bluuebunny/crossref_metadata_2025_split huggingface dataset:
Optimizations for identifying reference genes in bone and cartilage bioengineering
Authors: Xiong Fei , Cheng Xiangyun , Zhang Chao , Klar Roland Manfred , He Tao 
Published: March 2021

Abstract
Background
Reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR) remains one of the best-established techniques to assess gene expression patterns. However, appropriate reference gene(s) selection remains a critical and challenging subject in which inappropriate reference gene selction can distort results leading to false interpretations. To date, mixed opinions still exist in how to choose the most optimal reference gene sets in accodrance to the Minimum Information for Publication of Quantitative Real-Time PCR Experiments (MIQE) guideline. Therefore, the purpose of this study was to investigate which schemes were the most feasible for the identification of reference genes in a bone and cartilage bioengineering experimental setting. In this study, rat bone mesenchymal stem cells (rBMSCs), skeletal muscle tissue and adipose tissue were utilized, undergoing either chondrogenic or osteogenic induction, to investigate the optimal reference gene set identification scheme that would subsequently ensure stable and accurate interpretation of gene expression in bone and cartilage bioengineering.

Results
The stability and pairwise variance of eight candidate reference genes were analyzed using geNorm. The V0.15- vs. Vmin-based normalization scheme in rBMSCs had no significant effect on the eventual normalization of target genes. In terms of the muscle tissue, the results of the correlation of NF values between the V0.15 and Vmin schemes and the variance of target genes expression levels generated by these two schemes showed that different schemes do indeed have a significant effect on the eventual normalization of target genes. Three selection schemes were adopted in terms of the adipose tissue, including the three optimal reference genes (Opt3), V0.20 and Vmin schemes, and the analysis of NF values with eventual normalization of target genes showed that the different selection schemes also have a significant effect on the eventual normalization of target genes.

Conclusions
Based on these results, the proposed cut-off value of Vn/n + 1 under 0.15, according to the geNorm algorithm, should be considered with caution. For cell only experiments, at least rBMSCs, a Vn/n + 1 under 0.15 is sufficient in RT-qPCR studies. However, when using certain tissue types such as skeletal muscle and adipose tissue the minimum Vn/n + 1 should be used instead as this provides a far superior mode of generating accurate gene expression results. We thus recommended that when the stability and variation of a candidate reference genes in a specific study is unclear the minimum Vn/n + 1 should always be used as this ensures the best and most accurate gene expression value is achieved during RT-qPCR assays.
Analysis of the relationship between periodontitis and osteoporosis/fractures: a cross-sectional study
Authors: Hong Seok-Jin , Yang Byoung-Eun , Yoo Dae-Myoung , Kim Sung-Jae , Choi Hyo-Geun , Byun Soo-Hwan 
Published: March 2021

AbstractBackgroundChronic periodontitis is a multifactorial inflammatory disease resulting in patients exhibiting high levels of inflammatory factors causing systemic inflammatory bone destruction that may lead to osteoporosis development. The association between periodontitis and osteoporosis has been documented; however, the findings remain unclear. This study aimed to identify the association between periodontitis and osteoporosis using a cross-sectional study design and Korean Genome and Epidemiology Study (KoGES) health examinee data.MethodsThis cross-sectional study used epidemiological data from the KoGES during 2004–2016. Of 125,324 participants (age, 40–79 years), 9969 with periodontitis and 115,332 controls (without periodontitis) were selected. We analyzed the history of osteoporosis and fractures of all participants. All participants were examined according to age, sex, income group, obesity, smoking habits, alcohol consumption, and food intake. To analyze the odds ratio (OR) of periodontitis for those with osteoporosis and fractures, a logistic regression model was used.ResultsThe adjusted odds ratio (aOR) of periodontitis for osteoporosis was 2.16 (95% confidence interval [CI], 2.01–2.31;P < 0.001). The aOR of periodontitis for any fracture was 1.54 (95% CI 1.46–1.62;P < 0.001).ConclusionOsteoporosis and fractures are associated with periodontitis. Performing regular oral hygiene and examinations of bone mineral density are recommended to prevent aggravation of osteoporosis and periodontitis.
An ecological study on the association between universal health service coverage index, health expenditures, and early childhood caries
Authors: Folayan Morenike Oluwatoyin , Tantawi Maha El , Virtanen Jorma I. , Feldens Carlos Alberto , Rashwan Maher , Kemoli Arthur M. , Villena Rita , Al-Batayneh Ola B. , Amalia Rosa , Gaffar Balgis , Mohebbi Simin Z. , Arheiam Arheiam , Daryanavard Hamideh , Vukovic Ana , Schroth Robert J. ,   for the Early Childhood Caries Advocacy Group
Published: March 2021

