Miracle-dz/UniFAR-FTUs huggingface dataset:
Split and Join: Strong Partitions and Universal Steiner Trees for Graphs

We study the problem of constructing universal Steiner trees for undirected graphs. Given a graph G and a root node r, we seek a single spanning tree T of minimum stretch, where the stretch of T is defined to be the maximum ratio, over all terminal sets X, of the cost of the minimal sub-tree TX of T that connects X to r to the cost of an optimal Steiner tree connecting X to r in G. Universal Steiner trees (USTs) are important for data aggregation problems where computing the Steiner tree from scratch for every input instance of terminals is costly, as for example in low energy sensor network applications. graphs with 2O(√log n)-stretch. We also give a polynomial time We provide a polynomial time UST construction for general polylog(n)-stretch construction for minor-free graphs. One basic building block of our algorithms is a hierarchy of graph partitions, each of which guarantees small strong diameter for each cluster and bounded neighbourhood intersections for each node. We show close connections between the problems of constructing USTs and building such graph partitions. Our construction of partition hierarchies for general graphs is based on an iterative cluster merging procedure, while the one for minor-free graphs is based on a separator theorem for such graphs and the solution to a cluster aggregation problem that may be of independent interest even for general graphs. To our knowledge, this is the first subpolynomial-stretch (o(nε) for any ε >; 0) UST construction for general graphs, and the first polylogarithmic-stretch UST construction for minor-free graphs.
Comparative assessment of content-based face image retrieval in different color spaces

Content-based face image retrieval is concerned with computer retrieval of face images (of a given subject) based on the geometric or statistical features automatically derived from these images. It is well known that color spaces provide powerful information for image indexing and retrieval by means of color invariants, color histogram, color texture, etc. This paper assesses comparatively the performance of content-based face image retrieval in different color spaces using a standard algorithm, the Principal Component Analysis (PCA), which has become a popular algorithm in the face recognition community. In particular, we comparatively assess 12 color spaces (RGB, HSV, YUV, YCbCr, XYZ, YIQ, L*a*b*, U*V*W*, L*u*v*, I1I2I3, HSI, and rgb) by evaluating 7 color configurations for every single color space. A color configuration is defined by an individual or a combination of color component images. Take the RGB color space as an example, possible color configurations are R, G, B, RG, RB, GB, and RGB. Experimental results using 1,800 FERET R, G, B images corresponding to 200 subjects show that some color configurations, such as R in the RGB color space and V in the HSV color space, help improve face retrieval performance.
Revisiting Interacting Subsystems Accounts of Cognitive Architecture: The Emergence of Control and Complexity in an Algebra Task

Symbolic accounts of cognitive architecture most often have a central hub where information is processed (e.g. the production process in ACT-R [1]). An alternative approach is to model cognition as the interaction of multiple largely autonomous subsystems [2, 3]. This latter, Interacting Subsystems, approach is explored in the GLAM-PS cognitive architecture, a theory that operationalizes many of the assumptions of strongly grounded approaches to cognition [4]. The GLAM-PS model of problem solving in algebra is described. Control in the algebra model is passed between three subroutines when solving a problem. These subroutines emerge from the interaction of different subsystems and are not explicitly programmed into the model. By systematically varying two short-term memory parameters it is shown that the model’s successful performance of the task depends on the interaction of the contributing modules, and that this interaction demonstrates complexity, with additional memory resources not always improving performance.
Atomic Constraints between the Voltage Sensor and the Pore Domain in a Voltage-gated K+ Channel of Known Structure

