Miracle-dz/UniFAR-FTUs huggingface dataset:
Expressed Protein Ligation, a Novel Method for Studying Protein-Protein Interactions in Transcription*

Expressed protein ligation is a novel protein semi-synthesis method that permits the in vitro ligation of a chemically synthesized C-terminal segment of a protein to a recombinant N-terminal segment fused through its C terminus to an intein protein splicing element. In principle, the practical convenience of this method, combined with the expanded opportunities in protein engineering that it provides, makes it well suited for probing the molecular basis of complex processes such as transcription. Here we describe the successful application of expressed protein ligation to the ∼600 amino acid ς70 subunit of Escherichia coli RNA polymerase. The resulting semi-synthetic ς70 constructs are shown to be fully functional and have been used to map the binding region of the bacteriophage T4 anti-sigma protein, AsiA, to within amino acids 567–600 of ς70. The success of these semi-synthesis studies sets the stage for the future generation of semi-synthetic ς70 molecules in which unnatural amino acids and biophysical probes are site-specifically incorporated in the RNA polymerase complex.
Rickettsia helvetica in Ixodes ricinus Ticks in Sweden

ABSTRACT In the present study further characterization of the amplified sequence of the citrate synthase gene of the spotted fever groupRickettsia isolated from Ixodes ricinus ticks in Sweden showed that it has 100% homology with the deposited sequence of the citrate synthase gene of Rickettsia helvetica. The restriction fragment length polymorphism (RFLP) pattern of an amplified 382-bp product of the citrate synthase sequence, defined by primers RpCS877 and RpCS1258, yielded fragments for our isolate that could be visualized as a double band that migrated at approximately 44 bp, another double band at 85 bp, and a single band at nearly 120 bp after digestion with the restriction enzyme AluI. When calculating a theoretical PCR-RFLP pattern of the sequence of the citrate synthase gene of R. helvetica from the known positions where the AluI enzyme cuts, we arrived at the same pattern that was obtained for our isolate, a pattern distinctly different from the previously published PCR-RFLP pattern for R. helvetica. Investigation of 125 living I. ricinusticks showed a higher prevalence of rickettsial DNA in these ticks than we had found in an earlier study. Rickettsial DNA was detected by amplification of the 16S rRNA gene, for which a seminested primer system consisting of two oligonucleotide primer pairs was used. Of the 125 ticks, some were pooled, giving a total of 82 tick samples, of which 20 were found to be positive for the rickettsial DNA gene investigated. When considering the fact that some of the positive samples were pooled, the minimum possible prevalence in these ticks was 20 of 125 (16%) and the maximum possible prevalence was 46 of 125 (36.8%). These prevalence estimates conform to those of other studies of spotted fever group rickettsiae in hard ticks in Europe.
Real-Time Musculoskeletal Model for Injury Simulation on 3D Human Characters

We describe a real-time musculoskeletal model created for the purpose of simulating localized injuries on animated 3D human characters. The baseline experiment will include projectile injuries that are compared and validated against experimental data from the science of ballistics. The research will also include an injury assessment model suitable for motion editing purposes that looks at the total combined injury from separate biological layers such as bone, muscle, and fat tissues.
Cross–age Peer Tutoring of Thinking Skills in the High School

Teaching thinking skills has been characterised by the teacher-directed ‘embed ded’, ‘infusion’ and ‘bolt-on’ approaches, for which outcomes have been mixed. Peer tutoring in thinking skills offers a fourth way of wide applicability. This study evaluated such a method (Paired Thinking) in a high school setting. A substantial gain in reading comprehension was found for tutees. Triangulated subjective feedback indicated development in thinking skills, self-esteem and social skills for tutees and tutors. Paired Thinking appeared to yield considerable potential impact for minimal time input. Recommendations for refining organisation and for future research and practice were made.
Visual Analysis of Eye Movements by Hierarchical Filter Wheels

