bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phenotypic and genetic characterization of a near-isogenic line pair: insights into flowering time in chickpea
Authors: Perez-Rial Adrian , Carmona Alejandro , Ali Latifah , Rubio Josefa , Millan Teresa , Castro Patricia , Die Jose V. 
Published: July 2024

Abstract
Background
Cicer arietinum is a significant legume crop cultivated mainly in short-season environments, where early-flowering is a desirable trait to overcome terminal constraints. Despite its agricultural significance, the genetic control of flowering time in chickpea is not fully understood. In this study, we developed, phenotyped, re-sequenced and genetically characterized a pair of near-isogenic lines (NILs) with contrasting days to flowering to identify candidate gene variants potentially associated with flowering time.

Results
In addition to days to flowering, noticeable differences in multiple shoot architecture traits were observed between the NILs. The resequencing data confirms that the NILs developed in this study serve as appropriate plant materials, effectively constraining genetic variation to specific regions and thereby establishing a valuable resource for future genetic and functional investigations in chickpea research. Leveraging bioinformatics tools and public genomic datasets, we identified homologs of flowering-related genes from Arabidopsis thaliana, including ELF3 and, for the first time in chickpea, MED16 and STO/BBX24, with variants among the NILs. Analysis of the allelic distribution of these genes revealed their preservation within chickpea diversity and their potential association with flowering time. Variants were also identified in members of the ERF and ARF gene families. Furthermore, in silico expression analysis was conducted elucidating their putative roles in flowering.

Conclusions
While the gene CaELF3a is identified as a prominent candidate, this study also exposes new targets in chickpea, such as CaMED16b and LOC101499101 (BBX24-like), homologs of flowering-related genes in Arabidopsis, as well as ERF12 and ARF2. The in silico expression characterization and genetic variability analysis performed could contribute to their use as specific markers for chickpea breeding programs. This study lays the groundwork for future investigations utilizing this plant material, promising further insights into the complex mechanisms governing flowering time in chickpea.
Fulvic acid application increases rice seedlings performance under low phosphorus stress
Authors: Lv Xiaomeng , Li Qingchao , Deng Xuan , Ding Shitao , Sun Ruibo , Chen Shunquan , Yun Wenjing , Dai Changrong , Luo Bingbing 
Published: July 2024

Abstract
Background
Fulvic acid enhances plant growth and interacts synergistically with phosphate fertilizer to alleviate the agricultural production problem of low phosphorus fertilizer utilization efficiency. However, the underlying mechanism of its action remains poorly understood. In this study, we investigated the impact of fulvic acid application with varying concentrations (0, 40, 60, 80 and 120 mg/L) on rice performance in plants grown in a hydroponic system subjected to low phosphorus stress. The rice growth phenotypes, biomass, root morphology, phosphorus uptake, and the impact of fulvic acid on the rhizosphere environment of rice, were assessed.

Results
The findings showed that adding appropriate concentrations of exogenous fulvic acid could promote the growth performance of rice under low phosphorus stress. Particularly at T1 (40 mg/L) and T2 (60 mg/L) over the control effectively increased rice biomass by 25.42% and 24.56%, respectively. Fulvic acid treatments stimulated root morphogenesis, up-regulated phosphate transporter genes, and facilitated phosphorus absorption and accumulation. Especially T1 (20.52%), T2 (18.10%) and T3 (20.48%) treatments significantly increased phosphorus uptake in rice, thereby alleviating low phosphorus stress. Additionally, fulvic acid elevated organic acids concentration in roots and up-regulated plasma membrane H+-ATPase genes, promoting organic acids secretion. This metabolic alteration can also alleviate low phosphorus stress in rice.

Conclusions
The effect of exogenous fulvic acid on physiological indicators is concentration-dependent under low phosphorus stress, enhances rice performance and reduces reliance on phosphorus fertilizer. This provides new insights to shed light on the mechanism of alleviating low phosphorus stress in rice through fulvic acid application, an eco-friendly tool.
A retrospective cross-sectional study: comparison of the clinicopathological features of schistosomal and non-schistosomal colorectal cancer in Central China
Authors: Zhu Yuanting , Wu Xiaoxue , Ran Xiaoshan , Rao Chun , Gong Ping 
Published: July 2024

Abstract
Aim
To analyze the clinicopathological features of schistosomal and non-schistosomal colorectal cancer in Central China and compare them with other areas of the Yangtze River Basin.

