bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comprehensive Mutation Profiling of Colorectal Cancer Patients With Lung or Liver Metastasis by Targeted Next-Generation Sequencing
Authors: Hu Chun-Ting , Wang Jing-Long , Hou Ting , Yan Zhao-Wen , Zu Li-Dong , Fu Guo-Hui , Shen Wei-Wei 
Published: July 2023

Objectives Primary tumor tissue is often analyzed to search for predictive biomarkers and DNA-guided personalized therapies, but there is an incomplete understanding of the discrepancies in the genomic profiles between primary tumors and metastases, such as liver and lung metastases. Methods We performed in-depth targeted next-generation sequencing of 520 key cancer-associated genes for 47 matched primary and metastatic tumor samples which were retrospectively collected. Results A total of 699 mutations were detected in the 47 samples. The coincidence rate of primary tumors and metastases was 51.8% (n = 362), and compared to patients with liver metastases, patients with lung metastases had a significantly greater coincidence rate ( P = .021). The number of specific mutations for the primary tumors and liver and lung metastases was 186 (26.6%), 122 (17.5%), and 29 (4.1%), respectively. Analysis of a patient with all three occurrences, including a primary tumor, liver metastasis, and lung metastasis, indicated a possible polyclonal seeding mechanism for liver metastases. Remarkably, multiple samples from patients with primary and metastatic tumors supported a mechanism of synchronous parallel dissemination from primary tumors to metastatic tumors that were not mediated through pre-metastatic tumors. We also found that the PI3K-Akt signaling pathway significantly altered lung metastases compared to matched primary tumors ( P = .001). In addition, patients with mutations in CTCF, PIK3CA, or TP53 and LRP1B, AURKA, FGFR1, ATRX, DNMT3B, or GNAS had larger primary tumor sizes and metastases, especially patients with both LRP1B and AURKA mutations. Interestingly, CRC patients with TP53-disruptive mutations were more likely to have liver metastases ( P = .016). Conclusion In this study, we demonstrate significant differences in the genomic landscapes of colorectal cancer patients based on the site of metastasis. Notably, we observe a larger genomic variation between primary tumors and liver metastasis compared to primary tumors and lung metastasis. These findings can be used for tailoring treatments based on the specific metastatic site.
Estimating the adoption of electric vehicles: A case study of four Indian states
Authors: Saw Krishna , Kedia Ashu 
Published: July 2023

Rapid growth in petrol and diesel-powered vehicles has resulted in significant increases in tailpipe greenhouse gas emissions and air pollution, both of which harm public health in Indian cities. Furthermore, India’s dependence on imported fuel to transport people and goods threatens its fuel security. Therefore, electric mobility has been sought to deal with these issues. The governments have framed several plans and policies to promote electric vehicles (EVs) and achieve the target of EV30@30. However, EV adoption in Indian states has been slow. Therefore, this paper aims to estimate the number of EVs needed to be registered to achieve the desired target by 2030 by taking a case study of four states: Delhi, Uttar Pradesh, Karnataka, and Gujarat. The vehicular registration data used in this paper has been obtained from the government database. The study looks at the EV adoption rates of passenger vehicles such as two-wheelers, cars, auto-rickshaws (including e-rickshaws), and buses. According to the findings, the average annual share of passenger EVs is less than 2% in Delhi, less than 1% in Uttar Pradesh, and less than 0.5% in Karnataka and Gujarat during the study period. According to the models’ estimates, Delhi, Uttar Pradesh, Gujarat, and Karnataka will need to register 0.31 million, 1.51 million, 0.88 million, and 0.79 million passenger EVs, respectively, in FY 2030–2031 to achieve a 30% EV share of total registrations.
A pilot project investigating the use of ONCOpatient®—An electronic patient-reported outcomes app for oncology patients
Authors: Macanovic Bojan , O’Reilly David , Harvey Harry , Hadi Danial , Cloherty Maeve , O’Dea Pauline , Power Derek G. , Collins Dearbhaile C. , Connolly Roisin M. , Bambury Richard M. , O’Reilly Seamus 
Published: July 2023

