bluuebunny/crossref_metadata_2025_split huggingface dataset:
Seasonal Variation in Antimicrobial Activity of Crude Extracts of Psammaplysilla Sp. 1 From Phillip’s Reef, South Africa
Authors: Kibungu Cuthbert , Otigbu Anthony , Clarke Anna-Maria , Justine Fri , Njom Henry 
Published: March 2021

Abstract
Marine invertebrates constitute a diverse group of marine organisms beneficial to humankind due to their therapeutic significance. The marine sponge species Psammaplysilla sp. 1 was collected from Philips Reef, South Africa, over a four-season period and assayed for antimicrobial potential. The physicochemical parameters of the collection site were also recorded. The sponge crude extracts' antimicrobial activity was evaluated using an agar well diffusion assay against five pathogens. Phytochemical screening was conducted to identify the presence of 7 critical phytochemical groups. During the four seasons, the temperature was 17.35 oC ± 2.06, with autumn recording the highest (20 oC) temperature. Antifungal activity was observed by Psammaplysilla sp. 1 (30 mm) against C. albicans, and this was higher than that shown by standard drugs ICZ-10µg (15 ± 0.1 mm), FLU-15µg (21 ± 0.2 mm), VCZ-5µg (17 ± 0.1 mm) respectively. Similar bioactivities were observed seasonally with Psammaplysilla sp. 1 (22 mm and 24 mm) during autumn and spring, respectively, against C. difficile, while only crude extracts collected in spring showed bioactivity against C. albicans. Psammaplysilla sp crude extracts showed broad-spectrum bioactivity against all test pathogens. DCM:ME crude extracts tested positive for the presence of 2/7 of the phytochemicals (terpenoids and flavonoids). GC-MS revealed several previously reported biologically active compounds such as Bicyclo[4.2.0]octa-1,3,5-trien-7-ol and Phenol, 2,6-dibromo has been found in plants. This study revealed that sponge bioactivity is dependent on the season and further validated the antimicrobial potential of South African marine sponges.
Comparative Assessment and Outlook on Methods for Imputing Proteomics Data
Authors: Shen Minjie , Chang Yi-Tan , Wu Chiung-Ting , Parker Sarah J , Saylor Georgia , Wang Yizhi , Yu Guoqiang , Eyk Jennifer E. Van , Clarke Robert , Herrington David M. , Wang Yue 
Published: March 2021

Abstract
Background: Missing values are a major issue in quantitative proteomics data analysis. While many methods have been developed for imputing missing values in high-throughput proteomics data, comparative assessment on the accuracy of existing methods remains inconclusive, mainly because the true missing mechanisms are complex and the existing evaluation methodologies are imperfect. Moreover, few studies have provided an outlook of current and future development.Results: We first report an assessment of eight representative methods collectively targeting three typical missing mechanisms. The selected methods are compared on both realistic simulation and real proteomics datasets, and the performance is evaluated using three quantitative measures. We then discuss fused regularization matrix factorization, a popular low-rank matrix factorization framework with similarity and/or biological regularization, which is extendable to integrating multi-omics data such as gene expressions or clinical variables. We further explore the potential application of convex analysis of mixtures, a biologically-inspired latent variable modeling strategy, to missing value imputation. The preliminary results on proteomics data are provided together with an outlook into future development directions.Conclusion: While a few winners emerged from our comparative assessment, data-driven evaluation of imputation methods is imperfect because performance is evaluated indirectly on artificial missing or masked values not authentic missing values. Imputation accuracy may vary with signal intensity. Fused regularization matrix factorization provides a possibility of incorporating external information. Convex analysis of mixtures presents a biologically plausible new approach.
Changes of the Blood Lymphocytes On Severe&nbsp;Trauma Patients in Early Time
Authors: Cao Feng , He Ru , Huang Yan , Li Zi , Wu Xiaoheng , Chen Ronglin , Wang Meixia 
Published: March 2021

