bluuebunny/crossref_metadata_2025_split huggingface dataset:
Estimating the Mortality Rate using Statistical Variance and Reduced set of Clinical and Non-Clinical Attributes for Diagnosing Chronic Kidney Disease
Authors: K Meena , A Vadivel , p Sumathy , Zamani Abu Taha , Alanazi Sultan M , Varish Naushad 
Published: June 2023

Abstract
It is found that, Chronic Kidney Disease (CKD) is prevalence worldwide. Quality of Life (QoL) in terms of health became an essential measure for patients with CKD. This paper uses the real-time dataset of CKD patients collected from reputed medical dialysis unit in Chennai, India. We measure the inter and intra class variations between the clinical and non-clinical attributes. Principal Component Analysis (PCA) is applied on twelve clinical (biomarkers) and eight non-clinical (comorbiditity) attributes to find salient among them. ANOVA is applied only on reduced attributes to calculate the correlation between the target variables such as mortality, age and gender. The characteristics of the attributes and its discriminating nature is evaluated using various well known classifiers such as Logistic Regression, K-Nearest Neighbor, Support Vector Machine, Neive Bayes, Decision Tree, Random Forest and Artificial Neural Network. The performance of the classifiers are evaluated using parameters such as confusion matrix, accuracy, F-measure, precision and Recall. It is found that, the covariance of the attributes linearly separates the output space of target variables that are considered and the performance is encouraged.
tRF-27 competitively Binds to G3BPs and Activates MTORC1 to Enhance HER2 Positive Breast Cancer Trastuzumab Tolerance
Authors: He Yaozhou , Liu Yincheng , Gong Jue , Sun Chunxiao , Yan Xueqi , Duan Ningjun , Hua Yijia , Zeng Tianyu , Fu Ziyi , Yang Fan , Liang Yan , Huang Zebo , Huang Xiang , Tang Jinhai , Yin Yongmei 
Published: June 2023

Abstract
Breast cancer, one lethal malignant tumor, is positive for HER2 in about 20% of patients. The efficacy of current treatments is limited by primary and secondary resistance to trastuzumab. tRNA-derived fragments (tRFs) have shown crucial regulatory roles in various cancers. This study aimed to evaluate the role of tRF-27 in regulating the resistance of HER2-positive breast cancer against trastuzumab.tRF-27 was highly expressed in trastuzumab-resistant cells, and its expression level could predict the resistance to trastuzumab. High expression of tRF-27 promoted the growth and proliferation of trastuzumab-exposed cells.RNA-pulldown assay and mass spectrometry were performed to identify Ras GTPase-activating protein-binding proteins 1 and 2 (G3BPs) (two proteins targeted by tRF-27); RNA-immunoprecipitation (RIP) to confirm their bindings; co-immunoprecipitation (co-IP) and RNA-pulldown assay to determine the binding domains between G3BPs and tRF-27.tRF-27 bound to the nuclear transport factor 2 like domain(NTF2 domain) of G3BPs through a specific sequence. tRF-27 relied on G3BPs and NTF2 domain to increase trastuzumab tolerance. tRF-27 competed with lysosomal associated membrane protein 1(LAMP1) for NTF2 domain, thereby inhibiting lysosomal localization of G3BPs and tuberous sclerosis complex(TSC). Overexpression of tRF-27 inhibited phosphorylation of TSCs and promoted the activation of mechanistic target of rapamycin complex 1(MTORC1) to enhance cell proliferation and entice the resistance of HER2-positive breast cancer against trastuzumab.
Integrating genomics and transcriptomics to identify candidate genes for high egg production in Wulong geese
Authors: Liu Jingjing , Xiao Yu , Ren Pengwei , Zhang Shuer , Liu Yang , Zhu Mingxia 
Published: June 2023

