Miracle-dz/UniFAR-FTUs huggingface dataset:
Characterization and expression of the Escherichia coli Mrr restriction system

The mrr gene of Escherichia coli K-12 is involved in the acceptance of foreign DNA which is modified. The introduction of plasmids carrying the HincII, HpaI, and TaqI R and M genes is severely restricted in E. coli strains that are Mrr+. A 2-kb EcoRI fragment from the plasmid pBg3 (B. Sain and N. E. Murray, Mol. Gen. Genet. 180:35-46, 1980) was cloned. The resulting plasmid restores Mrr function to mrr strains of E. coli. The boundaries of the mrr gene were determined from an analysis of subclones, and plasmids with a functional mrr gene produce a polypeptide of 33.5 kDa. The nucleotide sequence of the entire fragment was determined; in addition to mrr, it includes two open reading frames, one of which encodes part of the hsdR. By using Southern blot analysis, E. coli RR1 and HB101 were found to lack the region containing mrr. The acceptance of various cloned methylases in E. coli containing the cloned mrr gene was tested. Plasmid constructs containing the AccI, CviRI, HincII, Hinfl (HhaII), HpaI, NlaIII, PstI, and TaqI N6-adenine methylases and SssI and HhaI C5-cytosine methylases were found to be restricted. Plasmid constructs containing 16 other adenine methylases and 12 cytosine methylases were not restricted. No simple consensus sequence causing restriction has been determined. The Mrr protein has been overproduced, an antibody has been prepared, and the expression of mrr under various conditions has been examined. The use of mrr strains of E. coli is suggested for the cloning of N6-adenine and C5-cytosine methyl-containing DNA.
Speech recognition using HMM-state confusion characteristics

In our previous work, we proposed a re-entry modeling of missing phonemes which are lost during search process. In the re-entry modeling, the recognition results are postprocessed and originally recognized phoneme sequences are converted to new phoneme sequences using HMM-state confusion characteristics spanning several phonemes. We con(cid:12)rmed that HMM-state confusions are e(cid:11)ective for the re-entry modeling. In this paper, we propose a re-entry modeling during recognition us-ing a multiple pronunciation dictionary where pronunciations are added using HMM-state confusion characteristics. The pronunciations are added considering part-of-speech (POS) dependency of confusion characteristics. As a result of continuous recognition experiments, we con(cid:12)rmed that the following two points are e(cid:11)ective to improve word recognition rates:
Trends in dietary intakes of vitamins A, C and E among Japanese men and women from 1974 to 2001

Abstract Objective To investigate long-term trends in dietary intakes of vitamins A, C and E in Japanese adults. Design Time series by community-based nutrition survey. Setting Two rural communities (Ikawa and Kyowa) between 1974 and 2001 in Japan. Subjects A total of 3713 men and 3726 women aged 40–69 years. Methods Dietary intake data were collected by the 24 h dietary recall. Results In Ikawa, mean intake of vitamin A (β-carotene and retinol) increased by 13–40 %; vitamins C and E increased by approximately 23–33 % among men and women from 1974–1977 to 1998–2000. In Kyowa, mean intake of vitamin A, primarily retinol, increased by 13–21 % among men and women; vitamin C from fruits decreased by 16 % among men; and vitamin E increased by 29 % among women from 1982–1986 to 1998–2001. Mean intake of vitamin E in the latest survey period was lower than the Adequate Intake among men and women in both communities. Generally, there were increased intakes of β-carotene and vitamin C from green/yellow and other vegetables; increased retinol intake from fish/shellfish, eggs, milk/dairy products and fats/oils; and increased vitamin E intake from green/yellow and other vegetables, fish/shellfish, eggs, milk/dairy products and fats/oils. Conclusions Mean intakes of the antioxidant vitamins A, C and E increased among middle-aged Japanese men and women between the 1970s and the 1990s except for decreased vitamin C among Kyowa men. The lower mean intake of vitamin E than the Adequate Intake should be considered a potential public health issue for the prevention of CVD.
FEATURES: Real-time adaptive feature and document learning for web search

