Miracle-dz/UniFAR-FTUs huggingface dataset:
Mining sandboxes: Are we there yet?

The popularity of Android platform on mobile devices has attracted much attention from many developers and researchers, as well as malware writers. Recently, Jamrozik et al. proposed a technique to secure Android applications referred to as mining sandboxes. They used an automated test case generation technique to explore the behavior of the app under test and then extracted a set of sensitive APIs that were called. Based on the extracted sensitive APIs, they built a sandbox that can block access to APIs not used during testing. However, they only evaluated the proposed technique with benign apps but not investigated whether it was effective in detecting malicious behavior of malware that infects benign apps. Furthermore, they only investigated one test case generation tool (i.e., Droidmate) to build the sandbox, while many others have been proposed in the literature. In this work, we complement Jamrozik et al.'s work in two ways: (1) we evaluate the effectiveness of mining sandboxes on detecting malicious behaviors; (2) we investigate the effectiveness of multiple automated test case generation tools to mine sandboxes. To investigate effectiveness of mining sandboxes in detecting malicious behaviors, we make use of pairs of malware and benign app it infects. We build a sandbox based on sensitive APIs called by the benign app and check if it can identify malicious behaviors in the corresponding malware. To generate inputs to apps, we investigate five popular test case generation tools: Monkey, Droidmate, Droidbot, GUIRipper, and PUMA. We conduct two experiments to evaluate the effectiveness and efficiency of these test case generation tools on detecting malicious behavior. In the first experiment, we select 10 apps and allow test case generation tools to run for one hour; while in the second experiment, we select 102 pairs of apps and allow the test case generation tools to run for one minute. Our experiments highlight that 75.5%-77.2% of malware in our dataset can be uncovered by mining sandboxes — showing its power to protect Android apps. We also find that Droidbot performs best in generating test cases for mining sandboxes, and its effectiveness can be further boosted when coupled with other test case generation tools.
Exploring possible choices of the Tikhonov regularization parameter for the method of fundamental solutions in electrocardiography

The inverse problem of electrocardiographic imaging (ECGI), i. e. computing epicardial potentials from the body surface measured potentials, is a challenging problem. In this setting, Tikhonov regularization is commonly employed, weighted by a regularization parameter. This parameter has an important influence on the solution. In this work, we show the feasibility of two methods to choose the regularization parameter when using the method of fundamental solution, or MFS (a homogeneous meshless scheme based). These methods are i) a novel automatic technique based on the Discrete Picard condition (DPC), which we named ADPC and ii) the U-curve method introduced in other fields for cases where the well-known L-curve method fails or over-regularize the solution. We calculated the Tikhonov solution with the ADPC and U-curve methods for experimental data from the free distributed Experimental Data and Geometric Analysis Repository (EDGAR), and we compared them to the solution obtained with CRESO and L-curve procedures that are the two extensively used techniques in the ECGI.
Review of Sample Preparation Techniques for the Analysis of Selected Classes of Pesticides in Plant Matrices

ABSTRACT The aim of this article is to present the trends in extraction techniques applied for the isolation of pesticides from plant matrix. To fully compare the effectiveness of different extraction techniques, it was required to analyze compounds with possibly wide spectrum of physicochemical properties. Hence, compounds representing neonicotinoids, pyrethroids, sulfonylureas and phenylamides were selected. Based on literature studies, it may be concluded that there are three main approaches to make the analytical procedures for pesticides determination more effective: (i) the optimization of extraction conditions, however, according to ANOVA conducted on the collected literature data, not all parameters influence the extraction process equally; chemometric studies based on literature reports may lead to the conclusion that the most favorable conditions (criterion: analyte recovery, repeatability) for neonicotinoid, pyrethroid and sulfonylurea herbicide extraction from plant tissues are provided by QuEChERS – extraction with acetonitrile, while the mixtures of PSA and GCB (for neonicotinoids), and PSA, GCB, C18 (for pyrethroids) should be used in d-SPE step. For sulfonylurea compounds and metalaxyl it was impossible to identify a sorbent(s) that cleans up the extract more effectively than the others; (ii) to develop a new generation of sorbents; however, the range of their applicability is limited, mainly due to difficulties in their synthesis; (iii) to develop the new extraction techniques with as few “trouble spots” as possible.
Essential oil composition of aerial parts of Micromeria persica Boiss. from Western of Shiraz, Iran

