Miracle-dz/UniFAR-FTUs huggingface dataset:
Functional promoter modules can be detected by formal models independent of overall nucleotide sequence similarity

MOTIVATION Gene regulation often depends on functional modules which feature a detectable internal organization. Overall sequence similarity of these modules is often insufficient for detection by general search methods like FASTA or even Gapped BLAST. However, it is of interest to evaluate whether modules, often known from experimental analysis of single sequences, are present in other regulatory sequences. RESULTS We developed a new method (FastM) which combines a search algorithm for individual transcription factor binding sites (MatInspector) with a distance correlation function. FastM allows fast definition of a model of correlated binding sites derived from as little as a single promoter or enhancer. ModelInspector results are suitable for evaluation of the significance of the model. We used FastM to define a model for the experimentally verified NFkappaB/IRF1 regulatory module from the major histocompatibility complex (MHC) class I HLA-B gene promoter. Analysis of a test set of sequences as well as database searches with this model showed excellent correlation of the model with the biological function of the module. These results could not be obtained by searches using FASTA or Gapped BLAST, which are based on sequence similarity. We were also able to demonstrate association of a hypothetical GRE-GRE module with viral sequences based on analysis of several GenBank sections with this module. AVAILABILITY The WWW version of FastM is accessible at: http://www.gsf. de/cgi-bin/fastm. pl and http://genomatix.gsf. de/cgi-bin/fastm2/fastm.pl
An ellipse-shaped with slanted slot circularly polarized monopole antenna for UHF RFID readers

An ellipse-shaped circularly polarized (CP) monopole antenna is proposed in this paper. A slanted slot is added into the antenna to enhance 3-dB axial ratio bandwidth. The antenna operates at ultrahigh frequency (UHF) band for radio-frequency identification (RFID) reader applications. The measured bandwidth of standing wave ratio (SWR) < 2 is 535 MHz (553 MHz–1088 MHz) and the measured 3-dB axial ratio (AR) bandwidth 45MHz (900MHz–945MHz). The size of the radiating element is 137 mm × 122 mm.
Substantive hemodynamic and thermal strain upon completing lower-limb hot-water immersion; comparisons with treadmill running

ABSTRACT Exercise induces arterial flow patterns that promote functional and structural adaptations, improving functional capacity and reducing cardiovascular risk. While heat is produced by exercise, local and whole-body passive heating have recently been shown to generate favorable flow profiles and associated vascular adaptations in the upper limb. Flow responses to acute heating in the lower limbs have not yet been assessed, or directly compared to exercise, and other cardiovascular effects of lower-limb heating have not been fully characterized. Lower-limb heating by hot-water immersion (30 min at 42°C, to the waist) was compared to matched-duration treadmill running (65-75% age-predicted heart rate maximum) in 10 healthy, young adult volunteers. Superficial femoral artery shear rate assessed immediately upon completion was increased to a greater extent following immersion (mean ± SD: immersion +252 ± 137% vs. exercise +155 ± 69%, interaction: p = 0.032), while superficial femoral artery flow-mediated dilation was unchanged in either intervention. Immersion increased heart rate to a lower peak than during exercise (immersion +38 ± 3 beats·min-1 vs. exercise +87 ± 3 beats·min-1, interaction: p < 0.001), whereas only immersion reduced mean arterial pressure after exposure (−8 ± 3 mmHg, p = 0.012). Core temperature increased twice as much during immersion as exercise (+1.3 ± 0.4°C vs. +0.6 ± 0.4°C, p < 0.001). These data indicate that acute lower-limb hot-water immersion has potential to induce favorable shear stress patterns and cardiovascular responses within vessels prone to atherosclerosis. Whether repetition of lower-limb heating has long-term beneficial effects in such vasculature remains unexplored.
The Ideology of Consumption: A Structural-Syntactical Analysis of "Dallas" and "Dynasty."

