bluuebunny/crossref_metadata_2025 huggingface dataset:
Detecting Sparse Microbial Association Signals Adaptively From Longitudinal Microbiome Data Based on Generalized Estimating Equations
Authors: Sun Han , Huang Xiaoyun , Huo Ban , Tan Yuting , He Tingting , Jiang Xingpeng
Published: October 2021

Background: The relationship between the compositions of microbial communities and various host phenotypes is an important research topic. Microbiome association research addresses multiple domains, such as human disease, diet and medicine. Statistical methods for testing microbiome-phenotype associations have been studied recently to determine their ability to assess longitudinal microbiome data. However, existing methods fail to detect sparse association signals in longitudinal microbiome data. Methods: In this paper, we developed a novel method, namely, aGEEMiHC, which is a data-driven adaptive microbiome higher criticism analysis based on generalized estimating equations, to detect sparse microbial association signals from longitudinal microbiome data. aGEEMiHC adopts a generalized estimating equations framework that fully considers the correlation among different observations from the same cluster (individuals) in longitudinal data, and it integrates multiple microbiome higher criticism analyses based on generalized estimating equations by setting different working correlation structures. Thus, the proposed method is robust to diverse correlation structures for longitudinal data.Results: The proposed method shows a stable performance for diverse association patterns in both sparsity levels and phylogenetic relevance. Extensive simulation experiments demonstrate that it can control the type I error correctly and achieve superior performance according to a statistical power comparison. In our simulation, we applied aGEEMiHC to longitudinal microbiome data with various types of host phenotypes to demonstrate the stability of our method. aGEEMiHC is also utilized for real longitudinal microbiome data, and we found a significant association between the gut microbiome and Crohn's disease. Conclusions: aGEEMiHC is a statistical method that facilitates association testing for sparse microbial association signals from longitudinal microbiome data, and it can be applied to situations in which the true underlying correlations among different observations from the same cluster in longitudinal data are unknown. It is worth noting that our method also ranks the significant factors associated with the host phenotype to provide potential biomarkers. The R package GEEMiHC is available at https://github.com/xpjiang-ccnu/GEEMiHC.
Modeling Forest Carbon Estimation Using Sentinel-2 Derived Indices in Yayu Afro-Montane Forest, South West Ethiopia
Authors: Muhe Seid , Argaw Mekuria
Published: October 2021

Background: Empirical analyses were common methods for forest carbon estimation. Lately, satellite images are popularly used to study different attributes of forest vegetation. Sentinel-2 image provides a significant improvement in spectral coverage, spatial resolution and temporal frequency to assess forest biomass. This study assessed the potential of vegetation indices and biophysical variables derived from Sentinel-2 images in modeling above ground biomass (AGB) and carbon stock in the Yayu forest biosphere reserve. Method: About twenty variables extracted from the Sentinel-2 image were used in this study. Forest stand parameters such as DBH and tree height were used to calculate AGB using allometric equations. The correlation between the biomass values measured from plots and the variables extracted from Sentinel-2 images were examined using the Pearson correlation coefficients. A regression analysis was applied to select determinant variables for predicting AGB. The regression model results were validated based on the coefficients of determination between the observed and the predicted values.Results: A strong correlation (r = 0.65 - 0.74) was found between the biophysical variables from Sentinel-2 image and AGB measured from sampling plots. The multispectral (MS) Band 4, the biophysical vegetation variables from Sentine-2 images were strongly correlated with the AGB. The variables MS Band 4, IRECI, LAI, FCOVER and FAPAR are good predictors of the forest AGB. The model goodness of fit between the observed and predicted values of the AGB showed a coefficient of determination (r2) value of 0.74 and root mean square error (RMSE) of 0.16 ton C/pixel. Conclusion: The developed AGB prediction model was applied to successfully quantify and map the AGB and carbon stock of the forest in the biosphere reserve. Vegetation indices from Sentinel-2 images can effectively predict AGB in forest landscapes and can avoid costly ground surveys to quantify AGB and carbon stock in difficult terrains.
Establishment and Fractionation of Metastatic Axillary Lymph Node Cell Suspension for Determination of Protein Expression Levels of Nuclear cFOS and Cytosolic TGFβ1 from Breast Cancer Patients
Authors: Ivanović Vesna , Dedović-Tanić Nasta , Milovanović Zorka , Stojiljković Bratislav , Demajo Miroslav , Mandušić Vesna
Published: October 2021

Background.

