bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cover crop-driven shifts in soil microbial communities could modulate tomato early crop growth via plant-soil feedbacks
Authors: Tosi Micaela , Drummelsmith John , Obregón Dasiel , Chahal Inderjot , Eerd Laura L. Van , Dunfield Kari E. 
Published: October 2021

Abstract
Sustainable agricultural practices such as crop diversification, cover crops and residue retention are increasingly applied to counteract detrimental effects of agriculture on natural resources. Since part of their effects occur via changes soil microbial communities, it is critical to understand how these respond to different practices. Our study analyzed five cover crop (cc) treatments (oat, rye, radish, rye-radish mixture and no-cc control) and two crop residue management strategies (retention/R+ or removal/R-) in an 8-year diverse horticultural crop rotation trial from ON, Canada. Cc effects were small but stronger than those of residue management. Radish-based cover crops tended to be the most beneficial for both microbial abundance and richness, yet detrimental for fungal evenness. Cc species, in particular radish, also shaped fungal and, to a lesser extent, prokaryotic community composition. Crop residues modulated cc effects on bacterial abundance and fungal evenness (i.e., more sensitive in R- than R+), as well as microbial taxa. Several microbial structure features, some affected by cc, were correlated with early tomato growth in the following spring (e.g., composition, taxa within Actinobacteria, Firmicutes and Ascomycota). Our study suggests that, whereas mid-term cc effects were small, they need to be better understood as they could be influencing crop productivity via plant-soil feedbacks.
Cancer Type Classification Using Plasma Cell Free RNAs Derived From Human and Microbes
Authors: Chen Shanwen , Jin Yunfan , Wang Siqi , Xing Shaozhen , Wu Yingchao , Tao Yuhuan , Ma Yongchen , Zuo Shuai , Liu Xiaofan , Hu Yichen , Chen Hongyan , Luo Yuandeng , Xia Feng , Xie Chuanming , Yin Jianhua , Wang Xin , Liu Zhihua , Zhang Ning , Xu Zhenjiang Zech , Lu Zhi John , Wang Pengyuan 
Published: October 2021

Abstract
Background: The utilities of cell free nucleic acids in monitoring cancer have been recognized by both scientists and clinicians. In addition to human transcripts, a fraction of cell free nucleic acids in human plasma were proved to derived from microbes, and reported to have some relevance to cancer. Methods: To get a better understanding of plasma cell free RNAs (cfRNAs) in cancer patients, we profiled cfRNAs in ~300 plasma samples of five cancer types (colorectal cancer, stomach cancer, liver cancer, lung cancer, esophageal cancer) and healthy donors with RNA-seq. Results: Microbe derived cfRNAs were consistently detected by different computational methods when potential contaminations were carefully filtered. Clinically relevant signals can be identified from human and microbial reads, and alteration in human cfRNA expression and virus abundance both suggests some cancer patients were immunosuppressed, as indicated by enriched KEGG pathways of downregulated human genes and higher prevalence torque teno virus. Our data supports the diagnostic value of human and microbe derived plasma cfRNAs for cancer detection, as an area under receiver operating characteristic (ROC) curve of 0.931 for distinguishing cancer patients from healthy donors was achieved on validation set, using both human and microbial features. Moreover, these cfRNAs both have some cancer type specificity, and could distinguish tumors of different primary locations. Compared to using human feature alone, combining human and microbial features improves the average validation accuracy of between cancer type classification by 11.5%. Conclusions: In summary, this work provides evidence for the clinical relevance of human and microbe derived plasma cfRNAs, and their potential utilities in cancer detection, and determination of tumor sites.
Incidence and Predictors of Mortality Among Neonates with Perinatal Asphyxia, Northwest Ethiopia, 2021: An Institution Based Retrospective Cohort Study.
Authors: Shibabaw Aster Tadesse , Belay Getaneh Mulualem , Desta Bogale Kassahun , Shiferaw Fasil Wagnew , Lakew Ayenew Molla 
Published: October 2021

