Miracle-dz/UniFAR-FTUs huggingface dataset:
Electronic Reprint Biological Crystallography Structure of the N-terminal Fragment of Escherichia Coli Lon Protease Biological Crystallography Structure of the N-terminal Fragment of Escherichia Coli Lon Protease

Author(s) of this paper may load this reprint on their own web site or institutional repository provided that this cover page is retained. Republication of this article or its storage in electronic databases other than as specified above is not permitted without prior permission in writing from the IUCr. Acta Crystallographica Section D: Biological Crystallography welcomes the submission of papers covering any aspect of structural biology, with a particular emphasis on the structures of biological macromolecules and the methods used to determine them. Reports on new protein structures are particularly encouraged, as are structure–function papers that could include crystallographic binding studies, or structural analysis of mutants or other modified forms of a known protein structure. The key criterion is that such papers should present new insights into biology, chemistry or structure. Papers on crystallographic methods should be oriented towards biological crystallography, and may include new approaches to any aspect of structure determination or analysis. The structure of a recombinant construct consisting of residues 1–245 of Escherichia coli Lon protease, the proto-typical member of the A-type Lon family, is reported. This construct encompasses all or most of the N-terminal domain of the enzyme. The structure was solved by SeMet SAD to 2.6 A ˚ resolution utilizing trigonal crystals that contained one molecule in the asymmetric unit. The molecule consists of two compact subdomains and a very long C-terminal-helix. The structure of the first subdomain (residues 1–117), which consists mostly of-strands, is similar to that of the shorter fragment previously expressed and crystallized, whereas the second subdomain is almost entirely helical. The fold and spatial relationship of the two subdomains, with the exception of the C-terminal helix, closely resemble the structure of BPP1347, a 203-amino-acid protein of unknown function from Bordetella parapertussis, and more distantly several other proteins. It was not possible to refine the structure to satisfactory convergence; however, since almost all of the Se atoms could be located on the basis of their anomalous scattering the correctness of the overall structure is not in question. The structure reported here was also compared with the structures of the putative substrate-binding domains of several proteins, showing topological similarities that should help in defining the binding sites used by Lon substrates. PDB Reference: N-terminal fragment of Lon protease, 3ljc.
Sliding-mode state observers for multi-output nonlinear systems with bounded noises on dynamics and measurements

A full-order sliding-mode state observer for a class of nonlinear continuous-time dynamic systems is proposed and conditions for the stability of the estimation error in the absence of noises are provided. If the system is affected by bounded disturbances, under such conditions the existence of an attractive invariant set for the estimation error is ensured. The design of the observer can be made via LMI techniques. Numerical results are reported to show the effectiveness of the proposed approach.
Navigating visually impaired travelers in a large train station using smartphone and bluetooth low energy

People with visual impairments face challenges when navigating indoor environments, such as train stations and shopping malls. Prior approaches either require dedicated hardware that is expensive and bulky or may not be suitable for such complex spaces. This paper aims to propose a practical solution that enables blind travelers to navigate a complex train station independently using a smartphone without the need for any special hardware. Utilizing Bluetooth Low Energy (BLE) technology and a smartphone's built-in compass, we developed StaNavi -- a navigation system that provides turn-by-turn voice directions inside Tokyo Station, one of the world's busiest train stations, which has more than 400,000 passengers daily. StaNavi was iteratively co-designed with blind users to provide features tailored to their needs that include interfaces for one-handed use while walking with a cane and a route overview to provide a picture of the entire journey in advance. It also offers cues that help users orient themselves in convoluted paths or open spaces. A field test with eight blind users demonstrates that all users could reach given destinations in real-life scenarios, showing that our system was effective in a complex and highly crowded environment and has great potential for large-scale deployment.
Bad Phages in Good Bacteria: Role of the Mysterious orf63 of λ and Shiga Toxin-Converting Φ24B Bacteriophages

Lambdoid bacteriophages form a group of viruses that shares a common schema of genome organization and lifecycle. Some of them can play crucial roles in creating the pathogenic profiles of Escherichia coli strains. For example, Shiga toxin-producing E. coli (STEC) acquired stx genes, encoding Shiga toxins, via lambdoid prophages (Stx phages). The results obtained so far present the evidence for the relation between the exo-xis region of the phage genome and lambdoid phage development, however molecular mechanisms of activities of the exo-xis genes' products are still unknown. In view of this, we decided to determine the influence of the uncharacterized open reading frame orf63 of the exo-xis region on lambdoid phages development using recombinant prophages, λ and Stx phage Φ24B. We have demonstrated that orf63 codes for a folded protein, thus, it is a functional gene. NMR spectroscopy and analytical gel filtration were used to extend this observation further. From backbone chemical shifts, Orf63 is oligomeric in solution, likely a trimer and consistent with its small size (63 aa.), is comprised of two helices, likely intertwined to form the oligomer. We observed that the deletion of phage orf63 does not impair the intracellular lambdoid phage lytic development, however delays the time and decreases the efficiency of prophage induction and in consequence results in increased survival of E. coli during phage lytic development. Additionally, the deletion of phage orf63 negatively influences expression of the major phage genes and open reading frames from the exo-xis region during prophage induction with hydrogen peroxide. We conclude, that lambdoid phage orf63 may have specific functions in the regulation of lambdoid phages development, especially at the stage of the lysis vs. lysogenization decision. Besides, orf63 probably participates in the regulation of the level of expression of essential phage genes and open reading frames from the exo-xis region during prophage induction.
Comparison of Optical Flow Algorithms for Speed Determination of Moving Objects

