bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transcriptome analysis of the lncRNAs and their mRNA networks associated with multiple myeloma
Authors: Yan Yan , wang Jiehao , Hu Yuhan , Du Jianwei , Gao Xue , Lyv Xiaodong , Zuo Wenli , Li Yufu , Song Yongping , Lin Quande 
Published: April 2022

Abstract
BackgroundTo study the lncRNA-mRNA interaction network structure and analyze the possible target mRNAs among the differentially expressed lncRNAs between healthy adults, newly diagnosed multiple myeloma patients, and refractory relapsed multiple myeloma patients.MethodsPublic sequence data files were downloaded from the Sequence Read Archive (SRA). Totally 23 RNA-seq samples (GSE110486) related to myeloma published in 2018 (including transcriptome data of bone marrow plasma cells from healthy adults, newly diagnosed multiple myeloma patients and recurrent patients) were acquired, further analyses of differential lncRNAs, lncRNAs-mRNA co-expression, and WGCNA expression module and cis regulatory gene were performed. In addition, we performed differential expression analysis of lncRNAs and enrichment analysis of target mRNA regulated by lncRNAs from multiple myeloma patients and healthy controls which in order to verify the functions of these lncRNAs and their target mRNAs.ResultsFrom the transcriptional samples in this study,1006 new lncRNAs were identified, which including 707 lncRNAs specifically up-regulated and 283 specifically down-regulated in relapsed myeloma. The mRNA genes co-expressed with specific lncRNAs in relapsed multiple myeloma were mainly enriched in the extracellular matrix organization, platelet activation, cell adhesion, inflammation response, T cell co-stimulation and immune response pathways. Target mRNA regulated by DE lncRNAs including IL23R, ELF3, IL32, TMIGD2, CD28, CD5, TNF, CX3CR1, ADAMTS20 etc, by GO analysis, these target genes were enriched into many biological processes, such as innate immunity, apoptosis and positive regulation of apoptosis. The cis-regulated lncRNA of these target mRNAs include U62631.5, XLOC_062939 and XLOC_027240, and their cis-regulatory targets include CD22, SSX1 and DCC. lncRNAs and enrichment analysis of target mRNA regulated by lncRNAs from multiple myeloma patients and healthy controls was consistent with the previous analysis.ConclusionTarget mRNAs regulated by DE lncRNAs and their cis-regulatory targets are involved in the immune cells remodeling of gene expression patterns during multiple myeloma relapse, and may have an important function in this pathological process, it deserves further study as a potential target for the treatment of multiple myeloma.
Development and validation of novel SSR markers using transcriptome data in okra (Abelmoschus esculentus L.)- A genetically orphan crop
Authors: V Puneeth P. , Yadav Ramesh Kumar , Lata Suman , Iquebal Mir Asif , Tomar B. S. , Choudhary H. , Tomer Avinash , Sharma Parva Kumar , Jaiswal Sarika 
Published: April 2022

Abstract
Background Okra is an important vegetable crop of the Malvaceae family grown for its tender pods. Unknown genome size, polyploidy and lack of sufficient molecular markers hindering the genetic improvement of okra. Molecular markers are imperative for marker assisted breeding programs. Genic SSR markers are the best DNA markers because of codominant inheritance and transferability across the species. Genomic tools like RNA- seq. for transcriptome analysis is a powerful tool to identify novel transcript or gene sequences in non-model plants like okra. In the present investigation, we have performed transcriptome sequencing of the okra leaf samples and identified EST-SSR markers.Methods and results In this study, EST-SSRs from okra transcriptome were mined and characterized to validate their use as genic microsatellite markers in diversity analysis. Out of the total (106224) EST-SSRs, 6913 were in compound formation and were not used for validation. Mononucleotide repeats were dominant with a frequency of 72.20% (71699) followed by trinucleotide 15% (14897) and dinucleotide 10.68%, (10604) repeats. In total, 183 primer pairs (156 di and 27 trinucleotides) were selected randomly for PCR using 12 Abelomoschus genotypes comprising of wild and cultivated species. Overall, 163 pairs produced expected PCR amplicons and the amplification efficiency was 89%. 23 pairs showed polymorphism accounting for 14.1% with an average value of 0.32 polymorphic information content. The identified markers were highly polymorphic for 12 genotypes. The UPGMA dendrogram analysis separated the okra genotypes into two main clusters.Conclusions This study provided insight into the distribution and frequency of EST-SSRs in the okra transcriptome. It demonstrated the successful employment of genic SSRs in okra diversity analysis. The markers developed in this study has potential application in the marker assisted breeding programs and genetic diversity analysis of okra germplasm. We expect the potential markers validated here will enrich the DNA markers repertoire for breeding and genetic studies in Abelomoschus sp.
Knowledge, attitude, and practice regarding oral health among college students in Eastern China
Authors: Li Wenhao , Yin Nan , Zhang Yanyong , Zhou Haoyun , Ge Hui , Ding Wei , Zhang Wei , Zhang Shunhua , Liao Shengkai 
Published: April 2022