Abstract
Background
Universal health care (UHC) may assist families whose children are most prone to early childhood caries (ECC) in accessing dental treatment and prevention. The purpose of this study was to determine the association between UHC, health expenditure and the global prevalence of ECC.

Methods
Health expenditure as percentage of gross domestic product, UHC service coverage index, and the percentage of 3–5-year-old children with ECC were compared among countries with various income levels using one-way analysis of variance (ANOVA). Three linear regression models were developed, and each was adjusted for the country income level with the prevalence of ECC in 3–5-year-old children being the dependent variable. In model 1, UHC service coverage index was the independent variable whereas in model 2, the independent variable was the health expenditure as percentage of GDP. Model 3 included both independent variables together. Regression coefficients (B), 95% confidence intervals (CIs), P values, and partial eta squared (ƞ2) as measure of effect size were calculated.

Results
Linear regression including both independent factors revealed that health expenditure as percentage of GDP (P < 0.0001) was significantly associated with the percentage of ECC in 3–5-year-old children while UHC service coverage index was not significantly associated with the prevalence of ECC (P = 0.05). Every 1% increase in GDP allocated to health expenditure was associated with a 3.7% lower percentage of children with ECC (B = − 3.71, 95% CI: − 5.51, − 1.91). UHC service coverage index was not associated with the percentage of children with ECC (B = 0.61, 95% CI: − 0.01, 1.23). The impact of health expenditure on the prevalence of ECC was stronger than that of UHC coverage on the prevalence of ECC (ƞ2 = 0.18 vs. 0.05).

Conclusions
Higher expenditure on health care may be associated with lower prevalence of ECC and may be a more viable approach to reducing early childhood oral health disparities than UHC alone. The findings suggest that currently, UHC is weakly associated with lower global prevalence of ECC.
Exploring why medical students still feel underprepared for clinical practice: a qualitative analysis of an authentic on‐call simulation
Authors: Hawkins Nichola , Younan Helen-Cara , Fyfe Molly , Parekh Ravi , McKeown Andrew 
Published: March 2021

Abstract
Background
Current research shows that many UK medical graduates continue to feel underprepared to work as a junior doctor. Most research in this field has focused on new graduates and employed the use of retrospective self-rating questionnaires. There remains a lack of detailed understanding of the challenges encountered in preparing for clinical practice, specifically those faced by medical students, where relevant educational interventions could have a significant impact. Through use of a novel on-call simulation, we set out to determine factors affecting perceived preparation for practice in final year medical students and identify ways in which we may better support them throughout their undergraduate training.

Methods
30 final year medical students from Imperial College London participated in a 90-minute simulation on hospital wards, developed to recreate a realistic on-call experience of a newly qualified doctor. Students partook in pairs, each observed by a qualified doctor taking field notes on their decisions and actions. A 60-minute semi-structured debrief between observer and student pair was audio-recorded for analysis. Field notes and students’ clinical documentation were used to explore any challenges encountered. Debrief transcripts were thematically analysed through a general inductive approach. Cognitive Load Theory (CLT) was used as a lens through which to finalise the evolving themes.

Results
Six key themes emerged from the on-call simulation debriefs: information overload, the reality gap, making use of existing knowledge, negative feelings and emotions, unfamiliar surroundings, and learning ‘on the job’.