Aspects of syntactics and structuralism are used to interpret two popular vehicles of consumption ideology, the television programs “Dallas” and “Dynasty. ” The primary structure encoded within “Dallas” and “Dynasty” is the binary opposition between secular consumption and sacred consumption. The consumer behaviors of characters associated with secular and sacred consumption are described, and processes of mediation and transformation between the sacred and secular consumption poles are illustrated.
This information is current as Mimics Recognition of Foreign and Self Molecular Conserved Binding Geometry in TCR Conformational Melding Permits a

Molecular mimicry between foreign and self Ags is a mechanism of TCR cross-reactivity and is thought to contribute to the development of autoimmunity. The ab TCR A6 recognizes the foreign Ag Tax from the human T cell leukemia virus-1 when presented by the class I MHC HLA-A2. In a possible link with the autoimmune disease human T cell leukemia virus-1–associated myelopathy/tropical spastic paraparesis, A6 also recognizes a self peptide from the neuronal protein HuD in the context of HLA-A2. We found in our study that the complexes of the HuD and Tax epitopes with HLA-A2 are close but imperfect structural mimics and that in contrast with other recent structures of TCRs with self Ags, A6 engages the HuD Ag with the same traditional binding mode used to engage Tax. Although peptide and MHC conformational changes are needed for recognition of HuD but not Tax and the difference of a single hydroxyl triggers an altered TCR loop conformation, TCR affinity toward HuD is still within the range believed to result in negative selection. Probing further, we found that the HuD–HLA-A2 complex is only weakly stable. Overall, these findings help clarify how molecular mimicry can drive self/nonself cross-reactivity and illustrate how low peptide-MHC stability can permit the survival of T cells expressing self-reactive TCRs that nonetheless bind with a traditional binding mode. T cell receptor recognition of peptide Ags presented by class I or class II MHC proteins is a cornerstone of cellular immunity. Recognition of foreign Ags forms the basis for defense against viruses and other pathogens, yet recognition of self Ags can lead to autoimmunity. Although the central tolerance mechanism of negative selection plays a protective role against autoimmunity, the high level of cross-reactivity present within the T cell repertoire can promote autoimmunity if T cells are activated by foreign Ags that share key structural or chemical features with self Ags. This concept of molecular mimicry has been implicated in a number of autoimmune pathologies, including type 1 diabetes, lupus, and multiple sclerosis (1–3). Previously determined structures of TCRs in complex with self Ags associated with autoimmunity have shown deviations from the binding mode traditionally seen in TCR recognition of foreign Ags. The traditional binding mode, typified by the structure of the ab A6 TCR with the human T cell leukemia virus-1 (HTLV-1) Tax peptide presented by HLA-A2 (4), has the TCR centered diagonally over the peptide-MHC (pMHC), with the …
Cognitive Retroactive Transfer (CRT) of Language Skills Among Bilingual Arabic-English Readers

This study examined the effects of an intervention helping struggling readers improve their reading and writing skills in English as a foreign language (L2), and those same skills in Arabic, which was their first language (L1). Transferring linguistic skills from L2 to L1 is termed cognitive retroactive transfer. Tests were administered to the experimental and control groups that assessed orthographic knowledge, phonological awareness, morphological awareness, syntax awareness, reading accuracy, and reading comprehension in Arabic and English. The experimental group received an intervention program in English, but not in Arabic, and the assessments were administered before and after the intervention. The findings indicated a significant improvement in the experimental group's achievements in all linguistic and metalinguistic skills in both Arabic and English after the English intervention program, with the exception of orthographic knowledge in Arabic. Therefore, foreign language learning can result in improvements in native language skills.
Targeting of Mutant p53 and the Cellular Redox Balance by APR-246 as a Strategy for Efficient Cancer Therapy

