Miracle-dz/UniFAR-FTUs huggingface dataset:
Genes involved in cell adhesion and signaling: a new repertoire of retinoic acid receptor target genes in mouse embryonic fibroblasts

ABSTRACT Nuclear retinoic acid (RA) receptors (RAR&agr;, &bgr; and &ggr;) are ligand-dependent transcription factors that regulate the expression of a battery of genes involved in cell differentiation and proliferation. They are also phosphoproteins and we previously showed the importance of their phosphorylation in their transcriptional activity. In the study reported here, we conducted a genome-wide analysis of the genes that are regulated by RARs in mouse embryonic fibroblasts (MEFs) by comparing wild-type MEFs to MEFs lacking the three RARs. We found that in the absence of RA, RARs control the expression of several gene transcripts associated with cell adhesion. Consequently the knockout MEFs are unable to adhere and to spread on substrates and they display a disrupted network of actin filaments, compared with the WT cells. In contrast, in the presence of the ligand, RARs control the expression of other genes involved in signaling and in RA metabolism. Taking advantage of rescue cell lines expressing the RAR&agr; or RAR&ggr; subtypes (either wild-type or mutated at the N-terminal phosphorylation sites) in the null background, we found that the expression of RA-target genes can be controlled either by a specific single RAR or by a combination of RAR isotypes, depending on the gene. We also selected genes that require the phosphorylation of the receptors for their regulation by RA. Our results increase the repertoire of genes that are regulated by RARs and highlight the complexity and diversity of the transcriptional programs regulated by RARs, depending on the gene.
Discovery of Selective and Potent Inhibitors of Palmitoylation

Palmitoylation is a reversible, post-translational modification of a protein through the addi‐ tion of the 16-carbon fatty acid, palmitate, to a cysteine residue. There are two types of pal‐ mitoylation, one called thioor S-palmitoylation in which palmitate is added to the thiol side chain of a cysteine residue via a labile thioester bond [1]. The other type, N-palmitoyla‐ tion, is the addition of palmitate to an N-terminal cysteine via a stable amide bond [2]. The two forms of palmitoylation are regulated by different families of palmitoyl acyltransferases (PATs)—S-palmitoylation via a family of multi-pass transmembrane proteins called DHHC (Asp-His-His-Cys) proteins [3] and N-palmitoylation via a family of multi-pass transmem‐ brane proteins termed membrane-bound O-acyltransferase [4]. S-palmitoylation, the focus of this chapter, is more common and because of the labile thioester bond, can dynamically regulate protein sorting and function.
Two-dimensional analog filtering and its implications on circuit theory

The objective of this paper is to focus on two-dimensional (2-D) analog linear systems. The potential of many 2-D concepts in analog domain have not been explored properly. Techniques of MDLT, in general, and 2DLT in particular, make it possible to characterize a large class of nonlinear analytic systems and the entire analog linear time-varying (LTV) systems and circuits including the entire communication networks. In this paper the development of a bifrequency theory for autonomous dynamic systems is outlined. The paper complements contents of existing literature more than duplicate.
Reliability of autoregressive error models as post-processors for probabilistic streamflow forecasts

Abstract. In this study, the reliability of different versions of autoregressive error models as post-processors for probabilistic streamflow forecasts is evaluated. Rank histograms and reliability indices are used as performance measures. An algorithm for the construction of confidence intervals to indicate ranges of reliable forecasts within the rank histograms is presented. To analyse differences in performance of the post-processors, scatter plots of the standardized residuals of the error models are generated to assess the homoscedacity of the residuals with respect to streamflow. A problem of distorted impressions may appear when such plots are generated with a regular x-scale. The problem is analysed with both synthetic and real data, and a rank scaled x-axis is proposed to remedy the problem. The results of the study reveal large differences in the reliability of the post-processors. Versions with empirical distribution functions are clearly superior to those with standard normal distribution, but for validations with independent data their rank histograms still lie outside of the confidence bands for reliable forecasts.
Saturation mutagenesis of the haloarchaeal bop gene promoter: identification of DNA supercoiling sensitivity sites and absence of TFB recognition element and UAS enhancer activity

