bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Multi-Centre Survey on Hospital Malnutrition: Result of PNSI Study
Authors: Poudineh Somayeh , Shayesteh Forough , Kermanchi Jamshid , Haghdoost Ali-Akbar , Torabi Parisa , Pasdar Yahya , Azimi-Nezhad Mohsen , Safarian Mohammad , Hajifaraji Majid , Eslami-Hasan-Abadi Saeed , Pournik Omid , Barkhidarian Bahareh , Norouzy Abdolreza 
Published: October 2020

Abstract
Background: Disease-related malnutrition is associated with adverse outcomes such as increased rates of morbidity and mortality, prolonged hospital stay, and extra costs of health care. This study was conducted to assess nutritional status among patients and to determine the risk factors for malnutrition in Iran university hospitals. Methods: Persian Nutritional Survey In Hospitals (PNSI) was a cross-sectional study that conducted in 20 university hospitals across Iran. All the patients with age range of 18 to 65 years, who were admitted or discharged, were assessed by subjective global assessment (SGA). Results: In total, 2306 patients were evaluated for malnutrition. Mean values of age and body mass index were 44.7±14 years and 25.2±6 kg/m2, respectively. Malnutrition (SGA-B & C) was identified in 23.9% of the patients, 26.2% and 21% of whom were among the admitted and discharged patients, respectively. The prevalence of malnutrition was higher in burns (78%) and heart surgery (58%) patients. Malnutrition was not associated with age (P=0.1). Multivariate analysis presented male gender (OR=1.023, P<0.001), malignant disease (OR=1.409, P<0.001), length of hospital stay (OR=1.206, P<0.001), and polypharmacy (OR=1.066, P<0.001) as independent risk factors for malnutrition.Conclusion: One out of four patients in the studied university hospitals was suffering from malnutrition; thus, appropriate measures should be taken to ameliorate this condition. Male gender, malignant disease, length of hospital stay, and polypharmacy were identified as independent risk factors for malnutrition.
Thousands of Previously Unknown Phages Discovered in Whole-community Human Gut Metagenomes
Authors: Benler Sean , Yutin Natalya , Antipov Dmitry , Raykov Mikhail , Shmakov Sergey , Gussow Ayal B , Pevzner Pavel A , Koonin Eugene 
Published: October 2020

Abstract
Background: Double-stranded DNA bacteriophages (dsDNA phages) play pivotal roles in structuring human gut microbiomes; yet, the gut phageome is far from being fully characterized, and additional groups of phages, including highly abundant ones, continue to be discovered by metagenome mining. A multilevel framework for taxonomic classification of viruses was recently adopted, facilitating the classification of phages into evolutionary informative taxonomic units based on hallmark genes. Together with advanced approaches for sequence assembly and powerful methods of sequence analysis, this revised framework offers the opportunity to discover and classify unknown phage taxa in the human gut.Results:A search of human gut metagenomes for circular contigs encoding phage hallmark genes resulted in the identification of 3,738 apparently complete phage genomes that represent 451 putative genera. Several of these phage genera are only distantly related to previously identified phages and are likely to found new families. Two of the candidate families, “Flandersviridae” and “Quimbyviridae”, include some of the most common and abundant members of the human gut virome that infect Bacteroides, Parabacteroides and Prevotella. The third proposed family, “Gratiaviridae”, consists of less abundant phages that are distantly related to the families Autographiviridae, Drexlerviridae and Chaseviridae. Analysis of CRISPR spacers indicates that phages of all three putative families infect bacteria of the phylum Bacteroidetes. Comparative genomic analysis of the three candidate phage families revealed features without precedent in phage genomes. Some “Quimbyviridae” phages possess Diversity-Generating Retroelements (DGRs) that generate hypervariable target genes nested within defense-related genes, whereas the previously known targets of phage-encoded DGRs are structural genes. Several “Flandersviridae” phages encode enzymes of the isoprenoid pathway, a lipid biosynthesis pathway that so far has not been known to be manipulated by phages. The “Gratiaviridae” phages encode a HipA-family protein kinase and glycosyltransferase, suggesting these phages modify the host cell wall, preventing superinfection by other phages. Hundreds of phages in these three and other families are shown to encode catalases and iron-sequestering enzymes that can be predicted to enhance cellular tolerance to reactive oxygen species.Conclusions:Analysis of phage genomes identified in whole-community human gut metagenomes resulted in the delineation of at least three new candidate families of Caudovirales and revealed diverse putative mechanisms underlying phage-host interactions in the human gut. Addition of these phylogenetically classified, diverse and distinct phages to public databases will facilitate taxonomic decomposition and functional characterization of human gut viromes.
Comprehensive Analysis of Genomic Mutation Signature and Tumor Mutation Burden for Prognosis of Intrahepatic Cholangiocarcinoma
Authors: Zhang Rui , Li Qi , Fu Jialu , Jin Zhechuan , Su Jingbo , Zhang Jian , Chen Chen , Geng Zhimin , Zhang Dong 
Published: October 2020

