bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Gut Microbiome as a Promising Biomarker of Cancer Progression Among Female Never-smokers With Lung Adenocarcinoma
Authors: Otoshi Takehiro , Nagano Tatsuya , Park Jonguk , Hosomi Koji , Yamashita Tomoya , Tachihara Motoko , Tabata Tokiko , Sekiya Reina , Tanaka Yugo , Kobayashi Kazuyuki , Mizuguchi Kenji , Itoh Tomoo , Maniwa Yoshimasa , Kunisawa Jun , Nishimura Yoshihiro 
Published: July 2022

Abstract
Background: The gut microbiome plays an important role in the immune system and has attracted attention as a new biomarker of various diseases, including cancer. As such, in this study, we examined the relationship between the gut microbiome and lung cancer progression. In addition, we assessed the correlation between the gut microbiome and epidermal growth factor receptor (EGFR) mutation status.Methods: Female never-smokers diagnosed with lung adenocarcinoma were consecutively enrolled between May 2018 and August 2019. Fecal samples were collected within 1 month before or after diagnosis and before administration of any lung cancer treatment. Principal coordinate analyses were performed using Bray-Curtis distance matrices to investigate the effects of clinical variables (age, body mass index, Tumor-Node-Metastasis stage, T category, N category, M category, primary tumor size, performance status, and EGFR mutation status) on the gut microbial community. A correlation analysis was also performed to determine the strength of association between the dominant taxonomy (comprising ≥1% of the relative abundance of bacterial DNA sequences) and clinical variables.Results: A total of 37 patients were enrolled. T category and primary tumor size were significantly correlated with the gut microbial community (p=0.018 and 0.041, respectively). At the genus level, a significant positive correlation was observed between the relative abundance of Faecalibacterium and both T category (correlation coefficient, R=0.51, p=0.0013) and primary tumor size (R=0.37, p=0.024), whereas a significant negative correlation was observed between the relative abundances of Fusicatenibacter and Bacteroides and T category (R=−0.35, p=0.034 and R=−0.32, p=0.05, respectively) and primary tumor size (R=−0.36, p=0.029 and R=−0.41, p=0.012, respectively). EGFR mutation status had no statistically significant effect on the gut microbial community (p=0.11). However, the relative abundances of Bifidobacterium and Faecalibacterium were significantly higher in EGFR mutation–negative patients than EGFR mutation–positive patients (p=0.012 and 0.041), whereas the relative abundance of Blautia was significantly lower in EGFR mutation–negative patients (p=0.036).Conclusions: This is the first study identifying the gut microbiome as a promising biomarker of lung cancer progression. Further elucidation of the role of the gut microbiome in lung cancer progression could facilitate development of new treatments for lung cancer.
Developing a Tailored Implementation Action Plan for A Suicide Prevention Clinical Intervention in an Australian Mental Health Service: A Qualitative Study Using the EPIS Framework.
Authors: Zbukvic Isabel , Rheinberger Demee , Rosebrock Hannah , Lim Jaclyn , McGillivray Lauren , Mok Katherine , Stamate Eve , McGill Katie , Shand Fiona , Torok Michelle , Moullin Joanna C 
Published: July 2022

Abstract
Background: Tailoring implementation strategies to local contexts is a promising approach to supporting implementation and sustainment of evidence-based practices in health settings. While there is increasing research on tailored implementation of mental health interventions, implementation research on suicide prevention interventions is limited. This study aimed to evaluate implementation and subsequently develop a tailored action plan to support implementation, sustainment and scale-up of an evidence-based suicide prevention intervention - Collaborative Assessment and Management of Suicidality (CAMS) - in an Australian public mental health service.Methods: This study took place within a larger randomised stepped-wedge design suicide prevention trial. Approximately 150 mental health staff working within a regional and remote community Local Health District in Australia were trained in CAMS. Semi-structured interviews and focus groups with frontline staff and clinical leaders were conducted to examine barriers and facilitators to using CAMS. Data were analysed using a reflexive thematic analysis approach and mapped to the Exploration, Preparation, Implementation and Sustainment (EPIS) framework. This was followed by stakeholder engagement to design a tailored implementation action plan based on a ‘tailored blueprint’ methodology.Results: A total of 22 barriers to implementing CAMS were identified. Based on the perceived impact on implementation fidelity and the feasibility of addressing identified barriers, six barriers were prioritised for addressing through an implementation plan. These barriers were mapped to evidence-based implementation strategies and, in collaboration with local health district staff, goals and actionable steps for each strategy were generated. This information was combined into a tailored implementation plan to support the sustainable use of CAMS as part of routine care within this mental health service. Conclusions: This study provides an example of a collaborative approach to tailoring strategies for implementation on a large scale. Novel insights were obtained into the challenges of evaluating the implementation process and barriers to implementing an evidence-based suicide prevention treatment approach within a geographically large and varied mental health service in Australia.Trial registration: This study was conducted as part of the LifeSpan suicide prevention trial. Trial registration for LifeSpan in Australia New Zealand Clinical Trials Register, ID: ACTRN12617000457347. Prospectively registered on 28 March 2017.
Correlation-driven organic 3D topological insulator with relativistic fermions
Authors: Nomoto Tetsuya , Imajo Shusaku , Akutsu Hiroki , Nakazawa Yasuhiro , Kohama Yoshimitsu 
Published: July 2022

