bluuebunny/crossref_metadata_2025_split huggingface dataset:
Differential transcriptome analysis of Dunaliella salina during flagellar assembly
Authors: Zhu Liqiang , Hu Lina , Li Aifang , Li Shuxuan , Li Yalan , Wang Qianqian , Huang Yu , Feng Yanxia , Li Qinghua , Feng Shuying 
Published: December 2022

Abstract
Background
Eukaryotic flagellum is highly conserved in basic structure and biogenesis, and defects in ciliary assembly or function lead to a wide range of human disease symptoms. The alga Dunaliella salina (D. salina), provides an excellent model for investigating flagellar/ciliary system. However, the genomes it carries is unpublished.
Results
In this study, using high-throughput illumina RNA sequencing, the transcriptomes from flagella-assembling D. salina were analyzed firstly at an unprecedented depth. About 4 gigabases of raw sequence data were generated and 197,295 unigenes were annotated with gene descriptions, conserved protein domains, or gene ontology terms against public databases. Among the annotated unigenes, 25,412 unigenes were differentially expressed during flagella regeneration, including 9,988 up-regulated unigenes and 15,407 down-regulated unigenes. Moreover, to functionally categorize the D. salina unigenes, the differentially expressed unigenes distributed into the category of biological process, molecular function and cellular component. These transcriptome datasets might reveal the mechanism of flagella assembly in D. salina cells, and serve as a public information platform for D. salina functional genomics and proteomics analysis. Furthermore, the differentially expressed unigenes involved in different signaling pathways of D. salina flagella assembly and human diseases were screened respectively.
Conclusion
These pathway-based results not only provide a further understanding to specific processes of ciliogenesis and ciliopathies, but also offer a cue to mechanism of human diseases.
Flooding in Freetown's urban coastal settlements: a community-based course of action
Authors: Turay Bashiru 
Published: December 2022

Abstract

The Sierra Leone government and its partners have been working hard to find a solution to the devastating flooding in Portee and Rokupa. However, information for understanding community-based actions in flood containment is limited, particularly at the household and organisation levels of coastal slum settlements. Consequently, there is insufficient knowledge to implement projects to change the current condition. In light of these concerns, this paper aims to present current information on this subject using a mixed methodology, with purposive and snowballing sampling techniques, to investigate 204 slum households and 12 community-based organisations. The findings show that word-of-mouth is the primary source of flood information for most household respondents (53%). This method of disseminating flood news is inefficient and indicates the widespread lack of flood information in the study sites. In their situation, a majority (83.2%) of household respondents and community-based organisations (58%) do not get support for flood management. The author recommends the urgent implementation of a people-centred early warning system. Also, future statistical studies are advised to use correlation and other relevant tests to assess the relationships between household characteristics and the potential to take or not take a particular flood management action. Such studies should look into the relative advantages and disadvantages of these actions. A comparative analysis of flood response and management strategies among the country's various coastal slum settlements is also recommended. Further investigation is required into the feasibility, socio-ecological and economic costs, and opportunities for transforming these slum settlements into modern flood-resistant structures.
A ferroptosis-related lncRNAs signature for prognosis prediction and its relationship with immune microenvironment in colon adenocarcinoma
Authors: Xu Zijie , Chen Yi , Yu Yue , Yu Ting , Wang Yiwen , Chen Tao , Zhu Lingjun , Shu Yongqian 
Published: December 2022

