bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analysis of critical protein-protein interactions of SARS-CoV-2 capping and proofreading molecular machineries towards designing dual target inhibitory peptides
Authors: Arabi-Jeshvaghani Fatemeh , Javadi‐Zarnaghi Fatemeh , Ganjalikhany Mohamad Reza 
Published: August 2022

Abstract
Coronaviruses (CoVs) have been the cause of human respiratory syndromes for many years. In recent years, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), as the cause of the coronavirus disease (COVID-19) global pandemic has imposed enormous health care issues and economic burden. The recent emerging SARS-CoV-2 variants with higher transmissibility and substantial immune evasion, have highlighted the importance of sustainable and imperative solutions to develop novel therapeutics other than vaccination to combat CoVs infections. In the search for promising antivirals for coronaviruses, besides receptor recognition and virus entry, efforts have concentrated on targeting other molecular machineries of the virus, such as the replication/transcription complex (RTC). Here, the key interacting residues that mediate the protein-protein interactions (PPIs) of nsp10 with nsp16 and nsp14 have been comprehensively analyzed. Consequently, the key residues' interaction maps, interaction energies, structural networks, and dynamics were investigated. Nsp10 stimulates nsp14's exoribonuclease (ExoN) as well as nsp16's 2′O-methyltransferase (2′O-MTase). Nsp14 ExoN is an RNA proofreading enzyme that supports replication fidelity. Nsp16 2′O-MTase is responsible for completion of the RNA capping to ensure efficient replication and translation and escape from the host cell's innate immune system. The results of PPIs analysis proposed crucial information which was applicable to anti SARS-CoV-2 drug design. Based on the PPIs analysis, a set of dual-target peptide inhibitors were designed on the basis of the predicted shared protein-protein interfaces of the nsp16-nsp10 and nsp14-nsp10 interactions. The peptides were evaluated by molecular docking, peptide-protein interaction analysis, and molecular mechanics Poisson–Boltzmann surface area (MM-PBSA) calculations, and then were further optimized by in silico saturation mutagenesis. According to the predicted evolutionary conservation among CoVs for the target residues that interact with the designed peptides, the designed peptides have the potential to be developed as dual target pan-coronavirus inhibitors.
High parenteral carbohydrate intakes in patients with chronic intestinal failure are associated with accumulation of advanced glycation end products.
Authors: Tetard Candice , Poullenot Florian , Pellet Gauthier , Clouzeau Haude , Rebouissoux Laurent , Wilsius Eva , Kerlogot Laurianne , Chevrier Constance , Laharie David , Lamireau Thierry , Enaud Raphaël 
Published: August 2022

Abstract
Advanced glycation end-products (AGE) are the product of non-enzymatic reactions between reduced carbohydrates, peptides, lipids, nucleic acids. AGE accumulate over time, they are considered as the metabolic memory. In certain pathologies such as diabetes mellitus, AGE accumulation is increased and correlated with vascular complications. Patients with chronic intestinal failure dependent on parenteral nutritional have long-term intravenous carbohydrate intakes. The assessment of AGE levels in this population has never been performed. We measured skin AGE levels by auto-fluorescence in 23 adults followed in a tertiary center for chronic intestinal insufficiency and treated with home parenteral nutrition that we compared to the values of the general population. We also analyzed factors associated with elevated AGE. More than half (n=13) had elevated AGE. The presence of elevated AGE was significantly associated with higher parenteral carbohydrate intakes. Patients with elevated AGE had higher intravenous carbohydrate intakes (median 3.3g/kg/day [1.84;3.62]), compared to patients with normal AGE (1.79g/kg/d [1.45;2.26], p=0.03). The presence of chronic renal failure was also associated with elevated AGE. This preliminary study suggests that AGE accumulation is increased in subjects on prolonged parenteral nutrition. Studies with larger numbers will be necessary to confirm this hypothesis and to evaluate the association with cardiovascular events.
Predictive value of TRPV2 expression from peripheral blood mononuclear cells on the early recurrence of atrial fibrillation after radiofrequency catheter ablation
Authors: Ling Xuebin , Wang Jun , Qin Xue , Lin Chufen , Jie Wei , Chen Yane , Fu Dajia , Yang Yang , Meng Qingwen , Lin Jing , Liu Hui , Li Tianfa , Guo Junli 
Published: August 2022