Abstract
Purpose: To evaluate the relationship between the change of blood lymphocyte counts in early stages of trauma patients and the secondary tissue injury after trauma. Method: A retrospective study was conduct to include trauma patients with Injury Severity Score(ISS) ≥16 between January 1 st , 2018 and December 31 st , 2019. Lymphocyte counts of each trauma patient were collected and recorded in first 3 hours, 6-12 hours, 24-48 hours, and 49-72 hours after trauma, separately. The degree of secondary on the trauma patients were evaluated according to the results of laboratory tests, the time stay in ICU and received mechanical ventilation, and 28-day outcome. Correlation analysis was performed between lymphocytes change and the score of the secondary tissue injury in severe trauma patients. Results: The lymphocyte count within first 3 hours after trauma was significantly high,the median was 4.03×10 9 /L, then dropped significantly in 6-72 hours after trauma (median: 0.85~0.99×10 9 /L), there was a significant statistical difference between the lymphocyte count within first 3 hours after trauma and that in 6-72 hours（P=0.000). The ratios of the lymphocytes counts in 6-72 hours to that within first 3 hours after trauma were very low, the median value was 0.22-0.27. The results of regression statistical analysis showed that the change of lymphocyte counts significantly associated with the severe degree of secondary injury (P=0.000). The lymphocyte ratio change can be used to predict the possibility of trauma patients secondary severe tissue injury occurred [Area Under the Curve( AUC) on the ratios of the lymphocytes counts in 6-72 hours to that within first 3 hours after trauma was 0.789, 0.840, 0.861, respectively]. The predictive thresholds of lymphocyte ratio of the trauma patients in the study were 0.31 to 0.35, the prediction sensitivity were 78% to 89% and specificity 74% to 84%. The lymphocyte counts there was significant difference between the patients with assessed as serious secondary tissue injury(87cases) and patients without(25 cases), the median value was 0.21-0.24 , 0.38-0.62, respectively , P=0.000. Conclusion: Lymphocytes counts was significantly increased in the trauma patients with ISS score ≥16 within the first 3 hours after trauma, then decreased significantly in 6-72 hours after trauma. The change of lymphocyte count was significant relationship with the degree of secondary tissue injury, that can be used to predict the degree of secondary severe tissue injury occurred by inflammatory reaction in trauma patients.
Characterisation of tumour immune microenvironment remodelling following oncogene inhibition in preclinical studies using an optimised imaging mass cytometry workflow
Authors: Maldegem Febe van , Valand Karishma , Cole Megan , Patel Harshil , Angelova Mihaela , Rana Sareena , Colliver Emma , Enfield Katey S , Bah Nourdine , Tsang Victoria , Mugarza Edurne , Moore Christopher , Hobson Philip , Levi Dina , Molina-Arcas Miriam , Swanton Charles , Downward Julian 
Published: March 2021

Abstract
Mouse models are critical in pre-clinical studies of cancer therapy, allowing dissection of mechanisms through chemical and genetic manipulations that are not feasible in the clinical setting. In studies of the tumour microenvironment (TME), novel highly multiplexed imaging methods can provide a rich source of information. However, the application of such technologies in mouse tissues is still in its infancy. Here we present a workflow for studying the TME using imaging mass cytometry with a panel of 27 antibodies on frozen mouse tissues. We optimised and validated image segmentation strategies and automated the process in a Nextflow-based pipeline (imcyto) that is scalable and portable, allowing for parallelised segmentation of large multi-image datasets. Incorporating user-specific plugins, imcyto can be flexibly tailored to a wide range of segmentation needs. With these methods we interrogated the dramatic remodelling of the TME induced by a KRAS G12C inhibitor in an immune competent mouse orthotopic lung cancer model, showcasing their potential as key discovery tools to enhance understanding of the interplay between tumour, stroma, and immune cells in the spatial context of the tissue.
Nanometer resolution in situ structure of SARS-CoV-2 post-fusion spike
Authors: Zhu Yun , Sun Fei , Wang Xiangxi , Tai Linhua , Zhu Guoliang , Yang Minnan , Cao Lei , Xing Xiaorui , Yin Guoliang , Chan Chun , Qin Cheng-Feng , Zihe Rao 
Published: March 2021

Abstract
The spike protein (S) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) mediates membrane fusion to allow entry of viral genome into host cell. To understand its detailed entry mechanism and develop specific entry inhibitor, the in situ structural information of SARS-CoV-2 spikes in different states are urgently important. Here, by using the cryo-electron microscopic tomograms, we observed spikes of inactivated SARS-CoV-2 virions in both pre-fusion and post-fusion states and solved the nanometer resolution structure of in situ post-fusion spike. With a more complete model compared to previous reports, the relative spatial position between fusion peptide and transmembrane domain was discovered. Novel oligomerizations of spikes on viral membrane were observed, likely suggesting a new mechanism of fusion pore formation.
Curcumin Promotes Anti-Tumor Effect of Cisplatin and Protects Against Cisplatin-Induced Kidney Injury in Lung Cancer
Authors: Zhao Miaoxin , Ma Yue , Hu Xiangka , Sun Yuqi , Liu Zuodong , Dong Sumin , Liu Hua , Dai Chunmei 
Published: March 2021