Abstract
Objective
The present study aimed to develop a prognostic ferroptosis-related long noncoding RNAs (lncRNAs) signature and to investigate its potential relationship with clinical characteristics and immune microenvironment in patients with colon adenocarcinoma (COAD).
Methods
Clinical information and RNA sequencing data were downloaded from The Cancer Genome Atlas (TCGA) database. Genes associated with ferroptosis were retrieved from the FerrDb database. Pearson’s correlation analysis was performed for the retrieved data, and differentially expressed ferroptosis-related lncRNAs (frlncRNAs) were screened out. A prognostic frlncRNAs signature was established based on the results of univariate Cox regression analysis and the least absolute shrinkage and selection operator algorithm. Survival analysis and receiver operating characteristic curve analysis were conducted to evaluate the prognostic efficacy of this signature. Gene set enrichment analysis (GSEA), somatic mutation analysis, drug sensitivity analysis, and immune analysis were performed. Quantitative real-time PCR was then used to confirm the expression of lncRNAs, and the regulatory functions of the screened lncRNAs LINC01138 and LINC01857 in ferroptosis were assessed.
Results
Eleven frlncRNAs were identified from the databases. A prognostic signature was constructed, and the risk score was calculated. Patients were classified into high-and low-risk groups according to their risk score. The prognostic signature showed a high efficacy for survival prediction, and the risk score was confirmed as an independent prognostic factor. GSEA showed differences between the two groups in terms of specific pathways involved in immune response, cell adhesion, mitochondrial function, and energy metabolism. Moreover, the high- and low-risk groups showed a significant difference in somatic mutation status such as that of TP53 gene. Patients in the high-risk group exhibited lower half-inhibitory concentration (IC50) values for cisplatin, bleomycin, gefitinib, veliparib, rapamycin, AZD8055, MK-2206, and Bay61-3606 and a higher IC50 value for sorafenib. Immune status and response of the patients to immunotherapy were also associated with the risk signature. The experiments also showed that LINC01138 and LINC01857 regulated ferroptosis processes in COAD.
Conclusion
The prognostic signature of frlncRNAs developed in this study facilitate the clinical diagnosis and treatment of patients with COAD and may enable to study the deeper functional mechanisms of frlncRNAs in immune microenvironment in COAD.
A literature review of methods for assessment of reproducibility in science
Authors: Nordling Torbjörn , Peralta Tomas Melo 
Published: December 2022

Abstract

Introduction: In response to the US Congress petition, the National Academies of Sciences, Engineering, and Medicine investigated the status of reproducibility and replicability in science. A piece of work is reproducible if the same results can be obtained while following the methods under the same conditions and using the same data. Unavailable data, missing code, and unclear or incomplete method descriptions are common reasons for failure to reproduce results. Objectives: The motivation behind this review is to investigate the current methods for reproducibility assessment and analyze their strengths and weaknesses so that we can determine where there is room for improvement. Methods: We followed the PRISMA 2020 standard and conducted a literature review to find the current methods to assess the reproducibility of scientific articles. We made use of three databases for our search: Web of Science, Scopus, and Engineering Village. Our criteria to find relevant articles was to look for methods, algorithms, or techniques to evaluate, assess, or predict reproducibility in science. We discarded methods that were specific to a single study, or that could not be adapted to scientific articles in general.
Results: We found ten articles describing methods to evaluate reproducibility, and classified them as either a prediction market, a survey, a machine learning algorithm, or a numerical method. A prediction market requires participants to bet on the reproducibility of a study. The surveys are simple and straightforward, but their performance has not been assessed rigorously. Two types of machine learning methods have been applied: handpicked features and natural language processing.
Conclusion: While the machine learning methods are promising because they can be scaled to reduce time and cost for researchers, none of the models reviewed achieved an accuracy above 75%. Given the prominence of transformer models for state-of-the-art natural language processing (NLP) tasks, we believe a transformer model can achieve better accuracy.
Epigenetics and Familial Hypercholesterolemia: a methylation study on the three canonical genes
Authors: RA Zorzo , VMM Suen , JE Santos , Silva-Jr  , VK Suazo , ALSC Honorato , RD Santos , CE Jannes , Pereira A , JE Krieger , Liberatore-Jr  
Published: December 2022

Abstract

Familial hypercholesterolemia (FH) is characterized by high low-density lipoprotein cholesterol (LDL-C) levels and a high risk of early coronary heart disease. Structural alterations in theLDLR,APOB, andPCSK9genes were not found in 20–40% of patients diagnosed using the Dutch Lipid Clinic Network (DCLN) criteria. We hypothesized that methylation in canonical genes could explain the origin of the phenotype in these patients. This study included 62 DNA samples from patients with a clinical diagnosis of FH according to the DCLN criteria, who previously tested negative for structural alterations in the canonical genes, and 47 DNA samples from patients with normal blood lipids (control group). All DNA samples were tested for methylation in the CpG islands of the three genes. The prevalence of FH relative to each gene was determined in both groups and the respective prevalence ratios (PRs) were calculated. The methylation analysis ofAPOBandPCSK9was negative in both groups, showing no relationship between methylation in these genes and the FH phenotype. Asthe LDLRgene has two CpG islands, we analyzed each island separately. The analysis ofLDLR-island1 showed PR = 0.982 (CI 0.33–2.95), also suggesting no relationship between methylation and the FH phenotype. Analysis ofLDLR-island2 showed a PR of 4.12 (CI 1.43–11.88), indicating a possible association between methylation on this island and the FH phenotype.
Optimizing the flash extraction process for total flavonoids from Edgeworthia gardneri (Wall) Meissn and antioxidant activity of the extracts
Authors: Ma Xinyu , Zhang Junwei , Liu Jiahao , Zhang Zhongtao , Liu Lu , Tian Jiahui , Guan Jiayu , Lu Zhao , Chen Huiyu 
Published: December 2022

