong radiation resonances with high electric field enhancement inside the gap. The use of silicon instead of metals as the material of choice in the design of such nanoantennas is advantageous since it allows the integration of nanoantenna-based structures into integrated-optoelectronics circuits manufactured using common fabrication methods in the electronic industry. It also allows the suggested devices to be mass-produced at a low cost. The proposed nanoantenna consists of a highly doped silicon nanorod and is placed on a dielectric substrate. Different shapes and different concentrations of doping for the nanoantenna structures that are resonant in the mid-infrared region are investigated and numerically analyzed. The wavelength of the enhancement peak as well as the enhancement level itself vary as the surrounding material changes. As a result, sensors may be designed to detect molecules via their characteristic vibrational transitions. The 3D FDTD approach via Lumerical software is used to obtain the numerical results. The suggested nanoantennas exhibit ultra-high local field enhancement inside the gap of the dipole structure.
Ultrafast electron dynamics in a topological surface state observed in two-dimensional momentum space
Authors: Reimann J. , Sumida K. , Kakoki M. , Kokh K. A. , Tereshchenko O. E. , Kimura A. , Güdde J. , Höfer U. 
Published: April 2023

AbstractWe study ultrafast population dynamics in the topological surface state of Sb$$_2$$

2

Te$$_3$$

3

in two-dimensional momentum space with time- and angle-resolved two-photon photoemission spectroscopy. Linearly polarized mid-infrared pump pulses are used to permit a direct optical excitation across the Dirac point. We show that this resonant excitation is strongly enhanced within the Dirac cone along three of the six $${\bar{\Gamma }}$$

Γ

¯

–$${\bar{M}}$$

M

¯

directions and results in a macroscopic photocurrent when the plane of incidence is aligned along a $${\bar{\Gamma }}$$

Γ

¯

–$${\bar{K}}$$

K

¯

direction. Our experimental approach makes it possible to disentangle the decay of transiently excited population and photocurent by elastic and inelastic electron scattering within the full Dirac cone in unprecedented detail. This is utilized to show that doping of Sb$$_2$$

2

Te$$_3$$

3

by vanadium atoms strongly enhances inelastic electron scattering to lower energies, but only scarcely affects elastic scattering around the Dirac cone.
An integrated analysis of air pollution and meteorological conditions in Jakarta
Authors: Handhayani Teny 
Published: April 2023

AbstractAir pollution and climate change are general problems for society. This paper proposes an integrated analysis of the Air Quality Index (AQI) and meteorological conditions in Jakarta. The column-based data integration model is applied to create integrated data of the Air Quality Index and meteorological conditions. The integrated data is then used to generate a causal graph using the PC algorithm. The causal graph reveals that there exist causal relationships between pollutants and meteorological conditions, e.g, humidity, rainfall, wind speed, and duration of sunshine affect particulate matter 10 (PM$$_{10}$$

10

); wind speed affects sulfur dioxide (SO$$_2$$

2

); temperature affects ozone (O$$_3$$

3

). The historical data records that the average wind speed is decreased and the number of unhealthy days has risen. Ozone and particulate matter are two pollutants that mainly influence poor air quality in Jakarta. The integrated data is also used to train Long Short-Term Memory (LSTM) and Gated Recurrent Unit (GRU) for forecasting. Experimental results show that LSTM using integrated data produces smaller errors for forecasting AQI and meteorological conditions.
Clinical impact of weight loss on mortality in patients with idiopathic pulmonary fibrosis: a retrospective cohort study
Authors: Lee Ju Kwang , Chung Chiwook , Kim Jiwon , Cho Hyo Sin , Kim Ho Cheol 
Published: April 2023