Abstract
Background: - Perinatal asphyxia is the third leading cause of neonatal mortality globally, which usually happens within the first week of life. Therefore, evidence-based estimation of neonatal mortality is a cornerstone for tracking progress towards child survival goal and identifying priority areas to improve progress towards eliminating preventable deaths due to perinatal asphyxia. Objective: To assess incidence and predictors of mortality among neonates with perinatal asphyxia admitted to the neonatal intensive care unit of Debre Markos Comprehensive Specialized Hospital, 2021.Methods: An institutional-based retrospective follow-up study was conducted among 402 neonates with perinatal asphyxia (PNA) admitted to the neonatal intensive care unit (NICU) of Debre Markos Comprehensive Specialized Hospital from January 1st, 2018 to the 30th of December, 2020. A simple random sampling technique was used to select the estimated sample. Data were entered using Epi data Version 4.6.0.0 and analyzed using Stata Version 14. The Kaplan–Meier and log-rank test were used to estimate and compare the survival time. Both the bi-variable and multivariable Weibull regression models were fitted to identify predictors of mortality. Finally, the Hazard ratio with a 95%CI was computed, and variables with p-values <0.05 were considered as statistically significant predictors of mortality. Results: A total of 125 (31.09%) neonates died during the follow-up period. The overall incidence rate of mortality was found to be 53.49 per 1000 neonate-days of observations (95%CI: 44.89-63.74). Neonatal sepsis (AHR=2.13;95%CI: 1.38-3.27), preterm birth (AHR= 3.42 95%CI; 2.13- 5.48), Hypoxic Ischemic Encephalopathy stage II (AHR=6.65 95%CI: 2.57-17.26), and III (AHR=16.8 95%CI; 6.28- 44.9), Antepartum hemorrhage (AHR=2;95%CI: 1.13-3.92), the induced onset of labor (AHR=3.90;95%CI; 1.83-8.27), and post-partum hemorrhage (AHR=2.12;95%CI: 1.32-3.38) were significant predictors of mortality among neonates with perinatal asphyxia.Conclusion: The study found that the overall incidence rate of mortality among neonates with PNA remains high. Neonatal sepsis, Hypoxic-ischemic encephalopathy stage II and III, preterm birth, antepartum hemorrhage, postpartum hemorrhage and induced onset of labor were independent predictors of mortality. Therefore, early anticipating high-risk pregnancies and newborns with the respective intervention could reduce neonatal due to perinatal asphyxia.
Development of a Questionnaire To Measure Teachers’ Student-Centred Perspectives Based On The Onion Model
Authors: Leatemia Lukas Daniel , Merrienboer Jeroen J. G. van , Susilo Astrid Pratidina 
Published: October 2021

Abstract
Background

Teachers with a teacher-centred perspective have difficulties applying student-centred approaches in Problem Based Learning (PBL) because they are inclined to show teacher-centred behaviours. The six aspects explained in Korthagen’s Onion Model (environment, behaviour, competencies, beliefs, identity, and mission) are assumed to contribute to teachers’ perspectives, showing that both the environment and personal characteristics influence behaviours. For teachers to function properly in PBL, those six aspects should reflect a student-centred perspective. Previous instruments to measure teaching perspectives focused on only a few of these relevant aspects. Therefore, we developed the Student-Centred Perspective of Teachers (SCPT) questionnaire with subscales for each aspect in the Onion Model. This study aimed to provide evidence for its internal and external validity.
Methods

The SCPT was distributed in a survey to 795 teachers from 20 medical schools. For the internal validation, Confirmatory Factor Analysis was performed to analyse theoretical fit model validation, convergent validation, and discriminant validation. For the external validation, teachers’ perspective scores were compared among three groups of amount of PBL training using Analysis of Variance (ANOVA) and post-hoc Least Significant Difference (LSD) tests. The p-value for all tests was set at .05.
Results

A total of 543 out of 795 teachers (68.3%) participated. Confirmatory Factor Analysis showed the evidence of the SCPT’s internal validation with acceptable fit for the six subscales measured by 19 items and the following Composite Reliability scores: environment (.72), behaviour (.74), competencies (.63), beliefs (.55), identity (.76), and mission (.60). All items’ factors loadings reached a good standard (.5 or greater). Only the environment subscale had the Average Variance Extracted (AVE) score higher than .5 and the Maximum Shared Variance score lower than the AVE score. ANOVA and Post-hoc LSD tests showed that teachers who participated in more PBL training showed significantly higher student-centred perspectives, providing evidence for external validity.
Conclusion