TP53 is the most frequently mutated gene in cancer. The p53 protein activates transcription of genes that promote cell cycle arrest or apoptosis, or regulate cell metabolism, and other processes. Missense mutations in TP53 abolish specific DNA binding of p53 and allow evasion of apoptosis and accelerated tumor progression. Mutant p53 often accumulates at high levels in tumor cells. Pharmacological reactivation of mutant p53 has emerged as a promising strategy for improved cancer therapy. Small molecules that restore wild type activity of mutant p53 have been identified using various approaches. One of these molecules, APR-246, is a prodrug that is converted to the Michael acceptor methylene quinuclidinone (MQ) that binds covalently to cysteines in p53, leading to refolding and restoration of wild type p53 function. MQ also targets the cellular redox balance by inhibiting thioredoxin reductase (TrxR1) and depleting glutathione. This dual mechanism of action may account for the striking synergy between APR-246 and platinum compounds. APR-246 is the only mutant p53-targeting compound in clinical development. A phase I/IIa clinical trial in hematological malignancies and prostate cancer showed good safety profile and clinical effects in some patients. APR-246 is currently tested in a phase Ib/II trial in patients with high-grade serous ovarian cancer.
Sensor fault detection and isolation for nonlinear systems based on a sliding mode observer

In this paper, a sensor fault detection and isolation scheme for nonlinear systems is considered. A nonlinear diffeomorphism is introduced to explore the system structure and a simple filter is presented to ‘transform’ the sensor fault into a pseudo‐actuator fault scenario. A sliding mode observer is designed to reconstruct the sensor fault precisely if the system does not experience any uncertainty, and to estimate the sensor fault when uncertainty exists. The reconstruction and estimation signals are based only on available information and thus can be implemented online. Finally, a mass–spring system is used to illustrate the approach. Copyright © 2007 John Wiley & Sons, Ltd.
Gender stereotypes in Italian television advertisements.

The present study attempted to replicate and extend American, Canadian and British studies on the portrayal of men and women in television commercials using advertisements broadcast in Italy, Three hundred and thirty‐three daytime and evening commercials were content analyzed by classifying the attributes of their central figures into eleven categories: gender, mode, credibility, role, location, reward, product price, argument, background, humor and comment. Gender stereotyping in Italy was constant across time‐of‐day and more apparent than in America, but as frequent as in England. The implications of results for the development and maintenance of gender roles are discussed.
Intrafamilial Adolescent Sex Offenders' Response to Psychological Treatment

This qualitative study examined perceptions of a community-based treatment program for intrafamilial adolescent sexual offenders, from the perspective of the adolescent clients. The post-treatment interviews of 12 adolescents generated information regarding the participants' experiences of treatment and the effect of treatment on individual and family functioning. Greatest improvements occurred in the areas of communication with family and friends, anger management, and impulsivity. All participants agreed that group therapy was the most beneficial component of the program. The space to express feelings about the inappropriate sexual behaviours, as well as other personal and family issues was regarded as key to positive change. Greater improvements in family functioning were reported when at least one parent also attended therapy. There were fewer indications of change in the expression of empathy and construction of relapse prevention plans.
Almost Invisible: Glimpsing the City and its Residents in the Urban Sustainability Discourse

‘Urban sustainability’ currently receives widespread and generally enthusiastic endorsement, yet concerns are emerging that recent expressions of the concept may actually be working against the city and its residents. Based on research in Christchurch, New Zealand (one of the most urbanised countries in the world), it is argued that the assimilation of social, economic and bio-physical environmental elements that gave the idea much of its original legitimacy has been reduced to a minimalist set of material and discursive ‘eco-friendly’ denominators. As a result, only occasional glimpses of the city and its human inhabitants are caught in attempts to operationalise sustainability in urban areas. The effect is that cities, in New Zealand at least, are less liveable and less likeable than they should be. It is suggested that there is a real need to re-urbanise and rehumanise the urban sustainability agenda as a means of realising its integrative and transformative potential.
Efficacy of interpersonal psychotherapy for postpartum depression.

