bluuebunny/crossref_metadata_2025_split huggingface dataset:
Toxicological effects of 2,3,7,8 tetrachlorodibenzo-p-dioxin on the skeletal muscle of mice during the perinatal period: a metabolomics study
Authors: Lam Gideon , Juricek Ludmila , Dayal Hiranya , Laserna Anna Karen Carrasco , Hichor Medhi , Blanc Etienne , Chauvet Caroline , Noirez Phillipe , Coumoul Xavier , Li Sam Fong Yau 
Published: June 2022

AbstractPersistent organic pollutants (POPs) accumulate in the organisms due to their hydrophobicity and resistance to xenobiotic metabolism. 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) is one of most representative POPs. Its pathophysiological effects have been extensively studied on many types of tissues but not on muscles. In this study, female C57BL/6J mouse model was used to analyze the long-term effects of maternal exposure to TCDD during gestation and lactation on the skeletal muscles (soleus, plantaris, and gastrocnemius) of the progeny during adulthood. The effects of re-exposure to TCDD in mice exposed during their development were also characterized. Female C57BL/6J mice were maternally exposed to TCDD or its vehicle (n-nonane in corn oil) and then re-exposed to TCDD or its vehicle at 9 weeks of age. The metabolites in the skeletal muscles were analyzed by gas chromatography–quadrupole time of flight-mass spectrometry (GC–qTOF-MS). Univariate analysis showed significant effects in certain metabolites in the skeletal muscle. It also showed that TCDD exerts a more significant impact on exposure to TCDD at 9 weeks of age than during maternal exposure for the soleus. On the other hand, TCDD exerts a more significant impact on mice maternally exposed to TCDD than at 9 weeks of age for the gastrocnemius. Multivariate analysis showed clear discrimination between the TCDD-exposed mice and the control. This study demonstrates the effects of TCDD observed following maternal exposure; some of them can be reinforced or attenuated by a re-exposure at the adult age, suggesting that the POP which mainly acts through the activation of the AhR leads to metabolic adaptation in the skeletal muscles. The period of exposure was a key factor in our study with TCDD playing a crucial role during the maternal period, as compared to when they were exposed at 9 weeks of age. It was inferred that disruption in amino acid metabolism might lead to a loss in muscle mass which may result in muscular atrophy. Our results also show that the metabolite profiles after perinatal exposure are different in different types of muscles even though they are all classified as skeletal muscles. Therefore, TCDD may affect the organism (specifically different skeletal muscles) in a non-homogenous manner.
A virus–target host proteins recognition method based on integrated complexes data and seed extension
Authors: Xia Shengrong , Xia Yingchun , Xiang Chulei , Wang Hui , Wang Chao , He Jin , Shi Guolong , Gu Lichuan 
Published: June 2022

AbstractBackgroundTarget drugs play an important role in the clinical treatment of virus diseases. Virus-encoded proteins are widely used as targets for target drugs. However, they cannot cope with the drug resistance caused by a mutated virus and ignore the importance of host proteins for virus replication. Some methods use interactions between viruses and their host proteins to predict potential virus–target host proteins, which are less susceptible to mutated viruses. However, these methods only consider the network topology between the virus and the host proteins, ignoring the influences of protein complexes. Therefore, we introduce protein complexes that are less susceptible to drug resistance of mutated viruses, which helps recognize the unknown virus–target host proteins and reduce the cost of disease treatment.ResultsSince protein complexes contain virus–target host proteins, it is reasonable to predict virus–target human proteins from the perspective of the protein complexes. We propose a coverage clustering-core-subsidiary protein complex recognition method named CCA-SE that integrates the known virus–target host proteins, the human protein–protein interaction network, and the known human protein complexes. The proposed method aims to obtain the potential unknown virus–target human host proteins. We list part of the targets after proving our results effectively in enrichment experiments.ConclusionsOur proposed CCA-SE method consists of two parts: one is CCA, which is to recognize protein complexes, and the other is SE, which is to select seed nodes as the core of protein complexes by using seed expansion. The experimental results validate that CCA-SE achieves efficient recognition of the virus–target host proteins.
eQTLs are key players in the integration of genomic and transcriptomic data for phenotype prediction
Authors: Wade Abdou Rahmane , Duruflé Harold , Sanchez Leopoldo , Segura Vincent 
Published: June 2022

Abstract
Background
Multi-omics represent a promising link between phenotypes and genome variation. Few studies yet address their integration to understand genetic architecture and improve predictability.

