Miracle-dz/UniFAR-FTUs huggingface dataset:
CREB Binds to Multiple Loci on Human Chromosome 22

ABSTRACT The cyclic AMP-responsive element-binding protein (CREB) is an important transcription factor that can be activated by hormonal stimulation and regulates neuronal function and development. An unbiased, global analysis of where CREB binds has not been performed. We have mapped for the first time the binding distribution of CREB along an entire human chromosome. Chromatin immunoprecipitation of CREB-associated DNA and subsequent hybridization of the associated DNA to a genomic DNA microarray containing all of the nonrepetitive DNA of human chromosome 22 revealed 215 binding sites corresponding to 192 different loci and 100 annotated potential gene targets. We found binding near or within many genes involved in signal transduction and neuronal function. We also found that only a small fraction of CREB binding sites lay near well-defined 5′ ends of genes; the majority of sites were found elsewhere, including introns and unannotated regions. Several of the latter lay near novel unannotated transcriptionally active regions. Few CREB targets were found near full-length cyclic AMP response element sites; the majority contained shorter versions or close matches to this sequence. Several of the CREB targets were altered in their expression by treatment with forskolin; interestingly, both induced and repressed genes were found. Our results provide novel molecular insights into how CREB mediates its functions in humans.
Rosiglitazone evaluated for cardiovascular outcomes--an interim analysis.

BACKGROUND A recent meta-analysis raised concern regarding an increased risk of myocardial infarction and death from cardiovascular causes associated with rosiglitazone treatment of type 2 diabetes. METHODS We conducted an unplanned interim analysis of a randomized, multicenter, open-label, noninferiority trial involving 4447 patients with type 2 diabetes who had inadequate glycemic control while receiving metformin or sulfonylurea, in which 2220 patients were assigned to receive add-on rosiglitazone (rosiglitazone group), and 2227 to receive a combination of metformin plus sulfonylurea (control group). The primary end point was hospitalization or death from cardiovascular causes. RESULTS Because the mean follow-up was only 3.75 years, our interim analysis had limited statistical power to detect treatment differences. A total of 217 patients in the rosiglitazone group and 202 patients in the control group had the adjudicated primary end point (hazard ratio, 1.08; 95% confidence interval [CI], 0.89 to 1.31). After the inclusion of end points pending adjudication, the hazard ratio was 1.11 (95% CI, 0.93 to 1.32). There were no statistically significant differences between the rosiglitazone group and the control group regarding myocardial infarction and death from cardiovascular causes or any cause. There were more patients with heart failure in the rosiglitazone group than in the control group (hazard ratio, 2.15; 95% CI, 1.30 to 3.57). CONCLUSIONS Our interim findings from this ongoing study were inconclusive regarding the effect of rosiglitazone on the overall risk of hospitalization or death from cardiovascular causes. There was no evidence of any increase in death from either cardiovascular causes or all causes. Rosiglitazone was associated with an increased risk of heart failure. The data were insufficient to determine whether the drug was associated with an increase in the risk of myocardial infarction. (ClinicalTrials.gov number, NCT00379769 [ClinicalTrials.gov].).
A Routing Based Time Synchronization Protocol for Multi-Hop Wireless Networks

Time synchronization is critical in distributed wireless networks to achieve and maintain coordination among distributed network nodes. In this paper, we propose a routing based time synchronization protocol (RBTSP) for multi-hop wireless networks. Different from many existing time synchronization protocols, our objective aims at minimizing the number of timing packet exchange and reducing the non-deterministic delay. We conduct mathematical analysis and simulation experiments to demonstrate the working of the proposed time synchronization method. The results manifest that our scheme can achieve better performance on synchronization accuracy and power efficiency.
A simple clinical colitis activity index

