bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparative physiology and transcriptome analysis reveals that chloroplast development influences silver-white leaf color formation in Hydrangea macrophylla var. maculata
Authors: Qi Xiangyu , Chen Shuangshuang , Wang Huadi , Feng Jing , Chen Huijie , Qin Ziyi , Deng Yanming 
Published: July 2022

Abstract
Background
Hydrangea macrophylla var. Maculata ‘Yinbianxiuqiu’ (YB) is an excellent plant species with beautiful flowers and leaves with silvery white edges. However, there are few reports on its leaf color characteristics and color formation mechanism.

Results
The present study compared the phenotypic, physiological and transcriptomic differences between YB and a full-green leaf mutant (YM) obtained from YB. The results showed that YB and YM had similar genetic backgrounds, but photosynthesis was reduced in YB. The contents of pigments were significantly decreased at the edges of YB leaves compared to YM leaves. The ultrastructure of chloroplasts in the YB leaves was irregular. Transcriptome profiling identified 7,023 differentially expressed genes between YB and YM. The expression levels of genes involved in photosynthesis, chloroplast development and division were different between YB and YM. Quantitative real-time PCR showed that the expression trends were generally consistent with the transcriptome data.

Conclusions
Taken together, the formation of the silvery white leaf color of H. macrophylla var. maculata was primarily due to the abnormal development of chloroplasts. This study facilitates the molecular function analysis of key genes involved in chloroplast development and provides new insights into the molecular mechanisms involved in leaf coloration in H. macrophylla.
Meta-QTL analysis explores the key genes, especially hormone related genes, involved in the regulation of grain water content and grain dehydration rate in maize
Authors: Wang Wei , Ren Zhaobin , Li Lu , Du Yiping , Zhou Yuyi , Zhang Mingcai , Li Zhaohu , Yi Fei , Duan Liusheng 
Published: July 2022

Abstract
Background
Low grain water content (GWC) at harvest of maize (Zea mays L.) is essential for mechanical harvesting, transportation and storage. Grain drying rate (GDR) is a key determinant of GWC. Many quantitative trait locus (QTLs) related to GDR and GWC have been reported, however, the confidence interval (CI) of these QTLs are too large and few QTLs has been fine-mapped or even been cloned. Meta-QTL (MQTL) analysis is an effective method to integrate QTLs information in independent populations, which helps to understand the genetic structure of quantitative traits.

Results
In this study, MQTL analysis was performed using 282 QTLs from 25 experiments related GDR and GWC. Totally, 11 and 34 MQTLs were found to be associated with GDR and GWC, respectively. The average CI of GDR and GWC MQTLs was 24.44 and 22.13 cM which reduced the 57 and 65% compared to the average QTL interval for initial GDR and GWC QTL, respectively. Finally, 1494 and 5011 candidate genes related to GDR and GWC were identified in MQTL intervals, respectively. Among these genes, there are 48 genes related to hormone metabolism.

Conclusions
Our studies combined traditional QTL analyses, genome-wide association study and RNA-seq to analysis major locus for regulating GWC in maize.
Biphasic positive airway pressure spontaneous breathing attenuates lung injury in an animal model of severe acute respiratory distress syndrome
Authors: Zhou Leilei , Yang Rui , Xue Chunju , Chen Zongyu , Jiang Wenqing , He Shuang , Zhang Xianming 
Published: July 2022

Abstract
Objective
To compare the effects of unassisted spontaneous breathing (SB) and complete muscle paralysis (PC) on early severe acute respiratory distress syndrome (ARDS) in an animal model, and to explore the possibility of biphasic positive airway pressure (BIPAP) as lung protective ventilation support for patients in the early stage of severe ARDS.

Methods
Twelve healthy beagle dogs between the ages of 10 and 15 months were randomly divided into two groups: the SB group (BIPAPSB) and the PC group (BIPAPPC). Arterial blood samples were drawn before modelling. Arterial blood gas analysis and mechanical tests were conducted. The animal model of severe ARDS was established using a deep intravenous injection of oleic acid, and BIPAP ventilation was performed for 8 hours. Lung tissue and blood were taken to detect lung function, inflammatory reactions and degree of pathological damage.

Results
At the beginning of the experiment, there was no significant difference in the arterial blood gas analysis between the two groups (p > 0.05). After successful modelling, the oxygenation index and the end-expiratory lung volume in the SB group were significantly higher than those in the PC group 8 hours after MV. Pathologically, the wet-dry ratio and pathological score of the PC group were higher than those of the SB group; the lung injury in the gravity-dependent area in the SB group was less than that in the PC group (p< 0.05).