Results
Our study used 241 poplar genotypes, phenotyped in two common gardens, with xylem and cambium RNA sequenced at one site, yielding large phenotypic, genomic (SNP), and transcriptomic datasets. Prediction models for each trait were built separately for SNPs and transcripts, and compared to a third model integrated by concatenation of both omics. The advantage of integration varied across traits and, to understand such differences, an eQTL analysis was performed to characterize the interplay between the genome and transcriptome and classify the predicting features into cis or trans relationships. A strong, significant negative correlation was found between the change in predictability and the change in predictor ranking for trans eQTLs for traits evaluated in the site of transcriptomic sampling.

Conclusions
Consequently, beneficial integration happens when the redundancy of predictors is decreased, likely leaving the stage to other less prominent but complementary predictors. An additional gene ontology (GO) enrichment analysis appeared to corroborate such statistical output. To our knowledge, this is a novel finding delineating a promising method to explore data integration.
Genome-scale metabolic network model of Eriocheir sinensis icrab4665 and nutritional requirement analysis
Authors: Li Jingjing , Gou Yifei , Yang Jiarui , Zhao Lingxuan , Wang Bin , Hao Tong , Sun Jinsheng 
Published: June 2022

Abstract
Background
Genome-scale metabolic network models (GEMs) provide an efficient platform for the comprehensive analysis the physical and biochemical functions of organisms due to their systematic perspective on the study of metabolic processes. Eriocheir sinensis is an important economic species cultivated on a large scale because it is delicious and nutritious and has a high economic value. Feed improvement is one of the important methods to improve the yield of E. sinensis and control water pollution caused by the inadequate absorption of feed.

Results
In this study, a GEM of E. sinensis, icrab4665, was reconstructed based on the transcriptome sequencing, combined with KEGG database, literature and experimental data. The icrab4665 comprised 4665 unigenes, 2060 reactions and 1891 metabolites, which were distributed in 12 metabolic subsystems and 113 metabolic pathways. The model was used to predict the optimal nutrient requirements of E. sinensis in feed, and suggestions for feed improvement were put forward based on the simulation results. The simulation results showed that arginine, methionine, isoleucine and phenylalanine had more active metabolism in E. sinensis. It was suggested that the amount of these essential amino acids should be proportionally higher than that of other amino acids in the feed to ensure the amino acid metabolism of E. sinensis. On the basis of the simulation results, we further suggested increasing the amount of linoleic acid, EPA and DHA in the feed to ensure the intake of essential fatty acids for the growth of E. sinensis and promote the accumulation of cell substances. In addition, the amounts of zinc and selenium in the feed were also suggested to be properly increased to ensure the basic metabolism and growth demand of E. sinensis.

Conclusion
The largest GEM of E. sinensis was reconstructed and suggestions were provide for the improvement of feed contents based on the model simulation. This study promoted the exploration of feed optimization for aquatic crustaceans from in vivo and in silico. The results provided guidance for improving the feed proportion for E. sinensis, which is of great significance to improve its yield and economic value.
A novel simulation-based approach to training for recruitment of older adults to clinical trials
Authors: Fisher Harriet , Zabar Sondra , Chodosh Joshua , Langford Aisha , Trinh-Shevrin Chau , Sherman Scott , Altshuler Lisa 
Published: June 2022

Abstract
Background
The need to engage adults, age 65 and older, in clinical trials of conditions typical in older populations, (e.g. hypertension, diabetes mellitus, Alzheimer’s disease and related dementia) is exponentially increasing. Older adults have been markedly underrepresented in clinical trials, often exacerbated by exclusionary study criteria as well as functional dependencies that preclude participation. Such dependencies may further exacerbate communication challenges. Consequently, the evidence of what works in subject recruitment is less generalizable to older populations, even more so for those from racial and ethnic minority and low-income communities.

