Miracle-dz/UniFAR-FTUs huggingface dataset:
CCAAT/Enhancer-binding Protein β Is an Accessory Factor for the Glucocorticoid Response from the cAMP Response Element in the Rat Phosphoenolpyruvate Carboxykinase Gene Promoter*

The cyclic AMP response element (CRE) of the rat phosphoenolpyruvate carboxykinase (PEPCK) gene promoter is required for a complete glucocorticoid response. Proteins known to bind the PEPCK CRE include the CRE-binding protein (CREB) and members of the CCAAT/enhancer-binding protein (C/EBP) family. We took two different approaches to determine which of these proteins provides the accessory factor activity for the glucocorticoid response from the PEPCK CRE. The first strategy involved replacing the CRE of the PEPCK promoter/chloramphenicol acetyltransferase reporter plasmid (pPL32) with a consensus C/EBP-binding sequence. This construct, termed pΔcreC/EBP, binds C/EBPα and β but not CREB, yet it confers a nearly complete glucocorticoid response when transiently transfected into H4IIE rat hepatoma cells. These results suggest that one of the C/EBP family members may be the accessory factor. The second strategy involved co-transfecting H4IIE cells with a pPL32 mutant, in which the CRE was replaced with a GAL4-binding sequence (pΔcreGAL4), and various GAL4 DNA-binding domain (DBD) fusion protein expression vectors. Although chimeric proteins consisting of the GAL4 DBD fused to either CREB or C/EBPα are able to confer an increase in basal transcription, they do not facilitate the glucocorticoid response. In contrast, a fusion protein consisting of the GAL4 DBD and amino acids 1–118 of C/EBPβ provides a significant glucocorticoid response. Additional GAL4 fusion studies were done to map the minimal domain of C/EBPβ needed for accessory factor activity to the glucocorticoid response. Chimeric proteins containing amino acid regions 1–84, 52–118, or 85–118 of C/EBPβ fused to the GAL4 DBD do not mediate a glucocorticoid response. We conclude that the amino terminus of C/EBPβ contains a multicomponent domain necessary to confer accessory factor activity to the glucocorticoid response from the CRE of the PEPCK gene promoter.
Recognizing thoracic breathing by ensemble empirical mode decomposition

Recognizing breathing pattern is important in many fields of medicine. Ensemble empirical mode decomposition (an adaptive algorithm) was used to investigate breathing pattern, including thoracic breathing (TB) and abdominal breathing (AB). This study recognizes TB and AB by correlation coefficient and power proportion. Results indicate that the recognition accuracy of TB by correlation coefficient and power proportion are 85.2% and 93.3% respectively, and that of AB by correlation coefficient and power proportion are 54.3% and 56.2% respectively. The TB can be well defined and recognized in complex time variation. These results can be used as references to develop the real time breathing evaluation system in the future.
Robust Inference of Strategic Interactions in Static

We present a new approach to inference in static games that allows for a rich strategy space. Assuming that payoff functions satisfy some general shape restrictions, we develop identification results and introduce an econometric procedure to do inference on the component of payoff functions that captures the direction of strategic interaction (i.e, patterns of substitutability/complementarity) as well as the relative effects of opponents' decisions on players' payoffs, leaving everything else about the model nonparametrically specified. As in De Paula and Tang (2012), we exploit the potential presence of multiple equilibria for identification. Our observable implications take the form of inequalities involving transformations of conditional moments. We introduce an econometric method to inference that exploits the information in these inequalities in a computationally simple way. We apply our approach to a model of entry which is modeled as an intensive capacity/investment decision rather than a binary choice. Using data from retail pharmacies, we show that our general model can reconcile largely positive correlations in capacity decisions across rival firms observed in the data with an underlying structural model of strategic substitutes. Our approach can also help us test conjectures about strategic interaction that have economic interest, such as whether players care equally about the decisions of each opponent or whether there is asymmetry in the effect of strategic interaction and how these effects vary with continuous market covariates (such as market size).
An Exploration of Innovation and Energy Efficiency in an Appliance Industry

