bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transcriptome and proteome profiling revealed the key genes and pathways involved in the fiber quality formation in brown cotton
Authors: Wang Zhenzhen , Rehman Abdul , Jia Yinhua , Dai Panhong , He Shoupu , Wang Xiaoyang , Li Hongge , Wang Liru , Qayyumd Abdul , Peng Zhen , Du Xiongming 
Published: September 2022

Abstract
Background
Colored cotton is also called eco-cotton because of its natural color fiber. However, the yield and quality of natural colored cotton are generally lower than white cotton. Now, little is known about the regulatory mechanisms involved in biochemical and metabolic pathways and critical genes between fiber quality and pigment synthesis. The present study used a pair of brown cotton near-isogenic lines (brown cotton ‘Z1-61’ and white cotton ‘RT’) to determine the transcriptomic and proteomic data of fiber (ovule) at 0DPA, 10DPA, and 20DPA.
Results
Integration analysis of the two-omics data demonstrated that the differential proteins with the same expression trend in the adjacent developmental stages were significantly and positively correlated with fold change. Enrichment analysis of metabolic pathway revealed that Z1-61, enriched in fiber elongation genes related to a flavonoid biosynthesis, phenylalanine metabolism, glutathione metabolism and many more genes (proteins) are up-regulated. Short Time-series Expression Miner analysis inferred that up-regulated genes of Z1-61 were specifically involved in the metabolism of carbohydrates, energy, and lipid, suggesting that these pathways play an important role in fiber elongation and pigmentation. We further analyzed the 164 glycosyltransferases genes were predominantly expressed in the early stage of Z1-61 fiber elongation while they were predominantly expressed during the later period of RT fibers elongation. And 15 MYB-bHLH-WD40 triple complex genes and other transcription factor genes such as C2H2 (12), ERF (11), and NAC (7) were also preferentially expressed in Z1-61. Weighted correlation network analysis exhibited that fatty acid synthesis and energy metabolism were the active metabolic pathways in both cotton genotypes during fiber development. The 10 hub genes obtained from the final screening can be considered to play a critical role in the process of fiber pigment deposition while ensuring that fiber quality does not degraded.
Conclusion
This is the first complementary analyses of the transcriptome and proteome related with the quality of brown cotton fiber. Those studies can be understood as better playing a major role in fiber quality enhancement and pigmentation during fiber elongation.
Correlation analysis of risk factors for cervical lymphatic metastasis in papillary thyroid carcinoma
Authors: Sun Haoying , Wang Xin , Zhao Xueyu , Ma Jinzhu , Liu Ming 
Published: September 2022

Abstract
Objective:To analyse the risk factors of cervical lymph node metastasis in patients with papillary thyroid carcinoma (PTC).
Methods: The clinicopathological data of 2384 PTC patients admitted to our hospital from January 2016 to December 2020 were retrospectively analysed. The risk factors for cervical lymph node metastasis of PTC were also analysed.
Results: Male (OR=1.564, 95%CI: 1.138-2.148, P < 0.001), age ≤55 years old (OR=2.874, 95%CI:1.600-5.161, P < 0.001), tumor lesion > 0.5cm (OR=1.777, 95%CI:1.289-2.448, P<0.001), Multifocal (OR=0.686, 95%CI:0.531- 0.886, P< 0.001) were risk factors for central lymph node metastasis (CLNM). ROC curve showed that the cutoff value of tumor lesion size for predicting CLNM was 0.855 (sensitivity was 57.9%, specificity was 69%, AUC was 0.269, P < 0.05). The metastatic rate of lateral cervical lymph nodes increased with the increase of tumor diameter. Lateral cervical lymph node metastasis (LLNM) was more common in area III (59.4%) and Ⅳ (53.1%) than Ⅴ (9.4%) (P < 0.008). The metastasis rate of area II was 40.6%, and there was no significant difference between the two regions. In this study, a total of 85 PTC patients were tested for BRAF gene, and 79 of them were found to have BRAF gene mutations, with a mutation rate of 93%. BRAF gene mutation is of certain value for the diagnosis of PTC, but there is no statistical significance for the assessment of CLNM (P=0.827).
Conclusion: CLNM in PTC patients is significantly related to male patients age ≤55 years old with tumor lesions > 0.855cm and multiple tumor lesions. Central lymph node dissection (CLND) should be performed actively for those patients. The lateral neck lymph node metastasis should be evaluated in detail before surgery. And areas Ⅱ, Ⅲ and Ⅳ should be the main focus if they need to be cleaned. Areas I and V were cleaned according to other risk factors of the patients.
Collaborative Cross mice are permissive to Salmonella enterica serovar Typhi infection
Authors: Alugupalli Kishore , Kothari Sudeep , Cravens Matthew , Walker Justin , Dougharty Darren , Dickinson Gregory , Gatto Louis , Wangdi Tamding , Miller Darla , Baumler Andreas , de Villena Fernando Pardo-Manuel , Siracusa Linda 
Published: September 2022

