bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identifies of key biomarkers associated with cell adhesion in multiple myeloma by integrated bioinformatics analysis
Authors: Peng Yue , Wu Dong , Zhang Peihua , Li Fangmei , Feng Yuandong , He Aili 
Published: March 2020

Abstract
Background: Multiple Myeloma (MM) is a hematologic malignancy whose underlying molecular mechanism has not yet fully understood. Cell adhesion plays a pivotal role in regulating MM progression. In this work, we aim to identify key genes involved in cell adhesion. Methods: Differentially expressed genes (DEGs) with p<0.05 and [logFC]≥1 were identified from the mRNA expression profiles of GSE6477 using GEO2R. Functional analysis and the protein-protein interaction (PPI) network analysis was performed to explore the biological function of the identified DEGs. Interactive networks of selected genes were built by STRING and Cytoscape software. Then,the prognostic and diagnostic values of hub genes were performed by the PrognoScan online tool and ROC curves. Moreover, a comprehensive analysis of candidate genes was performed using both clinical data and mRNA expression data. A retrospective clinical study was performed to evaluate the correlation between the expression of candidate proteins and the clinical characteristics of patients. Additionally, GSEA and transcription factor (TF) prediction were performed to identify biological progression that might be involved. Results: In total, 1383 DEGs were identified. GO enrichment analysis showed that these DEGs were enriched in the extracellular matrix (ECM) organization and cell adhesion. KEGG enrichment analysis showed that the DEGs were significantly associated with cell adhesion molecules (CAMs), and ECM-receptor interaction. To further identify key regulators involved in the cell adhesion process, we screened 180 overlapped genes between the DEGs and genes in GO terms of cell adhesion. Moreover, we built a PPI network to analyze filtered 123 proteins by STRING and Cytoscape software. 12 hub genes were identified as hub genes. Based on the PrognoScan database, ITGA9 and LAMB1 revealed the prognostic and diagnostic values of MM patients. They were both down-regulated in MM and had a correlation with some clinical characteristics of MM patients. Finally, GSEA analysis showed LAMB1 has a strong correlation with hypoxia, AKT1/mTOR signaling pathway, and oxidative phosphorylation. ITGA9 may be a target gene of MYC and has a strong correlation with oxidative phosphorylation. Moreover, based on TF prediction and the correlation analysis, we speculated that MYC may repress transcription of ITGA9 through binding to the promoter, which needs further verification. Conclusion: ITGA9 and LAMB1 were identified as key cell adhesion genes, serving as biomarkers and potential therapeutic targets for MM.
Influence of MoSi2 on oxidation protective ability of TaB2-SiC coating in oxygen-containing environments within a broad temperature range
Authors: Ren Xuanru , Lv Junshuai , Li Wei , Hu Yuwen , Sun Ke , Ma Can , Chu Hongao , Wang Weiguang , Xu Leihua , Li Ziyu , Feng Peizhong 
Published: March 2020

Abstract
TaB2-SiC coating modified by different content of MoSi2 was fabricated on graphite substrate with SiC inner coating by liquid phase sintering to elevate the anti-oxidation capability of the TaB2-SiC coatings. As compared to the sample with the TaB2-40wt.%SiC coating, the coating sample modified with MoSi2 exhibited a weight gain trend at lower temperatures, the fastest weight loss rate went down by 76%, and the relative oxygen permeability value reduced from about 1% to near 0. More importantly, the large amount of SiO2 glass phase produced over the coating during oxidation was in contact with the modification of MoSi2 , which was proved to be beneficial to the dispersion of Ta-oxides. A concomitantly formed continuous Ta-Si-O-B compound glass layer showed excellent capacity to prevent oxygen penetration. However, when the TaB2 content was sacrificed to increase the MoSi2 content, the relative oxygen permeability of the coating increased instead of decreased. Thus, on the basis of ample TaB2 content, increasing the MoSi2 content of the coating is conducive to reducing the relative oxygen permeability of the coatings in a broad temperature region.
Overcoming Recruitment Challenges in Nursing Home Research with Nurses and Health Care Aides
Authors: Peters Sheryl , Thompson Genevieve , McClement Susan 
Published: March 2020

