bluuebunny/crossref_metadata_2025_split huggingface dataset:
Whole-Genome Sequencing of 117 Chromosome Segment Substitution Lines for Genetic Analyses of Complex Traits in Rice
Authors: Fan Jiongjiong , Hua Hua , Luo Zhaowei , Zhang Qi , Chen Mengjiao , Gong Junyi , Wei Xin , Huang Zonghua , Huang Xuehui , Wang Qin 
Published: January 2022

AbstractRice is one of the most important food crops in Asia. Genetic analyses of complex traits and molecular breeding studies in rice greatly rely on the construction of various genetic populations. Chromosome segment substitution lines (CSSLs) serve as a powerful genetic population for quantitative trait locus (QTL) mapping in rice. Moreover, CSSLs containing target genomic regions can be used as improved varieties in rice breeding. In this study, we developed a set of CSSLs consisting of 117 lines derived from the recipient ‘Huanghuazhan’ (HHZ) and the donor ‘Basmati Surkb 89–15’ (BAS). The 117 lines were extensively genotyped by whole-genome resequencing, and a high-density genotype map was constructed for the CSSL population. The 117 CSSLs covered 99.78% of the BAS genome. Each line contained a single segment, and the average segment length was 6.02 Mb. Using the CSSL population, we investigated three agronomic traits in Shanghai and Hangzhou, China, and a total of 25 QTLs were detected in both environments. Among those QTLs, we found that RFT1 was the causal gene for heading date variance between HHZ and BAS. RFT1 from BAS was found to contain a loss-of-function allele based on yeast two-hybrid assay, and its causal variation was a P to S change in the 94th amino acid of the RFT1 protein. The combination of high-throughput genotyping and marker-assisted selection (MAS) is a highly efficient way to construct CSSLs in rice, and extensively genotyped CSSLs will be a powerful tool for the genetic mapping of agronomic traits and molecular breeding for target QTLs/genes.
Assembly and comparative analysis of the first complete mitochondrial genome of Acer truncatum Bunge: a woody oil-tree species producing nervonic acid
Authors: Ma Qiuyue , Wang Yuxiao , Li Shushun , Wen Jing , Zhu Lu , Yan Kunyuan , Du Yiming , Ren Jie , Li Shuxian , Chen Zhu , Bi Changwei , Li Qianzhong 
Published: January 2022

Abstract
Background
Acer truncatum (purpleblow maple) is a woody tree species that produces seeds with high levels of valuable fatty acids (especially nervonic acid). The species is admired as a landscape plant with high developmental prospects and scientific research value. The A. truncatum chloroplast genome has recently been reported; however, the mitochondrial genome (mitogenome) is still unexplored.

Results
We characterized the A. truncatum mitogenome, which was assembled using reads from PacBio and Illumina sequencing platforms, performed a comparative analysis against different species of Acer. The circular mitogenome of A. truncatum has a length of 791,052 bp, with a base composition of 27.11% A, 27.21% T, 22.79% G, and 22.89% C. The A. truncatum mitogenome contains 62 genes, including 35 protein-coding genes, 23 tRNA genes and 4 rRNA genes. We also examined codon usage, sequence repeats, RNA editing and selective pressure in the A. truncatum mitogenome. To determine the evolutionary and taxonomic status of A. truncatum, we conducted a phylogenetic analysis based on the mitogenomes of A. truncatum and 25 other taxa. In addition, the gene migration from chloroplast and nuclear genomes to the mitogenome were analyzed. Finally, we developed a novel NAD1 intron indel marker for distinguishing several Acer species.

Conclusions
In this study, we assembled and annotated the mitogenome of A. truncatum, a woody oil-tree species producing nervonic acid. The results of our analyses provide comprehensive information on the A. truncatum mitogenome, which would facilitate evolutionary research and molecular barcoding in Acer.
Developing indicators of age-friendly neighbourhood environments for urban and rural communities across 20 low-, middle-, and high-income countries
Authors: Rugel Emily J. , Chow Clara K. , Corsi Daniel J. , Hystad Perry , Rangarajan Sumathy , Yusuf Salim , Lear Scott A. 
Published: January 2022

Abstract
Background
By 2050, the global population of adults 60 + will reach 2.1 billion, surging fastest in low- and middle-income countries (LMIC). In response, the World Health Organization (WHO) has developed indicators of age-friendly urban environments, but these criteria have been challenging to apply in rural areas and LMIC. This study fills this gap by adapting the WHO indicators to such settings and assessing variation in their availability by community-level urbanness and country-level income.

