bluuebunny/crossref_metadata_2025_split huggingface dataset:
Significance of Glasgow prognostic scores in NSCLC patients treated with immunotherapy after platinum-based cytotoxic chemotherapy
Authors: Kang Hye Seon , Shin Ah Young , Yeo Chang Dong , Kim Sung Kyoung , Park Chan Kwon , Kim Ju Sang , Kim Seung Joon , Lee Sang Haak , Kim Jin Woo 
Published: February 2021

Abstract
Background: The Glasgow prognostic score (GPS) reflects the host’s systemic inflammatory response and is a validated prognostic factor in lung cancer. However, little is known about the prognostic role in non-small cell lung cancer (NSCLC) patients treated with immunotherapy after platinum-based cytotoxic chemotherapy.Methods: This study used a lung cancer cohort of the Catholic Medical Center of Korea between January 2018 and September 2020. We included patients who were diagnosed with unresectable advanced stage NSCLC or recurrent disease after pulmonary resection and had received at least one regimen of platinum-based chemotherapy before the administration of immunotherapy. The prognostic value of the GPS was assessed in patients with NSCLC treated with anti-PD1 or anti-PD-L1 (pembrolizumab, nivolumab, or atezolizumab). The GPS was calculated using C-reactive protein and albumin concentrations within one week before starting anti-PD1 or anti-PD-L1 treatment. Results: A total of 78 patients with NSCLC treated with immunotherapy as second or further-line therapy after platinum-based chemotherapy were included in the study. Kaplan-Meier analysis revealed that higher GPS values were significant predictors of shorter immune-related progression-free survival (irPFS) (log-rank P < 0.001) and overall survival (OS) (log-rank P < 0.001). In the Cox regression multivariate analysis, the hazard ratios for irPFS were 0.249 (95% confidence interval [CI]: 0.084 – 0.739, P = 0.012) for PD-L1 expression ≥ 50% and 9.73 (95% CI: 2.931 – 32.298, P < 0.001) for a GPS of 2 relative to a GPS of 0. Older age (P = 0.033), lower PD-L1 expression (P = 0.036), and higher GPS values (P = 0.007) were independently associated with shorter OS.Conclusions: Higher GPS values were identified as a poor prognostic factor for OS and irPFS in NSCLC patients who received immunotherapy as second or further-line therapy after platinum-based chemotherapy.
Ten-year follow up of cosmetic outcome, overall survival, and disease-free survival in endoscope-assisted partial mastectomy with filling of dead space using absorbable mesh for stage ≤IIA breast cancer: Comparison with conventional conservative method
Authors: Takemoto Nobuyuki , Koyanagi Ai , Yamamoto Hiroshi 
Published: February 2021

Abstract
Background

Data on long-term cosmetic outcome, overall survival, and disease-free survival of endoscope-assisted partial mastectomy (EAPM) for breast cancer are scarce. Thus, we examined these outcomes after a 10-year follow-up period, and compared with conventional conservative method (CCM).
Patients and Methods:

Data on 257 patients with stage ≤ IIA breast cancer who underwent CCM (n = 125) or EAPM (n = 132) were analyzed. Cosmetic outcome at 2, 5, and 10 years was evaluated by 5 criteria (breast retraction assessment, nipple deviation, atrophy, skin change, scar). For overall mortality, breast cancer-specific mortality, and recurrence, the risk by operation method was tested by Log-rank tests.
Results

EAPM performed significantly better than CCM in terms of cosmetic outcomes for location B at 2, 5, and 10 year-follow ups. As for cosmetic outcomes by individual criteria, EAPM had significantly higher proportions of satisfactory results for scar across all follow-up periods, and atrophy at 2-year and 10-year follow-up. There were no significant differences in terms of overall mortality, breast cancer-specific mortality, and recurrence between EAPM and CCM. The rates of patients who experienced local recurrence were similar between CCM and EAPM.
Conclusion

EAPM is better than CCM in terms of long-term cosmetic outcome, especially for location B. As a surgical treatment for breast cancer, EAPM is comparable to CCM in terms of mortality and recurrence.
Initiating a district-based public–private mix to overcome tuberculosis missing cases in Indonesia: readiness to engage.
Authors: Sunjaya Deni Kurniadi , Paskaria Cindra , Herawati Dewi Marhaeni Diah , Pramayanti Meisera , Riani Rini , Parwati Ida 
Published: February 2021