Transcription from the bop promoter in the haloarchaeon Halobacterium NRC‐1, is highly induced under oxygen‐limiting conditions. A DNA gyrase inhibitor, novobiocin, was previously shown to block bop gene induction and suggested that DNA supercoiling mediates transcriptional induction. A region of non‐B structure was found 3′ to the TATA box within an 11 bp alternating purine–pyrimidine sequence (RY box), which correlated to both increased DNA supercoiling and transcriptional induction. Here, saturation mutagenesis of the RY box region has been used to show that single‐base substitutions of A(r)G either 23 or 19 bp 5′ to the transcription start site temper the effect of DNA supercoiling based on novobiocin insensitivity of transcription. Mutagenesis of the region 5′ to the TATA box showed its involvement in DNA supercoiling modulation of transcription, defined the 3′ end of the upstream activator sequence (UAS) regulatory element, and ruled out the requirement for a TFB (TFIIB) Recognition Element. Spacing between the TATA box and UAS was found to be critical for promoter activity because insertion of partial or whole helical turns between the two elements completely inhibited transcription indicating that the UAS element does not function as a transcriptional enhancer. The results are discussed in the context of DNA melting and flexibility around the TATA box region and the involvement of multiple regulatory and transcription factors in bop promoter activity.
Light trapping by thin periodic planar structures

The problem of visible and IR light diffraction by planar 2-D periodic metaldielectric structures with a periodic cell consisted of two complex-shaped asymmetric metal elements was solved. The mapped PSTD method and ADE technique with complex-conjugate pole model were used for taking into account the dispersion of metal permittivity. The conditions of light confinement by an excitation of trapped mode resonances of the structures were studied. Existence of high order trapped mode resonance with a greater quality factor than the quality factor of lowest one was shown for the first time.
Case Studies and Theory Development in the Social Sciences

Case Studies and Theory Development in the Social Sciences. By Alexander L. George and Andrew Bennett. Cambridge, MA: MIT Press, 2005. 331p. $50.00 cloth, $20.00 paper. In recent years, there has been a surge in work on what has come to be known as “qualitative methods. ” The trend is essentially reactive, developing as a response to the outpouring of work on quantitative and formal methods and the assertions by scholars in those areas that case studies and historical work are impressionistic, unscientific, and noncumulative. To counter such claims, some of the field's most distinguished qualitative scholars (e.g., Stephan Van Evera, Guide to Methods for Students of Political Science, 1997; James Mahoney and Dietrich Rueschemeyer, eds., Historical Analysis in the Social Sciences, 2003; and Marc Trachtenberg, The Craft of International History, 2006) have spent much time and ink to show that researchers who eschew regressions or game theory can be just as methodologically aware and sophisticated as those who embrace them. Alexander George and Andrew Bennett's Case Studies and Theory Development in the Social Sciences is an impressive and welcome addition to this literature.
Comparison of GALS and Synchronous Architectures with MPEG-4 Video Encoder on Multiprocessor System-on-Chip FPGA

In large system-on-chip (SoC) architectures, balancing the clock network is increasingly difficult. Globally asynchronous locally synchronous (GALS) removes the need for global clock net, and also provides efficient means for managing the complexity and re-use in large architectures. However, quantitative comparisons of GALS against similar synchronous structures are rare for full SoC architectures. In this paper, we compare our SoC GALS architectures to a synchronous architecture with a fully functional MPEG-4 video encoder on FPGA. The results show that the area and performance overhead of GALS is only 1%. That is negligible compared to the benefits of the GALS architecture such as multiple clock frequencies for intellectual property (IP) blocks and dynamic frequency/voltage scaling, clock tree removal, and re-usability. Our architecture does not require modifications to the IP blocks already used with synchronous architectures, providing an ideal solution for rapid switch to GALS architecture
Guidelines for Hypermedia Usability Inspection