Purpose To investigate the feasibility of implementing a remote patient monitoring system using an electronic patient-reported outcomes (ePROs) platform in a tertiary cancer center in the Republic of Ireland. Methods Patients receiving oral chemotherapy and oncology clinicians were invited to participate in the study. Patients were asked to submit weekly symptom questionnaires through an ePRO mobile phone application (app)—ONCOpatient®. Clinical staff were invited to use the ONCOpatient® clinician interface. After 8 weeks all participants submitted evaluation questionnaires. Results Thirteen patients and five staff were enrolled in the study. The majority of patients were female (85%) with a median age of 48 years (range 22–73). Most (92%) were enrolled over telephone requiring on average 16 minutes. Compliance with the weekly assessments was 91%. Alerts were triggered by 40% of patients who then required phone calls to aid with symptom management. At the end of study, 87% of patients reported they would use the app frequently, 75% reported that the platform met their expectations, and 25% that it exceeded their expectations. Similarly, 100% of staff reported they would use the app frequently, 60% reported that it met their expectations, and 40% that it exceeded their expectations. Conclusions Our pilot study showed that it is feasible to implement ePRO platforms in the Irish clinical setting. Small sample bias was recognized as a limitation, and we plan to confirm our findings on a larger cohort of patients. In the next phase we will integrate wearables including remote blood pressure monitoring.
Analysis of the effect of glutamyltransferase on hyperlipidemia based on decision tree
Authors: Zhang Tingting , Ouyang Dantong , Sun Chenglin , Bi Yaru , He Lili , Bai Hongtao 
Published: July 2023

Objectives This study is designed to analyze the potential influencing factors of hyperlipidemia, and to explore the relationship between liver function indicators such as gamma-glutamyltransferase (GGT) and hyperlipidemia. Methods Data were derived from 7599 outpatients who visited the Department of Endocrinology of the First Hospital of Jilin University (2017–2019). A multinomial regression model is used to identify related factors of hyperlipidemia and the decision tree method is used to explore the general rules in hyperlipidemia patients and non-hyperlipidemia patients on these factors. Results The average of age, body mass index (BMI), systolic blood pressure (SBP), diastolic blood pressure, aspartate aminotransferase, alanine aminotransferase (ALT), GGT and glycosylated hemoglobin (HbA1c) in the hyperlipidemia group are higher than those in the non-hyperlipidemia group. In multiple regression analysis, SBP, BMI, fasting plasma glucose, 2-h postprandial blood glucose, HbA1c, ALT, GGT are associated with triglyceride. For people with HbA1c less than 6.0%, controlling GGT within 30 IU/L reduces the prevalence of hypertriglyceridemia by 4%, and for people with metabolic syndrome with impaired glucose tolerance controlling GGT within 20 IU/L reduces the prevalence of hypertriglyceridemia by 11%. Conclusions Even when GGT is in the normal range, the prevalence of hypertriglyceridemia increases with its gradual increase. Controlling GGT in people with normoglycemia and impaired glucose tolerance can reduce the risk of hyperlipidemia.
Learning Chemistry, Connecting Ecological Citizenship and Environmental Sustainability: “A Plate of Food” as a Learning Medium
Authors: Simanjuntak Familia Novita , Utomo Suyud Warno , Sika Ery Seda Francisia Saveria , Budhi Soesilo Tri Edhi , Sumiyati Sumiyati 
Published: July 2023

Highlights Using a new concept of “a plate of food” (aPoF), a symbol of meaningful chemical reaction products, this article addresses the Grade 10 students’ chemistry anxiety in Indonesia. In line with the ecological citizenship and pro-environmental behavior perspectives, the aPoF is conceptualized based on environmental concerns such as food sustainability, food-critical consciousness, and the earth's carrying capacity. This means that the aPoF is beneficial to support Sustainable Development Goals #2 Zero Hunger, #4 Quality Education, and #12 Responsible Consumption and Production. Based on our results, we suggest that chemistry teachers can give more space for students to express their difficulties in learning chemistry. The space can be delivered by giving assignments focusing on the students’ feelings and experiences related to a certain chemistry topic.
The Cause of Institutionalized Private Tutoring in Korea: Defective Public Schooling or a Universal Desire for Family Reproduction?
Authors: Bae (배상훈) Sang Hoon , Choi (최기호) Kee Ho 
Published: July 2023