In this article we report our research on building FEATURES—an intelligent web search engine that is able to perform real-time adaptive feature (i.e., keyword) and document learning. Not only does FEATURES learn from the user’s document relevance feedback, but it also automatically extracts and suggests indexing keywords relevant to a search query and learns from the user’s keyword relevance feedback so that it is able to speed up its search process and to enhance its search performance. We design two efficient and mutual-benefiting learning algorithms that work concurrently, one for feature learning and the other for document learning. FEATURES employs these algorithms together with an internal index database and a real-time meta-searcher to perform adaptive real-time learning to find desired documents with as little relevance feedback from the user as possible. The architecture and performance of FEATURES are also discussed.
Reduced‐complexity spatial and temporal processing of underwater acoustic communication signals

Multichannel processing of high‐speed underwater acoustic communication signals requires computationally intensive receiver algorithms. The size of adaptive filters, determined by the extent of ocean multipath, increases with signaling rate and limits system performance through large noise enhancement and increased sensitivity of computationally efficient algorithms to numerical errors. To overcome these limitations, reduction in receiver complexity is achieved by exploiting the relationship between optimal diversity combining and beamforming. Under relatively simple conditions, two adaptive receivers, one based on diversity combining which does not rely on any spatial signal distribution, and the other based on optimal beamforming, are shown to achieve the same performance. The beamforming approach, however, leads to a receiver of lower complexity. Carrying these observations over to a general case of broadband transmission through an unknown channel, a fully adaptive receiver is developed which incorpor.
Temperature aware energy-reliability trade-offs for mapping of throughput-constrained applications on multimedia MPSoCs

This paper proposes a design-time (offline) analysis technique to determine application task mapping and scheduling on a multiprocessor system and the voltage and frequency levels of all cores (offline DVFS) that minimize application computation and communication energy, simultaneously minimizing processor aging. The proposed technique incorporates (1) the effect of the voltage and frequency on the temperature of a core; (2) the effect of neighboring cores' voltage and frequency on the temperature (spatial effect); (3) pipelined execution and cyclic dependencies among tasks; and (4) the communication energy component which often constitutes a significant fraction of the total energy for multimedia applications. The temperature model proposed here can be easily integrated in the design space exploration for multiprocessor systems. Experiments conducted with MPEG-4 decoder on a real system demonstrate that the temperature using the proposed model is within 5% of the actual temperature clearly demonstrating its accuracy. Further, the overall optimization technique achieves 40% savings in energy consumption with 6% increase in system lifetime.
Evolution of the Internet-Dense Structure

As the Internet autonomous sytem (AS)-level topology grows over time, some of its structural properties remain unchanged. Such time-invariant properties are generally interesting because they tend to reflect some fundamental processes or constraints behind Internet growth. As has been shown before, the time-invariant structural properties of the Internet include some most basic ones, such as the degree distribution or clustering. Here, we add to this time-invariant list a nontrivial property— -dense decomposition. This property is derived from a recursive form of edge multiplicity, defined as the number of triangles that share a given edge. We show that after proper normalization, the -dense decomposition of the Internet has remained stable over the last decade, even though the Internet size has approximately doubled, and so has the -density of its -densest core. This core consists mostly of content providers peering at Internet eXchange Points, and it only loosely overlaps with the high-degree or high-rank AS core, consisting mostly of tier-1 transit providers. We thus show that high degrees and high -densities reflect two different Internet-specific properties of ASs (transit versus content providers). As a consequence, even though degrees and -densities of nodes are correlated, the relative fluctuations are strong, and related to that, random graphs with the same degree distribution or even degree correlations as in the Internet, do not reproduce its -dense decomposition. Therefore an interesting open question is what Internet topology models or generators can fully explain or at least reproduce the -dense properties of the Internet.
Multi-view proxemics: distance and position sensitive interaction

We present work at a previously unexplored intersection of two research areas: proxemic interaction and multi-view display technologies. Multi-view proxemic systems concurrently deliver distinct views from a single display to different viewers depending on a combination of their angle to the display and their distance from it. In this paper we demonstrate the capability to design such an interactive system using only commodity hardware and software. We describe two systems and present results of two user studies with 18 participants. The studies are based on two real-world scenarios of a departure board and a video player (with sub-titles). Our results show that multi-view proxemic systems are accurate and that users find them useful and would use them if they were available. We also discuss some of the design and technological implications of our work.
Calcium-dependent Epidermal Growth Factor Receptor Transactivation Mediates the Angiotensin II-induced Mitogen-activated Protein Kinase Activation in Vascular Smooth Muscle Cells*

