bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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.