2023: A year of accomplishments for the 13 Science Citation Index Expanded- and Emerging Sources Citation Index-indexed Baishideng journals

In 2023, Baishideng Publishing Group (Baishideng) routinely published 47 open-access journals, including 46 English-language journals and 1 Chinese-language journal. Our successes were accomplished through the collective dedicated efforts of Baishideng staffs, Editorial Board Members, and Peer Reviewers. Among these 47 Baishideng journals, 7 are included in the Science Citation Index Expanded (SCIE) and 6 in the Emerging Sources Citation Index (ESCI). With the support of Baishideng authors, company staffs, Editorial Board Members, and Peer Reviewers, the publication work of 2023 is about to be successfully completed. This editorial summarizes the 2023 activities and accomplishments of the 13 SCIE- and ESCI-indexed Baishideng journals, outlines the Baishideng publishing policy changes and additions made this year, and highlights the unique advantages of Baishideng journals.

Integrity of the editing and publishing process is the basis for improving an academic journal’s Impact Factor

BACKGROUND

Journal Impact Factor™ (JIF) is often used to evaluate the relative reputation and quality of academic journals in their respective fields, and can greatly influence the quality and scope of subsequent manuscript submissions. Therefore, many if not all academic journals are interested in increasing their JIF, to improve their academic impact.

AIM

To determine the importance of the integrity of the editorial and publication process in improving the academic influence of academic journals and the JIF of academic journals.

METHODS

In this paper, we describe our statistical analysis of bibliometric factors - including the 2021 JIFs released in the Journal Citation Report™ 2022, discipline rankings, received and published articles in 2019-2021, and webpage visits and downloads - for seven journals published by Baishideng Publishing Group (Baishideng) and indexed in Science Citation Index Expanded™; ultimately, we introduce and discuss the editing and publishing processes of Baishideng’s journals in their entirety, as they form the basis for our objective of safeguarding and bolstering integrity in academic publication.

RESULTS

For the seven journals assessed, their 2021 JIFs were basically unchanged from 2020, with the current metric ranging from 5.374 for World Journal of Gastroenterology (WJG) to 1.534 for World Journal of Clinical Cases (WJCC). Further assessments of the journals’ bibliometrics from 2019 to 2020, showed that World Journal of Stem Cells has the highest self-citation rate (1.43%) and World Journal of Gastrointestinal Surgery has the lowest (0.21%). Additionally, the total 3012 articles published during this period were cited by more than 20000 articles in approximately 8000 academic journals. Of note, the 1102 articles published in WJG were cited by articles in 3059 journals, among which 171 journals have a JIF of > 10, including internationally renowned academic journals such as CA-A Cancer Journal for Clinicians (2021 JIF 286.130, record count: 1), Lancet (2021 JIF 202.731, record count: 4), Nature Reviews Immunology (2021 JIF 108.555, record count: 2), Nature Reviews Gastroenterology & Hepatology (2021 JIF 73.082, record count: 9), Lancet Gastroenterology & Hepatology (2021 JIF 45.042, record count: 8), Gastroenterology (2021 JIF 33.883, record count: 19), and Gut (2021 JIF 31.793, record count: 21). This suggests that Baishideng’s journals have been widely recognized for their academic quality. In the Reference Citation Analysis (RCA) database, all seven Baishideng-published journals obtained a 2022 Journal Article Influence Index (JAII). For example, WJG has a 2022 JAII of 22.048, ranking 18^th out of 102 journals in the field of gastroenterology & hepatology in the RCA, with 469909 total citations (6/102) and 21313 total articles (5/102). The numbers of manuscripts received and published in 2021 were both higher than those in 2019-2020. For example, WJCC received a total of 3650 manuscripts in 2021, which is 91.1% higher than those in 2019-2020 (average: 1910 papers/year). In 2021, WJCC published 1296 articles, representing an increase of 105.1% compared to those in 2019-2020 (average: 632 articles/year). The numbers of webpage visits and downloads received by the seven journals have increased year by year. For example, the number of total visits received by WJG in 2019-2021 was 1974052 in 2019, 2317835 in 2020 (increased by 17.4% compared with that in 2019), and 2652555 in 2021 (increased by 4.4% compared with that in 2020). The visitors were from more than 220 countries and regions worldwide, such as the United States, China, and the United Kingdom. Open access (OA) plays a vital role in improving the quality, efficiency, transparency, and integrity of academic journal publishing. From 2019 to 2021, a total of 5543 OA articles were published in the seven journals, of which 2083 (37.6%) were invited and published free-of-charge. During the same period, 1683 articles were published in WJG, and the authors were from more than 70 countries and regions. For the total 5543 articles published in the seven journals from 2019 to 2021, 3903 article quality tracking reports were received after the online publication of these articles. The quality of the articles was further evaluated through the Baishideng’s article quality and author evaluation tracking system, with 4655 articles (84.0%) having received author evaluation and feedback, which contributes to tracking metrics for authors’ satisfaction with the collective publication processes. From March 25, 2021 to June 28, 2022, the seven journals received a total of 424 reader evaluations and 229 letters from readers; this subsequent reader engagement demonstrates that the popularity of the published articles and the volume of their readership audience were improved through the reader evaluation system.