Abstract
Background: People are increasingly concerned about the impact of oral health on the whole. College students represent the future trend of oral health in China. The purpose of this study was to investigate the status, influencing factors and differences in oral health knowledge, attitude, practice (KAP) between dental and non-dental students in Anhui Province, Eastern China. Methods: A cross-sectional survey was conducted on 1,822 college students in Anhui Province. The Mann-Whitney test and the Kruskal-Wallis test were used to test for differences in oral health KAP scores by different demographic factors and lifestyle habits. The Spearman test was used to determine the association between oral health knowledge, attitude and practice. The Person chi-square test was used to analyse the differences in oral health KAP between dental students and non-dental students. Results: The oral health KAP scores of dental, medical, and non-medical college students in Anhui Province decreased in the order. Gender, age, major, grade, place of birth, parents’ education, annual household income, and smoking status all had a difference on oral health KAP scores among college students. Positive correlations existed between oral health knowledge, attitude, and practice. Dental students had a better overall oral health KAP than non-dental students. Conclusions: The oral health knowledge and attitude of college students in Anhui Province were generally good. However, oral health practice was unsatisfactory. Our study has implications for targeted improvement of factors influencing oral health KAP.
Frontline therapy CLL without 17p del/p53 aberrations: systematic review and Bayesian network meta-analysis
Authors: Caridà Giulio , Pelaia Giulia , Ciliberto Domenico , Staropoli Nicoletta , Siciliano Maria Anna , Calandruccio Natale Daniele , Caracciolo Daniele , Riillo Caterina , Toscano Rosa , Tagliaferri Pierosandro , Tassone Pierfrancesco , Rossi Marco 
Published: April 2022

Abstract
Background. Chronic Lymphocytic Leukemia (CLL) is the most common adult leukemia. IgVh unmutated CLL without 17p del/p53 aberrations (UN-only CLL) still carry a poorer prognosis as compared to IgVh mutated (MU-only) cases. The best front line and sequencing treatment stratified by efficacy and tolerability for UN/MU-only CLL remains to be defined.Methods. A systematic review of frontline therapies was performed to conduct a Bayesian Network Meta-Analysis (NMA) and rank multiple treatments for PFS, ORR, MRD and Tolerability. Results. We built four different NMAs for the prespecified outcomes. Treatments included immunochemotherapy regimens, target agents [Acalabrutinib (ACA), Ibrutinib (IBR), Lenalidomide, Venetoclax (VEN)] w/without Rituximab (R)/Obinotuzumab (O). ACA-O scored the best result in PFS in unselected and UN/MU-only (SUCRA 100%). VEN-O ranked first for ORR (SUCRA value 100%) and MRD (SUCRA 90.4%), followed by VEN-O-IBR (SUCRA 84.0%) with no statistical difference between them (Odds Ratio 1.44, CrI 0.00,563.57). ACA monotherapy was the most tolerated therapy (SUCRA value 100%), IBR-O the most toxic treatment (SUCRA value 0%). IBR monotherapy ranked the 9th position in the network. Combination regimens including Obinotuzumab were weighted by high risk of toxicity.Conclusions. We compared PFS, tolerability, ORR and MRD in a consistent number of RCTs. ACA-O was the best treatment for PFS in MU/UN-only. ACA was equally efficacious in UN-only and the most tolerated regimen. VEN-O/BTKis-O regimens achieved the best positions, but with a higher toxicity profile. ACA-O turned to be the best treatment for prolonging the PFS in untreated, UN/MU-only CLL patients.
Composition tunability of semiconductor radiosensitizers for low-dose X-ray induced photodynamic therapy
Authors: Chen Lei , Zhang Jinghui , Zhu Luchao , Xu Lihua , Jing Jinpeng , Feng Yushuo , Wang Zongzhang , Liu Peifei , Sun Wenjing , Liu Xiangmei , Li Yimin , Chen Hongmin 
Published: April 2022

