bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dynamics and Functional Interplay of Non-histone Lysine Crotonylome and Ubiquitylome in Vascular Smooth Muscle Cell Phenotypic Remodeling
Authors: Cao Shan-Hu , Chen Zhi-Huan , Yue Lin , Jiang Han-Mei , Ma Ru-Yuan , Dong Li-Hua 
Published: September 2021

Abstract
BackgroundsCrotonylation of histones is a recently discovered type of post-translational modification that can regulate gene expression. However, the function of crotonylation on nonhistone proteins in vascular smooth muscle cells (VSMC) is unclear. Here, we aim to use modification and proteomic analysis to find the cellular characteristic of crotonylated nonhistone proteins and the crosstalk with ubiquitinated proteins in vascular smooth muscle cell (VSMC) phenotypic remodeling. ResultsWe performed modification and proteomic analysis of VSMCs before and after platelet-derived growth factor-BB (PDGF-BB) stimulation. The crotonylated and ubiquitinated pan-antibody was used to enrich the protein and then subjected to high-throughput mass spectrometry analysis. Then we compared the enrichment analysis of differentially modified proteins in regards to GO terms, KEGG pathway and protein domain. As a result, there were 2138 crotonylation sites in 534 proteins and 1359 ubiquitination sites corresponding to 657 proteins. The crotonylated proteins participate in a variety of important cellular pathways and perform different functions in VSMCs. Among them, some proteins were found to be closely involved in the physiological process of VSMC phenotypic remodeling including glycolysis/gluconeogenesis, vascular smooth muscle contraction, and PI3K-Akt signaling pathway. Furthermore, the KEGG pathway enrichment analysis showed that the ubiquitinated proteins were found to be closely involved in the physiological process of VSMC phenotypic remodeling including glycolysis/gluconeogenesis, vascular smooth muscle contraction, RAS signaling pathway or PI3K-Akt signaling pathway. Crosstalk analysis showed that there were 199 sites within 177 proteins modified by crotonylation and ubiquitination simultaneously. PPI network analysis indicated that crotonylated and ubiquitinated proteins played an important role in cellular bioprocess commonly and possible synergistic effect. ConclusionsIn summary, our bioinformatics show that nonhistone crotonylation and ubiquitination play an important role in the VSMC phenotypic transformation induced by PDGF-BB stimulation. The crosstalk of crotonylation and ubiquitination in glycolysis is possibly a novel mechanism underlying the VSMC phenotypic remodeling.
Validation of Acromegaly Quality of Life Questionnaire (AcroQol) for the Iranian Population
Authors: Danaei Mina , Bahadorizadeh Leyla , Dehnad Afsaneh , Mohamadzadeh Shirin , Hashemi-Madani Nahid , Khamseh Mohammad E 
Published: September 2021

Abstract
Background: Acromegaly is a chronic disease seriously impacting the patients' quality of life. This study aimed to validate the Acromegaly Quality of Life Questionnaire (AcroQoL) for the Persian-speaking population.Methods: This cross-sectional study recruited 73 Iranian patients with a confirmed diagnosis of acromegaly. The content validity of the scales was evaluated by an expert panel of eight endocrinologists. Construct validity was assessed by using confirmatory factor analysis. Internal consistency was assessed on the basis of Cronbach’s alpha, and a goodness-of-fit (GoF) index was calculated to display whether the model fitted the data.Results: The content validity index (CVI) and content validity ratio (CVR) yielded values of 0.85 and 0.80, respectively. The average variance extracted (AVE) from physical and psychological dimensions was 0.520 and 0.462, respectively, exceeding the minimum criterion of 0.40. Cronbach’s alpha for physical and psychological dimensions equaled 0.868 and 0.866, respectively, indicating the adequate internal consistency of multiple items for each construct. The subscales’ R square and path coefficient were greater than the recommended threshold (physical dimension: 0.778, psychological dimension: 0.873), demonstrating the suitability of this criterion. Finally, the GoF value of 0.29 indicated the model's moderate fit.Conclusions: The findings revealed that the Persian version of AcroQoL is of adequate validity and reliability for evaluating the quality of life of Iranian people with acromegaly.
A Capra Hircus Chromosome 19 Locus Linked to Milk Production Influences Mammary Conformation
Authors: Jiang Andrew , Ankersmit-Udy Alex , Turner Sally-Anne , Scholtens Megan , Littlejohn Mathew D , Lopez-Villalobos Nicolas , Proser Colin G , Snell Russell G , Lehnert Klaus 
Published: September 2021

