bluuebunny/crossref_metadata_2025_split huggingface dataset:
Development and validation of a novel immune-related prognostic signature in lung squamous cell carcinoma patients
Authors: Liu Xianyu , Shan Yunhan , Zhao Deze , Cui Weifang , Xie Qun , Jiang Junjie , Peng Wei , Zhang Chunfang , Duan Chaojun 
Published: July 2022

Abstract
Background. Lung Squamous Cell Carcinoma (LUSC) is an aggressive malignancy with limited therapeutic options. The response to immune therapy is a determining factor for the prognosis of LUSC patients. This study aimed to develop a reliable immune-related prognostic signature in LUSC.Methods. We extracted gene expression and clinical data of LUSC from The Cancer Genome Atlas (TCGA). A total of 502 patients enrolled and were divided into respond and non-respond groups by the TIDE algorithm. The CIBERSORT algorithm and the LM22 gene signature were used to analyze the distribution of immune cells in LUSC. Efficacy and response strength of immunotherapy are calculated by the tumor mutation burden (TMB) and ESTIMATE Score. Differentially expressed genes (DEGs) between the two groups were analyzed. The differential expression genes related to overall survival were pointed as hub DEGs, and a prognostic signature was constructed with lasso regression analysis.Results. LUSC patients were divided into responder and non-responder groups based on the response to immunotherapy. The distribution of immune cells was significantly different between the two groups. Forty-four DGEs were considered as overall survival-related genes. A prognostic signature was constructed, consisting of 11 hub-DGEs, including MMP20, C18orf26, CASP14, FAM71E2, OPN4, CGB5, DIRC1, C9orf11, SPATA8, C9orf144B, and ZCCHC5. The signature can accurately distinguish LUSC patients into high and low-risk groups. Moreover, the high-risk group had a shorter survival time than the low-risk group. The area under the ROC curve was 0.67. The multivariate Cox regression showed that the risk score calculated by the constructed signature was an independent prognostic predictor for LUSC patients.Conclusion. In short, we established a novel immune-related prognostic signature in LUCS, which has significant sensitivity and accuracy in predicting the prognosis of patients. Our research can guide the evaluation of the prognosis of LUSC patients in clinical, and the discovered immune-related genes can provide a theoretical basis for the discovery of new therapeutic targets.
Endometrial stem cell-derived exosomes repair cisplatin-induced premature ovarian failure via Hippo/YAP pathway
Authors: Wang Lijun , Wang Lihui , Wang Rongli , Xu Ting , Wang Jingyuan , Cui Zhiwei , Cheng Feiyan , Wang Wei , Yang Xinyuan 
Published: July 2022

Abstract
Background: Stem cells have been documented as a new therapeutic method for ovarian injuries such as premature ovarian failure (POF). However, effects of exosomes (Exos) derived from human endometrial stem cells (EnSCs) on diminished ovarian failure remain to be carefully elucidated. Our study aims to investigate the mechanisms of EnSC-Exos in the recovery of the cisplatin-induced granulosa cell injury model in vitro or POF mouses model in vivo and whether the Hippo signal pathway is involved in the regulation. Methods: Exosomes derived from human EnSCs were isolated by ultracentrifugation and identified by electron microscopy and western blot (WB) analysis, stained by PKH26, respectively. The mechanism involving suppression of Hippo signaling pathway and activation of Yes-associated protein (YAP) was investigated for evaluating EnSC-Exos therapeutic effects in the cisplatin-induced granulosa cell injury model in vitro using flow cytometry, WB, qRT-PCR, immunofluorescence and EdU staining. Hematoxylin-eosin staining, ELISA and immunohistochemistry analysis were used for evaluating EnSC-Exos therapeutic effects in POF mouses model.Results: In this study, we established successful construction of the cisplatin-induced granulosa cell injury model and evaluated Hippo signaling pathway activation in cisplatin-damaged granulosa cells (GCs). Furthermore, laser scanning confocal microscope and immunofluorescence demonstrated that EnSC-Exos can be transferred to cisplatin-damaged GCs to decrease apoptosis. In addition, the enhanced expression of YAP at the protein level as well as YAP/TEAD target genes, such as CTGF, ANKRD1 and the increase of YAP into the nucleus in immunofluorescence staining after the addition of EnSC-Exos to cisplatin-damaged GCs confirmed the suppression of Hippo signaling. While in vivo, EnSC-Exos successfully remedied POF in a mouse model. Conclusions: Collectively, our findings suggest that human EnSC-Exos is effective in recovery of ovarian function by chemotherapy-induced POF via activating YAP and inhibiting the Hippo signaling pathway. These findings provide new insights for further understanding of EnSC-Exos in the recovery of ovary function.
Study on the interaction mechanism between Crocus sativus and Fusarium oxysporum based on dual RNA-seq
Authors: Luo Juan , Zhang Aolai , Tan Kaifeng , Yang Shuting , Ma Xiaona , Bai Xiaolin , Hou Yutong , Bai Jie 
Published: July 2022

