Miracle-dz/UniFAR-FTUs huggingface dataset:
A Secure Network Detection System against Noisy Unlabeled Data

Today, the Internet along with the corporate network plays a major role in creating and advancing new business avenues. With the ever increasing deployment and usage of gigabit networks, traditional network anomaly detection based intrusion detection systems have not scaled accordingly. Most, if not all, systems deployed assume the availability of complete and clean data for the purpose of intrusion detection. We contend that this assumption is not valid. Factors like noise in the audit data, mobility of the nodes, and the large amount of data generated by the network make it difficult to build a normal traffic profile of the network for the purpose of anomaly detection. From this perspective, the leitmotif of the research effort described in this dissertation is the design of a novel intrusion detection system that has the capability to detect intrusions with high accuracy even when complete audit data is not available. In this dissertation, we take a holistic approach to anomaly detection to address the threats posed by network based denial-of-service attacks by proposing improvements in every step of the intrusion detection process. At the data collection phase, we have implemented an adaptive sampling scheme that intelligently samples incoming network data to reduce the volume of traffic sampled, while maintaining the intrinsic characteristics of the network traffic. A Bloom filters based fast flow aggregation scheme is employed at the data pre-processing stage to further reduce the response time of the anomaly detection scheme. Lastly, this dissertation also proposes an expectation-maximization algorithm based anomaly detection scheme that uses the sampled audit data to detect intrusions in the incoming network traffic. KeywordsNetwork Security, Anomaly Detection, Intrusion detection, Clustering.
Situated Incremental Natural Language Understanding using a Multimodal, Linguistically-driven Update Model

A common site of language use is interactive dialogue between two people situated together in shared time and space. In this paper, we present a statistical model for understanding natural human language that works incrementally (i.e., does not wait until the end of an utterance to begin processing), and is grounded by linking semantic entities with objects in a shared space. We describe our model, show how a semantic meaning representation is grounded with properties of real-world objects, and further show that it can ground with embodied, interactive cues such as pointing gestures or eye gaze.
Increased chemical acetylation of peptides and proteins in rats after daily ingestion of diacetyl analyzed by Nano-LC-MS/MS

Background Acetylation alters several protein properties including molecular weight, stability, enzymatic activity, protein–protein interactions, and other biological functions. Our previous findings demonstrating that diacetyl/peroxynitrite can acetylate L-lysine, L-histidine, and albumin in vitro led us to investigate whether diacetyl-treated rats suffer protein acetylation as well. Methods Wistar rats were administered diacetyl daily for four weeks, after which they were sacrificed, and their lung proteins were extracted to be analysed by Nano-LC-MS/MS (Q-TOF). A C18 reversed-phase column and gradient elution with formic acid/acetonitrile solutions from 2 to 50% over 150 min were used to separate the proteins. Protein detection was performed using a microTOF-Q II (QTOF) equipped with captive source and an electrospray-ionization source. The data from mass spectrometry were processed using a Compass 1.7 and analyzed using Protein Scape, software that uses Mascot algorithms to perform protein searches. Results A set of 3,162 acetylated peptides derived from 351 acetylated proteins in the diacetyl-treated group was identified. Among them, 23 targeted proteins were significantly more acetylated in the diacetyl-treated group than in the PBS control. Protein acetylation of the group treated with 540 mg/kg/day of diacetyl was corroborated by Western blotting analysis. Conclusions These data support our hypothesis that diacetyl exposure in animals may lead to the generation of acetyl radicals, compounds that attach to proteins, affecting their functions and triggering adverse health problems.
Decellularized Diaphragmatic Muscle Drives a Constructive Angiogenic Response In Vivo

