bluuebunny/crossref_metadata_2025_split huggingface dataset:
Exploring the configuration space of
elemental carbon with empirical and machine learned interatomic
potentials
Authors: Marchant George , Caro Miguel , Karasulu Bora , Bartok-Partay Livia 
Published: February 2023

Abstract
In the present work we detail how the many-body potential energy landscape of elemental carbon, as described by interatomic potentials, can be explored by utilising the nested sampling algorithm, allowing the calculation of their pressure-temperature phase diagram up to high pressures. We present a comparison of four interatomic potential models: Tersoff, EDIP, GAP-20 and its recently updated version, GAP-20U. Our evaluation is focused on their macroscopic properties, particularly on their melting transition and on identifying thermodynamically
stable solid structures up to at least 100 GPa. The studied models all form graphite structures upon freezing at lower pressure, then the diamond structure as the pressure increases. In the cases of the Tersoff, EDIP and GAP-20U potentials we were able to locate the transition between these phases. We placed particular focus on the state-of-the-art machine-learned models, the GAP-20 and GAP-20U, and calculated their phase diagrams up to 1 and 0.1 TPa, respectively, to evaluate their predictive capabilities well outside of the models’ fitting range. The phase diagrams of the GAP models showed remarkably good agreement with the experimental phase diagram up to 200 GPa. However, we found that the accuracy of the models’ descriptions of graphite was adversely affected by the relative stability of phases with incorrect layer spacing. By adding a suitable selection of graphite structures to the GAP training set and re-training the model, we have derived an improved model — referred to as the GAP-20U+gr — that suppresses erroneous local minima in the graphitic energy landscape. At extreme high pressure nested sampling identified two novel stable solid structures in the GAP-20 model, a strained diamond structure above 270 GPa and a strained hexagonal-close-packed structure above 890 GPa. However, the stability of these two phases were not confirmed by DFT calculations, highlighting potential routes to further improve the GAP model.
Gender Discrimination of Date Palm (Phoenix dactylifera L.) Using High-Resolution Melting Analysis
Authors: Sawongta Nipitpong 
Published: February 2023

Abstract
Date palm (Phoenix dactylifera L.) is dioecious plant, having separate male and female flowers with late initial reproductive age. In order to produce dates, it is important for the agriculturalist to know the gender of the date palm because the date can only be collected from females. High-Resolution Melting (HRM) analysis is a powerful molecular technique for identifying species, cultivars, and gender of living organisms. Therefore, this study aims to use the HRM analysis for sex discrimination of the date palm cultivar Deglet Nour. This research is divided into three main parts, including (i) collecting the nucleotide sequences of the 12th chromosome, which are the single nucleotide polymorphisms (SNPs) region and the gene region, as markers for gender identification; (ii) selecting candidate primers for sex identification requires designing primers and performing simulation HRM analysis using uMELT software; and (iii) conducting in vitro HRM analysis with the candidate primers to differentiate the gender of the date palm. The difference in melting curve profile and melting temperatures (Tm) between the genders were used to determine the sex of date palms. It is found that the most suitable primer for gender identification of the date palm by HRM analysis is the TIF2 primers (gene region). Male and female melting curves generated from TIF2 primers can be clearly separated. In addition, melting temperature of male and female date palm were also different. The results demonstrate that the HRM coupled with TIF2 primers is a powerful molecular technique for sex discrimination of the date palm cultivar Deglet Nour.
The Efficacy and Safety of Canaloplasty Vs Trabeculectomy Either Standalone or Combined with Cataract Surgery: An Updated Meta-Analysis
Authors: Abdelaal Abdelaziz , Badr Helmy , Serhan Hashem Abu , Elmallahy Mohamed , Ebrahim Mohamed , Abuelazm Mohamed , Abdallah Ahmed , Ebrahim Abdulrahman , Katamesh Basant E. , Abdelazeem Basel 
Published: February 2023

