bluuebunny/crossref_metadata_2025_split huggingface dataset:
Efficacy of nano-carbonate apatite dentifrice in relief from dentin hypersensitivity following non-surgical periodontal therapy: A randomized controlled trial
Authors: Ding Pei-Hui , Dai Anna , Hu Hua-Jiao , Huang Jia-Ping , Liu Jia-Mei , Chen Li-Li 
Published: November 2019

Abstract
Background: Dentine hypersensitivity (DH) could occur or intensify after non-surgical periodontal therapy because of the exposure of dentine tubules. It has been demonstrated that nano-sized particles could seal these the dentine tubules. This randomized controlled trial aimed to investigate the efficacy of dentifrice containing nano-carbonate apatite (n-CAP) in reducing dentine hypersensitivity (DH) after non-surgical periodontal therapy. Methods: 48 periodontitis patients with DH were included in this clinical trial. After non-surgical periodontal therapy, patients included were randomized to test and control group and the respective dentifrices were applied at chairside, after which they were instructed to brush teeth with the allocated dentifrices twice a day at home. Periodontal parameters were recorded at baseline and the last follow-up. DH was measured by air-blast test and recorded by visual analogue scale (VAS) and Schiff sensitivity scale at baseline, after polishing (0 week) and 2/4/6 weeks. Results: 45 participants completed the follow-up. Periodontal parameters were improved and comparable between groups. Significant reduction in DH was observed in both groups at all time-points compared to baseline in terms of VAS and Schiff score. The test group achieved significantly greater relief from hypersensitivity compared with the control group after 4-week at-home use (for VAS, test group: 0.66 ± 0.68 versus control group: 0.84 ± 0.78, p = 0.005; for Schiff score, test group: 0.69 ± 0.71 versus control group: 0.97 ± 0.77, p < 0.001). Conclusions: Home-use of n-CAP based dentifrice provided a significantly better alleviation of DH following non-surgical periodontal therapy after 4 weeks compared to the control product. Trail registration: Chinese Clinical Trials Registry (No. ChiCTR-IPR-17011678, http://www.chictr.org.cn/, registered 16 June, 2017)
Comparative analysis of the oral microbiota between iron-deficiency anaemia (IDA) patients and healthy individuals by high throughput sequencing
Authors: Xi Ranhui , Wang Renke , Wang Yuan , Xiang Zhenting , Su Zhifei , Cao Zaiqiang , Xu Xin , Zheng Xin , Li Jiyao 
Published: November 2019

Abstract
Background: The relationship between oral microbiota and IE (infective endocarditis) is well established. Opportunistic pathogens in normal oral flora enter the bloodstream through daily oral cleaning or invasive dental procedures, leading to the occurrence of infective endocarditis. An in vitro iron-deficient condition leads to a drastic community shift in oral microbiota with increasing proportion of taxa related to infective endocarditis. To investigate the relationship among insufficient iron supply, oral microbiota and the risk of IE and to conduct a population amplification study, iron-deficiency anaemia is used as an in vivo model. Results: High-throughput sequencing compared the dental plaque microbiota of 24 IDA(iron-deficiency anaemia) patients and 24 healthy controls. Sequences were classified into 12 phyla, 28 classes, 50 orders, 161 genera and 497 OTUs (the IDA and control groups shared the same 384 OTUs). Iron deficiency leads to lower internal diversity in the oral flora. The abundances of genera Corynebacterium, Neisseria, Cardiobacterium, Capnocytophaga, and Aggregatibacter were significantly higher in healthy controls, while genera Lactococcus, Enterococcus, Lactobacillus, Pseudomonas and Moraxella showed higher proportions in the IDA group (P<0.05). The relative abundances of genera Lactococcus, Enterococcus, Pseudomonas and Moraxella were significantly negatively correlated with the concentration of serum ferritin (P<0.05). Conclusions：Without an increase of oral streptococci, the main pathogen of IE, it is difficult to determine whether IDA can increase the risk of IE. However, the iron-deficient condition did lead to changes in the oral microbiota community structure. The genera that showed higher proportions in the IDA group were frequently reported as antibiotic resistant. As antibiotics are commonly recommended to prevent IE before dental procedures, this study offers new ideas of personalized prevention of IE.
Successful Infection Control of an Extended-Spectrum Beta-Lactamase-Producing Klebsiella pneumoniae ST307 Outbreak in a Neonatal Intensive Care Unit
Authors: Baek Eun-Hwa , Kim Se-Eun , Kim Sunjoo , Lee Seungjun , Cho Oh-Hyun , Hong Sun In , Do Hyun Jeong , Park Chan-Hoo , Shin Jeong Hwan , Hwang Inyeong , Park Eunhee 
Published: November 2019