Abstract
Exploring new topological phenomena and functionalities induced by strong electron correlation has been a central issue in modern condensed-matter physics. One example is a topological insulator (TI) state and its functionality driven by the Coulomb repulsion rather than a spin-orbit coupling. Here, we report a ‘correlation-driven’ TI state realized in an organic zero-gap system α-(BETS)2I3. The surface metallic state that emerges at low temperatures exhibits characteristic transport properties of a gapless Dirac semimetal, evidencing the presence of a topological surface state in this compound. Moreover, we observe a topological phase switching between the TI state and non-equilibrium Dirac semimetal state by a dc current, which is a unique functionality of a correlation-driven TI state. Our findings demonstrate that correlation-driven TIs are promising candidates not only for practical electronic devices but also as a field for discovering new topological phenomena and phases.
Does Medicaid Broaden the Choices of Patients with Low Socioeconomic Status? An Analysis of Bypassing Behaviors in Brooklyn
Authors: Lee Jae Bok 
Published: July 2022

Abstract
Background: Many governments worldwide have committed to extending choices in public service delivery. However, the extent to which policies ensure equity is unclear. We investigated whether Medicaid programs in the United States improve hospital accessibility among patients with low socioeconomic status, compared to those with non-low socioeconomic status who are non-Medicaid recipients or uninsured.Methods: We employed a difference-in-difference-in-differences approach using a rich dataset of information on inpatients and their choice of hospitals from Statewide Planning Research and Cooperative System and information on hospitals from the American Hospital Association in Brooklyn, New York, from 2003 to 2009Results: The findings indicated that Medicaid has failed to broaden the range of the hospital choices for patients with low socioeconomic status, assessed in terms of bypassing behaviors. Conclusions: Medicaid is a public program that offers choices driven by purchasing power. The findings of this study imply that this program has some limitations in alleviating existing socioeconomic inequities in available hospital choices.
A Combination Approach of Pseudotime Analysis And Mathematical Modeling For Understanding The Drug-Resistant Mechanisms
Authors: Magi Shigeyuki , Ki Sewon , Ukai Masao , Domínguez-Hüttinger Elisa , Naito Atsuhiko , Suzuki Yutaka , Okada Mariko 
Published: July 2022

Abstract
Cancer cells acquire drug resistance through the following nonresistant, pre-resistant, and resistant stages. Although the molecular mechanism of drug resistance is well investigated, the process of drug resistance acquisition remains largely unknown. Here we elucidate the molecular mechanisms underlying the process of drug resistance acquisition by sequential analysis of gene expression patterns in tamoxifen-treated breast cancer cells. Single-cell RNA-sequencing indicates that tamoxifen-resistant cells can be subgrouped into two, one showing altered gene expression related to metabolic regulation. The other showed high expression levels of adhesion-related molecules and histone-modifying enzymes. Pseudotime analysis showed a cell transition trajectory to the two resistant subgroups that stem from a shared pre-resistant state. An ordinary differential equation model based on the trajectory fitted well with the experimental results of cell growth. Based on the established model, it was predicted and experimentally validated that inhibition of transition to both resistant subtypes would prevent the appearance of tamoxifen resistance.
Comparison of endotracheal aspirate and bronchoalveolar lavage fluid metagenomic next-generation sequencing in severe pneumonia: a nested, matched case-control study
Authors: Bao Renren , Mei Qing , Yang Tianjun , Zhang Lei , Zhu Chunyan , Fan Xiaoqin , Wang Yinzhong , Tong Fei , He Yuxi , Fang Xiaowei , Geng Shike , Yang Yu , Sheng Ximei , Pan Aijun 
Published: July 2022