Abstract
To compare the efficacy and safety between trabeculectomy (TE) and canaloplasty (CP) either as standalone or combined with phacoemulsification (PTE and PCP). Nine databases were searched for studies reporting efficacy and safety of TE/PTE and CP/PCP. Efficacy endpoints included postoperative intraocular pressure (IOP), complete, and qualified success, while safety endpoints included failure, revision surgery, and complications. STATA was used to pool the crude mean difference (MD) or log odds ratio (logOR) for continuous and categorical outcomes, respectively. Fourteen studies were included. TE/PTE was associated with lower IOP when compared to CP/PCP [MD=-2.55; 95%CI=-3.30: -1.80, I2 = 61.43%]. Similarly, TE/PTE was associated with significantly higher odds of complete [logOR = 1.20; 95%CI = 0.79:1.61, I2 = 7.41] and qualified success [logOR = 0.64; 95%CI = 0.16:1.13, I2 = 0%] when compared to CP/PCP, respectively. Although no significant differences in failure and revision surgery were noted between TE/PTE and CP/PCP, in the TE subgroup, a significant reduction in failure was observed as compared to CP [logOR=-0.82; 95%CI=-1.61: -0.04, I2 = 28.18%]. TE/PTE was associated with higher odds for hypotony and choroidal detachment and lower odds for Descemet’s membrane detachment and hyphema. TE/PTE has superiority over CP/PCP regarding IOP control and revision surgery rates. However, the certainty of these findings is low to very low.
A method for mitigating the phase imbalance and insertion loss in the optical mm- wave system for 5G communication network
Authors: Mahmood Rawa Muayad , Yaakob Syamsuri , Ahmad Faisul Arif , Anas Siti Barirah Ahmad , Zan Zuraidah , Kadir Muhammad Zamzuri Abdul , Beson Mohd Rashidi Che , Mahmud Azwan 
Published: February 2023

Abstract
In this paper, an optical millimeter-wave (mm-wave) generated using a signal Mach Zehnder modulator (MZM) is proposed for a 5G communication network. This paper presents the mitigation process of phase imbalance and the insertion loss of the optical mm-wave signal. In the proposed system, the phase imbalance can be reduced by tuning the phase of the optical mm-wave signal at the optical stage. The best results are obtained when tuning the phase of 5π/12 at the phase shift. From the results, the phase imbalance influences the insertion loss and the amplitude of the mm-wave signal. In this study, the phase imbalance decreased from 0.4° to 0.1°. Mitigating the phase imbalance can lower the phase noise to 0.2°.
Morpho-physiological mechanisms of two different quinoa ecotypes to resist salt stress
Authors: Hussin Sayed A. , Ali Safwat H. , Lotfy Muhammad E. , El-Samad Emad H. Abd , Eid Mohamed A. , Abd-Elkader Ali M. , Eisa Sayed S. 
Published: February 2023

Abstract
Background: Quinoa (Chenopodium quinoa Wild.) is a facultative halophyte, showing various mechanisms of salt resistance among different ecotypes cultivars. This study aimed to determine salt resistance limits for a Peruvian sea level ecotype “Hualhuas” and Bolivian salar ecotype “Real” quinoa cultivars and elucidate individual mechanisms conferring differences in salt resistance of these cultivars. The plants were grown in sandy soil and irrigated with various water salinity levels (0, 100, 200, 300, 400, and 500 mM NaCl) under greenhouse conditions.
Results: At high salinity treatment, plant growth was reduced by 80% and 87% in Hualhuas and Real, respectively. Both cultivars were able to lower the osmotic potential of all organs due to substantial Na+ accumulation. However, Hualhuas plants exhibited distinctly lower Na+ contents and consequently higher K+/Na+ ratio compared to Real plants, suggesting a more efficient control mechanism on Na+ loading and better K+ retention in Hualhuas plants. Net CO2 assimilation rates (Anet) were reduced, being only 22.4% and 36.2% of the control values in Hualhaus and Real, respectively, at the highest salinity level. At full-strength salinity, Hualhuas plants showed lower stomatal conductance and transpiration rates, but higher photosynthetic water use efficiency, indicative of an efficient control mechanism over the whole gas-exchange machinery.
Conclusion: These results reveal that Hualhuas is a promising candidate in terms of salt resistance and biomass production compared to Real.
Ubiquitin Ligase MDM2 mediated endothelial inflammation in Kawasaki disease vasculitis development
Authors: Xu Lei , Zhu Li-yan , Qian Guang-Hui , Huang Hong-Biao , Huang Cheng-Cheng , Qin Jie , Zheng Yi-Ming , Sun Ling , Ren Yan , Lv Hai-Tao , Ding Yue-Yue 
Published: February 2023

