bluuebunny/crossref_metadata_2025 huggingface dataset:
Integrating expert opinions with clinical trial data to analyse low-powered subgroup analyses: a Bayesian analysis of the VeRDiCT trial
Authors: Thirard Russell , Ascione Raimondo , Blazeby Jane , Rogers Chris A
Published: October 2020

Background Typically, subgroup analyses in clinical trials are conducted by comparing the intervention effect in each subgroup by means of an interaction test. However, trials are rarely, if ever, adequately powered for interaction tests, so clinically important interactions may go undetected. We discuss the application of Bayesian methods by using expert opinions alongside the trial data. We applied this methodology to the VeRDiCT trial investigating the effect of preoperative volume replacement therapy (VRT) versus no VRT (usual care) in diabetic patients undergoing cardiac surgery. Two subgroup effects were of clinical interest, a) preoperative renal failure and b) preoperative type of antidiabetic medication. Methods Clinical experts were identified within the VeRDiCT trial centre in the UK. A questionnaire was designed to elicit opinions on the impact of VRT on the primary outcome of time from surgery until medically fit for hospital discharge, in the different subgroups. Prior beliefs of the subgroup effect of VRT were elicited face-to-face using two unconditional and one conditional questions per subgroup analysis. The robustness of results to the ‘community of priors’ was assessed. The community of priors was built using the expert priors for the mean average treatment effect, the interaction effect or both in a Bayesian Cox proportional hazards model implemented in the STAN software in R. Results Expert opinions were obtained from 7 clinicians (6 cardiac surgeons and 1 cardiac anaesthetist). Participating experts believed VRT could reduce the length of recovery compared to usual care and the greatest benefit was expected in the subgroups with the more severe comorbidity. The Bayesian posterior estimates were more precise compared to the frequentist maximum likelihood estimate and were shifted toward the overall mean treatment effect. Conclusions In the VeRDiCT trial, the Bayesian analysis did not provide evidence of a difference in treatment effect across subgroups. However, this approach increased the precision of the estimated subgroup effects and produced more stable treatment effect point estimates than the frequentist approach. Trial methodologists are encouraged to prospectively consider Bayesian subgroup analyses when low-powered interaction tests are planned.Trial registration ISRCTN, ISRCTN02159606. Registered 29th October 2008.
Cerebrospinal fluid analysis in 108 patients with progressive multifocal leukoencephalopathy
Authors: Möhn Nora , Yi Luo , Skripuletz Thomas , Schwenkenbecher Philipp , Ladwig Anne , Warnke Clemens , Meuth Sven G. , Wiendl Heinz , Gross Catharina C. , Schröder Christoph , Haghikia Aiden , Stangel Martin
Published: October 2020

Background: Progressive multifocal leukoencephalopathy (PML) is caused by an opportunistic infection with JC polyoma virus (JCPyV) and mainly affects immunocompromised patients. It leads to pronounced demyelination of the central nervous system (CNS) resulting in severe disability or even death. Detection of JCPyV DNA in the cerebrospinal fluid (CSF) is usually accepted as proof for the diagnosis of PML. Routine CSF parameters, like CSF cell count, protein concentration, Qalbumin, or intrathecal immunoglobulin synthesis are mostly considered normal. However, this has not been investigated systematically. Methods: We analyzed routine CSF parameters in a cohort of 108 PML patients that were treated at four different neurological centers in Germany. The patients exhibited different underlying conditions with natalizumab-treated multiple sclerosis (n=54) and human immunodeficiency virus (HIV)-infection (n=25) being the most frequent. The data were collected at the respective centers in accordance with local requirements and then jointly analyzed. The total PML cohort was compared with a control group of patients with normal pressure hydrocephalus (NPH) and idiopathic intracranial hypertension (IIH). Multiple sclerosis and HIV patients were additionally compared with their own non-PML control groups. Results: The PML group showed an elevated cell count (p<0.001) compared to the control group, however, this effect was mainly driven by HIV-PML patients. This subgroup also demonstrated a significantly higher proportion of patients with a disturbed blood-CSF-barrier function. Conclusions: This comprehensive, retrospective study on CSF diagnostic analysis in PML patients provides insight into the CSF of those patients. It demonstrates that CSF composition in PML patients may be specific for the underlying condition that predisposes for the development of PML and thus data have to be interpreted in this context.
Integrative analysis of long non-coding RNA (lncRNA) and mRNA expression in TLR4-primed MSCs of ankylosing spondylitis
Authors: Li Yuxi , Li Ming , Liu Ting , Huang Jiajun , Liang Yuwei , Huang Junshen , Liu Xiangge , Cheng Ziying , Lu Shixin , Shen Huiyong , Huang Lin
Published: October 2020