Conclusions
In the early stage of severe ARDS induced by oleic acid, compared with PC, retention of the BIPAP mode of SB can reduce the risk of lung injury and improve respiratory function.
Excimer laser ablation combined with drug-coated balloon versus drug-coated balloon in the treatment of de novo atherosclerotic lesions in lower extremities (ELABORATE): study protocol for a real-world clinical trial
Authors: Jiang Xiaolang , Fan Longhua , Chen Bin , Jiang Junhao , Liu Jianjun , Qiao Guanyu , Ju Shuai , Shi Yun , Ma Tao , Lin Changpo , Fang Gang , Guo Daqiao , Xu Xin , Dong Zhihui , Fu Weiguo 
Published: July 2022

Abstract
Background
The efficacy and validity of excimer laser ablation (ELA) in the in-stent restenosis (ISR) has been confirmed. However, its application in de novo atherosclerotic lesions of lower extremity artery disease (LEAD) has not been clearly defined and its procedure has not been standardized.

Methods
ELABORATE is a prospective, multicenter, real-world study designed to evaluate the efficacy and safety between ELA combined with drug-coated balloon (DCB) and DCB alone in de novo atherosclerotic lesions of LEAD.

Discussion
ELABORATE is a prospective, multicenter, real-world study designed to assess the efficacy and safety between ELA combined with drug-coated balloon (DCB) and DCB alone in patients with de novo atherosclerotic lesions of LEAD. According to the real-world situation, eligible patients will be allocated to ELA + DCB group (group E) and DCB group (group C). Baseline and follow-up information (at 3, 6, and 12 months) will be collected. The primary efficacy point is primary patency at 12-months, and the secondary efficacy points include clinically driven target lesion reintervention (CD-TLR), change of Rutherford class, ankle-brachial index and ulcer healing rate. These indexes will be assessed and recorded at 3, 6, and 12-month follow-up. Also, safety evaluation, including major adverse event, all-cause mortality through 30-day follow-up, unplanned major amputation, bailout stent and distal embolization, will also be evaluated by an independent core laboratory. All the data will be collected and recorded by the electric data capture system. This study will be finished in 3 years and the 12-month results will be available in 2023. All the patients will be followed for 5 years.
Trial registration number Chinese Clinical Trial Registry (ChiCTR2100051263). Registered 17 September 2019. http://www.chictr.org.cn/listbycreater.aspx.
Epstein–Barr virus-associated gastric adenosquamous carcinoma with concurrent gastric carcinoma with lymphoid stroma: a case report and review of the literature
Authors: Cao Fang , Yan Yan , Niu Dongfeng , Huang Xiaozheng , Jia Ling , Diao Xinting , Li Zhongwu 
Published: July 2022

Abstract
Background
Adenosquamous carcinoma (ASC)with concurrent gastric carcinoma with lymphoid stroma (GCLS) are extremely rare tumors. There are only limited cases reported in the literature. Epstein–Barr virus (EBV) infection was found in the concomitant GCLS, but none in the ASC. Here, we report the first case of gastric cancer with EBV infection detected in both ASC and GCLS.

Case presentation
A 59-year-old man complained of intermittent upper abdominal pain. The gastric endoscopy revealed a type IIc tumor located in the gastric body near the fundus of the stomach. Histological examination of the gastric tumor showed the coexistence of ASC and GCLS. Both components were positive for EBV-encoded RNA (EBER) in situ hybridization. Neoplastic nests of the former were positive for p63, p40 and CK5/6. The glandular components showed positive acid mucus in the Alcian-blue periodic-acid-schiff (AB-PAS) staining. There was significant difference in the expression of epidermal growth factor receptor (EGFR) between adenocarcinoma and squamous carcinoma, but not in other proteins such as human epidermal growth factor receptor 2 (HER2), p53 and mismatch repair proteins. The role of EGFR signaling pathway needs to be further explored in the differentiation of squamous carcinoma in the gastric ASC. Finally, a diagnosis of early EBV associated gastric ASC with concurrent GCLS (pT1bN1) was made. The patient took a single-drug S1 periodically for half a year after the surgery and has been disease free during 8 months of medical follow-up.

