Miracle-dz/UniFAR-FTUs huggingface dataset:
A Cell Culture Model of Lipopolysaccharide-induced Endothelial Activation Comparison of THP-1 Cells & PBMC-derived Monocytes

Sepsis is a systemic inflammatory host response to infection and leading cause of death in non-coronary ICUs. This disease coincides with a high mortality rate ranging from 30% to 50% and more for patients with septic shock. It is expensive to treat and therefore an enormous economic burden for worldwide healthcare resources. 750,000 people are annually affected by sepsis in the U.S. and 7,000–9,000 in Austria. Therapeutic options to treat sepsis are limited, as pathogenic mechanisms involved are still not fully understood. This thesis aims to characterize an existing cell culture model that mimics the initial events in gram-negative sepsis. The model is based on lipopolysaccharide (LPS)-induced activation of endothelial cells. The continuous monocytic cell line THP-1 was stimulated for 4 hours with 10 ng/ml LPS from Pseudomonas aeruginosa in media containing 10% human plasma. The culture supernatants containing LPS and factors secreted by the stimulated THP-1 cells were subsequently applied to primary Human Umbilical Vein Endothelial Cells (HUVEC). To compare the stimulation patterns of THP-1 cells to those of human monocytes, monocytes were isolated from human blood and used in the cell culture model. In the second part of this work, HUVEC were compared to the cell line Human Pulmonary Microvascular Endothelial Cells ST1.6R (HPMEC ST1.6R). For this purpose HPMEC ST1.6R were stimulated with supernatants containing LPS and secreted factors received from either monocytes or THP-1 cells. Endothelial activation in the model was monitored by different read-out assays. Cytokine secretion [Interleukin-6 (IL-6), Interleukin-8 (IL-8) and Tumor necrosis factoralpha (TNF-α)] was measured after 1 hour and 16 hours. Additionally, the expression of the adhesion molecules ICAM-1 and E-selectin as well as nuclear factor-κB (NF-κB) activity were quantified after 16 hours. Different levels of cytokine release by stimulated THP-1 cells and monocytes could be observed. However, stimulated HUVEC and HPMEC ST1.6R showed comparable secreted amounts of IL-6, IL-8 and TNF-α for both stimulating media. The expression of ICAM-1 was comparable for HUVEC stimulated with supernatants from THP-1 cells and monocytes. HPMEC ST1.6R showed a slightly increased expression of ICAM-1 for either of the stimulation media. Generally, the upregulation of ICAM-1 could be observed more clearly on HUVEC than on HPMEC ST1.6R. The determination of E-selectin as well as the quantification of NF-κB concluded in ambiguous results, most probably due to the low amount of protein available for the experiments. In conclusion, the cell culture model used in this diploma work simulates relevant processes of sepsis in a cell culture system and may serve as a useful tool for preclinical studies of gram-negative sepsis. Nevertheless, further studies to evaluate the model, especially regarding the LPS stimulation patterns of THP-1 and monocytes, are necessary.
First-Principles Thermodynamics of Graphene Growth on Cu Surfaces

Chemical vapor deposition (CVD) is an important method to synthesis graphene on a substrate. Recently, Cu became the most popular CVD substrate for graphene growth. Here, we combine electronic structure calculation, molecular dynamics simulation, and thermodynamics analysis to study the graphene growth process on Cu surfaces. As a fundamentally important but previously overlooked fact, we find that carbon atoms are thermodynamically unfavorable on a Cu surface under typical experimental conditions. The active species for graphene growth should thus mainly be CHx instead of atomic carbon. On the basis of this new picture, the nucleation behavior can be understood, which explains many experimental observations and also provides us a guide to improve graphene sample quality.
Synthesis of Poly(Lactic Acid): A Review

