bluuebunny/crossref_metadata_2025_split huggingface dataset:
Candidate gene analysis of watermelon stripe pattern locus ClSP ongoing recombination suppression
Authors: Yue Zhen , Ma Rongxue , Cheng Denghu , Yan Xing , He Yaping , Wang Chunxia , Pan Xiaona , Yin Lijuan , Zhang Xian , Wei Chunhua 
Published: February 2021

Abstract
Stripe pattern is an important commodity trait in watermelon, displaying diverse types. In this study, two segregating populations were generated for genetic mapping the single dominant locus ClSP, which was finally delimited to a 611.78 Kb interval with suppression of recombination. According to polymorphism sites detected among genotypes, four discrete haploblocks were characterized in this target region. Based on reference genomes, 81 predicted genes were annotated in the ClSP interval, including seven transcription factors namely as candidate No1-No7. Meanwhile, the ortholog gene of cucumber ist responsible for the irregular stripes was considered as candidate No8. Strikingly, gene structures of No1-No5 completely varied from their reference descriptions and subsequently re-annotated. Notably, the adjacent distribution candidates No2 and No3, as well as No4 and No5, were confirmed to derive from longer transcripts designated as No2_3 and No4_5, respectively. Sequence analysis demonstrated the third polymorphism in CDS of re-annotated No4_5 resulting in truncated proteins in non-stripe plants. Furthermore, only No4_5 was down-regulated in non-stripes relative to stripes contrast to other candidates. Transcriptome analysis identified 356 DEGs between striped and non-striped peels, with genes involved in photosynthesis and chloroplast development down-regulated in non-stripes but calcium ion binding related genes up-regulated. Additionally, 38 DEGs were annotated as transcription factors, with the majority up-regulated in non-stripes, such as ERFs and WRKYs. This study not only contributes to a better understanding of the molecular mechanisms underlying watermelon stripe development, but also provides new insight into the genomic structure of ClSP locus and valuable candidates.
Experimental Investigations to Analyze Surface Contact Fatigue Wear by Using a Dynamic Response of the Roller Bearing System
Authors: Pandey Shashikant , Muniyappa Amarnath 
Published: February 2021

Abstract
Bearings are used to reduce friction between two rolling /sliding members of the machines. Under normal operating conditions, an increase in the fatigue load cycles on the bearing contact surfaces results in surface defects viz. micro pitting, macro pitting, spalling and scuffing, thereby causing lubricant degradation. Hence, to maintain a better operating performance of rotating machines, it is essential to keep track of operating parameters. This paper describes the results of experimental investigations carried out to assess wear propagation on bearing contact surfaces using tribological and vibration parameters. Results obtained from experimental investigations provide a good correlation between the increase in surface fatigue wear and corresponding effects on transition in lubrication regimes, increased vibration levels, variations in rheological properties of lubricant and wear mechanisms developed on the contact surfaces of the roller bearing. The proposed approach can be used as a promising tool to assess incipient faults developed in roller bearing.
The Effectiveness of Salavadora Persica (Siwak) Petroleum Ether Extract As An Intracanal Medicament Used in Endodontic Therapy: An In Vitro Study
Authors: Ayoub Nahla , Badr Nadia , Alghamdi Saeed , Alzahrani Arwa , Alsulimani Rahaf , Nassar Afnan , Qadi Rawabi , Swilam Noha , Afifi Ibtesam 
Published: February 2021