AbstractPatients with idiopathic pulmonary fibrosis (IPF) often experience weight loss during the follow-up period. However, the prevalence and clinical impact of weight loss in these patients still need to be elucidated. This retrospective single-center study reviewed 134 consecutive patients diagnosed with IPF. Weight loss of 5% or more over 1 year was defined as significant weight loss. Clinical data of patients were compared according to the significant weight loss. We analyzed whether the clinical impact of significant weight loss differed regarding the pirfenidone dose. The median follow-up period was 22.1 months. The mean age of patients was 67.3 years, and 92.5% were men. Of the 134 patients, 42 (31.3%) showed significant weight loss. Multivariate cox regression analysis revealed that significant weight loss was independently associated with mortality (hazard ratio [HR]; 2.670; 95% confidence interval [CI] 1.099–6.484; p = 0.030) after adjusting for lung function and other significant risk factors (6-min walk test distance: HR, 0.993; 95% CI 0.987–0.998; p = 0.005). The median survival of patients with significant weight loss (n = 22) was relevantly shorter than that of those without significant weight loss (n = 43) in the reduced dose pirfenidone group (28.2 ± 3.3 vs. 43.3 ± 3.2 months, p = 0.013). Compared with patients without significant weight loss (n = 38), patients with significant weight loss (n = 15) also showed a marginally-significant shorter survival in the full-dose pirfenidone group (28.9 ± 3.1 vs. 39.8 ± 2.6 months, p = 0.085). Significant weight loss is a prognostic factor in patients with IPF regardless of pirfenidone dose. Vigilant monitoring might be necessary to detect weight loss during the clinical course in these patients.
Hepatic phosphate uptake and subsequent nerve-mediated phosphaturia are crucial for phosphate homeostasis following portal vein passage of phosphate in rats
Authors: Yasuda Seiichi , Inoue Kazunori , Matsui Isao , Matsumoto Ayumi , Katsuma Yusuke , Okushima Hiroki , Imai Atsuhiro , Sakaguchi Yusuke , Kaimori Jun-ya , Yamamoto Ryohei , Mizui Masayuki , Isaka Yoshitaka 
Published: April 2023

AbstractFibroblast growth factor 23, parathyroid hormone, and 1,25-dihydroxyvitamin D are critical in phosphate homeostasis. Despite these factors’ importance, regulators of phosphaturia in the acute postprandial phase remain largely unknown. This study investigated the mechanism of acute phosphate regulation in the postprandial phase in rats. Duodenal administration of radiolabeled phosphate (32P) showed that 32P levels in the inferior vena cava (IVC) blood were lower than those in the portal vein (PV) blood. Serum phosphate concentration transiently increased 5 min after phosphate solution administration through IVC, while it was maintained after the administration through PV. Phosphate administration through both IVC and PV resulted in increased fractional excretion of phosphate (FEPi) at 10 min without elevation of the known circulating factors, but urinary phosphate excretion during the period was 8% of the dose. Experiments using 32P or partial hepatectomy showed that the liver was one of the phosphate reservoirs. The elevation of FEPi and suppression of sodium-phosphate cotransporter 2a in the kidney at 10 min was attenuated in rats with SCH23390, hepatic denervation, or renal denervation, thus indicating that the liver communicated with the kidney via the nervous system to promote phosphaturia. These results revealed previously unknown mechanisms for serum phosphate maintenance.
Quantum transports in two-dimensions with long range hopping
Authors: Wang Si-Si , Li Kangkang , Dai Yi-Ming , Wang Hui-Hui , Zhang Yi-Cai , Zhang Yan-Yang 
Published: April 2023

AbstractWe investigate the effects of disorder and shielding on quantum transports in a two dimensional system with all-to-all long range hopping. In the weak disorder, cooperative shielding manifests itself as perfect conducting channels identical to those of the short range model, as if the long range hopping does not exist. With increasing disorder, the average and fluctuation of conductance are larger than those in the short range model, since the shielding is effectively broken and therefore long range hopping starts to take effect. Over several orders of disorder strength (until$$\sim 10^4$$∼104times of nearest hopping), although the wavefunctions are not fully extended, they are also robustly prevented from being completely localized into a single site. Each wavefunction has several localization centers around the whole sample, thus leading to a fractal dimension remarkably smaller than 2 and also remarkably larger than 0, exhibiting a hybrid feature of localization and delocalization. The size scaling shows that for sufficiently large size and disorder strength, the conductance tends to saturate to a fixed value with the scaling function$$\beta \sim 0$$β∼0, which is also a marginal phase between the typical metal ($$\beta >0$$β>0) and insulating phase ($$\beta <0$$β<0). The all-to-all coupling expels one isolated but extended state far out of the band, whose transport is extremely robust against disorder due to absence of backscattering. The bond current picture of this isolated state shows a quantum version of short circuit through long hopping.
Clinical prognostic value of OSGIN2 in gastric cancer and its proliferative effect in vitro
Authors: Wang Peipei , Zhu Ying , Jia Xinru , Ying Xiangchang , Sun Leitao , Ruan Shanming 
Published: April 2023