Conclusions
This is the first case of EBV associated gastric ASC with concurrent GCLS, and pathologists and clinicians should recognize and pay attention to this type of tumor.
A dynamic predictive nomogram of long-term survival in primary gastric lymphoma: a retrospective study
Authors: Yang Jinru , Liu Tao , Zhu Ying , Zhang Fangyuan , Zhai Menglan , Zhang Dejun , Zhao Lei , Jin Min , Lin Zhenyu , Zhang Tao , Zhang Liling , Yu Dandan 
Published: July 2022

Abstract
Background
Primary gastric lymphoma (PGL) is the most common extranodal non-Hodgkin lymphoma (NHL). Due to the rarity of the disease, it is important to create a predictive model that provides treatment and prognosis for patients with PGL and physicians.

Methods
A total of 8898 and 127 patients diagnosed with PGL were obtained from the SEER database and from our Cancer Center as training and validation cohorts, respectively. Univariate and multivariate Cox proportional hazards models were used to investigate independent risk factors for the construction of predictive survival nomograms, and a web nomogram was developed for the dynamic prediction of survival of patients with PGL. The concordance index (C-index), calibration plot, and receiver operating characteristics (ROC) curve were used to evaluate and validate the nomogram models.

Results
There were 8898 PGL patients in the SEER cohort, most of whom were married men over the age of 60, 16.1% of the primary tumors were localized in the antrum and pylori of the stomach, which was similar to the composition of 127 patients in the Chinese cohort, making both groups comparable. The Nomogram of overall survival (OS) was compiled based on eight variables, including age at diagnosis, sex, race, marital status, histology, stage, radiotherapy and chemotherapy. Cancer-specific survival (CSS) nomogram was developed with eight variables, including age at diagnosis, sex, marital status, primary tumor site, histology, stage, radiotherapy and chemotherapy. The C-index of OS prediction nomogram was 0.948 (95% CI: 0.901–0.995) in the validation cohort, the calibration plots showed an optimal match and a high area below the ROC curve (AUC) was observed in both training and validation sets. Also, we established the first web-based PGL survival rate calculator (https://yangjinru.shinyapps.io/DynNomapp/).

Conclusion
The web dynamic nomogram provided an insightful and applicable tool for evaluating PGL prognosis in OS and CSS, and can effectively guide individual treatment and monitoring.
Association between dependency on community resources and social support among elderly people living in rural areas in China: a cross-sectional study
Authors: Aierken Ayizuhere , Ding XiWen , Pan YiYang , Chen Yuan , Li Ying 
Published: July 2022

AbstractBackgroundThe prevalence of dependency personality disorder (DPD) is high among elderly people living in rural areas. This study aims to explore the association between dependency on community resources and social support among elderly individuals living in rural areas.MethodsA cross-sectional study was conducted in 26 locations in China. A total of 1160 participants aged ≥ 60 years were selected using a complex multistage sampling design. All data were obtained using questionnaires via face-to-face interviews. DPD was measured using the Minnesota Multiphasic Personality Inventory-II in the standardized Chinese version. Self-efficacy was assessed using the Chinese version of the General Self-Efficacy Scale. Social support was measured using the Chinese version of the questionnaires of the Older American Resources and Services scale. Community services and resources comprised 44 items. The association between DPD and levels of social support and self-efficacy was evaluated using a logistic regression model. The association between social support and self-efficacy was assessed using analysis of covariance.ResultsUnivariate analysis results showed that elderly people living in rural areas had higher DPD scores and lower levels of self-efficacy compared with those living in urban areas (P < 0.001). Logistic regression analysis showed that DPD was positively associated with the received frequencies of community health service, contracted family doctor services, and regular lectures on health knowledge among the elderly people with odd ratios of 1.58 (P < 0.001), 2.03 (P = 0.013), and 2.67 (P = 0.005), respectively. Logistic regression analysis showed significant interaction between social support and self-efficacy effect on DPD was found in the additive model (P < 0.001).ConclusionDPD was associated mainly with the community resources among elderly people living in rural areas. Social support and self-efficacy were commonly associated with DPD through a synergistic effect. These results suggest that DPD among elderly people may be reduced through effective social support to directly and indirectly promote the elderly’s use of community resources and improve their self-efficacy.
Biomarker discovery for practice of precision medicine in hypopharyngeal cancer: a theranostic study on response prediction of the key therapeutic agents
Authors: Kawata-Shimamura Yumiko , Eguchi Hidetaka , Kawabata-Iwakawa Reika , Nakahira Mitsuhiko , Okazaki Yasushi , Yoda Tetsuya , Grénman Reidar , Sugasawa Masashi , Nishiyama Masahiko 
Published: July 2022

Abstract
Background
Hypopharyngeal cancer is a relatively rare malignancy with poor prognosis. Current chemotherapeutic algorithm is still far from personalized medicine, and the identification of the truly active therapeutic biomarkers and/or targets is eagerly awaited.