Background—The appropriate medical treatment of patients with ulcerative colitis is determined largely by the severity of symptoms. Hospital assessment of the severity of disease activity includes investigation of laboratory indices and sigmoidoscopic assessment of mucosal inflammation. Aims—To develop a simplified clinical colitis activity index to aid in the initial evaluation of exacerbations of colitis. Methods—The information for development of the simple index was initially evaluated in 63 assessments of disease activity in patients with ulcerative colitis where disease activity was evaluated using the Powell-Tuck Index (which includes symptoms, physical signs, and sigmoidoscopic appearance). The new index was then further evaluated in 113 assessments in a different group of patients, by comparison with a complex index utilising clinical and laboratory data, as well as five haematological and biochemical markers of disease severity. Results—The newly devised Simple Clinical Colitis Activity Index, consisting of scores for five clinical criteria, showed a highly significant correlation with the Powell-Tuck Index (r=0.959, p<0.0001) as well as the complex index (r=0.924, p<0.0001) and all laboratory markers (p=0.0003 to p<0.0001). Conclusions—This new Simple Colitis Activity Index shows good correlation with existing more complex scoring systems and therefore could be useful in the initial assessment of patients with ulcerative colitis.
PCR amplification of the spliced leader gene for the diagnosis of trypanosomatid parasites of plants and insects in methanol-fixed smears.

A PCR-based method was adapted for the amplification of DNA from methanol-fixed smears of insects and plants parasitized by trypanosomatids. The PCR target was the multicopy spliced leader (SL) gene. Amplicons were hybridized with an oligonucleotide probe (SL3') specific for Phytomonas. The method has the advantage of dispensing with the cultivation of parasites, many of which are very fastidious or non-cultivable. The technique was applied to archival glass slides and to newly collected material. It proved to specific for Phytomonas spp. , enabling their detection in plants and insects. Sequence comparison of the amplicons obtained revealed the existence of different strains/species of Phytomonas circulating among diseased palsms and fruit.
Managing the Threat of Impending Implicit Attitude Feedback

People facing potentially threatening feedback sometimes opt to avoid it in an attempt to preserve a cherished self-view. In three studies, we examined whether people would adopt such a strategy in the context of the Black–White Implicit Association Test (IAT), which has the potential to reveal implicit prejudice. Study 1 demonstrated that people expect their IAT results to indicate less implicit prejudice than the results actually do, and perceive feedback from the Black–White IAT as potentially threatening. In addition, people who would rather avoid learning their results regretted receiving their feedback. In Studies 2 and 3, more participants declined to learn their IAT results when cued to expect unfavorable, rather than favorable, IAT results. Importantly, participants who received no expectation cue generally opted to receive their IAT feedback, suggesting that participants likely expect favorable IAT feedback.
The effects of three types of goal setting conditions on tennis performance: a field-based study.

Utilizing a two-stage random sampling technique, this study investigated the effect of three types of goal setting conditions (self-set, instructor-set, and “do your best” control) on tennis serving performance of college students (N = 156) in nine beginning tennis classes. A 3 × 2 × 5 (goal setting conditions × gender × trials) ANCOVA with repeated measures on the last factor and baseline performance as the covariate was computed. A significant interaction of goal setting conditions by trials was revealed (p < .003) with follow-up procedures favoring the instructor-set and self-set goal groups over the “do your best" group at the second and fourth trials. Further, at trial two, the instructor-set group was statistically superior to the self-set group. From this significant interaction, it appeared that the instructor-set and self-set goals enhanced students’ performance on the tennis serving task.
The system identification in industrial control: Case study on the differential wheeled mobile robot

This paper presents the modeling of a dynamic system through the System Identification Process, respectively of a wheeled mobile robot running on a flat factory terrain. The system control relies on the same control algorithms applied in industrial controllers, Decoupled PID control and Model Predictive Control (MPC). The simulation results, and the comparison between these control algorithms, subjected to the same identified model, are presented at the end of each section.
Prototyping novel collaborative multimodal systems: simulation, data collection and analysis tools for the next decade