In voltage-gated K+ channels (Kv), membrane depolarization promotes a structural reorganization of each of the four voltage sensor domains surrounding the conducting pore, inducing its opening. Although the crystal structure of Kv1.2 provided the first atomic resolution view of a eukaryotic Kv channel, several components of the voltage sensors remain poorly resolved. In particular, the position and orientation of the charged arginine side chains in the S4 transmembrane segments remain controversial. Here we investigate the proximity of S4 and the pore domain in functional Kv1.2 channels in a native membrane environment using electrophysiological analysis of intersubunit histidine metallic bridges formed between the first arginine of S4 (R294) and residues A351 or D352 of the pore domain. We show that histidine pairs are able to bind Zn2+ or Cd2+ with high affinity, demonstrating their close physical proximity. The results of molecular dynamics simulations, consistent with electrophysiological data, indicate that the position of the S4 helix in the functional open-activated state could be shifted by ∼7–8 Å and rotated counterclockwise by 37° along its main axis relative to its position observed in the Kv1.2 x-ray structure. A structural model is provided for this conformation. The results further highlight the dynamic and flexible nature of the voltage sensor.
Trip Router with Individualized Preferences (TRIP): Incorporating Personalization into Route Planning

Popular route planning systems (Windows Live Local, Yahoo! Maps, Google Maps, etc.) generate driving directions using a static library of roads and road attributes. They ignore both the time at which a route is to be traveled and, more generally, the preferences of the drivers they serve. We present a set of methods for including driver preferences and time-variant traffic condition estimates in route planning. These methods have been incorporated into a working prototype named TRIP. Using a large database of GPS traces logged by drivers, TRIP learns time-variant traffic speeds for every road in a widespread metropolitan area. It also leverages a driver's past GPS logs when responding to future route queries to produce routes that are more suited to the driver's individual driving preferences. Using experiments with real driving data, we demonstrate that the routes produced by TRIP are measurably closer to those actually chosen by drivers than are the routes produced by routers that use static heuristics.
Induction of cell migration by pro-urokinase binding to its receptor: possible mechanism for signal transduction in human epithelial cells

A human epithelial cell line, WISH, and a mouse cell line, LB6-uPAR, transfected with the human urokinase receptor (uPAR), both expressed high affinity uPAR but undetectable levels of urokinase (uPA). In two independent assays, binding of exogenous pro-uPA produced an up to threefold enhancement of migration. The migration was time and concentration dependent and did not involve extracellular proteolysis. This biologic response suggested that uPAR can trigger an intracellular signal. Since this receptor is a glycosyl-phosphatidylinositol-linked protein, we postulated that it must do so by interacting with other proteins, among which, by analogy to other systems, would be a kinase. To test this hypothesis, we carried out a solid phase capture of uPAR from WISH cell lysates using either antibodies against uPAR or pro-uPA adsorbed to plastic wells, followed by in vitro phosphorylation of the immobilized proteins. SDS-PAGE and autoradiography revealed two phosphorylated protein bands of 47 and 55 kD. Both proteins were phosphorylated on serine residues. Partial sequence of the two proteins showed a 100% homology to cytokeratin 18 (CK18) and 8 (CK8), respectively. A similar pattern of phosphorylation was obtained with lysates from A459 cells, a lung carcinoma, but not HL60, LB6-uPAR or HEp3 cell lysates, suggesting that the identified multiprotein uPAR- complex may be specific for simple epithelia. Moreover, immunocapture with antibody to another glycosyl-phosphatidylinositol-linked protein, CD55, which is highly expressed in WISH cells, was ineffective. The kinase was tentatively identified as protein kinase C, because it was inhibited by an analogue of staurosporine more specific for PKC and not by a PKA or tyrosine kinase inhibitors. The kinase was tentatively identified as PKC epsilon because of its resistance to PMA down- modulation, independence of Ca2+ for activity, and reaction with a specific anti-PKC epsilon antibody in Western blots. Cell fractionation into cytosolic and particulate fractions revealed that all four proteins, the kinase, uPAR, CK18, and CK8, were present in the particulate fraction. In vivo, CK8, and to a lesser degree CK18, were found to be phosphorylated on serine residues. Occupation of uPAR elicited a time-dependent increase in the phosphorylation intensity of CK8, a cell shape change and a redistribution of the cytokeratin filaments. These results strongly suggest that uPAR serves not only as an anchor for uPA but participates in a signal transduction pathway resulting in a pronounced biological response.
Autonomous Feature-Based Exploration using Multi-Sensors

