Miracle-dz/UniFAR-FTUs huggingface dataset:
MessageGuard: A Browser-based Platform for Usable, Content-Based Encryption Research

This paper describes MessageGuard, a browser-based platform for research into usable content-based encryption. MessageGuard is designed to enable collaboration between security and usability researchers on long-standing research questions in this area. It significantly simplifies the effort required to work in this space and provides a place for research results to be shared, replicated, and compared with minimal confounding factors. MessageGuard provides ubiquitous encryption and secure cryptographic operations, enabling research on any existing web application, with realistic usability studies on a secure platform. We validate MessageGuard's compatibility and performance, and we illustrate its utility with case studies for Gmail and Facebook Chat.
Qualitative control of periodic solutions in piecewise affine systems; application to genetic networks

Hybrid systems, and especially piecewise affine (PWA) systems, are often used to model gene regulatory networks. In this paper we elaborate on previous work about control problems for this class of models, using also some recent results guaranteeing the existence and uniqueness of limit cycles, based solely on a discrete abstraction of the system and its interaction structure. Our aim is to control the transition graph of the PWA system to obtain an oscillatory behaviour, which is indeed of primary functional importance in numerous biological networks; we show how it is possible to control the appearance or disappearance of a unique stable limit cycle by hybrid qualitative action on the degradation rates of the PWA system, both by static and dynamic feedback, i.e. the adequate coupling of a controlling subnetwork. This is illustrated on two classical gene network modules, having the structure of mixed feedback loops.
Galois Substitution Counter Mode (GSCM)

In this paper, we present the Galois substitution counter mode (GSCM) of operation. GSCM is based on the Galois/counter mode (GCM). GSCM is an enhancement of GCM (specially in software implementations), which is characterized by its high throughput and low memory consumption in network applications.
ProTISA: a comprehensive resource for translation initiation site annotation in prokaryotic genomes

Correct annotation of translation initiation site (TIS) is essential for both experiments and bioinformatics studies of prokaryotic translation initiation mechanism as well as understanding of gene regulation and gene structure. Here we describe a comprehensive database ProTISA, which collects TIS confirmed through a variety of available evidences for prokaryotic genomes, including Swiss-Prot experiments record, literature, conserved domain hits and sequence alignment between orthologous genes. Moreover, by combining the predictions from our recently developed TIS post-processor, ProTISA provides a refined annotation for the public database RefSeq. Furthermore, the database annotates the potential regulatory signals associated with translation initiation at the TIS upstream region. As of July 2007, ProTISA includes 440 microbial genomes with more than 390 000 confirmed TISs. The database is available at http://mech.ctb. pku.edu. cn/protisa
A framework for developing research protocols for evaluation of microbial hazards and controls during production that pertain to the quality of agricultural water contacting fresh produce that may be consumed raw.

Agricultural water may contact fresh produce during irrigation and/or when crop protection sprays (e.g., cooling to prevent sunburn, frost protection, and agrochemical mixtures) are applied. This document provides a framework for designing research studies that would add to our understanding of preharvest microbial food safety hazards and control measures pertaining to agricultural water. Researchers will be able to use this document to design studies, to anticipate the scope and detail of data required, and to evaluate previously published work. This document should also be useful for evaluating the strength of existing data and thus should aid in identifying future research needs. Use of this document by the research community may lead to greater consistency or comparability than currently exists among research studies, which may ultimately facilitate direct comparison of hazards and efficacy of controls among different commodities, conditions, and practices.
Competition between CO and N2 Desorption from Interstellar Ices