Abstract
Objectives: To compare clinical outcomes in patients with severe pneumonia according to the diagnostic strategy used. Methods: In this retrospective, nested, case-control study, patients with severe pneumonia who had undergone endotracheal aspirate (ETA) metagenomic next-generation sequencing of (mNGS) testing (n=53) were matched at a ratio of 1 to 2 (n=106) by sex, age, underlying diseases, immune status, disease severity scores, and type of pneumonia with patients who had undergone bronchoalveolar lavage fluid (BALF) mNGS. The microbiological characteristics and patient’s prognosis of the two groups were compared. Results: An overall comparison between the two groups showed no significant differences in bacterial, fungal, viral, or mixed infections. However, subgroup analysis of 18 patients who received paired ETA and BALF mNGS showed a complete agreement rate for the two specimens of 33.3%. There were more cases for whom targeted treatment was initiated (36.79% vs. 22.64%; P=0.043) and fewer cases who received no clinical benefit after mNGS (5.66% vs. 15.09%; P=0.048) in the BALF group. The pneumonia improvement rate in the BALF group was significantly higher than in the ETA group (73.58% vs. 87.74%, P=0.024). However, there were no significant differences in ICU mortality or 28-day mortality. Conclusions: We do not recommend using ETA mNGS as the first-choice method for analyzing airway pathogenic specimens from severe pneumonia patients.
Sirt1 regulates microglial activation and inflammation following oxygen-glucose deprivation/reoxygenation injury by targeting the Shh/Gli-1 signaling pathway
Authors: Liao Hongyan , Huang Jiagui , Liu Jie , Zhu Huimin , Chen Yue , Li Xuemei , Wen Jun , Yang Qin 
Published: July 2022

Abstract
Background: Cerebral ischemic injury leads to over-activation of microglia, which release pro-inflammatory factors that deteriorate neurological function during the acute phase of stroke. Thus, inhibiting microglial over-activation is crucial for reducing ischemic injury. Sirtuin 1 (Sirt1) has been shown to play a critical role in stroke, neurodegenerative diseases and aging. However, the effect of Sirt1 on the regulation of microglial activation following cerebral ischemic injury, as well as the underlying mechanism, remain unclear. The aim of the present study was to examine the effect of Sirt1 on oxygen-glucose deprivation/reoxygenation (OGD/R)-treated N9 microglia following treatment with the Sirt1 agonists resveratrol and SRT1720 and the Sirt1 antagonist sirtinol. Methods: Cell viability, Apoptosis, activation and inflammatory responses of microglia, expressions and activity of Shh signaling pathway proteins were detected by Cell Counting Kit 8, Flow Cytometry, immunocytochemistry, ELISA, and Western blotting, respectively.Results: The results demonstrated that treatment with resveratrol or SRT1720 could inhibit the activation of microglia and inflammation during OGD/R. Moreover, these treatments also led to the translocation of the GLI family zinc finger-1 (Gli-1) protein from the cytoplasm to the nucleus and upregulated the expression of Sonic hedgehog (Shh), Patched homolog-1 (Ptc-1), smoothened frizzled class receptor and Gli-1. By contrast, the inhibition of Sirt1 using sirtinol had the opposite effect. Conclusions: These findings suggested that Sirt1 may regulate microglial activation and inflammation by targeting the Shh/Gli-1 signaling pathway following OGD/R injury.
Low Energy Consumption Routing Protocol for Oil and Gas Pipeline Internet of Things
Authors: Liu Miao , Liu Yangyang , Yao Rong , Sun Zhenxing 
Published: July 2022