Abstract
Background:: Recent study has shown that the transient receptor potential vanilloid 2 (TRPV2) channel was exclusively upregulated in patients with atrial fibrillation (AF), and that this overexpression might be detrimental for occurrence and maintenance of AF. We aimed to characterize the expression levels of TRPV2 mRNA in peripheral blood mononuclear cells (PBMCs) with/without early recurrence of atrial fibrillation (ERAF) after radiofrequency catheter ablation (RFCA), and to find a reliable predictor for ERAF. Methods: 65 patients of AF, who underwent RFCA successfully, then divided into two groups according to ERAF during following 3 months. PBMCs were isolated from whole blood by Ficoll gradient centrifugation before and after RFCA. Gene set enrichment analysis (GSEA) was performed to evaluate TRPV channels expression levels and KEGG mapping was used for pathway enrichment analysis. Results: There was no significant difference in the TRPV2 mRNA expression level between the two groups before RFCA, while without ERAF group of TRPV2 expression was markedly reduced compared to ERAF group after RFCA. Moreover, the number of TRPV2 expression was confirmed as an independent predictor for the first time through receiver operation characteristic (ROC) and Kaplan-Meier survival curve analysis. It should be pointed out that the above results were only used to predict ERAF, and have no predictive significance for late recurrence of atrial fibrillation (LRAF) according to the current data. Additionally, ERAF was inversely correlated with P wave dispersion (PWD). KEGG mapping further clustered 41 pathways, revealing that ‘‘cGMP-PKG signaling pathway’’ was significantly enriched. Conclusions: We firstly assume that downregulated expression of peripheral TRPV2 appear in patients without ERAF after RFCA. TRPV2 may thus represent a novel predictor of early phase after successful radiofrequency ablation.
Investigating nicotine pathway-related long noncoding RNAs in Nicotiana tabacum
Authors: Xie Xiaodong , Jin Jingjing , Wang Chen , Lu Peng , Li Zefeng , Tao Jiemeng , Cao Peijian , Xu Yalong 
Published: August 2022

Abstract
Background
Long noncoding RNAs (lncRNAs) are transcripts longer than 200bp with low or no protein-coding ability, which play essential roles in various biological processes in plants. Tobacco is an ideal model plant for studying nicotine biosynthesis and metabolism, and there is little research on lncRNAs in this field. Therefore, how to take advantage of the mature tobacco system to profoundly investigate the lncRNAs involved in the nicotine pathway is intriguing.
Results
By exploiting 549 public RNA-Seq datasets of tobacco, 30,212 lncRNA candidates were identified, including 24,084 large intervening noncoding RNAs (lincRNAs) and 5,778 natural antisense transcripts (NATs), and 350 intronic noncoding RNAs (incRNAs). Compared with protein-coding genes, lncRNAs have distinct properties in terms of exon number, sequence length, A/U content, and tissue-specific expression pattern. incRNAs showed an asymmetric evolutionary pattern, with a higher proportion (68.71%) expressed from N.sylvestris (S) subgenome. We predicted the potential cis/trans-regulatory effects on protein-coding genes. One hundred four lncRNAs were detected as precursors of 30 known miRNA family members, and 110 lncRNAs were expected to be the potential endogenous target mimic for 39 miRNAs. By combining the results of weighted gene co-expression network analysis with the differential expressed gene analysis of topping RNA-seq data, we constructed a sub-network containing eight lncRNAs and 25 nicotine-related coding genes. We confirmed that seven lncRNAs could be affected by MeJA treatment and transcription factor NtMYC2 using a quantitative PCR assay.
Conclusions
Nicotine pathway-related lncRNA candidates were predicted and investigated in our study. We verified that seven lncRNAs could be affected by MeJA treatment and the transcription factor NtMYC2. Results suggested that they are involved in the nicotine pathway. Our findings further deepened the understanding of the features and functions of lncRNAs and provided new candidates for regulating nicotine biosynthesis in tobacco.
Templing and Temple Search-Same Height Hashing
Authors: Tripathi Rajeev Ranjan Kumar , Singh Pradeep Kumar , Singh Sarvpal 
Published: August 2022