Abstract
Background: Wulong geese are known for their excellent egg-laying performance. However, there are considerable population differences in egg-laying performance among Wulong geese. This study combined genome-wide selection signal analysis with transcriptome analysis (RNA-seq) to screen candidate genes related to high egg production in Wulong geese.
Results: A total of 132 selected genomic regions were screened using genome-wide selection signal analysis, and 130 genes related to high egg production were annotated in these regions. These selected genes were enriched for egg production-related pathways such as oocyte meiosis, estrogen signaling pathway, oxytocin signaling pathway, and progesterone-mediated oocyte maturation. Furthermore, a total of 890 differentially expressed genes (DEGs), including 340 up-regulated and 550 down-regulated genes, were identified by RNA-seq. Importantly, two genes — GCG and FAP — were identified both as selected genes and DEGs. A non-synonymous single nucleotide polymorphism was identified in an exon of FAP.
Conclusions: Based on genome-wide selection signal analysis and transcriptome data, GCG and FAPwere identified as candidate genes associated with high egg production in Wulong geese. These findings could serve as a reference for breeding Wulong geese varieties with high egg production abilities. They also provide a theoretical basis for exploring the mechanisms of reproductive regulation in poultry.
Employment of a high-throughput functional assay to define the critical factors that influence vaccine-induced, cross-variant neutralizing antibodies for SARS-CoV-2.
Authors: Gu Yue , Shunmuganathan Bhuvaneshwari , Qian Xinlei , Gupta Rashi , Tan Rebecca See Weng , Kozma Mary , Purushotorman Kiren , Murali Tanusya M. , Tan Nikki Y.J. , Preiser Peter R. , Lescar Julien , Nasir Haziq , Somani Jyoti , Tambyah Paul , Smith Kenneth G.C. , Renia Laurent , Ng Lisa F.P. , Lye David C. , Young Barnaby E. , MacAry Paul A. , Wai SCOPE cohort study group Fong Siew 
Published: June 2023

Abstract
The scale and duration of neutralizing antibody responses targeting SARS-CoV-2 viral variants represents a critically important serological parameter that predicts protective immunity for COVID-19. In this study, we describe the development and employment of a new functional assay that measures neutralizing antibodies for SARS-CoV-2 and present longitudinal data illustrating the impact of age, sex and comorbidities on the kinetics and strength of vaccine-induced antibody responses for key variants in an Asian volunteer cohort. We also present an accurate quantitation of serological responses for SARS-CoV-2 that exploits a unique set of in-house, recombinant human monoclonal antibodies targeting the viral Spike and nucleocapsid proteins and demonstrate a reduction in neutralizing antibody titres across all groups six months post-vaccination. We also observe a marked reduction in the serological binding activity and neutralizing responses targeting recently newly emerged Omicron variants including XBB 1.5 and highlight a significant increase in cross-protective neutralizing antibody responses following a third dose (boost) of vaccine. These data illustrate how key virological factors such as immune escape mutations combined with host demographic factors such as age and sex of the vaccinated individual influence the strength and duration of cross-protective serological immunity for COVID-19.
Novel Biphenylidene-Thiopyrimidine Derivatives as Corrosion Inhibitors for Carbon-Steel in Oilfield Produced Water
Authors: Ali Hagar , Shaban Mahmoud , Abousalem Ashraf Salem Elsayed , Ghaith Eslam , Fouda Abdelaziz , Ismail Mohamed 
Published: June 2023

Abstract
Three biphenylidene-thiopyrimidine derivatives were newly synthesized, characterized and their corrosion inhibition effect on corrosion of API 5L X52 carbon steel in oilfield produced water was measured by using electrochemical methods: Potentiodynamic polarization technique and electrochemical impedance spectroscopy (EIS). EIS results using an equivalent circuit to model the corrosion inhibition process were analyzed and discussed. The results of Tafel polarization indicate the tested inhibitors are of mixed-type. The adsorption of these compounds followed Langmuir isotherm. The surface of uninhibited and inhibited carbon steel was investigated by Atomic Force Microscopy (AFM), observing surface improvement when carbon steel samples exposed to inhibited corrosive solution. Quantum chemical calculations and molecular simulations were employed to elucidate the corrosion inhibition mechanism. The HM-1228 inhibitor exhibited corrosion inhibition efficiency at 94.8%, and the increase in performance is attributed to the presence of di-N-ethyl groups, which enhances the electron donating ability as well as lipophilic properties.
Impact of BMI on the Survival Outcomes of non-Small Cell Lung Cancer Patients Treated with Immune Checkpoint Inhibitors: A Meta-Analysis
Authors: Zhang Tongtong , Li Shuluan , Chang Jianhua , li Chao 
Published: June 2023

