Miracle-dz/UniFAR-FTUs huggingface dataset:
Assurance and Assurance Cases

Assurance provides confidence that a system will work as required and not cause harm. Confidence is based on justified beliefs about the system and its environment, and justification can be developed and documented as an assurance case comprised of a structured argument grounded on evidence. For justification to be compelling, the argument must be indefeasible, meaning that we have so thoroughly considered everything that can go wrong (i.e., hazards to the system and defeaters to the argument) that there is no new information that could change our assessment. I show how the obligation for indefeasible justification can guide construction and interpretation of the argument and the evidence in an assurance case and how confidence in the case translates to bounds on the risk posed by the system. Assurance requires predictability in both the system and its environment; I speculate how credible assurance may be provided for recent and forthcoming systems where both kinds of predictability may be lacking.
Simulations of nanosecond pulsed plasmas in supersonic flow

Thermal and chemical kinetic phenomena associated with nanosecond pulsed plasmas in supersonic flows are investigated. We determine if significant thermal effects occur in a nanosecond pulsed plasma and to determine what role they play in the production of combustion radicals such as O, H and OH. Simulations of pulse widths varying between 100 ns and 1 us have been performed for H 2 ‐ O 2 and argon Mach 3 flows over a flat ‐ plate geometry with two 0.8 mm 2 ‐ D electrodes. The resulting gas temperatures, pressures, and radical densities are presented from which it is concluded that at the voltages investigated, electron ‐ impact dissociation is the primary driver of radical production. Thermal (gas heating) effects are primarily produced by ion Joule heating in the vicinity of the cathode and are coupled strongly with pressure increases in the flowing gas. thermal effects in nanosecond pulses of various determine how significant thermal effects are, and what role they play in producing radicals. Supersonic flows of an H 2 ‐ O 2 mixture and a pure argon flow over a flat ‐ plate geometry with experimental work electron ‐ impact dissociation is the dominant producer of combustion enhancing radicals . the temperature increase for the H 2 ‐ O 2 mixture was on the order of 100 K, the presence of much higher temperature increase in argon which includes metastable excitation, suggests that the gas temperature increase in H 2 ‐ O noticeably oxygen excitation. on the H 2 ‐ O 2 chemistry by including excitation reactions and by investigating mixtures
Scaling participation in payments for ecosystem services programs

Payments for ecosystem services programs have become common tools but most have failed to achieve wide-ranging conservation outcomes. The capacity for scale and impact increases when PES programs are designed through the lens of the potential participants, yet this has received little attention in research or practice. Our work with small-scale marine fisheries integrates the social science of PES programs and provides a framework for designing programs that focus a priori on scaling. In addition to payments, desirable non-monetary program attributes and ecological feedbacks attract a wider range of potential participants into PES programs, including those who have more negative attitudes and lower trust. Designing programs that draw individuals into participating in PES programs is likely the most strategic path to reaching scale. Research should engage in new models of participatory research to understand these dynamics and to design programs that explicitly integrate a broad range of needs, values, and modes of implementation.
Evaluation of Acoustic, Thermal, and Morphological Properties in the Egg White Phantom

The egg white phantom is a thermal lesion visualization phantom able to illustrate a thermal lesion. It is often used to evaluate the performance of HIFU and is less expensive than the BSA phantom. This study determined the optimal phantom composition for evaluated therapeutic ultrasound machines by varying the egg white concentration in the egg white phantom and demonstrated its utility as a therapeutic ultrasound phantom. The egg white phantom at varying egg white concentrations (10-40% in 10% intervals) was fabricated, and its thermal properties and acoustic properties were assessed. In addition, the size and shape of the formed lesion were compared between the egg white phantom and bovine liver tissue according to the electrical power. The results showed that 30% egg white phantom was optimal for the performance evaluation due to its thermal and acoustic properties. The generated thermal lesions formed sequentially as a cigar, ellipse, tadpole, and cone shapes according to the electrical power; a similar tendency was observed in the liver tissue. Hence, we conclude that the egg white phantom will prove useful in quantitatively evaluating the thermal effects of therapeutic ultrasound.
Lysyl Oxidase Is Downregulated by the EWS/FLI1 Oncoprotein and Its Propeptide Domain Displays Tumor Supressor Activities in Ewing Sarcoma Cells