Method
The 501 cases of colorectal cancer (CRC) were retrospectively analyzed from 2020 to 2022. They were divided into two groups: 406 cases of colorectal cancer without schistosomiasis (CRC-NS) and 95 cases of colorectal cancer with schistosomiasis (CRC-S).The clinicopathological characteristics included the distribution of schistosomiasis eggs, patient age, sex, tumor differentiation, lymph node metastasis, and clinical stage. By retrieving the database, this study compared the clinicopathological differences of colorectal cancer with schistosomiasis in other areas of the Yangtze River basin.

Results
The cases of colorectal cancer with schistosomiasis accounted for 18.9%(95/501) in the study. The patients of CRC-S were older than the patients of CRC-NS (P = 0.002, P < 0.05). There was a statistical difference in the location of occurrence (P = 0.000, P < 0.05) between the two groups. There were no significant differences between CRC-S and CRC-NS in other clinicopathological features, such as sex (P = 0.054), Type(P = 0.242), histological type(P = 0.654), infiltrative depth(P = 0.811), differentiation(P = 0.837), lymph node metastasis(P = 0.574), intravascular tumor thrombus(P = 0.698), T stage(P = 0.354). In other areas of the Yangtze River Basin, there were statistical differences in the age of occurrence and T stage (P < 0.05) between colorectal cancer with schistosomiasis and non-schistosomal colorectal cancer.

Conclusion
In Central China, colorectal cancer with chronic schistosomiasis infection occurs more in the rectum and sigmoid colon. It is more common in individuals over 60 years old, consistent with the findings in the Yangtze River Basin. Additionally, schistosomal colorectal cancer had a higher T stage in the Yangtze River Basin. This may be related to the malignant biological behavior of colorectal cancer and could result in a relatively poor prognosis. Therefore, the elderly population in schistosomiasis endemic areas should pay more attention to early screening and tumor prevention.
Is chronic kidney disease associated with osteoarthritis? The United States national health and nutrition examination survey 2011–2020
Authors: Gao Kuiliang , Zhang Chao , Zhang Yifan , Zhang Longyao , Xu Jiankang , Xue Hongfei , Jiang Lingling , Zhang Jinwei 
Published: July 2024

Abstract
Objective
Chronic kidney disease (CKD) and osteoarthritis (OA) represent two frequently seen disorders among the general population, and they share several similar risk factors. The present work focused on assessing the relation of CKD with OA.

Methods
This cohort study included 26,280 eligible participants aged ≥ 20 years who had valid data on CKD and OA from the National Health and Nutrition Examination Survey (NHANES) 2011–2020. The association between CKD and OA was studied by logistic regression, adjusting for demographics, body mass index (BMI), socioeconomic factors, physical activity, ever smoking, alcohol using, diabetes status and hypertension status.

Results
Among the participants of this study, 26.69% of OA patients had concurrent CKD, whereas this proportion was only 13.83% among non-OA patients.CKD was related to OA[OR:2.269 (95%CI:2.266–2.271), p < 0.01] and the relation was of significance [OR:1.031 (95%CI:1.030–1.033),p < 0.01] following adjustments. In subgroup analyses based on age, the relation between osteoarthritis and chronic kidney disease remained significant, and in the subgroup analyses based on gender the previously mentioned relation between OA and CKD showed opposite directions in men [OR:0.869(95%CI0.867-0.871), p < 0.01] and women [OR:1.178(95%CI1.177-1.180), p < 0.01].

Conclusions
In the present 10-year large-scale national-wide survey, OA is closely related to CKD, and women with OA showed a higher risk of developing CKD compared to men. This study suggests that the relationship between OA and CKD deserves further investigation, and we suggest that patients with OA need to pay extra attention to their own kidney health.
Ubiquitin-specific proteases (USPs) in leukemia: a systematic review
Authors: Zangooie Alireza , Tavoosi Shima , Arabhosseini Mahan , Halimi Aram , Zangooie Helia , Baghsheikhi Amir Hossein , Rahgozar Soheila , Ahmadvand Mohammad , Jarrahi Alireza Mosavi , Salehi Zahra 
Published: July 2024

Abstract
Background
Leukemia, a type of blood cell cancer, is categorized by the type of white blood cells affected (lymphocytes or myeloid cells) and disease progression (acute or chronic). In 2020, it ranked 15th among the most diagnosed cancers and 11th in cancer-related deaths globally, with 474,519 new cases and 311,594 deaths (GLOBOCAN2020). Research into leukemia’s development mechanisms may lead to new treatments. Ubiquitin-specific proteases (USPs), a family of deubiquitinating enzymes, play critical roles in various biological processes, with both tumor-suppressive and oncogenic functions, though a comprehensive understanding is still needed.

