bluuebunny/crossref_metadata_2025_split huggingface dataset:
BRAF mutant colorectal cancer: ErbB2 expression levels as predictive factor for the response to combined BRAFi/ErbB1 inhibitors
Authors: Miele Evelina , Abballe Luana , Spinelli Gian Paolo , Besharat Zein Mersini , Catanzaro Giuseppina , Chiacchiarini Martina , Vacca Alessandra , Po Agnese , Capalbo Carlo , Ferretti Elisabetta 
Published: January 2020

Abstract
Background: Colorectal cancer (CRC) is a heterogeneous disease with a complex biology and a wide number of altered genes such as BRAF, KRAS and PIK3CA. Advances with new-targeted therapies have been achieved and available treating options have prolonged patient’s survival. However, BRAF-mutated CRC patients remain unresponsive to available therapies with RAF inhibitors (RAFi) alone or combined with ErbB inhibitors (ErbBi). These unmet needs require further exploitation of oncogenic signaling in order to set up individualized treatments.
Methods: To this end, we tested the efficacy of single agent or combined treatments using the BRAFi, vemurafenib and two different ErbBi: panitumumab and afatinib in CRC cells characterized by different molecular phenotypes.
Results: Combination strategies with BRAFi and ErbBi achieved a better response in BRAF V600E mutated cells expressing high levels of ErbB2.
Conclusions: Our findings support the importance of ErbB2 evaluation in BRAF-mutated CRC patients and its role as a positive predictor factor of response to BRAFi/ErbBi combination.
Downregulation of S100 Calcium Binding Protein A12 inhibits the growth of glioma cells
Authors: Lu Chunhe , Liu Jia , Yao Mingze , Li Lun , Li Guangyu 
Published: January 2020

Abstract
Introduction: S100 Calcium Binding Protein A12 (S100A12) is a member of the S100 protein family and is widely expressed in neutrophil and low expressed in lymphocytes and monocyte. However, the role of S100A12 in glioma has not yet been identified. Methods: In the present study, we carried out immunohistochemical investigation of S100A12 in 81 glioma tissues to determine the expression of s100A12 in glioma cells, and evaluate the clinical significance of S100A12 in glioma patients. Futher we knockdown the S100A12 by ShRNA, and evaluated cell proliferation, cell migration and cell apoptosis by MTT,clony formation assay, transwell assay ,flow cytometry assa and westernblot. Results: We found that S100A12 was upregulated in tissues of glioma patients and the expression was correlated to WHO stage and tumor size. Further, we found that knockdown S100A12 inhibits the proliferation, migration and invasion of glioma cells through regulating cell apoptosis and EMT. Conclusions: These findings demonstrated a novel function for S100A12 in glioma progression and suggested that S100A12 may be served as a new marker in the tumorigenesis and progression of glioma.
Transcriptomic analysis of flower induction for long-day pitaya by supplementary lighting in short-day winter season
Authors: Xiong Rui , Liu Chengli , Xu Min , Wei Shuang-Shuang , Huang Jia-quan , Tang Hua 
Published: January 2020

Abstract
Background: Pitayas are currently attracting considerable interest as a tropical fruit with numerous health benefits. However, as a long-day plant, pitaya plants cannot flower in the winter season from November to April in Hainan, China. To harvest pitayas with high economic value in the winter season, it is necessary to provide supplementary lighting at night to induce flowering. To further explore the molecular regulating mechanisms of flower induction in pitaya plants exposed to supplementary lighting, we used de novo RNA sequencing-based transcriptomic analysis for four stages of pitaya plants subjected to light induction. Results: We assembled 68113 unigenes in total, comprising 29782 unigenes with functional annotations in the NR database, 20716 annotations in SwissProt, 18088 annotations in KOG, and 11059 annotations in KEGG. Comparisons between different samples revealed different numbers of significantly differentially expressed genes (DEGs). A number of DEGs involved in energy metabolism-related processes and plant hormone signaling were detected. Moreover, we identified many CONSTANS-LIKE, FLOWERING LOCUS T, and other DEGs involved in the direct regulation of flowering including CDF and TCP, which function as typical transcription factor genes in the flowering process. At the transcriptomic level, we verified 13 DEGs with different functions in the time-course response to light-induced flowering by quantitative reverse-transcription PCR analysis. Conclusions: The identified DEGs may include some key genes controlling the pitaya floral-induction network, the flower induction and development is very complicated, and it involves photoperiod perception and different phytohormone signaling. These findings will increase our understanding to the molecular mechanism of floral regulation of long-day pitaya plants in short-day winter season induced by supplementary lighting.
Prevalence, risk factors, phenotypic and molecular characteristics for Staphylococcus aureus carriage in community-based drug users in Guangzhou, China
Authors: Wang Yingying , Lin Jialing , Zhou Junli , Han Zhigang , Yao Zhenjiang 
Published: January 2020