CONCLUSION

Ultimately, the findings from our bibliometric assessments indicate that establishing, promoting and actively practicing processes that safeguard and bolster the integrity of the editing and publication process also help to improve the academic influence of academic journals, which itself is the cornerstone for improving JIF.

Baishideng’s Reference Citation Analysis database announces the first Journal Article Influence Index of 104 core journals and a list of high-quality academic journals in orthopedics

After three rounds of rigorous evaluation of core journals in orthopedics conducted by the Reference Citation Analysis (RCA) editorial team of Baishideng Publishing Group (Baishideng), the RCA database of Baishideng officially released the 2022 Journal Article Influence Index (2022 JAII) of 104 core journals and a list of high-quality academic journals in orthopedics, for the first time on August 9, 2022. The list of 104 core journals can be found at: https://www.referencecitationanalysis.com/SearchJournal. Among them, the highest 2022 JAII is 55.015 and the lowest is 3.076. This article introduces the 21 high-quality academic journals and describes the calculation method for the 2022 JAII, the evaluation process, and the inclusion principles for journals in the RCA. These steps are the underpinning of the RCA’s empirical journal academic evaluation service by which the digital platform addresses the needs of authors to select reliable journals for submission, readers to select high-quality literature for reading, and editors to track their own journal citation performance. As such, the RCA core journal list will serve as a useful Find-a-Journal tool. Any interested party is welcome to use this journal list and recommend it to their peers.

Baishideng’s Reference Citation Analysis database announces the first Article Influence Index of multidisciplinary scholars

After three rounds of rigorous evaluation of registered scholars conducted by the Reference Citation Analysis (RCA) editorial team of Baishideng Publishing Group (Baishideng), the RCA database of Baishideng officially released the 2022 Article Influence Index (2022 AII) of 632 scholars from 74 countries/territories in 98 research categories, for the first time. The list of 632 scholars can be found at: https://www.referencecitationanalysis.com/searchscholar. Among them, the highest 2022 AII is 348.211, the highest number of total citations is 42830, and the highest number of total articles is 901. The category with the largest number of RCA scholars is Gastroenterology & Hepatology, with a total of 100 (15.8%), and the second is Surgery, with a total of 46 (7.3%). This article summarizes the RCA scholars and describes the mission of RCA, the openness and transparency of RCA evaluation, the calculation method for the 2022 AII, and the evaluation process of RCA scholars. The RCA scholar list will effectively serve as a useful Find-a-Scholar tool. Any interested scholar is welcome to register and join this RCA scholar list.

