Miracle-dz/UniFAR-FTUs huggingface dataset:
Serum Mac-2 Binding Protein Glycosylation Isomer to Predict the Severity of Hepatic Fibrosis in Patients with Hepatitis C Virus Infection

Large-scale studies to assess the utility of the Mac-2 binding protein glycosylation isomer (M2BPGi) in predicting hepatic fibrosis in patients with hepatitis C virus (HCV) infection are limited. Serum M2BPGi level determination was performed in 1460 patients with HCV who received liver stiffness measurement (LSM) using transient elastography (TE). The correlation of LSM and grade of hepatic fibrosis as staged by TE with M2BPGi was assessed. Receiver operating characteristic (ROC) curves were constructed to evaluate the diagnostic power of M2BPGi for fibrosis stages of ≥F2, ≥F3, and F4. The selected M2BPGi cutoff values were chosen based on the maximal Youden index, a positive likelihood ratio (LR) ≥ 10, and a negative LR ≤ 0.1. Serum M2BPGi level was highly correlated with LSM (Pearson correlation coefficient: 0.567, p < 0.001) and hepatic fibrosis stage (Spearman’s rank correlation coefficient: 0.772, p < 0.001). The areas under ROC curves (AUROCs) of M2BPGi for ≥F2, ≥F3, and F4 were 0.865 (95% confidence interval [CI]: 0.846–0.884), 0.937 (95 % CI: 0.922–0.952), and 0.962 (95% CI: 0.951–0.972). The maximal Youden indices for ≥F2, ≥F3, and F4 were 1.72, 2.65, and 3.93. By selecting M2BPGi cutoff values with a positive LR ≥ 10 and a negative LR ≤ 0.1, clinicians were able to correctly discriminate F2, F3, and F4 in 69.1%, 77.8%, and 90.1% of patients. In conclusion, serum M2BPGi is a good diagnostic tool to predict the severity of hepatic fibrosis in patients with HCV infection.
Trichostatin A-Mediated Epigenetic Modulation Predominantly Triggers Transcriptomic Alterations in the Ex Vivo Expanded Equine Chondrocytes

Epigenetic mechanisms of gene regulation are important for the proper differentiation of cells used for therapeutic and regenerative purposes. The primary goal of the present study was to investigate the impacts of 5-aza-2′ deoxycytidine (5-AZA-dc)- and/or trichostatin A (TSA)-mediated approaches applied to epigenomically modulate the ex vivo expanded equine chondrocytes maintained in monolayer culture on the status of chondrogenic cytodifferentiation at the transcriptome level. The results of next-generation sequencing of 3′ mRNA-seq libraries on stimulated and unstimulated chondrocytes of the third passage showed no significant influence of 5-AZA-dc treatment. Chondrocytes stimulated with TSA or with a combination of 5-AZA-dc+TSA revealed significant expressional decline, mainly for genes encoding histone and DNA methyltransferases, but also for other genes, many of which are enriched in canonical pathways that are important for chondrocyte biology. The TSA- or 5-AZA-dc+TSA-induced upregulation of expanded chondrocytes included genes that are involved in histone hyperacetylation and also genes relevant to rheumatoid arthritis and inflammation. Chondrocyte stimulation experiments including a TSA modifier also led to the unexpected expression incrementation of genes encoding HDAC3, SIRT2, and SIRT5 histone deacetylases and the MBD1 CpG-binding domain protein, pointing to another function of the TSA agent besides its epigenetic-like properties. Based on the transcriptomic data, TSA stimulation seems to be undesirable for chondrogenic differentiation of passaged cartilaginous cells in a monolayer culture. Nonetheless, obtained transcriptomic results of TSA-dependent epigenomic modification of the ex vivo expanded equine chondrocytes provide a new source of data important for the potential application of epigenetically altered cells for transplantation purposes in tissue engineering of the equine skeletal system.
Integrated Analysis of the Fecal Metagenome and Metabolome in Bladder Cancer in a Chinese Population