Methods
We used data from the Prospective Urban and Rural Epidemiology (PURE) study’s environmental-assessment tools, which integrated systematic social observation and ecometrics to reliably capture community-level environmental features associated with cardiovascular-disease risk factors. The results of a scoping review guided selection of 18 individual indicators across six distinct domains, with data available for 496 communities in 20 countries, including 382 communities (77%) in LMIC. Finally, we used both factor analysis of mixed data (FAMD) and multitrait-multimethod (MTMM) approaches to describe relationships between indicators and domains, as well as detailing the extent to which these relationships held true within groups defined by urbanness and income.

Results
Together, the results of the FAMD and MTMM approaches indicated substantial variation in the relationship of individual indicators to each other and to broader domains, arguing against the development of an overall score and extending prior evidence demonstrating the need to adapt the WHO framework to the local context. Communities in high-income countries generally ranked higher across the set of indicators, but regular connections to neighbouring towns via bus (95%) and train access (76%) were most common in low-income countries. The greatest amount of variation by urbanness was seen in the number of streetscape-greenery elements (33 such elements in rural areas vs. 55 in urban), presence of traffic lights (18% vs. 67%), and home-internet availability (25% vs. 54%).

Conclusions
This study indicates the extent to which environmental supports for healthy ageing may be less readily available to older adults residing in rural areas and LMIC and augments calls to tailor WHO’s existing indicators to a broader range of communities in order to achieve a critical aspect of distributional equity in an ageing world.
A randomised controlled trial on roles of prostaglandin E1 nebulization among patients undergoing one lung ventilation
Authors: Li Pengyi , Gu Lianbing , Tan Jing , Song Zhenghuan , Bian Qingming , Jiao Dian , Xu Zeping , Wang Lijun 
Published: January 2022

Abstract
Background
Prostaglandin E1 (PGE1) has been reported to maintain adequate oxygenation among patients under 60% FiO2 one-lung ventilation (OLV). This research aimed to explore whether PGE1 is safe in pulmonary shunt and oxygenation under 40% FiO2 OLV and provide a reference concentration of PGE1.

Methods
Totally 90 esophageal cancer patients treated with thoracotomy were enrolled in this study, randomly divided into three groups (n = 30/group): Group A (60% FiO2 and 0.1 µg/kg PGE1), Group B (40% FiO2 and 0.1 µg/kg PGE1), and Group C (40% FiO2, 0.2 µg/kg PGE1). Primary outcomes were oxygenation and pulmonary shunt during OLV. Secondary outcomes included oxidative stress after OLV.

Results
During OLV, patients in Group C and B had lower levels of PaO2, SaO2, SpO2, MAP, and Qs/Qt than those in Group A (P < 0.05). At T2 (OLV 10 min), patients in Group C and B exhibited a lower level of PaO2/FiO2 than those in Group A, without any statistical difference at other time points. The IL-6 levels of patients in different groups were different at T8 (F = 3.431, P = 0.038), with IL-6 in Group C being lower than that in Group B and A. MDA levels among the three groups differed at T5 (F = 4.692, P = 0.012) and T7 (F = 5.906, P = 0.004), with the MDA level of Group C being lower than that of Group B and A at T5, and the MDA level of Group C and B being lower than that of Group A at T7. In terms of TNF-α level, patients in Group C had a lower level than those in Group B and A at T8 (F = 3.598, P = 0.033). Compared with patients who did not use PGE1, patients in Group C had comparable complications and lung infection scores.