Abstract
Salmonella enterica serovar Typhi is the causative agent of typhoid fever restricted to humans and does not replicate in commonly used inbred mice. Genetic variation in humans is far greater and more complex than that in a single inbred strain of mice. The Collaborative Cross (CC) is a large panel of recombinant inbred strains which has a wider range of genetic diversity than laboratory inbred mouse strains. We found that the CC003/Unc and CC053/Unc strains are permissive to S. Typhi infection and show histopathological changes characteristic of human typhoid. These CC strains are immunocompetent, and immunization induces antigen-specific responses that can kill S. Typhi in vitro and control S. Typhi in vivo. Our results indicate that CC003/Unc and CC053/Unc strains can help identify the genetic basis for typhoid susceptibility, S. Typhi virulence mechanism(s) in vivo, and serve as a preclinical mammalian model system to identify effective vaccines and therapeutics strategies.
The Differences in Insights of Social-ecological Resilience between Organic Farmers and Extension Agents
Authors: Panpakdee Chaiteera 
Published: September 2022

Abstract

The objective of this research was to compare insights of organic farmers and extension agents regarding social-ecological resilience. To achieve that, forty-seven social-ecological components were used as the base. These components are features that can be applied to build resilience in organic rice production. In 2017, the components were systematically constructed by fifty-three organic farmers in four districts of Chiang Mai Province, Thailand, who grouped the four critical properties. The informants were twenty-eight extension agents working in the same districts. They were asked to assign a score to each vital property, and to gauge its significance contributed to building resilience. The scoring values were computed using the normalized method to produce the intensity of the importance of the properties. Next, an analysis of one sample t-test at the level of significance of 0.05 was carried out to compare the two parties’ intensities. The results pointed out three out of the four properties had been homogenous. The difference was only found in the property of ‘Learning to live with change and uncertainty’ due to the organic farmers’ unaltered hindrances, such as living in an aging society. This drawback can be solved by allowing organic farmers to gain access to programs facilitated by extension agents. This collective action motivates organic farmers to engage in those programs since it is designed to meet their needs.
Tooth Root Surface Area Calculation in Cone-Beam CT via Deep Segmentation
Authors: Su Sha , Jia Xueting , Zhan Liping , Fan Xiaochuan , Gao Siyuan , Cai He , Huang Xiaofeng 
Published: September 2022

Abstract
Purpose
Periodontitis is the main cause of tooth loss in adults. It is important to calculate healthy periodontal membrane area to evaluate the severity of periodontitis. The aim of this study is to develop a computer-assisted system based on convolutional neural network (CNN) to segment and calculate the tooth root surface area (RSA) on cone-beam CT(CBCT).
Methods
We presented a deep learning system to automatically identify the alveolar bone and tooth regions by applying an advanced Mask R-CNN segmentation on clinically dataset of 2000 CBCT images. Twenty-four teeth from 20 patients who required tooth extraction were selected. Before extraction, pre-treatment CBCT images of all the patients were recorded. The RSA of each tooth was calculated by CNN. After extraction, all the teeth were scanned by CBCT again. The RSA of each extracted tooth was calculated by CNN again and also calculated by medical image control system (Mimics version 15.01; Materialise, Leuven, Belgium). RSA of 24 teeth calculated using these two measurement methods were analyzed by the paired t-test (P < 0.05) and Bland-Altman plot consistency analysis.
Results
The paired t-test result showed that there was no statistical difference of RSA of 24 teeth calculated by CNN and Mimics (p > 0.05). The Bland-Altman plot test also showed the good consistency.
Conclusion
We applied Mask R-CNN to segment tooth root and calculate the RSA on CBCT. Such approach presents a novel, fast, automatic and accurate approach to measure the RSA and can be used for estimating the non-extracted teeth.
Hepatitis A virus seroprevalence among children and adolescents in a high-burden HIV setting in urban South Africa
Authors: Du Plessis Nicolette M , Mazanderani Ahmad Haeri , Motaze Nkengafac Villyen , Ngobese Makhosazane , Avenant Theunis 
Published: September 2022