Metastatic Axillary Lymph Node (mALN) status is currently the most important prognostic factor in the management of primary breast cancer (BC). Thus, development of specimens which enable identification of new mALN markers, involved in the progression of the disease, are of considerable interest. The specific aim of this work was to describe the method of establishment of Metastatic Axillary Nodal Cell Suspension and its fractionation, termed Fractionated Nodal Cell Suspension (FNCS), into nuclear and cytosolic extracts to enable determination of protein expression levels of nuclear cFOS and cytosolic Transforming Growth Factor β1 (TGFβ1) in BC patients.
Results.

To standardize the procedure, HeLa cells were successfully fractionated into nuclear/cytosolic extracts with confirmed presence of nuclear cFOS and cytosolic TGFβ1 proteins. Subsequently, the ALN Cell Suspension specimens were obtained and further fractionated from a pilot sample of six ALN tissue pairs, mALN versus autologous normal ALN (nALN), dissected from invasive BC patients. The mALN results revealed statistically significant overexpression in nuclear cFOS and cytosolic TGFβ1 protein levels, which was proportional to the respective values of mALN diameter of tumor deposits.
Conclusions.

Detailed protocol for establishment and fractionation of mALN cell suspension specimens, termed FNCS, into nuclear and cytosolic extracts is here described for the first time. This approach might be a convenient ex vivo model for simultaneous analysis of protein, RNA and DNA biomarkers from nuclear/cytosolic extracts of the same mALN tissue sample. It might have potential to enable, in the age of genomics and personalized medicine, an identification of novel mALN biomarkers and thus improve the screening, diagnosis and prognosis of invasive BC.
Body Composition Assessment in Patients with Periampullary Neoplasma Undergoing Pancreaticoduodenetomy and its Predictive Value for Postoperative Complications
Authors: Cai Zhenghua , Xu Shanshan , Zhang Yifan , Yang Yifei , He Jian , Qiu Yudong
Published: October 2021

BackgroundTo observe body composition parameters variance in patient with periampullary neoplasmas with different clinical characteristics and assess its predictive value for postoperative complications after pancreaticoduodenectomy. MethodsIn this study, we retrospectively reviewed the clinical and image data of 144 patients with periampullary neoplasmas.The area of subcutaneous adipose tissue (SAT), visceral adipose tissue (VAT) and total abdominal muscle area (TAMA) were measured from preoperative CT images at the 3rd lumbar vertebra level, the TAMA was normalized to stature and termed as skeleton muscle index (SMI). The perioperative and pathological data were collected. ResultsOf the included 144 patients, 80(55.6%), 29(20.1%) and 24(16.7%) patients were classified as sarcopenia, visceral obesity and sarcopenic obesity. 84(58.3%) patients were jaundiced and 28 (19.4%)，50 (34.7%)，66(45.8%) patients were diagnosed with benign pancreatic tumors, pancreatic cancer and non-pancreatic cancer respectively. The incidence rate of clinical postoperative pancreatic fistula(POPF) and other major complications were 38.2% and 16%.In the univariate analysis, jaundiced patients experienced more weight loss and had higher nutrition risk score, the TAMA[103.1(61.1-176.7) vs 111.8(74.1-198.2),P=0.021] and SMI(39.2±7.0 vs 42.6±9.1,P=0.012)were lower compared with non-jaundiced group. However, no significant difference were founded between different pathological results and it was not associated with occurrence of POPF and major complications.ConclusionJaundiced patients may experience more weight loss and have lower TAMA and SMI. Body morphometric analysis of preoperative CT did not show predictive value for postoperative complications and further multicenter studies are needed.Trail registrationRegistration number：2021-437-01.
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

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.
A Study of The Equilibrium, Kinetics, and Thermodynamics of Malachite Green Dye Adsorption Onto Lignin
Authors: Gandham Vani , Addepally UMA , T Bala Narsaiah
Published: October 2021

The authors have requested that this preprint be removed from Research Square.
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

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

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

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

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

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

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&3D Object Detection with Deep Learning
Authors: Ge Yunfei , Zhang Qing , Sun Yuantao , Shen Yidong , Wang Xijiong
Published: October 2021

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

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

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

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

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.
The New Probiotic Lactobacillus Plantarum Strain Isolated from Traditional Dairy Showed The Synergistic Effect on Aflatoxin B1 Detoxification Along with Nanochitosan Particles
Authors: Zamani Neda , Sepahi Abbas Akhavan , Fazeli Mohammad Reza , Shariatmadari Farid
Published: October 2021