Skeletal muscle tissue engineering (TE) aims to efficiently repair large congenital and acquired defects. Biological acellular scaffolds are considered a good tool for TE, as decellularization allows structural preservation of tissue extracellular matrix (ECM) and conservation of its unique cytokine reservoir and the ability to support angiogenesis, cell viability, and proliferation. This represents a major advantage compared to synthetic scaffolds, which can acquire these features only after modification and show limited biocompatibility. In this work, we describe the ability of a skeletal muscle acellular scaffold to promote vascularization both ex vivo and in vivo. Specifically, chicken chorioallantoic membrane assay and protein array confirmed the presence of pro-angiogenic molecules in the decellularized tissue such as HGF, VEGF, and SDF-1α. The acellular muscle was implanted in BL6/J mice both subcutaneously and ortotopically. In the first condition, the ECM-derived scaffold appeared vascularized 7 days post-implantation. When the decellularized diaphragm was ortotopically applied, newly formed blood vessels containing CD31+, αSMA+, and vWF+ cells were visible inside the scaffold. Systemic injection of Evans Blue proved function and perfusion of the new vessels, underlying a tissue-regenerative activation. On the contrary, the implantation of a synthetic matrix made of polytetrafluoroethylene used as control was only surrounded by vWF+ cells, with no cell migration inside the scaffold and clear foreign body reaction (giant cells were visible). The molecular profile and the analysis of macrophages confirmed the tendency of the synthetic scaffold to enhance inflammation instead of regeneration. In conclusion, we identified the angiogenic potential of a skeletal muscle-derived acellular scaffold and the pro-regenerative environment activated in vivo, showing clear evidence that the decellularized diaphragm is a suitable candidate for skeletal muscle tissue engineering and regeneration.
Turbulence Simulation on Sparse Grids Using the Combination Method

In this paper, we study the parallel numerical solution of the Navier-Stokes equations with the sparse grid combination method. This algorithmic concept is based on the independent solution of many problems with reduced size and their linear combination. We describe the algorithm for three-dimensional problems and we report on its application to turbulence simulation. Furthermore, statistical results on a pipe ow for Reynolds number Re cl = 6950 are presented and compared to results obtained from other numerical simulations and physical experiments. 1. Summary Sparse grid techniques are very promising for the solution of linear PDEs. There, for three-dimensional problems, only O(h ? 1 m (log(h ? 1 m)) 2) grid points are needed instead of O(h ? 3 m) grid points like in the conventional full grid case. Here, h m = 2 ? m denotes the mesh size in the unit cube. However, the accuracy of the sparse grid solution is of the order O(h 2 m (log(h ? 1 m)) 2) (with respect to the L 2 ? and L 1 ? norm) provided that the solution is suuciently smooth (i.e. j 6 u(x;y;z) x 2 y 2 z 2 jj 1). This is only slightly worse than the order O(h 2 m) obtained for the usual full grid solution. For further details on sparse grids, see 4], 9]. For the solution of problems arising from the sparse grid discretization approach, two diierent methods have been developed in the last years. First, multilevel-type solvers for the system that results from hierarchical basis like nite element//nite volume or nite diierence discretization (FE, FV, FD) and second, the so-called combination method. There, the solution is obtained on a sparse grid by a certain linear combination of discrete solutions on diierent meshes. The multilevel-type solvers need hierarchical data structures. Thus, specially designed solvers are necessary (see 3]). In the case of the combination method, however, only simple data structures are needed. This method merely handles three-dimensional arrays. Furthermore, it is possible to use any PDE solver as a "black-box" solution method within the combination approach to get a solution on the diierent meshes involved.
Caffeic Acid Phenethylester Increases Stress Resistance and Enhances Lifespan in Caenorhabditis elegans by Modulation of the Insulin-Like DAF-16 Signalling Pathway