Abstract
Radiation therapy is one of the most commonly used methods in clinical cancer treatment, and radiosensitizers could achieve enhanced therapeutic efficacy by incorporating heavy elements into structures. However, the secondary excitation of these high-Z elements-doped nanosensitizers still imply intrinsic defects of low efficiency. Herein, we designed Bi-doped titanium dioxide nanosensitizers in which high-Z Bi ions with adjustable valence state (Bi3+ or Bi4+) replaced some positions of Ti4+ of anatase TiO2, increasing both X-rays absorption and oxygen vacancies. The as-prepared TiO2:Bi nanosensitizers indicated high ionizing radiation energy-transfer efficiency and photocatalytic activity, resulting in efficient electron-hole pair separation and reactive oxygen species production. After further modification with cancer cell targeting peptide, the obtained nanoplatform demonstrated good performance in U87MG cell uptakes and intracellular radicals-generation, severely damaging the vital subcellular organs of U87MG cells, such as mitochondrion, membrane lipid, and nuclei etc. These combined therapeutic actions mediated by the composition-tunable nanosensitizers significantly inhibited the U87MG tumor growth, providing a refreshing strategy for X-ray induced dynamic therapy of malignant tumors.
Effects of separated and combined amaranth, quinoa and chia flours on the characteristics of gluten-free bread with different concentrations of hydrocolloids
Authors: Alsaiqali Ahmed , Dizlek Halef , Özer Mehmet Sertaç 
Published: April 2022

Abstract
Rice and corn flour/starch are frequently used in producing gluten-free products which are usually characterized with high starch and low fiber content, poor texture, insufficient volume, short shelf life, fast staling, and easy crumbling. The objective of this study was to use amaranth, quinoa, chia flours by separately or as a mixture and corn starch with different ratios as an alternative to wheat/rice flour using several hydrocolloids at different levels to improve the technological properties of dough and bread, to enhance the nutritive value of gluten-free breads, and to avoid the negative effects caused by ingestion of gluten for coeliacs. The increasing of moisture content, specific volume, L values of crumb color, and hardness of the crumb texture of all breads was associated with the increase in the level of hydrocolloids. Increasing the ratio of pseudocereal flours showed a dark dough, also, resulted in a reduction in specific volume, L values of bread color, and an increase in the moisture content and hardness of the crumb texture in all bread formulations. The formulations prepared with the lowest ratio of pseudocereal flours (10%) at the high hydrocolloid concentration (4%) produced bread with good quality better than that of the control bread in the acceptability. Amaranth, quinoa, and chia flours can be successfully incorporated into gluten-free formulation with hydrocolloids to produce gluten-free breads without negatively affecting the sensory properties of the loaves. Present study suggests that pseudocereals can represent a good-healthy alternative to ingredients used in the manufacture of gluten-free breads.
Multi-omics characterization of the Canada goose fecal microbiome reveals selective efficacy of simulated metagenomes
Authors: Gil Joshua C. , Hird Sarah M. 
Published: April 2022

