bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Niche Differentiation and Biogeography of Bathyarchaeia in Paddy Soil Ecosystems: A Case Study in Eastern China
Authors: Yi Xingyun , Brandt Kristian Koefoed , Xue Shu-Dan , Peng Jingjing , Wang Yi-Fei , Li Meng , Deng Ye , Duan Guilan 
Published: November 2023

Abstract
Bathyarchaeia (formerly Bathyarchaeota) is a group of highly abundant archaeal communities that play important roles in global biogeochemical cycling. Bathyarchaeia is predominantly found in sediments and hot springs. However, their presence in arable soils is relatively limited. In this study, we aimed to investigate the spatial distributions and diversity of Bathyarchaeia in paddy soils across eastern China, which is a major rice production region. The relative abundance of Bathyarchaeia among total archaea ranged from 3–68% in paddy soils, and Bathy-6 was the dominant subgroup among the Bathyarchaeia (70–80% of all sequences). Bathyarchaeia showed higher migration ability and wider niche width based on the neutral and null model simulations. Bathy-6 was primarily assembled by deterministic processes. Soil pH and C/N ratio were identified as key factors influencing the Bathyarchaeia composition, whereas C/N ratio and mean annual temperature influenced the relative abundance of Bathyarchaeia. Network analysis showed that specific Bathyarchaeia taxa occupied keystone positions in the archaeal community and co-occurred with some methanogenic archaea, including Methanosarcinia and Methanobacteria, and ammonia-oxidizing archaea belonging to Nitrososphaeria. This study provides important insights into the biogeography and niche differentiation of Bathyarchaeia particularly in paddy soil ecosystems.
Piloting a language translation device for Mandarin-speaking patients presenting for radiotherapy treatment – assessing patient and radiation therapist perspectives
Authors: Hunter Darren , Anderson Nigel , Oates Richard , Kok David , Sapkaroski Daniel , Treffry Nicola , Wright Caroline 
Published: November 2023

Abstract

Purpose
Culturally and linguistically diverse (CALD) cancer patients report unmet informational and emotional needs when receiving radiotherapy (RT). This feasibility study aimed to evaluate the clinical use of an instant translation device (ITD) to facilitate communication between Mandarin-speaking patients and radiation therapists (RTTs) within the Australian public RT setting. The primary aim was to assess the ability to convey information relating to daily patient care and build rapport using the device.
Methods
A single-arm prospective interventional trial was employed with patient and RTT participants. Eligible patient participants were aged 18 years or older, diagnosed with cancer, referred for RT with self-reported Mandarin as the primary language spoken at home. Patients who had previously received RT were excluded. Consenting patient participants completed a baseline assessment of health literacy (REALM-SF) and English proficiency (LexTALE). Surveys were administered to patients and consenting RTTs at the cessation of treatment, forming two distinct participant groups. Descriptive statistics were used to compare participant groups.
Results
Eleven patients and 36 RTTs were recruited to the study. Descriptive statistics demonstrated participant group agreement in conveying treatment instructions, though differing experiences were reported against general conversation. Although the reporting of technical difficulties were inconsistent, both groups recommended the application of the ITD within the RT domain.
Conclusion
This feasibility study demonstrated encouraging accounts of patients and RTTs with regard to ITD use in the context of RT treatment. Expanded, multi-institutional recruitment is required to yield statistical significance, inform the impact of the device and determine requisite training requirements.
miRNA Profiling of 3'UTR Variations in Sporadic Lung Carcinoma Tumours
Authors: Bagci Ozkan 
Published: November 2023