Abstract
Background: Economically important milk production traits including milk volume, milk fat and protein yield vary considerably across dairy goats in New Zealand. A significant portion of the variation is attributable to genetic variation. Discovery of genetic markers linked to milk production traits can be utilised to drive selection of high-performance animals.A previously reported genome wide association study across dairy goats in New Zealand identified a quantitative trait loci (QTL) located on chromosome 19. The most significantly associated single nucleotide polymorphism (SNP) marker for this locus is located at position 26,610,610 (SNP marker 19:26,610,610). This locus is associated with multiple milk production traits including fat, protein and volume. The predicted effect of selection for the beneficial haplotype would result in an average production increase of 2.2kg fat, 1.9kg protein and 73.6kg volume.An outstanding question was whether selection for the beneficial allele would co-select for any negative pleiotropic effects. An adverse relationship between milk production and udder health traits has been reported at this locus. Therefore, a genome wide association study was undertaken looking for loci associated with udder traitsResults: The QTL and production associated marker 19:26,610,610 was identified in this study to also be associated with several goat udder traits including udder depth (UD), fore udder attachment (FUA) and rear udder attachment (RUA). Our study replicates the negative relationship between production and udder traits with the high production allele at position 19:26,610,610 associated with an adverse change in UD, FUA and RUAConclusions: Our study has confirmed this negative relationship between udder traits and production traits in the NZ goat population. We have found that the frequency of the high production allele is relatively high in the NZ goat population, indicating that its effect on udder conformation is not significantly detrimental on animal health. It will however be important to monitor udder conformation as the Chromosome 19 locus is progressively implemented for marker assisted selection. It will also be of interest to determine if the gene underlying the production QTL has a direct effect on mammary gland morphology or whether the changes observed are a consequence of the increased milk volume.
Evaluation of Flexibility in Adaptation Projects for Climate Change
Authors: Kim Myung-Jin , Nicholls Robert J. , Preston John M. , De Almeida Gustavo A. M. 
Published: September 2021

Abstract
Climate change adaptation inherently entails investment decision-making under the high levels of uncertainty. Under these circumstances, the option of deferring a decision to adapt is one of possible strategies to address uncertainty. However, this decision will potentially leave people and areas exposed to the risk of coastal flooding during the deferral. In order to address this issue, a single fixed large investment can be divided into two or more sequential investments. This reduces the initial investment cost and adds flexibility about the size and timing of subsequent investment decisions as the magnitude of climate change becomes more available. This paper employs a real option analysis framework, as an analytical tool, to evaluate adaptations including flexibility to reduce both the risk and uncertainty of climate change, against increasing coastal flooding due to sea-level rise as an example. This paper considers (i) how to design the sequence of adaptation options under the growing risk of sea-level rise, and (ii) how to make the efficient use of flexibility included in adaptations for addressing uncertainty. This research incorporates a set of flexibilities (i.e. wait or future growth) into single-stage investments (i.e. raising coastal defence from 2.5 mAOD to 3.5mAOD or 4.0 mAOD) in two or three stages so that a set of multiple-stage adaptations are created to address both the risk and uncertainty of climate change. The proposed method compares the multiple-stage adaptations in economic terms, including optimisation, providing important additional information on the efficiency of flexible adaptation strategies given the uncertainty of climate change. The results from the analysis suggest that an efficient and robust strategy can be chosen for a short- and long- term adaptation.
Infection with a Hypervirulent Strain of Helicobacter Pylori Primes Gastric Cells Toward Intestinal Transdifferentiation
Authors: Saberi Samaneh , Esmaeili Maryam , Tashakoripour Mohammad , Hosseini Mahmoud Eshagh , Baharvand Hossein , Mohammadi Marjan 
Published: September 2021

