The utilization of paper-level classification system on the evaluation of journal impact

CAS Journal Ranking, a ranking system of journals based on the bibliometric indicator of citation impact, has been widely used in meso and macro-scale research evaluation in China since its first release in 2004. The ranking's coverage is journals which contained in the Clarivate's Journal Citation Reports (JCR). This paper will mainly introduce the upgraded version of the 2019 CAS journal ranking. Aiming at limitations around the indicator and classification system utilized in earlier editions, also the problem of journals' interdisciplinarity or multidisciplinarity, we will discuss the improvements in the 2019 upgraded version of CAS journal ranking (1) the CWTS paper-level classification system, a more fine-grained system, has been utilized, (2) a new indicator, Field Normalized Citation Success Index (FNCSI), which ia robust against not only extremely highly cited publications, but also the wrongly assigned document type, has been used, and (3) the calculation of the indicator is from a paper-level. In addition, this paper will present a small part of ranking results and an interpretation of the robustness of the new FNCSI indicator. By exploring more sophisticated methods and indicators, like the CWTS paper-level classification system and the new FNCSI indicator, CAS Journal Ranking will continue its original purpose for responsible research evaluation

An Explorative Study on Document Type Assignment of Review Articles in Web of Science, Scopus and Journals' Website

Accurately assigning the document type of review articles in citation index databases like Web of Science(WoS) and Scopus is important. This study aims to investigate the document type assignation of review articles in web of Science, Scopus and Journals' website in a large scale. 27,616 papers from 160 journals from 10 review journal series indexed in SCI are analyzed. The document types of these papers labeled on journals' website, and assigned by WoS and Scopus are retrieved and compared to determine the assigning accuracy and identify the possible reasons of wrongly assigning. For the document type labeled on the website, we further differentiate them into explicit review and implicit review based on whether the website directly indicating it is review or not. We find that WoS and Scopus performed similarly, with an average precision of about 99% and recall of about 80%. However, there were some differences between WoS and Scopus across different journal series and within the same journal series. The assigning accuracy of WoS and Scopus for implicit reviews dropped significantly. This study provides a reference for the accuracy of document type assigning of review articles in WoS and Scopus, and the identified pattern for assigning implicit reviews may be helpful to better labeling on website, WoS and Scopus

Extensive tRNA gene changes in synthetic Brassica napus

Allopolyploidization, where two species come together to form a new species, plays a major role in speciation and genome evolution. Transfer RNAs (abbreviated tRNA) are typically 73-94 nucleotides in length, and are indispensable in protein synthesis, transferring amino acids to the cell protein synthesis machinery (ribosome). To date, the regularity and function of tRNA gene sequence variation during the process of allopolyploidization have not been well understood. In this study, the inter-tRNA gene corresponding to tRNA amplification polymorphism method was used to detect changes in tRNA gene sequences in the progeny of interspecific hybrids between Brassica rapa and B. oleracea, mimicking the original B. napus (canola) species formation event. Cluster analysis showed that tRNA gene variation during allopolyploidization did not appear to have a genotypic basis. Significant variation occurred in the early generations of synthetic B. napus (F and F generations), but fewer alterations were observed in the later generation (F). The variation-prone tRNA genes tended to be located in AT-rich regions. BlastN analysis of novel tRNA gene variants against a Brassica genome sequence database showed that the variation of these tRNA-gene-associated sequences in allopolyploidization might result in variation of gene structure and function, e.g., metabolic process and transport

A signature of saliva-derived exosomal small RNAs as predicting biomarker for esophageal carcinoma:a multicenter prospective study