Baishideng’s Reference Citation Analysis database announces the first Journal Article Influence Index of 101 core journals and a list of high-quality academic journals in gastroenterology and hepatology

After three rounds of rigorous evaluation of core journals in gastroenterology and hepatology conducted by the Reference Citation Analysis (RCA) editorial team of Baishideng Publishing Group (Baishideng), the RCA database of Baishideng officially released the 2022 Journal Article Influence Index (2022 JAII) of 101 core journals in gastroenterology and hepatology, for the first time. The list of 101 core journals can be found at: https://www.referencecitationanalysis.com/SearchJournal. Among them, the highest 2022 JAII is 48.014 and the lowest is 3.900. This article highlights the top 20 journals, describes the calculation method for the 2022 JAII, the evaluation process, and the inclusion principles for journals in the RCA. These steps are the underpinning of the RCA’s empirical journal academic evaluation service by which the digital platform addresses the needs of authors to select reliable journals for submission, readers to select high-quality literature for reading, and editors to track their own journal citation performance. As such, the RCA core journal list will serve as a useful Find-a-Journal tool. Any interested party is welcome to use this journal list and recommend it to their peers.

Meeting report of the chief editorial board meeting for World Journal of Diabetes 2021

The 2021 online editorial board meeting of the World Journal of Diabetes (WJD) was held on November 9, 2021. Jin-Lei Wang, General Manager on behalf of the Baishideng Publishing Group, and Professor Islam, one of the Editors-in-Chiefs (EiCs) of the WJD, organized the meeting. Three EiCs and 18 Baishideng Publishing Group staff attended the meeting. The meeting goal was to brief the EiCs on the journal’s performance, discuss the issues of concern of the EiCs, and gather ideas for the journal’s development in 2022. As of November 8, the WJD had received 287 manuscripts since the year’s start, among which 122 met the criteria for publication. These numbers represent an increase of 117.4% for submissions and 110.3% for publications compared to those in 2020. However, how to effectively control the academic quality of manuscripts and attract high-quality original article submissions remain a challenge. The EiCs provided feedback and suggestions centered on three topics: (1) Who should and how to control the academic quality of the manuscripts; (2) How the EiCs perform their responsibilities; and (3) The distinctive and shared responsibilities of the publisher and the EiCs.

Meeting report of the editorial board meeting for World Journal of Hepatology 2021

The 2021 online editorial board meeting of the World Journal of Hepatology (WJH) was held on January 16, 2021. Xiang Li, Director of Production Office on behalf of the Baishideng Publishing Group, organized the meeting. Three Editors-in-Chiefs (EiCs) and 15 Baishideng Publishing Group staff attended the meeting. The meeting goal was to brief EiCs on journal performance and gather ideas for journal development in 2021. In 2020, WJH published 204 articles, a 20% increase compared to 2019, authors were from 32 countries and regions, and the average citation per article was three times. However, attracting high quality original article submissions remains a challenge. The EiCs provided feedback and suggestions centered on four topics: (1) Improve journal quality by building editorial; (2) Improve board engagement by establishing a clear policy and consistent internal communications; (3) Improve peer review quality and efficiency; and (4) Refine the current journal marketing strategy to increase visibility and discoverability.

5-Hydroxymethylcytosine signatures in cell-free DNA provide information about tumor types and stages

5-Hydroxymethylcytosine (5hmC) is an important mammalian DNA epigenetic modification that has been linked to gene regulation and cancer pathogenesis. Here we explored the diagnostic potential of 5hmC in circulating cell-free DNA (cfDNA) using a sensitive chemical labeling-based low-input shotgun sequencing approach. We sequenced cell-free 5hmC from 49 patients of seven different cancer types and found distinct features that could be used to predict cancer types and stages with high accuracy. Specifically, we discovered that lung cancer leads to a progressive global loss of 5hmC in cfDNA, whereas hepatocellular carcinoma and pancreatic cancer lead to disease-specific changes in the cell-free hydroxymethylome. Our proof-of-principle results suggest that cell-free 5hmC signatures may potentially be used not only to identify cancer types but also to track tumor stage in some cancers.