CAPE is an active constituent of propolis which is widely used in traditional medicine. This hydroxycinnamic acid derivate is a known activator of the redox-active Nrf2 signalling pathway in mammalian cells. We used C. elegans to investigate the effects of this compound on accumulation of reactive oxygen species and the modulation of the pivotal redox-active pathways SKN-1 and DAF-16 (homologues of Nrf2 and FoxO, respectively) in this model organism; these results were compared to the effects in Hct116 human colon carcinoma cells. CAPE exerts a strong antioxidative effect in C. elegans: The increase of reactive oxygen species induced by thermal stress was diminished by about 50%. CAPE caused a nuclear translocation of DAF-16, but not SKN-1. CAPE increased stress resistance of the nematode against thermal stress and finally a prolongation of the median and maximum lifespan by 9 and 17%, respectively. This increase in stress resistance and lifespan was dependent on DAF-16 as shown in experiments using a DAF-16 loss of function mutant strain. Life prolongation was retained under SKN-1 RNAi conditions showing that the effect is SKN-1 independent. The results of CAPE obtained in C. elegans differed from the results obtained in Hct116 colon carcinoma cells: CAPE also caused strong antioxidative effects in the mammalian cells, but no activation of the FoxO4 signalling pathway was detectable. Instead, an activation of the Nrf2 signalling pathway was shown by luciferase assay and western blots. CONCLUSION: CAPE activates the insulin-like DAF-16, but not the SKN-1 signalling pathway in C. elegans and therefore enhances the stress resistance and lifespan of this organism. Since modulation of the DAF-16 pathway was found to be a pivotal effect of CAPE in C. elegans, this has to be taken into account for the investigation of the molecular mechanisms of the traditional use of propolis.
Opus: University of Bath Online Publication Store Multimodal Electrochemical and Nanoplasmonic Biosensors Using Ferrocene Crowned Nanoparticles for Kinase Drug Discovery Applications

(2015) Multimodal electrochemical and nanoplasmonic biosensors using ferrocene crowned nanoparticles for kinase drug discovery applications. This version is made available in accordance with publisher policies. Please cite only the published version using the reference above. Abstract The use of on-chip multimodal sensing approaches is very promising towards integrated biosensing systems, which measure different parameters involved in biomolecular interactions and provide automated validation of true positives. In this report we investigate a proof of concept that enables multiple detection technologies for screening inhibitors of kinase activity, which is a crucial process in drug discovery applications. We demonstrate the integration of electrochemical techniques on the same chip, namely differential pulse voltammetry, impedance spectroscopy and direct open circuit potential measurements. Gold nanoparticles that attach to the thio-phosphorylated proteins facilitate localized surface plasmon resonance detection. The addition of thiolated ferrocene, which attaches to the nanoparticles like a crown, enables sensitive electrochemical amperometric detection of kinase activity. This novel multimodal biosensor provides a more rigorous measurement of biomolecules, with wide significance in biomedical, environmental and pharmaceutical applications.
Defining malware families based on analyst insights

Determining whether arbitrary files are related to known malicious files is often useful in network and host-based defense. Doing so can give network defenders sufficient exemplars of a particular threat to develop comprehensive signatures and heuristics for identifying the threat, leading to decreased response time and improved prevention of a cyber attack. Identifying these malicious families is a complex process involving the categorization of potentially malicious code into sets that share similar features, while being distinguishable from unrelated threats or non-malicious code. Current methods for automatically or manually describing malware families are typically unable to distinguish between indicators derived from the structure of the malware and indicators derived from the behavior of the malware. Further, attempts to cluster potentially related files by mapping them into alternate domains, including histograms, fuzzy hashes, Bloom filters, and so on often produces clusters of files solely derived from structural information. These similarity measurements are often very effective on crudely similar files, yet they fail to identify files that have similar or identical behavior and semantics. We propose an analytic method, driven largely by human experience and based on objective criteria, for assigning arbitrary files membership in a malicious code family. We describe a process for iteratively refining the criteria used to select a malicious code family, until such criteria described are both necessary and sufficient to distinguish a particular malicious code family. We contrast this process with similar processes, such as antivirus signature generation and automatic and blind classification methods. We formalize this process to describe a roadmap for practitioners of malicious code analysis and to highlight opportunities for improvement and automation of both the process and the observation of relevant criteria. Finally, we provide experimental results of applying this methodology to real-world malware.
Measurement results of within-die variations on a 90nm LUT array for speed and yield enhancement of reconfigurable devices

