Miracle-dz/UniFAR-FTUs huggingface dataset:
Scaffold-Based Pan-Agonist Design for the PPARα, PPARβ and PPARγ Receptors

As important members of nuclear receptor superfamily, Peroxisome proliferator-activated receptors (PPAR) play essential roles in regulating cellular differentiation, development, metabolism, and tumorigenesis of higher organisms. The PPAR receptors have 3 identified subtypes: PPARα, PPARβ and PPARγ, all of which have been treated as attractive targets for developing drugs to treat type 2 diabetes. Due to the undesirable side-effects, many PPAR agonists including PPARα/γ and PPARβ/γ dual agonists are stopped by US FDA in the clinical trials. An alternative strategy is to design novel pan-agonist that can simultaneously activate PPARα, PPARβ and PPARγ. Under such an idea, in the current study we adopted the core hopping algorithm and glide docking procedure to generate 7 novel compounds based on a typical PPAR pan-agonist LY465608. It was observed by the docking procedures and molecular dynamics simulations that the compounds generated by the core hopping and glide docking not only possessed the similar functions as the original LY465608 compound to activate PPARα, PPARβ and PPARγ receptors, but also had more favorable conformation for binding to the PPAR receptors. The additional absorption, distribution, metabolism and excretion (ADME) predictions showed that the 7 compounds (especially Cpd#1) hold high potential to be novel lead compounds for the PPAR pan-agonist. Our findings can provide a new strategy or useful insights for designing the effective pan-agonists against the type 2 diabetes.
Letters to Blood To the editor : A pharmacogenetic analysis of the Canadian Cancer Trials Group MY . 10 clinical trial of maintenance therapy for multiple myeloma

Biology, University of New Brunswick, Saint John, NB, Canada; Southern Alberta Cancer Research Institute, University of Calgary, Calgary, AB, Canada; Hematology, Vancouver General Hospital, Vancouver, BC, Canada; Queen Elizabeth II Health Sciences Center, Dalhousie University, Halifax, NS, Canada; Oncology, Princess Margaret Hospital, Toronto, ON, Canada; Oncology, London Health Sciences Centre, London, ON, Canada; Cancer Clinical Research Unit, Princess Margaret Cancer Centre, Toronto, ON, Canada; Centre for Individualized Medicine, Mayo Clinic Arizona, Scottsdale, AZ; Laboratory Medicine, Saint John Regional Hospital, Saint John, NB, Canada; Department of Internal Medicine, Queen’s University, Kingston, ON, Canada; Canadian Cancer Trials Group, Queen’s University, Kingston, ON, Canada; Juravinski Hospital and Cancer Centre and McMaster University, Hamilton ON, Canada; and Department of Oncology, Saint John Regional Hospital, Dalhousie University and University of New Brunswick, Saint John, NB, Canada
Refuting the OECD-World Bank development narrative: was East Asia’s ‘Economic Miracle’ primarily driven by education quality and cognitive skills?*

ABSTRACT Founded on several highly influential quantitative studies, the past decade has witnessed the OECD and World Bank increasingly converge on the view that cognitive levels of students and education quality, as proxied by international large-scale assessments (ILSAs), are the primary determinant of national economic growth worldwide. More recent OECD and World Bank pronouncements have further suggested these dynamics are clearly illustrated in East Asia’s education and ‘Economic Miracle’, in particular the cases of South Korea and Singapore. Herein we utilise the OECD’s own data to examine this new development narrative, finding little evidence in support of these claims.
Temporally Coherent Bayesian Models for Entity Discovery in Videos by Tracklet Clustering