Abstract
BackgroundRecruiting busy health care providers into research can be challenging. Yet, the success of a research project can hinge on recruitment response rates. This article uses a case study to demonstrate how qualitative researchers creatively readjusted their methods when standard methods were not yielding enough recruitment response with the aim of supporting other researchers with their recruitment. MethodsCase Example – Interest was expressed but response rates were low among nurses and health care aides in a research project on person-centred health care in a personal care home research site. The research team reconceptualized the participation design, creating a research ‘event’, which accommodated the time constraints and work culture of the respondents. The research event was much better attended than standard interview recruitment.ResultsThe research event approach overcame barriers to participation. An 80% response rate resulted. Standard response rates for research interviews tend to be well under 20%.DiscussionSuccessful recruitment hinged on the researcher’s willingness to reconceptualize the recruitment approach part-way through, when recruitment difficulties were encountered. The high response could be attributed to the methods’ alignment to the available time and work culture in respondent-centred ways. The results suggest that attending to aspects of the work culture can increase recruitment, improve the chances of successful data collection, and reduce the likelihood of research ‘stall’.ConclusionNew and creative approaches to recruiting nurses and health care aides to qualitative research studies can help to meet recruitment targets. Rethinking and redesigning recruitment strategies after research begins, can be a mark of a successful research strategy and not a failure of research design.
An in vivo multimodal feasibility study in a rat brain tumour model using flexible multinuclear MR and PET systems
Authors: Choi Chang-Hoon , Stegmayr Carina , Shymanskaya Aliaksandra , Worthoff Wieland A. , Silva Nuno A da , Felder Jörg , Langen Karl-Josef , Shah Nadim Jon 
Published: March 2020

Abstract
Background : In addition to the structural information afforded by 1 H MRI, the use of X-nuclei, such as sodium-23 ( 23 Na) or phosphorus-31 ( 31 P), offers important complementary information concerning physiological and biochemical parameters. By then combining this technique with PET, which provides valuable insight into a wide range of metabolic and molecular processes by using of a variety of radioactive tracers, the scope of medical imaging and diagnostics can be significantly increased. While the use of multimodal imaging is undoubtedly advantageous, identifying the optimal combination of these parameters to diagnose a specific dysfunction is very important and is advanced by the use of sophisticated imaging techniques in specific animal models.Methods : In this pilot study, rats with intracerebral 9L gliosarcomas were used to explore a combination of sequential multinuclear MRI using a sophisticated switchable coil set in a small animal 9.4 T MRI scanner and, subsequently, a small animal PET with the tumour tracer O-(2-[ 18 F]-fluoroethyl)-L-tyrosine ( 18 F-FET). This enabled in vivo multinuclear MR-PET experiments to be conducted without compromising the performance of either multinuclear MR or PET.Results : High-quality in vivo images and spectra including high-resolution 1 H imaging, 23 Na-weighted imaging, detection of 31 P metabolites and 18 F-FET uptake were obtained, allowing the characterisation of tumour tissues in comparison to a normal brain. These parameters have been shown to be useful in the identification of the genetic profile of gliomas, particularly concerning the mutation of the isocitrate hydrogenase gene, which is highly relevant for treatment strategy.Conclusions : The combination of multinuclear MR and PET in, for example, brain tumour models with specific genetic mutations will enable the physiological background of signal alterations to be explored and the identification of the optimal combination of imaging parameters for the non-invasive characterisation of the molecular profile of tumours.
Comparative transcriptomics analysis revealing flower trichome development during flower development in two Lonicera Japonica Thunb. cultivars using RNA-seq
Authors: Li Jianjun , Ye Chenglin , Chang Cuifang 
Published: March 2020