Aim
This systematic review aimed to provide a comprehensive review of how Ubiquitin-specific proteases are involved in pathogenesis of different types of leukemia.

Methods
We systematically searched the MEDLINE (via PubMed), Scopus, and Web of Science databases according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines (PRISMA) to identify relevant studies focusing on the role of USPs in leukemia. Data from selected articles were extracted, synthesized, and organized to present a coherent overview of the subject matter.

Results
The review highlights the crucial roles of USPs in chromosomal aberrations, cell proliferation, differentiation, apoptosis, cell cycle regulation, DNA repair, and drug resistance. USP activity significantly impacts leukemia progression, inhibition, and chemotherapy sensitivity, suggesting personalized diagnostic and therapeutic approaches. Ubiquitin-specific proteases also regulate gene expression, protein stability, complex formation, histone deubiquitination, and protein repositioning in specific leukemia cell types.

Conclusion
The diagnostic, prognostic, and therapeutic implications associated with ubiquitin-specific proteases (USPs) hold significant promise and the potential to transform leukemia management, ultimately improving patient outcomes.
Robot-assisted resection of choledochal cyst in neonates
Authors: Chen Sai , Gao Zhigang , Chen Qingjiang , Qian Yunzhong 
Published: July 2024

Abstract
Objective
Laparoscopic choledochectomy and hepatojejunostomy have been reported in children since 1995, but this procedure is technically demanding. Robotic surgical systems can simplify complex minimally invasive procedures. Currently, few reports have been made on neonates. We present the experience of 6 cases of neonatal CC(choledochal cysts).

Study design
Between January 2022 and December 2023, 6 neonates underwent robotic resection of choledochal cyst and hepaticojejunostomy using the Da Vinci surgical system at Children’s Hospital, Zhejiang University School of Medicine, a high-volume hepatobiliary disease center. demographic data of the patients and surgical outcomes were collected and analyzed.

Results
All 6 patients were successfully treated by robotic cystectomy and hepaticojejunostomy. The mean age was 17.3 days (range 4–25) and the mean weight was 3.6 kg (range 2.55–4.4). 5 cysts were type Ia and 1 was type Iva. The mean diameter of the cysts was 3.8 cm (range 1.25-5). The mean time to establish feeding was 4.83 days (range 4–6), and patients were discharged after a median time of 16.83 days (range 7–42) without postoperative complications.

Conclusions
This procedure is safe and effective for neonates. The authors found that the use of robot-assisted surgery has ergonomic advantages in this delicate, minimally invasive procedure.
Learning curve analysis of transvaginal natural orifice transluminal endoscopic surgery in treating ovarian cysts: a retrospective cohort study
Authors: Feng Dan , Liu Tianjiao , Li Xin , Huang Lu , Xiao Li , He Li , Lin Yonghong 
Published: July 2024

Abstract
Background
Transvaginal Natural Orifice Transluminal Endoscopy (vNOTES) is regarded as a challenging surgical technique to learn but is promising in reducing perioperative pain and significantly improves the cosmetic outcomes. Previous studies on the learning curve analysis of vNOTES mainly focuses on the hysterectomy approach, while the vNOTES ovarian cystectomy’s learning curve was merely reported though more frequently performed than vNOTES hysterectomy. Therefore, this study seeks to analyze the learning curve of three surgeons with varying levels of experience in performing endoscopic surgery and vaginal surgeries for the treatment of ovarian cysts using vNOTES.

Methods
A total of 127 patients with ovarian cysts of a variety of pathological types were treated by ovarian vNOTES performed by three surgeons of different levels of endoscopic and transvaginal surgical experience. Each surgeon’s learning curve was plotted using the Cumulative Sum method and divided into three or four phases of technique learning at the turning point of the learning curve. The sociodemographic and clinical features of patients in each phase were then compared and factors potentially associated with operation time were also screened.