We have recently reported that angiotensin II (Ang II)-induced mitogen-activated protein kinase (MAPK) activation is mainly mediated by Ca2+-dependent activation of a protein tyrosine kinase through Gq-coupled Ang II type 1 receptor in cultured rat vascular smooth muscle cells (VSMC). In the present study, we found Ang II rapidly induced the tyrosine phosphorylation of the epidermal growth factor (EGF) receptor and its association with Shc and Grb2. These reactions were inhibited by the EGF receptor kinase inhibitor, AG1478. The Ang II-induced phosphorylation of the EGF receptor was mimicked by a Ca2+ionophore and completely inhibited by an intracellular Ca2+chelator. Thus, AG1478 abolished the MAPK activation induced by Ang II, a Ca2+ ionophore as well as EGF but not by a phorbol ester or platelet-derived growth factor-BB in the VSMC. Moreover, Ang II induced association of EGF receptor with catalytically active c-Src. This reaction was not affected by AG1478. These data indicate that Ang II induces Ca2+-dependent transactivation of the EGF receptor which serves as a scaffold for pre-activated c-Src and for downstream adaptors, leading to MAPK activation in VSMC.
Description of Staphylococcus Serine Protease (ssp) Operon in Staphylococcus aureus and Nonpolar Inactivation of sspA-Encoded Serine Protease

ABSTRACT Signature tagged mutagenesis has recently revealed that the Ssp serine protease (V8 protease) contributes to in vivo growth and survival of Staphylococcus aureus in different infection models, and our previous work indicated that Ssp could play a role in controlling microbial adhesion. In this study, we describe an operon structure within the ssp locus of S. aureusRN6390. The ssp gene encoding V8 protease is designated assspA, and is followed by sspB, which encodes a 40.6-kDa cysteine protease, and sspC, which encodes a 12.9-kDa protein of unknown function. S. aureus SP6391 is an isogenic derivative of RN6390, in which specific loss of SspA function was achieved through a nonpolar allelic replacement mutation. In addition to losing SspA, the culture supernatant of SP6391 showed a loss of 22- to 23-kDa proteins and the appearance of a 40-kDa protein corresponding to SspB. Although the 40-kDa SspB protein could degrade denatured collagen, our data establish that this is a precursor form which is normally processed by SspA to form a mature cysteine protease. Culture supernatant of SP6391 also showed a new 42-kDa glucosaminidase and enhanced glucosaminidase activity in the 29 to 32 kDa range. Although nonpolar inactivation of sspA exerted a pleiotropic effect, S. aureus SP6391 exhibited enhanced virulence in a tissue abscess infection model relative to RN6390. Therefore, we conclude that SspA is required for maturation of SspB and plays a role in controlling autolytic activity but does not by itself exert a significant contribution to the development of tissue abscess infections.
Compelling Engagements: Feminism, Rape Law and Romance Fiction

Introduction: feminism, rape law and romance fiction Section I: Enduring Stabilities Consent and intent: gendering subjectivity in rape law Desire and love: gendering subjectivity in Harlequin Mills and Boon fiction Section II: The Fortitude of Heroines Victims and the dis/qualification of rape complainants Heroines and the in/security of romance readers Section III: Fear and Hope False complain(an)ts and other legal fictions Preferred readers and other romances Conclusion: compelling engagements Works cited
MINRES-QLP: A Krylov Subspace Method for Indefinite or Singular Symmetric Systems