Abstract
Background: The intrahepatic cholangiocarcinoma (iCCA) is highly lethal malignancy of biliary tract cancer. Analysis of somatic mutational profiling could help to reveal new prognostic markers and actionable targets for treatment. We aim to explore the impact of genomic mutation signature and tumor mutation burden (TMB) on prognosis of iCCA patients. Methods: The whole-exome sequencing and corresponding clinical data were collected from ICGC portal and cBioPortal database to detect the mutation prognostic genes and TMB values. To identify the hub prognostic mutant signature, Cox regression and Lasso feature selection were conducted. We built a mutation related signature (MRS) through multivariate Cox regression. The predictive performance of MRS and TMB were assessed using Kaplan-Meier (KM) analysis and receiver operating characteristic (ROC). We performed a functional enrichment pathway analysis with gene set enrichment analysis (GSEA) for mutated genes were conducted. Moreover, on the base of MRS, TMB and TNM stage, a nomogram was constructed to visualize the prognosis of iCCA patients.Results: The mutation landscape illustrated the distributions of mutation frequencies and types on iCCA, and revealed a list of most frequent mutation genes (such as Tp53, KRAS, ARID1A, IDH1). We obtain a 6- gene signature using the Lasso and Cox method. The AUC of MRS in 1, 3, 5-year OS prediction were 0.759, 0.732, 0.728, respectively. Moreover, Kaplan-Meier analysis showed a significant difference on the prognosis of iCCA with high and low MRS score (P <0.001). Interestingly, GSEA was utilized to show several signaling pathways including MAPK signaling pathway, PI3K-AKT signaling pathway and proteoglycans in cancer. On the other hand, survival analysis indicated that TMB was significantly associated with prognosis. And GSEA indicated that samples with high MRS or TMB upregulated signaling pathways involved in tumor signaling and immune system. At last, we constructed a predictive nomogram (included MRS, TMB and TNM stage) with satisfactory performance in survival prediction. Conclusions: The mutation genes signature and TMB were associated with prognosis in patients with iCCA. Our study provides a valuable prognostic predictor for further uncovering molecular pathogenesis in iCCA.
Radiomic Analysis of Gd-EOB-DTPA-enhanced MRI&nbsp;Predicts Ki-67 Expression in Hepatocellular Carcinoma
Authors: Fan Yanfen , Yu Yixing , Wang Ximing , Hu Mengjie , Hu Chunhong 
Published: October 2020

