bluuebunny/crossref_metadata_2025_split huggingface dataset:
Irreversible Alteration of Extracellular Vesicle and Cell-Free Messenger RNA Profiles in Human Plasma Associated With Ex Vivo Platelet Activation
Authors: Kim Hyun Ji , Rames Matthew , Yunga Samuel Tassi , Armstrong Randall , Morita Mayu , Ngo Anh , McCarty Owen , Civitci Fehmi , Morgan Terry , Ngo Thuy 
Published: January 2021

Abstract
The discovery and utility of clinically relevant circulating biomarkers depend on standardized methods that minimize preanalytical errors. Here, we examined the preanalytical variations of extracellular vesicles (EVs) and cell-free mRNA (cf-mRNA) profiles in human plasma and how post-freeze/thaw processing removes and retains EVs and cf-mRNA subtypes. Using multiparametric nanoscale flow cytometric analysis, which utilized forward light scatter, side scatter, and fluorescence intensity, we characterized the effect of specific preanalytical variables on vesicle subpopulations in human plasma. Cf-mRNA levels were measured by multiplexed RT-qPCR with a panel including housekeeping, platelet, and tissue-specific genes. We found that blood processing centrifugation and temperature strongly impacted the levels of residual platelets and platelet microvesicles. Intriguingly, exosome-sized events were more resistant to processing methods. We also examined the morphology of quiescent and activated platelets and platelet-derived EVs by electron microscopy. We demonstrated that platelet activation and fragmentation generated ex vivo vesicles similar to EVs in size, morphology, and canonical surface markers. Critically, freezing plasma containing residual platelets yielded irreversible ex vivo generation of new EV subpopulations and cf-mRNA transcripts, which were not removable by additional processing after freeze-thaw. In summary, we identified distinct subpopulations of EVs and cf-mRNA in human plasma that are differentially influenced by platelet activation and fragmentation during sample collection, processing, and banking via post freeze/thaw processing.
Transcriptomic and genomic analysis highlights the basis of ZYMV tolerance in zucchini
Authors: Amoroso Ciro , Andolfo Giuseppe , Capuozzo Claudio , Donato Antimo Di , Martinez Cecilia , Tomassoli Laura , Ercolano Maria 
Published: January 2021

Abstract
Background: Cucurbita pepo is high susceptible to Zucchini yellow mosaic virus (ZYMV) and the resistance found in several wild species does not provide complete or broad-spectrum resistance. In this study, a source of tolerance introgressed in C. pepo (381e) from C. moschata, in True French (TF) background, was investigated 12 days post inoculation (DPI) at transcriptomic and genomic levels. Results: A comparative RNA-seq experiment on TF (susceptible to ZYMV) and 381e (tolerant to ZYMV), allowed to evaluate 33,000 expressed transcripts and to identify 146 differentially expressed genes (DEGs) in 381e, mainly involved in photosynthesis, transcription, cytoskeleton organization and callose synthesis. By contrast, the susceptible line True French triggered oxidative processes related to response to biotic stimulus, and key regulators of plant virus intercellular movement. Moreover, the genome mapping of transcripts allowed the identification of two chromosome regions rich in SNPs (Single Nucleotide Polymorphisms), putatively introgressed from C. moschata, containing genes exclusively expressed in 381e. Conclusion: The transcriptome reprogramming of 381e ZYMV challenged revealed a globally restoring of cellular activities and a reduced virus movement and replication. Furthermore, genes putatively involved in ZYMV tolerance were detected in C. moschata introgressed genomic regions. Our work provides new insight into the plant virus recovery process and a better understanding of the molecular basis of 381e tolerance.
The information provided at the antenatal clinic regarding foetal diagnostics -how is it perceived? A qualitative interview study
Authors: Carlsson Ylva , Strömbäck Pernilla , Lundgren Ingela 
Published: January 2021

