bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation of screening tests for autoimmune gastritis in histopathologically confirmed Japanese patients, and re-evaluation of histopathological classification
Authors: Wada Yasuhiro , Nakajima Shigemi , Mori Naoko , Takemura Shizuki , Chatani Rena , Ohara Mariko , Fujii Makoto , Hasegawa Hiroshi , Hayafuji Kiyoyuki , Kushima Ryoji , Murakami Kazunari 
Published: March 2022

Abstract
Background: The aims of the present study are to evaluate non-invasive screening tests for autoimmune gastritis (AIG) and re-evaluate histopathological classification.Methods: We screened candidates of AIG in JCHO Shiga Hospital between May 2012 and January 2020. The screening criteria were as follows: endoscopic O-p atrophy with Updated Kimura-Takemoto classification, 3+ pepsinogen (PG) test, low serum vitamin B12 or elevated serum gastrin with positive anti-parietal cell (PC) or intrinsic factor antibodies. We evaluated the screening criteria in the patients who were histopathologically confirmed as AIG, and re-evaluated histopathological staging in clinical aspects. Results: Twenty-two of 28 (78.6%) patients who met the screening criteria were histopathologically confirmed as AIG. Common clinical findings in the AIG patients were 10x or greater anti-PC antibody, elevated serum gastrin greater than 172 pg/mL and endoscopic atrophy O-1 or greater. The areas under the curve of PG I, PG II and PG I/II ratio were 0.81, 0.29 and 0.98, respectively. Among histopathologically confirmed AIG patients, 4 and 18 patients were histopathologically classified into florid and end stages, respectively, while no patients into early stage. We could not find a significant difference between florid and end stages in the screening items studied. Conclusions: Florid and end stages in histopathological classification are both advanced-stage AIG in clinical aspects. Our screening criteria without biopsy are applicable to screen clinically-advanced AIG with 78.6% positive predictive value. PG I and PG I/II ratio may be useful to screen AIG. However, we may need other criteria to screen early stage of AIG.
Visual Clustering of Transcriptomic Data from Primary and Metastatic Tumors: Dependencies and Novel Pitfalls
Authors: Marquardt Andre , Kollmannsberger Philip , Krebs Markus , Knott Markus , Solimando Antonio Giovanni , Kerscher Alexander 
Published: March 2022

Abstract
Background: Personalized Oncology is a rapidly evolving area and offers cancer patients therapy options more specific than ever. Yet, there is still a lack of understanding regarding transcriptomic similarities or differences of metastases and corresponding primary sites. Methods: Approaching this question, we used two different unsupervised dimension reduction methods – t-SNE and UMAP – on three different metastases datasets – prostate cancer, neuroendocrine prostate cancer, and skin cutaneous melanoma – including 682 different samples, with three different underlying data transformations – unprocessed FPKM values, log10 transformed FPKM values, and log10+1 transformed FPKM values – to visualize potential underlying clusters. Results: The approaches resulted in formation of different clusters that were independent of respective resection sites. Additionally, data transformation critically affected cluster formation in most cases. Of note, our study revealed no tight link between the metastasis resection site and specific transcriptomic features. Instead, our analysis demonstrates the dependency of cluster formation on the underlying data transformation and the dimension reduction method applied. Conclusion: These observations propose data transformation as another key element in the interpretation of visual clustering approaches apart from well-known determinants such as initialization and parameters. Furthermore, the results show the need for further evaluation of underlying data alterations based on the biological question and subsequently used methods and applications.
Strengthening Research Ethics Systems In Liberia: Challenges, Prospects and Implications
Authors: Kennedy Stephen , Mason Gloria , Sherman Lawrence , Tegli Jemee , Taylor Curtis , Morris Cecelia , Bolay Fatorma , Scaramuzz Dario 
Published: March 2022

Abstract
Despite the tremendous growth of Research Ethics systems in resource-limited settings, structural and systematic challenges persist. Therefore, effective ethical frameworks must be cultivated and further implemented to promote the rights of human subjects and vulnerable populations, strengthen the implementation of high quality research, and engage the participation of communities for the sustainable growth of research ethics systems in low and middle income countries (LMICs). To explore those challenges, we conducted a cross-sectional study among prior and current members of research ethics committees in order to determine the facilitators and gaps that are impeding the growth of the research ethical systems in Liberia, a resource-limited country, and subsequently utilize the findings to formulate country-specific ethical and regulatory frameworks. The results revealed plethora of ethical challenges, ranging from the inadequacy of infrastructure to limited, non-inclusive, funder-driven, capacity building initiatives. While the findings have program and policy implications, the results could likely create a platform to support future ethics-based research efforts directed at developing effective ethical frameworks to strengthen and sustain research ethical systems in resource-limited settings.
Exosomal miR-221-3p derived from bone marrow mesenchymal stem cells alleviates asthma progression by targeting FGF2 and inhibiting the ERK1/2 signaling pathway
Authors: Liu Weike , Lin Hui , Nie Wuhui , Wan Jieting , Jiang Qian , Zhang Aimei 
Published: March 2022