Background: Ankylosing spondylitis (AS) is a chronic autoimmune disease, and the precise pathogenesis is largely unknown at present. Our previous study found that the expression of toll-like receptor 4 (TLR4) of mesenchymal stem cells from AS patients (AS-MSCs) was reduced and activation of TLR4 by lipopolysaccharide (LPS) could enhance the immunoregulatory ability of AS-MSCs. However, the potential mechanism by which TLR4 affect the immunoregulatory function of AS-MSCs remains unclear. Objective: The goal of this study was to explore the expression profiles and functional networks of lncRNAs and mRNAs in TLR4-primed AS-MSCs and to clarify the potential mechanisms by which TLR4-primed AS-MSCs exert immunoregulatory effects.Methods: Immunoregulatory effects of MSCs were determined after TLR4 activation. Then, the differentially expressed (DE) long non-coding RNAs (lncRNA) and messenger RNAs (mRNA) between AS-MSCs and TLR4-primed AS-MSCs (stimulated by LPS) were identified through high-throughput sequencing followed by qRT-PCR confirmation. Finally, bioinformatic analyses were performed to identify the critical biological functions, signalling pathways and associated functional networks involved in the TLR4-primed immunoregulatory function of AS-MSCs.Results: A total of 147 DE lncRNAs and 698 DE mRNAs were identified between TLR4-primed AS-MSCs and unstimulated AS-MSCs. Of total, 107 lncRNAs were upregulated and 40 were downregulated (fold change ≥2, P <0.05), while 504 mRNAs upregulated and 194 downregulated (fold change ≥2, P <0.05). 5 lncRNAs and 5 mRNAs with largest fold changes were respectively verified by qRT-PCR. GO and KEGG analysis demonstrated that the DE mRNAs and lncRNAs were highly associated with the inflammatory response, such as NOD-like receptor (NLR) signalling pathway, the TNF signalling pathway and the NF-kappa B signalling pathway. Cis-regulation prediction revealed 8 novel lncRNAs while trans-regulation prediction revealed 15 lncRNAs, respectively. 8 core pairs of LncRNA and target mRNA in the lncRNA-TF-mRNA network were: PACERR-PTGS2, LOC105378085-SOD2, LOC107986655-HIVEP2, MICB-DT-MICB, LOC105373925-SP140L, LOC107984251-IFIT5, LOC112268267-GBP2 and LOC101926887-IFIT3, respectively.Conclusion: In AS, TLR4 activation can enhance the immunoregulation ability of MSCs. Eight core pairs of lncRNA and target mRNA have been found in TLR4-primed AS-MSCs, which could contribute to elucidate the potential mechanism of immunoregulatory dysfunction of AS-MSCs.
In silico Analysis of Epitope-Based CadF Vaccine Design against Campylobacter jejuni
Authors: Naseri Mona Moballegh , Shams Saeed , Naseri Mohammad Moballegh , Bakhshi Bita
Published: October 2020

Objective: Vaccination is an important strategy for the eradication of infectious diseases. CadF protein of Campylobacter jejuni is one of the important factors in the pathogenesis of this bacterium. The purpose of this work was to perform a bioinformatics study to identify an epitope-based CadF vaccine, as a subunit vaccine. Full protein sequences of CadF were extracted from the NCBI and UniProt databases and subjected to in silico evaluations, including sequence analysis, allergenicity, antigenicity, epitope conservancy, and molecular docking assessments done by different servers. Results: The results showed that CadF was a highly conserved protein belonging to the outer member proteins superfamily. Among the evaluated epitopes, LSDSLALRL was identified as an antigenic and non-allergenic peptide with a suitable structure for vaccine development. It was also able to stimulate both T and B cells. This 9-mer peptide was located in 136-144 segment of CadF protein and interacted with both HLA-A 0101 and HLA-DRB1 0101 alleles. Overall, the obtained theoretical results showed that CadF protein could be used for designing and evaluating a new effective vaccine against C. jejuni.
lncRNA F11-AS1 Suppresses Glioma by Regulation miRNA-3146/PTEN
Authors: Qin Hao , Yang Qixia , Wang Tiantian , Liu Long , Di Chao , Zhuang Qiang , Xiao Longhai , Yin Hang
Published: October 2020

BACKGROUND: LncRNAs play key roles in glioma development, however, lncRNA F11-AS1’s effects has been unclearly in glioma.OBJECTIVE: F11-AS1 is an anti-tumor factor in glioma has been clearly until now.METHODS: Evaluating F11-AS1 expression by ISH in difference tissues and analysis the correlation with glioma prognosis in clinical. Using U87 and U251 cell to discuss lncRNA F11-AS1’s effect in glioma cancer cell biological activities by MTT, flow cytometry, transwell and wound healing assay. And measuring the relative miRNA and gene expressions by RT-qPCR and relative proteins expressions by WB assay. In next step, discuss the miR-3146 in F11-AS1 depressing cancer cell biological activities.RESULTS: The authors observed in this study that F11-AS1 was down-regulation in glioma and negatively correlated with miRNA-3146. Servival analysis showed that low level of F11-AS1 predicted poor survival. In glioma cells, F11-AS1 knockdown led to up-regulate, whereas F11-AS1 overexpression led to down-regulated miRNA-3146. Analysis of cell biological activities showed that F11-AS1 overexpression had effects to suppress glioma cell lines biological activities.CONCLUSION: Therefore, F11-AS1 down-regulates miRNA-3146 to depress cell biological activities in glioma.
Endoscopic submucosal dissection for gastric tube carcinoma after esophagectomy contributes to long-term outcomes: a retrospective case series
Authors: Hashimoto Satoru , Sato Hiroki , Mizuno Ken-ichi , Takahashi Kazuya , Takatsuna Masafumi , Yokoyama Junji , Ichikawa Hiroshi , Takeuchi Manabu , Kobayashi Masaaki , Terai Shuji
Published: October 2020

Background: Gastric tube carcinoma (GTC) after esophagectomy has been observed increasingly in recent years after advanced treatment of esophageal carcinoma. Surgical removal of the reconstructed gastric tube is not usually preferred; however, endoscopic submucosal dissection (ESD) is greatly anticipated to be a promising option. This study investigated the efficacy and safety of ESD for GTC. Methods: This study was designed based on a retrospective survey performed at our single center between 2003 and 2018. Patients with GTC were treated with ESD and followed-up according to the policy of our institution. The curability of ESD was evaluated histologically according to the Japanese gastric cancer treatment guidelines. Patient characteristics, outcomes of ESD procedures, and long-term outcomes were analyzed. Results: A total of 31 patients (2 females; median age, 73 years) with 45 GTC cases were treated with ESD. The mean period from esophagectomy to the diagnosis of GTC was 10.6 years. The only adverse event due to ESD was bleeding (2 patients: 6.5%). No fatal events, such as perforation, occurred. The rates of complete resections and curative resections were 80.6% and 48.4%, respectively. The 3-year and 5-year overall survival rates were 67.6% and 47.7%, respectively. The 3-year and 5-year disease-specific survival rates were 100% and 92.9%, respectively. One patient died of GTC and 14 patients died of other diseases, including five primary carcinomas. Conclusions: ESD for GTC can be a safe treatment and contribute to positive long-term outcomes. Long-term regular gastroscopy is required for early detection. Moreover, additional care should be given to GTC patients who are at high risk for other primary carcinomas or comorbidities.
Paternity in male kidney transplant recipients: A French national survey, the PATeRNAL study.
Authors: Boyer Annabel , Lobbedez Thierry , Ouethrani Mohamed , Lecouf Angélique Thuillier , Bouvier Nicolas , Châtelet Valérie , de Ligny Bruno Hurault
Published: October 2020

