Miracle-dz/UniFAR-FTUs huggingface dataset:
SEPIA: Security through Private Information Aggregation

Secure multiparty computation (MPC) allows joint privacy-preserving computations on data of multiple parties. Although MPC has been studied substantially, building solutions that are practical in terms of computation and communication cost is still a major challenge. In this paper, we investigate the practical usefulness of MPC for multi-domain network security and monitoring. We first optimize MPC comparison operations for processing high volume data in near real-time. We then design privacy-preserving protocols for event correlation and aggregation of network traffic statistics, such as addition of volume metrics, computation of feature entropy, and distinct item count. Optimizing performance of parallel invocations, we implement our protocols along with a complete set of basic operations in a library called SEPIA. We evaluate the running time and bandwidth requirements of our protocols in realistic settings on a local cluster as well as on PlanetLab and show that they work in near real-time for up to 140 input providers and 9 computation nodes. Compared to implementations using existing general-purpose MPC frameworks, our protocols are significantly faster, requiring, for example, 3 minutes for a task that takes 2 days with general-purpose frameworks. This improvement paves the way for new applications of MPC in the area of networking. Finally, we run SEPIA's protocols on real traffic traces of 17 networks and show how they provide new possibilities for distributed troubleshooting and early anomaly detection.
Primary teachers’ understanding of concepts of science: impact on confidence and teaching

The specification of the science to be taught in primary schools has thrown into sharper focus the matter of primary teachers’ own understanding of the subject matter which has, for some time, been an area of concern. Research carried out in Scotland has explored in some depth the problems primary teachers encounter in science and technology and the extent to which these are associated with lack of confidence and/or background knowledge. The findings indicate that there are some ideas which primary teachers can quite quickly come to understand while others require more extensive in‐service attention. Confidence is not only dependent on subject knowledge; teachers with low confidence employ various strategies for coping, some of which when regularly applied have a severely limiting effect on children's learning.
A Semantics and Complete Algorithm for Subsumption in the CLASSIC Description Logic

This paper analyzes the correctness of the subsumption algorithm used in CLASSIC, a description logic-based knowledge representation system that is being used in practical applications. In order to deal efficiently with individuals in CLASSIC descriptions, the developers have had to use an algorithm that is incomplete with respect to the standard, model-theoretic semantics for description logics. We provide a variant semantics for descriptions with respect to which the current implementation is complete, and which can be independently motivated. The soundness and completeness of the polynomial-time subsumption algorithm is established using description graphs, which are an abstracted version of the implementation structures used in CLASSIC, and are of independent interest.
The detectability lemma and quantum gap amplification

The quantum analogue of the constraint satisfaction problem is the fundamental physics question of finding the minimal energy state of a local Hamiltonian --- each term of the Hamiltonian specifies a local constraint whose violation contributes to the energy of the given quantum state. However, in general it is not meaningful to ask for the probability that a given quantum state violates at least one constraint; the difficulty being that the terms of the Hamiltonian do not commute. We show how to make sense of this notion under mild restrictions on the form of the Hamiltonian. We then provide two main results. We first prove the quantum detectability lemma, which states that the probability of detecting a violation of a constraint in a local Hamiltonian system is bounded from below by some constant times the minimal energy of the system. The proof reveals some intrinsic structure of the Hilbert space of local Hamiltonians, which is captured in the "exponential decay" lemma, and formalized using a novel decomposition of the Hilbert space called the XY decomposition. As an application of the detectability lemma, we prove our second main result: a quantum analogue of the classical gap amplification lemma using random walks over expander graphs, which was the seed for Dinur's celebrated new proof of the PCP theorem [6]. We hope that these results will pave the way to better understandings of the computational properties of local Hamiltonians systems, and to the evolving field of quantum Hamiltonian complexity.
Applications of Fourier Transform Ion Cyclotron Resonance (FT-ICR) and Orbitrap Based High Resolution Mass Spectrometry in Metabolomics and Lipidomics

Metabolomics, along with other “omics” approaches, is rapidly becoming one of the major approaches aimed at understanding the organization and dynamics of metabolic networks. Mass spectrometry is often a technique of choice for metabolomics studies due to its high sensitivity, reproducibility and wide dynamic range. High resolution mass spectrometry (HRMS) is a widely practiced technique in analytical and bioanalytical sciences. It offers exceptionally high resolution and the highest degree of structural confirmation. Many metabolomics studies have been conducted using HRMS over the past decade. In this review, we will explore the latest developments in Fourier transform mass spectrometry (FTMS) and Orbitrap based metabolomics technology, its advantages and drawbacks for using in metabolomics and lipidomics studies, and development of novel approaches for processing HRMS data.
An Empirical Comparison of Tree-Based Learning Algorithms: An Egyptian Rice Diseases Classification Case Study