Bladder cancer (BLCA) is a common malignancy of the urinary system. The gut microbiome produces various metabolites that play functional roles in tumorigenesis and tumor progression. However, the integrative analysis of the gut microbiome and metabolome in BLCA has still been lacking. Thus, the aim of this study was to identify microbial and functional characteristics and metabolites in BLCA in a Chinese population. Metagenomics, targeted metabolomics, bioinformatics, and integrative analysis were used in fecal samples of BLCA patients and healthy individuals. We found gut microbiomes were significantly dysregulated in BLCA patients, including Bifidobacterium, Lactobacillus, Streptococcus, Blautia, and Eubacterium. We also found 11Z-eicosenoic acid, 3-methoxytyrosine, abrine, aniline-2-sulfonate, arachidic acid, conjugated linoleic acids, elaidic acid, glycylleucine, glycylproline, leucyl-glycine, linoelaidic acid, linoleic acid, nicotinamide hypoxanthine dinucleotide, oleic acid, petroselinic acid, and ricinoleic acid to be significantly decreased, while cholesterol sulfate was significantly increased in BLCA patients. Integration of metagenomics and metabolomics revealed interactions between gut microbiota and metabolites and the host. We identified the alterations of gut microbiomes and metabolites in BLCA in a Chinese population. Moreover, we preliminarily revealed the associations between specific gut microbiomes and metabolites. These findings determined potential causative links among gut dysbiosis, dysregulated metabolites, and BLCA.
Incorporating Open Educational Practices in Graduate Education: A Collaborative Autoethnographic Study

In this paper we describe the early steps of our journey through a collaborative autoethnographic research project and share preliminary findings. As distance educators who work at an open, online university, we embrace a philosophy of openness, drawing on open educational practices to facilitate collaborative and flexible learning. As faculty members who support masters and doctoral students, we conceptualize our virtual learning environments as spaces where reciprocal learning takes place between and among learners and professors in a form of co-mentorship. We chose collaborative autoethnography because it is an approach that allows us to interrogate our practice using experiences, archival data, and artifacts as accessible and reliable sources of information. Collaborative autoethnography, which permits us to both individually and collectively critique our practice, requires us to consider our personal experiences in relation to our identities as distance educators within the cultural context of an open and online research university in Canada. The initial data analysis process has uncovered three emergent themes to date. These themes include values linking open educational practices with student engagement and facilitating effective open educational practice through learning design. This research project enables us to experience the power of collaborative autoethnography as a research approach and to further our understanding of the potential of open educational practices in graduate education.
Optimal channel and frequency band‐based feature selection for motor imagery electroencephalogram classification

Common spatial pattern (CSP) is a widely adopted method for electroencephalogram (EEG) feature extraction in brain‐computer interface (BCI) based on motor imagery. Bandpass‐filtering EEG into several subbands related to brain activity tasks is an effective approach to improve the performance of CSP based algorithm. However, this approach tends to suffer the over‐fitting problem because of the increase in feature dimension. Therefore, we proposed an optimal channel and frequency band‐based CSP feature selection method in this paper. Firstly, the correlation coefficient was calculated to select the optimal channels, and these channels were bandpass‐filtered into multiple overlapping subbands. The subbands with higher power spectrum density were chosen for CSP feature extraction. Next, the pair‐wise relevance was utilized to remove subband features with less difference. And then the screened subband features were combined with features extracted from the broadband signal. The Fisher ratio was exploited to carry out further feature selection. Finally, a support vector machine (SVM) was trained to classify the selected CSP features. An experimental study was implemented on BCI competition III dataset IVa and BCI competition IV dataset 1. The average classification accuracy reached 89.33% and 84.08%, which indicated the rationality and effectiveness of the proposed method.
First-Year Wilkinson Microwave Anisotropy Probe (WMAP) Observations: Galactic Signal Contamination from Sidelobe Pickup