In this paper, we present a semi real-time vehicle tracking algorithm to determine the speed of the vehicles in traffic from traffic cam video. The results of this work can be used for traffic control, security and safety both by government agencies and commercial organizations. In this paper a method is described for tracking moving objects from a sequence of video frame. This method is implemented by using optical flow (Horn-Schunck)and (Lucas-Kanade) in mat lab and Simulink. It has a variety of uses, some of which are: human computer interaction, security and surveillance, video communication and compression, augmented reality, traffic control, medical imaging and video editing. Segmentation is performed to detect the object after reducing the noise from that scene. The object is tracked by plotting a rectangular bounding box around it in each frame. The velocity of the object is determined by calculating the distance that the object moved in a sequence of frames with respect to the frame rate that the video is recorded. Comparison and performance analysis of algorithms based on psnr and average angular error is done.
HIFOO - A MATLAB package for fixed-order controller design and H ∞ optimization

Abstract H∞ controller design for linear systems is a difficult, nonconvex and typically nonsmooth (nondifferentiable) optimization problem when the order of the controller is fixed to be less than that of the open-loop plant, a typical requirement in e.g. embedded aerospace control systems. In this paper we describe a new MATLAB package called HIFOO, aimed at solving fixed-order stabilization and local optimization problems. It depends on a new hybrid algorithm for nonsmooth, nonconvex optimization based on several techniques, namely quasi-Newton updating, bundling and gradient sampling. The user may request HIFOO to optimize one of several objectives, including H∞ norm, which requires either the Control System Toolbox for MATLAB or, for much better performance, the linorm function in the SLICOT package. No other external package is required, but the quadratic programming code quadprog from either MOSEK or the Optimization Toolbox for MATLAB is recommended. Numerical experiments on benchmark problem instances from the COMPleib database indicate that HIFOO could be an efficient and reliable computer-aided control system design (CACSD) tool, with a potential for realistic industrial applications.
Why Linear (and Piecewise Linear) Models Often Successfully Describe Complex Non-Linear Economic and Financial Phenomena: A~Fuzzy-Based Explanation

Economic and financial phenomena are highly complex and non-linear. However, surprisingly, in many cases, these phenomena are accurately described by linear models – or, sometimes, by piecewise linear ones. In this paper, we show that fuzzy techniques can explain the unexpected efficiency of linear and piecewise linear models: namely, we show that a natural fuzzy-based precisiation of imprecise (“fuzzy”) expert knowledge often leads to linear and piecewise linear models. We also discuss which expert-motivated nonlinear models should be used to get a more accurate description of economic and financial phenomena.
Marshalgen: A Package for Semi-Automatic Marshaling of Objects

Marshaling or serialization of objects is an important component of both distributed and parallel computing. Current systems impose a significant burden on the programmer for describing the marshaling of complex, recursive data structures. Marshalgen provides a semi-automatic process for marshaling in C and C++. Marshalgen avoids the need for complex IDLs and auxiliary routines. It is based on annotations of the existing source code.
Characterization of a minimal simian virus 40 late promoter: enhancer elements in the 72-base-pair repeat not required

A 272-base-pair (bp) portion of the simian virus 40 regulatory region containing the replication origin, Sp1-binding region, and part of the 72-bp direct repeats makes up a minimal late promoter that is able to direct late-direction RNA synthesis in vivo and in vitro. Fourteen linker-scan mutants within this region were characterized. Mutations in the Sp1-binding region decreased late expression both in vivo and in vitro. By contrast, mutations that eliminate genetically defined elements of the early transcriptional enhancer or that prevent binding of the transcription factors AP-1, AP-2, and AP-3 in the 72-bp repeat region had little or no effect on late-direction expression. These results argue that, at least under certain circumstances, the early transcriptional enhancer sequences are not required for simian virus 40 late gene expression.
Incidence and etiology of acute renal failure among ambulatory HIV-infected patients.

