Miracle-dz/UniFAR-FTUs huggingface dataset:
Functional Studies of ssDNA Binding Ability of MarR Family Protein TcaR from Staphylococcus epidermidis

The negative transcription regulator of the ica locus, TcaR, regulates proteins involved in the biosynthesis of poly-N-acetylglucosamine (PNAG). Absence of TcaR increases PNAG production and promotes biofilm formation in Staphylococci. Previously, the 3D structure of TcaR in its apo form and its complex structure with several antibiotics have been analyzed. However, the detailed mechanism of multiple antibiotic resistance regulator (MarR) family proteins such as TcaR is unclear and only restricted on the binding ability of double-strand DNA (dsDNA). Here we show by electrophoretic mobility shift assay (EMSA), electron microscopy (EM), circular dichroism (CD), and Biacore analysis that TcaR can interact strongly with single-stranded DNA (ssDNA), thereby identifying a new role in MarR family proteins. Moreover, we show that TcaR preferentially binds 33-mer ssDNA over double-stranded DNA and inhibits viral ssDNA replication. In contrast, such ssDNA binding properties were not observed for other MarR family protein and TetR family protein, suggesting that the results from our studies are not an artifact due to simple charge interactions between TcaR and ssDNA. Overall, these results suggest a novel role for TcaR in regulation of DNA replication. We anticipate that the results of this work will extend our understanding of MarR family protein and broaden the development of new therapeutic strategies for Staphylococci.
Base Vector Learning Mechanism for Fuzzy Model

Fuzzy model based on support vector machine(SVM-based fuzzy model) was proposed in recent years. Although SVM has an excellent generalization performance, it is considered to have lower computation speed, and a large number of support vectors may be found, which leads to a complex fuzzy model with too many rules. To deal with the problem, the paper presents a new approach called base vector learning(BVL) to build fuzzy model. There are two steps in the process of the BVLbased fuzzy modeling. First, the quadratic Renyi entropy is applied to select base vectors, which are used to span a subspace in feature space F. Then, all data are projected onto this subspace where classical algorithms such as classification or regression can be applied. If Gaussian kernel is onsidered, the structure of BVL is equivalent to fuzzy model. The performance of the proposed learning scheme is illustrated by experiments of classification and regression.
Who Wants to Learn More Science? The Role of Elementary School Science Experiences and Science Self-Perceptions

Background/Context Much science education reform has been directed at middle and high school students; however, earlier experiences in elementary school may well have an important impact on young people's future science literacy and preparation for possible STEM careers. Purpose/Objective This study explores the relationships among fifth-graders’ perceived learning opportunities in school science, their perceptions of self in science, and their desire to take more science courses in middle and high school. Research Design To directly address concerns about the reproducibility of results of small educational studies, this study explores whether results from one sample are replicated in a second, different sample. The fifth-grade students from two different samples of public elementary students in California (Sample 1: n = 363; Sample 2: n = 327) completed surveys about students’ perceived school science experiences, sense of themselves as science learners, and aspirations to learn more science in the future. The analyses of both samples included regression analyses to explore the relationship between science self-perceptions and wanting to take future science classes, as well as whether students’ perceived opportunities to participate in science activities might influence the relationship between self-perceptions and wanting to take more science in the future. Findings/Results There were positive and significant relationships between both school science learning opportunities and wanting to take more science courses, and science self-perceptions and wanting to take more science courses. Analyses indicate that both factors need to be considered when predicting who is eager to learn more science. These findings were consistent across both samples and were robust even after including student-level and school-level and controlling for the nested structure of the data. Conclusions/Recommendations Findings highlight the importance of fifth-graders’ self-perceptions in understanding the effects of science learning opportunities on their desire to learn more science. Thus, school science opportunities may be necessary but not sufficient for increasing student interest in learning more science. Since teachers have influence on both learning activities and a student's sense of self as a science learner, the results underscore the importance of preparing elementary teachers to foster student desire to learn more science in the future.
General Recursion and Formal Topology

It is well known that general recursion cannot be expressed within Martin-Loef's type theory and various approaches have been proposed to overcome this problem still maintaining the termination of the computation of the typable terms. In this work we propose a new approach to this problem based on the use of inductively generated formal topologies.
Finding good feedback documents