Abstract
Background : We experienced an outbreak of extended-spectrum-beta-lactamase-producing Klebsiella pneumoniae (ESBL-KPN) bacteremia in a neonatal intensive care unit (NICU) starting in August 2017. We implemented an active countermeasure to control the outbreak of ESBL-KPN successfully.
Methods: The incidence of ESBL-KPN based on clinical specimens and healthcare-associated infection (HAI) rate were evaluated before and after the initiation of enhanced infection control (IC) practices initiated in January, 2018. Surveillance cultures were carried out for neonates, medical personnel, and NICU environmental samples. Molecular analyses, including pulse-field gel electrophoresis (PFGE), sequence typing, and ESBL genotyping, were performed for the isolated KPN strains.
Results: The incidence of ESBL-KPN in clinical specimens decreased from 2.84 to 0.49 per 1,000 patient-days and the HAI rate decreased from 2.43 to 0.0 per 1,000 patient-days after the implementation of enhanced IC procedures. Eleven neonates (11/15, 73.3%), one (1/41, 2.4%) of the medical personnel, and six (6/181, 3.3%) samples from the surroundings and medical devices were positive for ESBL-KPN in the surveillance cultures. All isolates demonstrated the same antibiotic resistance pattern and similar PFGE patterns and were identified as ST307 containing CTX-M-15.
Conclusions: Contaminated neonate surroundings and medical devices as well as spreading by medical personnel appeared to be the source of the outbreak of ESBL-KPN. We used an enhanced IC strategy for 3 months and successfully resolved the clonal outbreak of CTX-M-15-producing KPN. ST307 has emerged as an important bacteremia-causing pathogen in the NICU and should be monitored carefully.
enChIP systems with MSCV-based retroviral plasmids expressing 3xFLAG-Sp-dCas9
Authors: Yuno Miyuki , Fujita Toshitsugu , Fujii Hodaka 
Published: November 2019

Abstract
Objective: Engineered DNA-binding molecule–mediated chromatin immunoprecipitation (enChIP) is a technology for purifying specific genomic regions to facilitate identification of their associated molecules, including proteins, RNAs, and other genomic regions. In enChIP, the target genomic region is tagged with engineered DNA-binding molecules, e.g., a variant of the clustered regularly interspaced short palindromic repeats (CRISPR) system consisting of a guide RNA (gRNA) and a catalytically inactive form of Cas9 (dCas9). In this study, to increase the flexibility of enChIP and expand the range of target cells, we generated murine stem cell virus (MSCV)-based retroviral plasmids for expressing dCas9.
Results: We constructed MSCV-based retroviral plasmids expressing Streptococcus pyogenes dCas9 fused to a 3xFLAG-tag (3xFLAG-Sp-dCas9) and various drug resistance genes. We showed that it is feasible to purify target genomic regions with high yields using these plasmids. These systems might give enChIP users greater flexibility in choosing optimal systems for drug selection of transduced cells. In addition, they could be used to analyze different types of target cells.
The anti-apoptotic, antioxidant and anti-inflammatory effects of curcumin on acrylamide-induced neurotoxicity in rats
Authors: Guo Jie , Cao Xiaolu , Hu Xianmin , Li Shulan , Wang Jun 
Published: November 2019