Abstract Micromeria persica Boiss. is medicinal and aromatic plant, belonging to the Lamiaceae family. The chemical composition of the essential oils (EOs) from aerial parts of M. persica were extracted using hydro-distillation method and analysed using GC and GC–MS. Fifty-two compounds were identified in the EOs of aerial parts of M. persica. The main chemical compositions were n-hexadecanoic acid (14.9%), thymol (9.5%), linoleic acid (8.0%), carvacrol (5.6%), (E)-nerolidol (5.5%), linolenic acid (5.5%), α-cadinol (2.7%), linalool (2.7%), borneol (2.6%), caryophyllene oxide (2.3%) and pulegone (2.0%). Presence of borneol, thymol, carvacrol and pulegone suggests the potential of this plant as a flavouring source in the food industry, being used in perfumery and cosmetics industry, vitamin E synthesis and exhibit strong fungicidal, antibacterial and antimicrobial activities.
Identifying normal, AF and other abnormal ECG rhythms using a cascaded binary classifier

In this paper, we present a methodology for classifying normal, atrial fibrillation (AF), non-AF related other abnormal heart rhythms and noisy recordings by analysing single lead ECG signal of short duration. In a two layer binary cascaded approach proposed in our methodology, an unlabelled recording is initially classified into one of the two intermediate classes (‘normal+others’ and ‘AF+noisy’) at the first layer before actual classification at the second layer The Physionet Challenge 2017 dataset containing more than 8500 ECG recordings are used for creation of training models and interval validation. The proposed methodology yields an average F1-score of 0.91, 0.79 and 0.77 respectively in classifying normal, AF and other rhythms on the training dataset using 5-fold cross validation. Results also show that, the said methodology, when applied on a hidden test set maintained by the challenge organisers yields F1-score values of 0.92, 0.86 and 0.74 in classifying the same.
Human papillomavirus and oropharyngeal squamous cell carcinoma: a New Zealand cohort study

Human papillomavirus (HPV)‐related oropharyngeal squamous cell carcinomas (OPSCC) are clinically, epidemiologically and prognostically distinct from other OPSCCs. The incidence of HPV‐related OPSCCs has increased significantly worldwide over the past few decades. However, no studies of OPSCC with direct molecular HPV testing has been conducted in New Zealand.
SGTA-Dependent Regulation of Hsc70 Promotes Cytosol Entry of Simian Virus 40 from the Endoplasmic Reticulum

ABSTRACT Membrane penetration by nonenveloped viruses remains enigmatic. In the case of the nonenveloped polyomavirus simian virus 40 (SV40), the virus penetrates the endoplasmic reticulum (ER) membrane to reach the cytosol and then traffics to the nucleus to cause infection. We previously demonstrated that the cytosolic Hsc70-SGTA-Hsp105 complex is tethered to the ER membrane, where Hsp105 and SGTA facilitate the extraction of SV40 from the ER and transport of the virus into the cytosol. We now find that Hsc70 also ejects SV40 from the ER into the cytosol in a step regulated by SGTA. Although SGTA's N-terminal domain, which mediates homodimerization and recruits cellular adaptors, is dispensable during ER-to-cytosol transport of SV40, this domain appears to exert an unexpected post-ER membrane translocation function during SV40 entry. Our study thus establishes a critical function of Hsc70 within the Hsc70-SGTA-Hsp105 complex in promoting SV40 ER-to-cytosol membrane penetration and unveils a role of SGTA in controlling this step. IMPORTANCE How a nonenveloped virus transports across a biological membrane to cause infection remains mysterious. One enigmatic step is whether host cytosolic components are co-opted to transport the viral particle into the cytosol. During ER-to-cytosol membrane transport of the nonenveloped polyomavirus SV40, a decisive infection step, a cytosolic complex composed of Hsc70-SGTA-Hsp105 was previously shown to associate with the ER membrane. SGTA and Hsp105 have been shown to extract SV40 from the ER and transport the virus into the cytosol. We demonstrate here a critical role of Hsc70 in SV40 ER-to-cytosol penetration and reveal how SGTA controls Hsc70 to impact this process.
Climate Factors Associated with Historic Spruce Beetle (Coleoptera: Curculionidae) Outbreaks in Utah and Colorado