Background: Reduction of aflatoxin toxins in food products is of great importance. Therefore, in the present study, the effects of new Lactobacillus plantarum strain isolated from dairy products as well as chitosan nanoparticles were studied on reducing of aflatoxin B1 (AFB1) toxicity in vitro.Methods: After collection and preparation yogurt, cheese, milk and whey products, lactic acid bacteria (LABs) were isolated and identified using biochemical and molecular methods. To measure probiotic activity, pH, bile and salt tolerance tests were used. Then, the antimicrobial activity of LABs against gastrointestinal pathogens was studied. Next, the cheese-separated strain (C1) was selected as the superior strain and antibiotic susceptibility testing was performed. Then, the effect of C1 isolate and chitosan nanoparticles on reducing aflatoxin B1 (AFB1) in the medium was studied by measuring AFB1 using the enzyme-linked immunosorbent assay (ELISA) and high performance liquid chromatography (HPLC).Results: The results of biochemical evaluations indicated the separation of different strains of Lactobacillus plantarum. Antimicrobial activity test showed extensive antimicrobial activity of C1 isolate. The results showed that this strain has good probiotic activities. This strain was shown to be resistant to the antibiotics erythromycin, fusidic acid, gentamicin, kanamycin, nalidixic acid, neomycin, ofloxacin and vancomycin. C1 strain together with chitosan nanoparticles had the ability to reduce AFB1 in the medium and when both were used simultaneously, and synergistic effect in reducing AFB1 from the medium was seen.Conclusion: In general, it was concluded that the new C1 L. plantarum strains together with chitosan nanoparticles could have synergistic effects in reducing AFB1 toxin in food products.
Nutritional and Fungal Load Dynamics of Fresh Brewers’ Grain Stored Under Aerobic Conditions
Authors: Degefu Getu Kitaw , Faji Mulisa , Terefe Geberemariyam
Published: October 2021

Brewers’ spent grain (BSG) is the amplest by-product of the brewing process. Fresh BSG is currently used as low-cost cattle feed due to its microbiological instability and high perishability. While recent research has looked the effects of storage time and temperature on the characteristics of wet brewers grains (WBG) as ruminant feeds. Three storage temperatures (15°C, 20°C, and 25°C) and periods (2, 4 and 6 days) were arranged in a 3×3 factorial design. Surface spoilage was not apparent at 15 °C throughout the storage periods. Deterioration was not also observed at 20 °C until the fourth day of storage where slight mold growth was apparent. Extensive mold growth was detected late in the sixth day at 20° C and continued manifestations up until the last day of storage at 25°C. Changes in major nutrients, DM losses, and yeast and mold colony count were significantly affected by the interaction of storage temperatures and durations (P<0.05). Except for samples stored at 15° C, nutrients contents decreased concomitantly (exceptions are ADF, lignin, and loss in DM) with prolonged storage times (p<0.05) and increasing temperatures (p<0.05). Contrast analysis indicated that it would be safe to store under aerobic storage conditions and feed the WBG for dairy cattle.
A Novel Modified Cotton Fabric with Durable Anti-Fouling Performance for Separation of Surfactant-stabilized Oil-in-water Emulsions
Authors: Yang Pu , Hu Ruimin , Bin Yu , Sun Yiwei , Liu Yiping , Lu Ming
Published: October 2021

Membrane applications for the separation of surfactant-stabilized emulsions are often constrained by a deficiency in permeability and anti-fouling properties. Herein, special wetted cotton fabric with a protective layer (P-MH@CF) for durable anti-fouling performance was designed by a two-step method, which was related to interfacial ion migration technology and unilateral spraying treatment. In detail, the immobilization of magnesium hydroxide caused the formation of the rough micro/nano structure of the cotton fabric surface. The stearic acid acted as a protective layer, like a quilt, protecting the membrane from contamination. Permeability of water and separation performance of P-MH@CF membrane were investigated systematically. For emulsion stabilized by SDS (SDS/Oil/H2O), the separation flux driven by gravity was approximately 500 L m -2 h -1 , and all separation efficiencies were over 99.3 %. CTAB/Oil/H2O emulsion and the Tween-60/Oil/H2O emulsion also could be successfully separated with high separation efficiency and separation flux. During the whole separation process, the oil droplets surrounded by surfactants were difficult to demulsify and gathered physically on the surface of the fabric to form a "creamy layer", which could be cleaned off so that the P-MH@CF membrane was not contaminated. In addition, the P-MH@CF membrane exhibited robust reusability for separation, which was promising for the remediation of oily wastewater containing surfactants.
Triple-negative breast cancer in children: a case report
Authors: SHI Lexiang , Chi Chengtao , Zhang Yinan , Sun Zhongwen , Yang Wenxian , Zhang Yuchi , Wu Jingcheng , Li Jinping , Zhang Wanli
Published: October 2021

