bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transformer-based tool recommendation system in Galaxy
Authors: Kumar Anup , Grüning Björn , Backofen Rolf 
Published: November 2023

Abstract
Background
Galaxy is a web-based open-source platform for scientific analyses. Researchers use thousands of high-quality tools and workflows for their respective analyses in Galaxy. Tool recommender system predicts a collection of tools that can be used to extend an analysis. In this work, a tool recommender system is developed by training a transformer on workflows available on Galaxy Europe and its performance is compared to other neural networks such as recurrent, convolutional and dense neural networks.

Results
The transformer neural network achieves two times faster convergence, has significantly lower model usage (model reconstruction and prediction) time and shows a better generalisation that goes beyond training workflows than the older tool recommender system created using RNN in Galaxy. In addition, the transformer also outperforms CNN and DNN on several key indicators. It achieves a faster convergence time, lower model usage time, and higher quality tool recommendations than CNN. Compared to DNN, it converges faster to a higher precision@k metric (approximately 0.98 by transformer compared to approximately 0.9 by DNN) and shows higher quality tool recommendations.

Conclusion
Our work shows a novel usage of transformers to recommend tools for extending scientific workflows. A more robust tool recommendation model, created using a transformer, having significantly lower usage time than RNN and CNN, higher precision@k than DNN, and higher quality tool recommendations than all three neural networks, will benefit researchers in creating scientifically significant workflows and exploratory data analysis in Galaxy. Additionally, the ability to train faster than all three neural networks imparts more scalability for training on larger datasets consisting of millions of tool sequences. Open-source scripts to create the recommendation model are available under MIT licence at https://github.com/anuprulez/galaxy_tool_recommendation_transformers
Strontium ranelate enriched Ruminococcus albus in the gut microbiome of Sprague–Dawley rats with postmenopausal osteoporosis
Authors: Xiao Xiao , Cui Yuanyuan , Lu Huigai , Wang Jiaqi , Yang Jing , Liu Long , Liu Zhixin , Peng Xiaohong , Cao Hong , Liu Xinghui , Wei Xiuli 
Published: November 2023

Abstract
Background
Gut microbiome is critical to our human health and is related to postmenopausal osteoporosis (PMO). Strontium ranelate (SrR) is an anti-osteoporosis oral drug that can promote osteoblast formation and inhibit osteoclast formation. However, the effect of SrR on gut microbiome has been rarely studied. Therefore, we investigated the effect of oral SrR on gut microbiome and metabolic profiles.

Results
In this study, we used ovariectomized (OVX) Sprague–Dawley rats to construct a PMO model and applied oral SrR for 6 weeks. The relative abundance of intestinal microbiome was investigated by 16S rRNA metagenomic sequencing. Ultra-high-performance liquid chromatography-mass spectrometry (UHPLC-MS) was used to analyze changes in metabolites of intestinal contents. Results demonstrated that 6-week oral SrR alleviated osteoporosis and significantly changed the composition of the gut microbiome and metabolic profiles of OVX rats. Ruminococcus, Akkermansia and Oscillospira were significantly enriched in the gut of OVX rats after 6-week oral SrR. Especially, the species R. albus showed the greatest importance by a random forest classifier between OVX and OVX_Sr group. The enrichment of R. albus in the gut was positively correlated with bone mineral density and the accumulation of lycopene and glutaric acid, which also significantly elevated after oral SrR.

Conclusions
We discovered that oral SrR can improve bone health while stimulate the accumulation of gut microbe R. albus and metabolites (lycopene and glutaric acid). The results suggested possible connections between oral SrR and the gut-bone axis, which may provide new insight into the treatment/prevention of osteoporosis.
Relationship between clinical features and droplet digital PCR copy number in non-HIV patients with pneumocystis pneumonia
Authors: Bian Wenjie , Xie Yu , Shang Ying , Zhao Lili , Yang Zhengwu , Ma Xinqian , He Yukun , Yu Wenyi , Xi Wen , Yang Donghong , Wang Fang , Chen Yanwen , Gong Pihua , Gao Zhancheng 
Published: November 2023

Abstract
Objective
Droplet digital PCR (ddPCR) is a novel assay to detect pneumocystis jjrovecii (Pj) which has been defined to be more sensitive than qPCR in recent studies. We aimed to explore whether clinical features of pneumocystis pneumonia (PCP) were associated with ddPCR copy numbers of Pj.