It is possible to enhance speed and yield of reconfigurable devices utilizing WID variations. An LUT array LSI is fabricated on a 90nm process to measure WID and D2D variations. Performance fluctuations are measured by counting the number of LUTs through which a signal is passing within a certain time. D2D and WID variations are clearly observed by the measurement
Generating and Justifying Design Theory 2 Relevant Literature

This paper applies Simon's Sciences of the Artificial to elaborate a set of structures and processes for developing design theory. Goals, kernel theory, and artifacts inform an interrelated prototyping cycle of design, evaluation, and appropriation / generation to produce strategic design theory. The paper identifies DSR project types to provide signposts for starting and ending the cycle, artifact and evaluation iteration to facilitate the process and provide a chain of evidence, a simplified format for representing design theory iterations, and stopping rules to end the cycle. A detailed example illustrates the ideas, followed by a discussion of related work, and identification of limitations and future research opportunities. the development of design theory and justificatory knowledge within existing DSR methods. The research is important because even though current approaches address the 'what' and the overall meta-cycle of DSR, there is still much to be done on the 'how', the steps needed to produce theories and practical insights. Further, recent research continues to identify design theory generation as an important but problematic task (e. the research question: How do you develop design theory in DSR? Simon (1996) introduced the notion of a design theory and the need to make it explicit and precise – to make it a science of the artificial. Science requires the scientific method, i.e., to be systematic, observable, empirical, and measurable. In IS, Gregor and Jones (2007) make the case that for the field to rise " above the level of a craft " (p. 314) it is important to express design knowledge as theory. Yet the central focus of DSR, the artifact, by itself cannot easily be added to the knowledge base of science. It is hard to systematically show, measure, and justify the scientific contribution of an artifact. Consider a ground breaking lab experiment and compare to creating an interesting artifact. The experiment is a contribution and should be published, in addition, to add to knowledge in a way that is systematic and measurable, there is also a need to infer the theoretical contribution. In the case of artifacts, the option of (only) publishing the artifact is challenging. Modern IT artifacts are built on top of complex hierarchies of components (e.g., user interface components such as buttons) and unless 3 explicitly elaborated it will be hard to discern the unique contribution. The signal to noise ratio in leaving the contribution embedded inside the artifact is problematic. …
On the class of graphs with strong mixing properties

We study three mixing properties of a graph: large algebraic connectivity, large Cheeger constant (isoperimetric number) and large spectral gap from 1 for the second largest eigenvalue of the transition probability matrix of the random walk on the graph. We prove equivalence of this properties (in some sense). We give estimates for the probability for a random graph to satisfy these properties. In addition, we present asymptotic formulas for the numbers of Eulerian orientations and Eulerian circuits in an undirected simple graph.
Dramatic increase in the numbers of functionally mature dendritic cells in Flt3 ligand-treated mice: multiple dendritic cell subpopulations identified

Dendritic cells (DC) are the most efficient APC for T cells. The clinical use of DC as vectors for anti-tumor and infectious disease immunotherapy has been limited by their trace levels and accessibility in normal tissue and terminal state of differentiation. In the present study, daily injection of human Flt3 ligand (Flt3L) into mice results in a dramatic numerical increase in cells co-expressing the characteristic DC markers-class II MHC, CD11c, DEC205, and CD86. In contrast, in mice treated with either GM-CSF, GM-CSF plus IL-4, c-kit ligand (c-kitL), or G-CSF, class II+ CD11c+ cells were not significantly increased. Five distinct DC subpopulations were identified in the spleen of Flt3L-treated mice using CD8 alpha and CD11b expression. These cells exhibited veiled and dendritic processes and were as efficient as rare, mature DC isolated from the spleens of untreated mice at presenting allo-Ag or soluble Ag to T cells, or in priming an Ag-specific T cell response in vivo. Dramatic numerical increases in DC were detected in the bone marrow, gastro-intestinal lymphoid tissue (GALT), liver, lymph nodes, lung, peripheral blood, peritoneal cavity, spleen, and thymus. These results suggest that Flt3L could be used to expand the numbers of functionally mature DC in vivo for use in clinical immunotherapy.
Progress guarantee for parallel programs via bounded lock-freedom