Reversal of cancer gene expression correlates with drug efficacy and reveals therapeutic targets

The decreasing cost of genomic technologies has enabled the molecular characterization of large-scale clinical disease samples and of molecular changes upon drug treatment in various disease models. Exploring methods to relate diseases to potentially efficacious drugs through various molecular features is critically important in the discovery of new therapeutics. Here we show that the potency of a drug to reverse cancer-associated gene expression changes positively correlates with that drug's efficacy in preclinical models of breast, liver and colon cancers. Using a systems-based approach, we predict four compounds showing high potency to reverse gene expression in liver cancer and validate that all four compounds are effective in five liver cancer cell lines. The in vivo efficacy of pyrvinium pamoate is further confirmed in a subcutaneous xenograft model. In conclusion, this systems-based approach may be complementary to the traditional target-based approach in connecting diseases to potentially efficacious drugs.

Computational Discovery of Niclosamide Ethanolamine, a Repurposed Drug Candidate That Reduces Growth of Hepatocellular Carcinoma Cells In Vitro and in Mice by Inhibiting Cell Division Cycle 37 Signaling

BACKGROUND & AIMS

Drug repositioning offers a shorter approval process than new drug development. We therefore searched large public datasets of drug-induced gene expression signatures to identify agents that might be effective against hepatocellular carcinoma (HCC).

METHODS

We searched public databases of messenger RNA expression patterns reported from HCC specimens from patients, HCC cell lines, and cells exposed to various drugs. We identified drugs that might specifically increase expression of genes that are down-regulated in HCCs and reduce expression of genes up-regulated in HCCs using a nonparametric, rank-based pattern-matching strategy based on the Kolmogorov-Smirnov statistic. We evaluated the anti-tumor activity of niclosamide and its ethanolamine salt (NEN) in HCC cell lines (HepG2, Huh7, Hep3B, Hep40, and PLC/PRF/5), primary human hepatocytes, and 2 mouse models of HCC. In one model of HCC, liver tumor development was induced by hydrodynamic delivery of a sleeping beauty transposon expressing an activated form of Ras (v12) and truncated β-catenin (N90). In another mouse model, patient-derived xenografts were established by implanting HCC cells from patients into livers of immunocompromised mice. Tumor growth was monitored by bioluminescence imaging. Tumor-bearing mice were fed a regular chow diet or a chow diet containing niclosamide or NEN. In a separate experiment using patient-derived xenografts, tumor-bearing mice were given sorafenib (the standard of care for patients with advanced HCC), NEN, or niclosamide alone; a combination of sorafenib and NEN; or a combination sorafenib and niclosamide in their drinking water, or regular water (control), and tumor growth was monitored.

RESULTS

Based on gene expression signatures, we identified 3 anthelmintics that significantly altered the expression of genes that are up- or down-regulated in HCCs. Niclosamide and NEN specifically reduced the viability of HCC cells: the agents were at least 7-fold more cytotoxic to HCCs than primary hepatocytes. Oral administration of NEN to mice significantly slowed growth of genetically induced liver tumors and patient-derived xenografts, whereas niclosamide did not, coinciding with the observed greater bioavailability of NEN compared with niclosamide. The combination of NEN and sorafenib was more effective at slowing growth of patient-derived xenografts than either agent alone. In HepG2 cells and in patient-derived xenografts, administration of niclosamide or NEN increased expression of 20 genes down-regulated in HCC and reduced expression of 29 genes up-regulated in the 274-gene HCC signature. Administration of NEN to mice with patient-derived xenografts reduced expression of proteins in the Wnt-β-catenin, signal transducer and activator of transcription 3, AKT-mechanistic target of rapamycin, epidermal growth factor receptor-Ras-Raf signaling pathways. Using immunoprecipitation assays, we found NEN to bind cell division cycle 37 protein and disrupt its interaction with heat shock protein 90.

CONCLUSIONS

In a bioinformatics search for agents that alter the HCC-specific gene expression pattern, we identified the anthelmintic niclosamide as a potential anti-tumor agent. Its ethanolamine salt, with greater bioavailability, was more effective than niclosamide at slowing the growth of genetically induced liver tumors and patient-derived xenografts in mice. Both agents disrupted interaction between cell division cycle 37 and heat shock protein 90 in HCC cells, with concomitant inhibition of their downstream signaling pathways. NEN might be effective for treatment of patients with HCC.

