bluuebunny/crossref_metadata_2025_split huggingface dataset:
Glandular orientation and shape determined by computational pathology could identify aggressive tumor for early colon carcinoma: a triple-center study
Authors: Ji Meng-Yao , Yuan Lei , Lu Shi-Min , Gao Meng-Ting , Zeng Zhi , Zhan Na , Ding Yi-Juan , Liu Zheng-Ru , Huang Ping-Xiao , Lu Cheng , Dong Wei-Guo 
Published: March 2020

Abstract
Background
Identifying the early-stage colon adenocarcinoma (ECA) patients who have lower risk cancer vs. the higher risk cancer could improve disease prognosis. Our study aimed to explore whether the glandular morphological features determined by computational pathology could identify high risk cancer in ECA via H&E images digitally.

Methods
532 ECA patients retrospectively from 2 independent data centers, as well as 113 from The Cancer Genome Atlas (TCGA), were enrolled in this study. Four tissue microarrays (TMAs) were constructed across ECA hematoxylin and eosin (H&E) stained slides. 797 quantitative glandular morphometric features were extracted and 5 most prognostic features were identified using minimum redundancy maximum relevance to construct an image classifier. The image classifier was evaluated on D2/D3 = 223, D4 = 46, D5 = 113. The expression of Ki67 and serum CEA levels were scored on D3, aiming to explore the correlations between image classifier and immunohistochemistry data and serum CEA levels. The roles of clinicopathological data and ECAHBC were evaluated by univariate and multivariate analyses for prognostic value.

Results
The image classifier could predict ECA recurrence (accuracy of 88.1%). ECA histomorphometric-based image classifier (ECAHBC) was an independent prognostic factor for poorer disease-specific survival [DSS, (HR = 9.65, 95% CI 2.15–43.12, P = 0.003)]. Significant correlations were observed between ECAHBC-positive patients and positivity of Ki67 labeling index (Ki67Li) and serum CEA.

Conclusion
Glandular orientation and shape could predict the high risk cancer in ECA and contribute to precision oncology. Computational pathology is emerging as a viable and objective means of identifying predictive biomarkers for cancer patients.
In vitro modeling of the neurovascular unit: advances in the field
Authors: Bhalerao Aditya , Sivandzade Farzane , Archie Sabrina Rahman , Chowdhury Ekram Ahmed , Noorani Behnam , Cucullo Luca 
Published: March 2020

AbstractThe blood–brain barrier (BBB) is a fundamental component of the central nervous system. Its functional and structural integrity is vital in maintaining the homeostasis of the brain microenvironment. On the other hand, the BBB is also a major hindering obstacle for the delivery of effective therapies to treat disorders of the Central Nervous System (CNS). Over time, various model systems have been established to simulate the complexities of the BBB. The development of realistic in vitro BBB models that accurately mimic the physiological characteristics of the brain microcapillaries in situ is of fundamental importance not only in CNS drug discovery but also in translational research. Successful modeling of the Neurovascular Unit (NVU) would provide an invaluable tool that would aid in dissecting out the pathological factors, mechanisms of action, and corresponding targets prodromal to the onset of CNS disorders. The field of BBB in vitro modeling has seen many fundamental changes in the last few years with the introduction of novel tools and methods to improve existing models and enable new ones. The development of CNS organoids, organ-on-chip, spheroids, 3D printed microfluidics, and other innovative technologies have the potential to advance the field of BBB and NVU modeling. Therefore, in this review, summarize the advances and progress in the design and application of functional in vitro BBB platforms with a focus on rapidly advancing technologies.
Enhancing A82846B production by artificial attB-assisted overexpression of orf10–orf11 genes in Kibdelosporangium aridum SIPI-3927
Authors: Tian Xun , Huang He , Hu Hai-Feng 
Published: March 2020