Abstract
Background: Lung cancer patients will develop strong drug resistance and serious complications, especially severe renal injuries, after long-term treatment of platinum-based drugs. Curcumin (Cur) combined with cisplatin (DDP) has a synergistic and attenuating effect on lung cancer. However, the role of curcumin in protection against DDP kidney injury in lung cancer remains unknown. Methods: We conducted in vitro experiments to evaluate the anti-tumor effect of cur combined with DDP such as MTT, mitochondrial membrane potential (ΔΨm) analysis, and flow cytometry. The serology and histopathology were used to assess kidney injury induced by DDP in vivo experiments. Western blotting analysis was utilized to detect P38 levels in mouse kidneys. Results: A significant synergistic antitumor effect in A549 and LLC-1 cells based on the activation of the mitochondrial apoptosis pathway. Moreover, Cur could reduce the nephrotoxicity of DDP treatment through the P38MAPK signaling pathway. Conclusion: Cur in combination with DDP may be considered as a beneficial combination regimen for enhancing DDP sensitivity and providing a promising renoprotective effect against nephrotoxicity induced by DDP.
Synthesis, Characterization and Anticancer Evaluation of Nitrogen Substituted 1-(3-Aminoprop-1-ynyl)-4-Hydroxyanthraquinone Derivatives
Authors: Sirazhetdinova Nafisa S. , Baev Dmitry S , Savelyev Victor A. , Golubeva Tatyana S. , Klimenko Lyubov S. , Tolstikova Tatyana G. , Ganbaatar Jamsranjav , Shults Elvira E 
Published: March 2021

Abstract
Anthraquinones are of significant interest due to their biological activity, coloring properties and synthetic applications. Here, we describe a mild and convenient method for modification of 1-ethynyl-4-hydroxyanthraquinone that was obtained from the Sonogashira reaction of 1-hydroxy-4-iodoanthraquinone with alkynes. The copper(I) catalyzed one-pot three component reaction (A3-coupling) of the new 1-ethynyl-4-hydroxyanthraquinone with secondary amines and formaldehyde was the main approach for the synthesis of nitrogen substituted 1-[3-(amino)prop-1-ynyl]-4-hydroxyanthraquinones. The influence of different substituent in the amine on reaction rate and yield has been evaluated. The cytotoxicity of 1-ethynyl-4-hydroxyanthraquinones was evaluated using the conventional MTT assay. Among all the compounds synthesized, anthraquinone-propargylamine derivatives 28, 29, 30 and 34 possess most promising cytotoxic potential towards glioblastoma cancer cells; compounds 14 and 19 shown selectivity towards the prostate cancer cells DU-145, and 18, and 24 – towards breast cancer cells MCF-7. The grown inhibition on these cancer cells of 18 and 24 was comparable to those of standard drug Doxorubicin. Molecular modeling of new compounds in DNA G-quadruplex binding site was performed to help understand the observed SAR trends.
Comparison of Ngenuity and Traditional Microscope in Vitreoretinal Surgeries from Surgeon’s Perspective
Authors: Singh Niharika , Priya Swathi , Shah Haard , Raman Rajiv 
Published: March 2021