Abstract
Background: Salvadora persica L. (Siwak) of the family Salvadoraceae has been used for many centuries as oral hygiene tools, particularly in Saudi Arabia. The current study aimed at developing a new root canal medicament based on the extract of Salvadora persica (SP). The antibacterial activity against Enterococcus faecalis was determined compared with the gold standard intracanal medicament, Ca (OH)2. Materials and Methods: Freeze-dried Siwak sticks were extracted with Petroleum ether to yield an oily extract (SPE). GC-MS analysis was carried out to identify SPE components, whereas 32 compounds were identified (89.09%), with main components of benzyl isothiocyanate (BITC) (33.32%) and steroids (34%). Firstly, the consistency of the experimental medicament was accomplished according to ANSI/ADA Specification no 57. SPE assessment as intracanal medicament was conducted through an in vitro assay on 45 single-rooted mandibular premolars inoculated of 5 μL of E. faecalis. Colony-forming units (CFU) were counted before the application of experimental intracanal medicament (CFU-1) and then after seven days of its application (CFU-2). Group I: Siwak extract-based intracanal medicament, Group II positive control group received Ca(OH)2 paste, and Group III: negative control group received no medication. Results: CFU before and after using Siwak based medicament recorded statistically significant reduction (P=0.006) as well as those of Group II when Ca(OH)2 was applied (P=0.01). On comparing both medicaments with Group III, there were significant differences; (P=0.00) and (P=0.007), respectively. Siwak oil extract-based medication proved complete eradication of E. faecalis.Conclusion: SPE has a good potential as an intracanal medicament, besides the cleaning and shaping during endodontic therapy. This finding could be referred to as the high content of BITC bactericidal against pulpal and periodontal pathogens, in synergism with other antimicrobial components, representing 70.71% of SP oil extract.
Leveraging GWAS Data Derived From a Large Cooperative Group Trial to Identify a SNP Cluster Associated With the Risk of Taxane-induced Peripheral Neuropathy
Authors: Lustberg Maryam , Wu Xuan , Fernández-Martínez Juan Luis , de Andrés-Galiana Enrique J. , Philips Santosh , Leibowitz Jeffrey , Schneider Bryan , Sonis Stephen 
Published: February 2021

Abstract
BackgroundChemotherapy-induced peripheral neuropathy (CIPN) is a common toxicity of taxanes for which there is no effective intervention. Genomic CIPN risk determination has yielded promising, but inconsistent results. The present study assessed the utility of a collective SNP cluster identified using novel analytic to describe taxane-associated CIPN risk.MethodsWe analyzed GWAS data derived from ECOG-5103, first identifying SNPs that were most strongly associated with CIPN using Fisher’s ratio. We then ranked ordered those SNPs which discriminated CIPN-positive from CIPN-negative phenotypes based on their discriminatory power and developed the cluster of SNPs which provided the highest predictive accuracy using leave-one-out cross validation (LOOCV).ResultsUsing GWAS aggregate data, we identified a 267 SNP cluster which was associated with a CIPN+ phenotype with an accuracy of 96.1%. ConclusionsIdentification of a 267 SNP cluster could accurately predict CIPN risk. Validation using an independent patient cohort should be performed.
Innate and early immune responses to Yersinia ruckeri in the spleen of rainbow trout (Oncorhynchus mykiss)
Authors: Wang Di , Sun Simeng , Li Shaowu , Lu Tongyan , Shi Dongfang 
Published: February 2021

Abstract
Background: Yersinia ruckeri is a pathogen that can cause enteric redmouth disease in salmonid species, damaging global production of economically important fish including rainbow trout (Oncorhynchus mykiss). Herein, we conducted the transcriptomic profiling of spleen samples from rainbow trout at 24 h post-Y. ruckeri infection via RNA-seq in an effort to more fully understand their immunological responses. Results: We identified 2498 differentially expressed genes (DEGs), of which 2083 and 415 were up- and down-regulated, respectively. We then conducted a more in-depth assessment of 78 DEGs associated with the immune system including CCR9, CXCL11, IL-1β, CARD9, IFN, CASP8, NF-κB, NOD1, TLR8α2, HSP90, and MAPK11, revealing these genes to be associated with 20 different immunological KEGG pathways including the Cytokine-cytokine receptor interaction, Toll-like receptor signaling, RIG-I-like receptor signaling, NOD-like receptor signaling, and MAPK signaling pathways. Additionally, the differential expression of 8 of these DEGs was validated by a qPCR approach and their immunological importance was then discussed. Conclusions: Our findings provide preliminary insight regarding the innate and early immune responses of rainbow trout following Y. ruckeri infection and the base for future studies of host-pathogen interactions in rainbow trout.
Genome Instability-related Long Non-coding RNA in Clear Renal Cell Carcinoma Determined using Computational Biology
Authors: Wang Yutao , Yan Kexin , Bi Jianbin 
Published: February 2021