Conclusion
The concentration of FiO2 could be reduced from 60 to 40% to maintain oxygenation. 40% FiO2 + 0.2 µg/kg PGE1 is recommended as a better combination on account of its effects on the inflammatory factors.
Trial registration: Chictr.org.cn identifier: ChiCTR1800018288, 09/09/2018.
Application of machine learning missing data imputation techniques in clinical decision making: taking the discharge assessment of patients with spontaneous supratentorial intracerebral hemorrhage as an example
Authors: Wang Huimin , Tang Jianxiang , Wu Mengyao , Wang Xiaoyu , Zhang Tao 
Published: January 2022

Abstract
Background
There are often many missing values in medical data, which directly affect the accuracy of clinical decision making. Discharge assessment is an important part of clinical decision making. Taking the discharge assessment of patients with spontaneous supratentorial intracerebral hemorrhage as an example, this study adopted the missing data processing evaluation criteria more suitable for clinical decision making, aiming at systematically exploring the performance and applicability of single machine learning algorithms and ensemble learning (EL) under different data missing scenarios, as well as whether they had more advantages than traditional methods, so as to provide basis and reference for the selection of suitable missing data processing method in practical clinical decision making.

Methods
The whole process consisted of four main steps: (1) Based on the original complete data set, missing data was generated by simulation under different missing scenarios (missing mechanisms, missing proportions and ratios of missing proportions of each group). (2) Machine learning and traditional methods (eight methods in total) were applied to impute missing values. (3) The performances of imputation techniques were evaluated and compared by estimating the sensitivity, AUC and Kappa values of prediction models. (4) Statistical tests were used to evaluate whether the observed performance differences were statistically significant.

Results
The performances of missing data processing methods were different to a certain extent in different missing scenarios. On the whole, machine learning had better imputation performance than traditional methods, especially in scenarios with high missing proportions. Compared with single machine learning algorithms, the performance of EL was more prominent, followed by neural networks. Meanwhile, EL was most suitable for missing imputation under MAR (the ratio of missing proportion 2:1) mechanism, and its average sensitivity, AUC and Kappa values reached 0.908, 0.924 and 0.596 respectively.

Conclusions
In clinical decision making, the characteristics of missing data should be actively explored before formulating missing data processing strategies. The outstanding imputation performance of machine learning methods, especially EL, shed light on the development of missing data processing technology, and provided methodological support for clinical decision making in presence of incomplete data.
Hospital management practices in county-level hospitals in rural China and international comparison
Authors: Hu Min , Chen Wen , Yip Winnie 
Published: January 2022

Abstract
Background
Although management is important in healthcare, low- and middle-income countries (LMICs) have little experience measuring the competence of hospital management. While improving hospital management is the main focus of hospital reform in China, few studies have empirically documented the baseline situation to inform policy design.

Methods
We assessed the management practices of county-level hospitals in Guizhou in southwest China during 2015. We used the Development World Management Survey (D-WMS) instrument to interview 273 managers in 139 hospitals. We scored the management practices of the sampled hospitals, overall and in four dimensions (operations, monitoring, targets, personnel management) and three processes (implementation, usage, monitoring). We then converted the scores to the WMS scale and compared these with data from two other LMICs and seven high-income countries (HICs).

Results
On a scale of 1 (‘worst practice’) to 5 (‘best practice’), the mean (SD) hospital D-WMS scores were 2.57 (0.46) overall; 2.71 (0.48), 2.64 (0.58), 2.40 (0.64), and 2.56 (0.40) for operation, monitoring, target, and personnel, respectively; and 2.43 (0.48), 2.62 (0.48), and 2.66 (0.47) for implementation, usage, and monitoring, respectively. After conversion to WMS scores, China ranked seventh of 10 countries, after six HICs and higher than one HIC and two other LMICs (Brazil and India). China ranked higher than the two LMICs in each of the four dimensional scores.

Conclusions
Chinese county-level hospitals should improve their low quality of management by prioritizing target-setting and process implementation, particularly in personnel management. Meanwhile, modern management training should be given to most clinical managers.
Relationship between housing insecurity, diabetes processes of care, and self-care behaviors
Authors: Mosley-Johnson Elise , Walker Rebekah J. , Thakkar Madhuli , Campbell Jennifer A. , Hawks Laura , Pyzyk Sarah , Egede Leonard E. 
Published: January 2022

Abstract
Background
The aim of this analysis was to examine the influence of housing insecurity on diabetes processes of care and self-care behaviors and determine if that relationship varied by employment status or race/ethnicity.

Methods
Using nationally representative data from the Behavioral Risk Factor Surveillance System (2014-2015), 16,091 individuals were analyzed for the cross-sectional study. Housing insecurity was defined as how often respondents reported being worried or stressed about having enough money to pay rent/mortgage. Following unadjusted logistic models testing interactions between housing insecurity and either employment or race/ethnicity on diabetes processes of care and self-care behaviors, stratified models were adjusted for demographics, socioeconomic status, health insurance status, and comorbidity count.