BACKGROUND: The tRNA-derived small RNAs (tsRNAs) are produced in a nuclease-dependent manner in responses to variety of stresses that are common in cancers. We focus on a cancer-enriched tsRNA signature to develop a salivary exosome-based non-invasive biomarker for human esophageal squamous cell carcinoma (ESCC). METHODS: Cancer-enriched small RNAs were identified by RNA sequencing of salivary exosomes obtained from ESCC patients (n = 3) and healthy controls (n = 3) in a pilot study and further validated in discovery cohort (n = 66). A multicenter prospective observational study was conducted in two ESCC high-incidence regions (n = 320 and 200, respectively) using the newly developed biomarker signature. RESULTS: The tsRNA (tRNA-GlyGCC-5) and a previously undocumented small RNA were specifically enriched in salivary exosomes of ESCC patients, ESCC tissues and ESCC cells. The bi-signature composed of these small RNAs was able to discriminate ESCC patients from the controls with high sensitivity (90.50%) and specificity (94.20%). Based on the bi-signature Risk Score for Prognosis (RSP), patients with high-RSP have both shorter overall survival (OS) (HR 4.95, 95%CI 2.90–8.46) and progression-free survival (PFS) (HR 3.69, 95%CI 2.24–6.10) than those with low-RSP. In addition, adjuvant therapy improved OS (HR 0.47, 95%CI 0.29–0.77) and PFS (HR 0.36, 95%CI 0.21–0.62) only for patients with high but not low RSP. These findings are consistent in both training and validation cohort. CONCLUSIONS: The tsRNA-based signature not only has the potential for diagnosis and prognosis but also may serve as a pre-operative biomarker to select patients who would benefit from adjuvant therapy. TRIAL REGISTRATION: A prospective study of diagnosis biomarkers of esophageal squamous cell carcinoma, ChiCTR2000031507. Registered 3 April 2016 - Retrospectively registered. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12943-022-01499-8

A signature of saliva-derived exosomal small RNAs as predicting biomarker for esophageal carcinoma:a multicenter prospective study

BACKGROUND: The tRNA-derived small RNAs (tsRNAs) are produced in a nuclease-dependent manner in responses to variety of stresses that are common in cancers. We focus on a cancer-enriched tsRNA signature to develop a salivary exosome-based non-invasive biomarker for human esophageal squamous cell carcinoma (ESCC). METHODS: Cancer-enriched small RNAs were identified by RNA sequencing of salivary exosomes obtained from ESCC patients (n = 3) and healthy controls (n = 3) in a pilot study and further validated in discovery cohort (n = 66). A multicenter prospective observational study was conducted in two ESCC high-incidence regions (n = 320 and 200, respectively) using the newly developed biomarker signature. RESULTS: The tsRNA (tRNA-GlyGCC-5) and a previously undocumented small RNA were specifically enriched in salivary exosomes of ESCC patients, ESCC tissues and ESCC cells. The bi-signature composed of these small RNAs was able to discriminate ESCC patients from the controls with high sensitivity (90.50%) and specificity (94.20%). Based on the bi-signature Risk Score for Prognosis (RSP), patients with high-RSP have both shorter overall survival (OS) (HR 4.95, 95%CI 2.90–8.46) and progression-free survival (PFS) (HR 3.69, 95%CI 2.24–6.10) than those with low-RSP. In addition, adjuvant therapy improved OS (HR 0.47, 95%CI 0.29–0.77) and PFS (HR 0.36, 95%CI 0.21–0.62) only for patients with high but not low RSP. These findings are consistent in both training and validation cohort. CONCLUSIONS: The tsRNA-based signature not only has the potential for diagnosis and prognosis but also may serve as a pre-operative biomarker to select patients who would benefit from adjuvant therapy. TRIAL REGISTRATION: A prospective study of diagnosis biomarkers of esophageal squamous cell carcinoma, ChiCTR2000031507. Registered 3 April 2016 - Retrospectively registered. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12943-022-01499-8

STUDY ON ANTI-OSTEOSARCOMA ACTIVITY OF ETHANOL EXTRACT OF VENENUM BUFONIS IN VITRO

Background: Venenum bufonis is the dried white secretion of the auricular and skin glands of Bufo gargarizans Cantor, or Bufo melanostictus Schneider, Bufonidae. It is used in the treatment of deep-rooted carbuncle, boils and swelling; pain in the throat, heart stroke, coma, abdominal pain, vomiting and diarrhea. The objective of this paper is to preliminarily observe the effects of ethanol extract of Venenum bufonis on growth, and proliferation of human osteosarcoma U2OS cell lines, and to provide a theoretical basis for an in-depth study of the clinical application of Venenum bufonis for osteosarcoma inhibition, with its mechanism of action. Materials and Methods: SRB assay was used to determine the effect of Venenum bufonis ethanol extract on U2OS cell line activity, and to detect its inhibitory dose-effect on osteosarcoma cells. FCM was applied to determine the effect of Venenum bufonis ethanol extract on U2OS cell apoptosis and to perform cell cycle analysis. Results: As results, different Venenum bufonis ethanol extracts showed apparent concentration-effect relationships on U2OS cell lines. FCM analysis showed that it had a U2OS apoptosis promoting effect, which increased with increasing concentration. Cell cycle analysis revealed that the Venenum bufonis ethanol extract mainly arrested U2OS in the G0/G1 phase, preventing the cells from progressing to the S phase. Conclusion: The study concluded that Venenum bufonis ethanol extract has an inhibitory effect on proliferation of osteosarcoma U2OS cells