Purpose In Korea, private tutoring is considered a social evil that damages the capacity of public schooling and undermines social justice. Although the government has implemented various policies to reduce private tutoring, ranging from improving the quality of education to providing “quasi-private tutoring” programs and regulating the shadow education market, total spending on private tutoring has continued to increase. This study examines a little noticed but important cause of institutionalized private tutoring in Korea. Design/Approach/Methods The study employed a socio-ecological perspective to analyze both education and socio-structural factors. An extensive review of the government's private tutoring reduction policies and related literature was conducted. Findings Private tutoring functions as a means by which parents can help their children compete for admission to prestigious universities and pass on wealth and social status to their children. Participation in private tutoring has become a social norm that is taken for granted. The root causes of institutionalized private tutoring lie in both educational and socio-structural factors. Originality/Value The study suggests that government policies, when ignoring the long-established “grammar” of parents about children's education, may either end in failure or produce unintended consequences.
Impacts of COVID-19 Pandemic on the Price Volatility of Listed Commercial Bank Stocks in Vietnam
Authors: Lan Le Phuong , Phuong Dong Khanh 
Published: July 2023

This article aims to estimate the relationship between COVID-19 and the price volatility of listed commercial bank stocks in Vietnam during the two most severely affected years of the pandemic (2020–2021), and measuring the impacts of macroeconomic factors on those stocks’ returns and their price volatility (measured by standard deviation of returns) with previous studies’ results before the pandemic. Using the data from 16 listed commercial banks’ stock returns on Ho Chi Minh Stock Exchange (HOSE) and Hanoi Stock Exchange (HNX) during the study period, we used OLS to find the effect, with important findings: (1) COVID-19 daily reported cases had a weak negative effect on Vietnam listed banks’ stock returns and hardly any relation with stock returns’ standard deviation. (2) GDP influenced commercial bank stock returns positively, while CPI, number of COVID-19 cases, and businesses closed had a negative effect. Also, listed commercial bank stock returns were insignificantly impacted by the interest rate. (3) Macroeconomic factors’ impact on the standard deviation of returns were weak, during the pandemic. GDPs and CPIs effect turned out to be insignificant while interest rate had a negative effect on the volatility rate, and was only significant in two out of the three models, implying potential negative impacts of COVID-19 on the macroeconomy. JELClassification: G21, F62, F65, G18, G28
Clinical utility of lipid ratios as potential predictors of metabolic syndrome among the elderly population: Birjand Longitudinal Aging Study (BLAS)
Authors: Saeedi Farhad , Baqeri Elnaz , Bidokhti Ali , Moodi Mitra , Sharifi Farshad , Riahi Seyed Mohammad 
Published: July 2023

Abstract
Background
Elderly adults are at higher risk of developing metabolic syndrome (MetS). The present study aims to investigate the relationship between lipid ratios and MetS in the elderly population.

Methods
This study was conducted on elderly population of Birjand during 2018–2019. The data of this study was driven from Birjand Longitudinal Aging Study (BLAS). The participants were selected based on multistage stratified cluster sampling. Patients were categorized into quartiles according to the lipid ratios (TG/HDL-C, LDL-C/HDL-C, non-HDL/HDL-C), and the relationship between lipid ratio quartiles and MetS was determined by Logistic Regression using Odds Ratio. Finally, the optimal cut-off for each lipid ratio in MetS diagnosis was calculated according to the Area Under the Curve (AUC).

Results
This study included 1356 individuals, of whom 655 were men and 701 were women. In our study, the crude prevalence of MetS was 792 (58%), including 543 (77.5%) women and 249 (38%) men. Increasing trends were observed in quartiles of all lipid ratios for TC, LDL-C, TG, and DBP. TG/HDL was also the best lipid ratio to diagnose the MetS, based on NCEP ATP III criteria. One unit increased in level of TG/HDL resulted in 3.94 (OR: 3.94; 95%CI: 2.48–6.6) and 11.56 (OR: 11.56; 95%CI: 6.93–19.29) increasing risk of having MetS in quartile 3 and 4 compared to quartile 1, respectively. In men and women, the cutoff for TG/HDL was 3.5 and 3.0, respectively.