CG, SYMMLQ, and MINRES are Krylov subspace methods for solving symmetric systems of linear equations. When these methods are applied to an incompatible system (that is, a singular symmetric least-squares problem), CG could break down and SYMMLQ's solution could explode, while MINRES would give a least-squares solution but not necessarily the minimum-length (pseudoinverse) solution. This understanding motivates us to design a MINRES-like algorithm to compute minimum-length solutions to singular symmetric systems. MINRES uses QR factors of the tridiagonal matrix from the Lanczos process (where $R$ is upper-tridiagonal). MINRES-QLP uses a QLP decomposition (where rotations on the right reduce $R$ to lower-tridiagonal form). On ill-conditioned systems (singular or not), MINRES-QLP can give more accurate solutions than MINRES. We derive preconditioned MINRES-QLP, new stopping rules, and better estimates of the solution and residual norms, the matrix norm, and the condition number.
Harvesting Wiki Consensus: Using Wikipedia Entries as Vocabulary for Knowledge Management

Vocabularies that provide unique identifiers for conceptual elements of a domain can improve precision and recall in knowledge-management applications. Although creating and maintaining such vocabularies is generally hard, wiki users easily manage to develop comprehensive, informal definitions of terms, each one identified by a URI. Here, the authors show that the URIs of Wikipedia entries are reliable identifiers for conceptual entities. They also demonstrate how Wikipedia entries can be used for annotating Web resources and knowledge assets and give precise estimates of the amount of Wikipedia URIs in terms of the popular Proton ontology's top-level concepts.
School subjects and curriculum change : studies in curriculum history

Part 1 Becoming an academic subject - studies in the social history of the school curriculum: the growth of the English education system - changing patterns of curricula and examinations academic "subjects" and curriculum change. Part 2 School subjects - patterns of internal evolution: biology - aspects of subject history geography - aspects of subject history. Part 3 Relationships between subjects - the territorial nature of subject conflict: construction of an A level syllabus the defence of geography and biology the negotiation of environmental studies. Part 4 Conclusions, complexities and conjectures.
IBT: A Real-time Tempo and Beat Tracking System

This paper describes a tempo induction and beat tracking system based on the efficient strategy (initially introduced in the BeatRoot system [Dixon S., “Automatic extraction of tempo and beat from expressive performances.” Journal of New Music Research, 30(1):39-58, 2001]) of competing agents processing musical input sequentially and considering parallel hypotheses regarding tempo and beats. In this paper, we propose to extend this strategy to the causal processing of continuous input data. The main reasons for this are threefold: providing more robustness to potentially noisy input data, permitting the parallel consideration of a number of low-level frame-based features as input, and opening the way to real-time uses of the system (as e.g. for a mobile robotic platform). The system is implemented in C++, permitting faster than real-time processing of audio data. It is integrated in the MARSYAS framework, and is therefore available under GPL for users and/or researchers. Detailed evaluation of the causal and non-causal versions of the system on common benchmark datasets show performances reaching those of state-of-the-art beat trackers. We propose a series of lines for future work based on careful analysis of the results.
Workers Who Decline Employment-Related Health Insurance

Background:Families of workers who decline coverage represent a substantial share of the uninsured and publicly-insured population in the United States. Objective:We examined health status, access to health care, utilization, and expenditures among families that declined health insurance coverage offered by employers using data from the Medical Expenditure Panel Survey for 2001 and 2002. Results:We found differences in insurance status for adults and children among families with offers. We found that among low-income families with offers, children are less likely to have private insurance compared with adults. However, the majority of children who decline private insurance end up with public coverage, whereas most of adults who decline offers remain uninsured. Decliners are more likely to report poor health, yet they are also less likely to have high cost medical conditions. Families declining coverage have weaker preferences for insurance than families that take up. Although access to care is lower among the decliners who remain uninsured, decliners with public insurance have similar access to care as those with private insurance. Families turning down coverage are more likely to face high expenditure burdens as a percentage of income and more likely to have financial barriers to care. Families who decline coverage rely heavily on the safety net. Public sources and uncompensated care account for 72% of total expenditures among adults who decline coverage. Conclusions:Our results suggest that policy initiatives aimed at increasing take up among workers need to take into account the incentives workers face given the availability of care through public sources and uncompensated care.
Small-Bowel Capsule Endoscopy in Patients with Suspected Crohn's Disease—Diagnostic Value and Complications