Abstract
There is evidence that long non-coding RNA (lncRNA) is related to genetic stability. However, the complex biological functions of these lncRNAs are unclear. In the present study, we applied computational biology to identify genome-related long noncoding RNA and identified 26 novel genomic instability-associated lncRNAs in clear cell renal cell carcinoma. We identified a genome instability-derived six lncRNA-based gene signature that significantly divided clear renal cell samples into high-and low-risk groups. We validated it in test cohorts. Based on the above analysis, we identified six lncRNAs related to clear cell carcinoma outcomes and genome stability based on computational biology. To further elucidate the role of the six lncRNAs in the model's genome stability, we performed a gene set variation analysis (GSVA) on the matrix. We performed Pearson correlation analysis between the GSVA scores of genomic stability-related pathways and lncRNA. It was determined that LINC00460 and LINC01234 could be used as critical factors in this study. They may influence the genome stability of clear cell carcinoma by participating in mediating critical targets in the base excision repair pathway, the DNA replication pathway, homologous recombination, mismatch repair pathway, and the P53 signaling pathway. These data suggest that LINC00460 and LINC01234 are crucial for the stability of the clear cell renal cell carcinoma genome.
The Role of Weed Seed Contamination in Grain Commodities as Propagule Pressure
Authors: Ikeda Mafumi , Nishi Takeshi , Asai Motoaki , Muranaka Takashi , Konuma Akihiro , Tominaga Tohru , Shimono Yoshiko 
Published: February 2021

Abstract
The international grain trade is a major pathway for the introduction of alien plants because grain commodities can be contaminated with various weed seeds. To evaluate how alien weed seeds derived from imported grain commodities affect local vegetation in international trading ports, we conducted a vegetation survey on a set of grain landing ports and non-grain landing ports in nine regions throughout Japan to compare the vegetation between these two types of ports. We also surveyed weed seed contamination of wheat imported into Japan, and the contamination rate was calculated for each species based on our survey and previous studies on weed seed contamination. The vegetation clearly differed between the grain landing ports and the non-grain ports. In the grain landing ports, alien species were more abundant than in non-grain landing ports. All indicator species of the grain landing ports were reported to be contaminants in grain commodities. Furthermore, there was a tendency for the more abundant species at the grain landing ports to show higher contamination rates in grain commodities. These results indicate that contaminant seeds spill from imported grain in grain landing ports, and highly contaminated species are likely to become established. We clearly show that weed seed contamination in grain commodities plays an important role in propagule pressure. Gathering information about the prevalence of weeds in grain-exporting countries and monitoring the weed species composition in imported grain commodities is becoming increasingly important for predicting the unintentional introduction of troublesome weeds and identifying effective weed management options.
Computational Study on the Adsorption of H2SiCl2 by Pristine, Al-, and Ga-Doped Boron Nitride Nanosheets: A DFT Study
Authors: Mohammadi Mohsen Doust , abdullah hewa y 
Published: February 2021

Abstract
The density functional techniques (DFT) were put into practice to study the nature of the intermolecular interactions between Dichlorosilane (H2SiCl2) gas molecule with single-walled pristine, Al and Ga-doped boron nitride nanosheets (BNNS, BNAlNS, and BNGaNS, respectively). For performing optimization process, various functionals including PBE0, M06-2X, ωB97XD, and B3LYP-D3 were applied on both of the isolated and complex structures. All of the functionals were used together with split-valence triple-zeta basis sets with d-type Cartesian-Gaussian polarization functions (6-311G(d)). To consider the electronic structure, total density of state (DOS) analysis were employed. Natural bond orbital (NBO), quantum theory of atoms in molecules (QTAIM), and non-covalent interaction (NCI) analyses were also taken on board to discover the nature of intermolecular interactions between gas and nanosheets. The results of electronic structure calculations as well as population analyses has been carefully tabulated and partially depicted. The HOMO-LUMO energy gaps (HLG) were dramatically changed when the dopant atom added to the BNNS. It means the impurity can improve the sensivity and reactivity of the pristine nanosheet; therefore, by absorbing the H2SiCl2 onto the surface of the titled nanosheets, a salient signal can produce in a typical electronic circuit. Among all of the absorbents, BNGaNT shows the most favorable material to design a nanosensor for the studied gas molecule.
Evaluating the Presence of Paresthesia in Patients with Juxta-apical Radiolucency after Third Molar Surgery: A Case-control Study
Authors: Hasani Mahvash , Razavi Nasim , Haghnegahdar Abdolaziz , Zarifi Motahhareh 
Published: February 2021