Abstract
Background: As a chemical extensively used in industrial areas as well as formed during heating of carbohydrate-rich food and tobacco, acrylamide (ACR) has been known as well-established neurotoxic pollutant. Although the precise mechanism is unclear, enhanced apoptosis, oxidative stress and inflammation have been demonstrated to contribute to the ACR-induced neurotoxicity. In this study, we assessed the possible anti-apoptotic, antioxidant and anti-inflammatory effects of curcumin, the most active component in a popular spice known as turmeric, on the neurotoxicity caused by ACR in rats. Methods: Curcumin at the dose of 50 and 100 mg/kg was orally given to ACR- intoxicated Sprague-Dawley rats exposed by ACR at 40mg/kg for 4 weeks. All rats were subjected to behavioral analysis. The HE staining and terminal deoxynucleotidyl transferase mediated dUTP nick end labelling (TUNEL) staining were used to detect histopathological changes and apoptotic cells, respectively. The mRNA and protein expressions of apoptosis-related molecule telomerase reverse transcriptase (TERT) were detected using real-time PCR and immunohistochemistry, respectively. The contents of malondialdehyde (MDA) and glutathione (GSH) as well as the activities of superoxide dismutase (SOD) and glutathione peroxidase (GSH-Px) were measured as the indicators for evaluating the level of oxidative stress in brain. The levels of pro-inflammatory cytokinestumor necrosis factor-α (TNF-α) and interleukin-1β (IL-1β) in cerebral homogenates were detected using ELISA assay. Results: Concurrent administration of curcumin at the oral doses of 50 and 100 mg/kg with ACR significantly protected the rats from ACR-induced weigh loss and motor function deficits, and improved the pathological alterations in the ACR-intoxicated brains. Curcumin treatment especially at a high dose enhanced the TERT mRNA expression level and increased the number of TERT-positive nerve cells in cortex tissues of ACR intoxicated rats. The levels of MDA, TNF-α and IL-1β in the cerebral homogenates were reduced, the contents of GSH as well as the activities of SOD and GSH-Px were increased by curcumin treatment, compared to ACR control group. Conclusions: These data suggested the anti-apoptotic, antioxidant and anti-inflammatory effects of curcumin on ACR-induced neurotoxicity in rats. And maintaining TERT-related anti-apoptotic function might be one mechanism underlying the protective effect of curcumin on ACR-intoxicated brains.
Comparative transcriptome analysis reveals evolutionary divergence and shared network of cold and salt stress response in diploid D-genome cotton
Authors: Xu Yanchao , Magwanga Richard , Jin Dingsha , Cai Xiaoyan , Hou Yuqing , Zhou Zhongli , Wang Kunbo , Liu Fang 
Published: November 2019

Abstract
Background Wild species of cotton are excellent resistance to abiotic stress. Diploid D-genome cotton shown abundant phenotypic diversity and was the putative donor species of allotetraploid cotton which produce largest textile natural fiber.Results A total of 41,053 genes were expressed in all samples by mapping RNA-seq Illumina reads of G. thurberi (D 1 ), G. klotzschianum (D 3-k ), G. raimondii (D 5 ) and G. trilobum (D 8 ) to reference genome. The number of differently expressed genes (DEGs) were significantly higher under cold stress than salt stress. However, 34.1% DEGs under salt stress were overlapped with cold stress in four species. Notably, a potential shared network (cold and salt response, including 16 genes) was digged out by gene co-expression analysis. Totally, 47,180- 55,548 unique genes were identified in four diploid species by De novo assembly. Furtherly, 163, 344, 330 and 161 positive selected genes (PSGs) were detected in thurberi , G. klotzschianum , G. raimondii and G. trilobum by evolutionary analysis, respectively, and 9.5% - 17% PSGs of four species were DEGs in corresponding species under cold or salt stress. What’s more, most of PSGs were enriched GO term related to response to stimulation. G. klotzschianum shown best tolerance under both cold and salt stress. Interestingly, we found that a RALF-like protein coding gene not only is PSGs of G. klotzschianum, but also belongs to the potential shared network.Conclusion Our study provided a new evidence that gene expression variations of evolution by natural selection were essential drivers of the morphological variations related to environmental adaption during evolution. Additionally, there exist shared regulated networks under cold and salt stress, such as Ca 2+ signal transduction and oxidation reduction processes. Our work establishes a transcriptomic selection mechanism for altering gene expression of four diploid D-genome cotton, and provides available gene resource underlying multi-abiotic resistant cotton breeding strategy.
Molecular characterization and transcriptional profiling suggested structural and functional divergence in ascorbate peroxidase (APX) and APX-related (APX-R) genes in Triticum aestivum L.
Authors: Tyagi Shivi , . Shumayla , Verma Praveen Chandra , Singh Kashmir , Upadhyay Santosh Kumar 
Published: November 2019

