Miracle-dz/UniFAR-FTUs huggingface dataset:
Knowledge-Assisted Rule Building for Malware Analysis 103-Recent Advances in Multimedia Processing , Organization and Visualization beyond Domains and Disciplines

Due to the increasing threat from malicious software (malware), the monitoring of vulnerable systems is becoming increasingly important, which includes the need to log and analyze activity ranging from networks, individual computers, to mobile devices. Currently available tools in behavior-based malware analysis do not meet all experts’ needs, such as selecting different rules, categorizing them by their task and storing them in the database as well as manually adapting and/or tuning the rules identified. To close this gap, we designed CallNet, a knowledge-assisted visual analytics and rulebuilding tool for behavior-based malware analysis. The paper at hand is a design study which describes the design, a usage scenario, and the paper prototype evaluation. We report on the validation of CallNet by expert reviews, reflect on the insights gained from the reviews and, finally discuss the advantages and disadvantages of the prototype design including the visualization techniques applied.
Genome Wide Expression Analysis Suggests Perturbation of Vascular Homeostasis during High Altitude Pulmonary Edema

Background High altitude pulmonary edema (HAPE) is a life-threatening form of non-cardiogenic edema which occurs in unacclimatized but otherwise normal individuals within two to four days after rapid ascent to altitude beyond 3000 m. The precise pathoetiology and inciting mechanisms regulating HAPE remain unclear. Methodology/Principle findings We performed global gene expression profiling in individuals with established HAPE compared to acclimatized individuals. Our data suggests concurrent modulation of multiple pathways which regulate vascular homeostasis and consequently lung fluid dynamics. These pathways included those which regulate vasoconstriction through smooth muscle contraction, cellular actin cytoskeleton rearrangements and endothelial permeability/dysfunction. Some notable genes within these pathways included MYLK; rho family members ARGEF11, ARHGAP24; cell adhesion molecules such as CLDN6, CLDN23, PXN and VCAM1 besides other signaling intermediates. Further, several important regulators of systemic/pulmonary hypertension including ADRA1D, ECE1, and EDNRA were upregulated in HAPE. We also observed significant upregulation of genes involved in paracrine signaling through chemokines and lymphocyte activation pathways during HAPE represented by transcripts of TNF, JAK2, MAP2K2, MAP2K7, MAPK10, PLCB1, ARAF, SOS1, PAK3 and RELA amongst others. Perturbation of such pathways can potentially skew vascular homeostatic equilibrium towards altered vascular permeability. Additionally, differential regulation of hypoxia-sensing, hypoxia-response and OXPHOS pathway genes in individuals with HAPE were also observed. Conclusions/Significance Our data reveals specific components of the complex molecular circuitry underlying HAPE. We show concurrent perturbation of multiple pathways regulating vascular homeostasis and suggest multi-genic nature of regulation of HAPE.
Coordinated Optimization of Visual Cortical Maps (II) Numerical Studies

In the juvenile brain, the synaptic architecture of the visual cortex remains in a state of flux for months after the natural onset of vision and the initial emergence of feature selectivity in visual cortical neurons. It is an attractive hypothesis that visual cortical architecture is shaped during this extended period of juvenile plasticity by the coordinated optimization of multiple visual cortical maps such as orientation preference (OP), ocular dominance (OD), spatial frequency, or direction preference. In part (I) of this study we introduced a class of analytically tractable coordinated optimization models and solved representative examples, in which a spatially complex organization of the OP map is induced by interactions between the maps. We found that these solutions near symmetry breaking threshold predict a highly ordered map layout. Here we examine the time course of the convergence towards attractor states and optima of these models. In particular, we determine the timescales on which map optimization takes place and how these timescales can be compared to those of visual cortical development and plasticity. We also assess whether our models exhibit biologically more realistic, spatially irregular solutions at a finite distance from threshold, when the spatial periodicities of the two maps are detuned and when considering more than 2 feature dimensions. We show that, although maps typically undergo substantial rearrangement, no other solutions than pinwheel crystals and stripes dominate in the emerging layouts. Pinwheel crystallization takes place on a rather short timescale and can also occur for detuned wavelengths of different maps. Our numerical results thus support the view that neither minimal energy states nor intermediate transient states of our coordinated optimization models successfully explain the architecture of the visual cortex. We discuss several alternative scenarios that may improve the agreement between model solutions and biological observations.
A combinatorial algorithm for minimizing symmetric submodular functions