Conclusions
Our results showed that the TG/HDL-C is superior to the LDL-C/HDL-C and the non-HDL /HDL-C to predict MetS among the elderly adults.
Hepatitis C Virus in people with experience of injection drug use following their displacement to Southern Ukraine before 2020
Authors: Yakovleva Anna , Kovalenko Ganna , Redlinger Matthew , Smyrnov Pavlo , Tymets Olga , Korobchuk Anna , Kotlyk Lyudmyla , Kolodiazieva Anna , Podolina Anna , Cherniavska Svitlana , Antonenko Petro , Strathdee Steffanie A. , Friedman Samuel R. , Goodfellow Ian , Wertheim Joel O. , Bortz Eric , Meredith Luke , Vasylyeva Tetyana I. 
Published: July 2023

Abstract
Background
Due to practical challenges associated with genetic sequencing in low-resource environments, the burden of hepatitis C virus (HCV) in forcibly displaced people is understudied. We examined the use of field applicable HCV sequencing methods and phylogenetic analysis to determine HCV transmission dynamics in internally displaced people who inject drugs (IDPWID) in Ukraine.

Methods
In this cross-sectional study, we used modified respondent-driven sampling to recruit IDPWID who were displaced to Odesa, Ukraine, before 2020. We generated partial and near full length genome (NFLG) HCV sequences using Oxford Nanopore Technology (ONT) MinION in a simulated field environment. Maximum likelihood and Bayesian methods were used to establish phylodynamic relationships.

Results
Between June and September 2020, we collected epidemiological data and whole blood samples from 164 IDPWID (PNAS Nexus.2023;2(3):pgad008). Rapid testing (Wondfo® One Step HCV; Wondfo® One Step HIV1/2) identified an anti-HCV seroprevalence of 67.7%, and 31.1% of participants tested positive for both anti-HCV and HIV. We generated 57 partial or NFLG HCV sequences and identified eight transmission clusters, of which at least two originated within a year and a half post-displacement.

Conclusions
Locally generated genomic data and phylogenetic analysis in rapidly changing low-resource environments, such as those faced by forcibly displaced people, can help inform effective public health strategies. For example, evidence of HCV transmission clusters originating soon after displacement highlights the importance of implementing urgent preventive interventions in ongoing situations of forced displacement.
Systematic discovery of gene fusions in pediatric cancer by integrating RNA-seq and WGS
Authors: van Belzen Ianthe A. E. M. , Cai Casey , van Tuil Marc , Badloe Shashi , Strengman Eric , Janse Alex , Verwiel Eugène T. P. , van der Leest Douwe F. M. , Kester Lennart , Molenaar Jan J. , Meijerink Jules , Drost Jarno , Peng Weng Chuan , Kerstens Hindrik H. D. , Tops Bastiaan B. J. , Holstege Frank C. P. , Kemmeren Patrick , Hehir-Kwa Jayne Y. 
Published: July 2023

AbstractBackgroundGene fusions are important cancer drivers in pediatric cancer and their accurate detection is essential for diagnosis and treatment. Clinical decision-making requires high confidence and precision of detection. Recent developments show RNA sequencing (RNA-seq) is promising for genome-wide detection of fusion products but hindered by many false positives that require extensive manual curation and impede discovery of pathogenic fusions.MethodsWe developed Fusion-sq to overcome existing disadvantages of detecting gene fusions. Fusion-sq integrates and “fuses” evidence from RNA-seq and whole genome sequencing (WGS) using intron–exon gene structure to identify tumor-specific protein coding gene fusions. Fusion-sq was then applied to the data generated from a pediatric pan-cancer cohort of 128 patients by WGS and RNA sequencing.ResultsIn a pediatric pan-cancer cohort of 128 patients, we identified 155 high confidence tumor-specific gene fusions and their underlying structural variants (SVs). This includes all clinically relevant fusions known to be present in this cohort (30 patients). Fusion-sq distinguishes healthy-occurring from tumor-specific fusions and resolves fusions in amplified regions and copy number unstable genomes. A high gene fusion burden is associated with copy number instability. We identified 27 potentially pathogenic fusions involving oncogenes or tumor-suppressor genes characterized by underlying SVs, in some cases leading to expression changes indicative of activating or disruptive effects.ConclusionsOur results indicate how clinically relevant and potentially pathogenic gene fusions can be identified and their functional effects investigated by combining WGS and RNA-seq. Integrating RNA fusion predictions with underlying SVs advances fusion detection beyond extensive manual filtering. Taken together, we developed a method for identifying candidate gene fusions that is suitable for precision oncology applications. Our method provides multi-omics evidence for assessing the pathogenicity of tumor-specific gene fusions for future clinical decision making.
Development and validation of prognostic nomograms based on De Ritis ratio and clinicopathological features for patients with stage II/III colorectal cancer
Authors: Fu Jinming , Du Fenqi , Tian Tian , Huang Hao , Zhang Lei , Li Dapeng , Liu Yupeng , Zhang Ding , Gao Lijing , Zheng Ting , Liu Yanlong , Zhao Yashuang 
Published: July 2023