Abstract
Background: Nuclear protein Ki-67 indicates the status of cell proliferation and has been regarded as an attractive biomarker for the prognosis of HCC. The aim of this study is to investigate which radiomics model derived from different sequences and phases of gadolinium-ethoxybenzyl-diethylenetriamine pentaacetic acid (Gd-EOB-DTPA)-enhanced MRI was superior to predict Ki-67 expression in hepatocellular carcinoma (HCC), then further to validate the optimal model for preoperative prediction of Ki-67 expression in HCC. Methods: This retrospective study included 151 (training cohort: n=103; validation cohort: n=48) pathologically confirmed HCC patients. Radiomics features were extracted from the artery phase (AP), portal venous phase (PVP), hepatobiliary phase (HBP), and T2-weighted (T2W) images. A logistic regression with the least absolute shrinkage and selection operator (LASSO) regularization was used to select features to build a radiomics score (Rad-score). A final combined model including the optimal Rad-score and clinical risk factors was established. Receiver operating characteristic (ROC) curve analysis, Delong test and calibration curve were used to assess the predictive performance of the combined model. Decision cure analysis (DCA) was used to evaluate the clinical utility. Results: The AP radiomics model with higher decision curve indicating added more net benefit, gave a better predictive performance than the HBP and T2W radiomic models. The combined model (AUC = 0.922 vs 0.863) including AP Rad-score and serum AFP levels improved the predictive performance more than the AP radiomics model (AUC=0.873 vs 0.813) in the training and validation cohort. Calibration curve of the combined model showed a good agreement between the predicted and the actual probability. DCA of the validation cohort revealed that at a range threshold probability of 30-60%, the combined model added more net benefit compared with the AP radiomics model. Conclusions: A combined model including AP Rad-score and serum AFP levels based on enhanced MRI can preoperatively predict Ki-67 expression in HCC.
Exposure of Mesenchymal Stem Cells to an Alzheimer’s Disease Environment Enhances Therapeutic Effects
Authors: Park Sang eon , Kim Hyeong Seop , Kwon Soo Jin , Kim Min-Jeong , Choi Suk-joo , Oh Soo-young , Ryu Gyu Ha , Jeon Hong Bae , Na Duk L. , Chang Jong Wook 
Published: October 2020

Abstract
BackgroundMesenchymal stem cells (MSCs) have emerged as a promising tool for the treatment of Alzheimer’s disease (AD). Previous studies suggested that the co-culture of human MSCs with AD in an in vitro model reduced the expression of amyloid-beta 42 (Aβ42) in the medium as well as the overexpression of amyloid-beta (Aβ )-degrading enzymes such as neprilysin (NEP).MethodsIn this study, we focused on the role of primed MSCs (human Wharton's jelly-derived mesenchymal stem cells (WJ-MSCs) exposed to an AD cell line via a co-culture system) in reducing the levels of Aβ and inhibiting cell death. ResultsWe demonstrated that mouse groups treated with naïve MSCs and primed MSCs showed significant reductions in cell death, ubiquitin conjugate levels, and Aβ levels, but the effects were greater in primed MSCs. Also, mRNA sequencing data analysis indicated that high levels of TGF-β induced primed-MSCs. Furthermore, treatment with TGF-β reduced Aβ expression in an AD transgenic mouse model. ConclusionAD environmental preconditioning is a promising strategy to reduce cell death and ubiquitin conjugate levels and maintain the stemness of MSCs. Further, these data suggest that human WJ-MSCs exposed to an AD environment may represent a promising and novel therapy for AD.
Automatic Tooth Segmentation and Classification in Dental Panoramic X-ray Images
Authors: Zhao Shuxu , LUO QING , Liu Changrong 
Published: October 2020

Abstract
Background: The information of tooth shape, type and tooth position plays an important role in the understanding of pathological features in dental X-ray ﬁlms. It is of great signiﬁcance to realize the accurate tooth segmentation and tooth classiﬁcation of dental panoramic X-ray images for the construction of an intelligent dental diagnosis system.At present, the segmentation results of teeth are relatively rough, and most methods realize tooth recognition and segmentation as independent tasks, ignoring the parameter sharing between the two tasks. Therefore, an instance segmentation method which can realize tooth recognition and tooth segmentation at the same time is proposed. Methods: In model designing, the Mask R-CNN, an instance segmentation model , is adopted, which includes classiﬁcation branches and segmentation branches. The classiﬁcation branch can be used to complete the tooth recognition task and the segmentation branch to complete the tooth segmentation task. On this basis, the U-Net architecture is integrated to modify the segmentation branch to improve the segmentation eﬀect. In data engineering, two classiﬁcation schemes are designed, one according to the function of teeth, the other according to the position of teeth. Results: Based on the data of 400 panoramic X-ray ﬁlms of teeth, we combined migration learning to conduct experiments on the TensorFlow deep learning framework. The experimental results show that compared with other methods, the classiﬁcation and segmentation of teeth can be realized simultaneously in this paper, with an accuracy of more than 90%. Compared with the original model, the improved Mask R-CNN proposed in this paper improves the segmentation recall rate by 10%. In the proposed classiﬁcation scheme, the accuracy of classiﬁcation based on tooth function is 3% higher than that based on tooth position.Conclusions: The model proposed in this paper combines the two tasks of classiﬁcation and segmentation, avoids the repetitive training of the model, and improves the segmentation precision with the improved segmentation branch. Compared with the recall rate traditional methods of tooth function classiﬁcation, the proposed method based on tooth function has better classiﬁcation eﬀect.
520YS , Encoding an Ankyrin Repeat Protein, is Involved in Chloroplast Development in Rice
Authors: Wang Pingrong , Xiao Fuliang , Wang San , Guo Jia , Liu Qingsong , Tang Yulin , Zhang Xiangyu , Sun Changhui , Deng Xiaojian 
Published: October 2020