Background: There is concern about the impact of immunosuppressive agents taken by male kidney transplant (KT) recipients on the risk of foetal malformations. The aim of our survey was to estimate the paternity rate and the outcomes of pregnancies fathered by kidney transplanted males. Methods: This survey analysed 1332 male KT recipients older than 18 years, followed in 13 centres in France. A self-reported questionnaire was used to collect data on the patients, treatments at the time of conception and the pregnancy outcomes.Results: The study included data on 349 children from 404 pregnancies fathered by 232 male KT recipients. The paternity rate was 17% (95% CI [15–20]). There were 37 (9%, 95% CI [7–12]) spontaneous abortions, 12 (3%, 95% CI [2–5]) therapeutic abortions, 2 (0.5%, 95% CI [0.1–1]) still births, and 13 (4%, 95% CI [2–6]) malformations reported. Compared to the general population, there was no difference in the proportion of congenital malformations nor unwanted outcomes whether the father was exposed or not to immunosuppressive agents.Conclusions: This survey does not provide any warning signal that pregnancies fathered by male patients exposed to immunosuppressive agents, notably the debated MMF/MPA, have more complications than pregnancies in the general population.
Modified Nodal Stage of esophageal cancer based on the evaluation of the hazard rate of the negative and positive lymph node
Authors: Zhang Jinling , Li Hongyan , Zhou Liangjian , Yu Lianling , Che Fengyuan , Heng Xueyuan
Published: October 2020

Background: The study aimed to propose a modified N stage of esophageal cancer (EC) on the basis of the number of positive lymph node (PLN) and the number of negative lymph node (NLN) simultaneously. Method: Data from 13,491 patients with EC registered in the SEER database were reviewed. The parameters related to prognosis were investigated using a Cox proportional hazards regression model. A modified N stage was proposed based on the cut-off number of the re-adjusted ratio of the number of PLN (numberPLN) to the number of NLN (numberNLN), which were derived from the comparison of the hazard rate (HR) of numberPLN and numberNLN. The modified N stage was confirmed using the cross-validation method with the training and validation cohort, and it was also compared to the N stage from the American Joint Committee on Cancer (AJCC) staging system (7th edition) using Receiver Operating Characteristic (ROC) curve analysis.Results: The numberPLN on prognosis was 1.042, while numberNLN was 0.968. The modified N stage was defined as follows: N1 stage: the ratio range was from 0 to 0.21; N2 stage: more than 0.21, but no more than 0.48; N3 stage: more than 0.48. The log-rank test indicated that significant survival differences were confirmed among the N1, N2 and N3 sub-groups of patients in the training population. The difference of all the patients using the modified N stage method were more significant than AJCC N stage. The result of ROC analysis indicated that the modified N stage could represent the N stage of EC more accurately.Conclusion: The modified N stage based on the re-adjusted ratio of numberPLN to numberNLN can evaluate tumor stage more accurately than the traditional N stage.
Flow velocity and nutrients affect CO2 emissions from agricultural drainage channels in the North China Plain
Authors: Leng Peifang , Li Fadong , Du Kun , Li Zhao , Gu Congke , Koschorreck Matthias
Published: October 2020

Background Groundwater is typically over-saturated in CO2 with respect to atmospheric equilibrium. Irrigation with groundwater is a common agricultural practice in many countries, but little is known about the fate of dissolved inorganic carbon (DIC) in irrigation groundwater and its contribution to the CO2 emission inventory from land to the atmosphere. We performed a mesocosm experiment to study the fate of DIC entering agricultural drainage channels in the North China Plain. Specifically, we aimed to unravel the effect of flow velocity and nutrient on CO2 emissions. Results All treatments were emitting CO2. Approximately half of the DIC in the water was consumed by TOC production (1-16%), emitted to the atmosphere (14-20%), or precipitated as calcite (CaCO3) (14-20%). We found that DIC depletion was stimulated by nutrient addition, whereas more CO2 evasion occurred in the treatments without nutrients addition. On the other hand, about 50% of CO2 was emitted within the first 50h under high flow velocity. Thus, in the short term, high nutrient levels may counteract CO2 emissions from drainage channels, whereas the final fate of the produced biomass (burial versus mineralization to CO2 or even CH4) determines the duration of the effect. Conclusion Our study reveals that both hydrology and biological processes affect CO2 emissions from groundwater irrigation channels. The estimated CO2 emission from total groundwater depletion in the North China Plain is up to 0.52 ± 0.07 Mt CO2 y−1. Thus, CO2 emissions from groundwater irrigation should be considered in regional CO2 budgets, especially given that groundwater depletion is expected to acceleration in the future.
Value of AFP and PIVKA-II in diagnosis of primary hepatocellular carcinoma and prediction of vascular invasion and tumor differentiation
Authors: Si Yuan-quan , Wang Xiu-Qin , Fan Gang , Wang Chang-Yin , Zheng Yuan-Wen , Song Xie , Pan Cui-Cui , Chu Fu-Lu , Liu Zhan-Feng , Lu Bing-Ru , Lu Zhi-Ming
Published: October 2020