Abstract
Background: Staphylococcus aureus ( S. aureus ), particularly methicillin-resistant Staphylococcus aureus (MRSA), remains the predominant cause of infections in drug users. This cross-sectional study aims to elucidate the prevalence, risk factors, phenotypic and molecular characteristics of S. aureus carriage among community-based drug users.
Methods: All eligible drug users, with both injection and non-injection route of drug administration , were asked to complete questionnaires and collect nasal swabs by trained personal during the period between May and December 2017 in Guangzhou, China. Swabs were processed for identification of S. aureus . Antimicrobial susceptibility test and polymerase chain reaction assays were used to detect phenotypic and molecular characteristics for identified isolates. Univariate and multivariate logistic regression analyses were used to assess risk factors for S. aureus carriage.
Results: Overall, 353 drug users were included in the study and the prevalence of S. aureus carriage was 15.01% (53/353). The prevalence of MRSA carriage was 6.80% (24/353). Cohabitation was a risk factor for S. aureus (adjusted OR=8.80, 95% CI: 1.89-40.99). The proportion of multidrug resistance was 54.72% for S. aureus isolates and most of these isolates were resistant to penicillin, erythromycin and clindamycin. Seventeen MRSA isolates were multidrug resistant. The results of clonal complexes (CCs) and sequence types (STs) for S. aureus were diverse. The three predominant types for CCs were CC5 (64.15%, 34/53), CC59 (11.32%, 6/53), and CC7 (7.55%, 4/53); and for STs were ST188 (20.75%, 11/53), ST5 (11.32%, 6/53), and ST59 (11.32%, 6/53).
Conclusion: The prevalence of S. aureus nasal carriage was lower while the prevalence of MRSA carriage was moderate compared to previous studies. Phenotypic and molecular characteristics of S. aureus isolates, particularly MRSA isolates, revealed high proportions of antibiotic resistance, indicating the existence of cross-circulation, and implying high opportunity of virulence-related diseases. Decolonization and antibiotic stewardship might be implemented for drug users with MRSA carriage.
Pre-hospital CPR and early REBOA in trauma patients - Results from the ABOTrauma Registry.
Authors: Hilbert-Carius Peter , McGreevy David T , Abu-Zidan Fikri M. , Hörer Tal M. 
Published: January 2020

Abstract
Background: Severely injured trauma patients suffering from traumatic cardiac arrest (TCA) and requiring cardiopulmonary resuscitation (CPR) rarely survive. The role of Resuscitative Endovascular Balloon Occlusion of the Aorta (REBOA) performed early after hospital admission in patients with TCA is not well-defined. As the use of REBOA increases, there is great interest in knowing if there is a survival benefit related to the early use of REBOA after TCA. Using data from the ABOTrauma Registry, we aimed to study the role of REBOA used early after hospital admission in trauma patients who required pre-hospital CPR. Methods: Retrospective and prospective data on the use of REBOA were collected from the ABOTrauma Registry from 11 centers in seven countries globally between 2014 and 2019. In all patients with pre-hospital TCA, the predicted probability of survival, calculated with the Revised Injury Severity Classification II (RISC II), was compared with the observed survival rate. Results: Of 213 patients in the ABOTrauma Registry, 26 patients (12.2%) who had received pre-hospital CPR were identified. The median (range) Injury Severity Score (ISS) was 45.5 (25-75). Fourteen patients (54%) had been admitted to hospital with ongoing CPR. Nine patients (35%) died within the first 24 hours, while seventeen patients (65%) survived post 24 hours. The survival rate to hospital discharge was 27% (n=7). The predicted mortality using the RISC II was 0.977 (25 out of 26). The observed mortality (19 out of 26) was significantly lower than the predicted mortality (p=0.049). Patients not responding to REBOA were more likely to die. Only one (10%) out of 10 non-responders survived. Survival rate in the 16 patients responding to REBOA was 37.5% (n=6). REBOA with a median (range) duration of 45 (8-70) minutes significantly increases blood pressure from median (range) 56.5 (0-147) to 90 (0-200) mmHg. Conclusions: Mortality in patients suffering from TCA and receiving REBOA early after hospital admission is significantly lower than predicted by the RISC II. REBOA may improve survival after TCA. The use of REBOA in these patients should be further investigated.
HDAC inhibitor Givinostat targets DNA-binding of human CGGBP1
Authors: Patel Manthan , Patel Divyesh , Datta Subhamoy , Singh Umashankar 
Published: January 2020