Ewing sarcoma is the second most common bone malignancy in children and young adults. It is driven by oncogenic fusion proteins (i.e. EWS/FLI1) acting as aberrant transcription factors that upregulate and downregulate target genes, leading to cellular transformation. Thus, identificating these target genes and understanding their contribution to Ewing sarcoma tumorigenesis are key for the development of new therapeutic strategies. In this study we show that lysyl oxidase (LOX), an enzyme involved in maintaining structural integrity of the extracellular matrix, is downregulated by the EWS/FLI1 oncoprotein and in consequence it is not expressed in Ewing sarcoma cells and primary tumors. Using a doxycycline inducible system to restore LOX expression in an Ewing sarcoma derived cell line, we showed that LOX displays tumor suppressor activities. Interestingly, we showed that the tumor suppressor activity resides in the propeptide domain of LOX (LOX-PP), an N-terminal domain produced by proteolytic cleavage during the physiological processing of LOX. Expression of LOX-PP reduced cell proliferation, cell migration, anchorage-independent growth in soft agar and formation of tumors in immunodeficient mice. By contrast, the C-terminal domain of LOX, which contains the enzymatic activity, had the opposite effects, corroborating that the tumor suppressor activity of LOX is mediated exclusively by its propeptide domain. Finally, we showed that LOX-PP inhibits ERK/MAPK signalling pathway, and that many pathways involved in cell cycle progression were significantly deregulated by LOX-PP, providing a mechanistic explanation to the cell proliferation inhibition observed upon LOX-PP expression. In summary, our observations indicate that deregulation of the LOX gene participates in Ewing sarcoma development and identify LOX-PP as a new therapeutic target for one of the most aggressive paediatric malignancies. These findings suggest that therapeutic strategies based on the administration of LOX propeptide or functional analogues could be useful for the treatment of this devastating paediatric cancer.
speaq 2.0: A complete workflow for high-throughput 1D NMR spectra processing and quantification

Nuclear Magnetic Resonance (NMR) spectroscopy is, together with liquid chromatography-mass spectrometry (LC-MS), the most established platform to perform metabolomics. In contrast to LC-MS however, NMR data is predominantly being processed with commercial software. This has the effect that its data processing remains tedious and dependent on user interventions. As a follow-up to speaq, a previously released workflow for NMR spectral alignment and quantitation, we present speaq 2.0. This completely revised framework to automatically analyze 1D NMR spectra uses wavelets to efficiently summarize the raw spectra with minimal information loss or user interaction. The tool offers a fast and easy workflow that starts with the common approach of peak-picking, followed by grouping. This yields a matrix consisting of features, samples and peak values that can be conveniently processed either by using included multivariate statistical functions or by using many other recently developed methods for NMR data analysis. speaq 2.0 facilitates robust and high-throughput metabolomics based on 1D NMR but is also compatible with other NMR frameworks or complementary LC-MS workflows. The methods are benchmarked using two publicly available datasets. speaq 2.0 is distributed through the existing speaq R package to provide a complete solution for NMR data processing. The package and the code for the presented case studies are freely available on CRAN (https://cran.r-project.org/package=speaq) and GitHub (https://github.com/beirnaert/speaq). Author summary We present speaq 2.0: a user friendly workflow for processing NMR spectra quickly and easily. By limiting the need for user interaction and allowing the construction of workflows by combining R functions, metabolomics data analysis becomes fully reproducible and shareable. Such advances are critical for the future of the metabolomics field as it needs to move towards a fully open-science approach. This is no trivial goal as many researchers are still using black-box commercial software that often requires manually doing several steps, thus hampering reproducibility. To encourage the shift towards open source, we deliberately made our method usable for anyone with the most basic of R experience, something that is easily acquired. speaq 2.0 allows a stand-alone analysis from spectra to statistical analysis. In addition, the package can be combined with existing tools to improve performance, as it provides a superior peak picking method compared to the standard binning approach.
A Novel Immune-Inspired Shellcode Detection Algorithm Based on Hyperellipsoid Detectors