Abstract
Background: Juxta-apical radiolucency (JAR) has been presented as a radiographic sign, suggestive of the IAN injury through third molar surgery. This study aimed to evaluate the relation of JAR with paresthesia in cone-beam computed tomography (CBCT) images and to determine whether the presence of JAR is related to tooth angulation, proximity to the mandibular canal, position to the IAN and thinning of the cortical plates.Methods: Of an initial sample of 545 mandibular third molars, a total of 75 JAR and 75 control teeth were evaluated by CBCT. The association of JAR with the IAN, position to IAN, lingual cortical plate thinning, and tooth angulation was investigated in this study. Temporary and permanent paresthesia were also examined in the subjects. Descriptive statistics, Chi-square test, and Fisher’s exact test were performed for statistical analysis.Results: A significant relationship was found between JAR and temporary paresthesia (P=0.034). However, there was no case of permanent paresthesia. JAR showed no significant relationship with the tooth angulation, cortical plate thinning, position to IAN and proximity to the mandibular canal. The lingual position of JAR relative to the mandibular canal was related to the presence of paresthesia in the JAR group. Also, most cases of paresthesia showed some degree of lingual cortical plate thinning (P=0.012). Conclusion: JAR is generally in contact with the mandibular canal, and some degree of cortical thinning can be found in most cases. In this study, JAR was significantly related to temporary paresthesia. The present findings may indicate the increased risk of nerve injury during the surgical removal of third molars.
Impact of Gestational Weight Gain on Maternal and Neonatal Clinical Outcomes: A Retrospective Cohort Study.
Authors: Hassan Mahmoud F. , Rund Nancy Mohammed Ali , Yehia Amr Helmy , Alghanimi Salha A. , Abdallah Enas A.A. 
Published: February 2021

Abstract
We aim to explore the association between gestational weight gain and adverse events during pregnancy. A retrospective study was conducted to evaluate the perinatal outcomes in singleton women whose weight gain during pregnancy was below, within, or above the 2009 Institute of Medicine's (IOM) guidelines, and delivered between 24 and 42 weeks’ gestation. GWG was derived using weight at delivery minus the pre-pregnancy or first trimester weight. Our results indicated that mothers with low GWG had increased odds of having small-for-gestational-age neonates (adjusted OR 1.202; 95% CI 1.031-1.403), and preterm birth (adjusted OR 2.03; 95% CI 1.769-2.439), but decreased odds of having macrosomia (adjusted OR 0.523; 95% CI 0.24-0.991). Meanwhile, mothers with GWG above the IOM recommendations had higher odds of having hypertensive disease of pregnancy (adjusted OR 2.07; 95% CI 1.314-3.535), gestational diabetes (adjusted OR 1.227; 95% CI 1.038-1.448), cesarean section (adjusted OR 1.34; 95% CI 1.279-1.512), induced labor (adjusted OR 1. 219; 95% CI 1.051-1.409), failure of induced labor (adjusted OR 1.432; 95% CI 1.03-1.992), macrosomia (adjusted OR 1.987; 95% CI 1.384-2.725), and shoulder dystocia (adjusted OR 1.715; 95% CI 1.292-2.18. In conclusion, GWG is an important predictor of adverse maternal and neonatal outcomes during pregnancy.
Contraceptive situation and Influencing Factors in Guangdong Province: A comparative questionnaire study
Authors: JIANG FAN , Qu Yanxia , Lin Peixuan , Li Li , Xuan Qingshan , He Yaojuan , Zhang Aihua , Li Qingfeng 
Published: February 2021