A video can be represented as a sequence of tracklets, each spanning 10-20 frames, and associated with one entity (eg. a person). The task of \emph{Entity Discovery} in videos can be naturally posed as tracklet clustering. We approach this task by leveraging \emph{Temporal Coherence}(TC): the fundamental property of videos that each tracklet is likely to be associated with the same entity as its temporal neighbors. Our major contributions are the first Bayesian nonparametric models for TC at tracklet-level. We extend Chinese Restaurant Process (CRP) to propose TC-CRP, and further to Temporally Coherent Chinese Restaurant Franchise (TC-CRF) to jointly model short temporal segments. On the task of discovering persons in TV serial videos without meta-data like scripts, these methods show considerable improvement in cluster purity and person coverage compared to state-of-the-art approaches to tracklet clustering. We represent entities with mixture components, and tracklets with vectors of very generic features, which can work for any type of entity (not necessarily person). The proposed methods can perform online tracklet clustering on streaming videos with little performance deterioration unlike existing approaches, and can automatically reject tracklets resulting from false detections. Finally we discuss entity-driven video summarization- where some temporal segments of the video are selected automatically based on the discovered entities.
A poly-algorithm for parallel dense matrix multiplication on two-dimensional process grid topologies

In this paper, we present several new and generalized parallel dense matrix multiplication algorithms of the form C = AB + C on two-dimensional process grid topologies. These algorithms can deal with rectangular matrices distributed on rectangular grids. We classify these algorithms coherently into three categories according to the communication primitives used and thus we o er a taxonomy for this family of related algorithms. All these algorithms are represented in the data distribution independent approach and thus do not require a speci c data distribution for correctness. The algorithmic compatibility condition result shown here ensures the correctness of the matrix multiplication. We de ne and extend the data distribution functions and introduce permutation compatibility and algorithmic compatibility. We also discuss a permutation compatible data distribution (modi ed virtual 2D data distribution). We conclude that no single algorithm always achieves the best performance on di erent matrix and grid shapes. A practical approach to resolve this dilemma is to use poly-algorithms. We analyze the characteristics of each of these matrix multiplication algorithms and provide initial heuristics for using the poly-algorithm. All these matrix multiplication algorithms have been tested on the IBM SP2 system. The experimental results are presented in order to demonstrate their relative performance characteristics, motivating the combined value of the taxonomy and new algorithms introduced here. Revision and extension of our original paper entitled \The Multicomputer Toolbox Approach to Concurrent BLAS" submitted September 1, 1993. Address correspondence to: Mississippi State University, Engineering Research Center, PO Box 6176, Mississippi State, MS 39762. Tel: 601-325-8435. Email: tony@cs.msstate. edu.
ABVD plus radiotherapy versus EVE plus radiotherapy in unfavorable stage IA and IIA Hodgkin's lymphoma: results from an Intergruppo Italiano Linfomi randomized study.

BACKGROUND In 1997, the Intergruppo Italiano Linfomi started a randomized trial to evaluate, in unfavorable stage IA and IIA Hodgkin's lymphoma (HL) patients, the efficacy and toxicity of the low toxic epirubicin, vinblastine and etoposide (EVE) regimen followed by involved field radiotherapy in comparison to the gold standard doxorubicin, bleomycin, vinblastine and dacarbazine (ABVD) regimen followed by the same radiotherapy program. PATIENTS AND METHODS Patients should be younger than 65 years with unfavorable stage IA and IIA HL (i.e. stage IA or IIA with bulky disease and/or subdiaphragmatic disease, erythrocyte sedimentation rate higher than 40, extranodal (E) involvement, hilar involvement and more than three involved lymph node areas). RESULTS Ninety-two patients were allocated to the ABVD arm and 89 to the EVE arm. Complete remission (CR) rates at the end of treatment program [chemotherapy (CT) + RT] were 93% and 92% for ABVD and EVE arms, respectively (P = NS). The 5-year relapse-free survival (RFS) rate was 95% for ABVD and 78% for EVE (P < 0.05). As a consequence of the different relapse rate, the 5-year failure-free survival (FFS) rate was significantly better for ABVD (90%) than for EVE (73%) arm (P < 0.05). No differences in terms of overall survival (OS) were observed for the two study arms. CONCLUSIONS In unfavorable stage IA and IIA HL patients, no differences were observed between ABVD and EVE arms in terms of CR rate and OS. EVE CT, however, was significantly worse than ABVD in terms of RFS and FFS and cannot be recommended as initial treatment for HL.
Persistent deviations from market fundamentals or rational bubbles in stock market prices ?