Background. The aim of this work was to assess the value of capsule enteroscopy in the diagnosis of patients with suspected Crohn's Disease (CD). Methods. This was a retrospective study in a single tertiary care centre involving patients undergoing capsule enteroscopy for suspected CD. Patients taking nonsteroidal anti inflammatory drugs during the thirty preceding days or with a follow-up period of less than six months were excluded. Results. Seventy eight patients were included. The endoscopic findings included mucosal breaks in 50%, ulcerated stenosis in 5%, and villous atrophy in 4%. The diagnosis of CD was established in 31 patients. The sensitivity, specificity, positive and negative predictive value of the endoscopic findings were 93%, 80%, 77%, and 94%, respectively. Capsule retention occurred in four patients (5%). The presence of ulcerated stenosis was significantly more frequent in patients with positive inflammatory markers. The diagnostic yield of capsule enteroscopy in patients with negative ileoscopy was 56%, with a diagnostic acuity of 93%. Conclusions. Small bowel capsule endoscopy is a safe and valid technique for assessing patients with suspected CD. Capsule retention is more frequent in patients with positive inflammatory markers. Patients with negative ileoscopy and suspected CD should be submitted to capsule enteroscopy.
Electrochemical Oxidation of Ascorbic Acid on Gold Nanoparticles Coated Pt

Nanomaterials exhibit unique chemical [1-3], physical [47] and electronic [8] properties that are distinctly different from those of bulk materials and depend on size, shape and surface composition of the nanostructured materials. Nanomaterials of noble metals are finding worldwide interest in research communities [9-12]. Several reviews have highlighted the role of metal nanoparticles in catalysis [13-15]. The small size of the nanoparticles endows them with a high surface area, providing more active sites to catalyse reactions and with the ability to electronically interact with the reactant molecules, providing significant improvement in both detection and catalytic capabilities. Because of these properties, nanoparticles are finding applications in electroanalysis and electrochemical based sensors. In electrochemical experiments, nanoparticles based electrodes are rapidly replacing the conventional macroelectrodes because of the large effective surface area, increased mass transport, high catalytic activity and the ability to exert control over the local environment at the nanoparticles-modified electrode surface [16]. Gold nanoparticles have found applications as catalysts and biosensors in various chemical and biological reactions of interest, including biological labeling in medical imaging, because of the nanoparticles’ biocompatibility and easy functionalization of the surfaces. The surface of the gold nanoparticles is generally functionalized to prepare sensors, but some of the analytes can be detected at the nanoparticles-modified electrode. Electrochemical deposition is commonly used to synthesize and deposit metal nanoparticles onto the substrate simultaneously, with easy control of particle morphology. Therefore, electrochemical deposition is a potentially powerful and convenient technique, to regulate catalytic properties of the nanoparticles. This paper describes the electrochemical oxidation of ascorbic acid on nanostructured gold coated Pt electrode. The dependence of peak current (i p ) and peak potential (E p ) of ascorbic acid oxidation, on the numbers of cyclic voltammetry (CV) cycles used for gold deposition was studied.
Mid-range Ca 2 þ signalling mediated by functional coupling between store-operated Ca 2 þ entry and IP 3-dependent Ca 2 þ release

The versatility and universality of Ca2þ signals stem from the breadth of their spatial and temporal dynamics. Spatially, Ca2þ signalling is well studied in the microdomain scale, close to a Ca2þ channel, and at the whole-cell level. However, little is known about how local Ca2þ signals are regulated to specifically activate spatially distant effectors without a global Ca2þ rise. Here we show that an intricate coupling between the inositol 1,4,5 trisphosphate (IP3) receptor, SERCA pump and store-operated Ca2þ entry (SOCE) allows for efficient mid-range Ca2þ signalling. Ca2þ flowing through SOCE is taken up into the ER lumen by the SERCA pump, only to be re-released by IP3Rs to activate distal Ca 2þ -activated Cl channels (CaCCs). This CaCC regulation contributes to setting the membrane potential of the cell. Hence functional coupling between SOCE, SERCA and IP3R limits local Ca 2þ diffusion and funnels Ca2þ through the ER lumen to activate a spatially separate Ca2þ effector. DOI: 10.1038/ncomms4916