Results
38.1% of adults with diabetes reported housing insecurity. Those reporting housing insecurity who were employed were less likely to have a physicians visit (0.58, 95%CI 0.37,0.92), A1c check (0.45, 95%CI 0.26,0.78), and eye exam (0.61, 95%CI 0.44,0.83), while unemployed individuals were less likely to have a flu vaccine (0.84, 95%CI 0.70,0.99). Housing insecure White adults were less likely to receive an eye exam (0.67, 95%CI 0.54,0.83), flu vaccine (0.84, 95%CI 0.71,0.99) or engage in physical activity (0.82, 95%CI 0.69,0.96), while housing insecure Non-Hispanic Black adults were less likely to have a physicians visit (0.56, 95%CI 0.32,0.99).

Conclusions
Housing insecurity had an influence on diabetes processes of care and self-care behaviors, and this relationship varied by employment status and race/ethnicity. Diabetes interventions should incorporate discussion surrounding housing insecurity and consider differences in the impact by demographic factors on diabetes care.
Ultra-processed food and incident type 2 diabetes: studying the underlying consumption patterns to unravel the health effects of this heterogeneous food category in the prospective Lifelines cohort
Authors: Duan Ming-Jie , Vinke Petra C. , Navis Gerjan , Corpeleijn Eva , Dekker Louise H. 
Published: January 2022

Abstract
Background
The overall consumption of ultra-processed food (UPF) has previously been associated with type 2 diabetes. However, due to the substantial heterogeneity of this food category, in terms of their nutritional composition and product type, it remains unclear whether previous results apply to all underlying consumption patterns of UPF.

Methods
Of 70,421 participants (35–70 years, 58.6% women) from the Lifelines cohort study, dietary intake was assessed with a food frequency questionnaire. UPF was identified according to the NOVA classification. Principal component analysis (PCA) was performed to derive UPF consumption patterns. The associations of UPF and adherence to UPF consumption patterns with incidence of type 2 diabetes were studied with logistic regression analyses adjusted for age, sex, diet quality, energy intake, alcohol intake, physical activity, TV watching time, smoking status, and educational level.

Results
During a median follow-up of 41 months, a 10% increment in UPF consumption was associated with a 25% higher risk of developing type 2 diabetes (1128 cases; OR 1.25 [95% CI 1.16, 1.34]). PCA revealed four habitual UPF consumption patterns. A pattern high in cold savory snacks (OR 1.16 [95% CI 1.09, 1.22]) and a pattern high in warm savory snacks (OR 1.15 [95% CI 1.08, 1.21]) were associated with an increased risk of incident type 2 diabetes; a pattern high in traditional Dutch cuisine was not associated with type 2 diabetes incidence (OR 1.05 [95% CI 0.97, 1.14]), while a pattern high in sweet snacks and pastries was inversely associated with type 2 diabetes incidence (OR 0.82 [95% CI 0.76, 0.89]).

Conclusions
The heterogeneity of UPF as a general food category is reflected by the discrepancy in associations between four distinct UPF consumption patterns and incident type 2 diabetes. For better public health prevention, research is encouraged to further clarify how different UPF consumption patterns are related to type 2 diabetes.
Primary low-grade extrauterine endometrial stromal sarcoma: analysis of 10 cases with a review of the literature
Authors: Wu You , Li Nan , Zhang Rong , Bai Ping 
Published: January 2022

Abstract
Background
This study aimed to analyze the clinical and pathological features of extrauterine endometrial stromal sarcoma (EESS) and explore an effective therapeutic regimen to reduce the recurrence rate in low-grade EESS patients.

Methods
Ten LG-EESS patients who were treated at the Chinese Academy of Medical Sciences Cancer Institute and Hospital from June 1999 to June 2019 were collected and analyzed.