Tests for fractional integration in the log dividend yield of the S&P 500 are conducted in order to test the proposition that exogenous shocks have permanent effects. The presence of a unit root in the log dividend yield is consistent with “rational bubbles” in stock prices. Previous empirical studies employing univariate and bivariate tests for integer orders of integration or cointegration have had difficulty in rejecting the rational-bubbles hypothesis. Our findings, based on tests for fractional integration, yield robust rejections of the same hypothesis. The results strongly suggest that the log dividend yield is mean reverting.
Proposal Generalization Error Bounds for State Space Models with an Application to Economic Forecasting Version : July 14 , 2010

In this thesis, I propose to derive entirely data dependent generalization error bounds for state space models. These results can characterize the out-of-sample accuracy of many types of forecasting methods. The bounds currently available for time series data rely both on a quantity describing the dependence properties of the data generating process known as the mixing rate and on a quantification of the complexity of the model space. I will derive methods for estimating the mixing behavior from data and characterize the complexity of state space models. The resulting risk bounds will be useful for empirical researchers at the forefront of economic forecasting as well as for economic policy makers. The bounds can also be applied in other situations where state space models are employed.
Societal hierarchy and the health Olympics.

hat makes a population healthy? Advising individuals about the avoidance of risk factors is certainly important, but that is probably not the most efficient way to improve the overall health of a population. 1 The effects of the usual do’s and don’ts that we all preach pale in comparison with the effect of society’s structural factors on population health, especially the amount of hierarchy as measured by income distribution. With its life expectancies of 77.6 years for men and 84.3 years for women, Japan is the current leader in what might be called the health Olympics (the ranking of countries by life expectancy), a position it has held since 1977. Canada also ranks among the top countries, with life expectancies of 76.2 years for men and 81.9 years for women. Although Japan has twice as many male smokers per capita as Canada does, Japan’s smoking-related mortality rate is half that of
Z language based an algorithm for event detection, analysis and classification in machine vision

A common task in various machine learning (ML) application areas involves observing regularly gathered data for `interesting' events. This mission is predominant in reconnaissance, but also in responsibilities fluctuating from the investigation of scientific data to the observing of unsurprisingly happening events, and from controlling engineering procedures to noticing human behavior. We will refer to this observing procedure with the determination of classifying remarkable manifestations, as event detection, analysis and classification. With the appearance of personal computers (PCs) a lot of efforts have been made to substitute manual investigation by a computerized manner. Data, nevertheless, have become gradually difficult, and the sizes of gathered data have become enormously bulky in latest years. Text documents, JPEG images, MP3, videos and even relational data are now regularly gathered. In this paper, we propose an algorithm for event detection, analysis and classification in machine vision. Till proposed algorithm is deliberated a significant facility, required degree of event detection cannot be achieved. Finally, we use K-means algorithm for classification of incoming events and proposed algorithm has been validated by Z Formal specification language in general. The proposed algorithm has been implemented in Matlab and results have been gathered through a data mining tool. Using the proposed algorithm, the events are easily detected, analyzed and classified in machine vision.
Autism: A New Introduction to Psychological Theory and Current Debate

The autism research world has made considerable strides since the first edition of Happé’s book, so it is timely that a new version now emerges. As perspectives are frequently diverse (Pellicano, 2013; Fletcher-Watson, 2019), co-authoring this outsider perspective update was a good choice. Nevertheless, full advantage of this was not taken, as the potential for oiling the wheels of inclusion for the autistic voice did not happen.
Isolation of Functional RNA From Grapevine Tissues Poor in Nucleic Acid Content