Poly(lactic acid), a bio‐degradable polymer, has been studied extensively during the past 15 years. This paper presents a review on poly(lactic acid) (PLA) with focus on its stereochemistry, synthesis via ring‐opening polymerization, reaction kinetics and thermodynamics, synthesis of low molecular weight polymer, a continuous process for production of PLA from lactic acid, and blends. The different polymerization mechanisms, which have been proposed in the literature, are also summarized. Various catalyst systems, solvents, and reaction temperature and time give products of an entire range of molecular weights, ranging from a few thousand to over a million. Modeling and simulation of the ring‐opening polymerization of PLA is also discussed.
A practical method for the deconvolution of experimental curves

A general method is given for the correction of experimental spectra when they have been distorted according to the convolution integral described, where F(x) is the observed spectrum, f(x) is the true profile and S(x) is the slit function or intrinsic broadening function. The method is applied to the three main types of slit functions which are encountered in practice, namely the exponential, Gaussian and Cauchy distributions.
X‐ray photoelectron spectroscopy surface charge buildup used to study residue in deep features on integrated circuits

A major problem is encountered in characterizing the surfaces at the bottom of submicrometer holes formed by plasma etching operations in the fabrication of submicrometer circuitry. Using monochromated x rays to excite photoemission spectra, surface charge buildup can occur on insulating surfaces causing the spectra to shift relative to the spectra of electrically conductive surfaces. In the case of silicon dioxide on Si, the oxide surface can charge up to a significant voltage relative to the silicon substrate making the two regions spectroscopically resolvable. When an electron flood gun is used in conjunction with monochromatic x rays, the insulated regions can be made to shift in kinetic energy relative to the substrate thereby allowing precise identification of various electrically different regions. In this initial study, residues at the bottoms of 0.75‐μm‐wide paths etched in 0.9‐μm‐thick silicon dioxide were identified. Patterns were etched in silicon dioxide using Freon‐based plasma etching and v.
Nanomaterials and Analytical Chemistry

Abstract Nanomaterials play an important role in the area of sensor technology. In fact the sensitivity and the signal‐to‐noise ratio of many chemical sensors are significantly improved using nanomaterials. They have allowed the introduction of many strategies in sensors and biosensor technology. Recently, catalytic nanomotors were used for drug delivery, showing an oriented motion into the cells when they are assembled using magnetic nanowires. In this review, detailed bibliographic references are presented concerning the assembling of nanomaterial‐based sensors, and a brief discussion about the potential health risk of nanoparticles will be also presented.
An improved alkali reaction test for rice quality

An improved 9-point scoring scale for the alkali reaction test for rice (Little, Hilder & Dawson, 1958) has been devised by studying the successive stages of degradation of rice kernels of individual varieties by increasing concentrations of alkali. Each variety was just attacked by a certain concentration of potassium hydroxide and was essentially fully degraded by a 0-7-0-8% higher concentration of the alkali. Nine distinct stages could be distinguished in this degradation process based on the amount of residual chalky substance in the degraded kernel, the diameter of the collar, and the consistency of the collar. A concentration of 1.4% KOH was found to give the maximum spread of the scores among different varieties. The test could be conducted in ordinary Petri dishes and at room temperature for 18-24 hr. Different rice varieties exhibited three types of reaction. Reaction type A was characterized by progressive cracking and corrosion; type B by progressive grilling and cottony transformation; and type C by opening and splitting with gradual dense cottony transformation of the kernel when treated with successively higher concentrations of KOH. The implication of this reaction type on the quality characteristics of a variety is not known, but most indicas gave reaction of type A, and japonicas type C.
Mixed Policy Gradient

Reinforcement learning (RL) shows great potential in sequential decision-making. At present, mainstream RL algorithms are data-driven, which usually yield better asymptotic performance but much slower convergence compared with model-driven methods. This paper proposes mixed policy gradient (MPG) algorithm, which fuses the empirical data and the transition model in policy gradient (PG) to accelerate convergence without performance degradation. Formally, MPG is constructed as a weighted average of the data-driven and model-driven PGs, where the former is the derivative of the learned Q-value function, and the latter is that of the model-predictive return. To guide the weight design, we analyze and compare the upper bound of each PG error. Relying on that, a rule-based method is employed to heuristically adjust the weights. In particular, to get a better PG, the weight of the data-driven PG is designed to grow along the learning process while the other to decrease. Simulation results show that the MPG method achieves the best asymptotic performance and convergence speed compared with other baseline algorithms.
Deep ReLU Neural Network Approximation for Stochastic Differential Equations with Jumps