Results
The learning curve was presented in four phases. The operation time (OT) was significantly shorter in phases II (53.66 ± 16.55 min) and IV (54.39 ± 23.45 min) as compared with phases I (68.74 ± 15.85) and III (75.93 ± 30.55) (p < 0.001). More cases of serve pelvic adhesion and endometrioma were assigned in the later phases. The OT of endometriotic cysts had much longer than that of non-endometriotic cysts(62.57 ± 18.64 min vs. 49.88 ± 14.26 min, p = 0.15) The presence of pelvic adhesion [adjusted odds ratio (OR) 7.149 (0.506, 13.792), p = 0.035] and bilateral cyst [adjusted OR 16.996 (2.155, 31.837), p = 0.025], max diameter of cyst[adjusted OR 2.799 (0.174, 5.425), p = 0.037], and individual surgeon [adjusted OR -6.118 (-11.814, -0.423), p = 0.035] were significantly associated with OT.

Conclusion
There learning curve of ovarian vNOTES has four phases. ovarian vNOTES could be mastered after performing seven, nine, and 16 cases by surgeons #1, 2 and 3 respectively, in gynecologic endoscopic surgeries.

Trial registration
ChiCTR2200059282 (Registered on April 28th, 2022).
Distribution of EGFR fusions in 35,023 Chinese patients with solid tumors-the frequency, fusion partners and clinical outcome
Authors: Zhang Haiping , Wang Julei , Li Xiaoxiao , Zhang Dongfeng , Qi Yingxue , Zhang Qin , Luo Ningning , Wang Xiaoou , Wang Tuo 
Published: July 2024

Abstract
Background
Epidermal growth factor receptor (EGFR) fusions are rare but potentially actionable oncogenic drivers across multiple solid tumors. However, the distribution and molecular characteristics of EGFR fusions in Chinese patients with solid malignancies have not been explored.

Methods
Panel-based next-generation sequencing (NGS) data of 35,023 patients with various types of solid tumors was collected and analyzed from the Simcere Diagnostics (Nanjing, China) database. A 9563-patient cohort was derived from The Cancer Genome Atlas (TCGA) to explore the relationship between EGFR fusion status and overall survival (OS).

Results
In this study, prevalence of functional EGFR fusions was 0.303% (106/35,023) in total across solid tumors, which occur more commonly in gastroesophageal junction cancer (1/61, 1.613%), followed by medulloblastoma (1/66, 1.515%) and glioma (33/2409, 1.370%). Analysis showed a prevalence for fusion partners in different tumor types. The top 3 co-mutant genes with EGFR fusion were TP53 (mutation frequency, MF: 65%), BRCA2 (MF: 43%), and ALK (MF: 41%). Furthermore, patients in the EGFR fusion group had a significantly shorter OS than those in the non-EGFR fusion group (p < 0.0001) in the TCGA cohort, suggesting that EGFR fusion might be a high-risk factor for poor prognosis.

Conclusions
Our study is the first retrospective analysis of EGFR fusions in a large-scale solid tumor population, which may provide a reference for future EGFR-TKI clinical trials with EGFR fusions.
Elevated neutrophil extracellular traps in systemic sclerosis-associated vasculopathy and suppression by a synthetic prostacyclin analog
Authors: Kortam Neda , Liang Wenying , Shiple Claire , Huang Suiyuan , Gedert Rosemary , Clair James St. , Sarosh Cyrus , Foster Caroline , Tsou Pei-Suen , Varga John , Knight Jason S. , Khanna Dinesh , Ali Ramadan A. 
Published: July 2024

Abstract
Objectives
Neutrophils and neutrophil extracellular traps (NETs) contribute to the vascular complications of multiple diseases, but their role in systemic sclerosis (SSc) is understudied. We sought to test the hypothesis that NETs are implicated in SSc vasculopathy and that treatment with prostacyclin analogs may ameliorate SSc vasculopathy not only through vasodilation but also by inhibiting NET release.

Methods
Blood from 125 patients with SSc (87 diffuse cutaneous SSc and 38 limited cutaneous SSc) was collected at a single academic medical center. Vascular complications such as digital ulcers, pulmonary artery hypertension, and scleroderma renal crisis were recorded. The association between circulating NETs and vascular complications was determined using in vitro and ex vivo assays. The impact of the synthetic prostacyclin analog epoprostenol on NET release was determined.

Results
Neutrophil activation and NET release were elevated in patients with SSc-associated vascular complications compared to matched patients without vascular complications. Neutrophil activation and NETs positively correlated with soluble E-selectin and VCAM-1, circulating markers of vascular injury. Treatment of patients with digital ischemia with a synthetic prostacyclin analog boosted neutrophil cyclic AMP, which was associated with the blunting of NET release and reduced NETs in circulation.