Millimeter observations of pre- and protostellar cores show that the abundances of the gas-phase tracer molecules, C18O and N2H+, anticorrelate with each other and often exhibit "holes" where the density is greatest. These results are reasonably reproduced by astrochemical models, provided that the ratio between the binding energies of N2 and CO, RBE, is taken to be between 0.5 and 0.75. This Letter is the first experimental report of the desorption of CO and N2 from layered and mixed ices at temperatures relevant to dense cores, studied under ultrahigh vacuum laboratory conditions using temperature programmed desorption. From control experiments with pure ices, RBE = 0.923 ± 0.003, given Eb(N2-N2) = 790 ± 25 K and Eb(CO-CO) = 855 ± 25 K. In mixed (CO:N2 = 1:1) and layered (CO above or below N2) ice systems, both molecules become mobile within the ice matrix at temperatures as low as 20 K and appear miscible. Consequently, although a fraction of the deposited N2 desorbs at lower temperatures than CO, up to 50% of the N2 molecules leave the surface as the CO itself desorbs, a process not included in existing gas-grain models. This codesorption suggests that for a fraction of the frozen-out molecules, RBE is unity. The relative difference between the CO and N2 binding energies as derived from these experiments is therefore significantly less than that currently adopted in astrochemical models.
An Iranian roadmap for special protection scheme with challenges of wind farms integration

Flexibility of power system can increase by using of special protection scheme (SPS) rather than traditional protection systems. Implementation of SPS often can have the technical issues over than economic issues. This paper presents a new framework for analyze the SPS by considering of the economic and technical drivers. This might lead to the implementation of a special protection scheme in Iranian power system by considering of the integration of wind farms. As well as, maximum cost-effective integration of wind farms is a SPS capability. The proposed perspective shows the feasibility of the integration of wind farms in to the grid in presence of transmission congestions.
Mother's willingness to pay for her own and her child's health: a contingent valuation study in Taiwan.

We use the contingent valuation (CV) method to estimate mothers' willingness to pay (WTP) to protect themselves and their children from suffering a minor illness-a cold-in Taiwan. WTP is specified as a hedonic function of the duration and severity of the cold (measured alternatively by symptoms experienced and the Quality of Well-Being (QWB) index) and of respondents' socioeconomic characteristics. The average mother is willing to pay more to protect her child than herself from suffering a cold. Median WTP to avoid the average mother's and child's colds are US$37 and US$57, respectively. Adjusting for the greater duration and severity of the average mother's cold suggests that WTP to prevent comparable illnesses is approximately twice as large for the child as for the mother. We also find that mother's WTP is about 20% greater to prevent a son's than a daughter's illness.
On the Bragg Scattering Observed in L-Band Synthetic Aperture Radar Images of Flooded Rice Fields

This article presents the analysis of the Bragg scattering phenomenon which has been observed in the images of machine-planted rice paddies acquired by the JERS-1 L-band synthetic aperture radar (SAR). The simultaneous measurements of rice plants were made at the SAR data acquisition times. Large differences of 20-25 dB in image intensity between the transplanting and ripening stages are found to be dependent on the planting direction and bunch separation. This selective image enhancement is a result of the Bragg resonance backscatter due to the double-bounce of incident L-band microwave between the flooded water surface and periodically planted bunches of rice plants. Support for the idea of double-bounce scattering is provided by the decomposition analysis of L-band and X-band polarimetric Pi-SAR data; and a simple numerical simulation based on the physical optics model shows fairly good agreement with the JERS-1 SAR data. The results presented in this paper is mainly of academic interest, but a suggestion can be made on the selection of suitable microwave band for monitoring rice fields.
Linear programming upper bounds on permutation code sizes from coherent configurations related to the Kendall-tau distance metric

Recent interest on permutation rank modulation shows the Kendall-tau metric as an important distance metric. This note documents our first efforts to obtain upper bounds on optimal code sizes (for said metric) ala Delsarte's approach. For the Hamming metric, Delsarte's seminal work on powerful linear programming (LP) bounds have been extended to permutation codes, via association scheme theory. For the Kendall-tau metric, the same extension needs the more general theory of coherent configurations, whereby the optimal code size problem can be formulated as an extremely huge semidefinite programming (SDP) problem. Inspired by recent algebraic techniques for solving SDP's, we consider the dual problem, and propose an LP to search over a subset of dual feasible solutions. We obtain modest improvement over a recent Singleton bound due to Barg and Mazumdar. We regard this work as a starting point, towards fully exploiting the power of Delsarte's method, which are known to give some of the best bounds in the context of binary codes.
Exploring the sequence–structure relationship for amyloid peptides