The SCPT is a reliable and valid instrument to measure teaching perspectives. Identifying aspects that do not represent the adoption of a student-centred perspective may provide valuable input for faculty development in the context of PBL.
Processed Electroencephalogram-Based Monitoring to Guide Sedation in Critically Ill Patients: A Systematic Review and International Expert Panel-Based Consensus Recommendations
Authors: Rasulo Frank A , Hopkins Philip , Lobo Francisco Almeida , Pandin Pierre , Matta Basil , Carozzi Carla , Romagnoli Stefano , Absalom Anthony , Badenes Rafael , Bleck Thomas , Caricato Anselmo , Claassen Jan , Denault Andrè , Honorato Cristina , Meyfroidt Geert , Nardiello Ida , Radtke Finn M , Ricci Zaccaria , Robba Chiara , Taccone Fabio S , Vespa Paul , Lamperti Massimo 
Published: October 2021

Abstract
BackgroundThe literature related to the use of processed EEG (pEEG) for depth of sedation (DOS) monitoring is increasing, however it is unclear how to use this type of monitoring for critical care patients within the intensive care unit (ICU).MethodsWe performed a systematic review of the literature according to the Grade of Recommendation assessment, Development, and Evaluation (GRADE) approach. The modified Delphi method was utilised by a team of experts to produce statements and recommendations derived from study questions. Three separate online rounds discussing 89 statements categorized into four domains were formulated. The panelists rated the appropriateness of each statement and were able to suggest modifications or addition of statements. An analysis of anonymised ratings of the statements by part of the panel followed each Delphi round and previously validated criteria were used to define appropriateness and consensus.ResultsLevel of evidence regarding the four domains was very low. Fourteen panelists participated in the Delphi rounds and consensus was reached for 28 out of 89 statements, from which the reccomendations were created. The main findings were that DOS monitoring should be performed in critically ill patients whenever clinical evaluation is not possible, it should be performed by continuous pEEG techniques and the resulting data depicted with graphical tools to facilitate detection of excessive sedation, a potential cause of burst-suppression, and finally, structured training is suggested to achieve a basic pEEG competency.ConclusionsAlthough evidence on using DOS monitors in ICU is scarce and further research is required in order to better define the benefits of using pEEG, the results of this consensus highlight the general agreement that critically-ill patients would benefit from this type of neuromonitoring.
Using BERT to identify drug-target interactions from whole PubMed
Authors: Aldahdooh Jehad , Vähä-Koskela Markus , Tang Jing , Tanoli Ziaurrehman 
Published: October 2021

Abstract
Background: Drug-target interactions (DTIs) are critical for drug repurposing and elucidation of drug mechanisms, and are manually curated by large databases, such as ChEMBL, BindingDB, DrugBank and DrugTargetCommons. However, the number of articles providing this data (~0.1 million) likely constitutes only a fraction of all articles on PubMed that contain experimentally determined DTIs. Finding such articles and extracting the experimental information is a challenging task, and there is a pressing need for systematic approaches to assist the curation of DTIs. To this end, we propose Bidirectional Encoder Representations from Transformers (BERT) to identify such articles. Because DTI data intimately depends on the type of assays used to generate it, we also aimed to incorporate functions to predict the assay format.
Results: Our novel method identified ~2.1 million articles (along with drug and protein information) that are not previously included in public DTI databases. Using 10-fold cross-validation, we obtained ~99% accuracy for identifying articles containing quantitative drug-target profiles. The accuracy for the prediction of assay format is ~90%, which leaves room for improvement in future studies.
Conclusion: The BERT model in this study is robust and the proposed pipeline can be used to identify previously overlooked articles containing quantitative DTIs. Overall, our method provides a significant advancement in machine-assisted DTI extraction and curation. We expect it to be a useful addition to drug mechanism discovery and repurposing.
A Case Report of Toxic Anterior Segment Syndrome, A Rare Complication After Laser in Situ Keratomileusis
Authors: Ahmad Aline Ali , Hamwi Ali Othman , Hasan Rama Basem , Hamwi Sara Othman , Ahmad Hussein Ali , Darwish Taym Rafik 
Published: October 2021