Since the Galactic center is ∼1000 times brighter than fluctuations in the cosmic microwave background (CMB), CMB experiments must carefully account for stray Galactic pickup. We present the level of contamination due to sidelobes for the first-year CMB maps produced by the Wilkinson Microwave Anisotropy Probe (WMAP) observatory. For each radiometer, full 4π sr antenna gain patterns are determined from a combination of numerical prediction and ground-based and space-based measurements. These patterns are convolved with the WMAP first-year sky maps and observatory scan pattern to generate the expected sidelobe signal contamination, for both intensity and polarized microwave sky maps. When the main beams are outside of the Galactic plane, we find rms values for the expected sidelobe pickup of 15, 2.1, 2.0, 0.3, and 0.5 μK for the K, Ka, Q, V, and W bands, respectively. Except for at the K band, the rms polarized contamination is ≪1 μK. Angular power spectra of the Galactic pickup are presented.
Diffusionless hydromagnetic modes in rotating ellipsoids: a road to weakly nonlinear models?

We investigate free hydromagnetic eigenmodes of an incompressible, inviscid and ideal electrically conducting fluid in rotating triaxial ellipsoids. The container rotates with an angular velocity tilted from its figure. The magnetic base state is a uniform current density also tilted. Three-dimensional perturbations upon the base state are expanded onto a finite-dimensional polynomial basis. By combining symbolic and numerical computations, we are able to get the eigenmodes of high spatial complexity. Hydromagnetic modes of the sphere still exist in triaxial geometry. A plane-wave analysis is also carried on, explaining the dispersion relation observed in our model. Without magnetic field, the modes reduce to the inertial modes of the ellipsoids, which form a complete basis. We propose to use these modes to study the weakly nonlinear saturation of inertial instabilities, especially the elliptical one.
Serum Leucine-Rich α2 Glycoprotein: A Biomarker for Predicting the Presence of Ulcerative Colitis but Not Ulcerative Proctitis

The serum level of leucine-rich α2 glycoprotein (LRG) is a biomarker for active ulcerative colitis (UC). We examined the serum level of LRG as a biomarker for predicting the presence of UC. Patients with persistent diarrhea and/or bloody stool with no history of UC were consecutively enrolled at their initial visit. Serum LRG measurement and colonoscopy with histology were performed on the same day. We enrolled 103 patients (69 men; median age, 45 years) with suspected UC; 66 patients were diagnosed with active UC (proctitis, n = 10; left-sided colitis, n = 26; and pancolitis, n = 30) based on endoscopic and histological criteria. Although the median LRG value in patients with proctitis was similar to that of patients with normal colonoscopic findings (8.5 vs. 8.6 mg/mL, p = 0.24), the median LRG values were significantly elevated in patients with left-sided colitis and pancolitis compared with those of patients with normal colonoscopy (13.6 or 18.0 vs. 8.6 mg/mL, p < 0.0001). The LRG cut-off value of 10.8 μg/mL was derived from the ROC curve, showing 96% sensitivity and 97% specificity for active UC but not active proctitis. Using a cut-off value of 10.8 mg/mL serum, LRG could be a novel biomarker for predicting patients with active UC except for proctitis.
Energy vs. Nutritional Potential of Virginia Mallow (Sida hermaphrodita L.) and Cup Plant (Silphium perfoliatum L.)

The world today faces several pressing challenges: energy from non-renewable sources is becoming increasingly expensive, while at the same time the use of agricultural land for food production is decreasing at the expense of biofuel production. Energy crops offer a potential solution to maximizing the use of land. In order to provide new value to the by-product, it is necessary to investigate its possible nutritional and functional potential. Therefore, the main objective of this study was to determine the energetic, nutritional, and functional potential of the species Sida hermaphrodita L. and Silphium perfoliatum L. in different phenophases. The analyzed energy potential of the mentioned species is not negligible due to the high determined calorific value (17.36 MJ/kg for Virginia mallow and 15.46 MJ/kg for the cup plant), high coke content (15.49% for the cup plant and 10.45% for Virginia mallow), and desirably high carbon content, almost 45%, in both species. The phenophase of the plant had a significant influence on the content of the analyzed specialized metabolites (SM) in the leaves, with a high content of ascorbic acid at the full-flowering stage in Virginia mallow (229.79 mg/100 g fw) and in cup plants at the end of flowering (122.57 mg/100 g fw). In addition, both species have high content of polyphenols: as much as 1079.59 mg GAE/100 g were determined in the leaves of Virginia mallow at the pre-flowering stage and 1115.21 mg GAE/100 g fw in the cup plants at the full-flowering stage. An HPLC analysis showed high levels of ellagic acid and naringin in both species. In addition, both species have high total chlorophyll and carotenoid concentrations. Due to their high content of SM, both species are characterized by a high antioxidant capacity. It can be concluded that, in addition to their energetic importance, these two plants are also an important source of bioactive compounds; thus, their nutritional and functional potential for further use as value-added by-products should not be neglected.
A parallel and matrix free framework for global stability analysis of compressible flows