Background

Triple-negative breast cancer (TNBC) is often considered a breast tumor with a poor prognosis that lacks or decreases the expression of estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor 2 (HER-2). It tends to occur in middle-aged and older women, and cases of TNBC in children are rarely reported.
Methods
We report a case of basal-like TNBC in a child at our hospital and review the related literature.
Results

Based on the patient's condition we performed a local mass excision, and despite the postoperative pathological diagnosis of TNBC, this case of basic TNBC had a good prognosis and was very different from conventional basic TNBC in many ways.
Conclusions

Although secretory breast cancer is a subtype of basal-like TNBC, it has its peculiarities and is completely different from basal-like TNBC. There is a need to raise awareness of the disease, select individualized treatment options, and prevent medical errors.
Establishing a Risk Assessment Framework for Point-of-Care Ultrasound
Authors: Conlon Thomas W. , Yousef Nadya , Colungo Juan Mayordomo , Tissot Cecile , Fraga Maria V. , Bhombal Shazia , Suryawanshi Pradeep , Villanueva Alberto Medina , Siassi Brijan , Singh Yogen
Published: October 2021

Point of Care Ultrasound (POCUS) refers to the use of portable ultrasound (US) applications at the bedside, performed directly by the treating physician, for either diagnostic or procedure guidance purposes. It is being rapidly adopted by traditionally non-imaging medical specialties across the globe. Recent international evidence-based guidelines on POCUS for critically ill neonates and children were issued by the POCUS Working Group of the European Society of Pediatric and Neonatal Intensive Care (ESPNIC). Currently there are no standardized national or international guidelines for its implementation into clinical practice or even the training curriculum to monitor quality assurance. Further, there are no definitions or methods of POCUS competency measurement across its varied clinical applications.The Hippocratic Oath suggests medical providers do no harm to their patients. In our continued quest to uphold this value, providers seeking solutions to clinical problems must often weigh the benefit of an intervention with the risk of harm to the patient. Technologies to guide diagnosis and medical management present unique considerations when assessing possible risk to the patient. Frequently risk extends beyond the patient and impacts providers and the institutions in which they practice. Point-of-care ultrasound (POCUS) is an emerging technology increasingly incorporated in the care of children across varied clinical specialties. Concerns have been raised by clinical colleagues and regulatory agencies regarding appropriate POCUS use and oversight. We present a framework for assessing the risk of POCUS use in pediatrics and suggest methods of mitigating risk to optimize safety and outcomes for patients, providers and institutions.
Numerical investigation and Comparative analysis of tunable graphene-gold metasurface based polarizer structures for infrared frequency
Authors: Sorathiya Vishal , patel shobhit
Published: October 2021

We present the comparative analysis of tunable graphene-based metasurface polarizer structure THz frequency range. This polarizer structures have been numerically investigated over the 10 THz to 25 THz of the frequency range. Reflectance co-efficient, phase variation, and phase difference parameters have been investigated to identify the behavior of polarization effect over the range of 10 THz to 25 THz of the frequency. The proposed polarizer has been also investigated for the different shapes of the top gold resonator structure. The proposed structure is tunable for the range of 0.1 eV to 0.9 eV of the graphene Fermi energy. The proposed structure also works on the wide range of the input incident wave of the X and Y polarization. This structure having small, compact tunable design and it can be used as a basic building block in the large THz circuits and structures.
Corneal Nerve Loss in Patients With TIA and Acute Ischemic Stroke in Relation To Circulating Markers of Inflammation and Vascular Integrity
Authors: Khan Adnan , Parray Aijaz , Akhtar Naveed , Agouni Abdelali , Kamran Saadat , Pananchikkal Sajitha V. , Priyanka Ruth , Gad Hoda , Ponirakis Georgios , Petropoulos Ioannis N. , Chen Kuan-Han , Tayyab Kausar , Saqqur Maher , Shuaib Ashfaq , Malik Rayaz A.
Published: October 2021