Abstract
Background: District-based public–private mix (DPPM) is a variant of a relatively new PPM strategy of addressing missing cases in the tuberculosis (TB) care cascade in Indonesia. This research aims to analyze the readiness stakeholders' engagement in the context of initiating the implementation of DPPM.Methods: The research design was sequential exploratory mixed methods. A qualitative study in the first stage was carried out through participant observation, in-depth interviews and study documents. Data were analyzed through coding, categorizing, pattern matching and theorizing. The second stage was a survey conducted using instruments built in stage I. Data were analyzed using Rasch modeling and logistic regression.Results: District TB case detection rates (CDRs) has improved from 35% (2018) to 104% (2019). The contribution of private hospitals has increased considerably. However, there were none or minimal from the private primary healthcare facilities. The substantive theory generated indicates that awareness and concern of the TB problem, TB program comprehension and involvement, and institutional support are behind the readiness of private facilities to engage the TB program (the readiness to engage). The measurement results indicate the significant correlation of all dimensions on readiness to engage. Concern of the TB problem and institutional support are variables that influence readiness to engage (p < 0.05).Conclusions: Engaging private and public facility stakeholders is a challenge for local government. Intervention is through a personalized approach and encourages institutional support of health facilities for the TB program. Private sector engagement is a process that must be managed and not allowed to naturally happen.
Comparative Transcriptomic Analysis Provides Insight Into Carpel Petaloid in Lotus (Nelumbo Nucifera)
Authors: Lin Zhongyuan , Cao Dingding , Damaris Rebecca Njeri , Yang Pingfang 
Published: February 2021

Abstract
Background: Lotus (Nelumbo nucifera) is a famous flower with high ornamental value. Flower color and flower morphology are two main factors for flower lotus breeding. Petaloid is a universal phenomenon in lotus flowers. However, the genetic regulation of floral organ petaloid in lotus still remains unclear. Results: In this study, the transcriptomic analysis was performed among five organs, including petal, stamen petaloid, stamen, carpel petaloid, and carpel in lotus. 812 annotated DEGs related to carpel petaloid were identified. Our study showed that DNA methylation may be involved in regulating carpel petaloid. To identify the patterns of gene expression in the petaloid process using WGCNA analysis, 37 candidate genes were found to be related to carpel petaloid. Additionally, one floral homeotic gene encoded by MADS box transcription factor, AGAMOUS (AG), was identified as the candidate gene for petaloid in lotus. Meanwhile, a predicted labile boundary in floral organs of N. nucifera was hypothesized. Conclusions: In summary, the above results explored the candidate genes related to carpel petaloid, setting a theoretical basis for the molecular regulation of petaloid phenotype.
Inhibition of liver sinusoidal endothelial cells in rats with hepatic fibrosis by injection of VEGF 165 via the inferior vena cava
Authors: Sun Zhigang , Dong Tianyi , Zhang Zhun , Wang Tiantian , Zhang Chenyu , Tian Xingsong , Xu Hao 
Published: February 2021

Abstract
Background Although VEGF can maintain the normal phenotype of liver sinusoidal endothelial cells (LSECs), it has also been reported that VEGF exacerbates cirrhosis. The role of VEGF in the progression and recovery of cirrhosis has still remained controversial.Methods We established a cirrhotic rat model by thioacetamide that was used as drinking water; besides, 0, 1, 2, and 4 μg VEGF165 were then continuously injected into the rats. The serum level of hyaluronic acid was measured by ELISA at 0, 1, and 4 weeks, separately. Serum levels of ALT, AST, direct bilirubin, indirect bilirubin, and ALB were detected by an automatic biochemical analyzer. In addition, the levels of VEGF165, CD44, MMP9, MMP2, HIF-1α, and endothelin were detected by Western blotting. The expression level of CD44 in LSECs was detected by immunohistochemistry. Changes of fenestrations of LSECs and basement membranes of blood vessels were observed by transmission electron microscopy. Results With the increase of dosage and duration of VEGF treatment, the levels of liver function markers in the serum, the levels of CD44, HIF-1α, hydroxyproline and endothelin were significantly improved. With determination of the serum level of hydroxyproline in the blood, it was disclosed that the mentioned level was markedly decreased. In the Sirius Red staining, the stained red area was gradually reduced. Images captured by transmission electron microscopy also confirmed that the ultrastructure of LSECs tended to be normal.Conclusion VEGF165 can accelerate the resolution of liver fibrosis by promoting fenestration structure formation in LSECs, as well as promoting material exchange between sinusoids and hepatocytes. Our findings may provide a new insight for the study of the role of VEGF in liver fibrosis.
Bioaccumulation and phytotoxicity of ZnO nanoparticles in soil-grown Brassica chinensis and potential risks
Authors: Shen Meimei , Liu Weitao , Zeb Aurang , Lian Jiapan , Hu Xiji , Wu Jiani 
Published: February 2021