Results
(1) Patient demographics are summarized in manuscript. Preoperative CA125 examination showed that 8 patients had a median level of 49.5 U/L (15.4–168.0 U/L). (2) All ten patients underwent tumor cytoreductive surgery. Five patients underwent optimal tumor resection and achieved an R0 resection. After the initial surgery, 7 patients who had multiple metastasis were treated with adjuvant chemotherapy, 2 patients with vaginal ESS were treated with chemotherapy and radiation therapy, and 6 patients with ER/PR positive received hormone therapy with or without chemotherapy. (2) Most EESS patients had multiple tumors. The omentum was the most commonly affected site, followed by the ovaries. (3) The median follow-up was 94 (range: 27–228) months, and recurrence was observed in 3 patients (n = 10, 30%) who underwent non-optimal surgery and no hormone therapy. The 5-year and 10-year DFS rates were both 70%, as shown in Fig. 2. OS was both 100% at 5 and 10 years.

Conclusion
As a conclusion, EESS is a rare disease and LG-EESS has a good prognosis. Surgery remains the available treatment for patients. LG-EESS has a risk of late recurrence which requires a long-term follow-up. With a limited sample size, our study shows optimal tumor reductive surgery and adjuvant hormone therapy may significantly reduce the risk of recurrence.
Effect of lentivirus-mediated growth and differentiation factor-5 transfection on differentiation of rabbit nucleus pulposus mesenchymal stem cells
Authors: Zhu Kun , Zhao Rui , Ye Yuchen , Xu Gang , Zhang Changchun 
Published: January 2022

Abstract
Background
Intervertebral disc degeneration (IDD) is a natural progression of age-related processes. Associated with IDD, degenerative disc disease (DDD) is a pathologic condition implicated as a major cause of chronic lower back pain, which can have a severe impact on the quality of life of patients. As degeneration progression is associated with elevated levels of inflammatory cytokines, enhanced aggrecan and collagen degradation, and changes in the disc cell phenotype. The purpose of this study was to investigate the biological and cytological characteristics of rabbit nucleus pulposus mesenchymal stem cells (NPMSCs)—a key factor in IDD—and to determine the effect of the growth and differentiation factor-5 (GDF5) on the differentiation of rabbit NPMSCs transduced with a lentivirus vector.

Methods
An in vitro culture model of rabbit NPMSCs was established and NPMSCs were identified by flow cytometry (FCM) and quantitative real-time PCR (qRT-PCR). Subsequently, NPMSCs were randomly divided into three groups: a transfection group (the lentiviral vector carrying GDF5 gene used to transfect NPMSCs); a control virus group (the NPMSCs transfected with an ordinary lentiviral vector); and a normal group (the NPMSCs alone). FCM, qRT-PCR, and western blot (WB) were used to detect the changes in NPMSCs.

Results
The GDF5-transfected NPMSCs displayed an elongated shape, with decreased cell density, and significantly increased GDF5 positivity rate in the transfected group compared to the other two groups (P < 0.01). The mRNA levels of Krt8, Krt18, and Krt19 in the transfected group were significantly higher in comparison with the other two groups (P < 0.01), and the WB results were consistent with that of qRT-PCR.

Conclusions
GDF5 could induce the differentiation of NPMSCs. The lentiviral vector carrying the GDF5 gene could be integrated into the chromosome genome of NPMSCs and promoted differentiation of NPMSCs into nucleus pulposus cells. Our findings advance the development of feasible and effective therapies for IDD.
Intraosseous ganglion cyst mimicking chondrosarcoma on MRI: a case report
Authors: Seo Eun Hye , Yoon Yu Sung , Cha Jang Gyu , Kim Hee Kyung 
Published: January 2022

AbstractBackgroundThe intraosseous ganglia is a benign cyst, rarely locate in the olecranon process. As intraosseous ganglia can mimic malignant bone tumor, computed tomography (CT) is important for diagnosis even when magnetic resonance imaging (MRI) suggests malignant bone tumor, such as chondrosarcoma.Case presentationIn this paper, we report a 42-year-old woman with intraosseous ganglia in the olecranon process of the ulna. She complained pain in right elbow for 3 weeks. MRI revealed an intraosseous mass which initially diagnosed as chondrosarcoma. However, followed computed tomography (CT) demonstrated scattered intralesional gas and no underlying mineralization, and we can exclude chondrosarcoma from diagnosis.ConclusionsThe intraosseous ganglia can mimic bone tumor in MRI; therefore, CT is essential for accurate characterization of bone tumor. Even if MR imaging strongly suggests chondrosarcoma of the bone, CT should be performed as additional study.