A modified procedure for efficient isolation of intact and biologically active RNA from leaves, berries and cell cultures of grapevine (Vitis vinifera L.) is described. RNA is extracted in the presence of mild denaturants followed by sequential precipitations with potassium acetate and isopropanol. RNA is recovered free of contaminants after centrifugation through a CsCI cushion. Alternatively, RNA from grapevine callus and berry cell suspensions can be purified after the isopropanol step by high-salt precipitations, without a CsCI centrifugation step. The resulting RNA is of high-quality, as judged by agarose gel electrophoresis and northern blot analysis. Furthermore, RNA isolated by this method is biologically active as was evidenced by in vitro translation and analysis of the products by polyacrylamide gel electrophoresis and fluorography. This procedure can also be applied to other perennial woody plant species.
A Design Technique for Energy Reduction in NORA CMOS Logic

In this work, a design technique to reduce the energy consumption in NO RAce (NORA) circuits is presented. The technique is based on a unidirectional switch topology combined with a new clocking scheme permitting both charge recycling between circuit nodes and elimination of the short circuit current. Calculations proved that energy savings higher than 20% can be achieved. Simulation results from NORA designs in a 0.18-mum CMOS technology are presented to demonstrate the effectiveness of the proposed technique to achieve both energy and energy-delay product reduction
Transcriptional Regulation of Human NANOG by Alternate Promoters in Embryonic Stem Cells

Introduction The potential of pluripotent stem cells to be used for cell therapy depends on a comprehensive understanding of the molecular mechanisms underlying their unique ability to specify cells of all germ layers while undergoing unlimited self-renewal. Alternative splicing and alternate promoter selection contribute to this mechanism by increasing the number of transcripts generated from a single gene locus and thus enabling expression of novel protein variants which may differ in their biological role. The homeodomain-containing transcription factor NANOG plays a critical role in maintaining the pluripotency of Embryonic Stem Cells (ESC). Therefore, a thorough understanding of the transcriptional regulation of the NANOG locus in ESCs is necessary. Methods Regulatory footprints and transcription levels were identified for NANOG in human embryonic stem cells from data obtained using high-throughput sequencing methodologies. Quantitative real-time PCR following reverse transcription of RNA extracted human ESCs was used to validate the expression of transcripts from a region that extends upstream of the annotated NANOG transcriptional start. Promoter identification and characterization were performed using promoter reporter and electrophoretic mobility shift assays. Results Transcriptionally active chromatin marking and transcription factor binding site enrichment were observed at a region upstream of the known transcriptional start site of NANOG. Expression of novel transcripts from this transcriptionally active region confirmed the existence of NANOG alternative splicing in human ESCs. We identified an alternate NANOG promoter of significant strength at this upstream region. We also discovered that NANOG autoregulates its expression by binding to its proximal downstream promoter. Conclusion Our study reveals novel transcript expression from NANOG in human ESCs, indicating that alternative splicing increases the diversity of transcripts originating from the NANOG locus and that these transcripts are expressed by an alternate promoter. Alternative splicing and alternate promoter usage collaborate to regulate NANOG, enabling its function in the maintenance of ESCs.
Navigation Aid for Mobility Assistants

—This paper introduces Navigation Aid as the ﬁrst development of the European project Assistants for Safe Mobility (ASSAM). By fusing odometry, GPS and map information with the help of a Monte Carlo particle ﬁlter, we provide precise outdoor localization for assistive devices such as a walker. This allows for the application of a navigation system that considers device-speciﬁc environments including sidewalks, cycleways, etc. Target group needs are addressed by a simple and intuitive user interface running on Android-powered devices.
Kernel regression uniform rate estimation for censored data under α-mixing condition

In this paper, we study the behavior of a kernel esti- mator of the regression function in the right censored model with α-mixing data . The uniform strong consistency over a real compact set of the estimate is established along with a rate of convergence. Some simulations are carried out to illustrate the behavior of the estimate with different examples for finite sample sizes.
Innovations in Teaching Adult Education: Living History Museums and Transformative Learning in the University Classroom