Abstract
Background: Trichomes comprise specialized multicellular structures that have the capacity to synthesize and secrete secondary metabolites and protect plants from biotic and abiotic stresses. However, little is known about the trichome formation mechanism during flower development in Lonicera Japonica Thunb.Results: Here, we present a genome-wide comparative transcriptome analysis between two L. japonica cultivars, toward the identification of biological processes and functional gene activities that occur during flowering stage trichome development. In this study, the density and average lengths of flower trichomes were at their highest during three green periods. Using the Illumina RNA-Seq method, we obtained 134,304 unigenes, 33,733 of which were differentially expressed. In an analysis of 40 differentially expressed unigenes (DEGs) involved in trichome development, 29 of these were transcription factors. The DEGs analysis of plant hormone signal transduction indicated that plant growth and development may be independent of GA and CTK signaling pathways, and plant stress may be independent of JA and ET signaling pathways. We successfully isolated key genes involved in the floral biosynthesis of odors, tastes, colors, and plant hormones, and proposed biosynthetic pathways for sesquiterpenoid, triterpenoid, monoterpenoid, flavonoid, and plant hormones. Furthermore, 82 DEGs were assigned to cell cycles and 2,616 were predicted as plant resistance genes (PRGs).Conclusions: This study provides a comprehensive characterization of the expression profiles of flower development during the seven developmental stages of L. japonica, thereby offering valuable insights into the molecular networks that underly flower development in L. japonica.
Transcriptome and metabolome analyses revealing the potential mechanism of seed germination in Polygonatum cyrtonema
Authors: Liu Rong , Lu Jing , Xing Jiayi , Zhang Chihong , Zhou Min , Du Mei , Wang Mingxiu , Li Yunfang , Zhang Lei , Wu Yu 
Published: March 2020

Abstract
Background: Polygonatum cyrtonema Hua is a Chinese traditional medicine in the Liliaceae family. It have unique medical and edible value. However, the Polygonatum cyrtonema seeds are naturally difficult to germinate. Its reproductive and growth cycles should be accelerated through artificial technologies for meeting the market demand. Therefore, to beak the seeds dormancy and to elucidate the mechanism of germination, the metabolomics and transcriptomics analysis were performed in this study. Results: The results indicate that plant hormone (auxin, GA, ABA) were involved in seed germination. Furthermore, the expression levels of unigenes and α-amylase activity were increased in germinated seeds. In addition, the metabolites of phenylpropanoid and flavonoid biosynthesis were accumulated in Polygonatum cyrtonema seeds. Hhydroxycinnamyl (caffeic acid, coniferin and sinapic acid et al.), organic acids (benzoic acid, ferulic acid, and coumaric acid etc.) were significantly decreased, while flavonoids significantly accumulated during the germination. The results suggest that the metabolites of germinated seeds were mainly to promote flavonoids synthesis and to inhibit the lignin synthesis, which was beneficial to germination of Polygonatum cyrtonema. And hydrolysis of starch to glucose can provides necessary energy for germination. Conclusions: Our results give a novel insights into the regulating networks of seed germination and pave the way for Polygonatum cyrtonema seeds propagation and cultivation.
Antibiotic susceptibility pattern of biofilm producing Staphylococci isolated from different clinical samples
Authors: Tuladhar Ratna Shova , Shrestha Raju , Lekhak Sunil , Chaudhary Mahesh , Manandhar Sarita 
Published: March 2020

Abstract
Background: Biofilm mediated infection by Staphylococci have a significant negative impact on patient health and necessitate reliable method for detecting biofilm producers. The ability of isolates to produce biofilm make them resistant to host immune response as well as available antibiotics. This study aims to detect biofilm producing ability among clinical staphylococci by phenotypic methods and presence of icaAD genes as well as their antibiotic profile. Methods: A total of 4063 different clinical specimen received in the tertiary care hospital of Nepal were examined and Staphylococci were identified following standard microbiological procedure. The antibiotic resistivity pattern was detected by Kirby Bauer disc diffusion method whereas biofilm formation was detected by three phenotypic methods viz. congo red agar (CRA), tube method (TM) and tissue culture plate (TCP) method. Furthermore, icaAD genes were detected by PCR method. Results: A total of 161 Staphylococci were isolated comprising S. aureus (63, 39.1%) and CNS (98, 60.9%). The isolates were found to be resistant to penicillin and erythromycin. Strong biofilm formation was detected among 6 (3.7%), 22 (13.7%) and 35 (21.7%) by CRA, TM and TCP method respectively. Similarly, among 24 (14.9%) isolates icaAD genes were detected. Biofilm formation was found to be correlated with methicillin resistance. Conclusion: The study showed significant association between phenotypic production of biofilm and presence of ica genes. The biofilm producing isolates were found to be resistant to antibiotics than biofilm non producers.
Google analytics of a pilot study to characterize the visitor website statistics and implicate for enrollment strategies in Medical University
Authors: Chen Szu-Chieh , Tsao Thomas Chang-Yao , Lue Ko-Huang , Tsai Yafang 
Published: March 2020