Abstract
The antineoplastic agent Givinostat inhibits histone deacetylases. We present here our finding that the DNA-binding of human CGGBP1 is also inhibited by Givinostat. CGGBP1, a DNA-binding protein, is required for cancer cell proliferation. In our quest to exploit the potential anti-proliferative effects of CGGBP1 inhibition, we have developed a simple screening assay to identify chemical inhibitors of DNA-protein interactions. We have applied this screen for human CGGBP1 on a library of 1685 compounds and found that Givinostat is a direct inhibitor of CGGBP1-DNA interaction. The mechanism of action of Givinostat should thus extend beyond HDACs to include the inhibition of the myriad functions of CGGBP1 that depend on its binding to the DNA.
Effect of the Short-Segment Internal Fixation with Intermediate Inclined-Angle Screw at the Fractured Vertebrae on the Treatment of Denis type B thoracolumbar fracture
Authors: Xiong Chengjie , Huang Biwang , Wei Tanjun , Kang Hui , Xu Feng 
Published: January 2020

Abstract
Background Short-segment internal fixation with straight-forward screw (SSIF-SF) and long-segment internal fixation (LSIF) are two major surgical options for thoracolumbar (TL) fracture, however, limitations of two surgical options are obvious. SSIF with inclined-angle screw (SSIF-IA) have been lately developed to take advantage of their benefits and minimize their adverse effects. METHODS Three different treatments were randomly performed in 69 consecutive TL fracture. 26 were allocated to treatment with SSIF–IA, 24 were assigned to treatment with SSIF–SF, 19 patients were randomized to treatment with LSIF. Sagittal Cobb’s angle (SCA), anterior vertebral body height (AVBH), vertebral body index (VBI) and spinal canal encroachment (SCE) were measured and assessed. Functional recovery Visual Analogue Scale (VAS) and Oswestry disability index (ODI) were also evaluated. RESULTS The value of incision length, mean blood loss, duration of operation and hospital stay in the SSIF–IA group and SSIF-SF group were significantly lower than those in the LSIF group. During 6 months and the latest follow-ups, the AVBH and VBI in the SSIF-IA group and LSIF group were significantly more improved than those in the SSIF–SF group (p < 0.05). The correction losses of AVBH and VBI of the fractured vertebrae in the SSIF-IA group and LSIF group were significantly lower than those in the SSIF–SF group (P<0.05). There was no significant difference of SCA among three groups. The average ODI scores in SSIF-IA and SSIF-SF group were significantly lower than those in the LSIF group. CONCLUSIONS The bio-mechanical stability of SSIF-IA was comparable to LSIF, but less invasive as compared with LSIF. SSIF–IA was effective and reliable operative technique for patients with Denis type B TL fracture.
Global transcriptome and weighted gene co-expression network analyses of growth-stage-specific and hybrid-cultivar-specific drought stress responses in maize
Authors: Liu Songtao , Zenda Tinashe , Jin Hongyu , Liu Guo , Wang Xuan , Dong Anyi , Yang Yatong , Duan Huijun 
Published: January 2020