Abstract
Background
The aim of the study was to determine the exonic and 3'UTR sequences of EGFR, PIK3CA and KRAS genes in 39 sporadic lung cancer tumors and to reveal the relationship between the changes in the miRNA binding profile of tumors with somatic variation in the 3'UTR region and the metastatic status of the tumors.
Methods
The exonic and 3'UTR sequences of three genes in 39 sporadic lung carcinoma tumors were extracted by next generation sequencing. In tumors with somatic variation in the 3'UTR region, the changes caused by the variation in the miRNA binding profile were determined by bioinformatic analysis. The expression profile of miRNAs in lung cancer and other solid tumors compared to normal tissue was determined. Pathway analysis was performed to determine which signaling pathways are affected by miRNAs that differ depending on variation.
Results
A statistically significant correlation was found between the presence of miRNA that could not bind to the 3'UTR region due to variation in at least one of the EGFR or KRAS genes and the presence of metastasis in the tumor. It was revealed that variations in the 3'UTR regions of EGFR and KRAS oncogenes may be associated with the mechanism of metastasis and drug resistance as a result of their ability to cause increased expression of these oncogenes by preventing the binding of some miRNAs.
Conclusion
In this study, hsa-miR-124-3p, hsa-miR-506-3p, hsa-miR-1290 and hsa-miR-6514-3p were found to be particularly prominent in lung carcinoma in relation to these biological pathways.
In situ infrared of gas/particle conversion reaction of SO2, NO2 and NH3 mixture gases
Authors: Deng Wenye , Ai Ni , Yang Jing , Xie Yongxin , Liu Yi , Wu Yongmei , Yu Huailiang , Zhang Xuezhu 
Published: November 2023

Abstract
The gas/particle transformation reaction of gaseous precursors (SO2, NO2, NH3) at high concentrations is the main pathway for the generation of secondary inorganic particulate matter (SIPM), and the change of SIPM concentration is closely related to the change of PM2.5 mass concentration, so the control of the emission of SO2, NO2, and NH3 is the key to reduce the formation of secondary inorganic particulate matter (SIPM). This paper focuses on the gas/particle transformation process of SO2, NO2 and NH3 gas mixture in the atmosphere and explores the influence of environmental factors on the gas/particle transformation reaction. The results show that in the gas mixture of SO2, NO2 and NH3, NH3 is favorable for the gas/granule transformation reaction of mineral particles to generate (NH4)2SO4 and NH4NO3 after the oxidation of SO2 and NO2 into SO2- 4 and NO- 3. The environmental conditions have an effect on the gas/granule transformation reaction of secondary inorganic ions, and the gas/granule transformation reaction is favorable for the gas/granule transformation reaction with the appropriate gas/granule ratio of the pollutants, a certain amount of relative humidity, and a certain amount of illumination is favorable for the gas/granule conversion reaction.
Cytological Characteristics of Bone Marrow in Sepsis-Associated Thrombocytopenia: A Retrospective Case-control Study
Authors: Zhao Jiwei , Luo Qu , Zeng Fanlang , Xiang LeYang , Zhi Yaowei , Cai Yueqing , Zhang Meng , Zeng Zhifen 
Published: November 2023

Abstract
Objective To compare the cytological characteristics of bone marrow cells in patients with sepsis with or without thrombocytopenia and their clinical significance.
Methods Ninety-one patients diagnosed with sepsis in the Department of General Practice, Sun Yat-sen Memorial Hospital of Sun Yat-sen University between February 2016 and December 2022 were retrospectively recruited in this study, and their clinical parameters, bone marrow smears and examination results, and blood routine examination results were collected. Patients were divided into thrombocytopenia (TP) group and non-thrombocytopenia (non-TP) group according to the count of peripheral blood platelets, the clinical parameters and the cytological characteristics of bone marrow cells were compared between two groups.
Results Hypoplasia of marrow was more frequent in TP group (26.5%, 13/49) compared to the non-TP group (4.8%, 2/42; P = 0.005) and the occurrence of reduced megakaryocyte or dysmaturity was more common in TP group (31/49, 63.3%) compared to that in the non-TP group (13/42, 31.0%; P = 0.002). The number of bone marrow megakaryocytes was positively correlated with the count of peripheral blood platelets in all patients (r = 0.2884, P = 0.0056) and the non-TP group (r = 0.3316, p = 0.0319), but there was no correlation in the TP group; Moreover, the hemoglobin level, the white blood cell, granulocyte, lymphocyte, and monocyte count were lower in TP group than those in non-TP group. Furthermore，a significant higher incidence of MODS was observed in TP group (29/49, 59.2%) compared to non-TP group (14/42, 33.3%; P = 0.014) and the mean SOFA scores in TP group were higher than that in non-TP group (9.69 ± 3.92 vs 7.83±3.87, P = 0.026).
Conclusions The decreased production of platelets, which is secondary to marrow cell failure, is an exact mechanism of sepsis-associatedthrombocytopenia. Thus, precautions and intervention should been taken early during the treatment.
Leveraging Diverse Regulated Cell Death for Prognostic Prediction of Pancreatic Cancer Using Machine Learning and Multi-omics Analysis
Authors: wu zhaowei , Zhou Chao , Jiang Shiming , Chen Yong 
Published: November 2023