Abstract
Background
Hepatitis A virus (HAV) infection is one of the most important global causes of viral hepatitis. Recent reviews suggested that HAV endemicity in South Africa could be shifting from high to intermediate.
Methods
A hospital-based HAV-seroprevalence study was conducted between February 2018 to December 2019, in Pretoria, South Africa. Systematic sampling was done of children and adolescents (1–15 years) who attended outpatient services. Participants with a known HIV-status and valid HAV-serology results were included.
Results
Of 1220 participants, the median age was 7-years (IQR: 4–11) with 648 (53.11%) male and 572 (46.89%) female. Of 628 (51.48%) HIV-infected participants, most (329, 71.83%) were both immunologically and virologically controlled or with low level viremia (74, 16.16%). Almost three-quarters (894, 73.28%) were living in formal dwellings, and just over half (688, 56.39%) had access to clean water sources inside the house. Increasing age was associated with testing IgG-positive (OR 1.24; 95% CI 1.21–1.28), with 19.8% of participants one year of age compared with 86.7% of participants 15-years of age.
Conclusions
This study suggests that South Africa has an intermediate HAV-seroprevalence with rates < 90% by 10-years of age (68.6%). Increased age and informal dwellings are statistically associated with HAV-seropositivity, whilst HIV-status does not significantly influence HAV-seropositivity.
Correlation between physical activity, Sleep Components and Quality: in the Context of Type and Intensity : A Cross-Sectional study among Medical Students
Authors: Mahgoub Ahmed Abdelghyoum , Mustafa Shahenaz Satti 
Published: September 2022

Abstract
Background: Physical activity during the day is composed of different domains, specifically work-related, transportation, and recreation physical activity. We aimed at studying the correlation between energy expenditure and the corresponding metabolic equivalent of task and sleep in the context of the type, intensity and general level of physical activity.
Materials and Methods:a cross-sectional study, participants were n= 273 enrolled from Al-Neelain university faculty of medicine between January and April 2021 we used the global physical activity questionnaire to measure the standard metabolic equivalent of task (MET) for vigorous and moderate work & leisure MET, Transportation MET, and sedentary time. we used the Pittsburgh sleep quality index to assess sleep quality. Daytime sleepiness was assessed with (the Epworth sleepiness scale) and psychological distress was assessed with (the Kessler 10-item questionnaire).
Results: The Mean of Total-MET was (3533.36min/week) predominantly moderated work-MET (33%). Poor sleepers’ percentage was high (62%). Moreover, there was a significant difference between good and poor sleepers in moderate work MET mean (876.36,1334.2 min/week) (P<0.01).respectively. There was a significant difference between categories of activity in sleep duration (P<0.05) being higher for the low activity group(7.2h) than high and moderate categories (6.9h-6.3h) respectively. There were significant positive correlations between moderate work MET and roughly all sleep components namely (sleep latency, sleep disturbances, use of medications, daytime dysfunction) rho=(0.196, 0.182, 0.132, 0.149)(P<0.01, P<0.01, P<0.05, P<0.05) respectively and sleep quality rho=(. 211 P<0.001). Vigorous leisure MET positively correlated with increased sleep latency rho=(0. 134 P<0.01). Total MET correlated with increased sleep latency, use of medications, and poor sleep quality in general. (0.134, 0.124, 0.133) (P<0.05). Psychological distress significantly correlated with both moderate work MET (0.135)(P<0.05) and increased sleep latency (0.229 P<0.001) severe daytime sleepiness (0.295 P<0.001)and overall poor Sleep quality (0.330 P<0.001).
Conclusions: Our results show that poor sleep quality is primarily influenced by the type and intensity of physical activity. Eliciting a dose-response effect of different domains, being deleterious for work-related physical activity as work MET is of too low intensity or too long duration for maintaining or improving cardiorespiratory fitness and cardiovascular health subsequently imposing its deleterious effect.
STRIP2 motivates non-small cell lung cancer progression by modulating the TMBIM6 stability through IGF2BP3 dependent
Authors: Zhang Xilin , Chen Qiuqiang , He Ying , Shi Qian , Yin Chengyi , Xie Yanping , Yu Huanming , Bao Ying , Tang Chengwu , Dong Zhaohui 
Published: September 2022