Abstract
Background
Kawasaki Disease (KD), which is mainly characterized by systemic small and medium vasculitis in children, can lead to coronary artery lesions (CALs). Our previous study identified that STAT3 signaling plays essential roles during the acute phase of KD patients. However, whether its interacted protein MDM2 (Murine double minute 2), which functions as an E3 ligase is likewise involved in KD pathogenesis still unknown and remains to be investigated.
Methods
The role of MDM2 was investigated using the whole-blood samples from KD patients with CALs before and after IVIG treatment. The plasma and peripheral blood mononuclear cells were respectively isolated and collected. Meanwhile, a Candida albicans cell wall extracts (CAWS)‑induced KD mouse model was used to analyze the in vivo functions of MDM2. Real-time PCR, western blotting, and enzyme-linked immunosorbent methods were used respectively in the HCAECs or other cells to investigate the molecular mechanism of MDM2 involved in KD.
Results
MDM2 levels were downregulated, and STAT3 and VEGFA levels were upregulated in clinical blood samples from KD patients with CAL in the acute stage and in the mouse model. In the mouse model and HCAECs, MDM2 co-located with STAT3 . In vitro, the endogenous STAT3 protein level in HCAECs was upregulated after MDM2knockdown. Overexpression of MDM2 increased STAT3 ubiquitination and endogenous STAT3 and VEGFA levels decreased significantly. Additionally, the E3 ubiquitin ligase MDM2 can target its endogenous substrate STAT3 for ubiquitination.
Conclusions
Decreased MDM2 levels can reduce STAT3 ubiquitination, leading to STAT3 activation and the induction of VEGFA transcription, which is involved in the vascular endothelial inflammatory injury process of KD.
Segregation behavior of Cu and Sb with inclusion defects on local corrosion
Authors: Xiao Kui , Li Zhaoliang , Chen Junhang , Xue Wei , Yin Chenghui , Song Jialiang 
Published: February 2023

Abstract
The distribution characteristics of corrosion-resistant elements in low-alloy steel affected the initial corrosion behavior of matrix. In this article, the segregation behavior of elements at grain boundaries and pearlite defects in low-alloy steel and the precipitation behavior of Cu in inclusion had been studied. The precipitation of Cu in the inclusion was beneficial to the reduction of grain boundary segregation. And Cu had the ability to capture Sb and Ni. Cu was involved in the local corrosion initiation of inclusions, during which Cu and Sb were oxidized to corresponding Cu2O and Sb2O3, and distributed in the corrosion products. Under the influence of the segregation of elements at the grain boundaries, the local corrosion spreading process was carried out, and the internal part of the crystal was preferentially corroded. Cr was enriched in the cementite of pearlite and took part in the corrosion process, resulting in the formation of CrO3.
Effect of the tutorial training programme based on ADDIE model on research capacity of clinical nurses: a quasi-experimental study
Authors: Dong Xiaoqian , Wang Sha , Li Lijun , Duan Yinglong , Zheng Feng , Liu Min , Gan Gang , Xie Jianfei , Ding Siqing , Cheng Andy SK 
Published: February 2023

Abstract
Background
Over the last two decades, global continuous efforts have been devoted to improving nursing research capacity. However, it is currently at a low to medium level in China and the training measures still have shortcomings such as lack of theoretical guidance, single content, short time and poor learning effect. To design a training programme about research capacity based on the ADDIE(analysis, design, development, implementation, and evaluation, ADDIE) model and the tutor system for clinical nurses and evaluate its effect through before-and-after control.
Methods
A quasi-experimental, one-group, self-control, and pretest-posttest design study. From July 2020 to June 2021, forty-five clinical nurses from a hospital were enrolled and underwent the training programme based on ADDIE model, which included five stages. By special scales, the nurses’ levels of research capacity, self-efficacy and professional values were evaluated on a six months of theory training, a six months of practice training, and a follow-up six months after the training. Finally, forty nurses completed this study. SPSS25.0 software was used for analysis.
Results
The score of research capacity before training was 43.42 ± 22.50. The total scores of research capacity and its all dimensions, total scores of general self-efficacy and nurses professional values differed significantly in before, immediately after training and six months after training (P < 0.001). Six months after training, the numbers of application for scientific research projects, papers published and patent applications, were higher than those pre-training (P < 0.05).
Conclusions
The research capacity of clinical nurses was at a medium level. The tutorial training programme based on ADDIE model is beneficial to improve research capacity, self-efficacy and professional values of clinical nurses, and promote the output of research and innovation projects.
Comparison of the relative impacts of acute consumption of an inulin-enriched diet, milk kefir or a commercial probiotic product on the human gut microbiome and metabolome
Authors: Cotter Paul , Walsh Liam , Walsh Aaron , Perez Isabel Garcia , Crispie Fiona , Costabile Adele , Ellis Richard , Finlayson Jim , Finneganan Laura , Claesson Marcus , Holmes Elaine 
Published: February 2023

