bluuebunny/crossref_metadata_2025_split huggingface dataset:
Repeat to Gene Expression Ratios in Leukemic Blast Cells Can Stratify Risk Prediction in Acute Myeloid Leukemia
Authors: Onishi-Seebacher Megumi , Sawitzki Zoe , Ryan Devon , Erikson Galina , Greve Gabriele , Lübbert Michael , Jenuwein Thomas 
Published: July 2020

Abstract
BackgroundRepeat elements constitute a large proportion of the human genome and recent evidence indicates that repeat element expression has functional roles in both physiological and pathological states. Specifically for cancer, transcription of endogenous retrotransposons is often suppressed in order to attenuate an anti-tumor immune response, whereas aberrant expression of heterochromatin-derived satellite RNA has been identified as a tumor driver. These insights demonstrate separate functions for the dysregulation of distinct repeat subclasses in either the attenuation or progression of human solid tumors. For hematopoietic malignancies, such as AML, only very few studies on the expression/dysregulation of repeat elements were done. MethodsTo study the expression of repeat elements in acute myeloid leukemia (AML), we performed total-RNA sequencing of healthy CD34+ cells and of leukemic blast cells from primary AML patient material. We also developed an integrative bioinformatic approach that can quantify the expression of repeat transcripts from all repeat subclasses (SINE/ALU, LINE and ERV elements and satellite repeats) in relation to the expression of gene and other non-repeat transcripts. This novel approach can be used as an instructive signature (‘rep/gene’ ratio) for repeat element expression and has been extended to the analysis of poly(A)-RNA sequencing datasets from Blueprint and TCGA consortia that together comprise 120 AML patient samples. ResultsWe identified that repeat element expression is generally down-regulated during hematopoietic differentiation and that relative changes in repeat to gene expression (i.e. ‘rep/gene’ ratios) can stratify risk prediction of AML patients and correlate with overall survival probabilities. A high repeat to gene expression ratio identifies AML patient subgroups with a favorable prognosis, whereas a low repeat to gene expression is prevalent in AML patient subgroups with a poor prognosis. ConclusionsWe developed an integrative bioinformatic approach that defines a general model for the analysis of repeat element dysregulation in physiological and pathological development. We find that changes in repeat to gene expression (‘rep/gene’ ratios) correlate with hematopoietic differentiation and can sub-stratify AML patients into low-risk and high-risk subgroups. Thus, the definition of a ‘rep/gene’ expression ratio can serve as a valuable biomarker for AML and could also provide insights into differential patient response to epigenetic drug treatment.
Correlating Genomic Copy Number Alterations with Clinicopathologic Findings in A Case Series of Hepatocellular Carcinoma
Authors: Peng Gang , Chai Hongyan , Ji Weizhen , Lu Yufei , Wu Shengming , Li Peining , Hu Qiping 
Published: July 2020

Abstract
Background: Oligonucleotide array comparative genomic hybridization (aCGH) analysis has been used for detecting somatic copy number alterations (CNAs) in various types of tumors. This study aimed to assess the clinical utility of aCGH for a case series of hepatocellular carcinoma (HCC) and to evaluate the correlation between CNAs and clinicopathologic findings.Methods: Survival outcomes from this case series were analyzed based on Barcelona-Clinic Liver Cancer Stage (BCLC), Edmondson-Steiner grade (E-S), and recurrence status. aCGH was performed on 75 HCC cases with paired DNA samples from tumor and adjacent nontumor tissues. Correlation of CNAs with clinicopathologic findings was analyzed by Wilcoxon rank test and clustering vs. K means. Results: The survival outcomes indicated that BCLC stages and recurrence status could be predictors and E-S grades could be a modifier for HCC. The most common CNAs involved gains of 1q and 8q and a loss of 16q (50%), losses of 4q and 17p and a gain of 5p (40%), and losses of 8p and 13q (30%). Correlation and clustering analyses noted that losses of 4q13.2q35.2 and 10q22.3q26.13 seen in cases of stage A, grade III and nonrecurrence were likely associated with good survival, while loss of 1p36.31p22.1 and gains of 2q11.2q21.2 and 20p13p11.1 seen in cases of stage C, grade III and recurrence were possibly associated with worst prognosis. Conclusions: These results indicated that aCGH analysis could be used to detect recurrent CNAs and involved key genes and pathways in patients with HCC. Further analysis on a large case series to validate the association of CNAs with clinicopathologic findings of HCC could provide information to interpret CNAs and predict prognosis.
Risk Factors for post-Endoscopic Retrograde Cholangiopancreatography Abdominal Pain in Patients without post-ERCP Pancreatitis
Authors: Chen Mengjie , Zheng Ruhua , Cao Jun , Yao Yuling , Wang Lei , Zou Xiaoping 
Published: July 2020