Tankyrase inhibitors attenuate WNT/β-catenin signaling and inhibit growth of hepatocellular carcinoma cells

Deregulated WNT/β-catenin signaling contributes to the development of a subgroup of hepatocellular carcinoma (HCC), the second leading cause of cancer deaths worldwide. Within this pathway, the tankyrase enzymes (TNKS1 and TNKS2) degrade AXIN and thereby enhance β-catenin activity. We evaluate TNKS enzymes as potential therapeutic targets in HCC, and the anti-tumor efficacy of tankyrase inhibitors (XAV939, and its novel nitro-substituted derivative WXL-8) in HCC cells. Using semi-quantitative RT-PCR, we found significantly elevated levels of TNKS1/2 mRNA in tumor liver tissues compared to adjacent non-tumor livers, at protein levels only TNKS1 is increased. In HepG2, Huh7cells, siRNA-mediated knockdown suppression of endogenous TNKS1 and TNKS2 reduced cell proliferation, together with decreased nuclear β-catenin levels. XAV939 and WXL-8 inhibited cell proliferation and colony formation in HepG2, Huh7, and Hep40 cells (p < 0.05), with stabilization of AXIN1 and AXIN2, and decreased β-catenin protein levels. XAV939 and WXL-8 also attenuated rhWNT3A-induced TOPflash luciferase reporter activity in HCC cells, indicating reduced β-catenin transcriptional activity, consistent with decreased nuclear β-catenin levels. In vivo, intra-tumor injections of XAV939 or WXL-8 significantly inhibited the growth of subcutaneous HepG2 xenografts (P < 0.05). We suggest that tankyrase inhibition is a potential therapeutic approach for treating a subgroup HCC with aberrant WNT/β-catenin signaling pathway.

Epigenetics in hepatocellular carcinoma: An update and future therapy perspectives

Hepatocellular carcinoma (HCC), the predominant form of adult liver malignancies, is a global health concern. Its dismal prognosis has prompted recent significant advances in the understanding of its etiology and pathogenesis. The deregulation of epigenetic mechanisms, which maintain heritable gene expression changes and chromatin organization, is implicated in the development of multiple cancers, including HCC. This review summarizes the current knowledge of epigenetic mechanisms in the pathogenesis of HCC, with an emphasis on HCC mediated by chronic hepatitis B virus infection. This review also discusses the encouraging outcomes and lessons learnt from epigenetic therapies for hematological and other solid cancers, and highlights the future potential of similar therapies in the treatment of HCC.

Regulation of the gene encoding the intestinal bile acid transporter ASBT by the caudal-type homeobox proteins CDX1 and CDX2

The apical sodium-dependent bile acid transporter (ASBT) is expressed abundantly in the ileum and mediates bile acid absorption across the apical membranes. Caudal-type homeobox proteins CDX1 and CDX2 are transcription factors that regulate genes involved in intestinal epithelial differentiation and proliferation. Aberrant expression of both ASBT and CDXs in Barrett's esophagus (BE) prompted us to study, whether the expression of the ASBT gene is regulated by CDXs. Short interfering RNA-mediated knockdown of CDXs resulted in reduced ASBT mRNA expression in intestinal cells. CDXs strongly induced the activity of the ASBT promoter in reporter assays in esophageal and intestinal cells. Nine CDX binding sites were predicted in silico within the ASBT promoter, and binding of CDXs to six of them was verified in vitro and within living cells by electrophoretic mobility shift assays and chromatin immunoprecipitation assays, respectively. RNAs were extracted from esophageal biopsies from 20 BE patients and analyzed by real-time PCR. Correlation with ASBT expression was found for CDX1, CDX2, and HNF-1α in BE biopsies. In conclusion, the human ASBT promoter is activated transcriptionally by CDX1 and CDX2. Our finding provides a possible explanation for the reported observation that ASBT is aberrantly expressed in esophageal metaplasia that also expresses CDX transcription factors.