The visual exploration of spatio-temporal eye movement data is challenging, especially if we are interested in the movement patterns of a large number of study participants. For example, if popular visualization techniques like heat maps or gaze plots are used, we may lose the temporal information or get lost in visual clutter. To address these issues, we propose an approach for filtering saccadic eye movement data called hierarchical filter wheels, which employs a radial representation of saccade information. It supports the analysis of sequences of saccades by filtering them with respect to direction and length. The focus of our approach is a fast initial analysis of data from eye tracking studies without the need of defining areas of interest (AOIs) or other preprocessing of the data. The hierarchical filters are interactively generated on users' demand by creating a hierarchy of multiple filter wheels each filtering one element of the sequence. We use a bubble tree layout to represent the generated filter hierarchy. The node positions in our layout directly represent the spatial properties of the filter criteria allowing an intuitive incremental generation and understanding of filter hierarchies. We illustrate the approach by applying it to eye movement data formerly recorded in an eye tracking study investigating the readability of different node-link tree diagrams. We further demonstrate how the hierarchical filter wheels can be used in combination with gaze plots.
The Geographic Imagination of Civil War-Era American Fiction

Space is important in literary studies. This was true even before postmodernism’s spatial turn a generation ago, and our collective interest in spatial issues has only grown in recent years. Of course, what we mean by space varies widely across the discipline. We have studies of the relationship between literature and geography at scales ranging from the local to the global. We’re also interested in the smaller scales of built space and the lived environment. And then there’s the longstanding problem of mapping between space and time as organizing principles of narrative and other forms of cultural production. This variety doesn’t imply that we’ve made a hash of things. On the contrary, I think we’ve done well, considering the scope of the problem. But in nearly every case, we work in a way that makes some questions much easier to ask and to answer than others. By this I mean that our need to work with individual texts (and other cultural objects) has led us to study first and foremost specific representations of space and geography, which we’ve then used as symptomatic indices of larger social configurations. So we’ve become very good at, for example, determining what Kate Chopin’s stories reveal about the nexus of sexuality and Cajun regional culture or, in a different register, how the Las Vegas strip reveals the symbolic function of commercial built space. At the same time, it has often been difficult to assess the extent to which these symptomatic readings apply to larger groups of texts and objects, simply because we’ve lacked the capacity to apply our methods sequentially across, say, all of the fiction written in the nineteenth century.
Test data regeneration: generating new test data from existing test data

Existing automated test data generation techniques tend to start from scratch, implicitly assuming that no pre‐existing test data are available. However, this assumption may not always hold, and where it does not, there may be a missed opportunity; perhaps the pre‐existing test cases could be used to assist the automated generation of additional test cases. This paper introduces search‐based test data regeneration, a technique that can generate additional test data from existing test data using a meta‐heuristic search algorithm. The proposed technique is compared to a widely studied test data generation approach in terms of both efficiency and effectiveness. The empirical evaluation shows that test data regeneration can be up to 2 orders of magnitude more efficient than existing test data generation techniques, while achieving comparable effectiveness in terms of structural coverage and mutation score. Copyright © 2010 John Wiley & Sons, Ltd.
Parathyroid Hormone (PTH) and PTH-Related Peptide Domains Contributing to Activation of Different PTH Receptor–Mediated Signaling Pathways