Abstract
Background: Prenatal testing is voluntary and should be offered to all pregnant women in combination with sufficient information. Earlier studies have shown that pregnant women often felt the information given at the antenatal clinics about foetal diagnostics was lacking. Since new methods in foetal diagnostics are introduced into routine health care, there is an increased need for adequate information. The aim of this study was to examine how pregnant women and their partners perceive the information given at the antenatal clinic regarding foetal diagnostics, as well as to increase the understanding of how this information can be improved.Methods: A qualitative interview study was conducted in the Gothenburg area in Sweden. Ten women and seven partners expecting their first child were interviewed. The data was analysed using content analysis with an inductive approach.Results: The interview data generated three main categories and ten subcategories. The first category, ‘Diversity in the information perceived,’ concerned differences in the level of information perceived regarding voluntariness, the methods’ purpose and the possibility of abnormal findings. The second category, ‘Varying needs related to improved information,’ concerned the parents’ needs related to thorough information and pre-existing knowledge. The third category, ‘The midwife has a great impact on the information perceived,’ concerned sufficient and insufficient susceptibility and time to ask questions as well as varying experiences of the midwife’s attitude. Conclusions: Although previous research have already pointed out that information regarding foetal diagnostics is lacking, this study shows that there is still room for improvement. This is even more urgent now with new methods being introduced, which can make choices concerning foetal diagnostics even more complicated for the pregnant woman. The given information should be explicit concerning purpose, limitations and the voluntariness of prenatal testing. Sufficient time for questions and discussion was important to many who were interviewed. The diversity in answers among the participants in the study highlights the importance of considering the level of the parents’ pre-existing knowledge and their individual thoughts and questions and that it is important to adapt the information to the individual woman and partner.
A Novel Missense Mutation in NALCN Cause CLIFAHDD Syndrome and Prenatal Diagnosis in China
Authors: Li Yuping , Zhou Chenglong , Chen Yangran , shi Haihong , Chen Qiang , Li Ning , Zeng Qinlong , Hong Yan , Li Qing , Deng Choufen , Zhou Feng , Tan Jieliang , Yang Mei , Li Qiuli , Yang Yingsong , Feng Jianjiang , Sun Shuxiang , Tang Ziqian , Luo Liangping , Tang Jia 
Published: January 2021

Abstract
Background: CLIFAHDD is caused by mutation in NALCN and characterized by facial malformation, hypotonia, and developmental delay. Recently rare mutations in NALCN associated with of CLIFAHDD syndrome have been reported. Methods: Whole exome sequencing (WES) was applied to a diagnosis suspected CLIFAHDD syndrome proband based on clinical symptoms. Blood samples were taken from the parents of the proband for co-segregation analysis using Sanger sequencing. In addition, prenatal gene diagnosis was performed to the family. Finally bioinformatics analysis was utilized to predict the pathogenesis of novel variant. Result: We reported a 24-hour-old proband with a novel missense variant c.3016G>T (p.Val1006Phe) in NALCN by WES. The proband showed clinical symptoms of head abnormalities, neck shortage, thumbs adduction, positional foot deformities and elbows contracture. Prenatal diagnosis revealed that the proband’s sibling did not carry c.3016G>T. Conclusion: Our findings indicate c.3016G>T is a novel pathogenic mutation, while extending new phenotype CLIFAHDD syndrome and enriching the mutation spectrum of the NALCN gene.
Annotations of Recurrent Structural Variant Events in Pan-cancer Whole Genome Data for Precision Medicine
Authors: Koyama Takahiko , Hasegawa Takanori , Kasajima Rika , Shimizu Eigo , Tokumasu Reitaro , Yokoyama Kazuaki , Yamaguchi Kiyoshi , Tojo Arinobu , Furukawa Yoichi , Weeraratne Dilhan , Willis Van , Snowdon Jane , Nakagawa Hidewaki , Miyano Satoru , Parida Laxmi , Yamaguchi Rui , Imoto Seiya 
Published: January 2021