Abstract
Background: Most of the studies on the abdominal pain associated with endoscopic retrograde cholangiopancreatography (ERCP) are aimed at solving the pain during the procedure. Post-ERCP abdominal pain has rarely been investigated，and few studies have focused on the characteristics and risk factors of post-ERCP abdominal pain without post-endoscopic retrograde cholangiopancreatography pancreatitis (PEP).This study aimed to identify risk factors of post-ERCP abdominal pain without PEP and investigate characteristics of the abdominal pain in non-PEP patients.Methods: From August 6th, 2019, to January 15th, 2020, data of patients who underwent ERCP were retrospectively collected. The characteristics of the abdominal pain after ERCP were recorded and compared between PEP and non-PEP patients. Multivariate analysis was conducted to identify risk factors of non-PEP abdominal pain. Results: Data from 616 ERCP procedures were retrospectively investigated in this study, among which 51(8.28%) patients presented post-ERCP abdominal pain without PEP and 45 (7.31%) patients developed PEP. Multivariate analysis found that 5 risk factors were associated with non-PEP abdominal pain: female gender (OR:2.137), upper abdominal surgery history (OR:1.948), first time ERCP (OR:4.735), elevated serum γ-glutamyl transferase (𝛾-GT) (OR:2.570) and elevated serum direct bilirubin (DBIL) (OR:2.932). Visual analogue sale (VAS) score of PEP abdominal pain was higher than that of non-PEP pain group (P=0.05). There were no significant differences in the time of the onset of the pain, pain relief time, pain frequency, use of analgesic medicine, hospital stay and mortality between PEP and non-PEP pain group(P<0.05).Conclusion: This study indicated that female gender, upper abdominal surgery history, first time ERCP, elevated 𝛾-GT and elevated DBIL were independent risk factors for post-ERCP abdominal pain without PEP. Abdominal pain was severer in PEP patients than non-PEP patients.
Octreotide Safety and Efficacy in Pediatric Non-variceal Upper Gastrointestinal Bleeding, A Randomized Controlled Trial
Authors: Mirrahimi Bahador , Rohani Pejman , Moradi Omid , Hemmati Azin 
Published: July 2020

Abstract
Background: Octreotide as somatostatin analogue decrease the production of gastrointestinal (GI) peptides. Its consumption in pediatric population has been limited to control of bleeding episodes with variceal origin. In this randomized controlled trial, we aim to assess octreotide as an add-on therapy to conventional regimen of proton pump inhibitors in controlling upper GI bleeding in pediatric population.Methods: In a prospective randomized controlled clinical trial, in Mofid Children's Hospital, Tehran, Iran, pediatric patients with age of 0 to 15 years diagnosed with acute non-variceal upper GI bleeding allocated to receive Octreotide or placebo and pantoprazole concomitantly. Medication administration initiated after patient’s stabilization. Patients with hepatic failure, liver stigma, coagulopathy thrombocytopenia etc. were excluded. Demographic, clinical and preclinical data were recorded in prepared sheets. All patients were followed until therapy discontinuation.Results: Forty-three patients with the mean age of 4.98 ± 3.79 years with confirmed non-variceal upper GI bleeding included to the study. Most patients had no specific etiology for their bleeding episode. Patients in intervention and control group received pantoprazole in comparable doses. No differences in baseline hemoglobin values was observed but final hemoglobin values were higher in intervention group. No differences in bleeding duration observed. In regard of adverse drug reaction due to octreotide infusion, none was observed in any patient. Conclusions: Our study demonstrated that octreotide does not alter bleeding duration but need for transfusion in non-variceal upper GI bleeding but it may have effect on amount of blood loss.Trial registration: The study was registered in Iranian Registry of Clinical Trial by the code of IRCT20120415009475N6.
The Effect of Different Methods to Identify, and Scenarios Used to Address Energy Intake Misestimation on Dietary Patterns Derived by Cluster Analysis
Authors: Siou Geraldine Lo , Akawung Alianu K. , Solbak Nathan M. , McDonald Kathryn , Rajabi Ala Al , Whelan Heather K. , Kirkpatrick Sharon I. 
Published: July 2020