Abstract
In the current computing era, data are generating in exponential manner. These data are processed to extract information. This processing demands many query operations which in-turn requires the application of hashing for fast process of query operations. Cuckoo hashing is more efficient than conventional hashing techniques like open addressing, chaining and coalesced hashing. Because of simplicity and ease of use Cuckoo hashing has been used in real-world applications. Inherent problem associated with hashing is data collision and Cuckoo hashing also experiences the same. Cuckoo hashing uses endless loops,that results into high insertion latency and rehash operations. The idea behind Templing and Temple Search is to develop a robust hashing technique based on B-Tree that can efficiently handle the problem of data collisions without any changes in its underlying structure. In each bucket a separate B-Tree of same height is maintained to store the keys. Comprehensive analysis of experimental results demonstrate the potential of Templing and Temple Search. Templing and Temple Search addresses all challenges associated with Cuckoo hashing: intensive data migration, inefficient memory usages and high insertion latency.In future,Templing and Temple Search technique has great potential of its applications in the area of distributed hashing and in parallel hashing.
Adjunctive Nd:YAG laser irradiation in the treatment of stage III/IV periodontitis. A 12-month, randomized, controlled trial
Authors: Markou Nikolaos , Papadelli Anastasia , Nikolidakis Dimitris , Pepelassi Eudoxie , Madianos Phoebus , Karoussis Ioannis K. 
Published: August 2022

Abstract
Objectives: The aim of this triple-arm parallel prospective, randomized controlled 12-month trial was to evaluate in stage III/IV periodontitis the clinical efficacy of the adjunctive use of Nd:YAG laser, applied with two different protocols, to full-mouth scaling and root planing (FMS), compared to FMS alone. Materials and methods: Sixty healthy stage III/IV periodontitis patients were treated with FMS (control) or combined FMS/single Nd:YAG laser irradiation (3 W, 150 mJ, 20 Hz with Micro Short Pulse 100 µs) (Laser 1) or combined FMS/ double Nd:YAG laser irradiation (1 week interval, 2.0 W, 200 mJ, 10 Hz with Micro Short Pulse 100 µs) (Laser 2). Clinical parameters were evaluated at baseline, 6 weeks, 3, 6 and 12 months after treatment. Patient-reported parameters were also evaluated 1 week after treatment.Results: All groups presented significant (p<0.0001) clinical improvement for a 12-month period, except for clinical attachment level gain for Laser 2 at 12 months. Clinical improvement was similar among groups at all time points. The reported analgesic consumption was significantly higher for Laser 1.Conclusions: The combined FMS/Nd:YAG laser was significantly clinically effective for 12 months. The adjunctive use of Nd:YAG laser irradiation to FMS, applied with two different approaches, was similarly clinically effective to FMS for a 12-month period. A single post-FMS application of Nd:YAG laser for pocket epithelium removal and coagulation might non-statistically significantly further improve the PD reduction achieved with FMS alone. Clinical relevance: When Nd:YAG laser is used for sulcular epithelium removal and coagulation, it may provide minor improvements compared to FMS and Laser 2 long-term. The sense of discomfort seems to be more pronounced in Laser 1.
Social return on investment economic evaluation of supportive care for lung cancer patients in acute care settings in Australia
Authors: Hyatt Amelia , Chung Holly , Aston Ruth , Gough Karla , Krishnasamy Meinir 
Published: August 2022

Abstract
Background
Unmanaged consequences of cancer and its treatment are high among patients with lung cancer and their informal carers, resulting in avoidable healthcare use and financial burden. Provision of cancer supportive care has demonstrated efficacy in mitigating these consequences; however, globally, there is a lack of investment in these services. Paucity of robust economic evidence regarding benefit of cancer supportive care has limited policy impact and allocation of resources. In response to this, this study utilised a Social Return on Investment (SROI) methodology to conduct a forecast evaluation of lung cancer supportive care services, to ascertain social value and return on investment.
Methods
An SROI economic evaluation model was developed using qualitative stakeholder consultations synthesised with published evidence to compare the inputs, outcomes and financial value associated with the delivery of quality lung cancer supportive care services. SROI ratios were generated to determine the social value and cost savings associated per every $1AUD invested in cancer supportive care for both the healthcare system and patients. Deadweight, displacement, drop off and attribution were calculated, and sensitivity analysis was performed to confirm the stability of the model.
Results
The value generated from modelled supportive care service investments in a one-year period resulted in an SROI ratio of 1:9; that is, for every dollar invested in supportive care, AUD$9.00 return is obtained when savings to the healthcare system and benefits to the patients are combined. At five-years, these same investments resulted in greater cumulative value generated for both the patient and the healthcare system, with a SROI ratio of 1:11.
Conclusions
Our study provides strong evidence for policy makers, clinicians and consumers to advocate for further investment in cancer supportive care, as demonstrated cost savings can be achieved through implementation of the proposed supportive care service model, with these accruing over a five-year period. The SROI model provides a comprehensive framework detailing supportive care services and the health workforce necessary to achieve value-based outcomes for patients and the healthcare system.
Development and Validation of a duplex real-time PCR for the rapid detection and quantitation of HTLV-1
Authors: Ji Huimin , Chang Le , Yan Ying , Wang Lunan 
Published: August 2022