Methods
To support capacity of research staff, we developed a virtual, three station simulation (Group Objective Structured Clinical Experience—GOSCE) to teach research staff communication skills. This 2-h course included a discussion of challenges in recruiting older adults; skills practice with Standardized Participants (SPs) and faculty observer who provided immediate feedback; and debrief to highlight best practices. Each learner had opportunities for active learning and observational learning. Learners completed a retrospective pre-post survey about the experience. SP completed an 11-item communication checklist evaluating the learner on a series of established behaviorally anchored communication skills (29).

Results
In the research staff survey, 92% reported the overall activity taught them something new; 98% reported it provided valuable feedback; 100% said they would like to participate again. In the SP evaluation there was significant variation: the percent well-done of items by case ranged from 25–85%.

Conclusions
Results from this pilot suggest that GOSCEs are a (1) acceptable; (2) low cost; and (3) differentiating mechanism for training and assessing research staff in communication skills and structural competency necessary for participant research recruitment.
Osteosarcopenic obesity and its components—osteoporosis, sarcopenia, and obesity—are associated with blood cell count-derived inflammation indices in older Chinese people
Authors: Nie Yi-zhen , Yan Zhao-qi , Yin Hui , Shan Ling-han , Wang Jia-hui , Wu Qun-hong 
Published: June 2022

Abstract
Background
The aim of this study was to investigate the associations of osteosarcopenic obesity (OSO) and its components with complete blood cell count-derived inflammation indices.

Methods
In this cross-sectional study, data of 648 participants aged ≥60 years (men/women: 232/416, mean age: 67.21 ± 6.40 years) were collected from January 2018 to December 2020. Areal bone mineral density and body fat percentage were used to define osteopenia/osteoporosis and obesity, respectively. The criteria of the 2019 Asian Working Group for Sarcopenia were used to diagnose sarcopenia. Based on the number of these conditions, participants were divided into four groups: OSO/0, OSO/1, OSO/2, and OSO/3. Logistic regression analysis was conducted to identify associations between blood cell count-derived inflammation indices and the number of disorders with abnormal body composition.

Results
Systemic inflammation response index (SIRI), white blood cells, neutrophil-to-lymphocyte ratio (NLR), aggregate inflammation systemic index (AISI), platelet-to-lymphocyte ratio (PLR), and lymphocyte-to-monocyte ratio (LMR) showed statistically significant differences among the four groups (P < 0.05). Unlike in the OSO/0 group, in all other groups, AISI, SIRI, PLR, and NLR were significantly associated with increased likelihood of having multiple disorders with abnormal body composition after adjustment for confounders (P < 0.0001 for all). However, LMR showed an inverse correlation with the number of these conditions (P < 0.05).

Conclusion
Higher SIRI, AISI, NLR, and PLR values and lower LMR values are closely associated with OSO and its individual components—osteoporosis, sarcopenia, and obesity—in older adults, suggesting that the value of these indices in the evaluation of OSO warrants further investigation.
Genetic characterization of two G8P[8] rotavirus strains isolated in Guangzhou, China, in 2020/21: evidence of genome reassortment
Authors: Wang Si-Jie , Chen Li-Na , Wang Song-Mei , Zhou Hong-Lu , Qiu Chao , Jiang Baoming , Qiu Tian-Yi , Chen Sheng-Li , von Seidlein Lorenz , Wang Xuan-Yi 
Published: June 2022

Abstract
Background
The G8 rotavirus genotype has been detected frequently in children in many countries and even became the predominant strain in sub-Saharan African countries, while there are currently no reports from China. In this study we described the genetic characteristics and evolutionary relationship between rotavirus strains from Guangzhou in China and the epidemic rotavirus strains derived from GenBank, 2020–2021.