Abstract This study investigated relationships between climate and historic spruce beetle, Dendroctonus rufipennis Kirby (Coleoptera: Curculionidae), outbreaks in northern and southeastern Utah and western Colorado between 1905 and 1996. A chronology of outbreak years was constructed from historic records, research papers, newspapers, and other sources of information. Historic climate data for the region included annual and mean monthly temperature and precipitation, in addition to Palmer drought severity index (PDSI) values estimated from tree rings. Classification and regression tree analysis (CART) was used to identify those climate factors most important for predicting historic spruce beetle outbreaks. The factors identified by the best CART model included mean December temperature, mean September temperature 1 yr before outbreak years, the mean estimated PDSI value of the 5-yr period before outbreak years, and mean October precipitation. The resulting model correctly classified nonoutbreak and outbreak years 67 and 70% of the time, respectively.
Alcohol consumption in a general antenatal population and child neurodevelopment at 2 years

Background Prenatal alcohol exposure (PAE) is a community health problem with up to 50% of pregnant women drinking alcohol. The relationship between low or sporadic binge PAE and adverse child outcomes is not clear. This study examines the association between PAE in the general antenatal population and child neurodevelopment at 2 years, accounting for relevant contributing factors. Methods This prospective population-based cohort recruited 1570 pregnant women, providing sociodemographic, psychological and lifestyle information and alcohol use for five time periods. PAE categories were ‘low’, ‘moderate/high’, ‘binge’, in trimester 1 or throughout pregnancy. Measures of cognitive, language and motor development (Bayley Scales of Infant and Toddler Development) were available for 554 children, while measures of sensory processing (Infant/Toddler Sensory Profile) and social–emotional development (Brief Infant Toddler Social Emotional Assessment) were available for 948. Results A positive association in univariate analysis with low-level PAE throughout pregnancy and cognition (β=4.1, 95% CI −0.02 to 8.22, p=0.05) was attenuated by adjusting for environmental/social deprivation risk factors (β=3.06 (−1.19 to 7.30), p=0.16). Early binge drinking, plus continued PAE at lower levels, was associated with the child being more likely to score low in sensation avoidance (adjusted OR 1.88 (1.03 to 3.41), p=0.04). Conclusion Early binge exposure, followed by lower-level PAE, demonstrated an increase in sensation-avoiding behaviour. There were, however, no significant associations between PAE and neurodevelopment following adjustment for important confounders and modifiers. Follow-up is paramount to investigate subtle or later onset problems.
Geometrical Structures and Electronic Properties of Ga6 and Ga5X (X = B, C, N, O, F, Al, Si, P, S, Cl) Clusters

Based on the unbiased CALYPSO (Crystal structure Analysis by Particle Swarm Optimization) structure searching method in combination with density functional theory (DFT), the geometrical structures and electronic properties are investigated theoretically for Ga6 and Ga5X (X = B, C, N, O, F, Al, Si, P, S, Cl) clusters. The PBE0 exchange-correlation functional and the 6-311G(d) basis set is carried out to determine global minima on potential energy surfaces. The relative stabilities of the clusters are examined by the binding energies and substitution reaction. Following the predictions of the Jellium model, the Ga5B cluster with the 18 valence electrons is the most stable structure. At last, with the obtained lowest energy structures, some physical properties such as electrons transfer, molecular orbitals, and total and partial densities of states are discussed, respectively.
Linear and nonlinear viscoelastic and viscoplastic analysis of asphalt binders with warm mix asphalt additives