E RNEST O RLANDO L AWRENCE B ERKELEY N ATIONAL L ABORATORY An Exploration of Innovation and Energy Efficiency in an Appliance Industry Prepared by Margaret Taylor, K. Sydny Fujita, Larry Dale, and James McMahon For the European Council for an Energy Efficient Economy March 29, 2012 This work was supported by the Assistant Secretary for Energy Efficiency and Renewable Energy, Office of Building Technology, State, and Community Programs, of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231.
Sequential Superresolution Imaging of Multiple Targets Using a Single Fluorophore

Fluorescence superresolution (SR) microscopy, or fluorescence nanoscopy, provides nanometer scale detail of cellular structures and allows for imaging of biological processes at the molecular level. Specific SR imaging methods, such as localization-based imaging, rely on stochastic transitions between on (fluorescent) and off (dark) states of fluorophores. Imaging multiple cellular structures using multi-color imaging is complicated and limited by the differing properties of various organic dyes including their fluorescent state duty cycle, photons per switching event, number of fluorescent cycles before irreversible photobleaching, and overall sensitivity to buffer conditions. In addition, multiple color imaging requires consideration of multiple optical paths or chromatic aberration that can lead to differential aberrations that are important at the nanometer scale. Here, we report a method for sequential labeling and imaging that allows for SR imaging of multiple targets using a single fluorophore with negligible cross-talk between images. Using brightfield image correlation to register and overlay multiple image acquisitions with ~10 nm overlay precision in the x-y imaging plane, we have exploited the optimal properties of AlexaFluor647 for dSTORM to image four distinct cellular proteins. We also visualize the changes in co-localization of the epidermal growth factor (EGF) receptor and clathrin upon EGF addition that are consistent with clathrin-mediated endocytosis. These results are the first to demonstrate sequential SR (s-SR) imaging using direct stochastic reconstruction microscopy (dSTORM), and this method for sequential imaging can be applied to any superresolution technique.
Predictors of Student Commitment at Two-Year and Four-Year Institutions

Examining predictors of student institutional commitment at two-year and four-year institutions, HLM analyses reveal similar relationships between student predictors and institutional commitment, the strongest influences exerted by student academic integration, followed by social integration. Classroom experience is more influential at two-year institutions, while social integration has more impact for students at four-year institutions.
Testing the FR I/BL Lac unifying model with HST observations

Hubble Space Telescope (HST) observations provide a novel way of testing unified models for FR I radio sources and BL Lac objects. The detection of extended dust discs in some radio galaxies provides information on their jet orientation. Given this, the strength of the compact nuclear sources of FR I and BL Lacs can be compared with model predictions. As a pilot project towards using HST information in testing unified models, we selected five radio galaxies that show extended nuclear discs in the HST images. The relative orientation of the projected radio jets and of the extended nuclear discs indicates that they are not perpendicular, as the simplest geometrical model would suggest, but that they form an angle of ∼20--40 with the symmetry axis of the disc: a significant change of orientation occurs between the innermost AGN structure and the kiloparsec scale. Nevertheless, the discs appear to be useful indicators of the orientation of the radio source, since the angles formed by the disc axis and the jet with the line of sight differ by only ∼10--20. At the centre of each disc an unresolved nuclear source is present. We compared its luminosity with the optical core luminosity of BL Lacs selected for having similar host galaxy magnitude and extended radio luminosity. The BL Lac cores are between 2×102 and 3×105 times brighter than the corresponding radio galaxy ones. The FR I/BL Lac core luminosity ratio shows a suggestive correlation with the orientation of the radio galaxies with respect to the line of sight. The behaviour of this ratio is quantitatively consistent with a scenario in which the emission in the FR I and BL Lac sources is dominated by the beamed radiation from a relativistic jet with Doppler factor ∼5--10, thus supporting the basic features of the proposed unification schemes. Several observational tests, based on the method proposed here, can strengthen our conclusions and improve the statistical significance of the findings presented.
Walking Control of a Humanoid Robot via Explicit and Stable CoM Manipulation with the Angular Momentum Resolution