To support research and development of next-generation multimodal interfaces for complex collaborative tasks, a comprehensive new infrastructure has been created for collecting and analyzing time-synchronized audio, video, and pen-based data during multi-party meetings. This infrastructure needs to be unobtrusive and to collect rich data involving multiple information sources of high temporal fidelity to allow the collection and annotation of simulation-driven studies of natural human-human-computer interactions. Furthermore, it must be flexibly extensible to facilitate exploratory research. This paper describes both the infrastructure put in place to record, encode, playback and annotate the meeting-related media data, and also the simulation environment used to prototype novel system concepts.
Look out, there is a triangle behind you! The effect of primitive geometric shapes on perceived facial dominance

Previous research has shown that perceived facial valence is biased toward background valence. Here, we examine whether background dominance also affects perceived facial dominance. In particular, we hypothesized that downward-pointing triangles, which are known to convey threat, would affect perceived facial dominance. Participants judged perceived facial dominance of neutral faces presented overlaid on downward- or upward-pointing background triangles. Our results show that neutral faces are indeed judged more dominant when seen with a downward-pointing triangle in the background. The fact that simple geometric background shapes can affect facial judgments may have important implications for the design and experience of our daily environment and multimedia content.
Cidofovir Administered with Radiation Displays an Antiangiogenic Effect Mediated by E6 Inhibition and Subsequent TP53-Dependent VEGF Repression in HPV18+ Cell Lines

Abstract Amine, A. , Vozenin-Brotons, M-C. , Abdulkarim, B. , Violot, D. , Aubel, C. and Bourhis, J. Cidofovir Administered with Radiation Displays an Antiangiogenic Effect Mediated by E6 Inhibition and Subsequent TP53-Dependent VEGF Repression in HPV18+ Cell Lines. Radiat. Res. 166, 600–610 (2006). Therapeutic administration of the antiviral agent cidofovir with radiation markedly enhanced the antitumor effect of ionizing radiation in cells of two HPV18+ human cervical carcinoma cell lines. Although this potent radiosensitizing effect was associated with repression of the viral oncoproteins E6/ E7 and restoration of TP53 as shown previously, additional mechanisms may be involved. In the present study, we investigated the antiangiogenic effect of the combination of cidofovir and radiation in cells of two HPV18+ cervical cancer cell lines, HeLa and ME180, and assessed the molecular mechanisms associated with the antiangiogenic effect observed. Cells were exposed to cidofovir (10 μg/ml) and irradiated (1– 9 Gy). The angiogenic response was studied in vitro by a matrigel invasion assay. Modulations of E6, TP53 and VEGF mRNA and protein levels were studied by real-time RT-PCR, Western blot analysis and ELISA, respectively. Then a double RNA interference approach was used to analyze the connection between E6/TP53 and VEGF. The combination of cidofovir and radiation had a potent antiangiogenic effect. It induced E6 inhibition, restoration of TP53, and reduction of the proangiogenic phenotype of HPV18+ cells associated with VEGF inhibition. A siRNA strategy showed an anti-VEGF action of the combination mediated directly by E6 inhibition and TP53 restoration, since E6 siRNA inhibited VEGF whereas co-transfection with E6 and TP53 siRNA abrogated the anti-VEGF effect. This study showed that the combination of cidofovir with ionizing radiation has an antiangiogenic effect associated with VEGF inhibition subsequent to E6 inhibition and TP53 restoration.
TRUNCATED QZ METHODS FOR LARGE SCALE GENERALIZED EIGENVALUE PROBLEMS

This paper presents three methods for the large scale generalized eigenvalue problem Ax = Bx . These methods are developed within a subspace projection framework as a truncation and modification of the QZalgorithm for dense problems, that is suitable for computing partial generalized Schur decompositions of the pair (A;B). A generalized partial reduction to condensed form is developed by analogy with the Arnoldi process. Then truncated forward and backward QZ iterations are introduced to derive generalizations of the Implicitly Restarted Arnoldi Method and the Truncated RQmethod for the large scale generalized eigenvalue problem. These two methods require the accurate solution of linear systems at each step of the iteration. Relaxing these accuracy requirements forces us to introduce non-Krylov projection spaces that lead most naturally to block variants of the QZ i erations. A two-block method is developed that incorporates k approximate Newton corrections at each iteration. An important feature is the potential to utilize k matrix vector products for each access of the matrix pair ( A;B). Preliminary computational experience is presented to compare the three new methods.
EU external governance in 'wider Europe'