Abstract
A pot-culture experiment was carried out to explore the phytotoxicity and accumulation of ZnO nanoparticles (ZnO NPs) in pakchoi (Brassica chinensis), as well as its potential risk. Zn was mainly accumulated in the shoots of pakchoi and showed the order of cell wall fraction > soluble fraction > organelles fraction. Endosomes were observed in roots cell by transmission electron microscope (TEM) and it is proving that endocytosis is a possible way for NPs to enter the cells. The results showed that higher concentration of ZnO NPs treatments resulted in an increase in the content of photosynthetic pigments and malondialdehyde (MDA), Catalase (CAT) and ascorbate peroxidase (APX) activity, while the activity of superoxide dismutase (SOD) and guaiacol peroxidase (G-POD) decreased significantly compared with the control. These changes suggest that the mechanism of ZnO NPs phytotoxicity may induce strongly oxidative stress and damage biomembrane. Generally, ZnO NPs had a similar impact on the growth and absorption of Zn in pakchoi with Zn2+. Simultaneously, the treatment of ZnO NPs affected the nutritional quality and food safety of pakchoi at high concentration.
Genetic Characteristics of Systematic Juvenile Idiopathic Arthritis and The Bioinformatics Basis for Treatment
Authors: Liu Wenping , Wen Dawei , Liu Ziyi , Wang Kunyu , Wang Jibo 
Published: February 2021

Abstract
Objective

Systemic Juvenile Idiopathic Arthritis (sJIA) is a distinctive subtype of Juvenile Idiopathic Arthritis (JIA). The pathogenesis of sJIA is still unclear with the treatment options limited. Although previous bioinformatics analyses have identified some genetic factors underlying sJIA, these studies were mostly single center with a small sample size and the results were often inconsistent. Herein, we combined two datasets of GSE20307 and GSE21521 and select the matrix of patients diagnosed as sJIA in it for further analysis.
Methods

The GSE20307 and GSE21521 matrixs downloaded from the Gene Expression Omnibus (GEO) were analyzed using online-tool GEO2R, Venny, Metascape, STRING, and Cytoscape to identify differentially expressed genes (DEGs), enrichment pathways, protein-protein interaction (PPI), main Module and hub genes between sJIA individuals and healthy controls.
Results

A total of 289 overlapping genes (consisting of 41 downregulated genes and 248 upregulated genes) were identified. Hub genes were primarily related to erythropoiesis. And the KEGG (Kyoto Encyclopedia of Genes and Genomes) analysis of overlapping DEGs were maily involved in Malaria and non-small cell lung cancer. Besides, DEGs in main module were involved in ubiquitin mediated proteolysis.
Conclusions

our study suggests that the erythropoiesis signature indeed exists in sJIA similar to previous reports. And combining previous research and our results, we provide a basis for the application of proteasome inhibitors, hydroxychloroquine and kinase inhibitors in patients with sJIA from the perspective of bioinformatics.
Designing a new multi epitope-based vaccine against COVID-19 disease: an immunoinformatic study based on reverse vaccinology approach
Authors: Nemati Afshin Samimi , Tafrihi Majid , Sheikhi Fatemeh , Tabari Abolfazl Rostamian , Haditabar Amirhossein 
Published: February 2021

Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has currently caused a significant pandemic among worldwide populations. The transmission speed and the high rate of mortality caused by the disease necessitate studies for the rapid designing and effective vaccine production. The purpose of this study is to predict and design a novel multi-epitope vaccine against the SARS-CoV-2 virus using bioinformatics approaches. Coronavirus envelope proteins, ORF7b, ORF8, ORF10, and NSP9 were selected as targets for epitope mapping using IEDB and BepiPred 2.0 Servers. Also, molecular docking studies were performed to determine the candidate vaccine's affinity to TLR3, TLR4, MHC I, and MHC II molecules. Thirteen epitopes were selected to construct the multi-epitope vaccine. We found that the constructed peptide has valuable antigenicity, stability, and appropriate half-life. The Ramachandran plot approved the quality of the predicted model after the refinement process. Molecular docking investigations revealed that antibody-mode in the Cluspro 2.0 server showed the lowest binding energy for MHCI, MHCII, TLR3, and TLR4. This study confirmed that the designed vaccine has a good antigenicity and stability and could be a proper vaccine candidate against the COVID-19 infectious disease though, in vitro and in vivo experiments are necessary to complete and confirm our results.
Surgical site infection after delayed sternal closure in neonates with congenital heart disease:Retrospective Case-control study.
Authors: Yang Yuzhong , Wang Jie , Cai Lina , Peng Wei , Mo Xuming 
Published: February 2021

Abstract
Objectives: To determine the incidence of surgical site infections (SSIs) in neonatal congenital heart disease patients undergoing delayed sternal closure (DSC) and evaluate risk factors for SSI.Methods: Hospital records of 483 consecutive neonates who underwent surgical intervention between January 2013 and December 2017 were reviewed, and perioperative variables were recorded. Results: We found that the risk of SSI was 87.5% when the body weight was less than 1500 g. When the operative age was between seven and 14 days, the probability of no SSI is about 93.9%. When the duration of the aortic cross-clamp was more than 60 min, the risk of SSI was 91.2%. The incidence rate without SSI was 96.6% when the duration of DSC was less than 24 hours. However, when the duration of DSC was more than 120 hours, the risk of SSI was 88.9% (p = 0.000). Conclusions: With the prolongation of aortic clamping duration, the probability of occurrence of SSI increased in neonatal CHD with DSC. The age at operation and body weight are closely related to the occurrence of SSI in neonatal CHD patients with DSC.
Medical Student Wellness in the United States During the COVID-19 Pandemic: a Nationwide Survey
Authors: Nikolis Louis , Wakim Andrea , Adams William , Bajaj Prempreet 
Published: February 2021

Abstract
Background: As United States (US) medical students suffer higher rates of depression and anxiety than the general population, medical student wellness has been studied in recent years. One definition describes wellness as having eight dimensions: Intellectual, emotional, physical, social, occupational, financial, environmental, and spiritual. As the coronavirus (COVID-19) pandemic poses unique challenges for medical students, we aimed to compare medical student wellness before and during the COVID-19 pandemic.Methods: An informal survey was created to assess the eight wellness dimensions and distributed via Survey Monkey to US allopathic and osteopathic medical students via email and social media. The survey was administered from March 29, 2020 to June 23, 2020. Univariable and multivariable linear mixed-effects models were used to estimate the change in students’ overall wellness using an 11-point scale ranging from 0 (least well) to 10 (most well). Generalized estimating equations were used to compare students’ responses to the eight dimensions before and during the COVID-19 pandemic.Results: On multivariable analysis, students reported a decline in their overall wellness during COVID-19 (Mdiff = -1.04; p < .001), with Asian respondents reporting almost no change in overall wellness (M = -0.69) compared to White respondents (M = -1.18; p = .049) and Black respondents (M = -1.78; p = .03). Students felt less supported and comfortable with their social (OR = 0.47) and daily (OR = 0.45) environments and expressed decreased satisfaction with their exercise (OR = 0.85), sense of purpose (OR = 0.33), and financial status (OR = 0.75). Students also expressed lower confidence (OR = 0.15) and satisfaction (OR = 0.11) with their medical education and increased anxiety (OR = 3.37) and depression (OR = 2.05).Conclusions: Medical students reported declines in overall wellness and individual wellness dimensions. These findings can be used to implement changes to improve medical student wellness.
Screening and Identification of Genes Affecting Grain Quality and Spikelet Fertility During High-Temperature Treatment in Grain Filling Stage of Rice
Authors: Park Jae-Ryoung , Kim Eun-Gyeong , Jang Yoon-Hee , Kim Kyung-Min 
Published: February 2021