Abstract
Background: Intestinal metaplasia, gastric-to-intestinal transdifferentiation, occurs as a result of the misexpression of certain regulatory factors, leading to genetic reprogramming. Here, we have evaluated the H. pylori-induced expression patterns of these candidate genes.Methods: The expression levels of 1)tissue-specific transcription factors (RUNX3, KLF5, SOX2, SALL4, CDX1 and CDX2), 2)stemness factors (TNFRSF19, LGR5, VIL1) and 3)tissue-specific mucins (MUC5AC, MUC2) were evaluated by quantitative real-time PCR in gastric primary cells (GPCs), in parallel with two gastric cancer (MKN45 and AGS) cell lines, up to 96h following H. pylori infection. Results: Following H. pylori infection of GPCs, RUNX3 declined at 24h post infection (PI) (-6.2±0.3) and remained downregulated for up to 96h. Subsequently, overexpression of self-renewal and pluripotency transcription factors, KLF5 (3.6±0.2), SOX2 (7.6±0.5) and SALL4 (4.3±0.2) occurred. The expression of TNFRSF19 and LGR5, demonstrated opposing trends, with an early rise of the former (4.5±0.3) at 8h, and a simultaneous fall of the latter (-1.8±0.5). This trend was reversed at 96h, with the decline in TNFRSF19 (-5.5±0.2), and escalation of LGR5 (2.6±0.2) and VIL1 (1.8±0.3). Ultimately, CDX1 and CDX2 were upregulated by 1.9 and 4.7-fold, respectively. The above scenario was, variably observed in MKN45 and AGS cells.Conclusion: Our data suggests an interdependent gene regulatory network, induced by H. pylori infection. This interaction begins with the downregulation of RUNX3, upregulation of self-renewal and pluripotency transcription factors, KLF5, SOX2 and SALL4, leading to the downregulation of TNFRSF19, upregulation of LGR5 and aberrant expression of intestine-specific transcription factors, potentially facilitating the process of gastric-to-intestinal transdifferentiation.
Lubricant Coatings for Mobile Dry Drilling of Stacked Aluminium Alloys
Authors: Hassan Siti Rozakiyah Assurin , Mativenga Paul T , Cooke Kevin , Sun Hailin , Field Susan , Walker Mark , Chodynicki Jason , Sharples Colin , Jensen Boris , Mortensgaard Morten F. 
Published: September 2021

Abstract
Aluminium alloy stack materials offer good strength-to-weight ratio and are used for high strength airframe structures. For the panels to be joined, numerous holes have to be drilled and due to structure size mobile drilling heads are used. The drilling process releases lubricant oil which becomes airborne or collects on the shop-floor and presents a health and safety hazard. Avoiding this oil release is therefore a major driver for developing dry drilling processes. However, drilling aluminium alloys in the absence of cutting fluids is a challenging task due to its tendency to adhere to the cutting tool, and the high thermal conductivity of the workpiece. Owing to their low coefficient of friction, carbon-based coatings are an option to improve the machinability of aluminium alloys. This paper presents an industrial collaboration study on the performance of carbon-based coatings in dry drilling aluminium alloy 2024 and 7150 stacks. CVD Diamond, a hard DLC, Doped MoS2 and doped amorphous carbon (Doped a-C) were evaluated in comparison with an uncoated WC drills. Coating performance was assessed in terms of tool wear, hole diameter, and surface roughness. The results revealed that CVD diamond coated drills outperformed other coatings in terms of tool wear and hole quality. The coating enabled lower aluminium pick-up on the drills as well as minimised variations in diameter deviation and hole surface roughness. The work shows the capability for dry drilling of stacked aluminium alloys and hence eliminating the health and safety risk associated with use of oil in mobile drilling heads.
LncRNA ELFN1-AS1 Upregulates TRIM29 to Promote Gastric Cancer Progression by Suppressing miR-211-3p
Authors: Huang Jinxi , Yuan Weiwei , Chen Beibei , Li Gaofeng , Chen Xiaobing 
Published: September 2021

Abstract
BackgroundExtracellular leucine rich repeat and fibronectin type III domain containing 1-antisense RNA 1 (ELFN1-AS1) was upregulated in tumors. Nevertheless, the biological functions of ELFN1-AS1 in gastric cancer are not fully understood.MethodsThe ELFN1-AS1, miR-211-3p and TRIM29 expression levels were determined by reverse transcription-quantitative PCR. CCK8, EDU and colony formation assays were done to test the GC cell vitality. The migratory and invasive capabilities of GC cells were further measured by transwell invasion and cell scratch assays. The ceRNA activity of ELFN1-AS1 for TRIM29 via miR-211-3pp was ascertained through pull down, RIP and luciferase reporter assays.ResultsELFN1-AS1 and TRIM29 were robustly expressed in gastric cancer tissues and negatively associated overall survival time of patients. The ELFN1-AS1 silence blocked the proliferation, migration and invasion of GC cells. The oncogenic role of ELFN1-AS1 was recognized to be modulated by miR-211-3pp, which competitively bind to 3'UTR TRIM29 and resulted in the reduced expression of TRIM29.ConclusionELFN1-AS1 maintained the tumorigensis of GC cells by ELFN1-AS1/miR-211-3pp/TRIM29 axis, suggesting that intervention targeting this axis may be warranted for GC treatment.
Understanding Reasons for Lack of Acceptance in HIV Programs Among Indigenous: a Qualitative Study in Indonesia
Authors: Sianturi Elfride Irawati , Latifah E , Soltief S N , Sihombing R , Simaremare E S , Effendy C , Probandari A N , Suryawati S , Taxis K 
Published: September 2021