Abstract
It has been established that the human gut microbiota is central to health, and, consequently, there has been a growing desire to positively modulate its composition and/or function through, for example, the use of fermented foods, prebiotics or probiotics. Here, we compare the relative impact of the daily consumption of an inulin-enriched diet, a commercial probiotic-containing fermented milk product (FMP), or a traditional kefir FMP over a 28-day period on the gut microbiome and urine metabolome of healthy human adults. None of the treatments resulted in significant changes to clinical parameters or biomarkers tested. However, shotgun metagenomic analysis revealed that kefir consumption resulted in a significant change in taxonomy, in the form of an increased abundance of the sub-dominant FMP-associated species Lactococcus raffinolactis, which further corresponded to shifts in the urine metabolome. Overall, our results indicated that daily consumption of a single portion of kefir alone resulted in detectable changes to the gut microbiota and metabolome of consumers.
Comparison of Dental Flosses – An Investigation of Mechanical Properties and Subjective Preference
Authors: Huang Zhongjin , Broadbent Jonathan M. , Choi Joanne Jung Eun 
Published: February 2023

Abstract
Objective
To investigate the properties (tensile strength, roughness, abrasiveness) of different dental flosses and how these properties relate to subjective preference for floss by users.
Materials and method
Four flosses of differing compositions were selected (polytetrafluoroethylene, nylon, silk, and ultra-high-molecular-weight polyethylene). Tensile strength (TS) was measured utilising a universal testing machine (n = 10/group). Surface roughness (Ra) was measured on 3D reconstructed models of scanning electron microscope (n = 5/group). Abrasiveness was measured through block-on-ring tests against human enamel (n = 3/group). Subjective preference for floss was measured by asking a sample of 16 individuals to use each floss for an 8 day period using a split-mouth design.
Results
Highest TS was found in ultra-high-molecular-weight polyethylene floss (194.18 \(\pm\) 24.61 MPa) while the lowest TS was found in polytetrafluoroethylene floss (11.78 \(\pm\) 0.77 MPa). Silk floss had the highest Ra (0.304 \(\pm\) 0.025 µm) while polytetrafluoroethylene floss had the lowest (0.048 \(\pm\) 0.003 µm). In-vitro abrasion testing of the flosses identified in no significant differences between the flosses in causing wear on tooth enamel. Subjective ratings of flosses indicated polytetrafluoroethylene floss to be most preferred and nylon floss to be least preferred.
Conclusion
Polytetrafluoroethylene was rated more highly by participants than the other floss types. This floss had the lowest surface roughness and the lowest tensile strength.
Clinical Relevance:
This is the first study to comprehensively compare a wide range of mechanical properties of commercially available dental floss and the results of this study can provide guidance for the recommendation of dental floss for oral hygiene routines
A set of vectors and strains for chromosomal integration in fission yeast
Authors: Matsuyama Akihisa , Hashimoto Atsushi , Nishimura Shinichi , Yoshida Minoru 
Published: February 2023