Abstract

Pancreatic cancer is an aggressive form of cancer with poor prognosis. Recent findings indicate that regulated cell death (RCD) significantly contributes to tumor growth, which could be a potential prognostic indicator for pancreatic cancer. We utilized weighted gene co-expression network analysis to extract 103 genes shared by different subtypes of RCD (apoptosis, ferroptosis, necroptosis, pyroptosis, and entotic cell death). Following our analysis, we conducted cross-validation on 15 machine learning algorithms, testing a total of 167 combinations to establish a predictive model. The combination of deep learning and random survival forest achieved the highest C-index among the 167 evaluated machine learning algorithms. Therefore, it has been selected for further research. Patients were divided into high- and low-risk group. The high-risk group of pancreatic cancer patients had poorer prognosis when validated in three independent datasets. Further analysis revealed that individuals in the high-risk group were more likely to respond to immunotherapy and chemotherapy. Based on the proteome data, the protein expression of shared genes was significantly differentially expressed between pancreatic cancer and normal control. For MYOF, a shared gene, expression levels were significantly higher in pancreatic cancer tissues compared to adjacent tissues by PCR. Additional experimental results demonstrate MYOF's involvement in various processes, including proliferation, viability, invasion, and migration in pancreatic carcinoma cells. These results highlight its potential as a significant target for further investigation.
Toward neutral carbon integrated production y silvopastoral systems: an Uruguayan study case modeled using agent-based technique
Authors: Cameroni Francisco José Dieguez , Casadey Fabián Varela , Boscana Mariana , Bussoni Adriana 
Published: November 2023

Abstract
The aim of this study was to assess management practices, productivity, and greenhouse gas outcomes using multi-agent modeling of a livestock system incorporating agroforestry modules. The agent-based model simulates the dynamics of animal growth, forage, and tree vegetation in several scenarios. Simulation results were evaluated over 10-year periods using a case study. Rotational grazing and forestry presence in grazing paddocks induce changes in system-wide interactions and productivity. That combined production allows for adjusting animal stocking rates and achieving a balance between forage availability and cattle demand, considering also tree-cattle interactions. Through stocking rate management, a balance between forage supply and demand can be achieved, with an improvement in net greenhouse gas reduction as livestock weight gain increases. In our study case, carbon-neutral beef production is achieved with a ratio of 380 steers at 606 ha grazing area with 13% forested surface. Estimated greenhouse gas emission intensity exhibits an inverse exponential relationship with weight gain. The agent-based modeling is a valuable tool for understanding the complexity of these systems, generating emergent properties. The study underscores the importance of implementing sustainable livestock practices and integrating agroforestry systems as a mitigation strategy.
Two-sample Mendelian randomization study reveals no causal relationship between inflammatory bowel disease and urological cancers
Authors: Zhang Haoyang , Hu Can , Zhang Zhiyu , Li Peng , Shen Gang , Sun Jiale 
Published: November 2023

Abstract

Background:Relationships between inflammatory bowel disease (IBD) and urologic cancers have been identified in previous epidemiologic and observational studies, but causality remains uncertain. We tried to examine whether IBD was causally associated with urological cancers in this Mendelian randomization (MR) study.Methods:The causal relationship between IBD and its main subtypes and urological cancers were investigated using genome-wide association study (GWAS) data. To get a more reliable conclusion, all outcomes were then divided into training set and validation set. Eligible single-nucleotide polymorphisms (SNPs) were selected as instrumental variables (IVs) based on the assumptions of the MR analysis. The Inverse variance weighted (IVW) was applied as the main method with four others as complementary methods.Results:In this two-sample MR study, no genetic evidence for causal effect of IBD on urological cancers was found neither in the training set nor in the validation set using IVW method. Likewise, we did not observe any significant association of Crohn’s disease (CD) and ulcerative colitis (UC) on urological cancers. Results of other methods were in accordance with those of the IVW method.Conclusion:In this study, we confirmed that IBD was not a genetic causal risk factor for urological cancers in European population.
Identification of hypoxia- and immune- based prognostic signature and validation of TFRC as a potential biomarker and therapeutic target in BLCA
Authors: Tang Runhua , Wang Haoran , Liu Jianyong , Song Liuqi , Hou Huimin , Liu Ming , Wang Jianye , Wang Jianlong 
Published: November 2023