Abstract
For ensuring effective monitoring oil and gas pipelines deployed in the field or arears with poor environment, the wireless sensor network with flexibility, scalability and ease installation has become the basis of the Oil and Gas Pipeline Internet of Things (OGP-IoT). The energy limitation of sensor nodes is the key factor to restrict the performance of OGP-IoT. In addition, the end-to-end delay of the network determines the response time of OGP-IoT to pipeline accidents. It is also the key parameter to improve the real-time performance of OGP-IoT. For solving the problems of energy limitation and end-to-end delay, the Pipeline Internet of Things—Low Energy Consumption Routing Protocol (PIoT-LERP) is proposed in the paper. It can realize the energy balance of the Internet of Things by taking the remaining energy of nodes and the distance between nodes and aggregation nodes as the index of selecting candidate forwarding nodes. So, the life of network is extended and the end-to-end delay of the network is reduced by decreasing the number of data transmission hops. The simulation results show that PIoTLERP can effectively improve the network performance by extending the network life and reducing the network delay comparing with the classical opportunistic routing protocols ExOR and RE-OR.
A novel method for handling missing data in health care real-world study: Optimal Intact Subset Method
Authors: Wu Jingxian , Chang huan , Tong Rongsheng , Wu Xingwei 
Published: July 2022

Abstract
Background
Handling missing data is indispensable in health care real-world data processing. Deleting or imputing missing data may introduce error or lead to multicollinearity. Therefore, we tried to explore a novel missing data processing method to avoid the above issues.
Method
By exploring an optimal deleting way of columns and rows with missing data, we developed a missing data processing method which can retain most information of original datasets. Traditionally, the goal can be realized by traversing all possible deleting combinations. But the computational cost is too high to use in large datasets. Therefore, we established an Optimal Intact Subset Method (OIS.Method) by using an indicator containing missing information of both columns and rows to determine an optimal deleting order of columns. OIS.Method can ascertain the optimal deleting way and simplify computing meanwhile. In order to validate the effectiveness of OIS.Method, we compared OIS.Method with five other data-imputation methods in 700 classification datasets (simulated datasets 1) generated by computer. In order to simulate real-world datasets, we generated simulated datasets 2: introducing redundant variables in simulated datasets 1. We also compared OIS.Method with control methods on that. Finally, we validated OIS.Method in two real-world classification tasks: 1. predict the risk of hypotension during dialysis, 2. predict the risk of drug adverse reaction in elderly patients with type 2 diabetes.
Results
In simulated datasets 1, we found that OIS.Method performed well when the distribution of missing data was unbalanced among columns. In simulated datasets 2, the comprehensive performance of OIS.Method was better in all evaluating dimensions. In two real-world datasets, OIS.Method could acquire better classification performance. We used the area under ROC curve (AUC) to evaluate it: OIS.Method VS Simple Impute VS Random Forest VS Modified Random Forest, 0.8179 ± 0.0005VS0.8116 ± 0.0002VS0.8087 ± 0.0009VS0.8093 ± 0.0014 in task1, and 0.7028VS0.6963VS0.6957VS0.6699 in task2.
Conclusions
Our study provided a novel method for handing missing data in real-world study. Compared with other existing missing data processing methods, the calculation of OIS.Method is smaller, and OIS.Method can reflect the true data situation of original datasets. Moreover, OIS.Method is well-suited for real-world datasets with large sample size and multiple variables.
Insilco Vaccine Design of spike and hemagglutinin esterase proteins of Bovine Coronavirus
Authors: Awadelkareem Eman Ali , S Hamdoun 
Published: July 2022

Abstract

Background: Bovine coronavirus (BCoV) is a widespread, fatal illness in cattle that has a large economic impact in particularly disease-prone hosts. BCoV does not have an effective vaccine. As a result, the objective of this study was to use immunoinformatics and computational tools to design a multi-epitope vaccine against Spike and haemagglutinin proteins of Bovine coronavirus. BCoV proteins were also subjected to protein analysis.Methods: A variety of tools of bioinformatics were used for data analysis. Conserved B and T cell epitopes against BCoV target proteins were predicted using the Immune Epitope Database (IEDB). Proteins were characterized utilizing a variety of servers, including Protparam, PSIPRED and the GOR IV servers. The antigenicity, allergenicity, and toxicity of the anticipated epitopes were assessed as well. Results: Several MHCI epitopes were predicted from S and HE proteins. As top epitopes, the peptides 77NMALKGTLL85 and 56SYMDLNPAL65 were proposed from Spike and hemagglutinin proteins, respectively. These epitopes exhibited high scores of antigenicity, no allergenicity, no toxicity, and a strong connection to Bola alleles.Moreover, three epitopes (1204YYYPE1208, 379TCQPQ384, and 720QLQPINY726) from Spike glycoprotein were selected as surface, linear, and antigenic epitopes using B cell scales. The methods dropped to anticipate effective and safe epitope (s) to cover all B cell scales from HE protein. Conclusion: Three B cell epitopes (1204YYYPE1208, 379TCQPQ384, and 720QLQPINY726) were predicted from Spike protein (S) of BCoV only. MHC I epitopes of S and HE proteins of BCoV (77NMALKGTLL85 and 56SYMDLNPAL65) were shown to have a strong link to Bola alleles, as well as high antigenicity and safety. The predicted epitopes' activity should be tested experimentally as a multi-epitope vaccine against BCoV using in vitro and in vivo trials.
Accumulation of Toxic and Essential Elements in Patients with Gastrointestinal Carcinoma from Pakistan
Authors: Qayyum Muhammad Abdul , Mahmood Mian H.R. , Muddassir Khawaja , shahzad Muhammad , Shad Naveed Akhtar , Hussain Nazim , Ahmad Muhammad 
Published: July 2022