Abstract
Background
The HTLV-1 prevalence in China varies geographically, while HTLV-2 infection has rarely been found so far. Proviral load is one of the determining factors of pathogenesis and progression of HTLV-1 related diseases. However, neither molecular assays nor commercial kits are available for HTLV-1 diagnosis in China. The purpose of the present study was to develop and validate a TaqMan qPCR assay for HTLV-1 proviral load quantification.
Results
A plasmid containing both the HTLV-1 of interest and a fragment of the RNase P (RPPH1) gene was constructed and used to establish the standard curves. The assay has a wide dynamic range (2.5×108 copies/reaction ~ 25 copies/reaction) and sensitive to 1 copy for HTLV-1 and RPPH1. The limit of detection for Hut102 cell concentration was 0.0218% (95% confidence interval 0.0179 ~ 0.0298%). The assay gave coefficient of variation (CV) for both the HTLV-1 and RPPH1 Ct values. All of the HTLV-1 sero-negative samples and MOT cell line (infected with HTLV-2) amplified only the RPPH1 gene by our method, presenting 100% specificity. 85 Samples confirmed positive or indeterminate by LIA were performed by established qPCR assay and WB. 90.0% (27/30) of LIA-HTLV-1-positive, 33% (2/6) of LIA-untypeable and 2% (1/49) of LIA-indeterminate samples were defined as qPCR-positive. The median PVL of LIA-positive samples (n = 27, 1.780 copies/100 cells) was much higher than that of LIA-untypeable and (n = 2, 0.271 copies/100 cells) indeterminate samples (n = 1, 0.017 copies/ 100 cells). Additionally, the duplex qPCR confirmed more positive samples than WB, indicating a higher sensitivity than the later.
Conclusion
The duplex qPCR developed here with high sensitivity, good specificity and reproducibility could accurately and quantitatively detect the HTLV-1 PVLs, which can not only be used to confirm the initial reactive samples for a better cost/benefit ratio, but also to monitor the clinical progression and efficacy of therapy in patients with HTLV-1 related disease.
Cumulative Exposure to Oxidized Low-Density Lipoprotein is a Potential Predictor for Prognosis in Acute Ischemic Stroke: A Cohort Study
Authors: Kaili Cheng , Chen Xiuqi , Luo Yufan , Sun Wenbo , Yang Xiaoli , Huang Shengwen , Wang Yuanyuan , Wu Danhong 
Published: August 2022