This paper presents a walking algorithm for bipedal humanoid robots in the motion-embedded CoM Jacobian framework with angular momentum resolution. Walking constraints in the previous resolved momentum control framework are reformulated to utilize motion-embedded CoM Jacobian and reduce computational complexity. In this method, the conventional linear momentum control is replaced by the explicit CoM manipulation and the angular momentum equation only is used for upper body motion resolution without any other subject variables; whole body cooperative motions are completed with the walking constraints expressed by motion-embedded CoM Jacobian. The conventional resolved momentum control is able to play a more unified framework role owing to this method and lose computational weight while making compatibility with the motion-embedded CoM Jacobian framework. Validity and walking stability are demonstrated by the experiment on the real robot, MAHRU-II
DCU Search Runs at MediaEval 2014 Search and Hyperlinking

We described Dublin City University (DCU)’s participation in the Search sub-task of the Search and Hyperlinking Task at MediaEval 2014. Exploratory experiments were carried out to investigate the utility of prosodic prominence features in the task of retrieving relevant video segments from a collection of BBC videos. Normalised acoustic correlates of loudness, pitch, and duration were incorporated in a standard TF-IDF weighting scheme to increase weights for terms that were prominent in speech. Prosodic models outperformed a text-based TF-IDF baseline on the training set but failed to surpass the baseline on the test set.
Wide angle near-field diffraction and Wigner distribution

Summary Free-space propagation can be described as a shearing of the Wigner distribution function in the spatial coordinate; this shearing is linear in paraxial approximation but assumes a more complex shape for wide-angle propagation. Integration in the frequency domain allows the determination of near-field diffraction, leading to the well known Fresnel diffraction when small angles are considered and allowing exact prediction of wide-angle diffraction. The authors use this technique to demonstrate evanescent wave formation and diffraction elimination for very small apertures.
A MODIFIED HISTOGRAM BASED FAST ENHANCEMENT ALGORITHM

The contrast enhancement of medical images has an important role in diseases diagnostic, specially, cancer cases. Histogram equalization is considered as the most popular algorithm for contrast enhancement according to its effectiveness and simplicity. In this paper, we present a modified version of the Histogram Based Fast Enhancement Algorithm. This algorithm enhances the areas of interest with less complexity. It is applied only to CT head images and its idea based on treating with the soft tissues and ignoring other details in the image. The proposed modification make the algorithm is valid for most CT image types with enhanced results.
A Modeling and Verification Approach Based on Graph Transformation

—UML is a standard modeling language with an open notation and several concepts to be widely used in software modeling. However UML suffers from a lack of formal semantics. So, their models still need to be formally checked against incoherencies or inconsistencies. To reach this goal we propose in this paper, a framework and a tool based on graph transformation allowing an automatic translation of some UML diagrams to equivalent Maude formal specifications. To realize this automatic mapping we use UML Class diagram formalism to define three meta-models. The first one for Class Diagram, the second for State Machine Diagram and the third for the Communication Diagram. Then, we propose a graph grammar to generate Maude specifications of the UML diagrams based on theses meta-models. The meta-modeling tool AToM 3 is used to produce our visual modeling tool according to the proposed UML meta-models. An example is presented to illustrate our approach.
The Proteome Response to Amyloid Protein Expression In Vivo