Amyloid fibril formation is associated with misfolding diseases, as well as fulfilling a functional role. The cross-β molecular architecture has been reported in increasing numbers of amyloid-like fibrillar systems. The Waltz algorithm is able to predict ordered self-assembly of amyloidogenic peptides by taking into account the residue type and position. This algorithm has expanded the amyloid sequence space, and in the present study we characterize the structures of amyloid-like fibrils formed by three peptides identified by Waltz that form fibrils but not crystals. The structural challenge is met by combining electron microscopy, linear dichroism, CD and X-ray fibre diffraction. We propose structures that reveal a cross-β conformation with ‘steric-zipper’ features, giving insights into the role for side chains in peptide packing and stability within fibrils. The amenity of these peptides to structural characterization makes them compelling model systems to use for understanding the relationship between sequence, self-assembly, stability and structure of amyloid fibrils.
Abstract Representations and Frequent Pattern Discovery

We discuss the frequent pattern mining problem in a general setting. From an analysis of abstract representations, summarization and frequent pattern mining, we arrive at a generalization of the problem. Then, we show how the problem can be cast into the powerful language of algorithmic information theory. This allows us to formulate a simple algorithm to mine for all frequent patterns. 1
Extended phenotypes as signals

Animal signals may result from construction behaviour and can provide receivers with essential information in various contexts. Here we explore the potential benefits of extended phenotypes with a signalling function as compared to bodily ornaments and behavioural displays. Their independence of the body, their physical persistence and the morphological and cognitive conditions required for their construction allow unique communication possibilities. We classify various levels of information transfer by extended phenotype signals and explore the differences between secreted signals and signals resulting from collection and construction, which usually involve higher behavioural complexity. We examine evolutionary pathways of extended phenotypes with a signalling function with help of a comparative evaluation and conclude that often constructions first provide a direct fitness benefit, with a signalling function becoming more and more prominent during evolutionary progression. The abundance and variability of extended phenotypes as signals is impressive and provides unique possibilities for animal communication research.
Regulation of macrophage apoE secretion and sterol efflux by the LDL receptor Published, JLR Papers in Press, November 1, 2006.

Factors that regulate apolipoprotein E (apoE) secretion by macrophages will have important effects on vessel wall lipid flux and atherosclerosis. Macrophages express the LDL receptor, which binds apoE with high affinity and could thereby affect the net secretion of apoE from macrophages. In these studies, we demonstrate that treatment of J774 macrophages transfected to constitutively express a human apoE3 cDNA with simvastatin, to increase LDL receptor activity, reduces the secretion of apoE. To further examine the relationship between LDL receptor expression and apoE secretion from macrophages, mouse peritoneal macrophages (MPMs) were isolated from mice with constitutively high expression of human LDL receptor to increase overall LDL receptor expression by 2- to 3-fold. Cells with increased LDL receptor expression also showed reduced apoE secretion compared with MPMs with basal LDL receptor expression. The effect of changes in LDL receptor expression on apoE secretion was isoform-specific, with greater reduction of apoE4 compared with apoE3 secretion and no reduction of apoE2 secretion, paralleling the known affinity of each isoform for LDL receptor binding. The effect of the LDL receptor on apoE secretion for each isoform was further reflected in LDL receptor-dependent changes in apoE-mediated cholesterol efflux. These results establish a regulatory interaction between two branches of macrophage sterol homeostatic pathways that could facilitate a rapid response to changes in macrophage sterol content relative to need.
Evaluating Complex Semantic Artifacts