ABSTRACT Warm-Mix Asphalt (WMA) is a widely used product, which proved a contribution to the reduction in asphalt mixing and compaction temperatures. This reduction leads to lower fuel consumption and smoke emission in asphalt plants. Most of the characterisation of binders used in WMA has focused in the past on measuring linear viscoelastic properties and associated Superpave parameters. Several studies have shown that the average stresses and strains of the asphalt mixture remain mostly within the linear viscoelastic response. However, localised strains in the binder phase of the mixture could reach values high enough to induce nonlinear viscoelastic and viscoplastic deformations. Therefore, this study focuses on an experimental and analytical evaluation of linear, nonlinear viscoelastic and viscoplastic responses of selected binders modified for use in WMA. The first part of the paper analyses the linear viscoelastic material properties and their ability to evaluate permanent deformation resistance. Then, the non-recoverable creep compliance parameter obtained from the Multiple Stress Creep Recovery (MSCR) test is analysed to assess the nonlinear response and permanent deformation of asphalt binders. The paper utilises a nonlinear plasto-viscoelastic (NPVE) approach to assess and quantify the nonlinear plasto-viscoelastic response of binders by separating the recoverable and irrecoverable strains measured in the MSCR test. Two WMA additives were included in this study by mixing them with polymer-modified and unmodified asphalt binders. Analysis of results showed that the NPVE approach captured a higher percentage of recovery than the NLVE approach. However, binder’s performance evaluation and ranking did not change by adopting the NPVE approach. The nonlinear viscoelastic parameters provided insight on the behaviour of asphalt binders mixed with WMA additives during loading cycles. Sasobit showed higher influence than Advera on binders in resisting permanent deformation by increasing the recoverable strain during the unloading phase.
Phase Retrieval in X-ray Phase-contrast Imaging Suitable for Tomography

In-line phase-contrast X-ray imaging provides images where both absorption and refraction contribute. For quantitative analysis of these images, the phase needs to be retrieved numerically. There are many phase-retrieval methods available. Those suitable for phase-contrast tomography, i.e., non-iterative phase-retrieval methods that use only one image at each projection angle, all follow the same pattern though derived in different ways. We outline this pattern and use it to compare the methods to each other, considering only phase-retrieval performance and not the additional effects of tomographic reconstruction. We also outline derivations, approximations and assumptions, and show which methods are similar or identical and how they relate to each other. A simple scheme for choosing reconstruction method is presented, and numerical phase-retrieval performed for all methods. Phase-contrast imaging of weakly absorbing materials using hard X-rays, " Nature 373, 595–598 (1995). 6. V. N. Ingal and E. A. Beliaevskaya, " X-ray plane-wave topographyobservation of the phase contrast from a non-crystalline object, " J. On the possibilities of X-ray phase contrast microimaging by coherent high-energy synchrotron radiation, " Rev. Quantitative phase imaging using hard X-rays, " Phys. Phase objects in synchrotron radiation hard X-ray imaging, " J. Phase retrieval and differential phase-contrast imaging with low-brilliance X-ray sources, " Nat. Phase-contrast X-ray imaging with a liquid-metal-jet-anode micro-focus source, " App. Refracting Röntgen's rays: propagation-based X-ray phase contrast for biomedical imaging, " J. Appl. Implementation of a fast method for high resolution phase contrast tomography, " Opt.Ray cone-beam phase tomography formulas based on phase-attenuation duality, " Opt. Express 13, 6000–6014 (2005). Simultaneous phase and amplitude extraction from a single defocused image of a homogeneous object, " J. 2D and 3D X-ray phase retrieval of multi-material objects using a single defocus distance, " Opt. Optical phase retrieval by use of first Born-and Rytov-type approximations, " Appl.ray phase imaging: Demonstration of extended conditions with homogeneous objects, " Opt. Some simple rules for contrast, signal-to-noise and resolution in in-line phase-contrast imaging, " Opt. A new theory of phase-contrast X-ray imaging based on Wigner distributions, " Med. Phys. Polychromatic cone-beam phase-contrast tomography, " Phys. Low-dose high-resolution laboratory phase-contrast X-ray imaging, " manuscript in preparation.
A Teleo-Reactive Node for Implementing Internet of Things Systems