Abstract
Background: Laser in situ keratomileusis (LASIK) is increasingly used worldwide to correct a wide range of refractive errors. Toxic anterior segment syndrome (TASS), a noninfectious inflammatory disease with symptoms and signs that resemble bacterial infection, is a rare complication of LASIK. Case presentation: We report a case of TASS in a 42-year-old male patient after LASIK surgery in both eyes for hyperopia. Diagnosed clinically. Discussion and conclusion: Little information about complications after LASIK is available. TASS is a general term used to describe acute, sterile postoperative anterior segment reactions. Patients with TASS will often experience blurry vision with or without pain within 12 to 48 hours after surgery. Steroids have shown to be effective in resolving the inflammatory response, reducing the pain and recovering the vision.
Grayscale Medical Image Segmentation Method Based on 2D&amp;3D Object Detection with Deep Learning
Authors: Ge Yunfei , Zhang Qing , Sun Yuantao , Shen Yidong , Wang Xijiong 
Published: October 2021

Abstract
Background: Grayscale medical image segmentation is the key step in clinical computer-aided diagnosis. Model-driven and data-driven image segmentation methods are widely used for their less computational complexity and more accurate feature extraction. However, model-driven methods like thresholding usually suffer from wrong segmentation and noises regions because different grayscale images have distinct intensity distribution property thus pre-processing is always demanded. While data-driven methods with deep learning like encoder-decoder networks always are always accompanied by complex architectures which require amounts of training data. Methods: Combining thresholding method and deep learning, this paper presents a novel method by using 2D&3D object detection technologies. First, interest regions contain segmented object are determined with fine-tuning 2D object detection network. Then, pixels in cropped images are turned as point cloud according to their positions and grayscale values. Finally, 3D object detection network is applied to obtain bounding boxes with target points and boxes’ bottoms and tops represent thresholding values for segmentation. After projecting to 2D images, these target points could composite the segmented object. Results: Three groups of grayscale medical images are used to evaluate the proposed image segmentation method. We obtain the IoU (DSC) scores of 0.92 (0.96), 0.88 (0.94) and 0.94 (0.94) for segmentation accuracy on different datasets respectively. Also, compared with five state of the arts and clinically performed well models, our method achieves higher scores and better performance.Conclusions: The prominent segmentation results demonstrate that the built method based on 2D&3D object detection with deep learning is workable and promising for segmentation task of grayscale medical images.
Landscape of Infantile Hemangioma Management Trends on the 100 Top-Cited Articles Since 2010: Bibliometric Analysis
Authors: Li Meng-Ju , Wang Lin-Yen , Chien Tsair-wei , Lai Feng-Jie , Liao Kuang-Wen , Chou An-Kuo 
Published: October 2021

Abstract
Background: An infantile hemangioma (IH) is a type of benign vascular tumor that affects babies. They usually begin during the first four weeks of life, grow until about five months of life, and then shrink in size and disappear over the next few years. Complications may include pain, bleeding, ulcer formation, heart failure, or disfigurement. Numerous articles on IH have been published in literature, sharing expanded management strategies. Nevertheless, definite treatment guideline for IH is inconclusive due to differences in heterogenous presentations, varied severity and treatment strategy among countries. This study aimed to apply the medical subject headings (MeSH terms) to predict the number of article citations using 100 top-cited IH articles (T100IHs) and dissect their characteristics including the influential authors and affiliated counties since 2010.Methods: By searching the PubMed Central® (PMC) database, the T100IHs since 2010 were downloaded. Citation analysis was performed to compare the dominant countries and authors using social network analysis (SNA) and visual representations. MeSH terms were clustered by SNA when referring their citations in articles. The prediction effect was assessed based on its correlation coefficients (CC) between impact factors(IF) of MeSH terms and the T100IHs. Results: We observed that (1) the top three productive countries and journals in T100IHs were the US (49%), China (10%), France (8%); and Pediatrics (10%), Br J Dermatol (6%), Pediatr Dermatol (4%); (2) the most cited article (PMID=25693013 with 145 citations) was authored by Christine Léauté-Labrèze from France in 2015; (3) the most cited MeSH term was pharmacology with IF equal to 42.46 in T100IHs. MeSH terms were evident in prediction power on the number of article citations (correlation coefficient = 0.46; t = 5.11; p<0.01, n = 100). Conclusion: The breakthrough was made by making the citation prediction on T100IHs. MeSH terms are evident in predicting article citations using SNA and IF calculation approaches that can be applied to future research, and is not limited to the IH topic as we did in this study.
Investigation of Ecosystem Health of International Meighan Wetland
Authors: Abad Bahman Shams Esfand 
Published: October 2021