Abstract
Objectives
ICIs have become the standard treatment for advanced NSCLC patients. Currently, PD-L1 is the most widely useful biomarker to predict ICI efficacy, but the sensitivity and specificity are limited. Therefore, the useful predictive biomarkers of ICI efficacy is urgently needed. BMI is an internationally used measure of body health. Obesity may affect ICI efficacy by changing T cell functions. This meta-analysis aimed to clarify the relationship between BMI and survival outcomes of NSCLC patients treated with ICIs.
Methods
A systematic review was conducted to identify studies that assessed the association between BMI and survival outcomes in patients treated with ICIs. OS was the primary endpoint, and PFS was the secondary endpoint. Random-effect models or fixed-effect models were utilized to combine study effects according to the Cochran Q and I2 tests.
Results
Nine studies, including 4602 NSCLC patients treated with ICIs, that met the inclusion criteria were selected for this meta-analysis. There was no significant difference in PFS (HR 0.885; 95% CI 0.777–1.009, p = 0.068) or OS (HR 0.947; 95% CI 0.789–1.137, p = 0.560) between the low BMI group and the high BMI group. However, in the subgroup analysis, compared with normal-weight patients, overweight and obese patients achieved prolonged PFS (HR 0.862; 95% CI 0.760–0.978, p = 0.021) and OS (HR 0.818; 95% CI 0.741–0.902, p＜0.0001).
Conclusion
Overweight and obese NSCLC patients tend to achieve prolonged survival time with ICI regimens. Further prospective studies are needed to strengthen the association between ICI outcomes and BMI levels.
Optimization of vertically aligned carbon nanotube beam trajectory with the help of focusing electrode in the microchannel plate
Authors: Adhikari Bishwa Chandra , Ketan Bhotkar , Patil Ravindra , Choi Eun Ha , Park Kyu Chang 
Published: June 2023

Abstract
The focusing electrode plays an important role to reduce the electron beam trajectory with low dispersion and high brightness. This article summarizes the importance of the vertically aligned multi-walled carbon nanotube effect with the focusing electrode. First of all, the effect of electron beam trajectory is studied with the different heights, hole sizes, and applied voltage of the focusing electrode by the opera 3D simulation. The field emission electron beam spot is captured in the microchannel plate which helps to reduce the signal noise effect and damage of CNT tips by the joule heating effect. The high-dense bright spot is optimized at the focusing electrode hole size of 2 mm, and the height of 1 mm from the gate mesh electrode at the low bias voltage of -200 V without the loss of current. The FWHM of the electron beam is calculated 0.9 mm with its opening angle of 0.90 which could be applicable in high-resolution multi-electron beam microscopy and nano-focused X-ray system technology.
The lotus NnWOX1-1、NnWOX4-3 and NnWOX5-1 promoted root formation and enhanced stresses tolerance in transgenic Arabidopsis thaliana
Authors: quan Liu , Shiting Liang , Chen Zhao , Yuyan Han , Minrong Zhao , Shuyan Li , Libao Cheng 
Published: June 2023

Abstract
Background: Adventitious root (AR) is an important organ in water and nutrition uptake in lotus due to degeneration of principle root. Wox is involved in regulating plant development and growth by affecting multiple genes expression in plant kingdom. In this study, three genes including NnWOX1-1、NnWOX4-3 and NnWOX5-1were isolated, and genes function was assessed in Arabidopsis plants.
Results: The full-length of the NnWOX1-1、NnWOX4-3 and NnWOX5-1 were 1038 bp, 645 bp and 558 bp in nucleotide, and encoded 362, 345 and 185 amino acid residues respectively. Phylogenetic analysis showed that Nnwox1-1 and Nnwox4-3 was classified into one group, and Nnwox5-1 and Mnwox5 showed high genetic relationship. These three genes were all induced by sucrose and IAA, and had organ-speciﬁc expression characteristic. Aside from the improvement of root growth and salt tolerance, NnWOX1-1 and NnWOX4-3 could also promote stem development in transgenic Arabidopsis. A total of 751, 594 and 541genes including nineteen, nineteen and thirteen genes related with ethylene and IAA metabolism and response were enhanced expression in NnWOX1-1、NnWOX4-3 and NnWOX5-1 transgenic plants respectively. Further analysis showed that ethylene product rates was increased, and while IAA, POD and lignin content were no significantly changed. Exogenous application of ethephon promoted ARs formtion and dramaticly increased fresh weight and dry weight of lotus seedlings.
Conclusions: NnWOX1-1、NnWOX4-3 and NnWOX5-1 was involved in root formation, stem development and stresses adaptation in transgenic Arabidopsis plants by affecting multiple genes transcriptation. Among which, the change of genes expression in ethylene metabolism and respondings probably exerted criticle role on development in Arabidopsisplant. In addition, ethylene might be an important factor to affect ARs formation in lotus seedlings.
Rapid detection of lung cancer based on serum Raman spectroscopy and a support vector machine: a case-control study
Authors: Yan Linfang , Su Huiting , Liu Jiafei , Wen Xiaozheng , Luo Huaichao , Yin Yu , Guo Xiaoqiang 
Published: June 2023