Abstract
Background: Ascorbate peroxidases (APXs) are heme-dependent H2O2 scavenging enzymes providing the antioxidant defense and regulating myriad biological processes. APX-related (APX-R) is an additional form of APX protein which lacks peroxidase activity but form dimer with the chloroplastic APX (chlAPX). Despite of tremendous their functions, a systematic and comparative study of these genes is limited in Triticum aestivum L.
Results: Herein, a total of 21 TaAPX and six TaAPX-R genes were identified from the A, B and D sub genomes of Triticum aestivum, which form nine homeologous groups. These identified genes consisted of three pairs of paralogous genes which confronted pre-hybridization gene duplication under purifying selection. An unequal evolutionary rate after gene duplication suggested functional divergence between paralogous genes. The phylogenetic study classified TaAPXs into four distinct clades, where TaAPX-R proteins were clustered in clade I. The members of each clade showed similarity in gene and protein architecture, motifs distribution, sub-cellular localization that suggested their conserved nature. The tertiary structure analysis of three TaAPXs and one TaAPX-R revealed the presence of helices and coils, and residues involved in ligand binding. Transcriptional profiling of TaAPX and TaAPX-R genes suggested their specific role during development and abiotic and biotic stress response. Modulated transcript expression and APX enzyme activity during heat, drought and salt stress confirmed their role in these stress conditions. Co-expression analyses predicted interaction of these genes with the other genes involved in numerous biological processes. These genes were also found to be regulated by miRNAs associated with various developmental pathways and/or stress response. Further, they also exhibited interaction with the mediator compounds of Halliwell-Asada cycle.
Conclusions: Overall, the present study reported numerous molecular and structural features of TaAPXs and TaAPX-Rs, and their role in plant development and stress response. It provides a platform for detailed functional characterization of TaAPX and TaAPX-R genes in future studies.
Aberrant Functional Connectivity in Resting State Networks of ADHD Patients Revealed by Independent Component Analysis(ICA)
Authors: Zhang Huayu , Zhao Yue , Cao Weifang , Cui Dong , Jiao Qing , Lu Weizhao , Li Hongyu , Qiu Jianfeng 
Published: November 2019

Abstract
Background：ADHD is one of the most common psychiatric disorders in children and adolescents. Altered functional connectivity has been associated with ADHD symptoms. This study aimed to investigate abnormal changes in the functional connectivity of resting-state brain networks (RSNs) among adolescent patients with different subtypes of ADHD.
Methods: The data were obtained from the ADHD-200 Global Competition, including fMRI data from 88 ADHD patients (56 patients of ADHD-Combined，ADHD-C and 32 patients of ADHD-Inattentive, ADHD-I) and 67 Typically-Developing Controls (TD-C). Group ICA was utilized to research aberrant brain functional connectivity within different subtypes of ADHD.
Results: Compared with TD-C group, the clusters of decreased functional connectivity were located in the left inferior occipital gyrus (p=0.0041) and right superior occipital gyrus (p=0.0011) of DAN, supplementary motor area (p=0.0036) of ECN, left supramarginal gyrus (p=0.0081) of SN, middle temporal gyrus (p=0.0041) and superior medial frontal gyrus (p=0.0055) of DMN in ADHD-C group. In the ADHD-I group, decreased functional connectivity was found in the right superior parietal gyrus (p=0.0017) of DAN and left middle temporal gyrus (p=0.0105) of DMN. The decreased functional connectivity of ADHD-C group was found in superior temporal gyrus (p=0.0062) of AN, inferior temporal gyrus (p=0.0016) of DAN, dorsolateral superior frontal gyrus (p=0.0082) of DMN compared to ADHD-I group. All the clusters surviving at p<0.05 (AlphaSim correction).
Conclusion: The results suggested that decreased functional connectivity within the DMN and DAN was responsible, at least in part, for the symptom of inattention in ADHD-I patients. Similarly, we believed that the impaired functional connectivity within networks may contribute to the manifestations of ADHD-C patients, including inattention, hyperactivity/impulsivity, and unconscious movements.
Genome-wide associations for udder and teat conformational risk factors for mastitis in Holstein cows
Authors: Miles Asha M. , Posbergh Christian , Huson Heather Jay 
Published: November 2019