Conclusions
The combination of high fidelity on-call simulation, close observation and personalised debrief offers a novel insight into the difficulties faced by undergraduates in their preparation for work as a junior doctor. In using CLT to conceptualise the data, we can begin to understand how cognitive load may be optimised within this context and, in doing so, we highlight ways in which undergraduate curricula may be adapted to better support students in their preparation for clinical practice. Recommendations are centred around enhancing the expertise of the learner through ‘whole task’ training approaches and integrated learning, as well as navigating negative emotions and supporting lifelong ‘learning while working’.
A systematic review of theoretical constructs in CDS literature
Authors: Liu Siru , Reese Thomas J. , Kawamoto Kensaku , Del Fiol Guilherme , Weir Charlene 
Published: March 2021

Abstract
Background
Studies that examine the adoption of clinical decision support (CDS) by healthcare providers have generally lacked a theoretical underpinning. The Unified Theory of Acceptance and Use of Technology (UTAUT) model may provide such a theory-based explanation; however, it is unknown if the model can be applied to the CDS literature.

Objective
Our overall goal was to develop a taxonomy based on UTAUT constructs that could reliably characterize CDS interventions.

Methods
We used a two-step process: (1) identified randomized controlled trials meeting comparative effectiveness criteria, e.g., evaluating the impact of CDS interventions with and without specific features or implementation strategies; (2) iteratively developed and validated a taxonomy for characterizing differential CDS features or implementation strategies using three raters.

Results
Twenty-five studies with 48 comparison arms were identified. We applied three constructs from the UTAUT model and added motivational control to characterize CDS interventions. Inter-rater reliability was as follows for model constructs: performance expectancy (κ = 0.79), effort expectancy (κ = 0.85), social influence (κ = 0.71), and motivational control (κ = 0.87).

Conclusion
We found that constructs from the UTAUT model and motivational control can reliably characterize features and associated implementation strategies. Our next step is to examine the quantitative relationships between constructs and CDS adoption.
Clinical analysis and long-term treatment monitoring of 3 patients with glycogen storage disease type Ib
Authors: Du Caiqi , Li Zhuoguang , Wei Hong , Zhang Min , Hu Minghui , Zhang Cai , Luo Xiaoping , Liang Yan 
Published: March 2021

Abstract
Background
To investigate the clinical and genetic characteristics of patients with glycogen storage disease type Ib (GSD Ib).

Case presentation
This report retrospectively analyzed the clinical data of 3 patients with GSD Ib admitted into our hospital, and summarized their onset characteristics, clinical manifestations, related examinations and treatment as well as mutational spectrum. After gene sequencing, the diagnosis of GSD Ib was confirmed in all 3 patients. Five variants of SLC37A4 gene were detected, of which c. 572C > T was the common variant and c. 680G > A was a novel variant. The 3 cases of GSD Ib were mainly affected by liver enlargement, growth retardation, etc., and all had a history of repeated infections. At the onset, patients mainly manifested as mildly elevated alanine-aminotransferase (ALT), accompanied by decreased absolute neutrophil count (ANC), hypertriglyceridemia, and metabolic disorders (hypoglycemia, hyperlactic acidemia, metabolic acidosis, etc.). After long-term treatment by oral uncooked cornstarch, the abnormal liver enzymes gradually returned to normal, and metabolic abnormalities were basically controlled most of the time. With increasing age, ANC of 2 patients decreased progressively, whereas the times of infections was reduced.

Conclusions
We reported 3 cases with GSD Ib and a novel SLC37A4 variant. The possibility of GSD type Ib should be kept on alert when a patient suffers recurrent infections, accompanied by hepatomegaly, elevated liver enzymes, hypoglycemia, dyslipidemia, and metabolic disorders.
Combined genomic and proteomic approaches reveal DNA binding sites and interaction partners of TBX2 in the developing lung
Authors: Lüdtke Timo H. , Wojahn Irina , Kleppa Marc-Jens , Schierstaedt Jasper , Christoffels Vincent M. , Künzler Patrick , Kispert Andreas 
Published: March 2021