Abstract
Background: Melanesians are Indigenous Papuans that are racially and culturally different from most Indonesians. Poverty and inequalities remain high in this region despite having the highest revenues. Furthermore, Papua has the highest HIV prevalence rate, which is 24 times higher than other regions. Therefore, this study aimed to develop an understanding of the acceptance of HIV programs among Papuans.Methods: This is a qualitative study carried out using the grounded theory with data collected from 23 Papuans through semi-structured face-to-face interviews. All interviews were conducted in Bahasa Indonesia, audio-recorded, summarized, and transcribed for analysis.Results: The results showed that to “keep being a good Papuan," emerges from 4 interconnected categories, including 1) Culture and Religion, 2) Dealing with modernisms, 3) Tailoring program and 4) Stigma reduction. As a substantive theory underpinning the experiences of indigenous people with the programs, “Keep being a good Papuan” was a way of overcoming a series of problems and dealing with modernism to eliminating HIV. This is largely focused on the local culture, therefore any adjustment needs to balance keeping their tradition and welcoming modernism.Conclusions: Therefore, the future of the programs needs to be agreed upon, funded, implemented, measured, and achieved. One of the strategies used to achieve this is by elaborating a supportive culture and community-based interventions. Further, implementation needs to be prioritized to integrate and improve the quality of the programs due to the needs of the community and the available resources.
Efficacy of Alectinib in ALK-Positive Non-Small Cell Lung Cancer with Leptomeningeal Metastases Pretreated with Crizotinib
Authors: lu zhiqin , Liang Yuanyuan , Wang Xia , Zeng Zhimin , Zhong Congying , Liu Anwen 
Published: September 2021

Abstract
PurposeLeptomeningeal metastases is a fatal complication of advanced non-small cell lung cancer (NSCLC). This study aimed to assess the clinical efficacy of alectinib in ALK-positive NSCLC with LM patients previously treated with crizotinib.MethodsRetrospective study of NSCLC patients with alectinib-treated ALK- positive NSCLC and LM.ResultsFourteen patients (mean age, 55 years; 50% women) with adenocarcinoma NSCLC were included in the study. Before starting alectinib, all patients were treated with crizotinib. When LM was diagnosed, all patients had clinical symptoms. Sixteen (50%) patients had a performance status>2. Of 14 total patients, 85.7% (12/14) of the patients had a clinical and radiological responses. From the start of alectinib, median OS and PFS were 17.4 (95% CI, 8.9–25.9) and 11.6 months (95% CI: 8.4–14.8), respectively, one-year survival rate was 57.1%.ConclusionAlectinib had significant efficacy against NSCLC with LM, this efficacy was rapid in several patients, even some with poor performance status. Alectinib might be a suitable option for specific patient populations with advanced ALK-positive NSCLC with LM.
Tfet Biosensor Simulation and Analysis for Various Biomolecules
Authors: Vimala P , L Likith Krishna , SS Sharma , Ainapur Rakshanda , RH Swetha 
Published: September 2021

Abstract
This paper investigates the simulation and performance of Tunnel field effect transistor (TFET) with a nanocavity in it, which can be used for bio sensing application. The entire simulation is done using the tool Silvaco Atlas TCAD. This paper mainly aims in comparing the different parameters for few biomolecules which has different dielectric constant values, namely Streptavidin, Biotin, APTES, Cellulose and DNA. The device structure here consists of a nanocavity near the source end, which is used to place these biomolecules and hence observe the variation of the Drain current v/s Gate voltage characteristic graph, these biomolecules that are having unique dielectric constants are placed within this cavity and these graphs are observed. The energy band diagram of this device is obtained; on top of this various other parameters namely Surface Potential, Electric field are observed for the above-mentioned Biomolecules. The Length of the cavity of the biosensor is also varied to observe the difference, in addition to this Ion (ON current) variation is plotted for the change in the dielectric constant of the biomolecule.
Plasma Proteome Changes Linked to Late Phase Response After Inhaled Allergen Challenge in Asthmatics
Authors: Weitoft Maria , Kadefors Måns , Stenberg Henning , Tufvesson Ellen , Diamant Zuzana , Enes Sara Rolandsson , Bjermer Leif , Rosmark Oskar , Westergren-Thorsson Gunilla 
Published: September 2021