Abstract
BACKGROUND The objective of our study was to conduct high-density genome-wide association studies of dairy cow udder and teat conformation with direct phenotyping. We identified and compared quantitative trait loci ( QTL ) for a novel composite mastitis risk trait and considered environmental impact of milking by comparing primiparous cows only. Cows (N = 471) were genotyped on the Illumina BovineHD 777K beadchip and scored for front and rear teat length, width, end shape, and placement, fore udder attachment, udder cleft, udder depth, rear udder height, and rear udder width. Principal component analysis was performed on fore udder attachment, rear teat end shape, rear teat width, and rear udder height, to create a single new phenotype describing mastitis susceptibility based on these high-risk traits.RESULTS Over all 14 traits of interest, a total of 56 genome-wide associations were performed and 28 significantly associated (Bonferroni multiple testing correction < 0.05) QTL were identified. The linkage disequilibrium ( LD ) block surrounding the associated QTL or a 1 Mb window in the absence of LD was interrogated for candidate genes, resulting in the identification of genes with functions related to both cell proliferation and immune signaling, including ZNF683, DHX9, CUX1, TNNT1 , and SPRY1 . We assessed a primiparous only subset of cows (n = 144) to account for the possibility that the genetic variance component of the phenotype is greater for cows who have had less exposure to the environment, and observed different associated QTL and inheritance patterns for udder depth in primiparous cows compared to the total cohort.CONCLUSION Special focus was given to the aforementioned mastitis risk traits, and candidate gene investigation revealed both immune function and cell proliferation related genes in the areas surrounding significantly associated QTL, suggesting that selecting for mastitis resistant cows based on these traits would be an effective method for increasing mastitis resiliency in a herd.
Phenolics and related in vitro functional activities of different varieties of fresh waxy corn: a whole grain
Authors: Chen Lirong , Guo Yuqiu , Li Xiaoyue , Gong Kuijie , Liu Kaichang 
Published: November 2019

Abstract
The polyphenol distribution in fresh waxy corns of different color varieties and their in vitro functional activities, which may be useful for treating various chronic diseases, were investigated. The colored varieties contained more phenols than the common varieties (white and/or yellow). The total free phenolic acid content of the six varieties was 3151.57 μg/g DW (dry weight), which was slightly higher ( p >0.05) than that of the total bound form (3028.24 μg/g DW). The total free flavonoid content was 5850.09 μg/g DW, which was higher ( p < 0.05) than that of the total bound form (4874.51μg/g DW). No bound anthocyanin was detected in the methanol extracts of the tested varieties. For all the varieties, free polyphenols contributed 86-100% and 70-78% of the 2,2-diphenyl-1-picrylhydrazyl (DPPH) and hydroxyl radical scavenging abilities, respectively, and 100% of the ferric reducing capacity. The free phenolics in fresh waxy corn showed significantly better ( p < 0.05) hypoglycemic effect than the bound form in terms of inhibition of α-amylase activity, whereas the bound phenolics of most varieties showed higher α-glucosidase inhibitory activity than the free forms. The free phenolics showed significantly better ( p < 0.05) glycocholesterol binding than the bound form for all varieties. The bound polyphenols showed better sodium cholate and taurocholate binding than the free form for most varieties. In conclusion, the difference between free and bound polyphenol content and functional activities indicates that fresh waxy corn can be potentially used for the development of functional food.
A Sequence Embedding Method For Enzyme Optimal Condition Analysis
Authors: Li Xiangjun , Dou Zhixin , Sun Yuqing , Wang Lushan , Gong Bin 
Published: November 2019

Abstract
Background: An enzyme activity is influenced by the external environment condition. It is important to have an enzyme remain high activity in a specific condition. A usual way is to first determine the optimal condition of an enzyme by either the gradient test or by tertiary structure, and then to use protein engineering to mutate a wild type enzyme for a higher activity in an expected condition. Results: In this paper, we investigate the optimal condition of an enzyme by directly analyzing the sequence. We propose an embedding method to represent the amino acids and the construct information as vectors in the latent space. These vectors contain information about the correlations between amino acids and sites in the aligned amino acid sequences, as well as the correlations with the optimal conditions. We crawled and processed the amino acid sequence in glycoside hydrolase GH11 family, and got 125 amino acid sequences with optimal pH condition. We used probabilistic approximation method to implement the embedding learning method on these samples. Based on these embedding vectors, we design a computational score to determine the optimal condition for an enzyme and achieves the accuracy 80% on the test proteins in the same family. We also give the mutation suggestion such that it has a higher activity in the expected environment, which is consistent with the professional wet experiments and analysis. Conclusion: A new computational method is proposed for the sequence based enzyme optimal condition analysis. Compared with the traditional process that involves a lot of wet experiments and requires multiple mutations, this method can get the desired protein for an expected condition in an efficient and effective way. Keywords: Protein sequence analysis; Embedding; Bioinformatics