Abstract
BackgroundUnderstanding the composition and function of the microbiome is essential to understanding vertebrates. The taxonomic composition of a microbiome is often identified using amplicon sequencing of the 16S rRNA gene, but as a single marker, it cannot identify functions (genes). Metagenome and metatranscriptome sequencing can determine microbiome function but can be cost prohibitive. Therefore, computational methods have been developed to generate simulated metagenomes derived from 16S rRNA sequences and full-length genomes. Simulated metagenomes can be an effective alternative to empirical sequencing, but accuracy depends on the genomic database used and whether the database contains organisms closely related to the 16S sequences. The effectiveness of simulated metagenomes in non-model systems is poorly known. We sought to determine the accuracy of simulated metagenomes in a non-model organism, the Canada goose (Branta canadensis), by comparing metagenomes and metatranscriptomes to simulated metagenomes derived from 16S amplicon sequencing of the same samples. ResultsThe Canada goose fecal microbiome is rich in microbial taxa and functions, including those involved in fermentation. There were significant differences between the metagenomes, metatranscriptomes, and simulated metagenomes when comparing enzymes (ECs), KEGG orthologies (KOs), and metabolic pathways. The simulated metagenomes, when compared to the metagenomes, accurately identified the majority of the total ECs, KOs and pathways. The simulated metagenomes accurately identified the majority of the short-chain fatty acid metabolic pathways crucial to organisms with a nutrient poor diet. When narrowed in scope to specific groups of genes, the simulated metagenomes overestimated the number antimicrobial resistance genes and underestimated the number of genes relating to digestion in folivores.ConclusionsOur data show simulated metagenomes may be a useful tool when studying the functional potential of a non-model organism’s microbiome, depending on the question being asked. Simulated metagenomes were selectively accurate when identifying certain characteristics of the microbiome, like metabolic pathways, but not when compared to the entire sequenced metagenome. While simulated metagenomes are an important tool for inferring function, the lack of whole microbial genomes from understudied systems provides an impetus for continued study and sequencing of whole genomes and metagenomes from non-model systems.
TGF-β1 regulates the abnormal migration of rat vascular smooth muscle cells through affecting the expression of EMT related genes
Authors: Zhang Jing , Deng Yifan , Xu Xiaoting , Dai Chengye , Liu Juan , Zhu Mixue , He Shenghu , Zhou Wei 
Published: April 2022

Abstract
Purpose: This study aimed to investigate the effect of transforming growth factor-β1 (TGF-β1) on the migration capacity of rat vascular smooth muscle cells (VSMCs) and its potential mechanism.Methods: Different concentrations of TGF-β1 were used to treat rat VSMCs. The migration capacity of cells was observed by wound healing assay and Transwell assay. Western Blotting and Reverse transcription-quantitative real-time polymerase chain reaction (RT-qPCR) were performed to examine the expression of EMT related gene.Results: In a certain concentration range, the migration ability of rat VSMCs was enhanced with the increase of TGF-β1 concentration. Meanwhile, TGF-β1 increased the expression of N-cadherin and Vimentin (mesenchymal markers), and decreased the expression of E-cadherin and β-catenin (epithelial markers) at both protein and mRNA levels. Conclusion: TGF-β1 promoted abnormal migration of rat VSMCs by regulating the expression of EMT related genes. This may be one of the mechanisms of in-stent restenosis (ISR) in coronary arteries.
The resurrection of a species, Sarcocystis asinus Gadaev 1978, in donkeys that is distinct from Sarcocystis bertrami/fayeri currently found in horses based on mitochondrial cox1 sequences
Authors: Hu Junjie , Zhang Mingzhu , Wei Kaiwen , Wu Zhipeng , Sun Jun , Deng Shuangsheng , Tao Jianping 
Published: April 2022

Abstract
There is considerable confusion concerning the relationships among species of Sarcocystis found in donkeys and horses. Here, sarcocysts obtained from donkeys (Eqqus asinus) were morphologically and molecularly characterized. Sarcocysts were diagnosed in 12 of 32 (37.5%) Chinese donkeys and could be divided into two forms, thin-walled and thick-walled, with the aid of light microscopy (LM). The thin-walled sarcocysts were macroscopic (up to 4856 × 320 μm in size) and had short club-like protrusions of up to 2.7 μm; the thick-walled sarcocysts were microscopic (up to 3750 × 135 μm in size) and had hair-like protrusions of up to 5.4 μm. The ultrastructures of the two forms exhibited highly similar morphological characteristics, including bundled microtubules in the core of the villus protrusions penetrating diagonally into the ground substance, similar to wall type 11. Three genetic markers, 18S rDNA, 28S rDNA, and mitochondrial cox1, were sequenced and analyzed in the two forms. The three genetic markers presented high intraspecific similarity between the two forms, ranging from 97.2–99.5% (average 97.8%), 97.8-99.6% (average 98.4%) and 99.0−99.9% (average 99.4%), respectively. The comparison of these sequences with those of Sarcocystis spp. previously deposited in GenBank showed that the newly obtained sequences of 18S rDNA, 28S rDNA, and mitochondrial cox1 presented identities of 90.0−97.5% (average 94.7%), 94.7−95.1% (average 94.9%) and 82.6−84.5% (average 83.4%), respectively, with those of S. bertrami/fayeri obtained from horses. Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) based on the mitochondrial cox1 sequences of donkey and horse sarcocysts revealed three fragments (196, 243 and 641 bp) and two fragments (416 and 644 bp), respectively, upon digestion with the restriction enzymes HinifI and EcorRI. Phylogenetic analysis based on 18S rDNA or mitochondrial cox1 sequences revealed that donkey sarcocysts formed an individual clade that clustered with Sarcocystis spp. obtained from horses. Based on the divergence of the three sarcocyst genetic markers, especially mitochondrial cox1, between donkeys and horses, Sarcocystis asinus should be resurrected and regarded as a valid species in donkeys. The cross-infection of Sarcocystis between donkeys and horses needs to be attempted for further confirmation in the future.
Experimental Investigation with Optimal Prediction of Emission in Diesel Engine Using Combined SCR-NSR Catalyzer
Authors: Durairaj Rekha , Subramanian Neelakrishnan , Duraiswami Divakar 
Published: April 2022