Deep neural networks (DNNs) with ReLU activation function are proved to be able to express viscosity solutions of linear partial integrodiﬀerental equations (PIDEs) on state spaces of possibly high dimension d . Admissible PIDEs comprise Kolmogorov equations for high-dimensional diﬀusion, advection, and for pure jump L´evy processes. We prove for such PIDEs arising from a class of jump-diﬀusions on R d , that for any compact K ⊂ R d , there exist constants C, p , q > 0 such that for every ε ∈ (0 , 1] and for every d ∈ N the nomalized (over K ) DNN L 2 -expression error of viscosity solutions of the PIDE is of size ε with DNN size bounded by Cd p ε − q . In particular, the constant C > 0 is independent of d ∈ N and of ε ∈ (0 , 1] and depends only on the coeﬃcients in the PIDE and the measure used to quantify the error. This establishes that ReLU DNNs can break the curse of dimensionality (CoD for short) for viscosity solutions of linear, possibly degenerate PIDEs corresponding to Markovian jump-diﬀusion processes. As a consequence of the employed techniques we also obtain that expectations of a large class of path-dependent functionals of the underlying jump-diﬀusion processes can be expressed without the CoD.
Man-in-The-Middle Attacks and Defense in a Power System Cyber-Physical Testbed

Man-in-The-Middle (MiTM) attacks present numerous threats to a smart grid. In a MiTM attack, an intruder embeds itself within a conversation between two devices to either eavesdrop or impersonate one of the devices, making it appear to be a normal exchange of information. Thus, the intruder can perform false data injection (FDI) and false command injection (FCI) attacks that can compromise power system operations, such as state estimation, economic dispatch, and automatic generation control (AGC). Very few researchers have focused on MiTM methods that are difficult to detect within a smart grid. To address this, we are designing and implementing multi-stage MiTM intrusions in an emulation-based cyber-physical power system testbed against a large-scale synthetic grid model to demonstrate how such attacks can cause physical contingencies such as misguided operation and false measurements. MiTM intrusions create FCI, FDI, and replay attacks in this synthetic power grid. This work enables stakeholders to defend against these stealthy attacks, and we present detection mechanisms that are developed using multiple alerts from intrusion detection systems and network monitoring tools. Our contribution will enable other smart grid security researchers and industry to develop further detection mechanisms for inconspicuous MiTM attacks.
Testing Hamiltonicity (and other problems) in Minor-Free Graphs

In this paper we provide sub-linear algorithms for several fundamental problems in the setting in which the input graph excludes a fixed minor, i.e., is a minor-free graph. In particular, we provide the following algorithms for minor-free unbounded degree graphs. Both our algorithms use partition oracles, a tool introduced by Hassidim et al. (FOCS 2009), which are oracles that provide access to a partition of the graph such that the number of cut-edges is small and each part of the partition is small. The polynomial dependence in 1 /ϵ of our algorithms is achieved by combining the recent poly( d/ϵ )-query partition oracle of Kumar-Seshadhri-Stolman (ECCC 2021) for minor-free graphs with degree bounded by d . For bounded degree minor-free graphs we introduce the notion of covering partition oracles which is a relaxed version of partition oracles and design a poly( d/ϵ )-time covering partition oracle for this family of graphs. Using our covering partition oracle we provide the same results as above (except that the tester for Hamiltonicity has one-sided error) for minor-free bounded degree graphs, as well as showing that any property which is monotone and additive (e.g. bipartiteness) can be tested in minor-free graphs by making poly( d/ϵ )-queries. The benefit using the covering partition oracle rather than the partition oracle in our algorithms is its simplicity and an improved polynomial dependence in 1 /ϵ in the obtained query complexity.
Automating Test Case Identification in Open Source Projects on GitHub