Methods
Virus isolation and subsequent next-generation sequencing were performed for confirmed G8P[8] specimens. The genetic characteristics and evolutionary relationship were analyzed in comparison with epidemic rotavirus sequences obtained from GenBank.

Results
The two Guangzhou G8 strains were DS-1-like with the closest genetic distance to strains circulating in Southeast Asia. The VP7 genes of the two strains were derived from a human, not an animal G8 rotavirus. Large genetic distances in several genes suggested that the Guangzhou strains may not have been transmitted directly from Southeast Asian countries, but have emerged following reassortment events.

Conclusions
We report the whole genome sequence information of G8P[8] rotaviruses recently detected in China; their clinical and epidemiological significance remains to be explored further.
High expression level of CXCL1/GROα is linked to advanced stage and worse survival in uterine cervical cancer and facilitates tumor cell malignant processes
Authors: Man Xiaxia , Yang Xiaolin , Wei Zhentong , Tan Yuying , Li Wanying , Jin Hongjuan , Wang Baogang 
Published: June 2022

AbstractBackgroundCXCL1 belongs to a member of the ELR + CXC chemokine subgroups that also known as GRO-alpha. It has been recognized that several types of human cancers constitutively express CXCL1, which may serve as a crucial mediator involved in cancer development and metastasis via an autocrine and/or paracrine fashion. However, the expression pattern and clinical significance of CXCL1 in human uterine cervix cancer (UCC), as well as its roles and mechanisms in UCC tumor biology remains entirely unclear.MethodsThe expression and clinical significance of CXCL1 in UCC tissues was explored using immunohistochemistry and bioinformatics analyses. The expression and effects of CXCL1 in HeLa UCC cells were assessed using ELISA, CCK-8 and transwell assays. Western blotting experiments were performed to evaluate the potential mechanism of CXCL1 on malignant behaviors of HeLa UCC cells.ResultsThe current study demonstrated that CXCL1 was expressed in HeLa UCC cells, PHM1-41 human immortalized cervical stromal cells, as well as cervical tissues, with UCC tissues having an evidently high level of CXCL1. This high level of CXCL1 in cancer tissues was notably related to poor clinical stages and worse survival probability, rather than tumor infiltration and patient age. In addition, CXCL1 expression was extremely correlated with CCL20, CXCL8 and CXCL3 cancer-associated chemokines expression. In vitro, the growth and migration abilities of HeLa cells were significantly enhanced in the presence of exogenous CXCL1. Gain-function assay revealed that CXCL1 overexpression significantly promoted growth and migration response in HeLa cells in both autocrine and paracrine manners. Finally, we found that CXCL1 overexpression in HeLa cells influenced the expression of ERK signal-related genes, and HeLa cell malignant behaviors derived from CXCL1 overexpression were further interrupted in the presence of the ERK1/2 blocker.ConclusionOur findings demonstrate the potential roles of CXCL1 as a promoter and a novel understanding of the functional relationship between CXCL1 and the ERK signaling pathway in UCC.
Non-invasive diagnosis strategy of hepatocellular carcinoma in low-risk population
Authors: Xie Zonglin , Peng Zhenpeng , Zou Yujian , Xiao Han , Li Bin , Zhou Qian , Chen Shuling , Xu Lixia , Shen Jingxian , Mo Yunxian , Peng Sui , Kuang Ming , Long Jianting , Feng Shi-Ting 
Published: June 2022

Abstract
Aims
With prevalence of hepatocellular carcinoma (HCC) in low-risk population (LRP), establishing a non-invasive diagnostic strategy becomes increasingly urgent to spare unnecessary biopsies in this population. The purposes of this study were to find characterisics of HCC and to establish a proper non-invasive method to diagnose HCC in LRP.

Methods
A total of 681 patients in LRP (defined as the population without cirrhosis, chronic HBV infection or HCC history) were collected from 2 institutions. The images of computed tomography (CT) and magnetic resonance imaging (MRI) were manually analysed. We divided the patients into the training cohort (n = 324) and the internal validating cohort (n = 139) by admission time in the first institution. The cohort in the second institution was viewed as the external validation (n = 218). A multivariate logistic regression model incorporating both imaging and clinical independent risk predictors was developed. C-statistics was used to evaluate the diagnostic performance.