Abstract
Background
Bladder cancer is a common malignancy of the urinary system, and the survival rate and recurrence rate of patients with muscular aggressive (MIBC) bladder cancer are not ideal. Hypoxia is a pathological process in which cells acquire special characteristics to adapt to anoxic environment, which can directly affect the proliferation, invasion and immune response of bladder cancer cells. Understanding the exact effects of hypoxia and immune-related genes in BLCA is helpful for early assessment of the prognosis of BLCA. However, the prognostic model of BLCA based on hypoxia and immune-related genes has not been reported.
Purpose
Hypoxia and immune cell have important role in the prognosis of bladder cancer (BLCA). The aim of this study was to investigate whether hypoxia and immune related genes could be a novel tools to predict the overall survival and immunotherapy of BLCA patients.
Methods
Firstly, we downloaded transcriptomic data and clinical information of BLCA patients from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases. A combined hypoxia and immune signature was then constructed on the basis of the training cohort via least absolute shrinkage and selection operator (LASSO) analysis and validated in test cohort. Afterwards, Kaplan-Meier curves, univariate and multivariate Cox and subgroup analysis were employed to assess the accuracy of our signature. Immune cell infiltration, checkpoint and the Tumor Immune Dysfunction and Exclusion (TIDE) algorithm were used to investigate the immune environment and immunotherapy of BLCA patients. Furthermore, we We confirmed the role of TFRC in bladder cancer cell lines T24 and UMUC-3 through cell experiments.
Results
A combined hypoxia and immune signature containing 8 genes were successfully established. High-risk group in both training and test cohorts had significantly poorer OS than low-risk group. univariate and multivariate Cox analysis indicated our signature could be regarded as an independent prognostic factor. Different checkpoint was differently expressed between two groups, including CTLA4, HAVCR2, LAG3, PD-L1 and PDCD1. TIDE analysis indicated high-risk patients had poor response to immunotherapy and easier to have immune escape. The drug sensitivity analysis showed high-risk group patients were more potentially sensitive to many drugs. Meanwhile, TFRC could inhibit the proliferation and invasion ability of T24 and UMUC-3 cells.
Conclusion
A combined hypoxia and immune-related gene could be a novel predictive model for OS and immunotherapy estimation of BLCA patients and TFRC could be used as a potential therapeutic target in the future.
Smart City Digital Twin Framework for Real-Time Multi-Data Integration and Wide Public Distribution
Authors: Adreani Lorenzo , Bellini Pierfrancesco , Fanfani Marco , Nesi Paolo , Pantaleo Gianni 
Published: November 2023

Abstract

Digital Twins are becoming fundamental tools to monitor the status of entities, predict their future evolutions, and simulate alternative scenarios to understand the impact of possible changes. More recently, Digital Twin solutions have been applied in the context of Smart Cities. Thanks to the large deployment of sensors, together with the increasing amount of information available for municipalities and government organizations, it is possible to build wide virtual reproductions of urban environments including structural data and real-time information that can undoubtfully help city councils and decision makers to face future challenges in the urban development and improve the citizen quality of life. In this paper, the Snap4City Smart City Digital Twin framework is presented, which is capable to respond to requirements identified in recent literature and by international forums. The proposed architecture provides an integrated solution for data gathering, indexing, computing, and information distribution, therefore realizing a continuously updated digital twin of the urban environment at global and local scales. It addresses 3D building models, road networks, Internet of Things entities, point of interests, paths, as well as results from analytical processes for traffic density reconstruction, pollutant dispersion, predictions, and what-if analysis with dynamic and constrained routing, all integrated into a freely accessible interactive 3D web interface, enabling stakeholder and citizens participation to the city decision processes. As case of study, the digital twin of the city of Florence (Italy) is presented. The solution is released on top of the Snap4City platform as open-source and made available through our GitHub repository (https://github.com/disit) and as Docker compose.
Examining Surgeon Stress in Robotic and Laparoscopic Surgery
Authors: Sujka Joseph , Ahmed Abrahim , Kang Richard , Grimsley Emily A. , Weche Mcwayne , Janjua Haroon , Mi Zhiyong , English Diana , Martinez Carolina , Velanovich Vic , Bennett Robert , Docimo Salvatore , Saad Adham , DuCoin Christopher , Kuo Paul 
Published: November 2023