Background: To explore the value of alpha fetoprotein (AFP) and protein induced by vitamin K absence or antagonist-II (PIVKA-II) in diagnosis of primary hepatocellular carcinoma (HCC) and their relationship with vascular invasion, tumor differentiation and size.Methods: A total of 433 participants were enrolled in this study including 266 cases with HCC, 87 cases with liver cirrhosis and 80 healthy individuals. Then we explored the correlation between AFP, PIVKA-II serum level and several pathological features such as vascular invasion, tumor differentiation and size. The value of these two markers used singly or jointly in diagnosing HCC was evaluated by receiver operating characteristic (ROC) curve. The ROC curve was also plotted to identify AFP, PIVKA-II serum cut-off values that would best distinguish HCC patients with and without vascular invasion.Results: The level of AFP and PIVKA-II in HCC group was significantly higher (Z was 7.428, 11.243 respectively, all P<0.01). When AFP and PIVKA-II were used as the individual tumor marker, the areas under the ROC curve (AUC) of HCC diagnosis were 0.765 (95% CI, 0.713～0.8170) for AFP, 0.901 (95% CI, 0.868～0.935) for PIVKA-II, and 0.917 (95% CI, 0.886～0.948) for AFP and PIVKA-II simultaneously.The serum levels of AFP and PIVKA-II were positively correlated with tumor differentiation and size. High AFP and PIVKA-II expression was signiﬁcantly associated with the presence of vascular invasion (P was 0.007 and 0.014 respectively). The AFP level >64.4ng/ml or PIVKA-II level >957.61mAU/ml was the best critical value to predict the presence of vascular invasion.Conclusion: Our results validate that AFP and PIVKA-II play a significant role in the diagnosis of HCC. The diagnostic value of AFP and PIVKA-II combined detection or single assay of PIVKA-II is higher than that of separate assay of AFP. Moreover, their concentration has important clinical value in judging tumor size, tumor cell differentiation and vascular invasion.
Expression and Prognostic Analyses of the Insulin-like Growth Factor 2 mRNA Binding Protein Family in Human Pancreatic Cancer
Authors: Cui Xiao-Han , Hu Shu-Yi , Qin Xihu , Zhu Chun-Fu
Published: October 2020

Background: Despite advances in early diagnosis and treatment, cancer remains the leading cause of mortality worldwide. The insulin-like growth factor 2 mRNA binding protein (IGF2BP) family has been reported to be involved in a variety of human malignant tumours. However, little is known about their expression and prognostic value in human pancreatic cancer. Therefore, we performed a detailed cancer versus normal differential analysis.Methods: The Cancer Genome Atlas (TCGA) and Gene Expression Profiling Interactive Analysis (GEPIA) databases were used to analyse the mRNA expression levels of the IGF2BP family in various cancers, including pancreatic cancer. Then, the LinkedOmics and GEPIA databases were used to assess the relation between the expression levels of IGF2BPs and overall survival (OS). Then, univariate and multivariate Cox regression analyses were performed, and subgroups based on grade and stage were analysed. The signalling pathways associated with IGF2BP2 and IGF2BP3 were then investigated via gene set enrichment analysis (GSEA).Results: IGF2BP2 and IGF2BP3 were associated with each subset of OS based on grade and stage. Further clinical correlation analysis of IGF2BP2 and IGF2BP3 confirmed that IGF2BP2 and IGF2BP3 are fundamental factors in promoting pancreatic cancer progression.Conclusion: IGF2BP2 and IGF2BP3 are key factors in promoting the progression of pancreatic cancer and are closely related to overall survival.
Mortality calculator as a possible prognostic predictor of overall survival after gastrectomy in elderly patients with gastric cancer
Authors: Akaike Hidenori , Kawaguchi Yoshihiko , Maruyama Suguru , Shoda Katsutoshi , Satio Ryo , Furuya Shinji , Hosomura Naohiro , Amemiya Hidetake , Kawaida Hiromichi , Sudoh Makoto , Inoue Shingo , Kohno Hiroshi , Ichikawa Daisuke
Published: October 2020

Background: The number of elderly patients with gastric cancer has been increasing. Most elderly patients have associated reduced physiologic functions, that can sometimes become an obstacle to safe surgical treatment. The National Clinical Database Risk Calculator, which based on a large Japanese surgical database, provides predicted mortality and morbidity in each case as the surgical-related risks. The purpose of this study was to investigate the clinical significance of the risk for operative mortality (NRC-mortality), as calculated by the National Clinical Database Risk Calculator, during long-term follow-up after gastrectomy for elderly patients with gastric cancer.Methods: We enrolled 73 patients aged ≥80 years and underwent gastrectomy at our institution. Their surgical risk was evaluated based on the NRC-mortality. Several clinicopathologic factors, including NRC-mortality, were selected, and analyzed as the possible prognostic factors for elderly patients who have undergone gastrectomy for gastric cancer. Statistical analysis was performed using the log-rank test and Cox proportional hazard model.Results: NRC-mortality ranged from 0.5% to 10.6%, and the median value was 1.7%. Dividing the patients according to mortality, the overall survival was significantly worse in the high mortality group (≥1.7%, n = 38) than in the low mortality group (<1.7%, n = 35), whereas disease-specific survival was not different between the two groups. In the Cox proportional hazard model, multivariate analysis revealed NRC-mortality, performance status, and surgical procedure as the independent prognostic factors for overall survival. For disease-specific survival, the independent prognostic factors were performance status and pathological stage but not NRC-mortality.Conclusion: The NRC-mortality might be clinically useful for predicting both surgical mortality and overall survival after gastrectomy in elderly patients with gastric cancer.
Ex-vivo quantification of ovine pia arachnoid complex biomechanical properties under uniaxial tension
Authors: Natividad Gabryel Conley , Theodossiou Sophia K , Schiele Nathan R , Murdoch Gordon K , Tsamis Alkiviadis , Tanner Bertrand , Potirniche Gabriel , Mortazavi Martin , Vorp David , Martin Bryn
Published: October 2020