Methods
A total of 48 PCP patients were retrospectively included. Pj detection was implemented by ddPCR assay within 4 h. Bronchoalveolar fluid (BALF) samples were collected from 48 patients with molecular diagnosis as PCP via metagenomic next generation sequencing (mNGS) or quantitative PCR detection. Univariate and multivariate logistic regression were performed to screen out possible indicators for the severity of PCP. The patients were divided into two groups according to ddPCR copy numbers, and their clinical features were further analyzed.

Results
Pj loading was a pro rata increase with serum (1,3)-beta-D glucan, D-dimmer, neutrophil percentage, procalcitonin and BALF polymorphonuclear leucocyte percentage, while negative correlation with albumin, PaO2/FiO2, BALF cell count, and BALF lymphocyte percentage. D-dimmer and ddPCR copy number of Pj were independent indicators for moderate/severe PCP patients with PaO2/FiO2 lower than 300. We made a ROC analysis of ddPCR copy number of Pj for PaO2/FiO2 index and grouped the patients according to the cut-off value (2.75). The high copy numbers group was characterized by higher level of inflammatory markers. Compared to low copy number group, there was lower level of the total cell count while higher level of polymorphonuclear leucocyte percentage in BALF in the high copy numbers group. Different from patients with high copy numbers, those with high copy numbers had a tendency to develop more severe complications and required advanced respiratory support.

Conclusion
The scenarios of patients infected with high ddPCR copy numbers of Pj showed more adverse clinical conditions. Pj loading could reflect the severity of PCP to some extent.
Clinical efficacy and safety of tigecycline based on therapeutic drug monitoring for carbapenem-resistant Gram-negative bacterium pneumonia in intensive care units
Authors: Bai Xiang-rong , Wang Zhi-zhou , Li Wen-chao , Wang Yan-gai , Lou Ran , Qu Xin , Fan Linlin , Zhang Wei , Wu Yan-chuan , Yan Su-ying , Zhang Lan 
Published: November 2023

Abstract
Background
We investigated the associations between the different doses of tigecycline, its efficacy and safety, and the role of tigecycline therapeutic drug monitoring for patients in the intensive care unit.

Methods
This study was a single-center cohort including patients infected with multidrug-resistant Acinetobacter baumannii (MDR-AB) and multidrug-resistant Klebsiella pneumoniae (MDR-KP) causing pulmonary infections. The steady-state plasma concentration after tigecycline administration was determined by High-Performance Liquid Chromatography (HPLC) in patients admitted to the ICU between October 2020 and December 2021. Multivariate analyses of tigecycline’s clinical efficacy and safety were performed to control confounding factors.

Results
For this study, we included 45 patients and 45 blood samples to determine steady-state trough concentrations of tigecycline. All patients were divided into the High Dose (HD) and Standard Dose (SD) groups. The median trough concentration of tigecycline was 0.56 μg/mL in the HD group, which was higher than in the SD group (0,21 μg/mL), p = 0.000. There was no significant difference between the two groups of patients in terms of bacterial eradication rate, mortality rate, and clinical efficacy. Multiple regression analysis showed that the ICU days were correlated with mortality OR 1.030(1.005–1.056), p = 0.017. APACHE II was significantly associated with clinical efficacy OR 0.870(0.755–1.002), p = 0.045. The level of fibrinogen decline in the HD group was significantly higher than in the SD group (-3.05 ± 1.67 vs -1.75 ± 1.90), p = 0.038. We identified that age and tigecycline treatment duration influenced fibrinogen decline.