The 'wider Europe' initiative opens the possibility for a far-reaching association of the EU's eastern and southern European neighbours which, by offering 'everything but institutions' (Prodi), proposes an alternative to membership. This article presents this initiative as part of an ambitious external governance agenda by the enlarged Union with the aim to manage its new interdependence in an altered geopolitical context. Focusing on the conception of interdependence and the institutional configuration of EU relations with its near abroad, external governance is defined and examined in three prominent 'soft security' issues: justice and home affairs, environmental and energy policy. It is argued that external governance seeks to expand the 'legal boundary' of the Union with only limited openings of its 'institutional boundary', thereby oscillating between an inclusionary and exclusionary approach towards its near abroad.
Striving for Shared Understandings: Therapists' Perspectives of the Benefits and Dilemmas of Using a Child Self-Assessment

Pediatric client-centered intervention planning is particularly complex because children, parents, and professionals must form a “tridactic” partnership and reach a shared understanding for therapy. Therapists may use child self-reports to facilitate children's involvement in this process. The purpose of this study was to understand how therapists used and interpreted a child self-report to achieve a shared understanding in the context of a tridactic relationship, using the Children's Occupational Self-Assessment (COSA) as an exemplar. Thirty-three pediatric therapists participated in five focus groups and qualitative analysis was conducted in four iterative phases. Therapists' decision to use the COSA led to either “good” responses or unexpected tensions between the therapist's, child's, and parent's perspectives. Therapists used demonstration, negotiation, or reflection to shift beliefs to achieve a shared understanding for therapy. Findings suggest that although therapists valued children's voices, professional knowledge usually took precedence over child and parent self-knowledge during intervention planning.
OLAP Manipulations on RDF Data following a Constellation Model

Multidimensional analysis is an alternative way for summarising, aggregating and viewing RDF data on different axes (dimensions) and subjects of analysis (facts). From a RDF data collection conforming to the W3C Data Cube specification, we formalise a multidimensional model in terms of RDF data structures following a conceptual constellation model. This model regroups facts, which are studied according to several dimensions possibly shared between facts, with dimensions relating multi-hierarchies. We show how elementary OLAP operations can be translated into SPARQL queries using an OLAP algebra that is compliant to the constellation model. This algebra is based on a multidimensional table which displays data from one fact and two of its linked dimensions. Initial experiments have been carried out using both synthetic data sets and real data sets.
Separable Mechanisms of Attachment and Cell Uptake during Retrovirus Infection

ABSTRACT In the absence of viral envelope gene expression, cells expressing human immunodeficiency virus type 1 (HIV-1) gag andpol, accessory HIV functions, and a vector genome RNA produce and secrete large amount of noninfectious virus-like particles (VLPs) into the conditioned medium. After partial purification, such HIV-1 VLPs can be made infectious in cell-free conditions in vitro by complex formation with lipofection reagents or with the G protein of vesicular stomatitis virus (VSV-G). The resulting in vitro-modified HIV-1 particles are able to infect nondividing cells. Infectivity of envelope-free HIV VLPs can also be induced by prior modification of target cells through exposure to partially purified VSV-G vesicles. Similarly, infection can be carried out by attachment of envelope-free noninfectious VLPs to unmodified cells followed by subsequent treatment of cells with VSV-G. We interpret these findings to indicate that interaction between a viral envelope and a cell surface receptor is not necessary for the initial virus binding to the cells but is required for subsequent cell entry and infection.
Automated Video Editing for Aesthetic Quality Improvement