Abstract
In personalized cancer genomic medicine, characterizing a patient’s molecular profile based on comprehensive information is important for maximizing treatment benefits. However, current cancer genome analysis is centered on single nucleotide variation (SNV), gene expression, and copy number variation (CNV) but places little emphasis on structural variations (SV) beside fusions. To date, investigation of SVs has been limited because SV analysis entails a cumbersome annotation process. This study describes the design, development, and implementation of an annotation tool for SV, termed SVAnnotator. Detailed annotation was performed on the results of SV detection of 2,781 whole genome samples from the ICGC/TCGA PanCancer Analysis of Whole Genomes (PCAWG) with identifications of fusion, exon skipping, gene disruption, and tandem duplication SVs. These annotations of SVs will facilitate understanding of molecular events and further enhance utilities of precision medicine in stratifications, pathogenicity assessments and drug responses. Frequent novel SV events in MACROD2, FHIT, WWOX and CCSER1 were observed across many cancers. Importantly, SV events were frequently identified in well-established tumor suppressor genes including RB1, NF1, PTEN and TP53. As such, it is plausible that potential therapeutic opportunities are overlooked when SV analysis is not appropriately performed. Given the frequency of SVs detected in our study, SVanalysis with detailed annotation should be a routine part of comprehensive precision medicine analysis, and further studies are warranted to enhance clinical benefits as well as our understanding of uncharacterized SV events.
Association Between Serum Procalcitonin Levels and Disseminated Intravascular Coagulation in Patients With Septic Shock
Authors: Fu Guang , He Xi-si , Cao Xiao-peng , Li Hao-li , Zhan Hai-chao , Lu Jun-fu , Chen Yan-hong , Yang Zi-Long , Huang Jia-jia , Zhou Zhi-peng , Feng Yong-wen , Luan Ying-yi , Wu Ming 
Published: January 2021

Abstract
Objectives: To investigated the relationships between procalcitonin (PCT) and disseminated intravascular coagulation (DIC) during septic shock. Methods: A retrospective study was performed, which included septic shock patients admitted into intensive care unit (ICU) from January 1, 2015 to December 31, 2018. DIC was defined as international society of thrombosis and homeostasis criteria (ISTH≥5). PCT was based on the first value after admission into ICU and the routine biochemical coagulation data based on the worst value extracted from electronic medical records within 24 hours on admission into ICU.Results: Among 2156 patients screened, 164 patients with septic shock were included in the finally analysis and 35.4% (58/164) of whom developed DIC after admission. PCT level was significantly higher in septic shock patients who developed DIC than those who did not (54.6[13.6-200] vs12.6[2.4-53.3] ng/ml, P <0.001). Multivariable logistic regression revealed that PCT (OR=1.011, 95% CI 1.006- 1.016, P<0.001) was associated with DIC during septic shock. Curve fitting showed a positive correlation between PCT and DIC. The Receiver Operating characteristic (ROC) curve suggested that the cut-off point for PCT to predict DIC during septic shock was 42.1ng/ml, with sensitivity 60.34%, specificity72.74% and the area under the curve (AUC) 0.701(95% CI [0.619-0.784], P<0.001). Interestingly, PCT increased early detection of DIC during septic shock compared with other risk factors(P=0.012)Conclusions: Our data suggest that PCT level over 42.1ng/ml on admission is associated with DIC during septic shock, and PCT is a potential predictive factor of DIC induced by septic shock at early stage.
The Role of Early Growth Response 1 in the Prognostic Value and Cell Migration of Breast Cancer
Authors: Hao Leiyu , Huang Fengru , Yu Xinqian , Xu Bujie , Liu Yan , Zhang Yan , Zhu Yichao 
Published: January 2021