Abstract
Background: Striatin interacting protein 2 (STRIP2) is a core component of the striatin-interacting phosphatase and kinase (STRIPAK) complexes, which is involved in tumor initiation and progression via the regulation of cell contractile and metastasis. However, the underlying molecular mechanisms of STRIP2 in non-small cell lung cancer (NSCLC) progression remain largely unknown.
Methods: The expressions of STRIP2 and IGF2BP3 in human NSCLC specimens and NSCLC cell lines were detected using quantitative RT-PCR, western blotting, and immunohistochemistry (IHC) analyses. The roles and molecular mechanisms of STRIP2 in promoting NSCLC progression were investigated in vitro and in vivo. Results: Here, we found that STRIP2 expression was significantly elevated in NSCLC tissues and high STRIP2 expression was associated with a poor prognosis. Knockdown of STRIP2 suppressed tumor growth and metastasis in vitroand in vivo, while STRIP2 overexpression obtained the opposite effect. Mechanistically, P300/CBP-mediated H3K27 acetylation activation in the promoter of STRIP2 induced STRIP2 transcription, which interacted with insulin-like growth factor 2 mRNA-binding protein 3 (IGF2BP3) and upregulated IGF2BP3 transcription. In addition, STRIP2-IGF2BP3 axis stimulated m6A modification of TMBIM6 mRNA and enhanced TMBIM6 mRNA stability. Consequently, TMBIM6 involved NSCLC cell proliferation, migration and invasion dependent on STRIP2 and IGF2BP3. In NSCLC patients, high co-expression of STRIP2, IGF2BP3 and TMBIM6 was associated with poor outcomes.
Conclusions: Our findings indicate that STRIP2 interacts with IGF2BP3 to regulate TMBIM6 mRNA stability in an m6A-dependent manner and may represent a potential prognostic biomarker and therapeutic target for NSCLC.
Lysosomal-associated protein transmembrane 5 ameliorates non-alcoholic steatohepatitis through degradating CDC42
Authors: Jiang Lang , Zhao Jing , Yang Qin , Li Mei , Liu Hao , Xiao Xiaoyue , Tian Song , Hu Sha , Liu Zhen , Yang Peiwen , Chen Manhua , Ye Ping , Xia Jiahong 
Published: September 2022

Abstract
Non-alcoholic steatohepatitis (NASH) has received great attention due to its extremely high incidence. Our team screened LAPTM5 associated with NASH progression through extensive bioinformatics analysis. We found protein LAPTM5 markedly decreased in response to lipotoxicity both in liver tissues from human and mouse NASH groups, and protein level of LAPTM5 was negatively correlated with NAS score. Then, we found LAPTM5 degradation was mediated through its ubiquitination modification by the E3 ubquitin ligase NEDD4L. Hepatocyte specific depleting LAPTM5 exacerbated hepatic steatosis, inflammation and fibrosis in mouse NASH models. In contrast, LAPTM5 overexpression in hepatocyte exerted opposite effects. Mechanistically, LAPTM5 interacted with CDC42 and promoted its degradation through a lysosomal dependent manner, thus inhibited activation of the mitogen-activated protein kinase signaling pathway. Finally, adenovirus-mediated hepatic LAPTM5 overexpression ameliorated above symptoms in NASH models. These findings proved LAPTM5 as effective treatment in NASH and a potential biological marker for detecting NASH progression.
Early growth evaluation and biomass allocation differences of Cupressus funebris clones and families
Authors: Yang Tao , Zhang Zheng , Wang Pengcheng , Wang Wenyue , Jin Guoqing , Qiu Yongbin , Shen Han , Zhou Zhichun 
Published: September 2022