We describe a purely combinatorial algorithm which, given a submodular set function f on a finite set V, finds a proper subset A of V minimizing f[A]+f[V\A]. This algorithm, an extension of the Nagamochi-Ibaraki minimum cut algorithm as simplified by Stoer and Wagner (1994) and by F’rank (1994), minimizes any symmetric submodular function using O(lVl”) calls to a function value oracle.
SUZAKU WIDE BAND ANALYSIS OF THE X-RAY VARIABILITY OF TeV BLAZAR Mrk 421 IN 2006

We present the results of X-ray observations of the well studied TeV blazar Mrk 421 with the Suzaku satellite in 2006 April 28. During the observation, Mrk 421 was undergoing a large flare and the X-ray flux was variable, decreasing by ∼50%, from 7.8 × 10−10 to 3.7 × 10−10 erg s−1 cm−2 in about 6 hr, followed by an increase by ∼35%. Thanks to the broad bandpass coupled with high sensitivity of Suzaku, we measured the evolution of the spectrum over the 0.4–60 keV band in data segments as short as ∼1 ks. The data show deviations from a simple power-law model, but also a clear spectral variability. The time-resolved spectra are fitted by a synchrotron model, where the observed spectrum is due to a exponentially cutoff power-law distribution of electrons radiating in uniform magnetic field; this model is preferred over a broken power law. As another scenario, we separate the spectrum into “steady” and “variable” components by subtracting the spectrum in the lowest-flux period from those of other data segments. In this context, the difference (“variable”) spectra are all well described by a broken power-law model with photon index Γ ∼ 1.6, breaking at energy ϵbrk ≃ 3 keV to another photon index Γ ∼ 2.1 above the break energy, differing from each other only by normalization, while the spectrum of the “steady” component is best described by the synchrotron model. We suggest that the rapidly variable component is due to relatively localized shock (Fermi I) acceleration, while the slowly variable (“steady”) component is due to the superposition of shocks located at larger distance along the jet, or due to other acceleration process, such as the stochastic acceleration on magnetic turbulence (Fermi II) in the more extended region.
Internal Point Mutations of the Capsid Modify the Serotype of Rice Yellow Mottle Virus

ABSTRACT Rice yellow mottle virus is classified in five major serotypes; the molecular diversity of the coat protein (CP) is well established, but the amino acids involved in the recognition by discriminant monoclonal antibodies (MAbs) remain unknown. Reconstruction of a phylogenetic tree and sequence alignment of the CP gene of a sample representative of the continental-large diversity were used to identify 10 serospecific amino acids (i.e., conserved in all isolates belonging to the same serotype and distinct in other serotypes). Positions occupied by serospecific residues were localized on the crystal structure of the CP monomer and on modeled capsomers. Structural, molecular, and serological properties of each serotype were analyzed, and subsequently, hypotheses on the potential role of amino acids in discriminating reactions with antibodies were formulated. The residues 114 and 115 (serospecific of Sr1) and 190 (serospecific of Sr2) were localized on the outer surface of the capsid and might be directly involved in the immunoreactivity with MAb D and MAb A, respectively. In contrast, residues 180 (Sr3) and 178 (Sr5) lay within the inner surface of the capsid. To understand the role of these internal positions in the recognition with the antibodies, two substitutions (T180K and G178D) were introduced in the CP of an infectious clone. These mutations modified the antigenicity with MAb G and MAb E discriminating Sr3 and Sr5, respectively, while the reaction with MAb D remained unaffected. This result suggests an indirect effect of these two internal mutations on local immunostructure while the global structure was maintained.
Scaling Betweenness Centrality using Communication-Efficient Sparse Matrix Multiplication