AbstractA82846B, producing by Kibdelosporangium aridum, is an important precursor of the semi-synthetic glycopeptide antibiotic Oritavancin. K. aridum produces three components A82846A, B and C, so it is essential to increase A82846B titer and reduce A82846A and C titers by overexpressing halogenase and glycosyltransferase genes. Firstly, we constructed the genetically engineered strain SIPI-3927-attB harboring artificial attB site via homologous recombination. Secondly, two strains SIPI-3927-C1 and C2 were also constructed by integrating halogenase genes vcm8 and orf10 into artificial attB sites of SIPI-3927-attB, respectively. Meantime, three strains SIPI-3927-C3, C4 and C5 containing overexpressing glycosyltransferase A, B and C genes were obtained, respectively. Through fermentation analyses, the results showed that SIPI-3927-C1 and C2 could increase A82846B ratios, in which SIPI-3927-C1 showed a better performance. Moreover, the titer of SIPI-3927-C3 was highest in those of three strains. Finally, the strain SIPI-3927-C6 was constructed by integrating both orf10-encoded halogenase and orf11-encoded glycosyltransferase A, of which the yield and ratio of A82846B in shake-flask fermentation reached 1200 mg/L and 73.6%, respectively. Besides, the yield and ratio of A82846B in SIPI-3927-C6 grew up to 2520 mg/L and 86.5% in the 5-L fermenter culture, respectively. In conclusion, overexpressing orf10 gene can increase A82846B ratio,while overexpressing orf11 gene can increase A82846B titer as well. The artificial attB site is effective for inserting new genes.
Toeplitz matrix completion via a low-rank approximation algorithm
Authors: Wen Ruiping , Fu Yaru 
Published: March 2020

AbstractIn this paper, we propose a low-rank matrix approximation algorithm for solving the Toeplitz matrix completion (TMC) problem. The approximation matrix was obtained by the mean projection operator on the set of feasible Toeplitz matrices for every iteration step. Thus, the sequence of the feasible Toeplitz matrices generated by iteration is of Toeplitz structure throughout the process, which reduces the computational time of the singular value decomposition (SVD) and approximates well the solution. On the theoretical side, we provide a convergence analysis to show that the matrix sequences of iterates converge. On the practical side, we report the numerical results to show that the new algorithm is more effective than the other algorithms for the TMC problem.
Dynamics analysis on a class of delayed neural networks involving inertial terms
Authors: Zhang Jian , Huang Chuangxia 
Published: March 2020

AbstractThis paper explores a class of unbounded distributed delayed inertial neural networks. By introducing some new differential inequality analysis and abandoning the traditional order reduction technique, some new assertions are derived to verify the global exponential stability of the addressed networks, which improve and generalize some recently published articles. Finally, two cases of numerical examples and simulations are given to illustrate these analytical conclusions.
Collection and evaluation of thirty-seven pomegranate germplasm resources
Authors: Peng Yingshu , Wang Guibin , Cao Fuliang , Fu Fang-Fang 
Published: March 2020

AbstractPomegranates (Punica granatum L.) are gaining popularity among consumers because of their high antioxidant activity and multiple medical benefits. China is rich in pomegranate genetic resources, but how to use them effectively is a problem worthy of deep consideration. In this article, thirty-seven pomegranate varieties from seven provinces in China were collected and analyzed for twelve phenotypic traits and twelve biochemical indicators (seeds and juices). The fruit and aril fresh weight ranged between 210.5 and 576.5 g and 121.0 to 327.5 g, respectively, and the edible rate (42.58–64.80%), seed weight (1.80–3.41 g), seed number (249.1–838.9), fruit height (10.51–15.48 mm), fruit diameter (11.46–17.50 mm), skin thickness (2.14–6.98 mm), and shape index (0.82–0.96) varied among the different genotypes. The pomegranate juice total phenolic content ranged from 40.91 to 132.47 µg/mL, and the total flavonoid content (14.08–137.72 µg/mL), vitamin C content (12.80–66.63 µg/mL), pH (3.10–4.34), total soluble solids (13.13–17.50°Brix), and titratable acidity (0.26–2.71%) also varied; the pomegranate seed total phenolic content ranged from 0.62 to 1.78 mg/g, and the total flavonoid content (0.39–0.99 mg/g), vitamin C content (7.55–13.90 mg/g), DPPH radical scavenging capacity (85.98–98.24%), and ABTS scavenging ability (28.72–51%) were also measured. The coefficients of variation of the studied traits ranged from 5.62 to 54.02%, and the phenotypic traits’ Shannon–Weaver diversity indexes ranged from 0.67 to 1.53. Cluster analysis divided the 37 varieties into three categories, providing a reference for improved variety breeding. In addition, genotypic and environmental effects mainly affected the pomegranate flavor and antioxidant activity, respectively.
Characterization of antibiotic resistance and host-microbiome interactions in the human upper respiratory tract during influenza infection
Authors: Zhang Lingdi , Forst Christian V. , Gordon Aubree , Gussin Gabrielle , Geber Adam B. , Fernandez Porfirio J. , Ding Tao , Lashua Lauren , Wang Minghui , Balmaseda Angel , Bonneau Richard , Zhang Bin , Ghedin Elodie 
Published: March 2020