Abstract
BackgroundA subset of individuals with allergic asthma develops a late phase response (LPR) to inhaled allergens, which is characterized by a prolonged airway obstruction, airway inflammation and airway hyperresponsiveness. The aim of this study was to identify changes in the plasma proteome and circulating hematopoietic progenitor cells associated with the LPR following an inhaled allergen challenge. MethodsSerial plasma samples from asthmatics undergoing inhaled allergen challenge were analyzed by mass spectrometry and immunosorbent assays. Peripheral blood mononuclear cells were analyzed by flow cytometry. Mass spectrometry data was analyzed using a linear regression to model the relationship between airway obstruction during the LPR and plasma proteome changes. Data from immunosorbent assays was analyzed using linear mixed models.ResultsOut of 396 proteins quantified in plasma, 150 showed a statistically significant change 23 h post allergen challenge. Among the most upregulated were three protease inhibitors: alpha-1-antitrypsin, alpha-1-antichymotrypsin and plasma serine protease inhibitor. Altered levels of 13 proteins were associated with the LPR, including increased factor XIII A and a decreased von Willebrand factor. No relationship was found between the LPR and changes in the proportions of classical, intermediate, and non-classical monocytes.Conclusions﻿Allergic reactions to inhaled allergens in asthmatic subjects was associated with changes in a large proportion of the measured plasma proteome, whereof protease inhibitors showed the largest changes, likely to influence the inflammatory response. Many of the proteins altered in relation to the LPR are associated with coagulation, highlighting potential mechanistic targets for future treatments of type-2 asthma.
Penehyclidine Hydrochloride Has the Function of Lung Protection for Acute Lung Injury in Rat Models:A Systemic Review and Meta-analysis
Authors: Luo Shasha , Tan Hongbao , Chen Li , Wang Dongwei , Hua Rong 
Published: September 2021

Abstract
ObjectiveThis systematic review and meta-analysis aims to review the effects of penehyclidine hydrochloride (PHC) on acute lung injury in animal models. MethodsPubMed, Embase, CNKI were searched for collecting the randomized controlled trials(RCTs) on the effects of penehyclidine hydrochloride on acute lung injury in rat models from inception to July 1, 2021. We used Cochrane evaluating quality and RevMan 5.3 software performing Meta-analysis.(lung W/D ratio、PaO2/FiO2、SOD、MPO activity、IL-6 and TNF-α) ResultsOur search including 11 studies in 3 databases. Meta-analysis showed that, Compared with the acute lung injury model group, the PHC treatment group: lung W/D ratio[MD=-1.29，95%CI（-1.94，-0.64），P＜0.01]、PaO2/FiO2[MD=1.73，95%CI（0.01，3.45），P＜0.01]、SOD[MD=7.05，95%CI（5.58，8.52），P＜0.000,01]、IL-6 [MD=-1.03，95%CI（-1.29，-0.77），P＜0.0001]、IL-6 [MD=-3.35，95%CI（-5.29，-1.40），P＜0.001]and TNF-α[MD=-2.17，95%CI（-3.27，-1.07），P＜0.0001].Conclusions﻿penehyclidine hydrochloride has the function of lung protection in acute lung injury and provides a new therapy for future clinical treatment.
Chloroplast Genome Analysis of The Famous Chinese Herbal Medicine Yizhiren (Zingiberaceae)
Authors: Pan JiaoYi , Shiyun Sun , Qiong Xia , Xvhan Lv , Xinxian Yang , Fule He 
Published: September 2021

Abstract
Background: Yizhiren is the fruit of Alpinia oxyphylla(Zingiberaceae) ,a well-known Chinese herbal medicine from China. The complete chloroplast genome of Alpinia oxyphylla was studied in this paper, which laid the foundation of the further study of genetic information and data of Alpinia oxyphylla.Methods: The complete chloroplast sequences of 19 the family Zingiberaceae species were aligned using MEGAX software.The phylogenetic tree was constructed by the Maximum-Likelihood method and edited by the Evolview online.Results: The chloroplast gene group is a typical tetragonal structure, which is formed by 161,351 base pairs. Each genome has a large single-copy region (LSC) of 87,248 bp, a small single-copy region (SSC) of 16,175 bp and a pair of inverted-repeat regions (IRs) of 28,964 bp in each. The complete nucleotide composition of chloroplast genome is: 31.5% A, 32.4% T, 18.2% C, 17.9% G, and the total GC content is 36.2%. Among them 28 exons and 15 introns. A total of 137 genes were annotated, which included 92 protein coding genes (PCGs), 37 metastatic RNA (tRNAs) and 8 ribosomal RNA (rRNAs).Conclusions: The phylogenetic ML tree shown the conclusion that Alpinia oxyphylla is closely related to Alpinia chinensis on genetic position relationship. This result is of great value to the study of biological inheritance, species identification and medicinal value. Meanwhile, it provides references for the study of biological inheritance, species identification and medicinal value.