Abstract
The authors have requested that this preprint be removed from Research Square.
Elongin BC complex negatively regulates AXL and marks a differentiated phenotype in melanoma
Authors: Peeper Daniel , Schieven Sebastiaan , Traets Joleen , Vliet Alex , Baalen Martijn , Song Ji-Ying , Kuilman Thomas 
Published: July 2022

Abstract
High expression of the receptor tyrosine kinase AXL is implicated in epithelial-to-mesenchymal transition, cancer progression and therapy resistance. For example, AXL is abundant in BRAF mutant melanomas progressing on targeted BRAF/MEK inhibition. Therefore, AXL is thought to represent an attractive therapeutic target. This notwithstanding, little is known about the mechanisms governing expression of AXL. Here, we describe a fluorescence-activated cell sorting (FACS)-based whole genome-wide CRISPR-Cas9 screen to uncover regulators of AXL expression. We identified several genes, inactivation of which led to increased AXL expression. Most remarkable was the identification of five components that associate with the Elongin B/C heterodimer. The Elongin B/C heterodimer engages in multiple protein-protein interactions, including the transcription factor complex subunit Elongin A, the von Hippel-Lindau (VHL) tumor suppressor protein, and members of the SOCS-box protein family. The screen identified ELOB, ELOC, SOCS5, UBE2F and RNF7, each of which we demonstrate to serve as an inhibitor of AXL expression. Although the AXL promoter contains hypoxia response elements and Elongin B/C are found in the VHL complex, Elongin B/C unexpectedly regulate AXL independently of hypoxia. Instead, we demonstrate that the Elongin BC complex interacts with AXL through ELOB, and contributes to proteasomal AXL turnover. RNA-sequencing analysis of several melanoma datasets revealed a negative association between Elongin B/C and dedifferentiation. This was confirmed by immunohistochemistry in patient-derived melanoma xenografts. These results uncover the Elongin BC complex as a key determinant of AXL expression in melanoma, and that this correlates with a differentiated state.
Environmental Impact Assessment of Air-Purifying Paver Blocks Using Photocatalysis and Sensors Technology
Authors: Partheeban Pachaivannan , Christopher Chella Gifta , Anuradha Baskaran , Keerthana Sureshbabu , Haripriya Nagaraju 
Published: July 2022

Abstract
Air pollution is a major problem in India, and vehicular emissions cause about 27% of air pollution in urban areas. The major pollutants released from vehicles are carbon monoxide, carbon dioxide, nitrous oxide, photochemical oxidants, etc. The present investigation emphasizes the utilization of power plant waste materials effectively to replace the natural fine aggregate, leads to a new dimension of manufacturing concrete paver blocks. M-sand is replaced by bottom ash from 50–100%, and natural coarse aggregate is replaced with recycled coarse aggregates. Materials such as titanium dioxide (TiO2) and recycled glass particles are also incorporated to improve the photodegradation of air pollutants. Concrete paver blocks were prepared and tested, and the compressive strength of the various mixes were compared with other research works. Real-time air quality is monitored using an Internet of Things (IoT) device developed to assess the performance of paver blocks laid on the roadside. The results concluded that bottom ash could be replaced with natural fine aggregate and recycled coarse aggregate can be replaced with natural coarse aggregate. Real time study results of air quality monitoring IoT device concluded that the pollution concentrations have been reduced up to 50%.