Software testing is one of the very important Quality Assurance (QA) components. A lot of researchers deal with the testing process in terms of tester motivation and how tests should or should not be written. However, it is not known from the recommendations how the tests are actually written in real projects. In this paper the following was investigated: (i) the denotation of the test word in diﬀerent natural languages; (ii) whether the test word correlates with the presence of test cases; and (iii) what testing frameworks are mostly used. The analysis was performed on 38 GitHub open source repositories thoroughly selected from the set of 4.3M GitHub projects. We analyzed 20,340 test cases in 803 classes manually and 170k classes using an automated approach. The results show that: (i) there exists weak correlation ( r = 0 . 655) between the word test and test cases presence in a class; (ii) the proposed algorithm using static ﬁle analysis correctly detected 95% of test cases; (iii) 15% of the analyzed classes used main() function whose represent regular Java programs that test the production code without using any third-party framework. The identiﬁcation of such tests is very low due to implementation diversity. The results may be leveraged to more quickly identify and locate test cases in a repository, to understand practices in customized testing solutions and to mine tests to improve program comprehension in the future.
Metamagnetism of few-layer topological antiferromagnets

MnBi2Te4 (MBT) is a promising antiferromagnetic topological insulator whose films provide access to novel and technologically important topological phases, including quantum anomalous Hall states and axion insulators. MBT device behavior is expected to be sensitive to the various collinear and non-collinear magnetic phases that are accessible in applied magnetic fields. Here, we use classical Monte Carlo simulations and electronic structure models to calculate the ground state magnetic phase diagram as well as topological and optical properties for few layer films with thicknesses up to six septuple layers. Using magnetic interaction parameters appropriate for MBT, we find that it is possible to prepare a variety of different magnetic stacking sequences, some of which have sufficient symmetry to disallow non-reciprocal optical response and Hall transport coefficients. Other stacking arrangements do yield large Faraday and Kerr signals, even when the ground state Chern number vanishes.
Understanding and Controlling Hexagonal Patterns of Wrinkles in Neo-Hookean Elastic Bilayer Structures

A controlled surface wrinkling pattern has been widely used in diverse applications, such as stretchable electronics, smart windows, and haptics. Here, we focus on hexagonal wrinkling patterns because of their great potentials in realizing anisotropic and tunable friction and serving as a dynamical template for making non-flat thin films through self-assembling processes. We employ large-scale finite element simulations of a bilayer neo-Hookean solid (e.g., a film bonded on a substrate) to explore mechanical principles that govern the formation of hexagonal wrinkling patterns and strategies for making nearly perfect hexagonal patterns. In our model, the wrinkling instabilities are driven by the confined film expansion. Our results indicate robust hexagonal patterns exist at a relatively small modulus mismatch (on the order of 10) between the film and substrate. Besides, the film expansion should not exceed the onset of wrinkling value too much to avoid post-buckling patterns. By harnessing the imperfection insensitivity of one-dimension sinusoidal wrinkles, we apply a sequential loading to the bilayer structure to produce the nearly perfect hexagonal patterns. Lastly, we discuss the connection between the simple bilayer model and the gradient structures commonly existed in experiments.
Thermophoresis of a Near-Wall Particle at Great Knudsen Numbers

Analytical results are presented concerning the thermophoretic force acting on a spherical particle suspended near a planar wall at great Knudsen numbers (i.e., for the free-molecule regime). A combined specular and diffuse reflection at the wall and at the particle surface is included in the analysis. It has been shown that the thermophoretic force acting on the near-wall particle depends not only on the temperature gradient or heat flux within the bulk gas, but also on the gas pressure and gas/wall temperature ratio. The particle temperature and the specular reflection fraction at the particle surface do not affect the thermophoretic force. Dependent on the case conditions, the thermophoretic force acting on the near-wall particle may be greater or less than its counterpart without accounting for the near-wall effect.
Automatic Detection and Resolution of Software Merge Conflicts: Are We There Yet?