Abstract
Background:
Robotic surgery may decrease surgeon stress compared to laparoscopic. To evaluate intraoperative surgeon stress, we measured salivary alpha-amylase and cortisol. We hypothesized robotic elicited lower increases in surgeon salivary amylase and cortisol than laparoscopic.
Study Design:
Surgical faculty (n=7) performing laparoscopic and robotic operations participated. Demographics: age, years in practice, time using laparoscopic vs robotic, comfort level and enthusiasm for each. Operative data included operative time, WRVU (surgical “effort”), resident year. Saliva was collected using passive drool collection system at beginning, middle and end of each case; amylase and cortisol measured using ELISA. Standard values were created using seven-minute exercise (HIIT), collecting saliva pre- and post-workout. Linear regression and Student’s t test used for statistical analysis; p-values < 0.05 were significant.
Results:
Ninety-four cases (56 robotic, 38 laparoscopic) were collected (April-October 2022). Standardized change in amylase was 8.4±4.5 (p<0.001). Among operations, raw maximum amylase change in laparoscopic and robotic was 23.4±11.5 and 22.2±13.4; raw maximum cortisol change was 44.21±46.57 and 53.21±50.36 respectively. Values normalized to individual surgeon HIIT response, WRVU, and operative time, showing 40% decrease in amylase in robotic: 0.095±0.12, vs laparoscopic: 0.164±0.16 (p<0.02). Normalized change in cortisol was: laparoscopic 0.30±0.44, robotic 0.22±0.4 (p=NS). On linear regression (p<0.001), surgeons comfortable with complex laparoscopic cases had lower change in normalized amylase (p<0.01); comfort with complex robotic was not significant.
Conclusion:
Robotic may be less physiologically stressful, eliciting less increase in salivary amylase than laparoscopic. Comfort with complex laparoscopic decreased stress in robotic, suggesting laparoscopic experience is valuable prior to robotic.
Analyses of CTNNB1 mutation, β-catenin expression and clinicopathological characteristics in 179 cases of solid-pseudopapillary neoplasm of the pancreas
Authors: Zhao Shuai , Wang Jian , Lu Chenglu , Sun Lin , Shao Bing , Gao Song , Sun Yan 
Published: November 2023

Abstract

Solid-pseudopapillary neoplasm (SPN) of the pancreas is a low-grade malignant tumour, that mainly affects young females. Given its typical clinical characteristics, histopathological morphology and immunohistochemical nuclear expression of β-catenin, it is usually not difficult to diagnose SPN. However, nuclear expression of β-catenin is occasionally negative or false negative in SPN, leading to a missed diagnosis. In this study, we aimed to investigate the clinical significance of CTNNB1 mutation detection for diagnosing SPN and explore the difference in clinicopathological characteristics between female and male patients at different ages. We detected point mutations in exon 3 of CTNNB1 in 74.3% (133/179) of SPNs by Sanger sequencing. The main mutation sites were D32 (26%), S33 (23%), S37 (21%), G34 (14%) and T41 (11%). In the 3 SPNs without nuclear expression of β-catenin, Sanger sequencing showed the S33C mutation in exon 3 of CTNNB1 in two cases but not in one case in which next-generation sequencing detected the S37C mutation. Therefore, for atypical cases, testing for CTNNB1 mutations can help in the accurate diagnosis of SPN. The median age of the 179 patients was 31 years (6 ~ 64 years), and there were 32 male patients (17.9%) in this cohort. The tumour size, Ki-67 index, and the negative rates of β-catenin nuclear expression and syn expression in the paediatric group were higher than those in youth group and old group (P < 0.05 for all). There was no significant difference in age, tumour site; tumour size; expression of β-catenin, CD10, PR, Vimentin or Syn; Ki-67 index; or proportion of CTNNB1 mutations between male and female patients (P < 0.05 for all). Compared with middle-aged and elderly patients, paediatric with SPN may be more prone to recurrence, and their immunohistochemical phenotype is more complex, requiring additional care in the diagnosis and postoperative follow-up.