Abstract
Background: All self-report dietary intake data are characterized by measurement error, and validation studies indicate that the estimation of energy intake (EI) is particularly affected. Methods: Using self-report food frequency and physical activity data from Alberta’s Tomorrow Project participants (n=9,847 men 16,241 women), we compared the revised-Goldberg and the predicted total energy expenditure methods in their ability to identify misreporters of EI. We also compared dietary patterns derived by k-means clustering under different scenarios where misreporters are included in the cluster analysis (Inclusion); excluded prior to completing the cluster analysis (ExBefore); excluded after completing the cluster analysis (ExAfter); and finally, excluded before the cluster analysis but added to the ExBefore cluster solution using the nearest neighbor method (InclusionNN). Results: The predicted total energy expenditure method identified a significantly higher proportion of participants as EI misreporters compared to the revised-Goldberg method (50% vs. 47%). k-means cluster analysis identified 3 dietary patterns: Healthy, Meats/Pizza and Sweets/Dairy. Among both men and women, participants assigned to dietary patterns changed substantially between ExBefore and ExAfter and also between the Inclusion and InclusionNN scenarios. Conclusions: Different scenarios used to account for EI misreporters influenced cluster analysis and hence the composition of the dietary patterns.
Predictive Value of Platelet-to-Lymphocyte Ratio and Systemic Immune‐Inflammation Index in Adverse Pathology at Radical Prostatectomy in Patients with Low-Grade Prostate Cancer
Authors: Zhou Jiatong , Li Tao , Liu RanLu 
Published: July 2020

Abstract
Purpose: To determine the potential role of several biochemical and clinical markers in predicting adverse pathology (AP) and ISUP GG upgrading at radical prostatectomy (RP) with low-grade (ISUP Gleason Group (ISUP GG) 1 and 2) prostate cancer (PCa). Methods: We retrospectively reviewed the patients who underwent radical prostatectomy following criteria: clinical stage T2a or less,and were identified low-grade PCa (ISUP GG 1−2, prostate-specifific antigen (PSA) <20 ng/ml) through prostate biopsy, univariate and multivariate analyses were performed to evaluate the association of patient and tumor characteristics with reclassification, defined as defined as stage ≥T3 and/or ISUP GG ≥3.Results: A total of 155 patients were eligible for this study. AP at RP occurred in 20 of 97 (20.62%) patients with ISUP GG 1, and 28 of 58 (48.28%) with ISUP GG 2. At univariate analysis, bioptic ISUP GG emerged as significant risk factors of AP(p＜0.001). platelets to lymphocyte ratio(PLR) might be the risk factor of AP(p=0.059). At multivariate analysis, we found PLR and bioptic ISUP GG kept statistical significance. The area under the curve for PLR was 0.592. Multivariate analyses showed that systemic immune inflammation index(SII), and bioptic ISUP GG were significantly associated with ISUP GG upgrading (ORs ranging from 0.453 to 0.999) showing a protective effect. Conclusions: We found that SII could not be a significant risk factor of AP at low-grade prostate cancer (PCa) after RP. PLR might be used as an independent predictor which was inversely correlated with presence of AP in low-grade PCa after RP. While SII might be a predict factor for ISUP GG upgrading in low-grade PCa.
IgG Fc Binding Protein (FCGBP) Is Down-Regulated in Metastatic Lesions and Predicts Survival in Metastatic Colorectal Cancer Patients
Authors: Yuan Ziming , Zhao Zhixun , Hu Hanqing , Qiao Tianyu , Ma Tianyi , Zhu Yihao , Zhang Weiyuan , Wu Hongyu , Tang Qingchao , Huang Rui , Gao Feng , Zou Chaoxia , Wang Guiyu , Wang Xishan 
Published: July 2020