Shellcodes are machine language codes injected into target programs in the form of network packets or malformed files. Shellcodes can trigger buffer overflow vulnerability and execute malicious instructions. Signature matching technology used by antivirus software or intrusion detection system has low detection rate for unknown or polymorphic shellcodes; to solve such problem, an immune-inspired shellcode detection algorithm was proposed, named ISDA. Static analysis and dynamic analysis were both applied. The shellcodes were disassembled to assembly instructions during static analysis and, for dynamic analysis, the API function sequences of shellcodes were obtained by simulation execution to get the behavioral features of polymorphic shellcodes. The extracted features of shellcodes were encoded to antigens based on -gram model. Immature detectors become mature after immune tolerance based on negative selection algorithm. To improve nonself space coverage rate, the immune detectors were encoded to hyperellipsoids. To generate better antibody offspring, the detectors were optimized through clonal selection algorithm with genetic mutation. Finally, shellcode samples were collected and tested, and result shows that the proposed method has higher detection accuracy for both nonencoded and polymorphic shellcodes.
The Impacts of Human Activities on the Hydrogeological Regime of East Nile Delta, Egypt

Human activities contribute numerous hydrogeological threats including waterlogging, soil salinization and water pollution in East Nile Delta region. Landsat Thematic Images were utilized to detect the environmental changes in the study area during the last three decades. Remote sensing and Geographic Information Systems data were integrated to monitor and measure surface areas of agricultural and urban developments. Risk assessment maps were constructed for waterlogging and soil salinization threats. The results cleared that both evaporation from logged and flood irrigation water surfaces cause up to 30% of water loss. The logged areas increased from 25km in 1984 to 180km in 2014 along the El-Tina plain which represents the most threated zone. The total changes of waterlogging cover at east Nile Delta varies between 930km in 1989, 685km in 1998 after the construction of El-Salam Canal and 1044km in 2014. The total estimated water loss by direct evaporation was up to 23.6Mm/year. Following the construction of El-Salam Canal in 1998, water and drainage effluents into Manzala Lake were decreased creating shrinkage in its surface area by 45%. Consequently, water quality of Manzala Lake was severely deteriorated due to the throwing of municipal and irrigational sewages.
Modeling of Liquid Metal Infiltration of Porous Fiber Preform During Squeeze Casting

The present work adopts a new approach to the analytical modeling of infiltration of porous fiber preforms by liquid metal in the squeeze casting of metal matrix composites, with the assumption that the process is adiabatic and that the flow is unidirectional. Fluid dynamics is described on the basis of Darcy's law, while separate equations are derived to explain the thermal behavior of the liquid metal and the fiber, assuming that the thermal interactions between the two are interfacial. Unlike earlier models, this approach does not consider the thermal behavior of a “composite,” but instead studies the behavior of the liquid metal and the fiber preform separately. In addition to the conventional application of heat balance techniques and development of partial differential equations involving temperatures, this work introduces supplementary conditions for temperature calculations, specifically at the entry and front points during infiltration. Differential equations are solved by a method of finite differences, and the problem of additional unknowns (preform temperature) at the infiltration front position is overcome using the “virtual point” concept. Simple expressions are derived for the calculation of process parameters like total time for complete infiltration and time for solidification, on the basis of which the occurrence of complete infiltration is predicted. A novel attempt in generating the profiles of the preform and liquid temperatures at specific instants during infiltration has also been made. The relative influence of the liquid superheat temperature, the preform preheat temperature, and the squeeze pressure on the infiltration mechanism is analyzed by studying the infiltration characteristics for various squeeze conditions.
A novel piezoelectric dynamometer based on double-sensor for thermal compensation