Abstract

Background
Early screening and detection of lung cancer is essential for the diagnosis and prognosis of the disease. In this paper, we investigated the feasibility of serum Raman spectroscopy for rapid lung cancer screening.
Methods
Raman spectra were collected from 45 patients with lung cancer, 45 with benign lung lesions, and 45 healthy volunteers. The machine learning support vector machine (SVM) method was applied to build a diagnostic algorithm. Furthermore, 15 independent individuals were sampled for external validation, including 5 lung cancer patients, 5 benign lung lesion patients, and 5 healthy controls.
Results
Its diagnostic sensitivity, specificity, and accuracy were 91.67%, 92.22%, 90.56% (lung cancer vs. healthy control), 92.22%,95.56%,93.33% (benign lung lesion vs. healthy) and 80.00%, 83.33%, 80.83% (lung cancer vs. benign lung lesion). For the independent test, our model showed that all the samples were classified correctly.
Conclusion
Therefore, this study demonstrates that the serum Raman spectroscopy analysis technique combined with the SVM algorithm has great potential for the noninvasive identification of lung cancer.
“Mortality or not mortality, that is a question …” How to treat removals in tree survival analysis of managed forests
Authors: Lech Paweł , Kamińska Agnieszka 
Published: June 2023

Abstract

Tree mortality is an objective and easily definable criterion for forest health and is particularly suitable for long-term and large-scale studies of forest condition. However, it is not possible to accurately determine actual tree mortality in managed forests that are subject to silvicultural and sanitary, periodic or continuous tree removal. In this case, the only way to approximate actual tree mortality is to define the range in which it occurs by determining minimum and maximum mortality thresholds. For this purpose, we performed a survival analysis and considered the removals as either censored or complete observations. The results obtained showed significant differences, indicating the importance of how removals are classified in the analysis. An attempt to determine the similarity of removed trees to alive or dead trees in terms of defoliation, severity of damage, DBH and age of the trees revealed inconsistencies between species and the year for which this analysis was also performed. Removed trees from species in good health (pine) resembled alive, while removed trees from species in poor health (spruce) resembled dead trees more. This result suggests that in managed stands of healthy species the actual mortality is closer to the minimum, while in species in poor health it is closer to the maximum mortality.
Three-Input Logic Gate Based on DNA Strand Displacement Reaction
Authors: Ma Jingjing 
Published: June 2023

Abstract
In this paper, three kinds of three-input logic gates are designed based on DNA strand displacement reaction, which are three-input OR logic gate, three-input AND logic gate, and three-input MAJORITY logic gate. The logic gates designed in this paper takes different DNA strands as input and fluorescence signals as output. The biochemical experimental results verify my designs. The results show that DNA strand displacement technology has important application value in DNA computing, especially in the construction of DNA molecular logic gates.
Reliability and validity of the Patient Experiences Questionnaire for Interdisciplinary Treatment for Substance Dependence – Continuous Electronic Measurement (PEQ-ITSD – CEM)
Authors: Iversen Hilde Hestad , Haugum Mona , Ellingsen-Dalskau Lina Harvold , Bjertnaes Oyvind 
Published: June 2023