Abstract
Background
The abundance and diversity of antibiotic resistance genes (ARGs) in the human respiratory microbiome remain poorly characterized. In the context of influenza virus infection, interactions between the virus, the host, and resident bacteria with pathogenic potential are known to complicate and worsen disease, resulting in coinfection and increased morbidity and mortality of infected individuals. When pathogenic bacteria acquire antibiotic resistance, they are more difficult to treat and of global health concern. Characterization of ARG expression in the upper respiratory tract could help better understand the role antibiotic resistance plays in the pathogenesis of influenza-associated bacterial secondary infection.

Results
Thirty-seven individuals participating in the Household Influenza Transmission Study (HITS) in Managua, Nicaragua, were selected for this study. We performed metatranscriptomics and 16S rRNA gene sequencing analyses on nasal and throat swab samples, and host transcriptome profiling on blood samples. Individuals clustered into two groups based on their microbial gene expression profiles, with several microbial pathways enriched with genes differentially expressed between groups. We also analyzed antibiotic resistance gene expression and determined that approximately 25% of the sequence reads that corresponded to antibiotic resistance genes mapped to Streptococcus pneumoniae and Staphylococcus aureus. Following construction of an integrated network of ARG expression with host gene co-expression, we identified several host key regulators involved in the host response to influenza virus and bacterial infections, and host gene pathways associated with specific antibiotic resistance genes.

Conclusions
This study indicates the host response to influenza infection could indirectly affect antibiotic resistance gene expression in the respiratory tract by impacting the microbial community structure and overall microbial gene expression. Interactions between the host systemic responses to influenza infection and antibiotic resistance gene expression highlight the importance of viral-bacterial co-infection in acute respiratory infections like influenza.
Improved spectral imaging microscopy for cultural heritage through oblique illumination
Authors: Oakley Lindsay , Zaleski Stephanie , Males Billie , Cossairt Oliver , Walton Marc 
Published: March 2020

Abstract
This work presents the development of a flexible microscopic chemical imaging platform for cultural heritage that utilizes wavelength-tunable oblique illumination from a point source to obtain per-pixel reflectance spectra in the VIS–NIR range. The microscope light source can be adjusted on two axes allowing for a hemisphere of possible illumination directions. The synthesis of multiple illumination angles allows for the calculation of surface normal vectors, similar to phase gradients, and axial optical sectioning. The extraction of spectral reflectance images with high spatial resolutions from these data is demonstrated through the analysis of a replica cross-section, created from known painting reference materials, as well as a sample extracted from a painting by Pablo Picasso entitled La Miséreuse accroupie (1902). These case studies show the rich microscale molecular information that may be obtained using this microscope and how the instrument overcomes challenges for spectral analysis commonly encountered on works of art with complex matrices composed of both inorganic minerals and organic lakes.
Paediatric haemodynamic modelling: development and experimental validation using quantitative flow MRI
Authors: Mohammadyari Parvin , Gadda Giacomo , Taibi Angelo , Munuera del Cerro Josep 
Published: March 2020

Abstract
Background
Congenital vascular disease is one of the leading causes of death in paediatric age. Despite the importance of paediatric haemodynamics, large investigations have been devoted to the evaluation of circulation in adults. The novelty of this study consists in the development of a well calibrated mathematical model of cardiovascular circulation in paediatric subjects. To reach the purpose, a model for adult circulation was modified and recalibrated with experimental data and literature from children to be able to calculate the flow rates and pressures in the brain and neck.