Abstract
Background

Recent temperature increases due to rapid climate change have negatively affected rice yield and grain quality. Particularly, high temperatures during rice filling stage from the flowering stage reduce spikelet fertility, while interfering with sugar energy transport, and cause severe damage to grain quality by forming chalkiness grains. The effect of high-temperature on spikelet fertility and grain quality during grain filling stage was evaluated using a double haploid line derived from anther culture of F1 by crossing Cheongcheong and Nagdong cultivars. Quantitative trait locus (QTL) mapping identifies candidate genes significantly associated with spikelet fertility and grain quality at high temperatures.
Results

Our analysis screened OsSFq3 that contributes to spikelet fertility and grain quality at high-temperature. OsSFq3 was fine-mapped in the region RM15749-RM15689 on chromosome 3, wherein four candidate genes related to the synthesis and decomposition of amylose, a starch component, were predicted. Four major candidate genes, including OsSFq3, and 10 different genes involved in the synthesis and decomposition of amylose and amylopectin, which are starch constituents, together with relative expression levels were analyzed. OsSFq3 was highly expressed during the initial stage of high-temperature treatment. It exhibited high homology with FLOURY ENDOSPERM 6 in Gramineae plants and is therefore expected to function similarly.
Conclusion

The QTL, major candidate genes, and OsSFq3 identified herein could be effectively used in breeding rice varieties to improve grain quality, while tolerating high temperatures, to cope with climate changes. Furthermore, linked markers can aid in marker-assisted selection of high-quality and -yield rice varieties tolerant to high temperatures.
Geriatric Nutritional Risk Index Predicts Prognosis in Hepatocellular Carcinoma After Hepatectomy: A Propensity Score Matching Analysis
Authors: Kanno Hiroki , Goto Yuichi , Sasaki Shin , Fukutomi Shogo , Hisaka Toru , Fujita Fumihiko , Akagi Yoshito , Okuda Koji 
Published: February 2021

Abstract
The geriatric nutritional risk index (GNRI) is widely used for nutritional assessment in older inpatients and was recently reported to be associated with postoperative complications and cancer prognosis. We investigated the use of the GNRI to predict long-term outcomes in hepatocellular carcinoma of all etiologies after hepatectomy. 358 patients were reviewed after propensity score matching. We dichotomized the GNRI score into high GNRI (> 98: N = 179) and low GNRI (≤ 98: N = 179) and evaluated recurrence-free survival (RFS) and overall survival (OS) between the two groups. Clinicopathological characteristics between the low- and high-GNRI groups were similar after propensity score matching except for the components of the GNRI score (body mass index and serum albumin level), Child–Pugh score (consisting serum albumin level), and preoperative alpha-fetoprotein level (p < .0001, p < .0001, p = 0.0060, and p = 0.0049, respectively). A high GNRI was associated with significantly better RFS and OS (p = 0.0001 and p = 0.0055, respectively; log-rank test). Multivariate analysis revealed that GNRI is an independent prognostic factor of RFS and OS (low vs. high; HR, 1.8670; 95%CI, 1.4011–2.4880; p < .0001, HR, 1.7270; 95% CI, 1.1640–2.5623; p = 0.0066, respectively). The GNRI is an objective, inexpensive, and easily calculated assessment tool for nutritional status and can predict prognosis in hepatocellular carcinoma after hepatectomy.
Machine Learning Screening of Bile Acid-Binding Peptides in APeptide Database Derived From Food Proteins
Authors: Imai Kento , Shimizu Kazunori , Honda Hiroyuki 
Published: February 2021

Abstract
In the present study, a new bioactive peptide screening method was developed using BIOPEP-UWM and machine learning. Training data was initially obtained using high-throughput techniques, and positive and negative datasets were generated. The predictive model was generated by calculating the explanatory variables of the peptides. To understand both site-specific and global characteristics, amino acid features (for site-specific characteristics), and peptide features (for global characteristics) were generated. The constructed models were applied to the peptide database generated using BIOPEP-UWM, and bioactivity was predicted to explore candidate bile acid-binding peptides. Using this strategy, seven novel bile acid-binding peptides (VFWM, QRIFW, RVWVQ, LIRYTK, NGDEPL, PTFTRKL, and KISQRYQ) were identified. Our novel screening method could be easily applied to industrial applications using whole edible proteins. The proposed approach would be useful for identifying bile acid-binding peptides, as well as other bioactive peptides, as long as a large amount of training data can be obtained.