Salivary extracellular miRNAs for early detection and prognostication of esophageal cancer:a clinical study

BACKGROUND AND AIMS: Early detection of esophageal squamous cell carcinoma (ESCC) will facilitate curative treatment. We aimed to establish a micro-RNA (miRNA) signature derived from salivary extracellular vesicles and particles (EVPs) for early ESCC detection and prognostication.METHODS: Salivary EVP miRNA expression was profiled in a pilot cohort (n=54) using microarray. Area under the receiver-operator characteristic curve (AUROC) and lasso regression analyses were used to prioritize miRNAs that discriminated ESCC patients from controls. Using quantitative reverse transcription-polymerase chain reaction, the candidates were measured in a discovery cohort (n=72) and cell lines. The prediction models for the biomarkers were derived from a training cohort (n=342) and validated in an internal cohort (n=207) and an external cohort (n=226).RESULTS: The microarray analysis identified 7 miRNAs for distinguishing ESCC patients from control subjects. Since one was not always detectable in the discovery cohort and cell lines, the other 6 miRNAs formed a panel. A signature of this panel accurately identified all-stage ESCC patients in the training cohort (AUROC=0.968) and was successfully validated in two independent cohorts. Importantly, this signature could distinguish early-stage (stage Ⅰ/ Ⅱ) ESCC patients from control subjects in the training cohort (AUROC=0.969, sensitivity=92.00%, specificity=89.17%), internal (sensitivity=90.32%, specificity=91.04%) and external (sensitivity=91.07%, specificity=88.06%) validation cohorts. Moreover, a prognostic signature based on the panel was established and efficiently predicted the high-risk cases with poor progression-free survival and overall survival.CONCLUSION: The salivary EVP-based 6-miRNA signature can serve as noninvasive biomarkers for early detection and risk stratification of ESCC. Chinese Clinical Trial Registry, ChiCTR2000031507.</p

Salivary Extracellular MicroRNAs for Early Detection and Prognostication of Esophageal Cancer: A Clinical Study.

BACKGROUND & AIMS: Early detection of esophageal squamous cell carcinoma (ESCC) will facilitate curative treatment. We aimed to establish a microRNA (miRNA) signature derived from salivary extracellular vesicles and particles (EVPs) for early ESCC detection and prognostication. METHODS: Salivary EVP miRNA expression was profiled in a pilot cohort (n = 54) using microarray. Area under the receiver operator characteristic curve (AUROC) and least absolute shrinkage and selector operation regression analyses were used to prioritize miRNAs that discriminated patients with ESCC from controls. Using quantitative reverse transcription polymerase chain reaction, the candidates were measured in a discovery cohort (n = 72) and cell lines. The prediction models for the biomarkers were derived from a training cohort (n = 342) and validated in an internal cohort (n = 207) and an external cohort (n = 226). RESULTS: The microarray analysis identified 7 miRNAs for distinguishing patients with ESCC from control subjects. Because 1 was not always detectable in the discovery cohort and cell lines, the other 6 miRNAs formed a panel. A signature of this panel accurately identified patients with all-stage ESCC in the training cohort (AUROC = 0.968) and was successfully validated in 2 independent cohorts. Importantly, this signature could distinguish patients with early-stage (stage Ⅰ/Ⅱ) ESCC from control subjects in the training cohort (AUROC = 0.969, sensitivity = 92.00%, specificity = 89.17%) and internal (sensitivity = 90.32%, specificity = 91.04%) and external (sensitivity = 91.07%, specificity = 88.06%) validation cohorts. Moreover, a prognostic signature based on the panel was established and efficiently predicted the high-risk cases with poor progression-free survival and overall survival. CONCLUSIONS: The salivary EVP-based 6-miRNA signature can serve as noninvasive biomarkers for early detection and risk stratification of ESCC. Chinese Clinical Trial Registry, ChiCTR2000031507