Abstract
In order to efficiently extract natural medicines, response surface methodology (RSM)were used for the modeling and optimization of flash extraction of total flavonoids to determine the antioxidant activity of the extracts obtained from Edgeworthia gardneri (Wall). For the optimal combination of the comprehensive yield of total flavonoids (Y), the Box-Behnken design (BBD) was used to improve extract voltage (X1), extraction time (X2), ethanol concentration (X3), and liquid-solid ratio (X4). Based on the results of single factor test, the amount of total flavonoids extracted from Edgeworthia gardneri (Wall) Meissn was used as the evaluation index. The Box-Behnken experimental design was used to optimize the flash extraction process and to investigate the antioxidant activity in vitro. The results showed that the optimal extraction conditions were as follows: extraction voltage 150 V, flash extraction time 100 s, ethanol volume fraction 70%, solid-liquid ratio 1:30 mL/g, and total flavonoids extraction amount of 18.91 (mg/g). The total flavonoids of Edgeworthia gardneri (Wall) Meissn had significant scavenging ability against 2,2-diphenyl-1-picrylhydrazyl (DPPH), O2- and OH free radicals, and had good antioxidant activity. Furthermore, the HPLC separation conditions of total flavonoids of Edgeworthia gardneri (Wall) were explored. Under the set HPLC conditions (Hanbon benatach C18 250 mm × 4.6 mm, 5 μm, A: acetonitrile-B: 0.2% formic acid aqueous solution, 0→10→50→65→85 min, 5%→10%→30%→45%→90% A gradient elution, 1 mL/min, 314 nm, Column temperature: 25 ℃), the main components of total flavonoids of Edgeworthia gardneri (Wall) could achieve a good separation, which provide the separation conditions and basis for the identification of total flavonoids from Edgeworthia gardneri (Wall) Meissn.
Effectiveness and Safety of Normoxic Allogenic Umbilical Cord Mesenchymal Stem Cells Administered as Adjunctive Treatment in Patients with Severe COVID-19
Authors: Malueka Rusdy Ghazali , Nurudhin Arief , Purwoko Purwoko , Sumardi Sumardi , Wisaksana Rudi , Adhiputri Artrien , Sudadi Sudadi , Soeroto Arto Yuwono , Sidharta Brigitte Rina Aninda , Thobari Jarir At , Murni Tri Wahyu , Soewondo Widiastuti , Herningtyas Elizabeth Henny , Sudjud Reza Widianto , Trisnawati Ika , Ananda Nur Rahmi , Faried Ahmad , Soetjahjo Bintang 
Published: December 2022