Conclusions
Tigecycline plasma concentrations are significantly increased when using a high dose. However, the plasma concentration of tigecycline is not correlated with clinical efficacy and adverse reactions. Fibrinogen decline appears to be related to the patient’s age and days of tigecycline. Large sample data are still needed to confirm the clinical guidance significance of tigecycline TDM.
Quantitative CT parameters combined with preoperative systemic inflammatory markers for differentiating risk subgroups of thymic epithelial tumors
Authors: Gao Rongji , Zhou Jian , Zhang Juan , Zhu Jianzhong , Wang Tiantian , Yan Chengxin 
Published: November 2023

Abstract
Background
Thymic epithelial tumors (TETs) are the most common primary neoplasms of the anterior mediastinum. Different risk subgroups of TETs have different prognosis and therapeutic strategies, therefore, preoperative identification of different risk subgroups is of high clinical significance. This study aims to explore the diagnostic efficiency of quantitative computed tomography (CT) parameters combined with preoperative systemic inflammatory markers in differentiating low-risk thymic epithelial tumors (LTETs) from high-risk thymic epithelial tumors (HTETs).

Methods
74 Asian patients with TETs confirmed by biopsy or postoperative pathology between January 2013 and October 2022 were collected retrospectively and divided into two risk subgroups: LTET group (type A, AB and B1 thymomas) and HTET group (type B2, B3 thymomas and thymic carcinoma). Statistical analysis were performed between the two groups in terms of quantitative CT parameters and preoperative systemic inflammatory markers. Multivariate logistic regression analysis was used to determine the independent predictors of risk subgroups of TETs. The area under curve (AUC) and optimal cut-off values were calculated by receiver operating characteristic (ROC) curves.

Results
47 TETs were in LTET group, while 27 TETs were in HTET group. In addition to tumor size and CT value of the tumor on plain scan, there were statistical significance comparing in CT value of the tumor on arterial phase (CTv-AP) and venous phase (CTv-VP), and maximum enhanced CT value (CEmax) of the tumor between the two groups (for all, P < 0.05). For systemic inflammatory markers, HTET group was significantly higher than LTET group (for all, P < 0.05), including platelet-to-lymphocyte ratio (PLR), neutrophil-to-lymphocyte ratio (NLR) and systemic immune-inflammation index (SII). Multivariate logistic regression analysis showed that NLR (odds ratio [OR] = 2.511, 95% confidence interval [CI]: 1.322–4.772, P = 0.005), CTv-AP (OR = 0.939, 95%CI: 0.888–0.994, P = 0.031) and CTv-VP (OR = 0.923, 95%CI: 0.871–0.979, P = 0.008) were the independent predictors of risk subgroups of TETs. The AUC value of 0.887 for the combined model was significantly higher than NLR (0.698), CTv-AP (0.800) or CTv-VP (0.811) alone. The optimal cut-off values for NLR, CTv-AP and CTv-VP were 2.523, 63.44 Hounsfeld Unit (HU) and 88.29HU, respectively.

Conclusions
Quantitative CT parameters and preoperative systemic inflammatory markers can differentiate LTETs from HTETs, and the combined model has the potential to improve diagnostic efficiency and to help the patient management.
Comparison of the new self-contained darkroom refractive screener versus table-top autorefractor and cycloplegia retinoscopy in detecting refractive error
Authors: Wei Xianxian , Li Lili , Jiang Li , Lu Haiyan , Huang Huiyao , Zhong Dedong , Pan Liang , Wei Diefeng , Han Yun , Lin Hong , Chen Qi 
Published: November 2023

Abstract
Purpose
By comparing the results of the new self-contained darkroom refractive screener (YD-SX-A) versus table-top autorefractor and cycloplegic retinoscopy, to evaluate the performance of the YD-SX-A in detecting refractive error in children and adolescents and then judge whether it can be used in refractive screening.