Pseudo-relevance feedback finds useful expansion terms from a set of top-ranked documents. It is often crucial to identify those good feedback documents from which useful expansion terms can be added to the query. In this paper, we propose to detect good feedback documents by classifying all feedback documents using a variety of features such as the distribution of query terms in the feedback document, the similarity between a single feedback document and all top-ranked documents, or the proximity between the expansion terms and the original query terms in the feedback document. By doing this, query expansion is only performed using a selected set of feedback documents, which are predicted to be good among all top-ranked documents. Experimental results on standard TREC test data show that query expansion on the selected feedback documents achieves statistically significant improvements over a strong pseudo-relevance feedback mechanism, which expands the query using all top-ranked documents.
The incidence function approach to modeling of metapopulation dynamics

The incidence function approach to modelling of metapopulation dynamics is critically examined both from the biological perspective and for technical issues, the latter by placing the model in the context of Markov random fields and the statistical analysis of binary lattice systems. The claim that the model can be used to estimate time-process parameters from spatialpattern data is examined using real data sets for which process information was available. The incidence function approach is compared with the alternative approach of estimating extinction and colonization functions from time series data. We discuss the merits of the two approaches as potential tools in conservation of metapopulations and in landscape planning.
OBTAINING GOOD PERFORMANCE FROM A BADTEACHERMICHAEL KAISER

Programming by Demonstration (PbD) is an intuitive method to program a robot. The user, acting as a teacher or programmer, shows how a particular task can be performed. The demonstration is monitored using an interface device that allows the measurement and recording of both the applied commands as well as the data simultaneously perceived by robot's sensors. This paper considers the problems of not-at-all optimal examples that in general result from a human demonstration. It identiies the sources of non-optimality and presents methods to cope with it.
Acute and Chronic Effects of Intrathecal Morphine in Monkeys

In a double-blind study, seven Macaca fascicularis monkeys receiving intrathecal (i.t.) morphine in saline, 0.07 mg kg-1, were compared with a control group of four monkeys receiving either lumbar puncture alone (n = 1) or i.t. saline (n = 3). Neither morphine nor saline solutions contained preservatives. Arterial blood gas tensions, respiration, arterial pressure, e.c. g. , state of consciousness and motor function were recorded for 24 h. The control group was sacrificed 42 days later and the study group was sacrificed at 6 (n = 2) or 42 days (n = 5) after injection. The central nervous system, meninges, nerve roots and dorsal root ganglia were examined macroscopically and microscopically. Respiratory depression did not occur in either the control or the study groups. There were moderate but statistically significant decreases in systolic and diastolic arterial pressures following i.t. morphine. In both groups, the pathological findings were localized to the cauda equina region and characterized by mononuclear cell infiltration. In neither group was there evidence of demyelination, arachnoiditis or necrosis. Focal endoneurial fibrosis was found in only one animal in the control group following multiple lumbar punctures associated with paraesthesia. The features appeared to correlate with the physical trauma associated with lumbar puncture rather than with the injectate.
Brain-Inspired Conscious Computing Architecture

What type of artificial systems will claim to be conscious and will claim to experience qualia? The ability to comment upon physical states of a brain-like dynamical system coupled with its environment seems to be sufficient to make claims. The flow of internal states in such system, guided and limited by associative memory, is similar to the stream of consciousness. Minimal requirements for an artificial system that will claim to be conscious were given in form of specific architecture named articon. Nonverbal discrimination of the working memory states of the articon gives it the ability to experience different qualities of internal states. Analysis of the inner state flows of such a system during typical behavioral process shows that qualia are inseparable from perception and action. The role of consciousness in learning of skills, when conscious information processing is replaced by subconscious, is elucidated. Arguments confirming that phenomenal experience is a result of cognitive processes are presented. Possible philosophical objections based on the Chinese room and other arguments are discussed, but they are insufficient to refute claims articon’s claims. Conditions for genuine understanding that go beyond the Turing test are presented. Articons may fulfill such conditions and in principle the structure of their experiences may be arbitrarily close to human.
Image Segmentation Based on Inhomogeneity Pixel Using Complex Wavelet Transform for Medical Image

Abstract—The most widely used image segmentation algorithm are region based and typically rely on the homogeneity of the image intensities in the region of interest which is fail to provide accurate segmentation results due to the intensity of inhomogeneity. In this paper we have proposed novel region wavelet based method for image segmentation which is able to deal with intensity inhomogeneous. In segmentation the intensity inhomogeneity is identified by the efficient threshold technique in wavelet domain. This paper uses complex wavelet transform to segment the image based on inhomogeniety. Experiments demonstrate that t he Neighsureshrink threshold method using the complex wavelet transform achie ves better results than discrete wavelet transform in the terms of SS IM and CWSS IM. Index Terms—Segmentation, Inhomogeneity, Neighsuresh rink, SSIM, CWSSIM I. INTRO DUCTION
On Morphisms Preserving Primitive Words