Background: The pia arachnoid complex (PAC) is a cerebrospinal fluid-filled tissue conglomerate that surrounds the brain and spinal cord. Pia mater adheres directly to the surface of the brain while the arachnoid mater adheres to the deep surface of the dura mater. Collagen fibers, known as subarachnoid trabeculae (SAT) fibers, and microvascular structure lie intermediately to the pia and arachnoid meninges. Due to its structural role, alterations to the biomechanical properties of the PAC may change surface stress loading in traumatic brain injury (TBI) caused by sub-concussive hits. The aim of this study was to quantify the mechanical and morphological properties of ovine PAC. Methods: Ovine brain samples (n=10) were removed from the skull and tissue was harvested within 30 minutes post-mortem. To access the PAC, ovine skulls were split medially from the occipital region down the nasal bone on the superior and inferior aspects of the skull. A template was used to remove arachnoid samples from the left and right sides of the frontal and occipital regions of the brain. 10 ex-vivo samples were tested with uniaxial tension at 2 mm s-1, average strain rate of 0.59 s-1, until failure at <5 hours post extraction. The force and displacement data were acquired at 100 Hz using LabVIEW. PAC tissue collagen fiber microstructure was characterized using second-harmonic generation (SHG) imaging on a subset of n=4 stained tissue samples. To differentiate transverse blood vessels from SAT by visualization of cell nuclei and endothelial cells, samples were stained with DAPI and anti-von Willebrand Factor, respectively. The Mooney-Rivlin model for average stress-strain curve fit was used to model PAC material properties. Results: The elastic modulus, ultimate stress, and ultimate strain were found to be 7.7±3.0 MPa, 2.7±0.76 MPa, and 0.60±0.13, respectively. No statistical significance was found across brain dissection locations in terms of biomechanical properties. SHG images were post-processed to obtain average SAT fiber intersection density, concentration, porosity, tortuosity, segment length, orientation, radial counts, and diameter as 0.23%, 26.14%, 73.86%, 1.07±0.28, 17.33±15.25 µm, 84.66±49.18º, 8.15%, 3.46±1.62 µm, respectively. Conclusion: For the sizes, strain, and strain rates tested, our results suggest that ovine PAC mechanical behavior is isotropic, and that the Mooney-Rivlin model is an appropriate curve-fitting constitutive equation for obtaining material parameters of PAC tissues.
Improved Gossypium raimondii Genome Using a Hi-C-based Proximity-Guided Assembly
Authors: Song Guoli , Yang Qiuhong , Zuo Dongyun , Wang Qiaolian , Cheng Hailiang , Feng Xiaoxu , Ashraf Javaria , Zhang Youping , Li Simin , Chen Xiaoqin
Published: October 2020

Background: Genome sequence plays an important role in both the basic and applied studies. Gossypium raimondii, the putative contributor of the D subgenome of Upland cotton (Gossypium. hirsutum), highlights the need to improve the genome quality in a rapid and efficient way. Methods: we performed Hi-C sequencing of Gossypium raimondii and reassembled its genome based on a set of new Hi-C data and previously published scaffolds. We identified and corrected errors of initial scaffolds before reassembled into chromosomes. Result: A total of 98.42% of sequence was clustered successfully, among which 99.72% of the clustered sequence was ordered and 99.92% of the ordered sequence was oriented with high-quality. Further evaluation of results by heat-map and collinearity analysis revealed that the current reassembled genome is significantly improved than previous one. Conclusion: This improvement in Gossypium raimondii genome not only provides a better reference genome to increase study efficiency, but also offers a new way to assemble cotton genomes. Furthermore, Hi-C data of Gossypium raimondii may be used for 3D structure research or regulating analysis.
Ni-modified magnetic nanoparticles for affinity purification of His-tagged proteins from the complex matrix of the silkworm fat body
Authors: Minkner Robert , Xu Jian , Takamura Kenshin , Boonyakida Jirayu , Wätzig Hermann , Park Enoch Y.
Published: October 2020

Purification of recombinant proteins is often a challenging matter because high purity and high recovery are desired. If the expressed recombinant protein is also in a complex matrix, such as from the silkworm expression system, purification becomes more challenging. Even if purification from the silkworm expression system is troublesome, it benefits from a high capacity for the production of recombinant proteins. In this study, magnetic nanoparticles (MNPs) were investigated as a suitable tool for the purification of proteins from the complex matrix of the silkworm fat body. The MNPs were modified with nickel so that they have an affinity for His-tagged proteins, as the MNP purification protocol itself does not need special equipment except for a magnet. Among the three different kinds of investigated MNPs, MNPs with sizes of 100 nm to 200 nm and approximately 20 nm-thick nickel shells were the most suitable for our purpose. With them, the total protein amount was reduced by up to at least approximately 77.7%, with a protein recovery of around 50.8% from the silkworm fat body. The minimum binding capacity was estimated to be 83.3 µg protein/mg MNP. Therefore, these MNPs are a promising tool as a purification pretreatment of complex sample matrices.
Tribological Properties of Wax on Different Trees Leaf Surface Containing Different Chemical Components
Authors: Xia Yanqiu , Feng Xin , Zhang Wenyi
Published: October 2020