Applications of learning algorithms in knowledge discovery are promising and relevant area of research. The classification algorithms of data mining have been successfully applied in the recent years to predict Egyptian rice diseases. Various classification algorithms can be applied on such data to devise methods that can predict the occurrence of diseases. However, the accuracy of such techniques differ according to the learning and classification rule used. Identifying the best classification algorithm among all available is a challenging task. In this study, a comprehensive comparative analysis of a tree-based different classification algorithms and their performance has been evaluated by using Egyptian rice diseases data set. The experimental results demonstrate that the performance of each classifier and the results indicate that the decision tree gave the best results.
Cast Out: “Gender Role Outlaws” Seeking Asylum in the West and the Quest for Social Connections

Since 1994, increasing numbers of persons are fleeing persecution based upon their nonconformity with traditional gender roles. This qualitative study explores the experiences of 14 men and women from Islamic societies persecuted in their countries for resisting gender-role norms and, ultimately, gaining asylum in the United States. Findings suggest that “gender role outlaws” in resettlement may be alienated from families and more traditional coethnic others by their alignment, or perceived alignment, with Western constructs, and may also be marginalized by mainstream communities. Ultimately, findings contrast with received knowledge that family and coethnic affiliation is possible and positive for Muslims in resettlement and point to the need for alternative sources of social support.
Oral Contraceptives and HRT Risk of Thrombosis

Estrogen-containing medication, prescribed either for contraception in women of reproductive age or for prevention of cardiovascular events and osteoporosis as well as for alleviation of symptoms related to menopause, is associated with changes in the hemostatic balance and contributes to increased risk of development of venous thromboembolic complications. This risk is dose and medication dependent, increases with age, congenital and/or acquired predisposition to thrombosis, and mode of administration. This review attempts to summarize the current knowledge regarding the pathophysiology of oral contraceptive (OC) and hormone replacement therapy (HRT) -induced prothrombotic state in women, the risk of thrombosis associated with administration of various commercially available OCs and HRT, the additional risk in women with hereditary or acquired thrombophilia, and the currently available recommendations regarding massive screening of women for thrombophilia prior to initial prescription or continuation of treatment with OCs and HRT preparations.
Establishment and maintenance of Soybean Mosaic Virus in soybean callus culture

Susceptibility to inoculation with Soybean mosaic virus (SMV) and virus activity were investigated in soybean callus cultures growing in vitro. Excised hypocotyls of susceptible soybean, Glycine max (L.) Merr. ‘Essex’, were cultured in Msoy medium in the light at 25 °C. Established calluses were inoculated with SMV in vitro by a soak–prick method. In addition, SMV-infected leaves of soybean ‘Lee 68’ were surface sterilized, excised, and placed on callus-inducing medium. Calluses infected with SMV initiated by either method grew in vitro as well as calluses from uninfected tissues. Callus cultures turned brownish yellow after 6–8 weeks, when the media became depleted of nutrients. However, callus with an active SMV infection could be maintained by regular subculture to fresh medium. Longevity of SMV–callus cultures was increased by storage at 10–15 °C, thus reducing the frequency of transfers. The virus was detected in infected calluses by serological tests. Infectivity assays confirmed the presence and viability of SMV in callus cultures. Most callus cultures induced directly from infected leaves retained virus and high infectivity, whereas infective cultures from in vitro inoculated hypocotyls appeared to decrease in number and infectivity with repeated subcultures. However, selected infective cultures retained high infectivity after 10 successive transfers over a period of 20 months. These results demonstrate that SMV can be cultured and maintained active in callus cultures in vitro
Robust and reliable audio watermarking based on dynamic phase coding and error control coding

This paper proposes an audio watermarking method based on dynamic phase coding and error control coding. The technique of quantization index modulation is employed for embedding watermarks into the phase spectrum of audio signals. Since most of the audio information is distributed in moderately low frequencies, to increase robustness, this frequency region is chosen for embedding watermarks. Phase modification causes sound distortion in a manner that is proportional to the magnitude. Therefore, the amount of phase modification is adjusted according to the magnitude to balance inaudibility and robustness. Error control coding is incorporated to further increase reliability of watermark detection. The experimental results show that the watermarks could be kept inaudible in watermarked signals and robust against various attacks. Error control coding is effective in increasing watermark detection accuracy remarkably.
Model for the Peptide-Free Conformation of Class II MHC Proteins