Abstract
Purpose: To compare Ngenuity with traditional microscope in vitreoretinal surgeries from surgeon’s perspective Methods: In this retrospective study, we recruited patients who have underwent vitreoretinal (VR) surgeries from 1st August 2017 to 30th August 2017. Patient’s clinical parameters were extracted from electronic medical records (EMR), and also video recordings of the surgeries using the Ngenuity 3D visualization system were analysed. The surgeons were asked to compare Ngenuity 3D visualization system and traditional microscope during each step of the surgery. We administered a questionnaire to compare the two modalities in each step during the surgery in terms of the preferred system, comfort, ergonomic and visual parameters. Results: Out of 31 eyes, primary rhegmatogenous retinal detachment (RRD) was 35% (11 eyes), complex recurrent RRD was 13% (4 eyes) and diabetic TRD was 16% (3 eyes). The educational value, upper body comfort and image resolution was found to be better with Ngenuity than microscope. The depth of perception, field of view and the lower body comfort was graded as similar and time lag was experienced more with Ngenuity. On comparison of the preference of traditional microscope and Ngenuity during surgical steps, preference for Ngenuity was significantly more for posterior segment steps like the truncation of cone (p= <0.00001), PVD induction (p= 0.0001), Endo laser (p=0.0001), Fluid gas exchange (p= 0.0005) and tamponade injection (p=<0.00001). Conclusions: Ngenuity provided improved neck and upper body comfort, greater field of view and was more preferred for posterior segment procedures than anterior segment during VR surgeries.
Assessing Research Misconduct in Iran: A Perspective from Iranian Medical Faculty Members
Authors: Shamsoddin Erfan , Torkashvand Zahra , Sofi-Mahmudi Ahmad , Janani Leila , Kabiri Payam , Gooshki Ehsan Shamsi , Mesgarpour Bita 
Published: March 2021

Abstract
Background

Research misconduct is a global concern in almost every scientific field. There is no comprehensive data regarding the prevalence of research misconduct among Iran's medical faculties. This study aims to conduct a nationwide survey regarding research misconduct in the faculty members of medical universities in Iran.
Methods

We used the Persian version of the research misconduct questionnaire (PRMQ) in an online survey on the Google Forms platform. Using Google Froms, the survey link was sent to a systematic random sample of medical faculty members in Iran (N = 4986). Descriptive analyses were performed on the individual items of PRMQ, with frequencies and percentages for categorical and Likert-type response items and means and standard deviation (S.D.) for continuous variables. Chi-square analysis was conducted to test hypotheses examining differences in frequency of responses related to factors influencing misconduct. All the analyses were performed using R 3.6.0.
Results

The response rate was 13.8% (692 responses). Nearly three-quarters (N = 499, 72.1%) of the respondents had first-hand witted some instances of research misconduct during the previous year. Academic scholars in various tenure categories rated investigator competitiveness differently (df:9, p = 0.008), with the highest difference in the mean scores between tenure categories one (TC1) (2.7, SD:0.87) and four (2.4, SD:0.77). Only 18.5% of participants perceived the effectiveness of their associated organization’s rules for reducing research misconduct to be high or very high. Pressure for tenure was identified as the most perceived as having a strong behavioral influence on engaging in research misconduct (80.2%).
Conclusions

Research misconduct is a living trouble among medical faculty members in Iran and needs a more proactive approach to tackle.
Study the Oxygen Vacancies and Fe Oxidation States in CaFeO3-δ Perovskite Nanomaterial
Authors: khalaf eid , Abdel-Khalek E. K. , Motawea M. A. , Aboelnasr Mohamed A. , El-Bahnasawy H. H. 
Published: March 2021

Abstract
In this study, CaFeO3-δ perovskite nanomaterial has been synthesized by sol-gel method. The oxygen vacancies and Fe oxidation states in CaFeO3-δ perovskite nanomaterial were investigated by using X-ray diffraction (XRD), Mössbauer spectroscopy, X-ray photoelectron spectroscopy (XPS), thermogravimetry analysis (TG), differential scanning calorimetric (DSC), and vibrating sample magnetometer (VSM). Rietveld analysis of the XRD shows that the sample was crystallized in orthorhombic perovskite structure with space group pcmn. The oxygen vacancies and oxidation states of Fe ions in CaFeO3-δ sample were determined from Mössbauer spectroscopy. XPS shows the presence of different states of Fe ions and oxygen vacancies in the surface of CaFeO3-δ sample. The thermal and magnetic properties of this sample have been investigated.
lncRNA-ENST00000513396 is associated with multiple tumor signaling pathways, promotes the cell proliferation, invasion and migration in colorectal cancer
Authors: Zhu Jinxin , Wang Hui , Du Yangbin , He Zhenyu 
Published: March 2021

Abstract
Purpose

Recently, many studies have revealed that Long noncoding RNAs (lncRNAs) were abundant in kinds of cells and might have multiple functions in a wide range of biological processes, such as proliferation, apoptosis, or cell migration. However, the role of lncRNA in the development of colorectal cancer has not been systematically reported and needs to be studied.
Methods