Three kinds of leaf-surface waxes were extracted from different trees, and their chemical compositions were analyzed by Gas Chromatography-Mass Spectrometer (GC-MS). A MFT-R4000 tester was employed to investigate the tribological performances of samples, and the Scanning Electron Microscope (SEM) and Time of Flight Secondary Ion Mass Spectrometry (TOF-SIMS) were used to characterize the morphologies and chemical compositions on the worn surfaces, respectively. The result showed that waxes can effectively improve the friction reduction and anti-wear abilities of base oil, and different composition of waxes have different improve degree. This can be attributed to the chemical compositions and degree of chemical action.
Cross-linking peptide and repurposed drugs inhibit both entry pathways of SARS-CoV-2
Authors: Zhao Hanjun , Lam Hoiyan , Zhou Xinxin , To Kelvin , Chan Jasper , Lee Andrew C. Y. , Cai Jian-Piao , Chan Chris , Yeung Man Lung , Zhang Anna Jinxia , Yuen Kwok-Yung
Published: October 2020

So far, effective antivirals have not been widely available for treating COVID-19. In this study, we identify a dual-functional cross-linking peptide 8P9R which can inhibit the two entry pathways (endocytic pathway and TMPRSS2-mediated surface pathway) of SARS-CoV-2 in cells. The endosomal acidification inhibitors (8P9R and chloroquine) can synergistically enhance the activity of arbidol, a spike-ACE2 fusion inhibitor, against SARS-CoV-2 and SARS-CoV in cells. In vivo studies indicate that 8P9R or the combination of repurposed drugs (arbidol, chloroquine and camostat which is a TMPRSS2 inhibitor), simultaneously interfering with the two entry pathways of coronavirus, can significantly suppress SARS-CoV-2 replication in hamsters and SARS-CoV in mice. Here, we use drug combination (arbidol, chloroquine, and camostat) and a dual-functional 8P9R to demonstrate that blocking the two entry pathways of coronavirus can be a promising and achievable approach for inhibiting SARS-CoV-2 replication in vivo. Cocktail therapy of these drug combinations should be considered in treatment trials for COVID-19.
CRISPR/Cas9-engineered inducible gametocyte producer lines as a novel tool for basic and applied research on Plasmodium falciparum malaria transmission stages
Authors: Boltryk Sylwia , Passecker Armin , Alder Arne , de Vegte-Bolmer Marga van , Sauerwein Robert , Brancucci Nicolas , Beck Hans-Peter , Gilberger Tim , Voss Till
Published: October 2020

The malaria parasite Plasmodium falciparum replicates inside erythrocytes in the blood of infected humans. During each replication cycle, a small proportion of parasites commits to sexual development and differentiates into gametocytes, which are essential for parasite transmission to other human hosts via the mosquito vector. Detailed molecular investigation of gametocyte biology and transmission has been hampered by difficulties in generating large numbers of these highly specialized cells. Here, we engineered marker-free P. falciparum inducible gametocyte producer (iGP) lines for the routine mass production of synchronous gametocytes. Through targeted overexpression of the sexual commitment factor GDV1, iGP lines consistently achieve sexual commitment rates of 75% and produce gametocytes that are infectious to mosquitoes. Subsequent tagging of a nucleoporin allowed us to visualize marked nuclear transformations during gametocytogenesis and demonstrates that further genetic engineering of iGP lines is an invaluable tool for the targeted exploration of gametocyte biology. We believe the iGP approach developed here opens up unprecedented opportunities that will expedite future basic and applied research on P. falciparum transmission stages.
Flat band carrier confinement in magic-angle twisted bilayer graphene
Authors: Tilak Nikhil , lai xinyuan , Wu Shuang , Zhang Zhenyuan , Xu Mingyu , Ribeiro Raquel de Almeida , Canfield Paul , Andrei Eva
Published: October 2020

Magic angle twisted bilayer graphene has emerged as a powerful platform for studying strongly correlated electron physics, owing to its almost dispersionless low-energy bands and the ability to tune the band filling by electrostatic gating. Techniques to control the twist angle between graphene layers have led to rapid experimental progress, but improving sample quality is essential for separating the delicate correlation physics from disorder effects. Owing to the 2D nature of the system and the relatively low carrier density, the samples are highly susceptible to small doping inhomogeneity which can drastically modify the local potential landscape. This potential disorder is distinct from the twist-angle variation which has been studied elsewhere. Understanding and mitigating the effects of such disorder is important. Here, we demonstrate using low temperature scanning tunneling spectroscopy and planar tunneling junction measurements, how flat bands in twisted bilayer graphene can amplify small doping inhomogeneity leading to carrier confinement, thus obscuring magic-angle physics.
Effect of Endothelial Progenitor Cells Transplantation on Neointimal Hyperplasia and Reendothelialization after Balloon Catheter Injury in Rat Carotid Arteries
Authors: WANG WEI , Zhang Yingqian , Hui Hui , Tong Wei , Wei Zechen , Li Zhongxuan , Zhang Suhui , Yang Xin , Tian Jie , Chen Yundai
Published: October 2020