A piezoelectric dynamometer can produce thermal forces because of temperature fluctuations, thus affecting measurement precision. To investigate the influence of the thermal force on the dynamometer, this article proposes a hypothesis of decreasing the conduction power and establishes the function of a thermal force over time in an ordinary dynamometer based on the heat conduction differential equation. A novel double-sensor thermal compensation dynamometer is designed, with static calibration in constant temperature and force/heat coupling experiments, to solve the problem of the thermal force. The experimental results indicate that the nonlinearity and repeatability of the double-sensor thermal compensation dynamometer are less than 1% full scale (FS) of the static calibration at a constant temperature; in the force/heat coupling experiments, at a heating rate of 0.4 ℃/s to 110 ℃ with a loading force of 500 N, the maximal output deviation is less than 1.06% (FS), realizing the unidirectional thermal force compensation of the structure. The double-sensor thermal compensation dynamometer can be utilized in sharp temperature fluctuations environment, like rocket engine forces measurement.
Single-Molecule Study on Histone-Like Nucleoid-Structuring Protein (H-NS) Paralogue in Pseudomonas aeruginosa: MvaU Bears DNA Organization Mode Similarities to MvaT

Pseudomonas aeruginosa contains two distinct members of H-NS family of nucleoid-structuring proteins: MvaT and MvaU. Together, these proteins bind to the same regions of the chromosome and function coordinately in the regulation of hundreds of genes. Due to their structural similarity, they can associate to form heteromeric complexes. These findings left us wondering whether they bear similar DNA binding properties that underlie their gene-silencing functions. Using single-molecule stretching and imaging experiments, we found striking similarities in the DNA organization modes of MvaU compared to the previously studied MvaT. MvaU can form protective nucleoprotein filaments that are insensitive to environmental factors, consistent with its role as a repressor of gene expression. Similar to MvaT, MvaU filament can mediate DNA bridging while excessive MvaU can cause DNA aggregation. The almost identical DNA organization modes of MvaU and MvaT explain their functional redundancy, and raise an interesting question regarding the evolutionary benefits of having multiple H-NS paralogues in the Pseudomonas genus.
Challenges and Opportunities in the Multivariate Analysis of 3-D Spectral Images

Multivariate statistical methods have long proven powerful for extracting chemical information from spectroscopic images. The premise underlying this application of multivariate techniques is that the observed spectrum at any point can be described as an additive linear mixture of a limited number of base spectra or “pure components”. Recent interest has focused on applying these methods to data sets comprising full spectra acquired from samples in three spatial dimensions. Some examples include EDS tomographic images [1], ToF-SIMS imaging depth profiles [2] and atom probe tomography datasets [3]. Besides the obvious computational challenges posed by increasingly large data sets in 3-D, are more subtle concerns. Consider, for instance, a 10-pixel inclusion in a matrix whose characteristic size is 100 pixels. Spectra arising from the inclusion would account for about 10% of the total in a line scan, 1% in an image but only 0.1% of the voxels in a 3-D dataset. It appears that finding the proverbial needle is likely to be particularly difficult in a three-dimensional haystack. It will be shown, however, that Independent Component Analysis (ICA) is well suited for identifying minor components in a dataset. Furthermore, it will be shown that sparseness can be induced in a dataset via a wavelet transform, allowing ICA to extract more physically reasonable representations of all components, both major and minor.
EFFECTS OF FREEZING AND THAWING ON THE TENSION PROPERTIES OF HIGH-STRENGTH CONCRETE