The difficult times in which we live require innovative, creative, and hopeful pedagogies of adult education. This article describes a nontraditional experiential, “empathy-invoking” approach to the teaching of a graduate course on the theory and research of adult learning. The approach begins with the building of a safe learning community, a familiar “knowledge curriculum,” and a structured syllabus with academic readings, small group discussions, student “theory-to-practice” facilitation of learning activities, and an academic mid-term paper. Both the teacher and students design and lead learning activities which elaborate, “unpack,” and critique readings, and develop students’ capacity for experiential, emotional, spiritual, arts-based, and bodily learning as well as group process, all the while reinforcing trust, deeper relationships, cooperation, and better knowledge of each others’ lives, personalities, capabilities, and identities. The class culminates in creative presentations where learners transform the classroom into “living history museums” representing the sites of adult learning they have investigated in field research. Visitors to living history museums engage in a rich array of informal adult learning; they gain new knowledge, participate in hands-on learning and role playing, and at times even experience transformative learning. In this class, the museum and its learning opportunities come into the classroom, and are created by learners themselves.
Real-time estimation of the parameters and fluxes of induction motors

A novel method for the real-time estimation of the parameters and fluxes of induction motors is presented. The method is based on a standard model of the induction motor, expressed in rotor coordinates. It is assumed that current and position (or velocity) measurements are available. The interesting features of the method are: that it does not rely on special tests such as the locked rotor test or the no-load test (instead, a broad range of motor responses can be used); the method provides estimates of the rotor fluxes together with the estimates of the parameters; and measures of the uncertainties in the estimated motor parameters are provided. Results for both simulated and experimental data are provided. <<ETX>>
The effect of cybersickness on the affective appraisal of virtual environments

One application of virtual environments is to form an affective appraisal of an environment, such as a building before it is constructed. But the affective appraisal attributed to a real environment can differ from the affective appraisal of the simulated virtual environment. One virtual environment specific problem is that people can experience cybersickness by watching virtual scene movement. We hypothesize that people who experience cybersickness will affectively appraise a certain virtual environment differently from people who do not experience cybersickness. In order to test this, a virtual environment was created with the aid of a game level editor. Participants viewed a virtual tour through the environment with a superimposed camera oscillation with different amplitudes, on a 20 " computer screen. These amplitudes were subsequently tested as stimuli of cybersickness incidence. This yielded no significant result. Consequently a polygenic stimulus was implemented which did induce cybersickness and was mixed with an appraisal task. Results show that cybersickness significantly influences the affective appraisal of a virtual environment) 003. 0 , 30 (< = p N , which is mostly due to a decrease in pleasantness attributed to the environment. Detailed analysis and recommendations for future research have subsequently been given. 4 Preface I have always been an ardent videogame player, and was excited to find out the University of Utrecht was starting a center for Advanced Gaming and Simulation (AGS) in conjunction with TNO and the HKU. However, even after some delay in my study career, the thesis project came to early; the center was still in its preliminary buildup stage. Luckily at that moment I was doing an experimentation project at the university under Joske Houtkamp on the affective appraisal of virtual environments. This research is one of the objectives of AGS and consequently she was able to set me up with TNO to perform similar research there, which is this thesis project. Therefore my first thanks should go to Joske Houtkamp, who endured two consecutive projects with me and still remains friendly. Special praise should also go to my daily supervisor at TNO, Martijn van Emmerik, who was always available and willing to help me out, especially with my many questions on the statistical analysis. Further thanks go out to Jelte Bos and Lex Toet on their help with cybersickness and affective appraisal respectively. Additionally, this thesis wouldn't have been possible without my parents' patient and financial support, the support …
Legionella Effectors That Promote Nonlytic Release from Protozoa

Legionella pneumophila, the bacterial agent of legionnaires' disease, replicates intracellularly within a specialized vacuole of mammalian and protozoan host cells. Little is known about the specialized vacuole except that the Icm/Dot type IVsecretion system is essential for its formation and maintenance. The Legionella genome database contains two open reading frames encoding polypeptides (LepA and LepB) with predicted coiled-coil regions and weak homology to SNAREs; these are delivered to host cells by an Icm/Dot–dependent mechanism. Analysis of mutant strains suggests that the Lep proteins may enable the Legionella to commandeer a protozoan exocytic pathway for dissemination of the pathogen.