Abstract
Background: Under the lower fertility rate in Taiwan, colleges and universities face the harsh conditions of sourcing students. Therefore, each faculty must determine the strengths and weaknesses of its department, including the factors that students consider when choosing a major area.Methods: This study uses Google Analytics (GA) tools to perform a webpage analysis and conducts qualitative research to understand students’ needs. Among the webpage visitors, there were more women than men, with the highest frequency among those aged 18–24 years, followed by those aged 45–54 years.Results: The web information analysis provides information about the core content of the research department, the stay time, and the visitor characteristics.Conclusions: The website can enhance the introduction of the faculty-specific courses and highlight the differences in the characteristics of the curriculum design in competing departments to have clear market segmentation. The findings provide an information for the school’s enrollment strategies in each department.
New insights into patterns of first metastatic sites influencing survival of patients with hormone receptor-positive, HER2-negative breast cancer: a multicenter study of 271 patients
Authors: Yamamura Jun , Kamigaki Shunji , Fujita Junya , Osato Hiroki , Manabe Hironobu , Tanaka Yumiko , Shinzaki Wataru , Hashimoto Yukihiko , Komoike Yoshifumi 
Published: March 2020

Abstract
Background: The initial therapeutic strategy for hormone receptor-positive (HR+), HER2-negative (HER2-) breast cancer is based on the first metastatic site, but little evidence is available regarding the influence of metastatic distribution patterns of first metastatic sites on prognosis. In this study, we aimed to identify the metastatic distribution patterns of first metastatic sites that significantly correlate with survival after recurrence. Methods: We performed a retrospective review of records from 271 patients with recurrent metastatic HR+/ HER2- breast cancer diagnosed between January 2000 and December 2015. We assessed survival after recurrence according to the metastatic distribution patterns of first metastatic sites and identified significant prognostic factors among the patients with single and multiple metastases. Results: Prognosis was significantly better in patients with single metastasis than those with multiple metastases (median overall survival after recurrence: 5.86 years vs. 2.50 years, p<0.001). No metastatic organ site with single metastasis was significantly associated with prognostic outcome, though single metastasis with diffuse lesions was an independent risk factor for worse prognosis (HR: 3.641; 95% CI: 1.856-7.141), and more easily progressed to multiple metastases (p=0.002). Multiple metastases including liver metastasis (HR: 3.145; 95% CI: 1.802-5.495) or brain metastasis (HR: 3.289; 95% CI: 1.355-7.937) were regarded as a significant independent poor prognostic factor, but multiple metastases not involving liver or brain metastasis were not significantly related to prognosis after recurrence. Conclusions: Single metastasis with diffuse lesions could more easily disseminate systemically and progress to multiple metastases, leading to poor prognosis similar to multiple metastases. The metastatic distribution patterns of first metastatic sites may be important clinical clues for achieving optimal initial treatment for recurrent metastatic HR+/HER2- breast cancer. Our findings indicate that reconsideration of the determinant factors of therapeutic strategies for first recurrence may be needed.
Early screening of risk for multi-drug resistant organisms in the emergency department in patients with pneumonia and early septic shock: single-center, retrospective cohort study
Authors: Su Wen-Lin , Tzeng I-Shiang , Shui Hao-Ai , Wu Meng-Yu , Peng Ming-Yieh , Chan Chih-Yu , Chan Edward D. , Wu Yao-Kuang , Lan Chou-Chin , Yang Mei-Chen , Huang Kuo-Liang , Wu Chih-Wei , Chang Chia-Hui , Yiang Giou-Teng 
Published: March 2020

Abstract
Background

Pneumonia is the fourth leading cause of death globally, with rapid progression during septic shock. Multidrug-resistant organisms (MDROs) are becoming more common with some healthcare-associated pneumonia events. Early detection of MDRO risk may improve the outcomes; however, the risk of MDROs in patients with pneumonia and septic shock is unknown and may need broad spectrum multidrug antibiotic therapy. This study investigated the disease outcomes and multidrug antibiotic therapy of pneumonia with early septic shock in patients admitted in the emergency department (ED), a population with a high prevalence of MDROs, after early screening of MDROs risk.