In these days, a large number of videos is taken by various kinds of handheld devices, but many of them have poor aesthetic quality. In this paper, we present an automated video editing system that uses the shot length, camera motion, and color distribution as key aesthetic features. Given an amateur video, our system computes the original unrefined camera motion as homography and tries to remove some unreliable frames, which consequently splits the video into several shots. It then applies enhancement processes, including reconstruction of the overall camera motions and harmonization of color distributions. We apply our method to some amateur videos and evaluate the results through a subjective test. It is demonstrated that reducing the shot length in our method is a key point of editing that can lead enhanced satisfaction by viewers for the edited videos.
Modeling and Performance Analysis of P2P Live Streaming Systems under Flash Crowds

A fundamental problem that a peer-to-peer (P2P) live streaming system faces is how to support flash crowds effectively. A flash crowd occurs when a burst of join requests arrive at a system. When a flash crowd occurs, the sudden arrival of numerous peers may starve the upload capacity of a P2P system, and degrade the quality of service. By theoretical analysis and simulations, we find that a system has limited capacity to handle a flash crowd: It can recover to a new stable state when the size of flash crowd is small or moderate, but collapse when the flash crowd is excessively large. The capacity of a system is independent of initial state of the system while relevant to stable peers' departure rate, which suggests this capacity is an essential property of a P2P live streaming system. In addition, we prove that a P2P live streaming system with admission control has excellent capacity to handle flash crowds: It can recover from flash crowds of excessively large size and a startup peer's waiting time scales logarithmically with the size of flash crowds. Our theoretical model and simulation results provide a promising framework to understand the capacity of a P2P live streaming system for handling flash crowds.
Age, Gender and Training in Children's Performance of Piaget's Horizontality Task

Six-hundred children from the ages of 5 to 9 years, balanced for sex and age, were administered Piaget's horizontality tasks using a square water bottle. They were then divided into three experimental groups, and re-administered the task with or without instructions. The first group completed the task using gradually specific instructions until the participants performed each item to criterion level. The number of instructions needed to perform to criterion level was recorded (training scores). The second group completed the task with traditional training where the correct answer was demonstrated. The third group completed the task without feedback. After a month, all of the participants were given a post-test consisting of the square water bottle task, as well as a verticality task that required a related principle. Children's pre- and post-test performance scores were classified into six stages. It was found that there was a significant sex difference in the pretest performance of the horizontality task beginning at 8 years of age. The graduated training group evidenced higher stage scores on the post-test than the demonstration group and the control group. The former demonstrated a more integrated understanding of stable external reference frames compared to the other groups.
Doelbewuste controle en psychopathologie bij kinderen

Het doel van dit onderzoek was te bekijken of normale kinderen van 8 tot 12 jaar, die minder controle over hun aandacht hebben en minder doelbewuste controle hebben, meer psychopathologische symptomen (angst, depressie en agressie) ondervinden. Het voornaamste verschil met eerder onderzoek is dat er voor het in kaart brengen van aandachtscontrole en doelbewuste controle, naast vragenlijsten, gebruik is gemaakt van de Test of Everyday Attention for Children. Voor het huidige onderzoek zijn 207 kinderen getest op reguliere basisscholen in Rotterdam en omgeving. De opvallendste bevinding was dat de resultaten van de TEA-Ch niet of nauwelijks correleerden met de resultaten van de vragenlijsten. Kinderen die een lage doelbewuste controle en aandachtscontrole hadden, zoals gemeten met de vragenlijsten, hadden doorgaans meer psychopathologische symptomen. De scores op de TEA-Ch correleerden nauwelijks met symptomen van psychopathologie, alleen met depressie werd een klein negatief verband gevonden. Vervolgonderzoek is nodig om aan te tonen of vragenlijsten een juiste meting zijn voor het in kaart brengen van doelbewuste controle of dat de TEA-Ch als meer valide meting moet gelden.