Parathyroid hormone (PTH) and parathyroid hormone–related peptide (PTHrP), acting through the osteoblast PTH1 receptor (PTH1R), play important roles in bone remodeling. Intermittent administration of PTH(1-34) (teriparatide) leads to bone formation, whereas continuous administration paradoxically leads to bone resorption. Activation of PTH1R promotes regulation of multiple signaling pathways, including Gs/cAMP/protein kinase A, Gq/calcium/protein kinase C, β-arrestin recruitment, and extracellular signal-related kinase (ERK)1/2 phosphorylation, as well as receptor internalization, but their role in promoting anabolic and catabolic actions of PTH(1-34) are unclear. In the present investigation, a collection of PTH(1-34) and PTHrP(1-34) peptide analogs were evaluated in orthogonal human PTH1R (hPTH1R) functional assays capturing Gs- and Gq-signaling, β-arrestin recruitment, ERK1/2 phosphorylation, and receptor internalization to further define the patterns of PTH1R signaling that they stimulate and further establish peptide domains contributing to agonist activity. Results indicate that both N- and C-terminal domains of PTH and PTHrP are critical for activation of signaling pathways. However, modifications of both regions lead to more substantial decreases in agonist potency and efficacy to stimulate Gq-signaling, β-arrestin recruitment, ERK1/2 phosphorylation, and receptor internalization than to stimulate Gs-signaling. The substantial contribution of the peptide C-terminal domain in activation of hPTH1R signaling suggests a role in positioning of the peptide N-terminal region into the receptor J-domain. Several PTH and PTHrP peptides evaluated in this study promote different patterns of biased agonist signaling and may serve as useful tools to further elucidate therapeutically relevant PTH1R signaling in osteoblasts. With a better understanding of therapeutically relevant signaling, novel biased peptides with desired signaling could be designed for safer and more effective treatment of osteoporosis.
Amoebal Endosymbiont Protochlamydia Induces Apoptosis to Human Immortal HEp-2 Cells

Protochlamydia, an environmental chlamydia and obligate amoebal endosymbiotic bacterium, evolved to survive within protist hosts, such as Acanthamobae, 700 million years ago. However, these bacteria do not live in vertebrates, including humans. This raises the possibility that interactions between Protochlamydia and human cells could induce a novel cytopathic effect, leading to new insights into host-parasite relationships. Therefore, we studied the effect of Protochlamydia on the survival of human immortal cell line, HEp-2 cells and primary peripheral blood mononuclear cells (PBMC). Using mainly 4′,6-diamidino-2-phenylindole staining, fluorescent in situ hybridization, transmission electron microscopy, and also TUNEL and Transwell assays, we demonstrated that the Protochlamydia induced apoptosis in HEp-2 cells. The attachment of viable bacterial cells, but not an increase of bacterial infectious progenies within the cells, was required for the apoptosis. Other chlamydiae [Parachlamydia acanthamoebae and Chlamydia trachomatis (serovars D and L2)] did not induce the same phenomena, indicating that the observed apoptosis may be specific to the Protochlamydia. Furthermore, the bacteria had no effect on the survival of primary PBMCs collected from five volunteers, regardless of activation. We concluded that Protochlamydia induces apoptosis in human-immortal HEp-2 cells and that this endosymbiont could potentially be used as a biological tool for the elucidation of novel host-parasite relationships.
Central blood pressure measurements and antihypertensive therapy: a consensus document.

The 2003 European Society of Hypertension/European Society of Cardiology guidelines for the management of arterial hypertension1 included 2 important novel recommendations: assessment of the total cardiovascular risk should be taken into account in the management of the hypertensive patient, and quantification of risk should include subclinical target organ damage. These guidelines acknowledged that central (aortic) blood pressure (BP), which is the pressure exerted on the heart and brain, may be different from the pressure that is measured at the arm. They also recognized that central pressure may be predictive of outcome in specific populations2 and differently affected by antihypertensive drugs. However, although these guidelines accepted that central augmentation index and pulse wave velocity may be important as measures of subclinical organ damage, they also stressed the need for prospective trials to establish their predictive values given that such studies were lacking at that time (2003). After publication of these guidelines, additional data have strengthened the pathophysiological importance of central BP. Clinical studies have indicated that central BP may have predictive value independent of the corresponding peripheral (brachial) BP. More importantly, recent large-scale trials have shown that central hemodynamics may provide a worthwhile treatment target. In addition, central hemodynamics can now be reliably assessed noninvasively with a number of devices. Accordingly, because arterial stiffening and central hemodynamics are markers and manifestations of organ damage, the pertinent key question is whether the balance of evidence on their importance and issues related to clinical practice allows for implementation in patient management. Central (aortic and carotid) pressures are pathophysiologically more relevant than peripheral pressures for the pathogenesis of cardiovascular disease.3,4 It is aortic systolic pressure that the left ventricle encounters during systole (afterload), and the aortic pressure during diastole is a determinant of coronary perfusion. Furthermore, the distending pressure in the …
Top management demographic characteristics and company performance