AbstractBackgroundTbx2encodes a transcriptional repressor implicated in the development of numerous organs in mouse. During lung development TBX2 maintains the proliferation of mesenchymal progenitors, and hence, epithelial proliferation and branching morphogenesis. The pro-proliferative function was traced to direct repression of the cell-cycle inhibitor genesCdkn1aandCdkn1b, as well as of genes encoding WNT antagonists,FrzbandShisa3,to increase pro-proliferative WNT signaling. Despite these important molecular insights, we still lack knowledge of the DNA occupancy of TBX2 in the genome, and of the protein interaction partners involved in transcriptional repression of target genes.MethodsWe used chromatin immunoprecipitation (ChIP)-sequencing and expression analyses to identify genomic DNA-binding sites and transcription units directly regulated by TBX2 in the developing lung. Moreover, we purified TBX2 containing protein complexes from embryonic lung tissue and identified potential interaction partners by subsequent liquid chromatography/mass spectrometry. The interaction with candidate proteins was validated by immunofluorescence, proximity ligation and individual co-immunoprecipitation analyses.ResultsWe identifiedIl33andCcn4as additional direct target genes of TBX2 in the pulmonary mesenchyme. Analyzing TBX2 occupancy data unveiled the enrichment of five consensus sequences, three of which match T-box binding elements. The remaining two correspond to a high mobility group (HMG)-box and a homeobox consensus sequence motif. We found and validated binding of TBX2 to the HMG-box transcription factor HMGB2 and the homeobox transcription factor PBX1, to the heterochromatin protein CBX3, and to various members of the nucleosome remodeling and deacetylase (NuRD) chromatin remodeling complex including HDAC1, HDAC2 and CHD4.ConclusionOur data suggest that TBX2 interacts with homeobox and HMG-box transcription factors as well as with the NuRD chromatin remodeling complex to repress transcription of anti-proliferative genes in the pulmonary mesenchyme.
Comprehensive transcriptomic and proteomic analyses identify intracellular targets for myriocin to induce Fusarium oxysporum f. sp. niveum cell death
Authors: Wang Hengxu , Wang Zhigang , Xu Weihui , Wang Kexin 
Published: March 2021

Abstract
Background
Myriocin is a natural product with antifungal activity and is derived from Bacillus amyloliquefaciens LZN01. Our previous work demonstrated that myriocin can inhibit the growth of Fusarium oxysporum f. sp. niveum (Fon) by inducing membrane damage. In this study, the antifungal actions of myriocin against Fon were investigated with a focus on the effects of myriocin on intracellular molecules.

Results
Analysis of DNA binding and fluorescence spectra demonstrated that myriocin can interact with dsDNA from Fon cells. The intracellular-targeted mechanism of action was also supported by transcriptomic and proteomic analyses; a total of 2238 common differentially expressed genes (DEGs) were identified. The DEGs were further verified by RT-qPCR. Most of the DEGs were assigned metabolism and genetic information processing functions and were enriched in ribosome biogenesis in eukaryotes pathway. The expression of some genes and proteins in ribosome biogenesis in eukaryotes pathway was affected by myriocin, primarily the genes controlled by the C6 zinc cluster transcription factor family and the NFYA transcription factor. Myriocin influenced the posttranscriptional processing of gene products by triggering the main RI (retained intron) events of novel alternative splicing; myriocin targeted key genes (FOXG_09470) or proteins (RIOK2) in ribosome biogenesis in eukaryotes pathway, resulting in disordered translation.

Conclusions
In conclusion, myriocin was determined to exhibit activity against Fon by targeting intracellular molecules. The results of our study may help to elucidate the antifungal actions of myriocin against Fon.
Enhanced ascomycin production in Streptomyces hygroscopicus var. ascomyceticus by employing polyhydroxybutyrate as an intracellular carbon reservoir and optimizing carbon addition
Authors: Wang Pan , Yin Ying , Wang Xin , Wen Jianping 
Published: March 2021

Abstract
Background
Ascomycin is a multifunctional antibiotic produced by Streptomyces hygroscopicus var. ascomyceticus. As a secondary metabolite, the production of ascomycin is often limited by the shortage of precursors during the late fermentation phase. Polyhydroxybutyrate is an intracellular polymer accumulated by prokaryotic microorganisms. Developing polyhydroxybutyrate as an intracellular carbon reservoir for precursor synthesis is of great significance to improve the yield of ascomycin.