Abstract
Background: The aim of this study was to evaluate the ecosystem health of Meighan Wetland of Arak. Methods: To evaluate the Meighan Wetland of Arak, the status of benthic organisms and other parameters, sampling of sediments of the wetland floor was performed at 10 points of the wetland and at 5 replications at each point. Heavy metal pollution, biological, and water quality indices were also evaluated. Then, the map of ecosystem health was prepared. Results: The results showed that except for the nickel, zinc and lead, for other elements and compounds (EC, Na, Cl, Mg, Ca, HCO3, SO4 and TDS), the minimum and maximum values ​​belonged to stations 3 and 6, respectively. In the case of copper, zinc and lead, the lowest concentration was seen in the northwestern part of the wetland and the highest in the western and southeastern parts of the wetland. Conclusion: The high amount of the mentioned elements and compounds in station 6 may be due to the activity of a factory that produces sodium sulfate in the northern part of the wetland, which causes changes in the wetland ecosystem by removing sediments from the wetland floor. The high level of the copper, zinc and lead in the southern part of the wetland can be due to urban and domestic wastewaters that enter the wetland from the southwest of the wetland through the outlet channel of Arak refinery.
Do Artificial Neural Networks Always Provide High Prediction Performance? An Experimental Study on the Insufficiency of Artificial Neural Networks in Capacitance Prediction of the 6H-SiC/MEH-PPV/Al diode
Authors: Çolak Andaç Batur , Güzel Tamer 
Published: October 2021

Abstract
Recently, studies on artificial neural network model, which is one of the most effective artificial intelligence tools applied in many fields, reported that artificial neural networks are tools that offer very high prediction performance compared to traditional models. In this study, an artificial neural network model has been developed to predict the capacitance voltage outputs of the 6H-SiC/MEH-PPV/Al diode with organic polymer interface, depending on the frequency. In the multi-layer network model developed with a total of 186 experimental data, 70% of the data used for training, 15% for validation and 15% for testing. The prediction performances of three different artificial neural networks developed with 5, 10 and 15 neurons in their hidden layers have been analyzed. The results obtained, for the first time in the literature, show that the artificial neural network model cannot predict the capacitance voltage outputs of the organic polymer interface 6H-SiC/MEH-PPV/Al diode depending on the frequency.
Bismuth vanadate: A versatile heterogeneous catalyst for photocatalytic functionalization of C(sp2)–H bonds
Authors: Zeng Fan-Lin , Zhu Hu-lin , Wang Ru-Nan , Yuan Xiao-Ya , Sun Kai , Qu Lingbo , Chen Xiao-Lan , Yu Bing 
Published: October 2021

Abstract

Bismuth vanadate (BiVO4) could be prepared by the hydrothermal kettle method. Herein, the synthesized BiVO4-180 is demonstrated to be a versatile and stable heterogeneous photocatalyst for a series of C(sp2)–H functionalization reactions under visible light irradiation at ambient conditions. A series of functionalized compounds such as tetrahydroquinolines, 3-arylmethyl indoles, α-aryl α-amino acid esters, and sulfurized/selenized/thiocyanated heterocycles were successfully synthesized in good yields (>70 examples, including modification of drugs and peptides). The BiVO4 photocatalyst has the advantages of being recyclable, low-cost, air-tolerant, and high efficiency, which is the typical characteristic of overcoming the shortcomings of homogeneous catalysts.