Background: Reendothelialization is a natural pathway to inhibit neointimal hyperplasia and in-stent restenosis. Circulating endothelial progenitor cells (EPCs) derived from bone marrow might contribute to endothelial repair. However, the temporal and spatial distribution of injured vascular reendothelialization and neointimal hyperplasia in the presence of transplanted EPCs is not quite clear. Methods: We performed a carotid balloon injury model and treated by transplantation of bone marrow-derived EPCs. To evaluate the temporal and spatial distribution of neointimal hyperplasia and reendothelialization after injury, the carotid arteries were harvested at different time points after transplantation. Results: Transplanted EPCs labeled by PKH26 were clearly observed attaching on the injured luminal surface at day 1 post-injury. For the undamaged arteries, the transplanted EPCs never adhered to the luminal surface. From day 4 post-injury, the average value of PKH26 fluorescence decreased significantly. Although transplanted EPCs were decreased significantly at the site of injury on day 4 after transplantation, reendothelialization at the site of the injury and inhibition of neointimal hyperplasia were significantly promoted by transplanted EPCs. The degree of reendothelialization of EPC7d (group of EPCs transplantation after balloon injury and harvested at day 7 post-transplantation)/EPC14d was significantly better than that of the BI7d (group of medium injection after balloon injury and harvested at day 7 post-injection)/BI14d, and the statistical difference of neointimal hyperplasia began to appear between EPC14d and BI14d. The number of endothelial cells on the lumen surface of EPC14d increased than that of BI14d, and the number of infiltrated macrophages at the injury site decreased.Conclusions: Transplanted EPCs had chemotactic enrichment and attached to the injured arterial intima after transplantation. Although decreased significantly at the site of injury over time after transplantation, transplanted EPCs could still promote the reendothelialization at the site of the injury and inhibition of neointimal hyperplasia.
WITHDRAWN: lncRNA HAND2-AS1 is Down Regulated in Osteoarthritis and Regulates IL‐6 Expression in Chondrocyte
Authors: Si Zhenxing , Zhou Shifeng , Shen Zilong , Luan Feiyu , Yan Jinglong
Published: October 2020

Background: Osteoarthritis (OA) is a leading cause of disability. The incidence of OA is progressively rising due to the diminishing levels of physical activity and ever-expanding ageing population. However, the mainstay for OA treatment only can improve symptoms without delay the progression of this severe disease. This study aimed to explore the biological role and clinical function of lncRNA HAND2-AS1 in OA.Methods: Blood samples and synovial fluid were collected from OA patients and normal subjects. HAND2-AS1 expression was detected by qRT-PCR and IL-6 expression was detected by ELISA; The plasma levels of HAND2-AS1 were also detected in different ages, stages and gender of OA patients and controls. Furthermore, the ROC curve was used to analyze whether HAND2-AS1 can distinguish OA patients from normal subjects. Also, Pearson correlation coefficient analysis was used to analyze the correlation between lncRNA HAND2-AS1 and IL-6. In addition, western blot was used to detect the IL-6 level upon HAND2-AS1 overexpression in chondrocytes and qRT-PCR was used to detect the HAND2-AS1 level after endogenous IL-6 treatment. Results: HAND2-AS1 and IL-6 were dysregulated in plasma and synovial fluid of OA patients. The expression of HAND2-AS1 in plasma of OA patients was decreased with aging and progression. Furthermore, HAND2-AS1 downregulation effectively distinguished OA patients from the healthy controls. Overexpression of HAND2-AS1 inhibited IL‐6 expression in chondrocytes, while treatment with exogenous IL‐6 did not affect HAND2-AS1 expression. Conclusion: HAND2-AS1 effectively distinguished OA patients from the healthy controls and regulates IL‐6 expression in human chondrocytes. Abbreviations: Long non-coding RNA, lncRNA; Osteoarthritis, OA; Interleukin 6, IL‐6; Negative control plasmid, NC; Real‐time quantitative polymerase chain reaction, qRT-PCR; Enzyme‐linked immunosorbent assay, ELISA; Receiver operating characteristic curve, ROC; Trial registration: ChiCTR, ChiCTR2000038635. Registered 11 February 2019, http:// http://www.chictr.org.cn/ ChiCTR2000038635
Quantitation of Cancer Treatment Response by FDG PET/CT: Multi-center Assessment of Measurement Variability Using AUTO-PERCISTTM
Authors: O JooHyun , Lim Su Jin , Wang Hao , Leal Jeffrey P. , Shu Hui-Kuo G. , Wahl Richard L.
Published: October 2020

Background: The aim of this study was to assess the reader variability in quantitatively assessing pre- and post-treatment F-18 fluorodeoxyglucose positron emission tomography/computed tomography (FDG PET/CT) scans in a defined set of images of cancer patients using the same semi-automated analytical software (Auto-PERCIST™), which identifies tumor peak standard uptake value corrected for lean body mass (SULpeak) to determine 18F-FDG PET quantitative parameters.Methods: Paired pre- and post-treatment FDG PET/CT images from 30 oncologic patients and Auto-PERCIST™ semi-automated software were distributed to 13 readers across US and international sites. One reader was aware of the relevant medical history of the patients (readreference), whereas the 12 other readers were blinded to history but had access to the correlative images. Auto-PERCIST™ was set up to first automatically identify the liver and compute the threshold for tumor measurability (1.5 x liver mean) + (2 x liver standard deviation [SD]), and then detect all sites with SULpeak greater than the threshold. Next, the readers selected sites they believed to represent tumor lesions. The main performance metric assessed was the percent change in the SULpeak (%ΔSULpeak) of the hottest tumor identified on the baseline and follow up images. Results: The intra-class correlation coefficient (ICC) for the %ΔSULpeak of the hottest tumor was 0.87 (95%CI: [0.78, 0.92]) when all reads were included (n=297). Including only the measurements that selected the same target tumor as the readreference (n=224), the ICC for %ΔSULpeak was 1.00 (95%CI: [1.00, 1.00]). The Krippendorff alpha coefficient for response (complete or partial metabolic response, versus stable or progressive metabolic disease on PET Response Criteria in Solid Tumors 1.0) was 0.91 for all reads (n=380), and 1.00 including for reads with the same target tumor selection (n=270).Conclusion: Quantitative tumor FDG SULpeak changes measured across multiple global sites and readers utilizing Auto-PERCIST™ show very high correlation. Harmonization of methods to single software, Auto-PERCIST™, resulted in virtually identical extraction of quantitative tumor response data from FDG PET images when the readers select the same target tumor.
Preliminary Study of Ai-assisted Diagnosis Using FDG-PET/CT for Axillary Lymph Node Metastasis in Patients With Breast Cancer
Authors: Li Zongyao , Kitajima Kazuhiro , Hirata Kenji , Togo Ren , Takenaka Junki , Miyoshi Yasuo , Kudo Kohsuke , Ogawa Takahiro , Haseyama Miki
Published: October 2020