Abstract
Clonal forestry offers the opportunity to increase yields, enhance uniformity and improve wood characteristics. Evaluation of growth differences between clones and families has rarely been studied in slow-growing Cupressus funebris species, and whether such growth differences are related to biomass allocation patterns remains to be revealed and is essential for assessing the genetic selection potential and carbon sink capacity of superior species. We studied the genetic variation, heritability (replication power) and gain levels of 36 clones and 33 families of superior trees and analysed their biomass allocation patterns. The results showed that the early growth of Cupressus funebris was dominated by high growth, and the clones grew rapidly, with 253.36% and 51.77% higher diameter at breast height and height at 8 years old than the family lines, respectively. However, the genetic variation of growth traits in the families was higher than that of the clones. The clone repeatability and family heritability levels were evaluated. According to the 10% selection rate, the genetic gains of DBH and tree height of clones were 39.53% and 24.23%, respectively, 5.22 times and 2.05 times the genetic gains of families. The ratio of narrow and broad heritability of each trait was estimated to be 0.55–0.68, with an average value of 0.63, indicating that clones obtained higher additional genetic gains through nonadditive effects. The growth advantage of the clones was to increase the biomass of the aboveground part (86.03%) at the expense of the belowground biomass allocation, which was mainly reflected by the proportion of branch and leaf biomass allocation. The branches and leaves of the clones were dominated by the middle and upper layers, which accounted for 180.64% and 60.14%, respectively, while the middle and lower layers of the branches and leaves of the family lines accounted for a higher percentage. The model ln W=k0+k1 lnD + k2 lnH +k3 has the best prediction of biomass and could be used for early genetic evaluation of Cupressus funebris. In general, Cupressus funebris clones are fast growing and will help to improve the productivity and carbon storage of stands through genetic selection and utilization.
Diagnostic accuracy of a deep learning model using YOLOv5 for detecting developmental dysplasia of the hip on radiography images
Authors: Den Hiroki , Ito Junichi , Kokaze Akatsuki 
Published: September 2022

Abstract
Introduction
Developmental dysplasia of the hip (DDH) is a cluster of hip development disorders and one of the most common hip diseases in infants. Hip radiography is a convenient diagnostic tool for DDH, but its diagnostic accuracy is dependent on the interpreter’s level of experience.
The aim of this study was to develop a deep learning model for detecting DDH using YOLOv5.
Methods
Patients younger than 12 months who underwent hip radiography between June 2009 and November 2021 were selected. Using their radiography images, transfer learning was performed to develop a deep learning model using YOLOv5.
Results
A total of 305 anteroposterior hip radiography images (205 normal hip images and 100 DDH hip images) were collected. Of these, 30 normal hip images and 17 DDH hip images were used as the test set. The sensitivity and the specificity of our best deep learning model (YOLOv5l) were 0.94(95%CI 0.73-1.00) and 0.96 (95%CI:0.89-0.99), respectively.
Conclusion
This is the first study to establish a model for detecting DDH using YOLOv5. Our deep learning models provided good diagnostic performance for DDH. We believe our model is a useful diagnostic assistant tool.
Three nervous system-specific expressed genes are potential biomarkers for the diagnosis of sporadic amyotrophic lateral sclerosis through a bioinformatic analysis
Authors: Liao Yifu , Cai Haiping , Luo Feifei , Li Dongcheng , Li Hao , Liao Geng , Duan Jinhai , Xu Renshi , Zhang Xiong 
Published: September 2022

Abstract
Background
Amyotrophic lateral sclerosis (ALS) is the most common neurodegenerative disease in adults. However, ALS, especially sporadic ALS (sALS), is difficult to diagnose due to the lack of biomarkers.
Results
We used the Bioinformatics technology to find the potential biomarker and we found that two hundred seventy-four DEGs were identified and enrichment analysis showed DEGs were involved in nervous system activity, like axon_guidance and the neurotrophin_signaling_pathway. Five nervous system-specific expressed hub genes were further validated by three GEO datasets. APP, LRRK2, and PSEN1 might be potential diagnostic and prognostic biomarkers of sALS, and NEAT1-miR-373-3p/miR-302c-3p/miR-372-3p-APP, circ_0000002-miR-302d-3p/miR-373-3p-APP and XIST-miR-9-5p/miR-30e-5p/miR-671-5p might be potential ceRNA regulatory pathways. APP SNP analysis showed subjects harboring the minor G allele of rs463946, minor G allele of rs466433 and minor C allele of rs364048 had an increased risk of sALS development.
Conclusions
Our results identified three nervous system-specific expressed hub genes that might be diagnostic and prognostic markers of sALS and APP might be a genetic susceptibility factor contributing to sALS development.