Betweenness centrality (BC) is a crucial graph problem that measures the significance of a vertex by the number of shortest paths leading through it. We propose Maximal Frontier Betweenness Centrality (MFBC): a succinct BC algorithm based on novel sparse matrix multiplication routines that performs a factor of $p^{1/3}$ less communication on p processors than the best known alternatives, for graphs with n vertices and average degree $k=n/p^{2/3}$. We formulate, implement, and prove the correctness of MFBC for weighted graphs by leveraging monoids instead of semirings, which enables a surprisingly succinct formulation. MFBC scales well for both extremely sparse and relatively dense graphs. It automatically searches a space of distributed data decompositions and sparse matrix multiplication algorithms for the most advantageous configuration. The MFBC implementation outperforms the well-known CombBLAS library by up to 8x and shows more robust performance. Our design methodology is readily extensible to other graph problems. CCS CONCEPTS • Theory of computation → Massively parallel algorithms; • Mathematics of computing → Mathematical software performance; • Computing methodologies → Algebraic algorithms; Massively parallel algorithms;
Three‐dimensional Vp /Vs variations for the Coso Region, California

Recent seismological studies of the Coso region of southeastern California document both low P wave velocities and abnormal SV attenuation in Indian Wells Valley, south of the Pleistocene volcanics of the Coso Range. In order to learn more about the physical nature of these colocated anomalies, a tomographic inversion for the three-dimensional variations of Vp/Vs the ratio of compressional to shear velocity was performed. Iterative back projection of 2966 shear and compressional wave travel time residuals from local earthquakes recorded on vertical instruments reveals that Vp/Vs is generally high at the surface and decreases systematically to 10 km depth. Superimposed on this trend are several large anomalies. Near Devil's Kitchen in the Coso Geothermal Area, Vp/Vs values are very low near the surface, consistent with measured values for steam-dominated geothermal systems. Abnormally high values of Vp/Vs are observed in portions of Indian Wells Valley and also below the Cactus Peak rhyolite dome from 2 to 5 km in depth. In Indian Wells Valley the co-occurrence of low P velocities, low S velocities, high Vp/Vs, and anomalous SV attenuation are indicative of subsurface partial melt. Because the inversion is based on vertical data only, however, the results cannot be considered conclusive, only suggestive.
GPR processing using local planewave imaging

Local Plane-Wave processing is used to image synthetic GPR data. Numerically calculated Green's functions are used to back propagate the data down to a Green's function node, in the center of the region to be imaged. From the Green's function node a Plane-Wave approximation is used to back propagate the data over a local image. The data are correctly positioned in the wavenumber space and are re-sampled to a Cartesian grid. The data are then inverted using an IFFT.
Low-cost intelligent gesture recognition engine for audio-vocally impaired individuals

This paper presents a low-cost open source prototype of a gesture recognition and interpretation glove that aids audio-vocally impaired individuals in communication. A sensor based glove for recognition of the gestures in the American Sign Language (ASL) is the input module to the system. It incorporates resistive flex sensors and contact sensors appropriately positioned to obtain a theoretical efficiency of 96% in character recognition. When the sensors are subjected to change in orientation by the user, the variation in electrical resistance of each of the individual sensors is obtained as the input to an Arduino ATMega328 microcontroller that accurately maps it to the letters of the English alphabet through an efficient algorithm. An elegant methodology that is easy to implement using a microcontroller is employed for the mapping process to minimize the complexity of the system. The paper also presents a detailed study of the efficiency characteristics involved in the construction of the custom-designed flex sensors utilized in the system. The paper outlines the calibration and testing results of the sensors . The highlights of the system are its ergonomic and economical design, portability and intelligent gesture recognition and interpretation ability. The implemented system achieves a practical efficiency of up to 80% of theoretical efficiency. The cost of the system is approximately less than USD 5 at laboratory condition using off the shelf components.
Transglutaminase 2 Contributes to Apoptosis Induction in Jurkat T Cells by Modulating Ca2+ Homeostasis via Cross-Linking RAP1GDS1