Abstract
Background Drought is the major abiotic stress threatening maize ( Zea mays L.) production globally. Therefore, deciphering the molecular basis of maize drought tolerance remains pertinent. Results Here, through a comprehensive comparative leaf transcriptome analysis of drought-tolerant hybrid ND476 plants subjected to water-sufficient (control) and water-deficit (drought) treatment conditions at four (V12, VT, R1, and R4) crop growth stages, we report key cultivar-specific and growth-stage-specific molecular mechanisms regulating drought stress responses in maize. Based on the transcriptome analysis, a total of 3451 differentially expressed genes (DEGs) were identified from the four experimental comparisons, with 2403, 650, 397 and 313 DEGS observed at the V12, VT, R1, and R4 stages, respectively. The expression changes in these genes effected corresponding metabolic pathway responses related to drought tolerance in maize. Subsequently, 3451 DEGs were divided into 12 modules by weighted gene co-expression network analysis (WGCNA), comprising 277 hub genes covering drought-responsive genes involved in water-deficit stress and developmental signaling crosstalk. Interestingly, the co-expressed genes that clustered into similar modules exhibited diverse expression tendencies and got annotated to different GO terms at different stages. MapMan analysis revealed that DEGs related to stress signal transduction, detoxification, transcription factor regulation, hormone signaling and secondary metabolites biosynthesis were universal across the four growth stages. However, the DEGs associated with photosynthesis and amino acid metabolism; protein degradation; transport; and RNA transcriptional regulation were uniquely enriched at the V12, VT, R2, and R4 stages, respectively. Conclusions Our results affirmed that maize drought stress adaptation is a whole-plant response as well as a stage-specific response process. We hope that our findings will aid in clarifying the fundamental cultivar-specific and growth-stage-specific molecular mechanisms regulating drought stress responses in maize. In addition, the genes and metabolic pathways identified here can be valuable genetic resources or selection targets for developing new drought resistant maize cultivars.
Comparative phosphoproteome analysis to identify candidate phosphoproteins involved in blue light-induced brown film formation in Lentinula edodes
Authors: Song Tingting , Shen Yingyue , Jin Qunli , Feng Weilin , Fan Lijun , Cai Weiming 
Published: January 2020

Abstract
BackgroundLight plays an important role in the growth and differentiation of Lentinula edodes mycelia, and mycelial morphology is influenced by light wavelengths. The blue light-induced formation of brown film on the vegetative mycelial tissues of L. edodes is an important process. However, the mechanisms of L. edodes’ brown film formation, as induced by blue light, are still unclear. Using a high-resolution liquid chromatography-tandem mass spectrometry integrated with a highly sensitive immune-affinity antibody method, phosphoproteomes of L. edodes mycelia under red- and blue-light conditions were analyzed. ResultsA total of 11,224 phosphorylation sites were identified on 2,786 proteins, of which 9,243 sites on 2,579 proteins contained quantitative information. In total, 475 sites were up-regulated and 349 sites were down-regulated in the blue vs red group. To characterize the differentially phosphorylated proteins, systematic bioinformatics analyses, including gene ontology annotations, domain annotations, subcellular localizations, and Kyoto Encyclopedia of Genes and Genomes pathway annotations, were performed. These differentially phosphorylated proteins were correlated with light signal transduction, cell wall degradation, and melanogenesis, suggesting that these processes are involved in the formation of the brown film. ConclusionsOur study provides new insights into the molecular mechanisms of the blue light-induced brown film formation at the post-translational modification level.
SCC: An accurate modification method for scRNA-seq dropouts based on mixture model
Authors: zheng yan , Hu Jialu , Shang Xuequn 
Published: January 2020

Abstract
Single-cell RNA sequencing (scRNA-seq) technology has advanced in past decade, which enables gene expression analysis to be carried out at higher resolution. This technology is of great significance for exploring the dynamic development process of life, studying the regulation mechanism of genes and discovering new cell types. However, there are still some limitations in scRNA-seq technology. The primary limitation is the high noisy in scRNA-seq data. The main reason is the poor sensitivity of scRNA-seq technology. This technology only detect 5-15 percent of the mRNA molecules. Therefore, low-expression genes are difficult to detect in scRNA-seq data. The scRNA-seq data tend to be bimodal expression distribution because the expression is either strongly zero or high expression. In this paper, we proposal a method scRNA-seq complementation (SCC) to solve the dropouts in scRNA-seq data. Firstly, we find the nearest neighbor cells of every cell, and then use a mixture model to impute the dropouts of scRNA-seq data. The model can identifies the possibility of dropouts and estimates the reasonable gene expression value. The result shows that SCC significantly reduce the intra-class distance of cells and enhance the clustering of cell subpopulation, which is significant for future research on gene expression. The code is freely accessible at the website: https://github.com/nwpuzhengyan/SCC.
Protective Effects of Vitamin E on Chemotherapy-Induced Peripheral Neuropathy: A Meta-Analysis of Randomized Controlled Trials
Authors: Miao Huikai , Li Rongzhen , Chen Dongni , Hu Jia , Chen Youfang , Wen Zhesheng 
Published: January 2020