Abstract
Background: Liver is the most frequent metastatic spread sites for CRC patients and these patients have much poorer prognosis compared to those without metastasis. Previous studies have shown that IgG Fc binding protein (FCGBP) plays important roles in tumorigenesis, progression and prognosis. In this study, we are aimed to explore the significance of FCGBP in liver metastatic CRC (LMCRC) patients. Methods: The expression data of FCGBP was obtained from GEO and TCGA database, FCGBP RNA expression was evaluated between primary lesions (PC) and liver metastatic lesion (LM). 135 paired specimens including normal mucosa, primary tumor and liver metastasis tissues were all collected from CRC patients and adopted in Tissue microarrays (TMAs). Immunohistochemical staining was performed on the TMAs slides with FCGBP and the immunohistochemistry score (SI) was calculated by the staining intensity multiplied by the positive rate of stained cells. Survival curves were calculated by Kaplan–Meier method and the log-rank test was used to compare the overall survival (OS) and disease-free survival (DFS). Univariate and multivariate analysis for prognosis were using Cox proportional hazards regression model.Results: FCGBP RNA was down-regulated in PC and LM, and especially lower in LM in database. We also found FCGBP protein was down-regulated in primary lesion and metastatic lesion, especially in metastatic lesion in 135 paired tumor tissues. According to immunohistochemistry score (SI), each cohort (primary lesion and metastatic lesion) was divided into FCGBP-positive (SI=4-12) and FCGBP-negative (SI=0-3) group. In both groups, the level of CEA (PC group, 3.880 vs 77.049, p<0.001; LM group, 3.890 vs 14.239, p=0.008) and CA19-9 (PC group, 8.610 vs 111.700, p<0.001; LM group, 7.660 vs 19.380, p=0.037) was lower than those in FCGBP-negative group. FCGBP-positive in LM cohort was an independent risk factor both in OS (HR 1.573, 95% Cl [1.017-2.433], p=0.042) and DFS (HR 1.869, 95% Cl [1.256-2.781], p=0.002). Conclusions: This study has found the relationship between FCGBP and clinical information of LMCRC patients. FCGBP expression was much lower in liver metastasis tumor tissues compared with primary tumor tissues in liver metastatic CRC patients and associated with the OS and PFS. Our works illustrate that FCGBP can be a promising prognostic factor for LMCRC.
B7-H3 Blockade Decreases Macrophage Inflammatory Response and Alleviates Clinical Symptoms of Arthritis
Authors: Yang Jie , Guo Yundi , Gu Li , Liu Cuiping , Wu Pingping , Tong Min , Xiong Jian , Sun Jing 
Published: July 2020

Abstract
Background: The costimulatory molecule B7-H3 is an immunoregulatory protein that plays an important role in the course of autoimmune diseases. It is also involved in the regulation of inflammatory responses in the body. Studies have shown that B7-H3 is highly expressed in peripheral blood monocytes of rheumatoid arthritis (RA) patients and its expression is closely related to the clinical parameters of the disease. In this study we aimed to determine what the implication of high B7-H3 expression for the disease severity in human RA and mouse model of arthritis is, and whether targeting this molecule could constitute a new therapeutic approach.Methods: We combined histopathological scoring of the joint cavity of collagen-induced arthritis (CIA) mice with immunofluorescent studies of B7-H3 expression on macrophages. We assessed the function of B7-H3 in relation with the pro-inflammatory role of macrophage through small RNA interference. Then we studied the molecular pathways liking B7-H3 with the pro-inflammatory activity of macrophages by multiplex flow cytometry, western blot and quantitative real-time PCR. The therapeutic benefit of anti-B7-H3 blocking was probed in mouse with CIA.Results: Histopathological and histological examination showed a positive correlation between expression of B7-H3 on macrophages and disease activity score, degree of destruction of the joint cavity, and pannus formation. It was also correlated with increased expression of the pro-inflammatory cytokine TNF-α in the joint cavity tissue and TNF-α level in peripheral serum. Knocking down B7-H3 expression through stable expression of small interfering RNA in human and mouse mononuclear phagocytic cell lines weakened the inflammatory response of the cells. Further molecular analyses indicated that the regulation of the inflammatory response through B7-H3 involved NF-κB signaling. Treatment of CIA mice with anti-B7-H3 reduced the clinical manifestation of arthritis and downregulated the expression of pro-inflammatory cytokines. Conclusions: We confirmed increased expression of B7-H3 in arthritis and established a positive correlation between disease severity and expression of B7-H3 on macrophages. Through functional approaches in vitro and in vivo, we also demonstrated the therapeutic benefits of targeting B7-H3 for dampening macrophages’ inflammatory responses in RA.
DEVELOPING PERFORMANCE ASSESSMENT INSTRUMENT FOR MEASURING SCIENTIFIC ATTITUDES
Authors: Shinta Debi , Rosana Dadan 
Published: July 2020