Purpose – The importance of the performance of a firm and the essential role played by the management in their accomplishment has been discussed and recognised by many researchers from Drucker to Upper Echelon Theory. Nonetheless, currently, anybody has been able to determine the precious and reliable parameters which let the firm achieve required-level performance. The confusion around this objective is still sufficient and the controversial has being growing widely over time, being the findings achieved contradictory, insufficient, imprecise and unreliable. Regarding the demographical literature findings focus on the premises previous related to Upper Echelon Theory. The purpose of this paper is to go further and try to test how, not only the level, but also the diversity of constructs like top management teams (TMT)'s demographic characteristics influence the firm performance accomplished by the managers by applying a Hierarchical Linear Regression Model. Design/methodology/approach – Based on primary .
Harmonization of Commercial ELISA Methods for the Measurement of Prothrombin Fragment 1.2: Is It Feasible?

Poor comparability of two commercial ELISA methods for the measurement of prothrombin fragment 1.2 (FI.2) was recently reported (1). Because of the potential utility of plasma F1.2 measurement in the monitoring of the in vivo action of oral anticoagulant drugs (2), we con­ ducted a study aimed to evaluate the comparability of two commercial kits for the measurement of F 1.2 levels in normal controls (n = 80, 40 men and 40 females, mean age 40.8 ± 12.2 yrs, range 18-69) and in patients on stabilized oral anticoagulant treatment (n = 99, mean INR 2.62 ± 1.07, range 1.20-8.25). Blood was drawn sequentially - using a 20 gauge needle - into 5 ml vacutainer tubes (Becton Dickinson) con­ taining 0.129 M sodium citrate or sodium heparin. Plasma F1.2 levels were tested with the Enzygnost FI+2 (Behring, Marburg, Germany) in citrated plasma and with the FI.2 ELISA (Baxter, Miami, FI) in both citrated and heparinised plasma. The manufacturer’s instructions were followed closely except for omitting the 10 nM calibrator and adding a 1 nM calibrator - obtained by dilution of the 2nM calibrator in Tris-buffered saline - in the Behring calibration curve. In spite of the different mean values (Baxter-heparin 0.26 ±0.15 nM, Baxter-citrate 0.17 ± 0.10 nM, Behring-citrate 0.64 ± 0.29 nM) and of the moderate correlation observed between the values determined with the Behring-citrate and the Baxter-heparin methods (r = 0.712), there were good correlations between the FI.2 values
Advanced clinical MRI for better outcome in epilepsy surgery. Focusing on fMRI and prediction of verbal memory decline.