Abstract
Exosomes derived from human bone marrow mesenchymal stem cells (BMSCs) play potential protective roles in asthma. However, the underlying mechanisms remain not fully elucidated. Herein, exosomes were isolated from BMSCs, and their morphology, particle size and exosome marker proteins were identified by transmission electron microscopy (TEM) and nanoparticle tracking analysis (NTA) and Western blot, respectively. Then airway smooth muscle cells (ASMCs) were treated with transforming growth factor-β1 (TGF-β1) to construct proliferation model, and then incubated with BMSCs-derived exosomes. We found that exosome incubation increased miR-221-3p expression, and inhibited proliferation, migration, and the levels of extracellular matrix (ECM) proteins including fibronectin and collagen III. Moreover, FGF2 was identified as a target gene of miR-221-3p. FGF2 overexpression reversed the inhibitory effects of exosomal miR-221-3p on ASMC progression. Besides, the phosphorylation of extracellular signal-regulated kinase 1/2 (ERK1/2) is inhibited by exosomal miR-221-3p, which was reversed by FGF2 overexpression. And ERK1/2 signaling activator reversed the effects of exosomal miR-221-3p on ASMC progression. Additionally, an ovalbumin (OVA)-induced asthmatic mice model was established, and exosomes treatment alleviated airway hyper-responsiveness (AHR), histopathological damage and ECM deposition in asthmatic mice. Taken together, our findings indicated that exosomal miR-221-3p derived from BMSCs inhibited FGF2 expression and the ERK1/2 signaling, thus attenuating proliferation, migration and ECM deposition in ASMCs and alleviating asthma progression in OVA-induced asthmatic mice. Our findings may provide a novel therapeutic strategy for asthma.
Haplotype-aware modeling of cis-regulatory effects highlights the gaps remaining in eQTL data
Authors: Mohammadi Pejman , Ehsan Nava , Kotis Bence , Castel Stephane , Song Eric , Mancuso Nicholas 
Published: March 2022

Abstract
Expression Quantitative Trait Loci (eQTLs) are critical to understanding the mechanisms underlying disease-associated genomic loci. Nearly all protein-coding genes in the human genome have been associated with one or more eQTLs. Here we introduce a multi-variant generalization of allelic Fold Change (aFC), aFC-n, to enable accurate quantification of the cis-regulatory effects in genes with multiple conditionally independent eQTLs. Applying aFC-n to 458,465 eQTLs in the Genotype-Tissue Expression (GTEx) project data, we demonstrate significant improvement in accuracy over the current tools for estimating the eQTL effect size and predicting genetically regulated gene expression. We characterize some of the empirical properties of the eQTL data and use this framework to assess the current state of eQTL data in terms of characterizing cis-regulatory landscape in individual genomes. Notably, we show that 77.4% of the genes with an allelic imbalance in a sample show 0.5 log2 fold or more of residual imbalance after accounting for the eQTL data underlining the remaining gap in characterizing regulatory landscape in individual genomes. We further contrast this gap across tissue types, and ancestry backgrounds to identify its correlates and guide future studies.
Circular RNA hsa_circ_0023404 promotes the proliferation, migration and invasion in endometrial cancer cells through regulating miR-217/MAPK1 axis
Authors: Chen Zhuoying , Huang Meixiu , You Jiaying , Lin Yanhua , Huang Qiaoyun , He Caiping 
Published: March 2022