Our research addresses evaluating the usability of hypermedia systems oth offline (CD-ROMs) and online (Web) - and tries to capture the features that most characterize the specific nature of these systems. In this article, we describe an inspection technique that lets evaluators concentrate on the usability of specific aspects of hypermedia applications, such as information and navigation structuring, media integration and synchronization, and so on, without neglecting the surface aspects. Our technique uses operational guidelines, called abstract tasks (ATs), which systematically drive the inspection activities, allowing even less experienced evaluators to come up with valuable results. As they currently exist, we see ATs as evaluation patterns, which make it possible to maximize the reuse of an evaluator's expertise. That is, reuse takes advantage of previous work, thus reducing the effort to create a new one. ATs support the reuse of an evaluator's know-how. Their goal is to capture usability inspection expertise and to express it in a precise and understandable form, so that others can easily reproduce, communicate and exploit it. Our current work is devoted to extending the AT library to cover specific usability issues related to e-commerce Web sites.
Dimensional models of personality: the five-factor model and the DSM-5

It is evident that the classification of personality disorder is shifting toward a dimensional trait model and, more specifically, the five-factor model (FFM). The purpose of this paper is to provide an overview of the FFM of personality disorder. It will begin with a description of this dimensional model of normal and abnormal personality functioning, followed by a comparison with a proposal for future revisions to DSM-5 and a discussion of its potential advantages as an integrative hierarchical model of normal and abnormal personality structure.
From Turing machines to computer viruses

Self-replication is one of the fundamental aspects of computing where a program or a system may duplicate, evolve and mutate. Our point of view is that Kleene's (second) recursion theorem is essential to understand self-replication mechanisms. An interesting example of self-replication codes is given by computer viruses. This was initially explained in the seminal works of Cohen and of Adleman in the 1980s. In fact, the different variants of recursion theorems provide and explain constructions of self-replicating codes and, as a result, of various classes of malware. None of the results are new from the point of view of computability theory. We now propose a self-modifying register machine as a model of computation in which we can effectively deal with the self-reproduction and in which new offsprings can be activated as independent organisms.
Depot pipotiazine palmitate and undecylenate for schizophrenia.

BACKGROUND Antipsychotic drugs are usually given orally but compliance may be problematic. The development of depot injections in the 1960s gave rise to their extensive use as a means of long-term maintenance treatment. Pipotiazine palmitate is a depot from the phenothiazine family of antipsychotic drugs. OBJECTIVES To assess the clinical, social and economic effects of depot pipotiazine palmitate and undecylenate compared with placebo, oral antipsychotics and other depot antipsychotic preparations for people with schizophrenia. SEARCH STRATEGY For this update we searched the Cochrane Schizophrenia Group's Register (June 2003). We also inspected references of all identified trials for more studies and contacted relevant industries. SELECTION CRITERIA We included all randomised clinical trials comparing depot pipotiazine palmitate and undecylenate to oral antipsychotics or other depot preparations for people with schizophrenia. DATA COLLECTION AND ANALYSIS We reliably selected, quality rated and independently extracted data from relevant studies. We calculated the random effects relative risk (RR), the 95% confidence intervals (CI) and, where possible the number needed to treat (NNT) on an intention-to-treat basis. For continuous data, we calculated weighted mean differences (WMD). We only presented scale data for those tools that had attained pre-specified levels of quality. MAIN RESULTS When pipotiazine palmitate was compared with 'standard' oral antipsychotic no differences were found for outcomes of global impression (n=53, 1 RCT, RR 2.57, CI 0.8 to 8.6), relapse (n=124, 1 RCT, RR 1.55 CI 0.76 to 3.2), study attrition (n=219, 3 RCTs, RR 1.37 CI 0.8 to 2.4) and behaviour (n=124, 1 RCT, WMD 4.65, CI -1.1 to 10.4). There was also no reported difference in adverse effects such as tardive dyskinesia or the need for anticholinergic drugs. Sixteen studies compared pipotiazine palmitate with other depot preparations (n=1123). Pipotiazine palmitate was consistently equivalent to other depots in terms of a range of outcomes, including global impression (n=217, 4 RCTs, RR not improved 0.99 CI 0.91 to 1.07), relapse (n=239, 5 RCTs, RR relapse by 1 year 0.98 CI 0.55 to 1.75), and adverse effects (n=337, 5 RCTs, RR needing anticholinergic medication 0.98 CI 0.84 to 1.15). REVIEWERS' CONCLUSIONS Although well-conducted and reported randomised trials are still needed to fully inform practice (no trial data exists reporting hospital and services outcomes, satisfaction with care and economics) pipotiazine palmitate is a viable choice for both clinician and recipient of care.
Feynman's Path-Integral Approach for Intense-Laser-Atom Interactions