Abstract
Fusarium oxysporum is a widely distributed soil-borne fungus, which is the most serious pathogen in Crocus sativus production. Due to the lack of resistant cultivars of saffron，and the unclear disease resistance and pathogenic mechanism, there is no really effective control method at present. In this study, the process of F.oxysporum infection of saffron corms and the physiological responses of saffron were analyzed. On this basis, dual RNA-seq was performed on the saffron corms inoculated on the 3th and 6th days of F. oxysporum to analyze the defense-related genes of saffron and the pathogenicity-related genes of F. oxysporum. The results showed that on the third day of infection, it was observed that the hyphae completely entered the corm cells and colonized and spread in the cells; on the sixth day of infection, hyphae have appeared in xylem cells to block vessels. Interacting transcriptome results indicate that in the host saffron, its phenylpropanoid metabolism, plant hormone signal transduction and plant-pathogen interaction pathways were activated during infection process, which were conducive to the enhancement of cell wall, the occurrence of hypersensitivity, and the accumulation of various antibacterial proteins and phytoantitoxins. Meanwhile, in the fungus, the expression levels of cell wall degradationenzyme-related genes, growth and development -related genes and pathogenicity-related genes in F. oxysporum were up-regulated, indicating its strong pathogenicity. The study provides a new insight into the molecular mechanism of the interaction between C. sativus and F. oxysporum, and also provides a theoretical basis for mining saffron disease resistance genes.
Association between Interleukin-8 Polymorphism and Wheezing: A Meta-Analysis
Authors: Zhang Bo , Liu Ying , Qi Wen , Zhou Liting , Ye Lin 
Published: July 2022

Abstract
PurposeA number of studies reported on associations of single nucleotide polymorphisms (SNPs) present in Interleukin-8 with wheezing. The present study was then undertaken to perform a meta-analysis of all the results published to date.MethodsAll studies on the association of IL-8 gene polymorphisms with wheezing published before December 312020 were retrieved from the PubMed, Web of Science, Embase and ScienceDirect databases and Cochrane Library. RevMan 5.0 software was used to perform meta-analysis of the data that fulfilled the criteria for our meta-analysis. The effect size of 3 SNPs on IL-8 gene on wheezing was assessed based on the odds ratios (ORs) with calculation of 95% confidence interval (CI).ResultsA total of 6952 subjects (3755 cases and 3197 controls) from 13 studies were genotyped. Meta-analysis suggested the association of rs4073 AA, rs4073 AA + AT, rs2227306 TT, rs2227306 TT + TC, rs2227307 TT with wheezing was 0.90 (95% CI 0.71 ~ 1.15), 0.96 (95% CI 0.76 ~ 1.21), 0.85 (95% CI 0.72 ~ 1.00), 0.88 (95% CI 0.77 ~ 1.01), 0.67 (95% CI 0.32 ~ 1.40). Meta-analysis demonstrated asthma association for rs4073 AA (OR = 0.61, 95% CI 0.44 ~ 0.85, P = 0.004) and rs2227306 TT (OR = 0.54, 95% CI 0.38 ~ 0.78, P = 0.0009).ConclusionThe present meta-analysis suggests that rs4073 AA and rs2227306 TT genotype polymorphisms of IL-8 are associated with decreased risk for asthma.
Tapered PCF Mach-Zehnder interferometer based on Surface Plasmon Resonance (SPR) for estimating concentration Toxic metal ions (Lead)
Authors: Jassam Ghufran Mohammed 
Published: July 2022