AbstractThis study explored the promoting effect of oxidative stress-induced growth inhibitor family member 2(OSGIN2) on gastric cancer (GC) through public databases and in vitro experiments. The potential relationship between OSGIN2 expression, prognosis, functional enrichment of associated differential genes, immune infiltration, and mutational information in gastric cancer were comprehensively investigated using bioinformatics analysis. OSGIN2 was knocked down using small interfering RNA (siRNA) transfection for subsequent cell function testing. The results showed that gastric carcinoma cells and tissues contained high levels of OSGIN2, which was associated with a poor prognosis for GC patients. It was important in the cell cycle, autophagy, etc., and was related to a variety of tumor-related signal pathways. Knockdown of OSGIN2 inhibited tumor cell proliferation and contributed to cell cycle arrest. It was also correlated with tumor immune infiltrating cells (TILs), affecting antitumor immune function. Our analysis highlights that OSING2, as a new biomarker, has diagnostic and prognostic value in gastric cancer and is a potentially effective target in GC treatment.
The apoptotic effects of soybean agglutinin were induced through three different signal pathways by down-regulating cytoskeleton proteins in IPEC-J2 cells
Authors: Pan Li , E Tianjiao , Xu Chengyu , Fan Xiapu , Xia Jiajia , Liu Yan , Liu Jiawei , Zhao Jinpeng , Bao Nan , Zhao Yuan , Sun Hui , Qin Guixin , Farouk Mohammed Hamdy 
Published: April 2023

AbstractSoybean agglutinin (SBA) is a main anti-nutritional factor in soybean. SBA exhibits its anti-nutritional functions by binding to intestinal epithelial cells. Keratin8 (KRT8), Keratin18 (KRT18) and Actin (ACTA) are the representative SBA-specific binding proteins. Such cytoskeletal proteins act a crucial role in different cell activities. However, limited reports reveal what the signal transduction pathway of apoptosis caused by SBA when binding to KRT8, KRT18 and ACTA. We aimed to evaluate the effects of SBA on cell apoptosis and the expression of the cytoskeletal protein (KRT8, KRT18 and ACTA), reveal the roles of these cytoskeletal proteins or their combinations on SBA-induced cell apoptosis in IPEC-J2 cell line, evaluate the influences of SBA on the mitochondria, endoplasmic reticulum stress and death receptor-mediated apoptosis signal pathway and to show the roles of KRT8, KRT18 and ACTA in different apoptosis signal pathways induced by SBA. The results showed that SBA induced the IPEC-J2 cell apoptosis and decreased the mRNA expression of KRT8, KRT18 and ACTA (p < 0.05). The degree of effect of three cytoskeleton proteins on cell apoptosis was ACTA > KRT8 > KRT18. The roles of these three cytoskeletal proteins on IPEC-J2 apoptotic rates had a certain accumulation effect. SBA up-regulated mitochondrial fission variant protein (FIS1) and fusion protein (Mfn2) promoted CytC and AIF in mitochondria to enter the cytoplasm, activated caspase-9 and caspase-3, damaged or declined mitochondrial function and reduced ATP synthesis (p < 0.05). Also, SBA up-regulated the expression of GRP78, XBP-1, eIF2α, p-eIF2α and CHOP (p < 0.05), down-regulated the expression level of ASK1 protein (p < 0.05). SBA led to the recruitment of FADD to the cytoplasmic membrane and increased the expression of FasL, resulting in caspase-8 processing. SBA up-regulated the expression level of Bax protein and decreased cytosolic Bcl-2 and Bid (p < 0.05). In addition, there was a significant negative correlation between the gene expression of cytoskeleton proteins and apoptosis, as well as the expression of key proteins of apoptosis-related signal transduction pathways. In conclusion, SBA induced the activation of the mitochondria, endoplasmic reticulum stress and the death receptor-mediated apoptosis signal pathway and the crosstalk between them. The effect of SBA on these three pathways was mainly exhibited via down-regulation of the mRNA expression of the three cytoskeletal expressions. This study elucidates the molecular mechanism and signaling pathway of SBA that lead to apoptosis from the perspective of cell biology and molecular biology and provides a new perspective on the toxicity mechanism of other food-derived anti-nutrients, medical gastrointestinal health and related cancer treatment.