Abstract
Background
Inpatient experiences with interdisciplinary treatment for substance dependence and mental health care are measured using continuous electronic measurements in Norway. Major changes in data collection from cross-sectional surveys to continuous measurements necessitated the revalidation of the instrument. The main purpose of the present study was to determine the psychometric properties of the Patient Experiences Questionnaire for Interdisciplinary Treatment for Substance Dependence – Continuous Electronic Measurement (PEQ-ITSD – CEM). We also aimed to develop a short version of this tool, since completing the original version can be burdensome for some patients.
Methods
The study included adult inpatients (aged ≥16 years) who received substance-dependence treatment at 102 different sections in Norway during 2020–2022 (n=2,850). Levels of missing data, ceiling effects, factor structure, internal consistency and item performance were assessed. A short scale was developed based on the psychometric testing results that included item response theory analysis.
Results
The PEQ-ITSD – CEM comprised three empirically based scales with good internal consistency, reliability and validity, which cover treatment and personnel (14 items), milieu (6 items) and outcome (5 items). The results supported a seven-item short-formscale, with three items selected for the treatment and personnel scale, two items for the milieu scale and two items for the outcome scale.
Conclusions
The PEQ-ITSD – CEM can be recommended for future assessments of patient experiences with interdisciplinary treatment for substance dependence in Norway and in other countries with similar healthcare systems. This short-form scale can be applied when respondent burden is a crucial issue.
Faecal carriage and risk factors of carbapenemase-producing gram-negative bacteria resistant to third-generation cephalosporins in hospitalized and non- hospitalized patients, Kenya
Authors: Maina Anthony Karoki , Maingi John , Mutuma Caroline Kirito , Njeru John , Musyoki Abednego 
Published: June 2023

Abstract
The authors have requested that this preprint be removed from Research Square.
Multi-database analysis showed that genes associated with inflammatory response are important for prognosis prediction of renal clear cell carcinoma
Authors: Xiao Yonggui , Xu Danping , Jiang Chonghao , Li Hubo , Liu Jinzheng , Huili Youlong , Nie Shiwen , Cao Fenghong , Guan Xiaohai 
Published: June 2023

Abstract
Background
Clear cell carcinoma of the kidney is the largest subtype of kidney tumor. Inflammatory responses are involved in all stages of the tumor. The relationship between genes related to inflammatory response and renal clear cell carcinoma is expected to help the diagnosis and treatment of tumor patients.
Methods
First, we obtained all the data needed for this study free of charge from a public database. After differential analysis and COX regression, we obtained genes that were used to build the model. In addition, data from multiple databases were included in this study. To make the data from different sources comparable, we standardize all the data using the SVA package. Next, through LASSO regression, we constructed a prognostic model of genes related to inflammation (IRGM). The model contains 10 gene model signatures related to the inflammatory response (IRGMS). The data used for modeling and internal validation came from the TCGA database and the GSE29609 dataset. Clear cell renal carcinoma data from the ICGC database will be used for external validation. Tumor data from E-MTAB-1980 cohort will provide an additional external validation. The GSE40453 dataset and the GSE53757 dataset will be used to verify the differential expression of IRGMS. The immunohistochemistry of IRGMS will be queried through the HPA database. After adequate validation of IRGM, we explored the application of IRGM in greater depth by constructing nomograms, pathway enrichment analysis, immunocorrelation analysis, drug susceptibility analysis, and subtype identification.
Results
IRGM can robustly predict the prognosis of patient samples with clear cell carcinoma of the kidney from different databases. IRGMS (IGFBP3, SCNN1B, IFI16, LRRC19, GSTM3, IFI44, APOLD1, HPGD, CPA3, PROM1) is expected to become a new biomarker associated with clear cell carcinoma of the kidney. The construction of nomogram can use IRGM to predict patient survival more accurately, so as to adopt more reasonable treatment methods. Pathway enrichment analysis showed that patients in the HR group were associated with a variety of tumorigenesis biological processes. Immune-related analysis and drug susceptibility analysis suggest that patients with higher IRGM scores have more treatment options. The subtype identification results are conducive to further refinement of treatment.
Conclusion
IRGMS (IGFBP3, SCNN1B, IFI16, LRRC19, GSTM3, IFI44, APOLD1, HPGD, CPA3, PROM1) is valuable in predicting the prognosis of clear cell carcinoma of the kidney. Patients with higher IRGM scores may be better candidates for treatment with immune checkpoint inhibitors and have more chemotherapy options.