Abstract
BackgroundThe ankyrin repeat (ANK) proteins are widely distributed in organisms ranging from viruses to plants, which play key roles in plastid differentiation, embryogenesis, chloroplast biogenesis and so on. However, only a few ANK genes have been identified in rice.ResultsIn this study, we isolated a yellow-green leaf mutant, 520ys, from japonica rice cultivar Nipponbare through ethyl methane sulfonate mutagenesis. The mutant exhibited a yellow-green leaf phenotype throughout the life cycle, arrested development of chloroplasts, reduced levels of photosynthetic pigments, and accumulated reactive oxide species. Map-based cloning suggested that the candidate gene was LOC_Os07g33660, which encodes an expressed protein containing one ankyrin repeat and showing sequence similarity with the Arabidopsis LTD/GDC1 (At1g50900). Transgenic complementation experiment confirmed that LOC_Os07g33660 is the causal gene for the mutant type of 520ys. 520YS (LOC_Os07g33660) is mainly expressed in green tissues and its encoded protein is targeted to the chloroplast. In 520ys mutant, expression levels of four light-harvesting chlorophyll a/b-binding protein translocation-related genes and eight photosynthesis-related genes were significantly down-regulated.ConclusionWe characterized a novel ANK gene, 520YS, which plays a key role in chloroplast development in rice.
Chronic Ethanol Vapor Exposure Potentiates the Cardiovascular Responses to Acute Stress in Male but Not in Female Rats
Authors: Bianchi Paula Cristina , de-Souza Lucas Gomes , Costa-Ferreira Willian , Palombo Paola , de Oliveira Paulo E. Carneiro , Engi Sheila A. , Leão Rodrigo M. , Planeta Cleopatra S. , Crestani Carlos C. , Cruz Fabio C. 
Published: October 2020

Abstract
Background: Ethanol use is related to a wide variety of negative health outcomes, including cardiovascular diseases. Stress is also involved in numerous pathologies such as cardiovascular diseases and psychiatric disorders. Sexual dimorphism is an important factor affecting the cardiovascular response and have been proposed as a potentially risk factor for sex-specific health problems in human. Here, we evaluated the effect of prolonged ethanol vapor inhalation in arterial pressure, heart rate and tail skin temperature responses to acute restraint stress, investigating differences between male and female rats. Methods: We exposed male and female Long-Evans rats to ethanol vapor for 14 hours, followed by ethanol withdrawal for 10 hours, for 30 consecutive days or room air (control groups). The animals underwent surgical implantation of a cannula into the femoral artery for assessment of arterial pressure and heart rate values. The tail skin temperature was measured as an indirect measurement of sympathetic vasomotor response. Results: Chronic ethanol vapor inhalation reduced basal heart rate in both female and male rats. Sex-related difference was observed in the decrease of tail cutaneous temperature evoked by stress, but not in the pressor and tachycardiac responses. Furthermore, prolonged ethanol inhalation enhanced the blood pressure and heart rate increase caused by acute restraint stress in male, but not in female rats. However, no effect of chronic ethanol vapor was observed in the tail cutaneous temperature response to restraint in both sexes. Conclusion: Chronic ethanol vapor exposure increased the cardiovascular reactivity to stress in male, but not in female rats.
Effect of manual reduction and indirect decompression on thoracolumbar burst fracture: a comparison study
Authors: Huang Jian , Zhou Limin , Yan Zhaodong , Zhou Zongbo , Gou Xuejian 
Published: October 2020