A word is called primitive if it cannot be expressed as the power of another word. Morphisms preserving primitive words are investigated. Similarly to the word case, each square-free morphism is a primitive morphism but the converse does not hold. A precise characterization of primitive morphisms is provided in terms of pure codes. An easily testable characterization is given for uniform morphisms over the binary alphabet. TUCS Research Group Mathematical Structures of Computer Science
Trump Trumps Baldwin? How Trump’s Tweets Transform SNL into Trump’s Strategic Advantage

What happens when a politician responds through social media to critical humor, as in the case of Donald Trump’s hostile reactions toward Alec Baldwin’s appearances on Saturday Night Live (SNL)? Analysis of experimental data collected in December 2016 (N = 325) shows that viewing Trump’s Twitter response accusing SNL of media bias inoculates viewers against Baldwin’s anti-Trump satire that is present in the original skit. Moreover, viewing the SNL skit and an article detailing Trump’s continued Twitter engagement with the show over the course of the fall 2016 season encourages viewers to connect the anti-Trump SNL humor with Hillary Clinton and Tim Kaine, resulting in significantly lower favorability ratings for the Democratic opposition. The implications of the findings and their influence on strategic political communication are discussed.
Time-varying multiuser detection for DS-CDMA in doubly-selective channels

The problem of multiuser detection for DS-CDMA in doubly-selective (timeand frequency-selective) channels is considered, and a time-varying multiuser detector (TV-MUD) to solve this problem is proposed. Using a basis expansion model (BEM) to model the doubly-selective channel and the TV-MUD, we derive a closed-form expression for the BEM coefficients of the TV-MUD as a function of the BEM coefficients of the doubly-selective channel. The criterion we use is the symbol mean-square error.
ZOOMABLE USER INTERFACES IN SCALABLE VECTOR GRAPHICS

Zoomable user interfaces are an evolutionary outgrowth of graphical user interfaces. In this paper we propose a zoomable user interface based on Scalable Vector Graphics. Three-level zooming is proposed as a new paradigm to combine different zooming functionalities in a common interface and support zooming within the window manager. This helps to unify zooming techniques of different applications. To meet the demand of efficient and easy navigation on a user interface, several novel interaction techniques are shown that further support the integration of three-level zooming within the underlying presentation system. For mobile small-screen devices, where the benefit of zooming user interfaces is even higher, the proposed system can be operated with simple pen tap or tap and drag operations. We also present a prototypical implementation, which demonstrates how applications based on the SPARK toolkit can transparently benefit form the proposed technology.
Towards stabilizing parametric active contours

Numerical instability often occurs in evolving of parametric active contours. This is mainly due to the undesired change of parametrization during evolution. In this paper, we propose a new tangential diffusion term to compensate this undesired change. As a result, the parametrization will converge to a parametrization that is proportional to the natural parametrization which implies that the control points of the contour are uniformly distributed. We theoretically prove that this tangential diffusion term is bounded and therefore numerically stable. Several experiments were conducted and verified the feasibility of the proposed tangential diffusion force.
Stable maps and Hurwitz schemes in mixed characteristic

In this short note, we propose a definition of complete Hurwitz schemes (and stacks) in mixed characteristic. We follow an idea of R. Pandharipande, and define the complete Hurwitz stack as a substack of stable maps of degree d of nodal pointed curves of genus g to the universal curve over the moduli stack of stable pointed curves of genus h. This substack is simply the closure of the locus of Hurwitz covers in characteristic 0. We describe in detail the reduction modulo 2 of the complete Hurwitz stack of genus 1 double covers of the projective line. The result is wilder than you would imagine in your wildest dreams. We end by speculating about a possible relationship with the work of Abramovich-Vistoli about stable maps into Deligne-Mumford stacks.
Heating of X-Ray Hot Gas in Groups by Blast Waves

In order to find the conditions that determine whether X-ray hot gas in galaxy groups (intragroup gas [IGG]) is heated externally or internally, we investigate the evolution of blast waves in galaxy groups growing on a hierarchical clustering scenario. We find that the blast waves driven by quasars are confined in groups and heat the IGG internally at z ≲ 1. However, at z ≳ 1, they expel the IGG from groups; the expelled gas may fall back into the groups later as externally heated gas. Moreover, this may explain the observed low metal abundance of IGG. For blast waves driven by strong starbursts, the shift of the fate of blast waves occurs at z ~ 3. On the other hand, although blast waves driven by weak starbursts do not expel IGG from groups, the heating efficiency decreases at z ≳ 3 because of radiative cooling. It will be useful to compare these results with XMM-Newton observations.
Computers Seeing People