We applied Agilent microarray in tumoral tissues and paired para-cancer tissues for detecting different expression of lncRNAs and mRNAs. Bioinformatics analysis were used to identify the relationship between lncRNAs and corresponding mRNAs and the potential function of the lncRNAs. lncRNA-ENST00000430471 was chosen for further functional study through constructing overexpression plasmid, cell invasion, and cell migration.
Results

We found that 460 lncRNAs were significantly deregulated in cancer tissues. More importantly, they may participate in a variety of tumor-related signaling pathways through functional enrichment analysis with their co-expressed mRNAs, suggesting that these lncRNAs might play critical roles in tumorigenesis and development. Recently, we found lncRNA-ENST00000513396 was significantly upregulated in cancer tissues compared with para-cancer tissues. The overexpression of ENST00000513396 promotes tumor cell proliferation. Meanwhile ENST00000430471 could promote migration and invasion ability of colorectal cells.
Conclusion

LncRNAs play an important role in the development of colorectal cancer. Differentially expressed lncRNAs are associated with multiple tumor signaling pathways. Overexpression of lncRNA- ENST00000513396 in colorectal cancer cells can promote tumor cell proliferation and increase the ability of cell invasion and migration, which leads to the development of tumor.
Investigation of the Polishing Mechanism of Magnetorheological Elastic Polishing Composites
Authors: Xu Zhiqiang , Wang Jun , Wang Qiuliang , Wu Heng , Zhang Gaofeng , Jiang Shengqiang 
Published: March 2021

Abstract
Computer-controlled ultra-precision polishing technology is widely used for high-quality surface processing. However, its polishing tool has some shortcomings, such as limited adaptability to the complex surface and easy to cause surface damage. Therefore, a new smart material-based abrasive tool named magnetorheological elastic polishing composites (MREPCs) and its flexible polishing method are proposed. This study first prepared MREPCs and developed a polishing tool for MREPCs. Then, the material properties of MREPCs were obtained by theoretical and experimental analysis, and the tool influence function (TIF) of the hemispherical MRPECs was established according to the Hertz contact theory, the variable rheological theory and the Preston equation. Finally, the TIF and the polishing performance of MREPCs were verified by polishing experiments. The results show that the theoretical and the experimentally measured TIF models have a high coincidence, and the developed MREPCs can remove surface material with high precision. The above preliminary study indicates that MREPCs are promising for ultra-precision machining of small-sized parts with complex profiles.
Cyclophilin A/CD147 Induces the Epithelial-to-mesenchymal Transition and Renal Fibrosis in Chronic Allograft Dysfunction by Regulating MAPK Signaling
Authors: Liu Xuzhong , Tang Zhiwang , Jiang Xi , Wang Tianwei , Zhao Lun , Xu Zongyuan , Liu Kun 
Published: March 2021

Abstract
Objectives: Our study was designed to explore the role of Cyclophilin A (CyPA)/CD147 interactions in renal allograft fibrosis and chronic allograft dysfunction (CAD). Methods and materials: A rat renal transplant model with significant CAD was successfully identified. Renal allograft tissues and blood samples were collected. HE, Masson and immunohistochemistry staining were performed. Then human HK-2 cells were intervened by certain concentrations of CyPA, and total protein and mRNA were extracted. Western blot assay and PCR were performed to explore the protein and mRNA expression of CyPA, CD147 and epithelial-to-mesenchymal transition (EMT)-related biomarkers. CD147 siRNA and specific inhibitor of MAPK were used to explore the involved cellular mechanism.Results: We have successfully established and identified a 20-weeks renal transplant CAD model. We observed significant distributed and expressed CyPA and CD147 in the renal allograft fibrosis tissues. We also found the significant expression of CD147 and EMT-related markers in the HK-2 cells stimulated by CyPA. The CD147 siRNA confirmed the previous results in vitro. The selective inhibition of MAPK suggested the notable role of MAPK signaling pathway in the CyP/CD147 interactions involved in renal allograft fibrosis.Conclusions: Our study reported the positive relationship of CyPA/CD147 interactions with the renal allograft dysfunction. In vitro study suggested that CyPA could bind to CD147 and then induce the development of EMT process by MAPK signaling, thus contributing to the renal allograft fibrosis and CAD.