Abstract
Background
Oxidized low-density lipoprotein (ox-LDL) is closely related to the recrudescence and prognosis of acute ischemic stroke (AIS). However, there are limited studies about the effect of a long-term elevation of ox-LDL in AIS. In this research, our porpose was to explore the relevence between cumulative ox-LDL exposure and the short-term prognosis of AIS.
Methods
This study recruited patients with AIS. AIS severity was evaluated by infarct volumes and National Institute of Health Stroke Scale (NIHSS) scores at admission. AIS prognosis was assessed by Modified Rankin Scale (mRS) scores at 90 days and the difference between NIHSS scores at admission and discharge. Cumulative ox-LDL exposure was defined as ox-LDL level (pg/mL) multiplied by age (y). A multivariate logistic regression model was employed to investigate the correlation between exposure factors and the prognosis of AIS. The predictive ability of cumulative ox-LDL exposure for the prognosis of AIS was compared with cumulative LDL exposure by the receiver operating characteristic curve (ROC).
Results
A total of 175 AIS patients were included with an average age of 66.00 (61.00, 73.00). Patients with higher cumulative ox-LDL exposure tended to manifest worse prognosis, including neurological worsening at discharge (NIHSS increasing more than 2 points) (OR = 3.02, 95% CI, 1.30–6.98, P = 0.01) and poor functional prognosis at 90 days (mRS ≥ 3) (OR = 21.21, 95% CI, 4.72–95.36, P < 0.001). After adjusting for potential confounders, multivariate regression analysis showed significantly increased cumulative ox-LDL exposure was elated to poor functional prognosis at 90 days (OR = 9.92, 95% CI, 1.23–79.76, P = 0.031), but not with neurological worsening at discharge (OR = 1.74, 95% CI, 0.46–6.55, P = 0.414). ROC curve revealed that ox-LDL cumulative exposure had higher predictive value (AUC = 0.843, P < 0.001) for the functional prognosis of AIS than cumulative LDL exposure (AUC = 0.629, P = 0.023).
Conclusion
High cumulative ox-LDL exposure is related to the poor prognosis at 3-month of AIS, and its predictive accuracy is better than cumulative LDL exposure.
Curiosity in wild orangutans: ecological, social, and intrinsic effects assessed during a field experiment
Authors: Schuppli Caroline , Nellissen Lara , Carvajal Luz , Ashbury Alison , Oliver-Caldwell Natalie , Rahmaeti Tri , Laumer Isabelle , Haun Daniel 
Published: August 2022

AbstractThe readiness to interact with, and explore, novel stimuli – i.e., curiosity – are cornerstones of innovation. Great apes show the broadest and most complex innovation repertoires. However, little is known about the factors that affect curiosity in wild apes. To shed light on wild apes’ curiosity, we measured the reactions of wild Sumatran orangutans (Pongo abelii) to an experimental apparatus. Compared to adults, immatures showed higher tendencies to visually explore and approach the apparatus but were more likely to show signs of agitation. The presence of conspecifics who approached the apparatus increased exploration and approach tendencies. Prevailing habitat food availability positively affected exploration but had a negative effect on approach tendencies. These findings show that intrinsic, social, and ecological factors affect reactions to novelty in wild orangutans and suggest that exploration, neophobia and neophilia are independently regulated. Therefore, to understand the evolution of innovative tendency, factors acting on different elements of curiosity must be considered.
Design of Double Functionalized Carbon Nanotube for Amphotericin B and Genetic Material Delivery
Authors: Yazdani Sara , Mozaffarian Mehrdad , Pazuki Gholamreza , Hadidi Naghmeh , Gallego Idoia , Puras Gustavo , Pedraz Jose Luis 
Published: August 2022

Abstract
In the present work, single wall carbon nanotubes (SWCNT) were functionalized with phospholipid DSPE-PEG carboxylic acid, and then, with ethylenediamine (EDA), to obtain double functionalized single wall carbon nanotube (DFSWCNT). We applied DFSWCNT as a carrier for delivering amphotericin B (Amb) and EGFP plasmid. FSWCNT’s concentration obtained via UV-visible analysis was 0.99 mg/mL. The TGA analysis results provided the lost weights of DSPE-PEG-COOH, EDA, Amb and SWCNT impurities. XPS results showed that carbon atoms’ percentage decreased during the functionalization process from 97.2% (SWCNT) to 76.4% (FSWCNT) and 69.9% (DFSWNCT). Additionally, the oxygen atoms’ percentage increased from 2.3% (SWCNT) to 21% and 22.5% for FSWCNT and DFSWCNT, respectively. New bonds such as C-N and N-C = O appeared in the synthesized nanocarrier. The IG/ID ratio in Raman analysis decrease from 7.15 (SWCNT) to 4.08 (FSWCNT). The amount of Amb released to phosphate buffer saline medium was about 33% at pH = 5.5 and 75% at pH = 7.4 after 48 h. CCK8 results confirmed that the toxicity of functionalized SWCNT decreased. In a 2:1 ratio of DFSWCNT/EGFP plasmid, the cell viability (87%) and live transfected cells (56%) were at their maximum values. processes indicate that carbon nanotubes have the potential to be applied as both drug/gene delivery systems with outstanding properties such as high loading capacity and easy penetration to the cell membrane.