Abstract
Background: Early growth response family members (EGRs), EGR1-4, have increasingly attracted attention in multiple cancers. However, the exact expression patterns and prognostic values of EGRs in the progress of breast cancer (BRCA) remain largely unknown. Methods: The mRNA expression and prognostic characteristics of EGRs were examined by the Cancer Genome Atlas (TCGA), Oncomine and Kaplan-Meier plotter. Enrichment analyses were conducted based on protein-protein interaction (PPI) network. The Tumor Immune Estimation Resource (TIMER) database and MethSurv were further explored. The protein expression level of EGR1 and cell migration were measured by Western blotting, immunohistochemistry, wound-healing assay and Boyden chamber assay in BRCA. Results: The transcriptional levels of EGR1/2/3 displayed significantly low expression in BRCA compared to that in normal tissues, while EGR4 was shown adverse expression pattern. Survival analysis revealed up-regulated EGR1-4 were remarkably associated with favorable relapse-free survival (RFS). A close correlation with specific tumor-infiltrating immune cells (TIICs) and several CpG sites of EGRs were exhibited. Immunohistochemistry assays showed that the protein expression of EGR1 was remarkably downregulated in BRCA compared to that in paracancerous tissues. Cell migration of MCF10A cells was increased after the silence of EGR1 by siRNA transfection.Conclusions: This study provides a novel insight to the role of EGR1 in the prognostic value and cell migration of BRCA.
Value added and Profitability analysis of bamboo products in case of Banja district Awi zone Amhara regional state Ethiopia
Authors: Mengistu Mulat , Alemu Asmamaw , Dagnew Abebe 
Published: January 2021

Abstract
Background

Bamboo meets a rising and diverse consumer demands and generates income and contribute to reforestation and climate change mitigation due to its rapid growth and environmentally friendly character. Most bamboo processing enterprises and farmer and consumers use manual technology and produce less durable products. Since there is no research conducted in the area related to profitability of different bamboo products and the distribution of value added Therefore, this study aims to analyse the profitability of bamboo products for producers, traders and processors in the same way it analyses the value added distribution among different agents.
Methods

To collect primary data 122 smallholder bamboo producers, 13 traders and 16 bamboo product processors were selected. To analyse the data descriptive statistics were employed.
Results

On average producers supply 374.79 bamboo culms and earn revenue of 7,623.23 ETB. The total value added at the producer level was 15.64 ETB per culm. On average local traders, retailers and wholesalers earn 7.52%, 9.51% and 9.23% of profit Margin and these traders earn average revenue of 66,420 ETB, 129,360ETB and 280,343 ETB respectively. Traditional bamboo product processors produce 687 traditional bamboo chairs on average per year and gained 3.06 ETB/culm as a net profit. Bamboo furniture enterprises on average process 823 modern bamboo chair per year and they earn 197.91 ETB per chair as a net profit. Higher value is added at bamboo furniture enterprise level and lower value is added at producer and trader level.
Conclusion

The result of the study revealed that all actors have positive profit and value is added by different chain actors and distributed to different agents. Bamboo furniture enterprises gained higher profit margin than traditional bamboo processors. The contribution of the bamboo sector to the government economy is limited. Based on the finding of the study, an effort should be made to increase the contribution of the sector to the national economy. In addition to this, providing working capital and working place and enhancing the processors’ skill and capacity to transform the business into more modern and profitable bamboo furniture enterprise is advisable.
WITHDRAWN: Highly Efficient Magnetic Phosphoric Acid Modified Defatted Chlorella Vulgaris Algae ( MDCV/Fe3O4)&nbsp;as a Novel Biosorbent for Methylene Blue Removal
Authors: Salehi Zeinab , Naziri Sahar 
Published: January 2021