This study was aimed at developing an instrument of performance assessment based on the 7E learning cycle model and finding out the result of students’ scientific attitude measurement using the instrument. The study was conducted by adapting the Borg and Gall research method. The subjects of this study were students of grade eight of State Junior High School 2 Binangun, Cilacap, Central Java. Data were obtained from: first, experts’ judgements in determining the content validity of the instrument. Second, scores of the limited field try-out used in determining the reliability of the instrument, data collection instruments in the form of observation sheet, self assessment, and peer assessment. Third, students’ scientific attitudes in field try-out used to show the result of the measurement using the instrument. Findings show that the developed instrument of performance assessment is valid and reliable; and feasible to be used for measuring scientific attittudes, with measurement results in the good category equally for the three data collection instrumentsPENGEMBANGAN INSTRUMEN PENILAIAN KINERJAUNTUK MENGUKUR SIKAP ILMIAHPenelitian ini bertujuan untuk mengembangkan instrumen performance assessment berbasis model learning cycle 7E yang layak digunakan dan mengetahui hasil pengukuran sikap ilmiah menggunakan instrumen yang telah dikembangkan. Penelitian ini dikembangkan dengan adaptasi model Borg and Gall. Subjek uji coba yaitu peserta didik kelas VIII SMP Negeri 2 Binangun, Kabupaten Cilacap, Provinsi Jawa Tengah. Data dalam penelitian ini diperoleh melalui: pertama, penilaian berdasarkan masukan para ahli, untuk menentukan validitas isi instrumen. Kedua, hasil uji coba terbatas untuk menentukan reliabilitas instrumen, instrumen pengumpulan data berupa lembar observasi, penilaian diri, dan penilaian antarteman. Ketiga, data hasil sikap ilmiah peserta didik pada uji coba lapangan digunakan untuk mengetahui hasil pengukuran dengan instrumen yang telah dikembangkan. Instrumen performance assessment berbasis model learning cycle 7E yang dikembangkan dinyatakan valid dan reliabel sehingga layak digunakan serta terbukti dapat digunakan untuk mengukur sikap ilmiah peserta didik dengan hasil ukur pada kategori baik yang setara pada ketiga instrumen pengumpulan data
THE EFFECT OF INQUIRY BASED LEARNING WITH SOCIOSCIENTIFIC ISSUES CONTEXT ON CRITICAL THINKING SKILLS AND SCIENTIFIC EXPLANATION
Authors: Mahanani Intan , Rahayu Sri , Fajaroh Fauziatul 
Published: July 2020

This study was aimed at investigating the application of inquiry learning in the context of socioscientific issues (SSI) influences students' skills in critical thinking and scientific explanation on the topic of reaction rates. This study was quantitative research used post test only control group design. A total of 90 students who were enrolled in the 3 classes from one public senior high school in Malang regency were selected as the research sample by convenience. The data of critical thinking ability were collected through critical thinking test. The data of scientific explanation were collected through scientific explanation test. The results of critical thinking test were categorized by Ennis’s critical thinking, while the results of scientific explanation test were categorized by SOLO taxonomy. The data were analysed quantitatively by statistical parametric. The result of One-Way ANOVA showed that there were significant differences in students' critical thinking skills and scientific explanation ability who were taught by inquiry with SSI learning, inquiry, and verification model. Students who were taught by inquiry with SSI learning had a higher average of critical thinking and scientific explanation skills than the students who were taught by inquiry and verification learning. PENGARUH PEMBELAJARAN INKUIRI BERKONTEKS SOCIOSCIENTIFIC-ISSUES TERHADAP KETERAMPILAN BERPIKIR KRITIS DAN SCIENTIFIC EXPLANATIONPenelitian ini bertujuan untuk menginvestigasi pengaruh penerapan pembelajaran inkuiri berkonteks socioscientific issues (SSI) terhadap keterampilan siswa dalam berpikir kritis dan scientific explanation pada topik laju reaksi. Penelitian kuantitatif dilakukan dengan posttest only control group design. Sampel penelitian berjumlah 90 siswa yang terbagi ke dalam 3 kelas dari satu SMA Negeri di Kota Malang yang dipilih menggunakan teknik convenience sampling. Data keterampilan berpikir kritis diperoleh dari tes keterampilan berpikir kritis. Data penjelasan ilmiah dikumpulkan dengan tes scientific explanation. Data kemampuan berpikir kritis dikategorikan menurut kategori berpikir kritis Ennis. Adapun data kemampuan scientific explanation siswa dikategorikan menurut taksonomi SOLO. One-Way ANOVA digunakan untuk menganalisis pengaruh perlakuan Hasil penelitian menunjukkan adanya perbedaan yang signifikan keterampilan berpikir kritis dan scientific explanation pada siswa yang dibelajarkan dengan pembelajaran inkuiri berkonteks SSI, inkuiri, dan verifikasi. Siswa yang dibelajarkan dengan pembelajaran inkuiri berkonteks SSI memiliki nilai rata-rata keterampilan berpikir kritis lebih tinggi dan lebih mampu membangun explanation hingga level tertinggi yaitu level extended abstract, dibandingkan dengan siswa yang dibelajarkan menggunakan pembelajaran inkuiri dan verifikasi.