An numerical iterative framework for global modal stability analysis of compressible flows using a parallel environment is presented. The framework uses a matrix-free implementation to allow computations of large scale problems. Various methods are tested with regard to convergence acceleration of the framework. The methods consist of a spectral Cayley transformation used to select desired Eigenvalues from a large spectrum, an improved linear solver and a parallel block-Jacobi preconditioning scheme.
A Bayesian Sample Size Estimation Procedure Based on a B-Splines Semiparametric Elicitation Method

Sample size estimation is a fundamental element of a clinical trial, and a binomial experiment is the most common situation faced in clinical trial design. A Bayesian method to determine sample size is an alternative solution to a frequentist design, especially for studies conducted on small sample sizes. The Bayesian approach uses the available knowledge, which is translated into a prior distribution, instead of a point estimate, to perform the final inference. This procedure takes the uncertainty in data prediction entirely into account. When objective data, historical information, and literature data are not available, it may be indispensable to use expert opinion to derive the prior distribution by performing an elicitation process. Expert elicitation is the process of translating expert opinion into a prior probability distribution. We investigated the estimation of a binomial sample size providing a generalized version of the average length, coverage criteria, and worst outcome criterion. The original method was proposed by Joseph and is defined in a parametric framework based on a Beta-Binomial model. We propose a more flexible approach for binary data sample size estimation in this theoretical setting by considering parametric approaches (Beta priors) and semiparametric priors based on B-splines.
Introduction to the Physics of the Quantum Hall Regime

These lecture notes attempt to explain the main ideas of the theory of the quantum Hall effect. The emphasis is on the localization and interaction physics in the extreme quantum limit which gives rise to the quantum Hall effect. The interaction physics in the extreme quantum limit which is responsible for the fractional quantum Hall effect is discussed at length and from an elementary point of view.
Large rapidity gap processes in proton-nucleus collisions

The cross sections for a variety of channels of proton-nucleus interaction associated with large gaps in rapidity are calculated within the Glauber-Gribov theory. We found inelastic shadowing corrections to be dramatically enhanced for such events. We employ the light-cone dipole formalism which allows to calculate the inelastic corrections to all orders of the multiple interaction. Although Gribov corrections are known to make nuclear matter more transparent, we demonstrate that in some instances they lead to an opaqueness. Numerical calculations are performed for the energies of the HERA-B experiment and the RHIC-LHC colliders.
Non-Supersymmetric T^2/Z_N and T^4/Z_N Orbifolds

We compute the perturbative tachyonic and massless spectra of Type II and Type 0 string theories on non-supersymmetric T^2/Z_N orbifolds, and those on T^4/Z_N ones. Comparing the spectra with one another, we obtain insight about the degeneracy of states and find several pairs of Type 0 orbifolds which could be identified with each other.
Static Mixers Producible by Additive Manufacturing: Novel Rapid Automatic Optimisation and Practical Evaluation