Background Transglutaminase 2 (TG2) is a protein cross-linking enzyme known to be associated with the in vivo apoptosis program of T cells. However, its role in the T cell apoptosis program was not investigated yet. Results Here we report that timed overexpression of both the wild type (wt) and the cross-linking mutant of TG2 induced apoptosis in Jurkat T cells, the wt being more effective. Part of TG2 colocalised with mitochondria. WtTG2-induced apoptosis was characterized by enhanced mitochondrial Ca2+ uptake. Ca2+-activated wtTG2 cross-linked RAP1, GTP-GDP dissociation stimulator 1, an unusual guanine exchange factor acting on various small GTPases, to induce a yet uncharacterized signaling pathway that was able to promote the Ca2+ release from the endoplasmic reticulum via both Ins3P and ryanodine sensitive receptors leading to a consequently enhanced mitochondrial Ca2+uptake. Conclusions Our data indicate that TG2 might act as a Ca2+ sensor to amplify endoplasmic reticulum-derived Ca2+ signals to enhance mitochondria Ca2+ uptake. Since enhanced mitochondrial Ca2+ levels were previously shown to sensitize mitochondria for various apoptotic signals, our data demonstrate a novel mechanism through which TG2 can contribute to the induction of apoptosis in certain cell types. Since, as compared to knock out cells, physiological levels of TG2 affected Ca2+ signals in mouse embryonic fibroblasts similar to Jurkat cells, our data might indicate a more general role of TG2 in the regulation of mitochondrial Ca2+ homeostasis.
Continuous subcutaneous hydrocortisone infusion versus oral hydrocortisone replacement for treatment of addison's disease: a randomized clinical trial.

CONTEXT Conventional glucocorticoid replacement therapy fails to mimic the physiological cortisol rhythm, which may have implications for morbidity and mortality in patients with Addison's disease. OBJECTIVE The objective of the study was to compare the effects of continuous sc hydrocortisone infusion (CSHI) with conventional oral hydrocortisone (OHC) replacement therapy. DESIGN, PATIENTS, AND INTERVENTIONS This was a prospective crossover, randomized, multicenter clinical trial comparing 3 months of treatment with thrice-daily OHC vs CSHI. From Norway and Sweden, 33 patients were enrolled from registries and clinics. All patients were assessed at baseline and after 8 and 12 weeks in each treatment arm. MAIN OUTCOME MEASURES The morning ACTH level was the primary outcome measure. Secondary outcome measures were effects on metabolism, health-related quality of life (HRQoL), sleep, and safety. RESULTS CSHI yielded normalization of morning ACTH and cortisol levels, and 24-hour salivary cortisol curves resembled the normal circadian variation. Urinary concentrations of glucocorticoid metabolites displayed a normal pattern with CSHI but were clearly altered with OHC. Several HRQoL indices in the vitality domain improved over time with CSHI. No benefit was found for either treatments for any subjective (Pittsburgh Sleep Quality Index questionnaire) or objective (actigraphy) sleep parameters. CONCLUSION CSHI safely brought ACTH and cortisol toward normal circadian levels without adversely affecting glucocorticoid metabolism in the way that OHC did. Positive effects on HRQoL were noted with CSHI, indicating that physiological glucocorticoid replacement therapy may be beneficial and that CSHI might become a treatment option for patients poorly controlled on conventional therapy.
Modular multiple dispatch with multiple inheritance

Overloaded functions and methods with multiple dispatch are useful for extending the functionality of existing classes in an object-oriented language. However, such functions introduce the possibility of ambiguous calls that cannot be resolved at run time, and modular static checking that such ambiguity does not exist has proved elusive in the presence of multiple implementation inheritance. We present a core language for defining overloaded functions and methods that supports multiple dispatch and multiple inheritance, together with a set of restrictions on these definitions that can be statically and modularly checked. We have proved that these restrictions guarantee that no undefined nor ambiguous calls occur at run time, while still permitting various kinds of overloading.
The acid flux dynamics of two artificial drains in acid sulfate soil backswamps on the Clarence River floodplain, Australia