Abstract
Aim
Studies indicated that Circular RNA hsa_circ_0023404 play a critical role in cancer progression. The aim of our research is to investigate the functions of hsa_circ_0023404 in endometrial cancer (EC) and the potential molecular mechanism.
Methods
We used RT-qPCR and Western blot approach to detect the expressed levels of related genes in EC cell lines. Transfected siRNAs were applied to knockdown the level of related mRNA in cells. Cell proliferation by CCK-8 assay and colony formation assay were applied to detect cell proliferation. Transwell migration and invasion assay was for detecting the migration and invasion of the cells.
Results
RT-qPCR showed that the level of hsa_circ_0023404 and MARK1 mRNA were upregulated but mirR-217 was decreased in three endometrial cancer cell lines. Knockdown of hsa_circ_0023404 by siRNA markedly increased the level of miR-217 and reduced the proliferation of the Ishikawa cells。 It also inhibited the cell migration and invasion. Anti-miR-217 can reverse the promoted proliferation, migrations and invasion of Ishikawa cells mediated by si-circ_0023404. si-MARK1 restored the inhibited cell proliferation, migration and invasion of the co-transfected Ishikawa cells with si- circ_0023404 and anti-miR-217.
Conclusion
hsa_circ_0023404 exerts a tumor-promoting role in endometrial cancer by regulating miR-217/MARK1 axis. hsa_circ_0023404 inhibit miR-217 as sponge which inhibit endometrial cancer cell growth and metastasis. MARK1 is downstream target of miR217 and upregulated by hsa_circ_0023404/miR-217 axis and involved in the endometrial cancer progression.
Sarcopenia is Associated with Non-motor symptoms in Han Chinese Patients with Parkinson's Disease: A Cross-Sectional Study
Authors: Liu Qiu-wan , Mao Cheng-jie , Lu Zhao-hui , Shi Rong-fang , Zhang Ying-chun , Zhao Ping , Liu Chun-Feng 
Published: March 2022

Abstract
Background: Sarcopenia is commonly seen in the older adults and increases in incidence with age, also in Parkinson’ s Disease (PD). There may be a vicious circle between the development of PD and sarcopenia, but the relationship between the two is not clear. We aimed to investigate the incidence of sarcopenia in patients with PD and the association between non-motor symptoms (NMS) in PD. Methods: The study included 123 patients with PD and 38 age- and sex-matched healthy controls. All participants were evaluated for sarcopenia using the 2019 Asian Sarcopenia Diagnostic Criteria, and patients with PD underwent standard assessments of motor and non-motor symptoms. Multiple logistic regression and receiver operating characteristic (ROC) curve analyses were used to examine the association between sarcopenia and NMS in PD patients.Results: The incidence of sarcopenia was significantly higher in patients with PD than in healthy controls (26.8% vs. 10.4%, p=0.035). Multiple logistic regression analysis revealed that poorer sleep quality (odds ratio [OR]: 1.305; 95% confidence interval [CI]: 1.026–1.622; p=0.030) and fatigue (OR: 1.097, 95% CI: 1.003–1.199, p=0.042) were independently associated with sarcopenia. ROC analysis indicated that the optimal cut-off value for Pittsburgh Sleep Quality Index (PSQI) scores was 10, with 72.7% sensitivity and 74.4% specificity (area under the curve [AUC]=0.776, 95% CI: 0.692–0.846, p<0.001). The optimal cut-off value for Fatigue Severity Scale (FSS) scores was 39, with 87% sensitivity and 50% specificity (AUC=0.725, 95% CI: 0.637 –0.802, p<0.001). joint use of FSS and PSQI increased the predictive value (AUC = 0.804, p<0.001).Conclusion: Patients with PD are more susceptible to sarcopenia than healthy older adults. Combined use of FSS and PSQI scores may be a valuable screening method for identifying sarcopenia in patients with PD.
Weather effects on offspring survival differ between reproductive stages in a Neotropical seabird.
Authors: Ortega Santiago , Rodriguez Cristina , Drummond Hugh 
Published: March 2022

Abstract
Weather conditions can profoundly affect avian reproduction. Thus far, most studies on weather effects have focused on how weather conditions prior to clutch initiation affect laying dates and, ultimately, breeding success. By contrast, little is known of how weather conditions after the onset of reproduction affect birds. Using a 32-year population study of the Blue-footed booby (Sula nebouxii) in Mexico, we show that effects of weather conditions on offspring survival and body condition at independence vary with the reproductive stage at which they occur. During most of the incubation period, warm sea surface temperatures and low to moderate rainfall depressed hatching success; while during the last month of brood care surface temperatures were unimportant but rainfall increased fledging success. In addition, chicks that experienced warm sea surface temperatures in the middle of the brood care stage had lower body condition at fledging. Our results provide insight of how weather effects vary between reproductive stages in a long-lived neotropical seabird.
Musa Acuminata Wastes as New Potential source of Anti-ulcerative Colitis Agents : Pharmacological and Metabolomics Profiles
Authors: Mohammed Mona A. , Ibrahim Bassant M.M. , Abdelatif Yasmin , Hassan Azza H. , Raey Mohamed A. El , Hassan Emad M. , El-Gengaihi Souad E. 
Published: March 2022