Abstract
Background:A novel biosorbent based on defatted Chlorella vulgaris (DCV) as a by-product of the biofuel industry was considered as an economical and inexpensive biosorbent in the form of magnetic modified defatted Chlorella vulgaris (MDCV/Fe3O4) for methylene blue (MB) removal. The lipid extraction was performed on raw Chlorella vulgaris (RCV). Phosphoric acid was selected as a DCV modifier. During acid modification, the variables affecting the biosorption capacity and the residual algae such as temperature (30-70 ), the contact time of DCV with acid (3-9 hr), the concentration of acid (2-6 mol/L), and the ratio of acid volume to DCV (30-70 mL/g) were investigated and optimized using Minitab-18 software. The modified defatted Chlorella vulgaris (MDCV) was prepared by acidification of DCV under optimal conditions. MDCV/ was prepared using the co-precipitation method for easy and low-cost separation of biosorbent. The XRD, FTIR, SEM, EDS, BET, and VSM analyses were performed to identify the structures and characteristics of RCV, DCV, MDCV, and MDCV/. Some experimentsere designed using Minitab-18 software to investigate the effects of temperature (5-45 ), contact time (30-90 min), biosorbent dosage (15-45 mg), initial concentration of MB (20-100 mg/L), and pH (5-9) on the biosorption capacity of MDCV/. The kinetic, isothermal and thermodynamic parameters were investigated on MDCV/.Results:The specific surface area of MDCV/ was 25.20 . RCV, DCV, and MDCV/ had a crystalline structure and MDCV had an amorphous structure. The data were most consistent with Pseudo-second-order and Freundlich models. The maximum biosorption capacity of MDCV/ was calculated in the amount of 32.44‌ mg/g. According to the positive values of and negative values of (-46.56 kJ/mol) and (-0.17 kJ/mol.K), the biosorption of MB on MDCV/ was non-spontaneous, exothermic with a decrease in irregularity.Conclusions:In this study, MDCV/ was applied as the MB biosorbent. Modifications such as lipid extraction, phosphoric acid modification and magnetization improved this biosorbent in its biosorption capacity and separation. Data were optimized in the acid modification and MB biosorption steps. Comparison of the characteristics of MDCV/ with unmodified species confirmed its high efficiency. Kinetic, isothermal and thermodynamic studies were also performed.
Different Timings of Early Cumulus Cells Removal Have Different Multiple Pronuclei Rates in Human in Vitro Fertilization
Authors: Liu Zhiren , Liu Qicai , Jiang Mingting , Chen Xingting , Lin Chen , Guo Yujia 
Published: January 2021

Abstract
Background: Cumulus cells removal 4 h post-insemination has a significantly higher multiple pronuclei (MPN) rate than cumulus cells removal 20 h post-insemination. And, cumulus cells removal 6 h post-insemination has a significantly lower MPN rate than cumulus cells removal 20 h post-insemination. However, it remains unclear whether the different timings of early cumulus cells removal, such as the timings of 4, 5 and 6 h post-insemination, have significantly different MPN rates.Methods: This was a retrospective study. The included cycles were early cumulus cells removal cycles (n=752) at our center from January 2015 to August 2020. The included cycles were divided into two groups according to whether MPN exist (MPN=0% and MPN>0%). The patient and cycle stimulation characteristics of the two groups were compared. Binary logistic regression was performed to investigate the correlation between the timing of early cumulus cells removal and MPN. The cohort study was also performed to compare the patient characteristics, cycle stimulation characteristics, fertilization outcomes, and cultivation outcomes.Results: In the population of our study, the timing of early cumulus cells removal had a significant effect on the MPN. The cumulus cells removal ≤4 h post-insemination group had a high MPN rate, and the 5.5<time≤6 h group had a high fertilization failure rate. However, 2PN rate was not significantly different among the different timings of early cumulus cells removal. In addition, the ≤4 h post-insemination group had a high grade 1–2 embryo rate at day 3.Conclusion(s): Even if all the timings of cumulus cells removal are early, the different timings of early cumulus cells removal still have a significant effect on the MPN.
Implementing Cloud Radio Access on a Multi-Core System
Authors: Gerai V. , Krishnamurty T.S. , Chakraborty K.L. 
Published: January 2021

Abstract
In this article, we propose the implementation of a Cloud Radio Access Network (C-RAN) on a multicore unified device that facilitates the processing of multiple distributed antennas in the base band. In order to decrease their runtime, we present a parallel processing model based on both functional and data decomposition of virtualized Base Band Unit (BBU) functions. We are investigating two parallel running BBU work scheduling techniques, where computational resources can be distributed by user equipment (UE) or by code blocks (CB). We implement a batch queuing model by using data obtained while running an open source RAN code to determine the necessary processing power in a data center while following tight latency criteria in the downlink and uplink directions. When processing a hundred LTE-cells in a multicore device, the proposed model is validated by simulation. The findings provide useful advice on the sizing and implementation of Cloud-RAN applications such as cryptography [9].