Evaluating complex Natural Language Processing (NLP) systems can prove extremely difficult. In many cases, the best one can do is to evaluate these systems indirectly, by looking at the impact they have on the performance of the downstream use case. For complex end-to-end systems, these metrics are not always enlightening, especially from the perspective of NLP failure analysis, as component interaction can obscure issues specific to the NLP technology. We present an evaluation program for complex NLP systems designed to produce meaningful aggregate accuracy metrics with sufficient granularity to support active development by NLP specialists. Our goals were threefold: to produce reliable metrics, to produce useful metrics and to produce actionable data. Our use case is a graph-based Wikipedia search index. Since the evaluation of a complex graph structure is beyond the conceptual grasp of a single human judge, the problem needs to be broken down. Slices of complex data reflective of coherent Decision Points provide a good framework for evaluation using human judges (Medero et al., 2006). For NL semantics, there really is no substitute. Leveraging Decision Points allows complex semantic artifacts to be tracked with judge-driven evaluations that are accurate, timely and actionable.
Implementation of stiff virtual walls in force-reflecting interfaces

The performance of a haptic interface is often reported in terms of the dynamic range of impedances it may represent. At the low end, the range is typically limited by inherent dynamics of the interface device, such as inertia and friction. At the high end, the range is typically limited by system stability. In a number of the applications, the principal limitation has proven to be the achievable upper limit on impedance. Therefore, a benchmark problem of considerable importance is the implementation of a stiff "wall". Contacting a wall may be described as the reversible transition from a region of very low impedance to one of very high impedance. A theoretical analysis (supplemented with discussion of experimental and simulation results) of stiff wall implementation is presented. The main result is a criterion for the passivity of a virtual wall in terms of two nondimensional parameters. <<ETX>>
Abciximab Reduces Monocyte Tissue Factor in Carotid Angioplasty and Stenting

Background and Purpose— Abciximab, a nonselective glycoprotein IIb/IIIa inhibitor, was shown to reduce peri-interventional stroke rate in carotid stenting. We evaluated the effect of adjunct abciximab therapy on monocyte-platelet cross talk and neurological deficit in unprotected carotid stenting and compared its efficacy with distal filter protection. Methods— Fifty patients were randomized to either standard antithrombotic therapy (n=30) consisting of aspirin, clopidogrel, and heparin or adjunct bolus (0.25 mg/kg) and 12-hour infusion (0.125 &mgr;g · kg−1 · min−1) of abciximab (n=20). A third cohort of patients was stented with filter protection (n=30). Monocyte-platelet aggregate formation and monocyte tissue factor expression were determined by whole blood flow cytometry, and F1.2 generation and soluble CD40 ligand (sCD40L) were determined by immunoassay. Results— The incidence of peri-interventional ischemic episodes (23% versus 10%; P =0.2) and the number of de novo ischemic lesions detected by diffusion-weighted MRI (47% versus 30%; P =0.17) were not significantly different between standard antithrombotic therapy and adjunct abciximab but were reduced with filter protection (P =0.023). However, the number of transient ischemic attacks was lower (P =0.05) and the National Institutes of Health Stroke Score rapidly decreased in patients with adjunct abciximab. This clinical improvement was paralleled by a reduction in the postinterventional percentage of activated monocyte-platelet aggregates (CD62P+/CD14+; P =0.018) and the number of tissue factor–positive monocytes (TF+/CD14+; P =0.005). Both abciximab and filter protection suppressed F1.2 generation and significantly reduced sCD40L. Conclusions— Abciximab limits thrombus propagation and thrombus stabilization after carotid stenting by reducing monocyte-platelet cross talk and sCD40L. Although abciximab seems inferior to filter devices in peri-interventional cerebral protection, it may be considered in patients who do not allow placement of protection devices.
Herpes Simplex Virus Type 1/Adeno-Associated Virus Hybrid Vectors Mediate Site-Specific Integration at the Adeno-Associated Virus Preintegration Site, AAVS1, on Human Chromosome 19