Atoms interacting with intense laser fields can emit electrons and photons of very high energies. An intuitive and quantitative explanation of these highly nonlinear processes can be found in terms of a generalization of classical Newtonian particle trajectories, the so-called quantum orbits. Very few quantum orbits are necessary to reproduce the experimental results. These orbits are clearly identified, thus opening the way for an efficient control as well as previously unknown applications of these processes.
Protein tyrosine kinase 2 beta (PTK2B), but not focal adhesion kinase (FAK), is expressed in a sexually dimorphic pattern in developing mouse gonads

Sexual reproduction is essential for the propagation and the maintenance of fitness of our species, and is dependent on the correct development of the bipotential genital ridges into testes and ovaries. Although several transcription factors, secreted signaling molecules, and their receptors have been found to be important for testis determination and early gonad development, comparatively little research has been carried out into intracellular signal transduction pathways activated during these processes. Focal adhesion kinase (FAK) and protein tyrosine kinase 2 beta (PTK2B) form one group of cytosolic tyrosine kinases that are known to be important for processes such as cell proliferation, differentiation, and motility. Here, we describe the temporal and spatial expression patterns of Fak and Ptk2b mRNA and protein during sex determination and early gonadogenesis in mouse embryos. Ptk2b mRNA and PTK2B protein were expressed in testes from 11.5 days post coitum onward, predominantly in developing Sertoli cells, in a SOX9‐dependent manner. Fak mRNA and FAK protein were expressed in gonads of both sexes at all stages examined. Our data suggest cell type‐ and stage‐specific roles for PTK2B during early testis development. Developmental Dynamics 239:2735–2741, 2010. © 2010 Wiley‐Liss, Inc.
Two steps natural actor critic learning for underwater cable tracking

This paper proposes a field application of a high-level Reinforcement Learning (RL) control system for solving the action selection problem of an autonomous robot in a cable tracking task. The underwater vehicle ICTINEUAUV learns to perform a visual based cable tracking task in a two step learning process. First, a policy is computed by means of simulation where a hydrodynamic model of the vehicle simulates the cable following task. Once the simulated results are accurate enough, in a second step, the learned-in-simulation policy is transferred to the vehicle where the learning procedure continues in a real environment, improving the initial policy. The natural actor-critic (NAC) algorithm has been selected to solve the problem in both steps. This algorithm aims to take advantage of policy gradient and value function techniques for fast convergence. Actor's policy gradient gives convergence guarantees under function approximation and partial observability while critic's value function reduces variance of the estimates update improving the convergence process.
Motives for accepting temporary employment : A typology

Purpose - This paper aims to offer a typology of temporary workers, based on their motives for accepting their work arrangement, which includes voluntary, involuntary and stepping-stone motives, and relate this typology to various individual and work-related variables. Design/methodology/approach - Latent class analysis of 645 European workers was used to construct a typology of temporary workers. Variation of individual and work-related variables between types of temporary workers was analyzed using ANOVA. Findings - The analyses suggest that there are three types of workers: involuntary temporary workers highlight the involuntary motive and the stepping-stone motive; the stepping-stone type stresses the stepping-stone motive only, and the non-involuntary group disagrees with all three motives. Moreover, the groups differed significantly on important work-related variables such as occupational position, tenure, employability, and work-involvement. However, differences in individual variables were limited. Research limitations/implications - The research puts forward a more complex typology of temporary workers than is usually suggested. Moreover, the study shows a non-involuntary group for which temporary employment can become a trap, and hence these workers should be targeted by future policy and interventions. Originality/value - The research offers a typology of temporary workers, which is founded on motivation theory, and existing research on motives for accepting temporary employment.
Exercise enhances memory consolidation in the aging brain