Abstract
Study designRetrospective cohort study.ObjectiveTo evaluate the effect of manual reduction and indirect decompression on thoracolumbar burst fracture.Methods60 patients with thoracolumbar burst fracture who were hospitalized from January 2018 to October 2019 were selected and divided into experimental group (33 cases) and control group (27 cases) according to different treatment methods. The experimental group was treated with manual reduction and indirect decompression, while the control group was not treated with manual reduction. The operation time and intraoperative blood loss were recorded. VAS score was used to evaluate the improvement of pain. The anterior height of injured vertebra, wedge angle of injured vertebral body, encroachment ratio of injured vertebral canal were used to evaluate spinal canal decompression and fracture reduction. JOA score was used to evaluate the improvement of spinal function.ResultsThere was no significant difference in operation time and intraoperative blood loss between the two groups. Compared with the control group, the VAS score and the wedge angle of injured vertebral body of the experimental group on 3 days after operation and the last follow-up were significantly lower than that of the control group, and the difference was statistically significant. The ratio of anterior height of injured vertebra of the experimental group on 3 days after operation and the last follow-up were significantly higher than that of the control group, and the difference was statistically significant. The difference of the encroachment ratio of injured vertebral canal between preoperation and 3 days after operation was significantly higher than that of the control group, and the difference was statistically significant. The bladder function of JOA on 3 days after operation of the experimental group was significantly higher than that of the control group, and the difference was statistically significant. And the rest aspect of JOA on 3 days after operation and last follow-up of the experimental group were no significant difference Compared with the control group.ConclusionManipulative reduction and indirect decompression can obtain better clinical effect in the treatment of thoracolumbar burst fractures.
Naringin Increases Osteoprotegerin Expression in Fibroblasts From Periprosthetic Membrane by the Wnt/β-catenin Signaling Pathway
Authors: Yang Chao , Liu Wei , Zhang Xianlong , Zeng Bingfang , Qian Yebin 
Published: October 2020

Abstract
Background: The osteoclast bone resorption is critical in aseptic loosening after joint replacemrent. The balance between activator of nuclear factor kappa B ligand (RANKL) and osteoprotegerin (OPG) is considered to play a central role in osteoclast maturation. Fibroblasts from the periprosthetic membrane express RANKL and promote osteoclast formation. Studies have demonstrated that naringin inhibited osteoclastogenesis and wear particles-induced osteolysis. In this study, the naringin-induced OPG/RANKL effects and its underlying mechanism were studied in fibroblasts from periprosthetic membrane. Methods: Fibroblasts were isolated from the periprosthetic membrane during hip arthroplasty for revision due to aseptic loosening. Fibroblasts were cultured and treated with or without naringin and DKK-1 (the classical inhibitor of Wnt/β-catenin signaling pathway). OPG and RANKL mRNA and protein levels, gene expression of β-catenin and cyclin D1, which participate in the Wnt signaling pathway, were examined by real-time polymerase chain reaction and enzyme- linked immunosorbent assay. Results: The mRNA and protein levels of OPG were enhanced by naringin in a dose dependent manner compared to that of the non-treated control. In contrast, naringin did not affect the expression of RANKL. Importantly, DKK-1 attenuated OPG expression in fibroblasts under naringin treatment. Moreover, naringin stimulated the gene expression of β-catenin and cyclin D1 in fibroblasts and the effect could be inhibited by DKK-1.Conclusion: The results indicated that naringin enhanced OPG expression through Wnt/β-catenin signaling pathway in fibroblasts from periprosthetic membrane, which may be useful to inhibit periprosthetic osteolysis during aseptic loosening after total joint arthroplasty.