Methods
Cross-sectional study. 1000 participants between the ages of 6 and 18 who visited the Optometry Center of the People's Hospital of Guangxi Zhuang Autonomous Region from June to December 2022 were selected. First, participants were instructed to measure their diopter with a table-top autorefractor (Topcon KR8800) and YD-SX-A in a noncycloplegic setting. After cycloplegia, they were retinoscopy by a professional optometrist. The results measured by three methods were collected respectively. To avoid deviation, only the right eye (1000 eyes) data were used in the statistical analysis. The Bland–Altman plots were used to evaluate the agreement of diopters measured by the three methods. The receiver operating characteristic (ROC) curves was used to analysis effectiveness of detecting refractive error of YD-SX-A.

Results
The average age of participants was 10.77 ± 3.00 years, including 504 boys (50.4%) and 496 girls (49.6%). When YD-SX-A and cycloplegia retinoscopy (CR) were compared in the myopia group, there was no statistical difference in spherical equivalent (SE) (P > 0.05), but there was a statistical difference in diopter spherical (DS) and diopter cylinder (DC) (P < 0.05). Comparing the diopter results of Topcon KR8800 and CR, the difference between each test value in the myopia group was statistically significant (P < 0.05). In the hyperopia group, the comparison between YD-SX-A and CR showed no statistically significant differences in the DC (P > 0.05), but there were significant differences in the SE and DS (P < 0.05). In the astigmatism group, the SE, DS, and DC were statistically different, and the DC of YD-SX-A was lower than that of CR and Topcon KR8800. Bland–Altman plots indicated that YD-SX-A has a moderate agreement with CR and Topcon KR8800. The sensitivity and specificity of YD-SX-A for detecting myopia, hyperopia and astigmatism were 90.17% and 90.32%, 97.78% and 87.88%, 84.08% and 74.26%, respectively.

Conclusion
This study has identified that YD-SX-A has shown good performance in both agreement and effectiveness in detecting refractive error when compared with Topcon KR8800 and CR. YD-SX-A could be a useful tool for large-scale population refractive screening.
Introduction of pediatric laparoscopic inguinal hernia repair in Guatemala
Authors: Cóbar Juan P. , Nichol Peter F. 
Published: November 2023

Abstract
Purpose
Introducing new surgical techniques in a developing country can be challenging. Inguinal hernias in children are a common surgical problem, and open repair is the standard surgical approach. Laparoscopic repair has gained popularity in developed countries because of similar results. This study aimed to determine the outcomes following the introduction of laparoscopic repairs in Guatemala.

Methods
This retrospective analysis of prospectively collected data from all patients under 18 years who underwent laparoscopic repair at Corpus Christi Hospital in Patzun, Guatemala, from September 5th to September 8th, 2022.

Results
A total of 14 patients were included in the study. A board-certified pediatric surgeon and a Guatemalan physician performed all cases. The mean patient age was 7.6 years; 7 boys and 7 girls. All patients were interviewed at 7 days, 30 days, and 6 months. There were no postoperative infections, pain requiring re-evaluation, gonadal atrophy, or hernia recurrence.

Conclusion
Under controlled circumstances with limited but proper equipment and disposables, laparoscopic inguinal hernia repairs can be introduced and performed in a developing country with a risk complication profile comparable to that in developed countries. This study provides promising evidence of laparoscopic repair feasibility and safety where surgical resources are limited.
A prediction model for identifying high-risk lymph node metastasis in clinical low-risk papillary thyroid microcarcinoma
Authors: Huang Hui , Liu Yunhe , Ni Song , Liu Shaoyan 
Published: November 2023

Abstract
Background
The presence of high-volume lymph node metastasis (LNM) and extranodal extension (ENE) greatly increases the risk of recurrence in patients with low-risk papillary thyroid microcarcinoma (PTMC). The goal of this research was to analyze the factors that contribute to high-risk lymph node metastasis in patients with low-risk PTMC.

Methods
We analyzed the records of 7344 patients who were diagnosed with low-risk PTMC and treated at our center from January 2013 to June 2018.LNM with a high volume or ENE was classified as high-risk lymph node metastasis (hr-LNM). A logistic regression analysis was conducted to identify the risk factors associated with hr-LNM. A nomogram was created and verified using risk factors obtained from LASSO regression analysis, to predict the likelihood of hr-LNM.