Methods
Venturing to focus on the conventional key chemotherapeutic drugs, we identified the most correlative genes (and/or proteins) with cellular sensitivity to docetaxel (TXT), cisplatin (CDDP) and 5-fluorouracil (5-FU) in the expression levels, through 3 steps approach: genome-wide screening, confirmation study on the quantified expression levels, and knock-down and transfection analyses of the candidates. The probable action pathways of selected genes were examined by Ingenuity Pathway Analysis using a large-scale database, The Cancer Genome Atlas.

Results
The first genome-wide screening study derived 16 highly correlative genes with cellular drug sensitivity in 15 cell lines (|R| > 0.8, P < 0.01 for CDDP and 5-FU; |R| > 0.5, P < 0.05 for TXT). Among 10 genes the observed correlations were confirmed in the quantified gene expression levels, and finally knock-down and transfection analyses provided 4 molecules as the most potent predictive markers-AGR2 (anterior gradient 2 homolog gene), and PDE4D (phosphodiesterase 4D, cAMP-specific gene) for TXT; NINJ2 (nerve Injury-induced protein 2); CDC25B (cell division cycle 25 homolog B gene) for 5-FU- in both gene and protein expression levels. Overexpression of AGR2, PDE4D signified worse response to TXT, and the repressed expression sensitized TXT activity. Contrary to the findings, in the other 2 molecules, NINJ2 and CDC25, there observed opposite relationship to cellular drug response to the relevant drugs. IPA raised the potential that each selected molecule functionally interacts with main action pathway (and/or targets) of the relevant drug such as tubulin β chain genes for TXT, DNA replication pathway for CDDP, and DNA synthesis pathway and thymidylate synthetase gene for 5-FU.

Conclusion
We newly propose 4 molecules -AGR2, PDE4D,NINJ2 and CDC25B) as the powerful exploratory markers for prediction of cellular response to 3 key chemotherapeutic drugs in hypopharyngeal cancers and also suggest their potentials to be the therapeutic targets, which could contribute to the development of precision medicine of the essential chemotherapy in hypopharyngeal patients. (339 words).
Transcriptome profiling and co-expression network analysis of lncRNAs and mRNAs in colorectal cancer by RNA sequencing
Authors: Li Mingjie , Guo Dandan , Chen Xijun , Lu Xinxin , Huang Xiaoli , Wu Yan’an 
Published: July 2022

Abstract
Background
Long non-coding RNAs (lncRNAs) are widely involved in the pathogenesis of cancers. However, biological roles of lncRNAs in occurrence and progression of colorectal cancer (CRC) remain unclear. The current study aimed to evaluate the expression pattern of lncRNAs and messenger RNAs (mRNAs).

Methods
RNA sequencing (RNA-Seq) in CRC tissues and adjacent normal tissues from 6 CRC patients was performed and functional lncRNA-mRNA co-expression network was constructed afterwards. Gene enrichment analysis was demonstrated using DAVID 6.8 tool. Reverse transcription quantitative polymerase chain reaction (RT-qPCR) was used to validate the expression pattern of differentially expressed lncRNAs. Pearson correlation analysis was applied to evaluate the relationships between selected lncRNAs and mRNAs.

Results
One thousand seven hundred and sixteenth differentially expressed mRNAs and 311 differentially expressed lncRNAs were screened out. Among these, 568 mRNAs were up-regulated while 1148 mRNAs down-regulated, similarly 125 lncRNAs were up-regulated and 186 lncRNAs down-regulated. In addition, 1448 lncRNA–mRNA co-expression pairs were screened out from 940,905 candidate lncRNA-mRNA pairs. Gene enrichment analysis revealed that these lncRNA-related mRNAs are associated with cell adhesion, collagen adhesion, cell differentiation, and mainly enriched in ECM-receptor interaction and PI3K-Akt signaling pathways. Finally, RT-qPCR results verified the expression pattern of lncRNAs, as well as the relationships between lncRNAs and mRNAs in 60 pairs of CRC tissues.