Abstract
Background
Metabolic derangements and systemic inflammation are related to the progression of colorectal cancer (CRC) and the prognoses of these patients. The survival of stage II and III CRC patients existed considerable heterogeneity highlighting the urgent need for new prediction models. This study aimed to develop and validate prognostic nomograms based on preoperative serum liver enzyme as well as evaluate the clinical utility.

Methods
A total of 4014 stage II/III primary CRC patients pathologically diagnosed from January 2007 to December 2013 were included in this study. These patients were randomly divided into a training set (n = 2409) and a testing set (n = 1605). Univariate and multivariate Cox analyses were used to select the independent factors for predicting overall survival (OS) and disease-free survival (DFS) of stage II/III CRC patients. Next, nomograms were constructed and validated to predict the OS and DFS of individual CRC patients. The clinical utility of nomograms, tumor-node-metastasis (TNM), and the American Joint Committee on Cancer (AJCC) system was evaluated using time-dependent ROC and decision curve analyses.

Results
Among seven preoperative serum liver enzyme markers, aspartate aminotransferase-to-alanine aminotransferase ratio (De Ritis ratio) was identified as an independent factor for predicting both OS and DFS of stage II/III CRC patients. The nomograms incorporated De Ritis ratio and significant clinicopathological features achieved good accuracy in terms of OS and DFS prediction, with C-index of 0.715 and 0.692, respectively. The calibration curve showed good agreement between prediction by nomogram and actual observation. The results of time-dependent ROC and decision curve analyses suggested that the nomograms had improved discrimination and greater clinical benefits compared with TNM and AJCC staging.

Conclusions
De Ritis ratio was an independent predictor in predicting both the OS and DFS of patients with stage II/III CRC. Nomograms based on De Ritis ratio and clinicopathological features showed better clinical utility, which is expected to help clinicians develop appropriate individual treatment strategies for patients with stage II /III CRC.
Pan-cancer analysis of whole-genome doubling and its association with patient prognosis
Authors: Kikutake Chie , Suyama Mikita 
Published: July 2023

AbstractBackgroundWhole-genome doubling (WGD) is a common mutation in cancer. Various studies have suggested that WGD is associated with a poor prognosis in cancer. However, the detailed association between WGD occurrence and prognosis remains unclear. In this study, we aimed to elucidate the mechanism by which WGD affects prognosis using sequencing data from the Pan-Cancer Analysis of Whole Genomes (PCAWG) and The Cancer Genome Atlas.MethodsWhole-genome sequencing data of 23 cancer types were downloaded from PCAWG project. We defined the WGD event in each sample using the WGD status annotated using PCAWG. We used MutationTimeR to predict the relative timings of mutations and loss of heterozygosity (LOH) in WGD, thus evaluating their association with WGD. We also analyzed the association between WGD-associated factors and patient prognosis.ResultsWGD was associated with several factors, e.g., length of LOH regions. Survival analysis using WGD-associated factors revealed that longer LOH regions and LOH in chr17 were associated with poor prognosis in samples with WGD (WGD samples) and samples without WGD (nWGD samples). In addition to these two factors, nWGD samples showed that the number of mutations in tumor suppressor genes was associated with prognosis. Moreover, we explored the genes associated with prognosis in both samples separately.ConclusionThe prognosis-related factors in WGD samples differed significantly compared with those in nWGD samples. This study emphasizes the need for different treatment strategies for WGD and nWGD samples.