Abstract
In this work, Mach-Zehnder interferometer (MZI) based Surface-Plasmon-Resonance (SPR), is created by fusing two regular single-mode fibers with a photonic crystal fiber (PCF) (SMF -PCF-SMF) for estimating the concentration and refractive index of Toxic lead ion. A little part (4cm) of Photonic crystal fiber is manufactured in the middle of the sensor, and then the tapering process is completed, the gold metal is then deposited at a thickness of about (40nm). Toxic lead ion are placed on gold coated core of a Photonic crystal fiber. The calculated the signal to noise ratio, sensitivity, resolution and Figures of merit are approaching SNR is 0.09, S 714 nm/RIU, Resolution is 2.8x10-3and the FOM is5.368 is a chivied.
Convergence of a modification of the Jacobi method particularly indicated on matrices with non-negative coefficients. Version 2
Authors: tagliaferro fulvio 
Published: July 2022

Abstract
The rate of convergence of an iterative method for linear systems analogous to Jacobi's method is tested. The method is particularly suitable for systems with a matrix with non-negative coefficients. An attempt is being made at this point to justify this fact.
Impact of the geometric parameters on the performance of silicon TG SOI N FinFET 5nm
Authors: lazzaz abdelaziz , Bousbahi Khaled , Ghamnia Mustapha 
Published: July 2022

Abstract
Semiconductor device dimensions have been downsized to nanoscale dimensions to upgrade the driving capacity and increasing speed. At the lower technology node, the performance of conventional CMOS circuits degrades because of the short channel effects (SCEs). the researchers expect to identify new solutions for different design issues as a result, the FinFET device has been introduced as an alternative to MOSFET for advanced scalability which allows the use of multi gates in order to dissipate lower power. This paper presents an analysis of TG N SOI (Semiconductor On insulator) FinFET 5 nm using Hafnium Dioxide and the Non-Equilibrium Green Function (NEGF) formalism to study the quantum effect. The different parameters such as leakage current, the ON current, the performance ratio ION/IOFF which are calculated and optimized. The aim and the novelty of this simulation is to present novel geometric parameters that improve the performance of the device, and hence to have optimized CMOS circuits.
Evaluation of the Agro-morphological traits, seed characterization and the genetic diversity of local Rice (Oryza sativa L.) Varieties of Pakistan
Authors: Fazal Urooj , Uddin Israr , Khan Amir Muhammad , Khan Fahim Ullah , Khan Mudassar Nawaz , Iqbal Navid , Ibrahim Muhammad , Bangash Sajid Ali Khan 
Published: July 2022

Abstract
Background: Broad base genetic diversity is essential for a sustainable crop yield to provide tolerance against biotic and abiotic stresses. In Pakistan, rice is ranked second as a staple food and cultivated under different climatic zones. However, very little is known in terms of rice genetic diversity.Methods and results: Present research were performed to evaluate the genetic diversity among 12 local rice varieties by using 5 SSR markers. Furthermore, agro-morphological parameters and seed characterization of these varieties were studied. The highest plant height (204.3 cm) and panicle length (40.1 cm) were observed for Hans-raj, the maximum number of panicles were recorded for dilrosh-97 (47.3). The maximum number of primary and secondary panicle branches were observed in Ratua-81 (51) and super basmati (62), respectively. Super basmati showed highest number of filled grains (264.3) and total number of grains per panicle (315). The minimum days to maturity was recorded for ratua-81 (140 days), and highest 1000 grains weight was recorded for Ksk-133 (27g). The highest concentration of elements, e.g. zinc (Zn) was observed in Ks-282 (44µg/g), Iron (Fe) in hansraj (190.3µg/g), manganese in bamla sufaid (111.3µg/g), copper (Cu) in hansraj (856.3µg/g), lead (Pb) in super basmati (3883.3µg/g), and nickel (Ni) was found in basmati-385 (314.6ug/g). For the genetic diversity analysis, five SSR markers were used and a total of 60 alleles were amplified with 20% polymorphism, RM28130 showed the highest PIC value (0.60). The maximum number (3) of alleles were produced by RM28089. Based on secondary panicle branches and total number of filled grains, Super basmati showed best panicle architecture and grain yield, which can be used in breeding program to develop high yielding aromatic rice genotypes.Conclusions: The highest number of filled grains and total number of grains per panicle were observed in super basmati, which indicated the potential adaptation. Basmati Hansraj, Ks-282, Super basmati and Basmati surkh-161 were found to be highly rich in micronutrients (iron, zinc, copper, lead and manganese). The maximum genetic distance was observed in basmati-2000 and basmati surkh 161 genotypes.
Enhancement in Performance of the PVC / Nanoclay Mixed Matrix Nanofiltration Membrane
Authors: Ferdowsi Amirhoosein , Kikhavani Tavan , Ashrafizadeh S.Nezamoddin 
Published: July 2022