Protein misfolding disorders such as Alzheimer, Parkinson and transthyretin amyloidosis are characterized by the formation of protein amyloid deposits. Although the nature and location of the aggregated proteins varies between different diseases, they all share similar molecular pathways of protein unfolding, aggregation and amyloid deposition. Most effects of these proteins are likely to occur at the proteome level, a virtually unexplored reality. To investigate the effects of an amyloid protein expression on the cellular proteome, we created a yeast expression system using human transthyretin (TTR) as a model amyloidogenic protein. We used Saccharomyces cerevisiae, a living test tube, to express native TTR (non-amyloidogenic) and the amyloidogenic TTR variant L55P, the later forming aggregates when expressed in yeast. Differential proteome changes were quantitatively analyzed by 2D-differential in gel electrophoresis (2D-DIGE). We show that the expression of the amyloidogenic TTR-L55P causes a metabolic shift towards energy production, increased superoxide dismutase expression as well as of several molecular chaperones involved in protein refolding. Among these chaperones, members of the HSP70 family and the peptidyl-prolyl-cis-trans isomerase (PPIase) were identified. The latter is highly relevant considering that it was previously found to be a TTR interacting partner in the plasma of ATTR patients but not in healthy or asymptomatic subjects. The small ubiquitin-like modifier (SUMO) expression is also increased. Our findings suggest that refolding and degradation pathways are activated, causing an increased demand of energetic resources, thus the metabolic shift. Additionally, oxidative stress appears to be a consequence of the amyloidogenic process, posing an enhanced threat to cell survival.
Implementing Box–Cox Quantile Regression

The Box–Cox quantile regression model introduced by Powell (1991) is a flexible and numerically attractive extension of linear quantile regression techniques. Chamberlain (1994) and Buchinsky (1995) suggest a two stage estimator for this model but the objective function in stage two of their method may not be defined in an application. We suggest a modification of the estimator which is easy to implement. A simulation study demonstrates that the modified estimator works well in situations, where the original estimator is not well defined.
Efficient recognition of Odiya numerals using low complexity neural classifier

The paper develops an efficient but simple adaptive nonlinear classifier for recognition of handwritten Odiya numerals. The standard gradient and curvature features are extracted and nonlinearly mapped by sine/cosine expansions. These nonlinear inputs are fed to a low complexity classifier. The simulation results show excellent classification accuracy when test features are used.
AN ONTOLOGICAL PROXY AGENT FOR WEB INFORMATION PROCESSING

This paper discusses how ontology helps Web information processing to provide better Web services. We propose the ontology-supported solution integration and proxy techniques for Web information processing, which not only helps the user find out proper, integrated query results in accord with his/her proficiency level or satisfaction degree, but supports proxy access of query solutions through a four-tier solution finding process. Our experiment shows around 79.1% of the user queries can be answered by Proxy Agent, leaving about 20.9% of the queries for Answerer Agent to take care, which can effectively alleviate the overloading problem that usually associated with a backend server.
Approximate Learning and Inference for Tracking with Non-overlapping Cameras

Tracking with multiple cameras requires partitioning of ob servations from various sensors into trajectories. In this paper we assume that the observations are generated by a hidden, stochastic 'partition' process and propose a hidden Markov model (HMM) as a generative model for the data. The state space for the hidden variable is intractable, so the inference and learning in our HMM are based on ap proximate representation of the distribution on this state space. The proposed approximation truncates the distri bution from unlikely states. We test our method on real observations; by tracking people in a university building. The tests show that the described approach is an useful al ternative to the existing approximate methods.
Draft Genome of the Scarab Beetle Oryctes borbonicus on La Réunion Island