Abstract
The expression of heterologous genes is an important technique in yeast genetics. In fission yeast, the leu1 and ura4 genes have been used mainly as selectable markers for heterologous expression. To expand the repertoire of selection markers available for heterologous expression of genes, here we developed new host-vector systems employing lys1 and arg3. By employing genome editing with the Crispr/Cas9 system, we isolated several alleles of lys1 and arg3, each having a critical mutation in the ORF region. In parallel, we developed a set of vectors that complement the amino acid auxotrophy of lys1 and arg3 mutants when integrated into each locus. Using these vectors in combination with the previously developed integration vector pDUAL, we successfully observed the localization of three proteins in a cell simultaneously by fusing them with different fluorescent proteins. Thus, these vectors enable combinational expression of heterologous genes, which addresses increasingly diverse experimental challenges.
Integrative analysis of uterine leiomyoma genetics, epigenomics, and single-cell transcriptomics reveals causal genetic variants, gene targets, and cell types
Authors: Buyukcelebi Kadir , Seker-Polat Fidan , Abdula Fatih , Kinali Meric , Adli Mazhar 
Published: February 2023

Abstract
Uterine fibroids (UF), also called leiomyomas, are observed in nearly 70% of women of reproductive age. These tumors disrupt normal uterine function and cause significant physical and psychological health problems. Although heritable genetics is a significant risk factor, specific genetic variations and gene targets causally associated with UL are poorly understood. We performed a meta-analysis on existing fibroid genome-wide association studies (GWAS) and integrated the identified risk loci and potentially causal single nucleotide polymorphisms (SNPs) with epigenomics (H3K27me3), transcriptomics (RNA-Seq), 3D chromatin organization (Hi-C) and single-cell atlas (scRNA-Seq) of primary samples from UF patients. The integrative analysis identified 24 risk loci and 394 potential gene targets associated with UF. Among these, 106 of them were differentially expressed in UF tumors. Critically, the integrative analysis with single-cell RNA sequencing revealed the cell types with aberrant expression of these target genes in normal and UF tissue. Finally, CRISPR-based epigenetic manipulation (dCas9-KRAB) of two risk loci in a disease-relevant cell type fine-mapped the gene targets. These findings and the methodological approach indicate the effectiveness of integrative multi-omics data combined with locus-specific epigenetic editing approaches to identify disease-relevant risk loci and their target genes.
A clinical experience-based Chinese herbal formula improves ethanol metabolism, drunken behavior and hepatic steatohepatitis based on both acute and acute-on-chronic (NIAAA) mice models
Authors: Gao Han , Li Zhen , Liu Yao , Zhao Yong-kang , Cheng Cheng , Qiu Feng , Gao Yuan , Lu Ya-wen , Song Xin-hua , Wang Jia-bo , Ma Zhi-tao 
Published: February 2023

Abstract
Background: Bao-Gan-Xing-Jiu pills (BGXJW) is a clinical experience-based Chinese herbal formula. Its efficacy, pharmacological safety, targeted function, process quality, and other aspects have met the evaluation standards and the latest requirements of preparations. It could prevent and alleviate the symptoms of drunkenness and alcoholic liver injury clinically. The present work aims to elucidate whether BGXJW could protect against drunkenness and alcoholic liver disease in mice and explore the associated mechanism.
Material and methods: We used acute-on-chronic (NIAAA) mice model to induce alcoholic steatosis, and alcohol binge-drinking model to reappear the drunk condition. BGXJW at indicated doses were administered by oral gavage respectively to analyze its effects on alcoholic liver injury and the associated molecular mechanisms.
Results: BGXJW had no cardiac, hepatic, renal, or intestinal toxicity in mice. Alcoholic liver injury and steatosis in the NIAAA mode were effectively prevented by BGXJW treatment. BGXJW increased the expression of alcohol metabolizing enzymes ADH, CYP2E1, and ALDH2 to enhance alcohol metabolism, inhibited steatosis through regulating lipid metabolism, counteracted alcohol-induced upregulation of lipid synthesis related proteins SREBP1, FASN, and SCD1, meanwhile it enhanced fatty acids β-oxidation related proteins PPAR-α and CPT1A. Alcohol taken enhanced pro-inflammatory TNF-α, IL-6 and down-regulated the anti-inflammatory IL-10 expression in the liver, which were also reversed by BGXJW administration. Moreover, BGXJW significantly decreased the blood ethanol concentration and alleviated drunkenness in the alcohol binge-drinking mice model.
Conclusions: BGXJW could effectively relieve drunkenness and prevent alcoholic liver disease by regulating lipid metabolism, inflammatory response, and alcohol metabolism.