Abstract
Mixed matrix membranes are considered as a novel generation of membranes that have favorable separation and stability properties of inorganic and polymeric membranes at the same time. In this study, the effects of presence of clay nanoparticles (CNs) on the enhancement of properties and performance of PVC nanofiltration membranes were investigated. FTIR, AFM, XRD, EDS, and FESEM analyses were used to evaluate the mixed matrix membranes. Significant improvements in the membrane hydrophilicity, porosity, permeation flux, and rejection were observed by incorporating CNs. The highest rejection of 94.8% was obtained with mixed matrix membranes containing 2 wt% of CNs. The permeation flux of this membrane was enhanced by 75% relative to the neat membrane.
Integrator complex subunit 15 controls mRNA splicing and is critical for eye development
Authors: Azuma Noriyuki , Yokoi Tadashi , Tanaka Taku , Matsuzaka Emiko , Saida Yuki , Nishina Sachiko , Terao Miho , Takada Shuji , Fukami Maki , Okamura Kohji , Maehara Kayoko , Yamasaki Tokiwa , Hirayama Jun , Nishina Hiroshi , Handa Hiroshi , Yamaguchi Yuki 
Published: July 2022

Abstract
The eye and brain are composed of elaborately organized tissues, development of which is supported by spatiotemporally precise expression of a number of transcription factors and developmental regulators. Here we report the molecular and genetic characterization of Integrator complex subunit 15 (INTS15). INTS15 was identified in search for the causative gene(s) for an autosomal-dominant eye disease with variable individual manifestation found in a large pedigree. While homozygous INTS15 knockout mice are embryonic lethal, mutant mice lacking a small C-terminal region of INTS15 show ocular malformations similar to the human patients. INTS15 is highly expressed in the eye and brain during embryogenesis and stably interacts with the Integrator complex to support snRNA 3′ end processing. Its knockdown resulted in missplicing of a large number of genes, probably as a secondary consequence, and substantially affected genes associated with eye and brain development. Moreover, studies using human iPS-derived neural progenitor cells showed that INTS15 is critical for axonal outgrowth in retinal ganglion cells. This study suggests a new link between general transcription machinery and a highly specific hereditary disease.
Circularly Polarized Tunable Graphene-Patch over SiO2 substrate for THz Applications
Authors: Narayaswamy Nagesh Kallollu , Bhosle Manju Ramrao , Penmatsa Krishna Kanth Varma , Dwivedi Ajay Kumar 
Published: July 2022

Abstract
In this communication, a graphene-based radiator is designed and analyzed at THz frequency. A tilted dumbbell-shaped aperture is loaded on a graphene patch for creating degenerated orthogonal mode with 900 phase shift, which in turn produces circularly polarized (CP) waves. Graphene patch is placed over SiO2 substrate. Slot loading in graphene patch shifts the frequency band due to a reduction in effective permittivity. Another important feature of the proposed antenna is to provide a tunable feature in the frequency response and axial ratio by changing the chemical potential. The proposed antenna operates from 5.85 THz to 6.05 THz. 3-dB axial ratio is obtained from 5.85 THz to 5.95 THz. Good value of gain, as well as left-handed circular polarization characteristics, makes the proposed THz antenna in biomedical applications
Anatomical Analysis of Sphenoid Sinus and its Surrounding Structures in Cone-beam Computed Tomography Images: A Retrospective Cross-sectional Study
Authors: Foroozandeh maryam , Salemi fatemeh , khodakarami leyla , alafchi behnaz 
Published: July 2022