Abstract
BackgroundThe aim of our study is to describe the status of induced abortion and contraceptive use in reproductive women and make clear the correlated factors in Guangdong province.MethodA self-administered questionnaire survey was conducted separately in 1839 individuals aged 18–49 and 900 health care providers from Guangdong province. The content of questionnaire was based on status of induced abortion and contraceptive use for the former and problems concerning contraceptive services for the latter. Systematic random sampling was used and data were analyzed using SPSS 19.0. Descriptive statistics and binary logistic regression were used in this study.Results30.61% of participants experienced the induced abortion. The rate of repeated abortion was 19.96% and it was 20.45% in persons under 20 years old. 18.23% of 1839 individuals chose LARC as the main contraceptive method. The females with college degree(Odds ratio, OR = 1.867; 95% confidence intervals 95%CI: 1.175–2.969), technologists(OR = 2.291; 95%CI: 1.063–4.936) and the persons whose monthly income were of between 3000–5000¥(OR = 1.920; 95%CI: 1.204–3.065) were more likely to use LARC. The younger females less than 30 years old and never using PAC services had lower odds of using LARC. The rate of post abortion care performance was merely 12.23%. Age, monthly income, occupation, living conditions and obtaining free contraceptives in time were all strongerly influence factors for the use of post-abortion care(P < 0.01). The satisfaction rate of free contraceptive services was about 57.44%. Variety uniformity, obtaining inconveniently and worrying about the quality were the main reasons. 66.22% of hospitals set up the department of family planning in our study. Highly work intensity(54.67%) and less leadership (40.22%) influenced health care providers to provide family planning services.ConclusionThe abortion rate was high especially in young women. There were many problems affecting contraceptive services which damaged women’reproductive health. Increasing government investment for family planning services, strengthening the construction of the family planning department and performing post abortion care and long-acting reversible contraception by taking relevant steps would be useful measures for improving current contraceptive status.
Oral Administration of Lactobacillus Rhamnosus Ameliorates the Progression of Osteoarthritis by Inhibiting Joint Pain and Inflammation
Authors: Jhun JooYeon , Cho Keun-Hyung , Lee Dong hwan , Kwon Ji Ye , Woo Jin Seok , Kim Jiyoung , Na Hyun Sik , Park Sung-Hwan , Kim Seok Jung , Cho Mi-La 
Published: February 2021

Abstract

Osteoarthritis (OA) is the most common form of arthritis and age-related degenerative joint disorder, which adversely affects quality of life and causes disability. However, the pathogenesis of OA remains unclear. This study was performed to examine the effects of Lactobacillus rhamnosus in OA progression. OA was induced in 6-week-old male Wistar rats by monosodium iodoacetate (MIA) injection, and the effects of oral administration of L. rhamnosus were examined in this OA rat model. Pain severity, cartilage destruction, and inflammation were measured in MIA-induced OA rats. The intestines were isolated from OA rats, and the intestinal structure and inflammation were measured. Protein expression in the dorsal root ganglion was analyzed by immunohistochemistry. The effects of L. rhamnosus on mRNA and protein expression in chondrocytes stimulated with interleukin (IL)-1β and lipopolysaccharide (LPS) were analyzed by real-time polymerase chain reaction (RT-PCR) and enzyme-linked immunosorbent assay (ELISA). Pain severity was decreased in L. rhamnosus-treated MIA-induced OA rats. The levels of expression of MCP-1, a potential inflammatory cytokine, and its receptor, CCR2, were decreased, and GABA and PPAR-γ expression were increased in L. rhamnosus-treated OA rats. The inflammation, as determined by IL-1β, and cartilage destruction, as determined by MMP3, were also significantly decreased by L. rhamnosus in OA rats. Intestinal damage and inflammation were also improved by L. rhamnosus. In human OA chondrocytes, TIMP1, TIMP3, SOX9 and COL2A1 which are tissue inhibitors of MMP, and IL-10, an anti-inflammatory cytokine, were increased by L. rhamnosus.L. rhamnosus treatment led to decreased pain severity and cartilage destruction in a rat model of OA. Intestinal destruction and inflammation were also decreased by L. rhamnosus treatment. Our findings suggested the therapeutic potential of L. rhamnosus in OA.