BACKGROUND Acute renal failure (ARF) is a cause of renal dysfunction in human immunodeficiency virus (HIV)-infected patients. Its incidence and causes have not been studied since the introduction of highly active antiretroviral therapy (HAART) in HIV ambulatory patients. METHODS This is a prospective cohort study of 754 HIV patients, 18 years or older, seen at a university-based infectious disease clinic between 2000 and 2002. ARF was identified using proportional increases in serum creatinine from baseline and by chart review. Clinical conditions were assessed at the time of the ARF event. ARF incidence rates (IR) were calculated by dividing the number of events by person time at risk. To compare patients with and without ARF, t test or chi-square test were used. RESULTS Patient's mean age was 40 years; 68% were male and 61% were black. One hundred-eleven ARF events occurred in 71 subjects (IR 5.9 per 100 person-years; 95% CI 4.9, 7.1). ARF was more common in men, in those with CD4 cell count <200 cells/mm(3), and HIV RNA levels >10,000 copies/mL. These patients more often had acquired immunodeficiency syndrome (AIDS), hepatitis C infection (HCV), and have received HAART. ARF was mainly community-acquired, due to prerenal causes or acute tubular necrosis, and associated with opportunistic infections and drugs. Liver disease was a cause of ARF in HCV-infected patients. CONCLUSION ARF is common in ambulatory HIV patients. Immunosuppression, infection, and HCV are important conditions associated with ARF in the post-HAART era.
Growth Factors, Cytokines, Cell Cycle Molecules Neuraminidase-1, a Subunit of the Cell Surface Elastin Receptor, Desialylates and Functionally Inactivates Adjacent Receptors Interacting with the Mitogenic Growth Factors PDGF-BB and IGF-2

We recently established that the elastin-binding protein, which is identical to the spliced variant of -galactosidase, forms a cell surface-targeted complex with two proteins considered “classic lysosomal enzymes”: protective protein/cathepsin A and neuraminidase-1 (Neu1). We also found that cell surface-residing Neu1 can desialylate neighboring microfibrillar glycoproteins and facilitate the deposition of insoluble elastin, which contributes to the maintenance of cellular quiescence. Here we provide evidence that cell surfaceresiding Neu1 contributes to a novel mechanism that limits cellular proliferation by desialylating cell membrane-residing sialoglycoproteins that directly propagate mitogenic signals. We demonstrated that treatment of cultured human aortic smooth muscle cells (SMCs) with either a sialidase inhibitor or an antibody that blocks Neu1 activity induced significant up-regulation in SMC proliferation in response to fetal bovine serum. Conversely, treatment with Clostridium perfringens neuraminidase (which is highly homologous to Neu1) decreased SMC proliferation, even in cultures that did not deposit elastin. Further, we found that pretreatment of aortic SMCs with exogenous neuraminidase abolished their mitogenic responses to recombinant platelet-derived growth factor (PDGF)-BB and insulin-like growth factor (IGF)-2 and that sialidosis fibroblasts (which are exclusively deficient in Neu1) were more responsive to PDGF-BB and IGF-2 compared with normal fibroblasts. Furthermore, we provide direct evidence that neuraminidase caused the desialylation of both PDGF and IGF-1 receptors and diminished the intracellular signals induced by the mitogenic ligands PDGF-BB and IGF-2. (Am J Pathol 2008, 173:1042–1056; DOI: 10.2353/ajpath.2008.071081)
Interactive Augmentation of Live Images using a HDR Stereo Camera

JVRB, 4(2007), no. 12. - Adding virtual objects to real environments plays an important role in todays computer graphics: Typical examples are virtual furniture in a real room and virtual characters in real movies. For a believable appearance, consistent lighting of the virtual objects is required. We present an augmented reality system that displays virtual objects with consistent illumination and shadows in the image of a simple webcam. We use two high dynamic range video cameras with fisheye lenses permanently recording the environment illumination. A sampling algorithm selects a few bright parts in one of the wide angle images and the corresponding points in the second camera image. The 3D position can then be calculated using epipolar geometry. Finally, the selected point lights are used in a multi pass algorithm to draw the virtual object with shadows. To validate our approach, we compare the appearance and shadows of the synthetic objects with real objects.
A survey on signature-based Gröbner basis computations

This paper is a survey on the area of signature-based Grobner basis algorithms that was initiated by Faugere's F5 algorithm in 2002. We explain the general ideas behind the usage of signatures. We show how to classify the various known variants by 3 different orderings. For this we give translations between different notations and show that besides notations many approaches are just the same. Moreover, we give a general description of how the idea of signatures is quite natural when performing the reduction process using linear algebra. This survey shall help to outline this field of active research.
The ‘Matchbox School’ (1927–1932): Anna Freud and the idea of a ‘psychoanalytically informed education’*