Background Major histocompatibility complex proteins are believed to undergo significant conformational changes concomitant with peptide binding, but structural characterization of these changes has remained elusive. Methodology/Principal Findings Here we use molecular dynamics simulations and experimental probes of protein conformation to investigate the peptide-free state of class II MHC proteins. Upon computational removal of the bound peptide from HLA-DR1-peptide complex, the α50-59 region folded into the P1-P4 region of the peptide binding site, adopting the same conformation as a bound peptide. Strikingly, the structure of the hydrophobic P1 pocket is maintained by engagement of the side chain of Phe α54. In addition, conserved hydrogen bonds observed in crystal structures between the peptide backbone and numerous MHC side chains are maintained between the α51-55 region and the rest of the molecule. The model for the peptide-free conformation was evaluated using conformationally-sensitive antibody and superantigen probes predicted to show no change, moderate change, or dramatic changes in their interaction with peptide-free DR1 and peptide-loaded DR1. The binding observed for these probes is in agreement with the movements predicted by the model. Conclusion/Significance This work presents a molecular model for peptide-free class II MHC proteins that can help to interpret the conformational changes known to occur within the protein during peptide binding and release, and can provide insight into possible mechanisms for DM action.
Molecular Characterization of Feline Immunodeficiency Virus Budding

ABSTRACT Infection of domestic cats with feline immunodeficiency virus (FIV) is an important model system for studying human immunodeficiency virus type 1 (HIV-1) infection due to numerous similarities in pathogenesis induced by these two lentiviruses. However, many molecular aspects of FIV replication remain poorly understood. It is well established that retroviruses use short peptide motifs in Gag, known as late domains, to usurp cellular endosomal sorting machinery and promote virus release from infected cells. For example, the Pro-Thr/Ser-Ala-Pro [P(T/S)AP] motif of HIV-1 Gag interacts directly with Tsg101, a component of the endosomal sorting complex required for transport I (ESCRT-I). A Tyr-Pro-Asp-Leu (YPDL) motif in equine infectious anemia virus (EIAV), and a related sequence in HIV-1, bind the endosomal sorting factor Alix. In this study we sought to identify and characterize FIV late domain(s) and elucidate cellular machinery involved in FIV release. We determined that mutagenesis of a PSAP motif in FIV Gag, small interfering RNA-mediated knockdown of Tsg101 expression, and overexpression of a P(T/S)AP-binding fragment of Tsg101 (TSG-5′) each inhibited FIV release. We also observed direct binding of FIV Gag peptides to Tsg101. In contrast, mutagenesis of a potential Alix-binding motif in FIV Gag did not affect FIV release. Similarly, expression of the HIV-1/EIAV Gag-binding domain of Alix (Alix-V) did not disrupt FIV budding, and FIV Gag peptides showed no affinity for Alix-V. Our data demonstrate that FIV relies predominantly on a Tsg101-binding PSAP motif in the C terminus of Gag to promote virus release in HeLa cells, and this budding mechanism is highly conserved in feline cells.
CRISPR / Cas 9 and mitochondrial gene replacement therapy : promising techniques and ethical considerations

Thousands of mothers are at risk of transmitting mitochondrial diseases to their offspring each year, with the most severe form of these diseases being fatal [1]. With no cure, transmission prevention is the only current hope for decreasing the disease incidence. Current methods of prevention rely on low mutant maternal mitochondrial DNA levels, while those with levels close to or above threshold (>60%) are still at a very high risk of transmission [2]. Two novel approaches may offer hope for preventing and treating mitochondrial disease: mitochondrial replacement therapy, and CRISPR/Cas9. Mitochondrial replacement therapy has emerged as a promising tool that has the potential to prevent transmission in patients with higher mutant mitochondrial loads. This method is the subject of many ethical concerns due its use of a donor embryo to transplant the patient’s nuclear DNA; however, it has ultimately been approved for use in the United Kingdom and was recently declared ethically permissible by the FDA. The leading-edge CRISPR/Cas9 technology exploits the principles of bacterial immune function to target and remove specific sequences of mutated DNA. This may have potential in treating individuals with disease caused by mutant mitochondrial DNA. As the technology progresses, it is important that the ethical considerations herein emerge and become more established. The purpose of this review is to discuss current research surrounding the procedure and efficacy of the techniques, compare the ethical concerns of each approach, and look into the future of mitochondrial gene replacement therapy.
MAZ-binding G4-decoy with locked nucleic acid and twisted intercalating nucleic acid modifications suppresses KRAS in pancreatic cancer cells and delays tumor growth in mice