Conclusions
In conclusion, these results of the RNA-seq and bioinformatic analysis strongly suggested that the dysregulation of lncRNA is involved in the complicated process of CRC development, and providing important insight regarding the lncRNAs involved in CRC.
Ruthenium-106 plaque radiotherapy for uveal melanoma: analysis of tumor dimension and location on anatomical and functional results
Authors: Mirshahi Reza , Sedaghat Ahad , Jaberi Ramin , Azma Zohreh , Mazloumi Mehdi , Naseripour Masood 
Published: July 2022

Abstract
Background
To report the long-term outcomes of Ru-106 plaque radiotherapy in eyes with uveal melanoma (UM) and to assess the effect of tumor thickness and location on final outcomes.

Methods
Medical records of 234 patients undergoing Ru-106 plaque radiotherapy for UM were reviewed, and the visual outcome, globe preservation, and patient survival were evaluated. The results of 2 groups were compared: 1. between thin (small and medium-sized, thickness < 7 mm, 148 eyes [63.2%]) and thick (thickness ≥ 7 mm, 86 eyes [36.8%]) tumors, and 2. between large (largest basal diameter [LBD] > 12 mm, 109 eyes [46.6%]) and medium/small (LBD ≤ 12 mm, 125 eyes [53.4%]). In addition, a comparison of the juxtapapillary location in 46 eyes (19.7%) versus tumors arising elsewhere and between tumors with and without ciliary involvement in 48 eyes (21.5%) were done.

Results
The patients were followed for a median of 54.2 months (range: 6–194.5 months). After adjusting for baseline visual acuity (VA), there was no significant association between final VA and different dimension and tumor location groups. Final globe preservation was 91.9%, and there was no significant difference between different dimension- and ciliary body involvement groups regarding anatomical success rate. The juxtapapillary tumors had lower globe preservation (80.4% vs .94.7%, p = 0.002). The hazard ratio (HR) for enucleation in juxtapapillary tumors was HR = 6.58 (95-CI: 3.84 to 11.21). The overall metastasis rate was 6.8%, with no significant difference in juxtapapillary tumors (4.3% vs.7.4%, p = 0.455).

Conclusions
Ru-106 plaque radiotherapy is an effective treatment for thick and large UM. With this type of treatment, the globe preservation rate is lower in juxtapapillary tumors, but there is no significant difference in the metastasis rate.
A prediction model for sulcus-to-sulcus diameter in myopic eyes: a 1466-sample retrospective study
Authors: Zhu Qiu-Jian , Zhu Wei-Jian , Chen Wen-Jing , Ma Lie , Yuan You 
Published: July 2022

Abstract
Background
To establish and verify the accuracy and reliability of a sulcus-to-sulcus diameter (STS) prediction model.

Methods
In this retrospective study, the prediction formula was established with the data from 1466 eyes from 733 subjects from July 2020 to April 2021 and verified with the data from 278 eyes from 139 subjects between May 2021 and June 2021. Each subject was measured with a Pentacam, IOLMaster 700, OPD-Scan III, and ultrasound biomicroscope. The prediction formulas were established with multiple linear regression, and intergroup correlation coefficients (ICCs) and Bland–Altman tests were used to assess the agreement between the predicted and actual STS (actual STS was measured by UBM).

Results
The explanatory variables relevant to the horizontal STS (STSH) were the Pentacam white-to-white diameter (WTWP; standardized partial regression coefficient [β] = 0.330; p < 0.001), the flat K value (β = -0.211; p < 0.001), and the anterior corneal diameter (ACD) (β = 0.178; p < 0.001). The corresponding multiple regression equation was : STSH (mm) = 8.061 + 0.510 × WTWP − 0.090 × Flat K value + 0.430 × ACD. The explanatory variables relevant to the vertical STS (STSV) were the WTWP (β = 0.435; p < 0.001), the steep K value (β = -0.271; p < 0.001), and the ACD (β = 0.187; p < 0.001). The corresponding multiple regression equation was : STSV (mm) = 8.540 + 0.492 × WTWP − 0.075 × Steep K value + 0.329 × ACD. The bias of the predicted to the actual STSH was − 0.021, with 95% limits of agreement (95% LoA) from − 0.499 to 0.457. The bias of the predicted to the actual STSV was 0.057, with 95% LoA from − 0.462 to 0.575. The ICC was 0.883 between the predicted and actual STSH and 0.859 between the predicted and actual STSV.

Conclusions
The Pentacam-measured WTW, the K value and the ACD are important for predicting the STS diameter. The prediction model has good accuracy and reliability.

Trial registration
Not applicable.