In this paper, we present an algorithm for feature based exploration of a prior unknown indoor environment. The mobile robot Odete equipped with two different types of sensors is used. Employing different sensor capabilities, 3D features are detected autonomously very quickly. The main contribution of the paper is to let the robot move to a new unexplored place, based on some prospect values of this place. One of these prospect values is the natural feature quality available at that place, whereas the second prospect value is the navigation cost to it. The vision-based feature extractor is demonstrated, showing how it is self motivated to search for an interesting region using a segmentation and detection process. The obtained region is classified into known objects, and the relative location information for the selected object is memorized. The mobile robot plans its motion such that it continuously builds up a geometrical model of the features, taking into consideration the cost of reaching a target point. The target point is chosen depending on the number of the features and their visibility that a robot can cover with its sensors upon reaching that location. The captured information from these sensors is transformed into different representations in order to achieve the task
Posttraumatic Stress Disorder Experienced by Survivors of School Violence in South Africa: Sex and Age Differences

The study investigated sex and age differences in the experiences of posttraumatic stress disorder by survivors of school violence in urban and rural schools in the Eastern Cape area of South Africa. One hundred and thirty five survivors of school violence (males =57, females =78, age range: 10 year or younger, 11–15 years, and 16 year or older) described their posttraumatic stress disorder (PTSD) symptoms using a numeric measures of PTSD on a 37 items scale. The survivors were learners in primary (n=73) as well as secondary schools (n=62). The study found that survivors experienced three forms of violence, namely: verbal, physical, and sexual in nature. The sex of survivors was not a significant factor in either the forms of violence or the PTSD symptoms experienced. Age differences were significant for four of the six PTSD symptom categories.
Extending the Size of Protein–RNA Complexes Studied by Nuclear Magnetic Resonance Spectroscopy

Increasing evidence supports a model of cellular biochemistry in which most proteins exert their biological role through either transient or relatively stable multicomponent macromolecular complexes. The key to understanding the functions of these complexes lies in their structural investigation by a variety of biophysical methods. For very large systems, cryoelectron microscopy can provide images of the overall shape of the biomolecules, and X-ray crystallographic methods can access the molecular details of multiprotein assemblies. However, the crystallization process is restricted to systems that are scarce in unstructured elements or structural heterogeneity, in contrast to the situation frequently found in the components of signal transduction pathways and transcriptional regulation, among others. Nuclear magnetic resonance spectroscopy is ideally suited to study these latter complexes, but only in recent years have techniques been developed to overcome the size limitation. The use of specific isotope-labeling strategies enables both a simplification of the NMR spectra and reduction in the detrimental relaxation effects that lead to signal degradation in large, slowly tumbling molecules. In addition, applications of orientational restraints from residual dipolar couplings (RDCs) and further developments in utilizing structural restraints derived from spin labels provide novel and powerful data for NMR studies of high-molecular-weight proteins and complexes. Here, we discuss the emerging potential of NMR to probe the structure and dynamics of increasingly large complexes, especially when structural information is available for smaller regions of such complexes. In particular, aspects of sample production and NMR techniques will discussed. A strategy for quaternary-structure determination based on structures of subdomains, RDCs, and distance restraints is outlined.
Towards Data-Driven Football Player Assessment