Abstract
Musa acuminata is a popular fruit in the world. Non-food parts of the plant have been investigated for their antioxidant and anti-ulcerative colitis activity. Metabolomic approaches was found to be informative as a screening tool. It discovered different metabolites depending on statistical analysis. The antioxidant activity content was measured by colorimetric method. Seventy six investigated metabolites were observed. The identities of some of these markers were confirmed based on their MS2 fragmentation and NMR spectroscopy. These include: Cinnamic acid and its dimer 2-hydroxy-4-(4-methoxyphenyl)-1H-phenalen-1-one beside Gallic acid and flavonoids; Quercetin, Quercetin-3-O-β-D-glucoside, Luteolin-7-O-β-D-glucopyranoside. The leaves, pseudostem and fruit peels extracts were tested for their safety and their antiUlcerative-colitis efficacy in rats. Rats were classified into:Normal, Positive, prednisolone reference group , Musa extracts pretreated groups(250-500mg/kg) for two weeks followed by induction of Ulcerative-colitis by per-rectal infusion of 8% acetic acid. Macroscopic and microscopic examination were done. Inflammatory markers (ANCA, CRP and Ilβ6) were measured in sera. The extracts showed good antioxidant and anti-inflammatory activities as they ameliorated macroscopic and microscopic signs of Ulcerativecolitis and lowered the inflammatory markers compared to untreated group. Musa wastes can be a potential source of bioactive metabolites for industrial use and future employment as promising anti-Ulcerativecolitis food supplements.
Integration of Mentimeter into the Classroom: A Scoping Review
Authors: Madiseh Fatemeh Ranjbaran , Abri Abdullah Al , Sobhanifar Hadi 
Published: March 2022

Abstract
The rapid development in technology and information has inspired educators to explore innovative technological resources and assets to promote the quality of teaching and learning. Student Response Systems (SRS) have been acknowledged as having a significant influence on student engagement, motivation, and overall achievement. This scoping review investigated the integration of Mentimeter in the educational context to determine its effectiveness for both teaching and learning processes. The included studies were screened for only those that investigated the use of Mentimeter in the classroom, while including peer-reviewed journal articles, conference proceedings, short articles, book chapters, and review articles from 2015 to 2022 that were available in English without limitation on discipline. The 57 publications that met the eligibility criteria were coded for various characteristics, the most significant of which are discipline, geographical region, publication type, research method and outcomes. Our results reveal the numerous merits gained from integrating Mentimeter in educational settings, including: 1) benefits not only to enriching student-centered pedagogy, but also encapsulating a diverse audience of cultural backgrounds and competencies; 2) providing immediate feedback for anonymous student responses; 3) enhancing student motivation; 4) engaging students’ active participation. The results of this study provide initiatives for teachers and educational researchers to conduct further research on various educational technology platforms, and highlight the advantages of integrating technology into the educational setting. While teachers and practitioners persevere to transform the learning experience through technology, we emphasize the necessity for continuous research to investigate different learning platforms that considerably improve learning outcomes.
The Efficacy of Casirivimab/Imdevimab in Solid Organ Transplant Recipients with Mild-To-Moderate COVID-19
Authors: Tagaya Etsuko , Kikuchi Ken , Mitsuda Toshihiro , Ebihara Fumiya , Maruyama Takumi , Hamada Yukihiro , Kimura Toshimi , Unagami Kohei , Kanzawa Taichi , Sekiguchi Haruki , Shimamoto Ken , Ishida Hideki , Egawa Hiroto , Tanaka Junji , Tanabe Kazunari , Kawana Masatoshi , Arimura Ken 
Published: March 2022