Exercise has been shown to reduce age-related losses in cognitive function including learning and memory, but the mechanisms underlying this effect remain poorly understood. Memory formation occurs in stages that include an initial acquisition phase, an intermediate labile phase, and then a process of consolidation which leads to long-term memory formation. An effective way to examine the mechanism by which exercise improves memory is to introduce the intervention (exercise), post-acquisition, making it possible to selectively examine memory storage and consolidation. Accordingly we evaluated the effects of post-trial exercise (10 min on a treadmill) on memory consolidation in aged canines both right after, an hour after, and 24 h after acute exercise training in concurrent discrimination, object location memory (OLM), and novel object recognition tasks. Our study shows that post-trial exercise facilitates memory function by improving memory consolidation in aged animals in a time-dependent manner. The improvements were significant at 24 h post-exercise and not right after or 1 h after exercise. Aged animals were also tested following chronic exercise (10 min/day for 14 consecutive days) on OLM or till criterion were reached (for reversal learning task). We found improvements from a chronic exercise design in both the object location and reversal learning tasks. Our studies suggest that mechanisms to improve overall consolidation and cognitive function remain accessible even with progressing age and can be re-engaged by both acute and chronic exercise.
Factors affecting disappearance of feedstuffs from bags suspended in the rumen.

Four experiments were conducted to examine the effect of various factors on in situ digestion of feedstuffs in the rumen of Holstein cows. In Exp. 1, the effect of various days, animals and animal diets on in situ digestion was evaluated. Measured disappearance of dry matter (DM) and nitrogen (N) from soybean meal (SBM) suspended in dacron bags was lowest when the host animal was fed a high grain diet. No effect due to animals, day of incubation or period of experimentation was observed. The effect of bag porosity and substrate particle size on DM and N disappearance from bags was studied in Exp. 2. Rip-stop nylon, a material with small pores, appeared to decrease the influx of digesting agents into bags and limited efflux of digested residues from bags when compared with bags made from dacron polyester material. Disappearance of DM and N from SBM and distillers grains (DG) in rip-stop nylon bags was greater when these feedstuffs were in the pulverized form rather than in the commercially processed form. In Exp. 3, dacron and Acropore bags, with pore sizes of 52 and 5 microns, respectively, were used to examine DM and N disappearance, in the rumen of cows, from total mixed diets containing various dietary N sources. Lower DM and N disappearance from Acropore bags was observed for each of the diets regardless of time spent in the rumen; much of the difference was established within the first hour. The effect of formaldehyde treatment on degradation of amino acids from SBM suspended in dacron bags in the rumen for 16 h was studied in Exp. 4. Increased resistance of SBM amino acids to degradation in the rumen was observed as a result of formaldehyde treatment levels as low as . 3% by weight. A possible increase in protection of lysine from degradation relative to other amino acids was also observed.
High-level Specification and Animation of Communicative Gestures

This paper describes a complete system for the specification and the generation of visual communicative gestures. A high-level language for the specification of hand? arm communication gestures was developed. This language is based on both a discrete description of space, and a movement decomposition inspired by sign language gestures. Communication gestures are represented by symbolic commands that can be described by qualitative data, and translated in terms of spatio-temporal targets that drive the generation system. This approach is well-suited for a class of generation models controlled by key-points information at the trajectory level. The animation model used in our approach is composed of a set of sensory-motor control loops. Each of these models computes in real-time updated angular coordinates of the articulatory structure from the minimization of the distance between target and current locations. At the same time, psycho-motor laws of biological movement are satisfied. The whole control system is applied to the synthesis of communication and sign language gestures. A synthetic character is animated and some results are presented.