Understanding the value of a football player is a challenging problem. Player valuation is not only critical for scouting, bidding and negotiation processes but also attracts a large media and fan interest. Due to the complexities which arise from the fact that player pool is distributed over hundreds of different leagues and many different playing positions, many clubs hire domain experts (often retired professional players) in order to evaluate the value of potential players. We argue that such human-based scouting has several drawbacks including high cost, inability to scale to thousands of active players and inevitable subjective biases. In this paper we present a methodology for data-driven player market value estimation which tackles these drawbacks. To examine the quality of the proposed methodology and demonstrate that our data-driven valuation outperforms widely used transfermarkt.com market value estimates in predicting the team performance.
Timing Analysis of Cyclic Combinational Circuits *

The accepted wisdom is that combinational circuits must have acyclic (i.e., loop-free or feed-forward) topologies. And yet simple examples suggest that this need not be so. In previous work, we advocated the design of cyclic combinational circuits (i.e., circuits with loops or feedback paths). We proposed a methodology for analyzing and synthesizing such circuits, with an emphasis on the optimization of area. In this paper, we extend our methodology into the temporal realm. We characterize the true delay of cyclic circuits through symbolic event propagation in the floating mode of operation, according to the up-bounded inertial delay model. We present analysis results for circuits optimized with our program CYCLIFY. Some benchmark circuits were optimized significantly, with simultaneous improvements of up to 10% in the area and 25% in the delay.
Forced Expiratory Volume in One Second Predicts Length of Stay and In-Hospital Mortality in Patients Undergoing Cardiac Surgery: A Retrospective Cohort Study

Objective An aging population and increasing use of percutaneous therapies have resulted in older patients with more co-morbidity being referred for cardiac surgery. Objective measurements of physiological reserve and severity of co-morbid disease are required to improve risk stratification. We hypothesised that FEV1 would predict mortality and length of stay following cardiac surgery. Methods We assessed clinical outcomes in 2,241 consecutive patients undergoing coronary artery bypass grafting and/or valve surgery from 2001 to 2007 in a regional cardiac centre. Generalized linear models of the association between FEV1 and length of hospital stay and mortality were adjusted for age, sex, height, body mass index, socioeconomic status, smoking, cardiovascular risk factors, long-term use of bronchodilators or steroids for lung disease, and type and urgency of surgery. FEV1 was compared to an established risk prediction model, the EuroSCORE. Results Spirometry was performed in 2,082 patients (93%) whose mean (SD) age was 67 (10) years. Median hospital stay was 3 days longer in patients in the lowest compared to the highest quintile for FEV1, 1.35-fold higher (95% CI 1.20–1.52; p<0.001). The adjusted odds ratio for mortality was increased 2.11-fold (95% CI 1.45–3.08; p<0.001) per standard deviation decrement in FEV1 (800 ml). FEV1 improved discrimination of the EuroSCORE for mortality. Similar associations were found after excluding people with known pulmonary disease and/or airflow limitation on spirometry. Conclusions Reduced FEV1 strongly predicted increased length of stay and in-hospital mortality following cardiac surgery. FEV1 is a widely available measure of physiological health that may improve risk stratification of complex patients undergoing cardiac surgery and should be evaluated for inclusion in new prediction tools.
Firms learning price in a monopolistic competition economic model

This paper aims to investigate the possibility for monopolistically competitive firms to set the price and the quantity of goods through a reinforcement learning approach. The model incorporates a set of firms that produce and sell differentiated goods in monopolistically competitive markets and households that supply different types of labor, purchase goods for consumption and hold money. The households behave optimally, maximizing their utility, while the firms learn their desired mark-up by a reinforcement learning algorithm in order to set the price.
Decay Kinetics of an Interferon Gamma Release Assay with Anti-Tuberculosis Therapy in Newly Diagnosed Tuberculosis Cases