ABSTRACT Herpes simplex virus type 1 (HSV-1)-based amplicon vectors have a large transgene capacity and can efficiently infect many different cell types. One disadvantage of HSV-1 vectors is their instability of transgene expression. By contrast, vectors based on adeno-associated virus (AAV) can either persist in an episomal form or integrate into the host cell genome, thereby supporting long-term gene expression. AAV expresses four rep genes, rep68, -78, -40, and -52. Of those, rep68 or rep78 are sufficient to mediate site-specific integration of the AAV DNA into the host cell genome. The major disadvantage of AAV vectors is the small transgene capacity (∼4.6 kb). In this study, we constructed HSV/AAV hybrid vectors that contained, in addition to the standard HSV-1 amplicon elements, AAV rep68, rep78, both rep68 and -78, or all four rep genes and a reporter gene that was flanked by the AAV inverted terminal repeats (ITRs). Southern blots of Hirt DNA from cells transfected with the hybrid vectors and HSV-1 helper DNA demonstrated that both the AAV elements and the HSV-1 elements were functional in the context of the hybrid vector. All hybrid vectors could be packaged into HSV-1 virions, although those containing rep sequences had lower titers than vectors that did not. Site-specific integration at AAVS1 on human chromosome 19 was directly demonstrated by PCR and sequence analysis of ITR-AAVS1 junctions in hybrid vector-transduced 293 cells. Cell clones that stably expressed the transgene for at least 12 months could easily be isolated without chemical selection. In the majority of these clones, the transgene cassette was integrated at AAVS1, and no sequences outside the ITR cassette, rep in particular, were present as determined by PCR, ITR rescue/replication assays, and Southern analysis. Some of the clones contained random integrations of the transgene cassette alone or together with sequences outside the ITR cassette. These data indicate that the long-term transgene expression observed following transduction with HSV/AAV hybrid vectors is, at least in part, supported by chromosomal integration of the transgene cassette, both randomly and site specifically.
Regularised Centre Recruitment in Radial Basis Function Networks

and this could either be applied between choosing sets of centres with multiple runs of RFS or between choosing individual centres within one run of RFS. In the latter case this requires continual adjustment of the matrix G m to account for the changing value of. I tried this with the example from gure 1 and from an initial value of = 1 the re-estimations converged to a value close to 0:02 after selecting the rst few centres. Perhaps this explains why my original guess of = 0:02 worked well to begin with! It is also possible to attempt to choose the best value of r (the basis function radii in (5)) from the training data. In the case of the above Bayesian scheme it is not possible to derive a re-estimation formula for r and it is necessary to resort to non-linear optimisation techniques to maximise the evidence. However, it is simpler to use a heuristic to set r (examples are in Moody and Darken (1989)) and then try to optimise. 7 Conclusions Ordinary centre selection terminated using a xed threshold on the unexplained variance and without any regularisation is liable to overrtting even when the true noise variance is known. Cross-validation as a termination criterion reduces the tendency to overrt but has no eeect in areas of the input space outside the training set. If, in addition to cross-validation, zero-order regularisation is used in the selection process then the behaviour of the tted function outside the training set is more constrained and this may lead to better extrapolation performance for target functions which are known a priori to be smooth. Centre selection, cross-validation and regularisation are an advantageous combination in RBF networks. Selection economises on centres, cross-validation avoids gross overrt and regularisation smooths the t outside the training set. Although regularisation alone may suuce to avoid overrt, parsimony is often an important consideration in practical applications. This is particularly true in high-dimensional spaces where local methods, like RBF networks, suuer from the \curse of dimensionality". Figure 3: Average RMS errors for OLS (solid curve) and RFS (dashed curve) using the naive stopping criterion (20) for diierent values of ^. The set of test points used covered the same regions from which the samples were drawn. to modify the method of section 4 to be able backwardly eliminate as well as forwardly select. However, parsimony, and not optimality, is …