BACKGROUND Postpartum depression causes women great suffering and has negative consequences for their social relationships and for the development of their infants. Research is needed to evaluate the efficacy of psychotherapy for postpartum depression. METHODS A total of 120 postpartum women meeting DSM-IV criteria for major depression were recruited from the community and randomly assigned to 12 weeks of interpersonal psychotherapy (IPT) or to a waiting list condition (WLC) control group. Subjects completed interview and self-report assessments of depressive symptoms and social adjustment every 4 weeks. RESULTS Ninety-nine of the 120 patients completed the protocol. Hamilton Rating Scale for Depression (HRSD) scores of women receiving IPT declined from 19.4 to 8.3, a significantly greater decrease than occurred in the WLC group (19.8 to 16.8). The Beck Depression Inventory (BDI) scores of women who received IPT declined from 23.6 to 10.6 over 12 weeks, a significantly greater decrease than occurred in the WLC group (23.0 to 19.2). A significantly greater proportion of women who received IPT recovered from their depressive episode based on HRSD scores of 6 or lower (37. 5%) and BDI scores of 9 or lower (43.8%) compared with women in the WLC group (13.7% and 13.7%, respectively). Women receiving IPT also had significant improvement on the Postpartum Adjustment Questionnaire and the Social Adjustment Scale-Self-Report relative to women in the WLC group. CONCLUSIONS These findings suggest that IPT is an efficacious treatment for postpartum depression. Interpersonal psychotherapy reduced depressive symptoms and improved social adjustment, and represents an alternative to pharmacotherapy, particularly for women who are breastfeeding.
Scalable Clustering of Correlated Time Series using Expectation Propagation

We are interested in finding clusters of time series such that series within a cluster are correlated and series between clusters are independent. Existing Bayesian methods for inferring correlated clusters of time series either: (i) require conditioning on latent variables to decouple time series, but results in slow mixing or (ii) require calculating a collapsed likelihood, but with computation scaling cubically with the number of time series per cluster. To infer the latent cluster assignments efficiently, we consider approximate methods that trade exactness for scalability. Our main contribution is the development of an expectation propagation based approximation for the collapsed likelihood approach. Our empirical results on synthetic data show our methods scale linearly instead of cubically, while maintaining competitive accuracy.
A relevance feedback approach for the author name disambiguation problem

This paper presents a new name disambiguation method that exploits user feedback on ambiguous references across iterations. An unsupervised step is used to define pure training samples, and a hybrid supervised step is employed to learn a classification model for assigning references to authors. Our classification scheme combines the Optimum-Path Forest (OPF) classifier with complex reference similarity functions generated by a Genetic Programming framework. Experiments demonstrate that the proposed method yields better results than state-of-the-art disambiguation methods on two traditional datasets.
Efficiency optimization of high power density Dual Active Bridge DC-DC converter

A DC-DC converter based on the Dual Active Bridge topology is designed, having high power density as main design target. To that aim, a simple structure has been proposed for the transformer with embedded inductor, allowing high frequency operation with low losses and requiring only readily available magnetic core shapes. Simple phase-shift control has been used, and the switching frequency is varied in order to minimize the peak transformer current, thus achieving high conversion efficiency. A fully operational prototype has been built and tested, demonstrating a power density figure of 7.1 kW/Liter with forced air cooling, and a peak efficiency at rated 4 kW load equal to 96.6 %.
Cytosolic Retention of Phosphorylated Extracellular Signal-Regulated Kinase and a Rho-Associated Kinase-Mediated Signal Impair Expression of p21Cip1/Waf1 in Phorbol 12-Myristate-13- Acetate-Induced Apoptotic Cells

ABSTRACT In response to treatment with phorbol-12-myristate-13-acetate (PMA), the half-population of erythromyeloblast D2 cells, a cytokine-independent variant of TF-1 cells, displayed adhesion and differentiated into a monocyte/macrophage-like morphology, while the other half-population remained in suspension and underwent apoptosis. Expression of the cell cycle inhibitor p21Cip1/Waf1 was induced after PMA treatment in the adherent cells but not in the proapoptotic cells. We investigated the mechanism responsible for the impairment of p21Cip1/Waf1 induction in PMA-induced proapoptotic cells. We demonstrated that in PMA-induced adherent cells, upregulation of p21Cip1/Waf1 requires the activation and nuclear translocation of phosphorylated extracellular signal-regulated kinase (phospho-ERK). Although ERK was phosphorylated to comparable levels in PMA-induced proapoptotic and adherent cells, nuclear distribution of phospho-ERK was seen only in the adherent, not in the proapoptotic cells. We also found that only PMA-induced proapoptotic cells contained the phosphorylated form of myosin light chain, which is dependent on Rho-associated kinase (ROCK) activation, and that expression of a dominant-active form of ROCK suppressed activation of the p21Cip1/Waf1 promoter during PMA induction. Finally, we demonstrated that inhibition of ROCK restores nuclear distribution of phospho-ERK and activation of p21Cip1/Waf1 expression. Based on these findings, we propose that a ROCK-mediated signal is involved in interfering with the process of ERK-mediated p21Cip1/Waf1 induction in PMA-induced proapoptotic TF-1 and D2 cells.
Designer Selves: Construction of Technologically Mediated Identity within Graphical, Multiuser Virtual Environments