Background
Vascular and inflammatory mechanisms are implicated in the development of cerebrovascular disease and corneal nerve loss occurs in patients with transient ischemic attack (TIA) and acute ischemic stroke (AIS). We have assessed whether serum markers of inflammation and vascular integrity are associated with the severity of corneal nerve loss in patients with TIA and AIS.
Methods
Corneal confocal microscopy (CCM) was performed to quantify corneal nerve fiber density (CNFD), corneal nerve branch density (CNBD), corneal nerve fiber length (CNFL) in 105 patients with TIA or AIS and age matched control subjects (n=56). Circulating levels of IL-6, MMP-2, MMP-9, E-Selectin, P-Selectin and VEGF were quantified in patients within 48 hours of presentation with a TIA or AIS.
Results
CNFL (P=0.000, P=0.000), CNFD (P=0.122, P=0.000) and CNBD (P=0.002, P=0.000) were reduced in patients with TIA and AIS compared to controls, respectively with no difference between patients with AIS and TIA. The NIHSS Score (P=0.000), IL-6 (P=0.011) and E-Selectin (P=0.032) were higher in patients with AIS compared to TIA with no difference in MMP-2 (P=0.636), MMP-9 (P=0.098), P-Selectin (P=0.395) and VEGF (P=0.831). CNFL (r=0.218, P=0.026) and CNFD (r=0.230, P=0.019) correlated with IL-6 and multiple regression analysis showed a positive association of CNFL and CNFD with IL-6 (P=0.041, P=0.043).
Conclusions
Patients with TIA and stroke have evidence of corneal nerve loss and elevated IL6 and E-selectin levels. Larger longitudinal studies are required to determine the association between inflammatory and vascular markers and corneal nerve fiber loss in patients with cerebrovascular disease.
Calpain-TRPC6 Signaling Pathway Contributes to Propofol-Induced Developmental Neurotoxicity in Rats
Authors: She Ying-Jun , Xu Hai-Ping , Gao Yin , Wang Qiong , Zheng Jun , Ruan Xiangcai
Published: October 2021

Background
Compelling experimental evidence suggests a risk of neuronal damage following early childhood exposure to anesthesia and sedation drugs, including propofol. We investigated whether the transient receptor potential canonical 6 (TRPC6) channel could protect neonatal rats against developmental neurotoxicity following prolonged exposure to propofol. The potential role of calpain, a neuronal TRPC6 protease, was also investigated.
Methods
Postnatal day 7 rats were exposed to five bolus injections of 25 mg/kg propofol or 10% intralipid at hourly intervals. Acute neuronal injury was assessed by the expression pattern of terminal deoxynucleotidyl transferase nick-end labeling staining and cleaved–caspase-3 in the prefrontal cortex. The Morris water maze test was used to evaluate learning and memory functions in later life. Pretreatments consisting of intracerebroventricular injections of a TRPC6 agonist, TRPC6 inhibitor, or calpain inhibitor were used to confirm the potential role of a calpain–TRPC6 pathway.
Results
Prolonged exposure to propofol induced acute neuronal injury, downregulation of TRPC6, and enhancement of calpain activity in the prefrontal cortex up to 24 h after anesthesia. It also induced later behavioral disorders, manifesting as longer escape latency and as fewer platform-crossing times and less time spent in the target quadrant during postnatal days 35–42. These propofol-induced effects were attenuated by TRPC6 agonist and calpain inhibitor while exaggerated by TRPC6 inhibitor. Treatment with calpain inhibitor also attenuated the propofol-induced TRPC6 downregulation in the prefrontal cortex.
Conclusions
A calpain–TRPC6 signaling pathway contributes to propofol-induced acute neuronal injury and long-term behavioral disorders in neonatal rats.
The order of macrophage 4D genome coordinates gene transcription during differentiation and infection
Authors: Cao Gang , Lin Da , Xu Weize , Hong Ping , Wu Chengchao , Zhang Zhihui , Zhang Siheng , Xing Lingyu , Yang Bin , Zhou Wei , Xiao Qin , Wang Jinyue , Wang Cong , He Yu , Man Jiangwei , Wu Xiaofeng , Hao Xingjie , Hu Zhe , Chen Chunli , Cao Zimeng , Yin Rong , Fu Zhen , Li Guoliang
Published: October 2021

The highly organized three-dimensional genome is crucial for gene transcription. However, it remains elusive how the order of the genome architecture related to its function. Here, we developed a single-cell Hi-C method and proposed TAD “degree of disorder” as a measure of genome organizational patterns, which is correlated with the chromatin epigenetic states, gene expression and co-regulation, and chromatin structure variability in individual cells. Upon Mycobacterium tuberculosis infection, NF-κB enters into the nucleus, binds to the target genome regions and initiates systematic chromatin conformation reorganization. Furthermore, we identified a remote NF-κB enriched enhancer promotes the expression of PD-L1 through chromatin loop, which could be a potential anti-tuberculosis and even anti-tumor therapeutic target. The integrated Hi-C, eQTL, and GWAS analysis depicted the atlas of the long-range target genes of tuberculosis susceptible loci. Among which SNP rs1873613 is located in the anchor of a dynamic chromatin loop with LRRK2, whose inhibitor AdoCbl could be an anti-tuberculosis drug candidate. Our study provides comprehensive resources for the 4D genome of immunocytes and sheds insights into the genome organization order and the coordinated gene transcription.