The Internet of Things (IoT) is one of today’s main disruptive technologies and, although massive research has been carried out in recent years, there are still some open issues such as the consideration of software engineering methods and tools. We propose the adoption of the Teleo-Reactive approach in order to facilitate the development of Internet of Things systems as a set of communicating Teleo-Reactive nodes. The software behavior of the nodes is specified in terms of goals, perceptions and actions over the environment, achieving higher abstraction than using general-purpose programming languages and therefore, enhancing the involvement of non-technical users in the specification process. Throughout this paper, we describe the elements of a Teleo-Reactive node and a systematic procedure for translating Teleo-Reactive specifications into executable code for Internet of Things devices. The case study of a robotic agent is used in order to validate the whole approach.
Coupling Coefficient Reconfigurable Wideband Branch-Line Coupler Topology With Harmonic Suppression

The need for a flexible coupler topology to support a wide variety of coupling coefficients and robust suppression of harmonics often results in severely increased insertion loss, system size, and fabrication complexity. In this paper, we propose a two-section branch-line coupler (BLC) topology that simultaneously achieves a wide bandwidth, reconfigurable coupling coefficient, and harmonic suppression. Closed-form equations and a design methodology are provided. To verify the proposed technique, a BLC prototype operating at 3 GHz was designed, fabricated, and measured. The circuit can work under four configurations providing the coupling coefficients of 4, 6, 8, and 10 dB. The prototype achieved a 15-dB harmonic suppression up to 7.5 GHz. The measured fractional bandwidth, defined by 1-dB amplitude imbalance and 5° phase stability, is 30% from 2.55 to 3.45 GHz, the widest of reported reconfigurable couplers.
DO 3 SE modelling of soil moisture to determine ozone flux to forest trees

The DO3SE (Deposition of O-3 for Stomatal Exchange) model is an established tool for estimating ozone (O-3) deposition, stomatal flux and impacts to a variety of vegetation types across Europe. It has been embedded within the EMEP (European Monitoring and Evaluation Programme) photochemical model to provide a policy tool capable of relating the flux-based risk of vegetation damage to O-3 precursor emission scenarios for use in policy formulation. A key limitation of regional flux-based risk assessments has been the assumption that soil water deficits are not limiting O-3 flux due to the unavailability of evaluated methods for modelling soil water deficits and their influence on stomatal conductance (g(sto)), and subsequent O-3 flux. This paper describes the development and evaluation of a method to estimate soil moisture status and its influence on g(sto) for a variety of forest tree species. This DO3SE soil moisture module uses the Penman-Monteith energy balance method to drive water cycling through the soil-plant-atmosphere system and empirical data describing g(sto) relationships with pre-dawn leaf water status to estimate the biological control of transpiration. We trial four different methods to estimate this biological control of the transpiration stream, which vary from simple methods that relate soil water content or potential directly to g(sto), to more complex methods that incorporate hydraulic resistance and plant capacitance that control water flow through the plant system. These methods are evaluated against field data describing a variety of soil water variables, g(sto) and transpiration data for Norway spruce (Picea abies), Scots pine (Pinus sylvestris), birch (Betula pendula), aspen (Populus tremuloides), beech (Fagus sylvatica) and holm oak (Quercus ilex) collected from ten sites across Europe and North America. Modelled estimates of these variables show consistency with observed data when applying the simple empirical methods, with the timing and magnitude of soil drying events being captured well across all sites and reductions in transpiration with the onset of drought being predicted with reasonable accuracy. The more complex methods, which incorporate hydraulic resistance and plant capacitance, perform less well, with predicted drying cycles consistently underestimating the rate and magnitude of water loss from the soil. A sensitivity analysis showed that model performance was strongly dependent upon the local parameterisation of key model drivers such as the maximum g(sto), soil texture, root depth and leaf area index. The results suggest that the simple modelling methods that relate g(sto) directly to soil water content and potential provide adequate estimates of soil moisture and influence on g(sto) such that they are suitable to be used to assess the potential risk posed by O-3 to forest trees across Europe.