Abstract Of all the applications of psychoanalysis to various fields, perhaps none has been as important – or as fraught – as the application of psychoanalytic insights to education. This paper re-constructs some of the early debates around psychoanalysis and pedagogy that Anna Freud engaged with during the 1920s in Vienna, when the whole question of what education should be became a central issue for politicians, pedagogues and psychoanalysts alike. The paper focuses on the period leading up to the creation of the so-called ‘Matchbox School’, operating under Anna Freud's guidance between 1927 and 1932, and describes the influence of pioneers such as Seigfried Bernfeld and August Aichhorn. Compared to her more well-known work at the Hampstead War Nurseries during the Second World War, Anna Freud's involvement with this earlier educational experiment is relatively neglected. Yet one can argue that this short-lived project not only laid the foundation for much of Anna Freud's later work; it also had some far-reaching consequences, both for psychoanalysis and for the practice of progressive education.
Universalistic handbook discourse and the local needs of writers

Drawing on a cross-disciplinary framework combining insights from discourse analysis, pragmatics, critical educational theory, cultural theory, and new literacy studies, this article describes how two American handbook series—the MLA Handbook for Writers of Research Papers and the (Chicago) Manual for Writers of Term Papers, Theses and Dissertations— construct academic writing and articulate their educational ideology. On the basis of a close analysis of content, language, and textual patterns, the article shows how the two series are nearly antithetical. Through their liberal instructive discourse, the MLA handbooks aim at socializing writers and guiding them towards membership in the community of academic writers, while the more conservative Chicago manuals strive to protect the institutionally valued research text from its writers. However, the handbooks are also similar in certain respects: in addition to providing instructions that can be quite empowering, they also delimit the options writers can have. From this perspective, the article also argues that particularly for non-native writers of English, handbook discourse can be quite problematic. The article concludes by arguing that in today’s heterogeneous academia, the purposes and aims of handbook discourse merit critical reevaluation so that they show more awareness and tolerance of difference and plurality.
Stability of the thermohaline circulation in a simple coupled model

In an analytical study, the stability of the thermohaline circulation with respect to freshwater perturbations in high latitudes is investigated. The study is based on a coupled ocean and atmosphere box model in an idealized North Atlantic geometry. The box model provides a qualitative understanding of how the thermohaline circulation is affected by feedback mechanisms associated with changes in atmospheric transports of heat and moisture. Within a linear analysis, we examine the stability of the thermohaline circulation for a range of different atmospheric boundary conditions. The stability of the coupled system depends on the imposed transport parameterizations and the basic state. For the underlying non-linear system, we examine the sensitivity with respect to the strength of salinity perturbation. DOI: 10.1034/j.1600-0870.1996. t01-2-00008.x
Effective Site Customization Based on Web Semantics and Usage Mining

The explosive growth of online data and the diversity of goals that may be pursued over the Web have significantly increased the monetary value of the Web traffic. To tap into this accelerating market, Web site operators try to increase their traffic by customizing their sites to the needs of specific users. Web site customization involves two great challenges: the effective identification of the user interests and the encapsulation of those interests into the sites' presentation and content. In this paper, we study how we can effectively detect the user interests that are hidden behind navigational patterns and we introduce a novel recommendation mechanism that employs Web mining techniques for correlating the identified interests to the sitespsila semantic content, in order to customize them to specific users. Our experimental evaluation shows that the user interests can be accurately detected from their navigational behavior and that our recommendation mechanism, which uses the identified interests, yields significant improvements in the sites' usability.
Long‐term outcome of per anum intersphincteric rectal dissection with direct coloanal anastomosis for lower rectal cancer

Objective The authors have performed per anum intersphincteric rectal dissection. With direct coloanal anastomosis for cases of lower rectal cancer in which the distal surgical margin is difficult to secure by the double stapling technique. The aim of this study was to evaluate the long‐term outcome and to clarify the surgical indications for this operation.
Explaining the gambler's fallacy: Testing a gestalt explanation versus the “law of small numbers”

The present study tests a gestalt (closure) explanation for the gambler's fallacy which posits that runs in random events will be expected to reverse only when the run is open or ongoing. This is contrasted with the law of small numbers explanation suggesting that people expect random outcomes to balance out generally. Sixty-one university students placed hypothetical guesses and bets on a series of coin tosses. Either heads or tails were dominant (8 versus 4). In a closed run condition the run ended prior to the critical trial (e.g., HHHT), and in an open run condition the run remained open (e.g., THHH). As hypothesised, participants showed the gambler's fallacy in the open run condition, but not in the closed run condition. This difference is not due to differential memory for the outcomes. Men, and people with more previous experience gambling, were also found to be more prone to the gambler's fallacy. It is argued that the gestalt explanation best explains the results.