Abstract
Inflammatory response in COVID-19 contributes greatly to disease severity. Mesenchymal Stem Cells (MSCs) have the potential to alleviate inflammation and reduce mortality and length of stay in COVID-19 patients. We investigated the safety and effectiveness of normoxic-allogenic umbilical cord (NA-UC)-MSCs as an adjunctive treatment in severe COVID-19 patients. A double-blind, multicentric, randomized, placebo-controlled trial involving severe COVID-19 patients was performed from January–June 2021 in three major hospitals across Java, Indonesia. Eligible participants (n = 42) were randomly assigned to two groups (1:1), namely the intervention (n = 21) and control (n = 21) groups. Either NA-UC-MSCs or NaCl placebo were administered daily. The primary outcome was the duration of hospitalization. Meanwhile, the secondary outcomes were radiographical progression (Brixia score), respiratory and oxygenation parameters, and inflammatory markers, in addition to the safety profile of NA-UC-MSCs. NA-UC-MSC administration did not affect the length of hospital stay of severe COVID-19 patients, nor did it improve the Brixia score or mMRC dyspnoea scale better than placebo. Nevertheless, NA-UC-MSCs led to a better recuperation in oxygenation index (120.80 ± 72.70 baseline vs 309.63 ± 319.30 D + 22, p = 0.038) and oxygen saturation (97.24 ± 4.10% vs 96.19 ± 3.75% in placebo, p = 0.028). Additionally, compared to the placebo group, the treatment group had a significantly smaller increase in PCT level at D + 22 (1.43 vs. 12.76, p = 0.011). No adverse effects, including serious ones, were recorded until D + 91. NA-UC-MSC therapy is a very safe adjunct for COVID-19 patients. It improves the oxygenation profile and carries potential to suppress inflammation.
The Role of Neutrophil - Lymphocyte ratio and Platelet - Lymphocyte ratio with High Sensitivity C-Reactive Protein level in patients on hemodialysis
Authors: Raji Sara , Rad Fatemeh Javadi , Mottaghi Mahdi , Kazerani Marzieh 
Published: December 2022

Abstract
Background: Hemodialysis (HD) is the most common treatment for chronic kidney insufficiency that can increase inflammation and mortality in these patients. We aimed to compare the relationship of neutrophil-lymphocyte ratio (NLR) and platelet-lymphocyte ratio (PLR) with high sensitivity C-reactive protein (hs-CRP) levels in predicting inflammatory conditions in HD patients.
Methods: This cross-sectional study included end-stage renal disease (ESRD) patients on regular HD in the Islamic Republic of Iran. Based on patients’ records, demographic and clinical data, and inflammatory markers, including NLR, PLR, and hs-CRP, were obtained.
Results: One hundred patients were enrolled, of which 46% were female. The mean age was 37.96 ± 10.29, and the mean HD time was 54.32 ± 50 months. The mean hs-CRP levels, NLR, and PLR were 6.08 ± 5.70mg/l, 2.79 ± 1.18, and 125.80 ± 57.14, respectively. Our results showed a statistically significant and direct relationship between PLR and hs-CRP levels (P = 0.01) but no correlation between NLR and hs-CRP levels (P = 0.8). In addition, PLR was correlated inversely with hs-CRP in hypertensive patients (r = -0.283, P = 0.04) and had significant relationships in the female population (r = 0.3, P = 0.04) and time of HD below five years (r = 0.3, P = 0.001).
PLR is a suitable and inexpensive inflammatory marker in HD patients with ESRD, correlating with hs-CRP. Further investigations emphasizing accuracy establishment are mandated to certify its application in clinical workups.
Differences and biocontrol potential of haustorial endophytic fungi from Taxillus Chinensis on different host plants
Authors: Song Li-sha , Huo Juan , Wan Lingyun , Pan Limei , Jiang Ni , Fu Jine , Wei Shugen , He Lili 
Published: December 2022

Abstract
Background
In order to explore the community composition and diversity of the endophytic fungi in Taxillus chinensis, samples of the parasites growing on seven different hosts, Morus alba, Prunus salicina, Phellodendron chinense, Bauhinia purpurea, Dalbergia odorifera, Diospyros kaki and Dimocarpus longan, were isolated. The strains were identified by their morphological characteristics and their internal transcribed spacer (ITS) sequences were analyzed.
Results
150 different endophytic fungi were isolated from the haustorial roots of the seven hosts, and the total isolation rate was 61.24%. These were found to belong to 1 phylum, 2 classes, 7 orders, 9 families, 11 genera and 8 species. Pestalotiopsis, Neopestalotiopsis and Diaporthe were the dominant genera, accounting for 26.67, 17.33 and 31.33% of the total number of strains, respectively. Diversity and similarity analyses showed that the endophytic fungi isolated from D. longan (H'=1.60) had the highest diversity index. The highest richness indexes were found in M. alba and D. odorifera (both 2.23). The evenness index of D. longan was the highest (0.82). The similarity coefficient of D. odorifera was the most similar to D. longan and M. alba (33.33%), while the similarity coefficient of P. chinense was the lowest (7.69%) with M. alba and D. odorifera. Nine strains showed antimicrobial activities. Among them, Pestalotiopsis sp., N. parvum and H. investiens showed significant antifungal activity against three fungal phytopathogens of medicinal plants. At the same time, the crude extracts from the metabolites of the three endophytic fungi had strong inhibitory effect on the three pathogens. Pestalotiopsis sp., N. parvum and H. investiens had the strongest inhibitory effects of S. cucurbitacearum, with inhibitory rates of 100%, 100% and 81.51%, respectively. Secondly, N. parvum had a strong inhibitory effect on D. glomerata and C. cassicola, with inhibitory rates of 82.35% and 72.80%, respectively.
Conclusions
These results indicate that the species composition and diversity of endophytic fungi in the branches of T. chinensis were varied in the different hosts and showed good antimicrobial potential in the control of plant pathogens.
WITHDRAWN: Prediction of fruit quality parameters using peel color in Citrus Reticulata L. fruit by multiple linear regression and artificial neural network approach
Authors: Ghanghas Sachin , Singh Vijay Kumar , Kumar Sunil , Kumar Nitin , Garg Mukesh Kumar 
Published: December 2022