Parallel platforms are becoming ubiquitous with modern computing systems. Many parallel applications attempt to avoid locks in order to achieve high responsiveness, aid scalability, and avoid deadlocks and livelocks. However, avoiding the use of system locks does not guarantee that no locks are actually used, because progress inhibitors may occur in subtle ways through various program structures. Notions of progress guarantee such as lock-freedom, wait-freedom, and obstruction-freedom have been proposed in the literature to provide various levels of progress guarantees. In this paper we formalize the notions of progress guarantees using linear temporal logic (LTL). We concentrate on lock-freedom and propose a variant of it denoted bounded lock-freedom, which is more suitable for guaranteeing progress in practical systems. We use this formal definition to build a tool that checks if a concurrent program is bounded lock-free for a given bound. We then study the interaction between programs with progress guarantees and the underlying system (e.g., compilers, runtimes, operating systems, and hardware platforms). We propose a means to argue that an underlying system supports lock-freedom. A composition theorem asserts that bounded lock-free algorithms running on bounded lock-free supporting systems retain bounded lock-freedom for the composed execution.
A Greedy Algorithm of Data-Dependent User Selection for Fast Fading Gaussian Vector Broadcast Channels

User selection (US) with Zero-forcing beamforming is considered in fast fading Gaussian vector broadcast channels with perfect channel state information (CSI) at the transmitter. A novel criterion for US is proposed, which depends on both CSI and the data symbols, while conventional criteria only depend on CSI. Since the optimization of US based on the proposed criterion is infeasible, a greedy algorithm of data-dependent US is proposed to perform the optimization approximately. An overhead issue arises in fast fading channels: On every update of US, the transmitter might inform each user whether he/she has been selected, using a certain fraction of resources. This overhead results in a significant rate loss for fast fading channels. In order to circumvent this overhead issue, iterative detection and decoding schemes are proposed on the basis of belief propagation. The proposed iterative schemes require no information about whether each user has been selected. The proposed US scheme is compared to a data-independent US scheme. The complexity of the two schemes is comparable to each other for fast fading channels. Numerical simulations show that the proposed scheme can outperform the data-independent scheme for fast fading channels in terms of energy efficiency, bit error rate, and achievable sum rate.
Morphological disambiguation of Hebrew: a case study in classifier combination

Abstract Morphological analysis and disambiguation are crucial stages in a variety of natural language processing applications, especially when languages with complex morphology are concerned. We present a system which disambiguates the output of a morphological analyzer for Hebrew. It consists of several simple classifiers and a module that combines them under the constraints imposed by the analyzer. We explore several approaches to classifier combination, as well as a back-off mechanism that relies on a large unannotated corpus. Our best result, around 83 percent accuracy, compares favorably with the state of the art on this task.
Faster solutions of the inverse pairwise Ising problem

Princeton Center for Theoretical Physics, Princeton University, Princeton, NJ 08544(Dated: February 4, 2008)Recent work has shown that probabilistic models based on pairwise interactions|in the simplestcase, the Ising model|provide surprisingly accurate descriptions of experiments on real biologicalnetworks ranging from neurons to genes. Finding these models requires us to solve an inverse prob-lem: given experimentally measured expectation values, what are the parameters of the underlyingHamiltonian? This problem sits at the intersection of statistical physics and machine learning, andwe suggest that more ecient solutions are possible by merging ideas from the two elds. We usea combination of recent coordinate descent algorithms with an adaptation of the histogram MonteCarlo method, and implement these techniques to take advantage of the sparseness found in data onreal neurons. The resulting algorithm learns the parameters of an Ising model describing a networkof forty neurons within a few minutes. This opens the possibility of analyzing much larger data setsnow emerging, and thus testing hypotheses about the collective behaviors of these networks.I. INTRODUCTION