Abstract Aim: The aim of the thesis was to evaluate the use of advanced MRI technology to improve results of epilepsy surgery, with focus on language and memory functions. Methods: In paper I, 25 patients with drug-resistant epilepsy were retrospectively included in the study for having been referred to high resolution 3T MRI with and without surface coils. The surface coils were placed over the suspected epileptogenic zone. The efficacy of the coils was assessed and graded in relation to their placement. In papers II, III and IV, a functional MRI (fMRI) paradigm, including both a verbal encoding task and a visuospatial task, was designed and implemented. The medial temporal lobe (MTL) for memory and the anterior language area were studied. In paper III, a standard word generation fMRI paradigm was also included. In these three studies, the test was performed in 15 healthy right handed subjects (paper II), 6 patients with drug-resistant temporal lobe epilepsy (TLE) with mixed handedness and 10 controls (paper III) and 14 TLE patients eligible for resective surgery (paper IV), respectively. A bootstrap algorithm was used to calculate lateralization indices (LI) and LI-curves. In paper IV, a clinical risk assessment score was created from collected clinical data. Additional value from fMRI LI was correlated to post-surgical memory decline. Results: Surface coil 3T MRI did not contribute to detection of previously undiagnosed lesions. In 20% of patients, 3T MRI, compared with previous 1.0-1.5T MRI, provided new information about cortical lesions. The fMRI paradigm visualized memory-related activity in the MTL and provided information regarding language processes. LI and LI-curves for memory at group level were consistent with previous studies, but a variety of activation effects were found at the individual level. LI-curves added complementary information for individual subjects with uncharacteristic results. The verbal encoding task provided information on verbal memory, which had equal lateralization as language in right-handed subjects, but not always in left-handed subjects and TLE patients. Bilateral fMRI language representation was seen in 2 right TLE patients who later suffered verbal memory decline post-operatively. Conclusion: High resolution 3T MRI is valuable for lesion detection, but surface coils do not provide further crucial information. The fMRI paradigm activates memory and language areas that can be studied at an individual level using LIcurves. Analysis of language patterns seems to be important for prediction of memory outcome in both left and right TLE. fMRI indices may identify an unexpected high risk for post-operative verbal memory decline in right TLE patients. (Less)
Intelligent Prediction System of Coal-Gas Outburst Based on Evolutionary Neural Nets

The novel coal-gas dangerous-level prediction model established has advantages of the EA and BP neural nets, and overcomes the shortcomings of misreport and missing-report of others. This approach can accurately capture the complicated relationships among feature values of coal-gas outbursts and dangerous circumstances. We considered the characteristic of coal-gas outburst carefully, combining with the raw data of coal-gas monitor system in the Daping colliery and the 10th colliery of Pingdingshan Company as well as real-time samples of accidents, and selected pattern sets to train the proposed model and generate the corresponding rules for prediction. Results show that the ENN has better performance than the ANN or the traditional method used individually, and enhances the practical techniques for prediction of coal and gas in coal mine to guarantee safety.
SMARTBIKE: Policy making and decision support for bike share systems

Bike share systems have been implemented in many cities to provide an alternative low-cost environmentally friendly and healthy public transportation. Citizens can pick up and drop off bikes among stations around the city. The system may be used for both work-related and leisure purposes including supporting last-mile transportation and tourism. In order to sustain and attract more users into the bike system, understanding demand and trip patterns is a key objective. Further, due to the asymmetric and dynamic nature of user demands, some stations tend to run out of bikes whereas other stations tend to be full (impeding returns). Rebalancing stations to provide high quality services to fit pick up and drop off demand is a major challenge in bike share systems. In this paper, we present a three-layer SMARTBIKE system to assist city administrators in Fortaleza, Brazil with bike share system decision making. This is an international cooperative effort between academia and government to aid in building a Smart City. The first layer of the proposed tool includes ¿-means clustering technology to understand the true demand of the city bike share system. We designed a novel station network analysis in the second layer to provide insights on system usage patterns and to help with the rebalancing strategy. The third layer provides rebalancing support at the facility and operation level. Finally, we discuss a dynamic visualization tool to support decision making.
Libertarian Populism, Neoliberal Rationality, and the Mandatory Long-form Census: Implications for Sociology

This article argues the Canadian government’s decision in 2010 to eliminate the mandatory long-form census constitutes a mobilizing appeal to libertarian populism commensurate not only with neoliberal concepts of individualism, private property, and the role of the state, but also with a redefinition of what counts as valid argumentation and a legitimate basis for making knowledge claims. This rationale has implications for sociological research and theory, for the profession of sociology, and for a sociological vision of society.