KRAS mutations are primary genetic lesions leading to pancreatic cancer. The promoter of human KRAS contains a nuclease-hypersensitive element (NHE) that can fold in G4-DNA structures binding to nuclear proteins, including MAZ (myc-associated zinc-finger). Here, we report that MAZ activates KRAS transcription. To knockdown oncogenic KRAS in pancreatic cancer cells, we designed oligonucleotides that mimic one of the G-quadruplexes formed by NHE (G4-decoys). To increase their nuclease resistance, two locked nucleic acid (LNA) modifications were introduced at the 3′-end, whereas to enhance the folding and stability, two polycyclic aromatic hydrocarbon units (TINA or AMANY) were inserted internally, to cap the quadruplex. The most active G4-decoy (2998), which had two para-TINAs, strongly suppressed KRAS expression in Panc-1 cells. It also repressed their metabolic activity (IC50 = 520 nM), and it inhibited cell growth and colony formation by activating apoptosis. We finally injected 2998 and control oligonucleotides 5153, 5154 (2 nmol/mouse) intratumorally in SCID mice bearing a Panc-1 xenograft. After three treatments, 2998 reduced tumor xenograft growth by 64% compared with control and increased the Kaplan–Meier median survival time by 70%. Together, our data show that MAZ-specific G4-decoys mimicking a KRAS quadruplex are promising for pancreatic cancer therapy.
Pattern-Based Evaluation of Scientific Workflow Management Systems

In recent years several scientific Workflow Management Systems (WfMSs) have been developed with the aim to automate large scale scientific experiments. As yet, many offerings have been developed, but none of them has been promoted as an accepted standard. In this paper we propose a pattern-based evaluation of three among the most widely used scientific WfMSs: Kepler, Taverna and Triana. The aim is to compare them with traditional business WfMSs, emphasizing the strengths and deficiencies of both systems. Moreover, a set of new patterns is defined from the analysis of the three considered systems.
Unary Constraints for Efficient Context-Free Parsing

We present a novel pruning method for context-free parsing that increases efficiency by disallowing phrase-level unary productions in CKY chart cells spanning a single word. Our work is orthogonal to recent work on "closing" chart cells, which has focused on multi-word constituents, leaving span-1 chart cells unpruned. We show that a simple discriminative classifier can learn with high accuracy which span-1 chart cells to close to phrase-level unary productions. Eliminating these unary productions from the search can have a large impact on downstream processing, depending on implementation details of the search. We apply our method to four parsing architectures and demonstrate how it is complementary to the cell-closing paradigm, as well as other pruning methods such as coarse-to-fine, agenda, and beam-search pruning.
Outline of chronohygiene.

Since chronotherapy already manipulates rhythmical functions, it is the important task of chronohygiene to outline the object of therapy i.e. health, from chronobiological points of view. Only on such a basis can chronohygiene be extended to the preventive provisions of health care and health education in regard to the biological time structure. Health can be characterized as an optimal state of harmonious time structure and its integration into the temporal orders of the environment. The circannual variations of an organism establish a seasonal risk cycle changing the inner preconditions of therapy as well. Moreover, chronohygiene must raise the question of whether the biological circannual rhythm is an integrating component of the human time organization, or if it may be levelled by civilization. Circadian variations of the organism not only modify the preconditions of therapy, but in particular those of activity and efficiency. The nocturnal maximum of functional economy normally is protected against exploitation by a simultaneous minimum of vigilance, which provides the nightly recovery. Therefore the destruction of this phase relationship by night-work must worsen recovery conditions. The disturbance of the time structure in the organism by night-work not only affects the circadian system, but faster rhythms as well. The phase position of the circadian rhythms is closely related to the individual responsiveness of the autonomous system as well as to the pulse-respiration-ratio. The latter can serve as a chronobiological criterion for evaluating suitability or risk of night- and shift-work. The effort of chronohygiene is based on the fact that disturbances of the time structure represent just a complementary aspect to disturbances of the spatial structure of the organism.
A Connectionist Symbol Manipulator that Discovers the Structure of Context-Free Languages

We present a neural net architecture that can discover hierarchical and recursive structure in symbol strings. To detect structure at multiple levels, the architecture has the capability of reducing symbols substrings to single symbols, and makes use of an external stack memory. In terms of formal languages, the architecture can learn to parse strings in an LR(O) context-free grammar. Given training sets of positive and negative exemplars, the architecture has been trained to recognize many different grammars. The architecture has only one layer of modifiable weights, allowing for a straightforward interpretation of its behavior.
Motion-Aware Gradient Domain Video Composition

For images, gradient domain composition methods like Poisson blending offer practical solutions for uncertain object boundaries and differences in illumination conditions. However, adapting Poisson image blending to video presents new challenges due to the added temporal dimension. In video, the human eye is sensitive to small changes in blending boundaries across frames and slight differences in motions of the source patch and target video. We present a novel video blending approach that tackles these problems by merging the gradient of source and target videos and optimizing a consistent blending boundary based on a user-provided blending trimap for the source video. Our approach extends mean-value coordinates interpolation to support hybrid blending with a dynamic boundary while maintaining interactive performance. We also provide a user interface and source object positioning method that can efficiently deal with complex video sequences beyond the capabilities of alpha blending.