Abstract
An expanding requirement for clean air motivates the vehicle makers to contribute a lot of time and cash to reduce toxic emissions. The utilization of catalytic converters is one of the well-known strategies to clean the exhaust. The catalytic converters oxidize the destructive carbon monoxide, hydrocarbon emissions into harmless CO2 and water vapor. In this experiment, the essential objective is to develop a catalytic converter with combined methods like selective catalytic reduction, NOx storage and reduction (SCR-NSR) procedure and test its effectiveness towards the NOx reduction from the exhaust of diesel engine. The combination of the two systems is proposed in this experimentation for building up an effective catalytic converter and distinguishing the optimal emission processes. The fabricated SCR-NSR catalytic converter fitted to the exhaust system and the emission rates are estimated with the help of a gas analyzer. The testing is done by utilizing diesel as fuel in the Kirloskar TV1 engine with NSR, Non-filter and combined NSR-SCR system. The investigation is experiencing for 20 trials with different emission parameters is analyzed. For improving the discharge level in the engine, the test data are predicted with the proposed numerical model and tested in Mat Lab software. The invasive weed optimization and particle swarm optimization together with a recurrent neural network are utilized for the prediction and optimization process and parameters like compression ratio, input power, and load are utilized as input to the experimentation. In the 20 trial, a low level of discharge is attained in the 17th trial. Subsequently, the prediction goes for the 20 sets individually and compared with 17th set and the experimental results demonstrates that the discharge rates acquired for consolidated NSR-SCR observed to be 0.01% of CO, 3% of HC, 0.1% of CO2, 20.74% of O2, and 68 ppm of NOx. At the point when compared to predicted outcomes demonstrates the ideal level of 0.001% of CO, 0.5% of HC, 0% of CO2, 21.76% of O2, and 60.6ppm of NOx respectively. The proposed invasive weed optimization and particle swarm optimization obviously reduce the emission rates of diesel engine than the other comparative methods.
A Deep Learning Method for MiRNA/IsomiR Target Detection
Authors: Talukder Amlan , Zhang Wencai , Li Xiaoman , Hu Haiyan 
Published: April 2022

Abstract
Motivation: Accurate identification of microRNA (miRNA) targets at base-pair resolution has been an open problem for over a decade. The recent discovery of miRNA isoforms (isomiRs) adds more complexity to this problem. Despite the existence of many methods, none considers isomiRs, and their performance is still suboptimal. We hypothesize that by taking the isomiR-mRNA interaction into account and applying a deep learning model to study miRNA-mRNA interaction features, we may improve the accuracy of miRNA target predictions.Results: We developed a deep learning tool called DMISO to capture the intricate features of miRNA/isomiR-mRNA interactions. Based on 10-fold cross-validation, DMISO showed high precision (95%) and recall (90%). Evaluated on three independent datasets, DMISO had superior performance to five tools, including three popular conventional tools and two recently developed deep learning-based tools. By applying two popular feature interpretation strategies, we demonstrated the importance of the miRNA regions other than their seeds and the potential contribution of the RNA-binding motifs within miRNAs/isomiRs and mRNAs to the miRNA/isomiR-mRNA interactions. Availability: The source code and tool are available at http://hulab.ucf.edu/research/projects/DMISO.