The export of acidity, iron, aluminium, and sulfate to an estuary from 2 drains in acid sulfate soil backswamps was monitored over 18 months. The backswamps had similar geomorphology, stratigraphy, and drainage density, and comparable soil and groundwater acidity. However, the flux rates, temporal dynamics, and export pathways of acid and other sulfide oxidation products varied greatly and were controlled to first order by (i) the saturated hydraulic conductivity (K) of sulfuric horizons and (ii) the tidally influenced groundwater gradients. The site with very high K and large tidally influenced groundwater gradients had high acid flux rates (5300 mol H+/ha.year), chronic acid discharge, high drain water acid and metal concentrations, and the primary flux pathway was direct groundwater seepage (interflow/bypass flow) to the drain. The site with lower K and smaller groundwater gradients displayed low acid flux rates (50 mol H+/ha.year), infrequent, highly episodic discharge, and the primary flux pathway was dilute surface runoff following dissolution of sulfide oxidation products accumulated on the soil surface. Importantly, the majority of acid export at both sites occurred while the backswamp groundwater level was within a very narrow elevation range.
A Study of Long‐Term Effects on Plasmid‐Containing Escherichia coli in Carbon‐Limited Chemostat Using 2D‐Fluorescence Spectrofluorimetry

Strain stability of plasmid‐containing recombinant organisms is clearly important for industrial applications. Stability is normally assessed by methods such as selective colony forming units or by simply measuring the recombinant product. These methods are typically performed off‐line, are time‐consuming, and do not give detailed information on the changes in the metabolism. In the current work, long‐term stability of a plasmid‐containing strain of Escherichia coli (W3110.shik1) capable of shikimic acid overproduction was studied by means of a 2D‐fluorescence sensor (BioView) able to emit and detect light in ranges of 260–560 nm and 300–600 nm, respectively. Long‐term carbon‐limited chemostat experiments were made under both selective (tetracycline‐containing medium) and nonselective conditions. It is shown that the fluorescence spectra provide information about metabolic changes at an earlier stage, thereby giving a noninvasive method for monitoring of strain stability. Further, the fluorescence measurements showed that (i) the metabolic changes in the strain W3110.shik1 with time were qualitatively different in selective and nonselective environment, (ii) plasmid recombination resulted primarily in increased biomass yield, and (iii) a change in metabolism probably involving FAD/FMN and pyridoxal‐5‐P occurred in all experiments. It was concluded that the strain was not stable in any growth condition for more than about 25 growth generations and even less if plasmid recombination took place.
PSO Algorithm with Transition Probability Based on Hamming Distance for Graph Coloring Problem

In this paper, we propose a PSO algorithm with transition probability based on Hamming distance for solving planar graph coloring problems. PSO was originally intended to handle only continuous optimization problems. To apply PSO to discrete problems, the standard arithmetic operators of PSO need to be redefined over discrete space. In this work, we propose a new algorithm that uses transition probability based on Hamming distance into PSO. The experimental results show that the new algorithm can get higher success rate and smaller average iterations than a Genetic Algorithm and the conventional PSO.
Use of a Needs Assessment in the Development of an Interprofessional Faculty Development Program

A needs assessment was conducted regarding an interprofessional faculty development program for promoting excellence in education. Nursing and medical faculty and administrators (N = 156) were surveyed about perceived need, program curriculum, and delivery. The results indicated strong support for the program, particularly related to teaching/learning strategies, leadership, and scholarship. Nursing faculty rated some topical areas significantly higher than did the medical faculty, including innovative classroom teaching, educational technology, interprofessional education, diversity/inclusion, and mentoring graduate students.
Trench geometry and resist profiles from modeling of polarized optical spectra

Profiles of trenches in silicon were calculated by fitting measured polarized reflectance spectra with theoretically calculated RCWA (rigorous coupled wave analysis) models. The agreement of trench geometry from optical measurements with SEM cross-sections was good. The contact-free optical measurement on productive wafers constitutes a serious alternative to the time consuming and destructive cross-section analyses. Critical dimensions (CD) of gratings of resist lines were obtained from RCWA modeling of optical spectra. An i-line resist with lines of larger spacing and a UV resist with lines of smaller pitch were investigated. In both cases the top and bottom CDs varied over a wide range due to the change in exposure dose across the wafer. The good agreement between optically obtained CD values, in-line CD SEM data and cross-section SEM data makes the optical method an ideal tool for process control.