The emergence of graphical, multiuser virtual environments has created new forums for the performance of identity, forums in which information system designers' decisions may influence people's presentation of self. Based on ethnographic research, this paper describes designers' actions affecting identity performance within graphical virtual environments, and the manner in which those decisions interact with larger social contexts of dominance based on race, class, and gender. I make explicit the social consequences of designer's decisions, in order to further the dialogue between social scientists and technologists, and make suggestions regarding how designers may approach the construction of virtual environments without unwittingly contributing to patterns of dominance in society.
Complete Genomic Sequence of an Avian Pathogenic Escherichia coli Strain of Serotype O7:HNT

ABSTRACT Avian pathogenic Escherichia coli (APEC) is associated with colibacillosis in poultry. Here, we present the first complete sequence of an APEC strain of the O7:HNT serotype and ST73 sequence type, isolated from a broiler with cellulitis. Complete genomes of APEC with distinct genetic backgrounds may be useful for comparative analysis.
VisFiles: presentation techniques for time-series data

This is the first in a series of columns on the subject of data visualization. I'm excited to have this opportunity because it will give me an excuse to finally learn about some subjects that I've wanted to learn about but never gave myself the time. Gordon Cameron, Computer Graphics Editor, has given me some latitude on topics so future visualization columns will deal with color selection, data visualization systems and APIs, data visualization research, information visualization, user interface issues, tips and hints, etc. If you have comments on this column or suggestions for future columns, please send me email (todd@acm.org). In this issue I will give an overview of some familiar, and some probably unfamiliar, time-series data presentation techniques. Time-series data visualization is becoming an increasingly important topic as data archives grow exponentially and computing becomes ubiquitous. Some researchers claim that time-series data can be imaged using techniques similar to those applied to spatial data (since time is most often linear), and some claim that temporal data is a much different beast. For example, temporal data can have multiple strands and events, features not present in spatial data. There are also many interesting unsolved problems and data handling issues associated with temporal data:&bull; Boolean and other mathematical operations&bull; Data storage and temporal databases&bull; Data query and retrieval&bull; Data generalization (handling data at vastly different resolutions)&bull; Data models and representation&bull; Data presentationI have lately been working on designing a user interface for a simple geographic information system capable of manipulating and compositing time-series geo-referenced data. This project started me thinking about the different ways of visually representing temporal data. Without going into much detail on any one method, following are all the methods I could find within arms length in my office. Most of these methods allow the scientist or visualizer to present the time-series in a single image, while the final method uses an animation technique. Good techniques for visually presenting time-series data will:&bull; Reveal spatial and temporal relationships&bull; Uncover patterns&bull; Show variability
An ecological design philosophy: Randolph T. Hester's Design for ecological democracy

This paper provides an extended review of Randolph T. Hester's Design for ecological democracy (2006). Initially, a brief introduction to the book, its author and the works position in the literature is given, before a broad summary of the book's central argument is provided. The paper then considers the three key themes Hester explores: enabling form, resilient form and impelling form. Through this discussion, linkages are made to wider concepts of ecology in planning practice as well as political and planning theory. The paper concludes that Design for ecological democracy provides not only an engaging philosophy for the future, but also a series of case study‐supported interlinked practical methods for change for the way the built environment is shaped.