Background: To improve the diagnostic accuracy of axillary lymph node (LN) metastasis in breast cancer patients using FDG-PET/CT, we constructed an artificial intelligence (AI)-assisted diagnosis system that uses deep-learning technologies.Materials and Methods: Two clinicians and the new AI system retrospectively analyzed and diagnosed 414 axillae of 407 patients with biopsy-proven breast cancer who had undergone FDG-PET/CT before a mastectomy or breast-conserving surgery with a sentinel lymph node (LN) biopsy and/or axillary LN dissection. We designed and trained a deep 3D convolutional neural network (CNN) as the AI model. The diagnoses from the clinicians were blended with the diagnoses from the AI model to improve the diagnostic accuracy.Results: Although the AI model did not outperform the clinicians, the diagnostic accuracies of the clinicians were considerably improved by collaborating with the AI model: the two clinicians' sensitivities of 59.8% and 57.4% increased to 68.6% and 64.2%, respectively, whereas the clinicians' specificities of 99.0% and 99.5% remained unchanged.Conclusions: It is expected that AI using deep-learning technologies will be useful in diagnosing axillary LN metastasis using FDG-PET/CT. Even if the diagnostic performance of AI is not better than that of clinicians, taking AI diagnoses into consideration may positively impact the overall diagnostic accuracy.
Feasibility of Self-Administered Electroencephalography-Based Sleep Assessment in Children and Adults: Data From The SCREENS Pilot Trial
Authors: Pedersen Jesper , Rasmussen Martin Gillies Banke , Olesen Line Grønholt , Kristensen Peter Lund , Grøntved Anders
Published: October 2020

Background Sleep is a crucial part of our lives and insufficient sleep has been linked to several health disorders in both children and adults. However, most studies are based on single night laboratory polysomnography, actigraphy, or sleep diaries. The primary aim of this study was to evaluate the feasibility of a novel self-administered electroencephalography-based (EEG-based) sleep assessment protocol in a sample of children and adults for six nights. The secondary aim was to report sleep parameters derived from the Zmachine.Methods We analyzed data from 12 families who participated in the SCREENS pilot trial (2018-2019). Children (n=14) and adults (n=19) had to undergo three nights of EEG-based sleep assessment at baseline and follow-up. We assessed compliance to the sleep assessment protocol and summarized perceived feasibility in children and adults. Summary estimates were computed for several sleep parameters.Results Compliance to the sleep assessment protocol was high with 92.9 % and 89.4% of children and adults meeting the a priori specified compliance goal of at least two out of three nights of complete sleep data at both baseline and follow-up. In general, the protocol was perceived as feasible, with low prevalence of sleep disruption and only minor issues, e.g. difficulties with removing sensors. Results on sleep parameters indicate large within group variation.Conclusions Our findings support the use of a self-administered EEG-based habitual sleep assessment protocol, including multiple days of measurement, in children and adults.Trial registration Cilinicaltrials.gov: NCT03788525 [Secondary outcome measures; Retrospectively registered; 27th December, 2018] https://clinicaltrials.gov/ct2/show/NCT03788525 .
DDB2 Regulates DNA Replication through PCNA-Independent Degradation of CDT2
Authors: Wu Xiaojun , Yu Min , Zhang Zhuxia , Leng Feng , Ma Yue , Xie Ni , Lu Fei
Published: October 2020

BackgroundTargeting ubiquitin-dependent proteolysis is one of the strategies in cancer therapy. CRLCDT2 and CRLDDB2 are two key E3 ubiquitin ligases involved in DNA replication and DNA damage repair. But CDT2 and DDB2 are opposite prognostic factors in kinds of cancers, and the underlining mechanism needs to be elucidated. MethodsSmall interfering RNAs were used to determine the function of target genes. Co-immunoprecipitation (Co-IP) was performed to detect the interaction between DDB2 and CDT2. Immunofluorescence assays and fluorescence activating cell sorting (FACS) were used to measure the change of DNA content. In vivo ubiquitination assay was carried out to clarify the ubiquitination of CDT2 mediated by DDB2. Cell synchronization was performed to arrest cells at G1/S and S phase. The mechanism involved in DDB2-mediated CDT2 degradation was investigated by constructing plasmids with mutant variants and measured by Western blot. Immunohistochemistry was performed to determine the relationship between DDB2 and CDT2. Paired two-side Student’s t-test was used to measure the signiﬁcance of the difference between control group and experimental group.Results Knockdown of DDB2 stabilized CDT2, while over-expression of DDB2 enhanced ubiquitination of CDT2, and subsequentially degradation of CDT2. Although both DDB2 and CDT2 contain PIP (PCNA-interacting protein) box, PIP box is dispensable for DDB2-mediated CDT2 degradation. Knockdown of PCNA had negligible effects on the stability of CDT2, but promoted accumulation of CDT1, p21 and SET8. Silencing of DDB2 arrested cell cycle in G1 phase, destabilized CDT1 and reduced the chromatin loading of MCMs, thereby blocked the formation of polyploidy induced by ablation of CDT2. In breast cancer and ovarian teratoma tissues, high level of DDB2 was along with lower level of CDT2.ConclusionWe found that CRL4DDB2 is the novel E3 ubiquitin ligases of CDT2, and DDB2 regulates DNA replication through indirectly regulates CDT1 protein stability by degrading CDT2 and promotes the assembly of pre-replication complex. Our results broaden the horizon for understanding the opposite function of CDT2 and DDB2 in tumorigenesis, and may provide clues for drug discovery in cancer therapy.