Conclusion
Our study demonstrates an association between NETs and vascular complications in SSc. We also identified the potential for an additional therapeutic benefit of synthetic prostacyclin analogs, namely to reduce neutrophil hyperactivity and NET release in SSc patients.
Reinforced protection of fragile bronze cultural relics based on nano-cuprammonium fiber material
Authors: Tan Jinlong , Chen Jiachang , Cui Xinzhan 
Published: July 2024

Abstract
Bronze artifacts often suffer from “bronze disease” due to the presence of chloride ions, which result from copper chlorides forming on their surfaces during storage. Therefore, reinforced protection is essential for these unearthed cultural artifacts, and new materials for the reinforced protection of fragile bronzes are urgently needed. In this study, cuprammonium solvent and nanocellulose (CNC) were utilized as reinforcement materials to protect fragile bronzes. The chemical and aesthetic properties before and after reinforcement were analyzed using ultra-depth field microscopes, SEM-EDX, XRD, and Raman spectroscopy. The results indicated that at a nano-cuprammonium reinforcer concentration of 2.5 mol/L, the optimal reinforcement effect on simulated bronze powdery rust samples was achieved.Mechanical strength increased by an average of 77.59%. The mass growth rate reached 84.8%, while the color difference

$$\Delta E$$

Δ
E

remained below 4.0. Additionally, aging resistance significantly improved, aligning with cultural artifact protection standards.Meanwhile, a compact and stable protective membrane formed on the surface of the bronzes, isolating the bronze matrix from direct contact with the external environment, which delayed bronze corrosion and contributed to long-term stable preservation.

Graphical Abstract
A fluorite bead from Bronze Age Tianshanbeilu cemetery, Xinjiang, Northwest China
Authors: Reheman Kuerban , Yan Meiting , Qin Chunlei , Li Xiaoguang , Simayi Mulati , Tang Zihua 
Published: July 2024

Abstract
The Tianshanbeilu cemetery is the largest Bronze Age cemetery in eastern Xinjiang, China, and plays important roles in connecting the Eurasian interior to the Hexi Corridor, and further to the Central Plains region. Utilizing micro-XRF and Raman spectroscopy techniques, we identified a fluorite bead at this cemetery. This barrel bead is the earliest record of such a fluorite bead in China, dating back to approximately 1385–1256 BCE. Comparing the unearthed records of fluorite beads in eastern China spanning from the Neolithic Age to the Western Zhou dynasty, we notice that in the early Western Zhou period, fluorite beads found in élite burials are only in barrel or biconical shapes, both of which first appeared in the eastern region of Xinjiang, such as the Tianshanbeilu cemetery in Hami and the Yanghai cemetery in the Turpan Basin. We proposed that the barrel fluorite bead drilled by metal tubular drill first appearing in the Tianshanbeilu cemetery might have spread eastward to the Central Plains region and finally constituted a component of the ritual revolutions during the Western Zhou dynasty.
Using deep learning for enrichment of heritage BIM: Al Radwan house in historic Jeddah as a case study
Authors: Miky Yehia , Alshawabkeh Yahya , Baik Ahmad 
Published: July 2024

Abstract
Building information modeling (BIM) can greatly improve the management and planning of historic building conservation projects. However, implementing BIM in the heritage has many challenges, including issues with modeling irregular features, surveying data occlusions, and a lack of predefined libraries of parametric objects. Indeed, surface features can be manually distinguished and segmented depending on the level of human involvement during data scanning and BIM processing. This requires a significant amount of time and resources, as well as the risk of making too subjective decisions. To address these bottlenecks and improve BIM digitization of building geometry, a novel deep learning based scan-to-HBIM workflow is used during the recording of the historic building in historic Jeddah, Saudi Arabia, a UNESCO World Heritage site. The proposed workflow enables access to laser scanner and unmanned aerial vehicle imagery data to create a complete integrated survey using high-resolution imagery acquired independently at the best position and time for proper radiometric information to depict the surface features. By employing deep learning with orthophotos, the method significantly improves the interpretation of spatial weathering forms and façade degradation. Additionally, an HBIM library for Saudi Hijazi architectural elements is created, and the vector data derived from deep learning-based segmentation are accurately mapped onto the HBIM geometry with relevant statistical parameters. The findings give stakeholders an effective tool for identifying the types, nature, and spatial extent of façade degradation to investigate and monitor the structure.