Abstract
Background Chemotherapy often causes chemotherapy-induced peripheral neuropathy (CIPN), but effective prevention measures are still lacking. Whether vitamin E can prevent peripheral neurotoxicity caused by chemotherapy is inconclusive. Therefore, we collected related randomized controlled trials (RCTs) and conducted a meta-analysis to examine whether vitamin E could prevent CIPN. Methods We searched PubMed, EMBASE and the Cochrane databases in November 2019 for eligible trials. Two reviewers conducted the analysis independently when studies were homogeneous enough. Results Eight RCTs, involving 555 patients, were identified. Upon pooling these RCTs, patients who received vitamin E supplementation of 600 mg/day had a significantly lower incidence of peripheral neuropathy (RR 0.31; 95% CI 0.14 to 0.65; P = 0.002) induced by chemotherapy compared with the placebo group. Vitamin E played a key role in decreasing the incidence of peripheral neuropathy in the cisplatin chemotherapy group (RR 0.28; 95% CI 0.14 to 0.54; P = 0.0001). With regard to improvements in sural amplitude, vitamin E supplementation significantly decreased patients’ sural amplitude after three rounds of chemotherapy (RR -2.66; 95% CI -5.09 to -0.24; P =0.03) in contrast with that of placebo supplementation, while no significant difference was observed when patients were treated with vitamin E after six rounds of chemotherapy. In addition, the vitamin E group had better improvement in the neurotoxicity score (RR -2.65; 95% CI -4.01to -1.29; P = 0.0001) and a lower incidence of reflexes and distal paraesthesias (RR 0.50; 95% CI 0.29 to 0.87; P = 0.01) compared to the control group. Conclusion Available data included in this meta-analysis showed that vitamin E supplementation can confer modest improvement in the prevention of CIPN. However, large-scale, well-designed RCTs are needed to confirm the exact role of vitamin E supplementation in the prevention of CIPN.
Study on prevalence and risk factors of falls among community-dwelling elderly adults: results from three consecutive waves of the national health interview survey in Taiwan
Authors: Tsai Yih-Jian , Yang Ping-Yen , Yang Yi-Ching , Lin Mau-Roung , Wang Ying-Wei 
Published: January 2020

Abstract
Background An aging society incurs great losses due to fall-related injuries and mortalities. The foreseeable increased burden of injury due to falls among elderly people requires a nationwide study on the fall epidemic in Taiwan. Methods The fall epidemic was examined using data from three consecutive waves of the National Health Interview Survey (2005, 2009, and 2013). Common explanatory variables across these surveys included socio-demographic factors (age, sex, and difficulty in performing activities of daily living or instrumental activities of daily living), biological factors (vision, comorbidities, urinary incontinence, and depressive symptoms), and behavioral risk factors (sleeping pill use, and frequency of exercise). After univariate and bivariate analyses were conducted, the prevalence of falls was investigated using multiple linear regression models adjusted for age group, sex, and the year of survey. A multivariate logistic regression model for falls with adjustments for these common explanatory variables was established across three waves of surveys. Results For each survey, there were consecutively 2,722; 2,900; and 3,200 respondents, with a mean age of 75.1, 75.6, and 76.4 years, respectively. The multiple linear regression model yielded a negative association between the prevalence of falls and the year of survey. Several sociodemographic and biological factors, including female gender, difficulty in performing one basic ADL, difficulty in performing two or more instrumental ADLs, unclear vision, comorbidities, urinary incontinence, and depressive symptoms, were significantly associated with falls. Conclusion Although information regarding the change in fall prevalence over time supports existing fall intervention strategies in Taiwan, the identification of risk factors in the elderly may increase the effectiveness of future fall prevention programs.