Abstract
Kinnow mandarin fruit color changes from deep green to completely orange during the period of peak maturity, which indicates if the fruit should be harvested. On the basis of the peel color, fifteen fruits were being selected for harvest, and their colors were measured with the chromameter which measures color in CIE-Lab color space. Green to Orange color fruits were divided into five regions (Green, Green-Yellow, Yellow, Yellow-Orange, Orange). The fruit samples in triplicate were used for all the laboratory analysis. The effects of color parameters i.e. L-value, a-value and b-value in different color regions on chemical parameters i.e. total soluble solids (TSS), titratable acidity (TA), fruit juice content (Juice %), maturity index (MI), ascorbic acid content (AA) and pH value of the fruit were studied using descriptive and correlation analysis. The model approaches i.e. multiple linear regression (MLR) and artificial neural network (multi-layer perceptron) (MLP-ANN) were implemented on the fruit sample data to predict the important fruit quality parameters which were prominent in determining the fruit color. The predicted data was plotted against the actual data using boxplot and scatter plot for both the models, the linearly best fitted and statistical significance was determined using R2, RMSE. Green and Green-Yellow colored region fruits have high in titratable acidity, ascorbic acid content and lower soluble sugars, maturity index and pH value. There was a steeper transition visible in TSS, juice content, maturity index, AA and pH value for the color shift from Yellow region to Yellow-Orange region. The better and optimal predictions were made with MLP-ANN for total soluble solids, titratable acidity and fruit juice content. The ANN model could be used in future for prediction of maturity indices of kinnow fruit in different maturity regions as per the consumer and market preferences.
The Low expression of PAI-1 increasing MC3T3-E1 cell proliferation by promoting glucose metabolism and activating BMP/TGF-β/Smad and Wnt/β-catenin pathways: a downstream regulatory role of PAI-1 in osteoblasts
Authors: aikebaier aobulikasimu , Chen Hongtao , Jiang Luoyong , zhuang Qianzheng , You Wei , Zhai Rihong , Sun Wei 
Published: December 2022

AbstractPAI-1 is a marker of aging and a mediator of aging induction. Our previous study showed that PAI-1 is highly expressed in bone tissues of osteoporosis patients. Gavage of osteoporosis model mice with PAI-1 inhibitor resulted in increased Osteoblasts and bone mineral density. Inhibition of PAI-1 expression in MC3T3-E1 cells found that the altered transcription factors were mainly enriched in zf-C2H2 (12.38%) and HMG (10.48%), and Zinc finger related proteins were significantly increased in the differential proteins. Transcription factors use the energy provided by ATP to regulate the transcription and translation of downstream genes. The low expression of PAI-1 in MC3T3-E1 cells promotes ATP synthesis, cell cycle progression through cellular ATP binding and cellular metabolic process, and as a result, Osteoblast proliferation. Runx1 is expressed at different stages of Chondrocyte and Osteoblast differentiation and promotes Chondrogenesis by regulating the BMP/TGF-β/Smad and Wnt/β-catenin signaling pathways. The low expression of PAI-1 in MC3T3-E1 cells promotes Runx1 expression. This may imply that the low expression of PAI-1 may promote Osteoblast proliferation by activating the BMP/TGF-β/Smad and Wnt/β-catenin pathways by Runx1.