Beetles represent the largest insect order and they display extreme morphological, ecological and behavioral diversity, which makes them ideal models for evolutionary studies. Here, we present the draft genome of the scarab beetle Oryctes borbonicus, which has a more basal phylogenetic position than the two previously sequenced pest species Tribolium castaneum and Dendroctonus ponderosae providing the potential for sequence polarization. Oryctes borbonicus is endemic to La Réunion, an island located in the Indian Ocean, and is the host of the nematode Pristionchus pacificus, a well-established model organism for integrative evolutionary biology. At 518 Mb, the O. borbonicus genome is substantially larger and encodes more genes than T. castaneum and D. ponderosae. We found that only 25% of the predicted genes of O. borbonicus are conserved as single copy genes across the nine investigated insect genomes, suggesting substantial gene turnover within insects. Even within beetles, up to 21% of genes are restricted to only one species, whereas most other genes have undergone lineage-specific duplications and losses. We illustrate lineage-specific duplications using detailed phylogenetic analysis of two gene families. This study serves as a reference point for insect/coleopteran genomics, although its original motivation was to find evidence for potential horizontal gene transfer (HGT) between O. borbonicus and P. pacificus. The latter was previously shown to be the recipient of multiple horizontally transferred genes including some genes from insect donors. However, our study failed to provide any clear evidence for additional HGTs between the two species.
Relationship Between Tightness of the Hip Joint and Elbow Pain in Adolescent Baseball Players

Background: Repetitive tensile stresses from valgus torque can induce elbow injury in adolescent baseball players. Insufficient hip range of motion (ROM) can change throwing mechanics, reducing the transfer of energy from the lower to the upper extremities. Thus, hip ROM limitations may force the upper extremities to bear the burden of a strong throw. Improper pitching mechanics caused by insufficient hip ROM are thought to increase valgus torque on the elbow when throwing, increasing the risk of elbow injury. Purpose: To investigate the relationship between elbow pain and hip ROM in adolescent baseball players. Study Design: Cross-sectional study; Level of evidence, 3. Methods: A total of 122 adolescent baseball players with a mean age of 12.0 years (range, 6-14 years) participated in this study. Elbow pain, hip flexion angle, and the internal rotation angles of the hip at 0° and 90° of flexion were assessed. Participants were divided into a pain group and a normal group based on the pain assessment, and each hip angle was compared between groups using Student t tests. P values <. 05 were considered statistically significant. Results: Thirty-one of 122 players had elbow pain. The hip flexion angle of the trail leg was 121.9° ± 12.3° for the normal group and 111.2° ± 11.3° for the pain group (P = .0001). The plant leg hip flexion angles were 122.0° ± 12.4° and 113.6° ± 11.3° (P = .0014) for the normal and pain groups, respectively. The internal rotation angle at 0° of hip flexion of the trail leg was 49.4° ± 12.6° and 45.6° ± 8.8° (not significant), and of the plant leg was 49.1° ± 12.5° and 48.7° ± 11.5° (not significant), for the normal and pain groups, respectively. The internal rotation of the trail leg at 90° of hip flexion was 46.9° ± 13.3° in the normal group and 36.1° ± 15.7° in the pain group (P = .0005). In the plant leg, the internal rotation angle at 90° of hip flexion was 46.9° ± 12.2° and 36.4° ± 18.1° for the normal and pain groups, respectively (P = .0013). Conclusion: Limitations to hip flexion and internal rotation at 90° of hip flexion were risk factors for elbow injury. Differences in internal rotation angles between 0° and 90° of hip flexion may be important criteria for identifying adolescent baseball players at risk of elbow pain.
Fourier Techniques for Very Long Astrophysical Time-Series Analysis

We present an assortment of both standard and advanced Fourier techniques that are useful in the analysis of astrophysical time series of very long duration—where the observation time is much greater than the time resolution of the individual data points. We begin by reviewing the operational characteristics of Fourier transforms of time-series data, including power-spectral statistics, discussing some of the differences between analyses of binned data, sampled data, and event data, and we briefly discuss algorithms for calculating discrete Fourier transforms (DFTs) of very long time series. We then discuss the response of DFTs to periodic signals and present techniques to recover Fourier amplitude "lost" during simple traditional analyses if the periodicities change frequency during the observation. These techniques include Fourier interpolation, which allows us to correct the response for signals that occur between Fourier frequency bins. We then present techniques for estimating additional signal properties such as the signal's centroid and duration in time, the first and second derivatives of the frequency, the pulsed fraction, and an overall estimate of the significance of a detection. Finally, we present a recipe for a basic but thorough Fourier analysis of a time series for well-behaved pulsations.