In the extrusion of plastics, the thermal and material homogeneity of the plastic melt at the die entry are of high importance for the extrudate quality. While static mixers are widely used to improve the melt homogeneity, previous attempts at optimisation for reduced pressure loss and improved mixing had to be performed by hand and human experience, limiting the degrees of freedom and efficiency. A new automatic optimisation method based on the open source software OpenFOAM was developed. Using immersed boundary methods, new target functions in the pre-existing routine adjointShapeOptimizationFoam and an additional algorithm checking the suitability for additive manufacturing and fixing the geometry during run-time is presented. The new algorithm is used to optimise an existing static mixer based on an X-type geometry with integrated oil channels, maximising the heat exchange between oil and melt. Based on the results of these simulative optimisations, the best candidates were manufactured using selective laser melting and experimental trials were run. Experimental validation shows that with our optimisation algorithm, a pressure loss reduction of 10% could be achieved. The core melt temperature was reduced by 6 ∘C, improving the thermal homogenisation as well. While the main advantage of this method is the rapid optimisation taking the operating point into account, the trials also showed positive results in off-design operating points. This allows the low-cost design and manufacture of individualised static mixers.
Efficient two-mode interferometers with spinor Bose-Einstein condensates

We consider general three-mode interferometers using a spin-1 atomic Bose-Einstein condensate with macroscopic magnetization. We show that these interferometers, combined with the measurement of the number of particles in each output port, provide an ultra-high phase sensitivity. We construct effective two-mode interferometers which involve two Zeeman modes showing that they also provide an ultra-high phase sensitivity but of a bit reduced factor in the corresponding Fisher information. A special case of zero magnetization is shown to persist the efficiency of the two-mode interferometry.
Towards topological quasifreestanding stanene via substrate engineering

In search for a new generation of spintronics hardware, material candidates for room temperature quantum spin Hall effect (QSHE) have become a contemporary focus of investigation. Inspired by the original proposal for QSHE in graphene, several heterostructures have been synthesized, aiming at a hexagonal monolayer of heavier group IV elements in order to promote the QSHE bulk gap via increased spin-orbit coupling. So far, however, the monolayer/substrate coupling, which can manifest itself in strain, deformation, and hybridization, has proven to be detrimental to the aspired QSHE conditions for the monolayer. Specifically focusing on stanene, the Sn analogue of graphene, we investigate how an interposing buffer layer mediates between monolayer and substrate in order to optimize the QSHE setting. From a detailed density functional theory study, we highlight the principal mechanisms induced by such a buffer layer to accomplish quasi-free standing stanene in its QSHE phase. We complement our theoretical predictions by presenting the first real attempts to grow a buffer layer on SiC(0001) on which stanene can be deposited.
A Scintillator and Radio Enhancement of the IceCube Surface Detector Array

An upgrade of the present IceCube surface array (IceTop) with scintillation detectors and possibly radio antennas is foreseen. The enhanced array will calibrate the impact of snow accumulation on the reconstruction of cosmic-ray showers detected by IceTop as well as improve the veto capabilities of the surface array. In addition, such a hybrid surface array of radio antennas, scintillators and Cherenkov tanks will enable a number of complementary science targets for IceCube such as enhanced accuracy to mass composition of cosmic rays, search for PeV photons from the Galactic Center, or more thorough tests of the hadronic interaction models. Two prototype stations with 7 scintillation detectors each have been already deployed at the South Pole in January 2018. These R&D studies provide a window of opportunity to integrate radio antennas with minimal effort.
Optoelectronic control of spin dynamics at near-terahertz frequencies in magnetically doped quantum wells

We use time-resolved Kerr rotation to demonstrate the optical and electronic tuning of both the electronic and local moment (Mn) spin dynamics in electrically gated parabolic quantum wells derived from II-VI diluted magnetic semiconductors. By changing either the electrical bias or the laser energy, the electron spin precession frequency is varied from 0.1 to 0.8 THz at a magnetic field of 3 T and at a temperature of 5 K. The corresponding range of the electrically-tuned effective electron g-factor is an order of magnitude larger compared with similar nonmagnetic III-V parabolic quantum wells. Additionally, we demonstrate that such structures allow electrical modulation of local moment dynamics in the solid state, which is manifested as changes in the amplitude and lifetime of the Mn spin precession signal under electrical bias. The large variation of electron and Mn-ion spin dynamics is explained by changes in magnitude of the sp−d exchange overlap.