Results
The fermentation characteristics of the parent strain S. hygroscopicus var. ascomyceticus FS35 showed that the accumulation and decomposition of polyhydroxybutyrate was respectively correlated with cell growth and ascomycin production. The co-overexpression of the exogenous polyhydroxybutyrate synthesis gene phaC and native polyhydroxybutyrate decomposition gene fkbU increased both the biomass and ascomycin yield. Comparative transcriptional analysis showed that the storage of polyhydroxybutyrate during the exponential phase accelerated biosynthesis processes by stimulating the utilization of carbon sources, while the decomposition of polyhydroxybutyrate during the stationary phase increased the biosynthesis of ascomycin precursors by enhancing the metabolic flux through primary pathways. The comparative analysis of cofactor concentrations confirmed that the biosynthesis of polyhydroxybutyrate depended on the supply of NADH. At low sugar concentrations found in the late exponential phase, the optimization of carbon source addition further strengthened the polyhydroxybutyrate metabolism by increasing the total concentration of cofactors. Finally, in the fermentation medium with 22 g/L starch and 52 g/L dextrin, the ascomycin yield of the co-overexpression strain was increased to 626.30 mg/L, which was 2.11-fold higher than that of the parent strain in the initial medium (296.29 mg/L).

Conclusions
Here we report for the first time that polyhydroxybutyrate metabolism is beneficial for cell growth and ascomycin production by acting as an intracellular carbon reservoir, stored as polymers when carbon sources are abundant and depolymerized into monomers for the biosynthesis of precursors when carbon sources are insufficient. The successful application of polyhydroxybutyrate in increasing the output of ascomycin provides a new strategy for improving the yields of other secondary metabolites.
miR-320a/SP1 negative reciprocal interaction contributes to cell growth and invasion in colorectal cancer
Authors: Zhang Wenjing , Yang Haitao , Wang Zhongqiu , Wu Yanting , Wang Jingzhai , Duan Guihua , Guo Qiang , Zhang Yu 
Published: March 2021

Abstract
Background
Transcription factors (TFs) may be engaged in reciprocal regulatory circuits with certain miRNAs to maintain cellular homeostasis. Disequilibrium of the reciprocities by certain tumor-related stimuli may give rise to deregulation of downstream cellular signaling pathways, thus promoting malignant tumor phenotypes. Specificity Protein 1 (SP1) is the most representative member of the tumor-related transcription factors. Previous studies disclosed that SP1 can transcriptionally regulate miRNAs and coding genes to facilitate tumor progression. In our study, we used bioinformatic analysis to predict several SP1-binding sites within the miR-320a promoter and found that SP1 is a predicted target gene of miR-320a. Therefore, we hypothesize a reciprocal regulatory link between SP1 and miR-320a that participates in colorectal cancer (CRC) development

Methods
We performed bioinformatic analysis, quantitative polymerase chain reaction (qPCR), immunoblotting, dual-luciferase reporter assays, and a series of in vitro and in vivo functional assays to describe a novel SP1/miR-320a reciprocal interaction in CRC

Results
First, we found that miR-320a was significantly downregulated in CRC tissues and cell lines. Consistent with findings in other cancers, miR-320a exhibited inhibitory effects on cell growth and invasion of CRC in vitro and in vivo. Moreover, we identified SP1 as a target gene of miR-320a, and ectopic SP1 expression partly abolished miR-320a-induced inhibitory effects. Conversely, we confirmed that SP1 interacts with the miR-320a promoter, leading to depression of miR-320a. This illustrates a double-negative feedback loop between miR-320a and SP1. Additionally, based on the fact that SP1 promotes MACC1 transcription, we determined via immunoblotting that the oncogenic MACC1/MET signaling pathway was inactivated in the context of miR-320a-induced SP1 downregulation

Conclusion
Taken together, our study is the first to describe a miR-320a/SP1 negative reciprocal interaction, which contributes to cell growth and invasion in CRC through modulation of the MACC1/MET signaling pathway.