Methods
The haemodynamic model simulates the 76 main arteries, together with the main veins in brain and neck. A proper magnetic resonance imaging (MRI) dataset of 29 volunteers aged 12 ± 5 years (mean ± standard deviation) was used to extract age-dependent physiological and clinical parameters such as heart rate, flow rate, vessel cross section area, and blood pressure. The computational model was calibrated using such experimental data. The paediatric and adult model results were compared.

Results
Increase of the vessels stiffness due to aging contributes to a flow rate decrease while blood pressure increases. In accordance, our simulation results show about 16% decrease in mean pressure of internal jugular vein in paediatric rather than adult subjects. The model outcomes indicated about 88% correlation with MRI data.

Conclusions
The mathematical model simulates the paediatric head and neck blood circulation. The model provides detailed information of human haemodynamics including arterial and venous network to study both paediatric and adult blood circulation.
Flare or foe? - Mycobacterium marinum infection mimicking rheumatoid arthritis tenosynovitis: case report and literature review
Authors: Schubert Nils , Schill Tillmann , Plüß Marlene , Korsten Peter 
Published: March 2020

AbstractBackgroundRheumatoid arthritis is the most common type of inflammatory arthritis affecting about 1% of the population. With the advent of disease-modifying anti-rheumatic drugs the disease can be well controlled in many cases. Patients, however, are prone to developing infectious complications. In rare cases, these can mimic a flare of the underlying itself.Case presentationWe report the case of a 45-year-old female patient with a history of seronegative rheumatoid arthritis (RA) who presented with swelling and tenderness of the third metacarpophalangeal joint of the right hand. A flare of her RA was suspected based on clinical and ultrasound findings which showed a tenosynovitis with intense power doppler activity. Her steroid dose was increased but the clinical response to glucocorticoid therapy was very limited. Subsequently, she developed skin manifestations of ‘swimmer’s granuloma’ over the next 2 weeks after first presentation. Finally, a diagnosis of aMycobacterium marinuminfection was established with the help of tissue biopsy and culture, and the patient received appropriate antibiotic treatment with the desired effect.ConclusionsThis case highlights the difficulty of distinction between infection and inflammation in patients with joint swelling and pain, especially in the age of disease-modifying drugs (DMARDs) and the concomitant risk of atypical infections. A review of the literature identified eight additional published cases, which suggests thatMycobacterium marinuminfection is a rare but recognized complication of DMARD therapy. It can mimic a flare of the underlying arthritis potentially leading to diagnostic delays, and requires differential diagnostic methods to identify the pathogen and pave the way for appropriate treatment.
DSMC modeling of rarefied ionization reactions and applications to hypervelocity spacecraft reentry flows
Authors: Fang Ming , Li Zhi-Hui , Li Zhong-Hua , Liang Jie , Zhang Yong-Hao 
Published: March 2020

AbstractThe DSMC modeling is developed to simulate three-dimensional (3D) rarefied ionization flows and numerically forecast the communication blackout around spacecraft during hypervelocity reentry. A new weighting factor scheme for rare species is introduced, whose key point is to modify the corresponding chemical reaction coefficients involving electrons, meanwhile reproduce the rare species in resultants and preserve/delete common species in reactants according to the weighting factors. The resulting DSMC method is highly efficient in simulating weakly inhomogeneous flows including the Couette shear flow and controlling statistical fluctuation with high resolution. The accurate reliability of the present DSMC modeling is also validated by the comparison with a series of experimental measurements of the Shenzhou reentry capsule tested in a low-density wind tunnel from the HAI of CARDC. The obtained electron number density distribution for the RAM-C II vehicle agrees well with the flight experiment data, while the electron density contours for the Stardust hypervelocity reentry match the reference data completely. In addition, the present 3D DSMC algorithm can capture distribution of the electron, N+and O+number densities better than the axis-symmetric DSMC model. The introduction of rare species weighting factor scheme can significantly improve the smoothness of the number density contours of rare species, especially for that of electron in weak ionization case, while it has negligible effect on the macroscopic flow parameters. The ionization characteristics of the Chinese lunar capsule reentry process are numerically analyzed and forecasted in the rarefied transitional flow regime at the flying altitudes between 80 and 97 km, and the simulations predict communication blackout altitudes which are in good agreement with the actual reentry flight data. For the spacecraft reentry with hypervelocity larger than the second cosmic speed, it is forecasted and verified by the present DSMC modeling that ionization reactions will cover the windward capsule surface, leading to reentry communication blackout, and the communication interruption must be considered in the communication design during reentry in rarefied flow regimes.
Advances in BeiDou Navigation Satellite System (BDS) and satellite navigation augmentation technologies
Authors: Li Rui , Zheng Shuaiyong , Wang Ershen , Chen Jinping , Feng Shaojun , Wang Dun , Dai Liwen 
Published: March 2020