Freeze-thaw cycles pose a serious problem for concrete structures in cold environments. This investigation deals with the exposure of high-strength concrete to rapid freezing and thawing in a controlled environment. Experimental tests consisted of measuring the relative dynamic modulus of elasticity, modulus of rupture, direct tensile strength, and change in mass of air-entrained concrete specimens. The tests were conducted on prisms for both high-strength concrete and normal strength concrete at intervals of every 100 cycles up to 700 cycles. Test results revealed that high-strength concrete was still durable after 700 cycles of freezing and thawing in accordance with American Society for Testing and Materials standards. After 700 cycles, standard prisms of high-strength concrete showed a reduction in mass of less than 1 percent, reduction in compressive strength between 10 to 15 percent, and reduction in modulus of rupture up to 15 percent. For the thin concrete specimens used for the direct tension tests, the direct tensile strength was reduced between 15 to 25 percent. The post-cracking behavior of high-strength concrete after 700 cycles of freezing and thawing was evaluated in terms of the stress-strain curve and fracture energy. Specimens of normal strength concrete were used as reference specimens. The normal strength concrete prisms had deteriorated severely after 250 to 300 cycles. For the thin concrete specimens, the average value of the relative dynamic modulus of elasticity based on resonant frequencies at 300, 600, and 700 cycles was 72, 54, and 39 percent, respectively, compared with the corresponding values of 82, 69, and 66 percent, respectively, for high-strength concrete.
Induction of Apoptosis and Antiproliferative Activity of Naringenin in Human Epidermoid Carcinoma Cell through ROS Generation and Cell Cycle Arrest

A natural predominant flavanone naringenin, especially abundant in citrus fruits, has a wide range of pharmacological activities. The search for antiproliferative agents that reduce skin carcinoma is a task of great importance. The objective of this study was to analyze the anti-proliferative and apoptotic mechanism of naringenin using MTT assay, DNA fragmentation, nuclear condensation, change in mitochondrial membrane potential, cell cycle kinetics and caspase-3 as biomarkers and to investigate the ability to induce reactive oxygen species (ROS) initiating apoptotic cascade in human epidermoid carcinoma A431 cells. Results showed that naringenin exposure significantly reduced the cell viability of A431 cells (p<0.01) with a concomitant increase in nuclear condensation and DNA fragmentation in a dose dependent manner. The intracellular ROS generation assay showed statistically significant (p<0.001) dose-related increment in ROS production for naringenin. It also caused naringenin-mediated epidermoid carcinoma apoptosis by inducing mitochondrial depolarization. Cell cycle study showed that naringenin induced cell cycle arrest in G0/G1 phase of cell cycle and caspase-3 analysis revealed a dose dependent increment in caspase-3 activity which led to cell apoptosis. This study confirms the efficacy of naringenin that lead to cell death in epidermoid carcinoma cells via inducing ROS generation, mitochondrial depolarization, nuclear condensation, DNA fragmentation, cell cycle arrest in G0/G1 phase and caspase-3 activation.
Low-Density-Lipoprotein Particle Size Predicts a Poor Outcome in Patients with Atherothrombotic Stroke

Background and Purpose Low-density lipoprotein (LDL) particle size is considered to be one of the more important cardiovascular risk factors, and small LDL particles are known to have atherogenic potential. The aim of this study was to determine whether LDL particle size is associated with stroke severity and functional outcome in patients with atherothrombotic stroke. Methods Between January 2009 and May 2011, 248 patients with first-episode cerebral infarction who were admitted to our hospital within 7 days after symptom onset were prospectively enrolled. LDL particle size was measured using the nondenaturing polyacrylamide gradient gel electrophoresis assay. Stroke severity was assessed by applying the National Institutes of Health Stroke Scale (NIHSS) at admission. Functional outcome was investigated at 3 months after the index stroke using the modified Rankin Scale (mRS), and poor functional outcome was defined as an mRS score of ≥3. Results The LDL particle size in the 248 patients was 25.9±0.9 nm (mean±SD). LDL particle size was inversely correlated with the degree of cerebral artery stenosis (p=0.010). Multinomial multivariate logistic analysis revealed that after adjustment for age, sex, and variables with p<0.1 in univariate analysis, LDL particle size was independently and inversely associated with stroke severity (NIHSS score ≥5; reference, NIHSS score 0-2; odds ratio=0.38, p=0.028) and poor functional outcome (odds ratio=0.44, p=0.038). Conclusions The results of this study demonstrate that small LDL particles are independently correlated with stroke outcomes. LDL particle size is thus a potential biomarker for the prognosis of atherothrombotic stroke.