AI researchers are interested in building intelligent machines that can interact with them as they interact with each other. Science fiction writers have given us these goals in the form of HAL in 2001: A Space Odyssey and Commander Data in Star Trek: The Next Generation. However, at present, our computers are deaf, dumb, and blind, almost unaware of the environment they are in and of the user who interacts with them. In this article, I present the current state of the art in machines that can see people, recognize them, determine their gaze, understand their facial expressions and hand gestures, and interpret their activities. I believe that by building machines with such abilities for perceiving, people will take us one step closer to building HAL and Commander Data.
Extensive range persistence in peripheral and interior refugia characterizes Pleistocene range dynamics in a widespread Alpine plant species (Senecio carniolicus, Asteraceae)

Recent evidence suggests that survival of arctic‐alpine organisms in peripheral or interior glacial refugia are not mutually exclusive and may both be involved in shaping an organism’s Pleistocene history, yet potentially at different time levels. Here, we test this hypothesis in a high‐mountain plant (diploid lineage of Senecio carniolicus, Asteraceae) from the Eastern European Alps, in which patterns of morphological variation and current habitat requirements suggest survival in both types of refugia. To this end, we used AFLPs, nuclear and plastid DNA sequences and analysed them, among others, within a graph theoretic framework and using novel Bayesian methods of phylogeographic inference. On the basis of patterns of genetic diversity, occurrence of rare markers, distribution of distinct genetic lineages and patterns of range connectivity both interior refugia in the formerly strongly glaciated central Alps and peripheral refugia along the southern margin of the Alps were identified. The presence of refugia congruently inferred by markers resolving at different time levels suggests that these refugia acted as such throughout several glacial cycles. The high degree of range persistence together with gradual range expansion, which contrasts with the extent of range shifts implied for other Alpine species, is likely responsible for incipient lineage differentiation evident from the genetic data. Replacing a simplistic peripheral vs. interior refugia dualism by more complex models involving both types of refugia and considering different time levels will help identifying common phylogeographic patterns with respect to, for instance, location of refugia and colonization routes and elucidating their underlying genetic and/or ecological causes.
Testing the concept of academic housework in a European setting: Part of academic career-making or gendered barrier to the top?

In the labour market women’s jobs have frequently been conceptually and literally tied to housework and hence thought of as unskilled and therefore undervalued. Although academic institutions have undergone changes, the fact that women still carry the main responsibility for domestic and caring tasks continues to follow them into the academic work environment. In this explorative study we focus on the gendered aspects of undervalued work in academia by examining how academic housework manifests itself in different academic contexts and how early career academics in six European countries contend with it. We will link the undervalued academic work to housework in a double sense. Firstly, we will discuss how domestic housework affects the working conditions of academic women and men differently in their early career. Secondly, we will approach academic work through the lenses of academic housework, hence making use of the notion of ‘housework’ in a transferred and more figurative meaning. The discussion is aimed at developing a new conceptual framework in the analysis of gendered academic careers. In this way the topic of academic housework, which seems to be accompanied by social taint, may become more easily discussable within the academic work environment.
Acoustic reconstruction of the geometry of an environment through acquisition of a controlled emission

This paper presents a novel solution for the reconstruction of an environment from the acquisition of a controlled emission, in particular for what concerns the estimation of the position of acoustic reflectors. The solution proposed in this paper makes use of a loudspeaker rotating on a circular pattern and emitting a controlled noise and a microphone located at the center of the circle. A likelihood map is built by means of a template matching between the signal acquired at the microphone and a template signal obtained by simulating the propagation of the signal to all the potential obstacles locations. The position of the reflectors is inferred by the analysis of the likelihood map. Simulations assess the best working conditions for the device in terms of test signal duration, radius of the circular trajectory and Signal to Noise Ratio. A simulation has been carried out also in the presence of multiple and interacting reflectors to show the feasibility of the approach also in more complex scenarios.
Accumulation of Phosphorylated Repressor for Gibberellin Signaling in an F-box Mutant

Gibberellin (GA) regulates growth and development in plants. We isolated and characterized a rice GA-insensitive dwarf mutant,gid2. The GID2 gene encodes a putative F-box protein, which interacted with the rice Skp1 homolog in a yeast two-hybrid assay. In gid2, a repressor for GA signaling, SLR1, was highly accumulated in a phosphorylated form and GA increased its concentration, whereas SLR1 was rapidly degraded by GA through ubiquitination in the wild type. We conclude that GID2 is a positive regulator of GA signaling and that regulated degradation of SLR1 is initiated through GA-dependent phosphorylation and finalized by an SCFGID2-proteasome pathway.