AbstractSeveral noteworthy breakthroughs have been made with the BeiDou Navigation Satellite System (BDS) and other global navigation satellite systems as well as the associated augmentation systems, such as the commissioning of the BDS-3 preliminary system and the successful launch of the first BDS-3 GEO satellite which carries the satellite-based augmentation payload. Presently, BDS can provide basic services globally, and its augmentation system is also being tested. This paper gives an overview of BDS and satellite navigation augmentation technologies. This overview is divided into four parts, which include the system segment technologies, satellite segment technologies, propagation segment technologies, and user segment technologies. In each part, these technologies are described from the perspectives of preliminary information, research progress, and summary. Moreover, the significance and progress of the BeiDou Satellite-based Augmentation System (BDSBAS), low earth orbit augmentation, and the national BeiDou ground-based augmentation system are presented, along with the airborne-based augmentation system. Furthermore, the conclusions and discussions covering popular topics for research, frontiers in research and development, achievements, and suggestions are listed for future research.
Evaluation of CD147 gene expression, lipid peroxidation, and antioxidants in cases of acute coronary syndrome in Egyptian population
Authors: Emam Wafaa A. , Ali Nader M. M. , Kamel Aliaa T. A. , Eladawy Mohamed I. M. , Raafat Nermin 
Published: March 2020

Abstract
Background
The main mechanism of acute coronary syndrome (ACS) is the rupture of atherosclerotic plaques. Matrix metalloproteinases (MMPs) play an important role in the rupture of the vulnerable plaques. MMP secretion is stimulated by CD147, one of the immunoglobulin families. Malondialdehyde is an important marker of oxidative damage, which is related to the atherosclerotic process. Superoxide dismutase normally prevents the oxidative process. This study was conducted to evaluate the association of ACS with CD147 gene expression, lipid peroxidation, and antioxidants in Egyptian population. The study included 124 people, 62 ACS patients and 62 healthy controls.

Results
CD147 gene expression in the ACS group was significantly increased compared to the control group (p < 0.001). The ACS was 9.71 ± 3.56-fold; the control group was 0.94 ± 0.19-fold. Also, the SOD activity in the ACS group was significantly increased when compared to the control group (t = 16.023, p < 0.001). There was a highly significant increase in the MDA level in ACS groups when compared to the control group (t = 35.536, p < 0.001). There was a highly significant increase in the creatine kinase-MB (CK-MB) and high sensitive troponin I levels in ACS groups when compared to the control group (p < 0.001).

Conclusion
There is a highly significant positive correlation between CK-MB and CD147 in both control and ACS groups (p = <0.001**); also, there is highly significant positive correlation between high sensitive troponin I and CD 147 in both control and ACS groups (p = <0.001**), but we did not find significant correlation between SOD and CD147 or between MDA and CD 147 in both control and ACS groups.
A new particle swarm intelligence-based graph partitioning technique for image segmentation
Authors: Kapade S. D. , Khairnar S. M. , Chaudhari B. S. 
Published: March 2020

AbstractThe advances in the image processing area demand for improvement in image segmentation methods. Effect of light and noise being ignored in image segmentation while tracing the objects of interest in addition to this texture is also one of the most important factors for analyzing an image automatically. Among the diverse segmentation methods, graph-based techniques are widespread because of their capabilities of generating accurate segmentation structures. In this paper, we have proposed a novel technique by using discrete particle swarm optimization and multilevel partitioning for segmentation of an image. The developed technique has lesser complexity, better efficiency and gives improved results than other methods.