Abstract
Background
Anatomical analysis of the sphenoid sinus is important because of its proximity to vital neurovascular structures. The aim of this study is investigating the anatomy of the SS and its surrounding structures in CBCT images.
Methodology:
In this retrospective cross-sectional study, 201 cone-beam computed tomography (CBCT) radiographs were analyzed. The analyzed images included the type of SS, protrusion of ICA and optic nerve and foramen rotundum, vidian canal type, the Onodi cell, pneumatization to surrounding bones, the ostium, the septum. The data were analyzed using chi-square and the t-test in SPSS 24 at a significance level of 0.05.
Results
The tilted septum had the highest frequency (46.3%). Ostium was bilateral in most images (56.2%). The protrusion of the ICA (54.7%) and optic nerve (62.2%) was smooth in most images. Foramen rotundum protrusion and Onodi cell prevalence were 25% and 22.9%, respectively. The postsellar type of sinus had the highest frequency (71.1%). Vidian canal Grade II had the highest frequency (40.3%). Greater wing pneumatization had the highest frequency (51.7%). No statistically significant relationship was found between the optic nerve protrusion and Onodi cell (P-value < 0.05). There was a significant relationship between the pneumatization of the pterygoid process and the protrusion of the vidian canal, and the foramen rotundum protrusion (p-value < 0.001).
Conclusion
CBCT imaging is very effective in the anatomical analysis of the SS and its surrounding structures. The postsellar type had the highest frequency.Vidian canal Grade II had the highest frequency; greater wing pneumatization was observed in more than half of the images; the most common type of septum was tilted; ostium was bilateral in most cases; the protrusion of the ICA and optic nerve was mostly smooth.
CRISPR/Cas9-mediated AtGATA25 mutant represents a novel model for regulating hypocotyl elongation in Arabidopsis thaliana
Authors: Kim Kihwan , Shin Juhyung , Kang Tae-An , Kim Byeonggyu , Kim Won-Chan 
Published: July 2022

Abstract
Background: Plants have evolved while adapting to the ever-changing environment through various morphological changes. The circadian clock is an endogenous oscillator with approximately 24 hours that enables an organism to anticipate and respond to changes in its environment. The circadian clock regulates various physiological processes, such as hypocotyl elongation in Arabidopsis thaliana. Phytochrome interacting factor 4 (PIF4), a member of the bHLH protein, plays a vital hub role in light signaling pathways and temperature-mediated growth response mechanisms. PIF4 is controlled under the circadian clock by interaction with several factors. However, the components regulating PIF4 transcription and activity are not clearly known.Methods and results: Here, we show that the Arabidopsis thaliana GATA25 (AtGATA25) transcription factor plays a fundamental role in promoting hypocotyl elongation by positively regulating the expression of PIF4. It was confirmed to in the loss-of-function mutant of AtGATA25 via CRISPR/Cas9-mediated gene editing inhibits hypocotyl elongation and decrease the expression of PIF4. In contrast, the overexpression of AtGATA25 in transgenic plants showed increased expression of PIF4 and enhanced hypocotyl elongation. To better understand AtGATA25-mediated PIF4 transcriptional regulation, we analyzed the promoter region of the target gene PIF4 and characterized the role of GATA25 through transcriptional activation analysis.Conclusion: our findings provide a new perspective on the adaptive development of plants along with the circadian clock, a critical environmental factor.
Role of Nanotechnology in Microbial mediated Remediation
Authors: CHAURASIA PREETI , Jasuja Nakuleshwar Dut , Kumar Sanjeev 
Published: July 2022

Abstract
Man-made pollution and pollutants are increasing day by day which has prompted alarming health issues and a declining availability of clean drinking water. Xenobiotic compounds from the waste of industries aggregate in agricultural soils and penetrates in the food chain. Thus, imposes a negative influence on the natural ecosystem and eventually impacts on human. The limitations of conventional methods used in remediation to get rid of the contaminants have given rise to trial nanotechnological aids for environmental clean-up by various researchers. The use of nanoparticles produced by microorganisms with the aid of nano biotechnology is known as nano bioremediation. This substitute for developing nanoparticles is an eco-compatible, environment-affable and cost-efficient method to eliminate the contaminants. Nanoparticles have shown their effectiveness over bulk materials as they confer easy handling, large surface area, economic viability, higher reactivity, and hence better performance. Microorganisms like bacteria, fungi, yeast, actinomycetes, and algae are exploited as a “biofactory” for the nanoparticle’s synthesis such as cadmium sulfide iron, silver, gold, platinum, titanium, titanium dioxide, palladium, magnetite, etc for the conversion and detoxification of the contaminants. Microbes have secured remarkable attentiveness as they possess the potency to synthesize nanoparticles in varying sizes, shapes and compositions with distinct physicochemical features for the elimination of heavy metals, organic, inorganic contaminants, organochlorines, dyes in soil and water treatment. Developments withinside the subject of nanoparticle biosynthesis will raise the commercial economic system through producing inexperienced energy. This manuscript emphasizes the importance and mechanism of environmental remediation of pollutants by microbe-driven nanoparticles.