Methods

In this retrospective cohort study, patients with pneumonia and sepsis (n=533) admitted to the ED at the Taipei Tzu Chi Hospital from 2013 to 2019 were enrolled. The study population was divided into the high-risk and low-risk groups (patients from the communities or long-term care facilities with high and low prevalence of MDROs) and further divided into four subgroups to those whose screening procedure completed within 1 or 6 h of admission (high-risk within 1 h, high-risk within 6 h, low-risk within 1 h, and low risk within 6 h groups). The ICU mortality and multidrug antibiotic therapy were compared.

Results

The high-risk MDROs groups had higher percentage of P. aeruginosa than the low-risk group. Furthermore, the appropriate ED first antibiotics were higher in the “within 1 h” than in the “within 6 h” subgroup of the high-risk MDROs group. In multivariate analysis, the “within 6 h” high-risk MDROs subgroup had an adjusted odds ratio of 7.191 (95% CI: 2.911–17.767, p <0.001) and 2.917 (95% CI:1.456–5.847, p=0.003) for the ICU mortality and multidrug therapy in the ICU, respectively, after adjusting for other confounding factors.

Conclusions

Delayed MDRO screening in the high risk group had significant higher ICU mortality and multidrug antibiotic therapy in patients with pneumonia and early septic shock in the ED, especially in areas with a high prevalence of MDROs.
Comparative analysis of the complete chloroplast genome of seven Nymphaea species
Authors: Sun chunqing , Chen fadi , Teng nianjun , Yao yuemei , Shan Xi , Dai zhongliang 
Published: March 2020

Abstract
Background: Although there has been a long history of cultivation and research on Nymphaea, the taxonomic relationships and evolutionary relationships among Nymphaea species remain controversial. The chloroplast (cp) genome can provide a new method to determine species origin, evolution, and phylogenetic relationships of Nymphaea. However, there are few studies on the cp genomes of Nymphaea, and the data of their genomes are very scarce. The complete cp genomes of seven Nymphaea species were sequenced by high-throughput sequencing technology, and the structural characteristics and phylogenetic relationships of cp genomes were analyzed.Results: A total of 126–129 genes were annotated in seven Nymphaea species, including 81–84 protein coding genes, eight rRNA, and 37 tRNA genes. A comparative cp genomic analysis of seven Nymphaea species showed that the cp gene sequence of Nymphaea was consistent, with no signs of reverse rearrangement. The codons preferentially ended with A/U. The cp genomes of seven Nymphaea species contained 147–168 dispersed repeats with a length of 15–19 bp and 979 simple sequence repeats (SSRs). Using N. colorata as the reference sequence, a total of 8,328 single nucleotide polymorphisms (SNPs) and 1,579 insertions/deletions were obtained. The degree of variation of the cp genome of the seven Nymphaea species in rpoA–rpl20, rbcL–ndhC, ndhD–ndhF, and trnN-GUU–ndhA regions is relatively high; related regions can be used as potential molecular markers for population genetics research. KaKs analysis showed that the ycf2 gene was positively selected. The results of the phylogenetic analysis showed that the genus Nymphaea can be divided into five branches: subgenus Nymphaea, subgenus Hydrocallis, subgenus Lotos, subgenus Anecphya, and subgenus Brachyceras. Conclusions: The cp genome of Nymphaea is very conservative in structure and composition, but it has rich variation in LSC and SSC regions. The phylogenetic analysis showed that Nymphaea could be further divided into five subgenera, and Euryale and Victoria were most closely related to Nymphaea. This study provided insight on the structure and composition of the cp genome of Nymphaea. Moreover, our results have provided more sequence information and genome resources for follow-up studies on Nymphaea.