Developers create software branches for tentative feature addition and bug fixing, and periodically merge branches to release software with new features or repairing patches. When the program edits from different branches textually overlap (i.e., textual conflicts), or the co-application of those edits lead to compilation or runtime errors (i.e., compiling or dynamic conflicts), it is challenging and time-consuming for developers to eliminate merge conflicts. Prior studies examined %the popularity of merge conflicts and how conflicts were related to code smells or software development process; tools were built to find and solve conflicts. However, some fundamental research questions are still not comprehensively explored, including (1) how conflicts were introduced, (2) how developers manually resolved conflicts, and (3) what conflicts cannot be handled by current tools. For this paper, we took a hybrid approach that combines automatic detection with manual inspection to reveal 204 merge conflicts and their resolutions in 15 open-source repositories. %in the version history of 15 open-source projects. Our data analysis reveals three phenomena. First, compiling and dynamic conflicts are harder to detect, although current tools mainly focus on textual conflicts. Second, in the same merging context, developers usually resolved similar textual conflicts with similar strategies. Third, developers manually fixed most of the inspected compiling and dynamic conflicts by similarly editing the merged version as what they did for one of the branches. Our research reveals the challenges and opportunities for automatic detection and resolution of merge conflicts; it also sheds light on related areas like systematic program editing and change recommendation.
Permeation of helium and hydrogen from glass‐microsphere laser targets

Isothermal outgassing curves of hollow glass microspheres filled with helium, hydrogen, or deuterium gas have been determined. Four million 40–45‐μm soda‐lime glass microspheres, similar to laser‐fusion targets, were filled by gas permeation at 693–763 K and outgassed at 292–573 K. The permeabilities were calculated by an exponential theory, and they agree to an order of magnitude with the literature values. The outgassing curves are not pressure dependent. Two irregularities are apparent. First, the counting of target‐quality individual D‐T–filled microspheres shows a permeability spread of an order of magnitude from one microsphere to the next, which may be caused by variable chemical composition. Second, all the gases show deviations from exponential behavior in the form of tails at long times. Chemical reaction of the hydrogen with the glass, as well as incomplete filling and outgassing, may cause the hydrogen tails; the cause of the helium tails is not known.
Feedback factory: multiple faint radio jets detected in a cluster at z = 2

We report the detection of multiple faint radio sources, that we identify as active galactic nucleus (AGN) jets, within CLJ1449+0856 at z = 2 using 3 GHz Very Large Array observations. We study the effects of radio-jet-based kinetic feedback at high redshifts, which has been found to be crucial in low-redshift clusters to explain the observed thermodynamic properties of their intracluster medium (ICM). We investigate this interaction at an epoch featuring high levels of AGN activity and a transitional phase of ICM in regards to the likelihood of residual cold gas accretion. We measure a total flux of $\rm 30.6 \pm 3.3\, \mu Jy$ from the six detected jets. Their power contribution is estimated to be $1.2 \, (\pm 0.6)\, \times 10^{44} \, \rm erg\, s^{-1}$, although this value could be up to $4.7 \, \times 10^{44} \, \rm erg\, s^{-1}$. This is a factor of ∼0.25–1.0 of the previously estimated instantaneous energy injection into the ICM of CLJ1449+0856 from AGN outflows and star formation that have already been found to be sufficient in globally offsetting the cooling flows in the cluster core. In line with the already detected abundance of star formation, this mode of feedback being distributed over multiple sites, contrary to a single central source observed at low redshifts, points to accretion of gas into the cluster centre. This also suggests a ‘steady state’ of the cluster featuring non-cool-core-like behaviour. Finally, we also examine the total infrared–radio luminosity ratio for the known sample of galaxies within the cluster core and find that dense environments do not have any serious consequence on the compliance of galaxies to the infrared–radio correlation.