Results
Besides the major imaging features of HCC (non-rim enhancement, washout and enhancing capsule), tumor necrosis or severe ischemia (TNSI) on imaging and two clinical characteristics (gender and alpha fetoprotein) were also independently associated with HCC diagnosis (all P < 0.01). A clinical model (including 3 major features, TNSI, gender and AFP) was built to diagnose HCC and achieved good diagnostic performance (area under curve values were 0.954 in the training cohort, 0.931 in the internal validation cohort and 0.902 in the external cohort).

Conclusions
The clinical model in this study developed a satisfied non-invasive diagnostic performance for HCC in LRP.
CMV retinitis and subsequent acute cystoid macular oedema after treatment with vitreous ganciclovir injection: a case report
Authors: Liu Mengyun , He Hengqian , Lu Qinkang , Zhang Juntao 
Published: June 2022

Abstract
Background
To report a very rare acute cystoid macular oedema following ganciclovir injection in patients receiving allogeneic haematopoietic stem cell transplantation.

Case presentation
A 44-year-old male patient experienced vision loss in his left eye eight months after allogeneic stem cell transplantation. Ophthalmologic examination showed posterior retinopathy with retinal haemorrhage, a yellow necrotic border, and a vascular white sheath involved in the superior temporal retina but not the posterior pole. Cytomegalovirus DNA results in both plasma and ocular fluid were positive. All tests combined with the patient’s medical history suggested that his ocular disease was cytomegalovirus retinitis. Consequently, he received a weekly ganciclovir vitreous injection. The disease was visibly controlled, and the fundus condition improved after the first three treatments. However, the patient had severe vision loss in his left eye and acute cystic oedema in the macula, while the original lesion was stable two hours after the fourth treatment. The macular oedema subsided significantly on the first day. Over the next week, daily OCT findings indicated that the patient's macular oedema gradually subsided and resolved completely by the second week, and his left eye vision partially improved.

Conclusion
Macular oedema may occur in patients with cytomegalovirus retinitis, but it rarely occurs during treatment. In this case, the patient's macular oedema appeared and resolved quickly. Macular oedema in patients with cytomegalovirus retinitis receiving vitreous cavity injections of ganciclovir needs to be further studied and discussed.
Reduced blood flow by laser speckle flowgraphy after 125I-plaque brachytherapy for uveal melanoma
Authors: Tamplin Michelle R. , Wang Jui-Kai , Vitale Anthony H. , Hashimoto Ryuya , Garvin Mona K. , Binkley Elaine M. , Hyer Daniel E. , Buatti John M. , Boldt H. Culver , Kardon Randy H. , Grumbach Isabella M. 
Published: June 2022

Abstract
Background
To determine whether reductions in retinal and choroidal blood flow measured by laser speckle flowgraphy are detected after 125I-plaque brachytherapy for uveal melanoma.

Methods
In a cross-sectional study, retinal and choroidal blood flow were measured using laser speckle flowgraphy in 25 patients after treatment with 125I-plaque brachytherapy for uveal melanoma. Flow was analyzed in the peripapillary region by mean blur rate as well as in the entire image area with a novel superpixel-based method. Relationships between measures were determined by Spearman correlation.

Results
Significant decreases in laser speckle blood flow were observed in both the retinal and choroidal vascular beds of irradiated, but not fellow, eyes. Overall, 24 of 25 patients had decreased blood flow compared to their fellow eye, including 5 of the 6 patients imaged within the first 6 months following brachytherapy. A significant negative correlation between blood flow and time from therapy was present.

Conclusions
Decreases in retinal and choroidal blood flow by laser speckle flowgraphy were detected within the first 6 months following brachytherapy. Reduced retinal and choroidal blood flow may be an early indicator of microangiographic response to radiation therapy.