Results
The rate of hr-LNM was 6.5%. LASSO regression revealed six variables that independently contribute to hr-LNM: sex, age, tumor size, tumor location, Hashimoto’s thyroiditis (HT), and microscopic capsular invasion. A predictive nomogram was developed by integrating these risk factors, demonstrating its excellent performance. Upon analyzing the receiver operating characteristic (ROC) curve for predicting hr-LNM, it was observed that the area under the curve (AUC) had a value of 0.745 and 0.730 in the training and testing groups showed strong agreement, affirming great reliability.

Conclusion
Sex, age, tumor size, tumor location, HT, and microscopic capsular invasion were determined to be key factors associated with hr-LNM in low-risk PTMC. Utilizing these factors, a nomogram was developed to evaluate the risk of hr-LNM in patients with low-risk PTMC.
ITRAQ-based proteomics analysis of human ectopic endometrial stromal cells treated by Maqian essential oil
Authors: Zhang Liu-yang , Huang Ting-ting , Li Li-ping , Liu Dan-ping , Luo Yong , Lu Wan , Huang Ning , Ma Peng-peng , Liu Yan-qiu , Zhang Ping , Yang Bi-cheng 
Published: November 2023

Abstract
Background
Endometriosis is a common and complex syndrome characterized by the presence of endometrial-like tissue outside the uterus. Chinese medicine has been recently found to show good efficacy in treating endometriosis. Our previous results revealed that Maqian fruit essential oil (MQEO) could inhibit the proliferation and induce apoptosis of ectopic endometrial stromal cells (EESCs), but the mechanisms remain unclear. In this study, we aim to explore the molecular mechanism of MQEO’s specific effects in EESCs.

Methods
We conducted a quantitative proteomics analysis by iTRAQ on EESCs treated with MQEO or DMSO. Then deep analysis was performed based on differentially expressed proteins, including Gene Ontology enrichment analysis, pathway enrichment analysis and protein interaction analysis. Candidate protein targets were subsequently verified by western blotting.

Results
Among 6575 identified proteins, 435 proteins exhibited altered expression levels in MQEO-treated EESCs. Of these proteins, most were distributed in signal transduction as well as immune system and the most significantly altered pathway was complement and coagulation cascades. Moreover, two differentially expressed proteins (Heme oxygenase 1 and Acyl-CoA 6-desaturase) were verified and they can be potential biomarkers for endometriosis treatment.

Conclusions
Our proteomic analysis revealed distinct protein expression patterns induced by MQEO treatment in EESCs, highlighting the potential of MQEO for endometriosis treatment and biomarker discovery.
Assessor discomfort and failure to fail in clinical performance assessments
Authors: Scarff Catherine E , Bearman Margaret , Chiavaroli Neville , Trumble Stephen 
Published: November 2023

Abstract
Background
Assessment of trainee performance in the workplace is critical to ensuring high standards of clinical care. However, some supervisors find the task to be challenging, and may feel unable to deliver their true judgement on a trainee’s performance. They may ‘keep MUM’ (that is, keep mum about undesirable messages) and fail to fail an underperforming trainee. In this study, we explore the effect of discomfort on assessors.

Methods
Using a survey method, supervisors of trainees in the Australasian College of Dermatologists were asked to self-report experiences of discomfort in various aspects of trainee workplace assessment and for their engagement in MUM behaviours including failure to fail.

Results
Sixty-one responses were received from 135 eligible assessors. 12.5% of assessors self-reported they had failed to fail a trainee and 18% admitted they had grade inflated a trainee’s score on a clinical performance assessment in the previous 12-month period. Assessors who reported higher levels of discomfort in the clinical performance assessment context were significantly more likely to report previously failing to fail a trainee. The study did not reveal significant associations with assessor demographics and self-reports of discomfort or MUM behaviours.

Conclusions
This study reveals the impact of assessor discomfort on the accuracy of assessment information and feedback to trainees, including as a contributing factor to the failure to fail phenomenon. Addressing assessor experience of discomfort offers one opportunity to impact on the complex and multifactorial issue that failure to fail represents.