Background Qualitative and quantitative changes in IGRA response offer promise as biomarkers to monitor Tuberculosis (TB) drug therapy, and for the comparison of new interventions. We studied the decay kinetics of TB-specific antigen T-cell responses measured with an in-house ELISPOT assay during the course of therapy. Methods Newly diagnosed sputum smear positive TB cases with typical TB chest radiographs were recruited. All patients were given standard anti-TB treatment. Each subject was followed up for 6 months and treatment outcomes were documented. Blood samples were obtained for the ESAT-6 and CFP-10 (EC) ELISPOT at diagnosis, 1-, 2-, 4- and 6-months. Qualitative and quantitative reversion of the ELISPOT results were assessed with McNemar test, conditional logistic regression and mixed-effects hierarchical Poisson models. Results A total of 116 cases were recruited and EC ELISPOT was positive for 87% (95 of 109) at recruitment. There was a significant decrease in the proportion of EC ELISPOT positive cases over the treatment period (p<0.001). Most of the reversion occurred between the start and first month of treatment and at completion at 6 months. ESAT-6 had higher median counts compared to CFP-10 at all time points. Counts for each antigen declined significantly with therapy (p<0.001). Reverters had lower median SFUs at the start of treatment compared to non-Reverters for both antigens. Apart from the higher median counts for non-Reverters, no other risk factors for non-reversion were found. Conclusions TB treatment induces qualitative and quantitative reversion of a positive in-house IGRA in newly diagnosed cases of active TB disease. As this does not occur reliably in the majority of cured individuals, qualitative and quantitative reversion of an IGRA ELISPOT has limited clinical utility as a surrogate marker of treatment efficacy.
The Light Field Attachment: Turning a DSLR into a Light Field Camera Using a Low Budget Camera Ring

We propose a concept for a lens attachment that turns a standard DSLR camera and lens into a light field camera. The attachment consists of eight low-resolution, low-quality side cameras arranged around the central high-quality SLR lens. Unlike most existing light field camera architectures, this design provides a high-quality 2D image mode, while simultaneously enabling a new high-quality light field mode with a large camera baseline but little added weight, cost, or bulk compared with the base DSLR camera. From an algorithmic point of view, the high-quality light field mode is made possible by a new light field super-resolution method that first improves the spatial resolution and image quality of the side cameras and then interpolates additional views as needed. At the heart of this process is a super-resolution method that we call iterative Patch- And Depth-based Synthesis (iPADS), which combines patch-based and depth-based synthesis in a novel fashion. Experimental results obtained for both real captured data and synthetic data confirm that our method achieves substantial improvements in super-resolution for side-view images as well as the high-quality and view-coherent rendering of dense and high-resolution light fields.
Direct conversion of root primordium into shoot meristem relies on timing of stem cell niche development

To understand how the identity of an organ can be switched, we studied the transformation of lateral root primordia (LRP) into shoot meristems in Arabidopsis root segments. In this system, the cytokinin-induced conversion does not involve the formation of callus-like structures. Detailed analysis showed that the conversion sequence starts with a mitotic pause and is concomitant with the differential expression of regulators of root and shoot development. The conversion requires the presence of apical stem cells, and only LRP at stages VI or VII can be switched. It is engaged as soon as cell divisions resume because their position and orientation differ in the converting organ compared with the undisturbed emerging LRP. By alternating auxin and cytokinin treatments, we showed that the root and shoot organogenetic programs are remarkably plastic, as the status of the same plant stem cell niche can be reversed repeatedly within a set developmental window. Thus, the networks at play in the meristem of a root can morph in the span of a couple of cell division cycles into those of a shoot, and back, through transdifferentiation. Highlighted article: Arabidopsis lateral roots can be directly transdifferentiated to shoot identity by cytokinin treatment during a narrow time window of lateral root development.
Assessing the Validity of the Social Communication Questionnaire in Adults with Autism Spectrum Disorders and Intellectual Disability

ii Dedication . iv Acknowledgments. v Vita . vi List of Tables . ix List of Figures . x Chapter 1: Introduction . 1 Chapter 2: Method . 23 Chapter 3: Results . 39 Chapter 4: Discussion . 45 Appendix: Tables, Figures, Questionnaires, and Consent Forms . 53 References . 96