Abstract
Background: Solid organ transplant recipients (SOTRs) are at high risk for severe coronavirus disease 2019 (COVID-19) due to comorbidities and immunosuppression. Moreover, the treatment for COVID-19 is limited. Neutralizing monoclonal antibodies (mAbs) against severe acute respiratory syndrome coronavirus 2 are used for treating mild-to-moderate COVID-19. However, reports comparing the efficacy of COVID-19 treatment with and without neutralizing mAbs in SOTRs are limited. Here, we assessed the efficacy of casirivimab/imdevimab as neutralizing mAbs against mild-to-moderate COVID-19 in SOTRs. Methods: Forty-one patients hospitalized from September 2020 to September 2021 at Tokyo Women’s Medical University Hospital were included. The duration until antifebrile and of hospitalization, requirement of oxygen (O2) ≥ 5 L, and neutralizing antibody levels were compared in SOTRs with COVID-19 who received and those who did not receive casirivimab/imdevimab therapy.Results: Casirivimab/imdevimab therapy correlated with less duration until antifebrile and of hospitalization and non-requirement of O2 ≥ 5 L in SOTRs with COVID-19 [mean days without vs. with casirivimab/imdevimab: 6 vs. 2; P = 0.0002, hazard ratio (HR) = 0.3333, 95% confidence interval (CI) = 0.1763–0.6301; mean days: 15 vs. 8; P < 0.0001, HR = 0.5333, 95% CI = 0.2878–0.9883; P = 0.0377, HR = 0.1502, 95% CI = 0.02511–0.8980, respectively]. Further, casirivimab/imdevimab therapy was associated with early antifebrile after adjusting for sex and age (P = 0.013, HR = 0.412, 95% CI = 0.205–0.826). Although no significant difference was observed in neutralizing antibody levels between patients without and with casirivimab/imdevimab therapy on the day of hospitalization (P = 0.1055), including 13 SOTRs who had received vaccination. Neutralizing antibody levels were higher in patients with casirivimab/imdevimab therapy at 3–5 days after hospitalization including such patients in whom the levels tended to stay lower despite vaccination than in those without casirivimab/imdevimab at 7–9 days after hospitalization (P < 0.0001, mean antibody without vs. with, 414.9 vs. 40000). Conclusion: Casirivimab/imdevimab therapy was effective and increased the neutralizing antibody levels in SOTRs with mild-to-moderate COVID-19. Therefore, casirivimab/imdevimab therapy could contribute to preventing the progression of mild-to-moderate COVID-19 in SOTRs.
Diminazene aceturate attenuates hepatic ischemia/reperfusion injury in mice
Authors: Yoon So Hye , Kang Hye Bin , Kim Jongwan , Han Sang Jun 
Published: March 2022

Abstract
Hepatic ischemia/reperfusion (I/R) injury is one of the leading causes of mortality following partial hepatectomy, liver transplantation, hypovolemic shock, and trauma; however, effective therapeutic targets for the treatment of hepatic I/R injury are lacking. Recent studies have shown that diminazene aceturate (DIZE) has protective effects against inflammation, oxidative stress, and cell death, which are the main pathogenetic mechanisms associated with hepatic I/R injury. However, the mechanistic effects DIZE exerts on hepatic I/R remain unknown. C57BL/6 male mice were pretreated with either 15 mg/kg DIZE or vehicle control (saline) and subjected to partial liver ischemia for 60 min. One day after induction of hepatic I/R, liver damage, inflammatory responses, oxidative stress and apoptosis were analyzed. By evaluating plasma alanine aminotransferase levels and histology, we found that DIZE treatment attenuated liver failure and was associated with a reduction in histologically-apparent liver damage. We also found that DIZE-treated mice had milder inflammatory responses, less reactive oxidative damage, and less apoptosis following hepatic I/R compared to vehicle-treated mice. Taken together, our study demonstrates that DIZE protects against ischemic liver injury by attenuating inflammation and oxidative damage and may be a potential therapeutic agent for the prevention and treatment of ischemic liver failure.
Predictors of Research Subject retention - Repetitive non-adherence or socioeconomic factors: Insights from a urological clinical trial
Authors: Liss Michael A. , Wheeler Allison J. , Garg Harshit , Kaushik Dharam , Mansour Ahmed , Pruthi Deepak 
Published: March 2022

Abstract
Background:To investigate various patient level variables, specifically socioeconomic status, as risk factors for withdrawal in a recently completed clinical study. We specifically investigate a recent study in men on adherence to an observational prostate cancer imaging and biomarkers study. Methods: We performed a retrospective study to investigate risk factors for withdrawal in a prostate cancer imaging study that enrolled men on active surveillance from January 2016 to June 2019. For each subject, we assessed their retention status and collected demographic data. We compared values between the two retention groups using T-test, Chi-Squared, and logistic regression. Results:Out of 273 men screened, 123 men were enrolled and included in the results of this study. Of those, 106 (86%) were retained in the study and 17 (14%) were withdrawn. While we found no significant relationship between low socioeconomic status and retention, we did find that the number of non-adherences was a significant factor in withdrawal from the study (OR 2.5, 95% CI 3.5-40.5, p<0.001). Conclusions: Expanding diverse inclusion and limiting withdrawal with real-time non-adherence monitoring will lead to more efficient clinical research and greater generalizability of results.