Miracle-dz/UniFAR-FTUs huggingface dataset:
LSU Digital Commons LSU Digital Commons Under the genomic radar: The Stealth model of Alu amplification Under the genomic radar: The Stealth model of Alu amplification

Alu elements are the most successful SINEs (Short INterspersed Elements) in primate genomes and have reached more than 1,000,000 copies in the human genome. The amplification of most Alu elements is thought to occur through a limited number of hyperactive “master” genes that produce a high number of copies during long evolutionary periods of time. However, the existence of long-lived, low-activity Alu lineages in the human genome suggests a more complex propagation mechanism. Using both computational and wet-bench approaches, we reconstructed the evolutionary history of the Alu Yb lineage, one of the most active Alu lineages in the human genome. We show that the major Alu Yb lineage expansion in humans is a species-specific event, as nonhuman primates possess only a handful of Alu Yb elements. However, the oldest existing Alu Yb element resided in an orthologous position in all hominoid primate genomes examined, demonstrating that the Alu Yb lineage originated 18–25 million years ago. Thus, the history of the Alu Yb lineage is characterized by ∼ 20 million years of retrotranspositional quiescence preceding a major expansion in the human genome within the past few million years. We suggest that the evolutionary success of the Alu family may be driven at least in part by “stealth-driver” elements that maintain low retrotranspositional activity over extended periods of time and occasionally produce short-lived hyperactive copies responsible for the formation and remarkable expansion of Alu elements within the genome. [The sequence data from this study have been submitted to GenBank under accession nos. AY791249–AY791290. ] As the most successful SINEs (Short INterspersed Elements) in primate genomes, Alu elements have enjoyed remarkable prolif-eration during the primate radiation and have expanded to more than 1,000,000 copies
State of rhetoric: neoliberal discourses for education in state of the state addresses and gubernatorial press releases

ABSTRACT Policy elites use rhetoric in speeches and press releases to provide framing that is intended to influence public opinion. These rhetorical events can be treated as instances in which speech usefully promotes particular discourses. Indeed, elected officials are able to influence how individuals think about problems and solutions through speeches and press releases. Two important rhetorical events in which political elites advance frames for social issues are annual state of the state addresses (SoSA) given by U.S. governors and gubernatorial press releases that inform media reporting about state policy. This study employed policy discourse and rhetorical analyses to examine SoSAs and press releases as rhetorical events within the context of educational policy. Our findings show that governors framed the roles of state government, governors, and educational stakeholders within a discourse that perpetuates a neoliberal version of education. In this framing, governors situated education’s purpose as being workforce and economic development, ignoring its role in addressing social issues and preparing informed, engaged participants for democratic society. Given that individuals make decisions about how to address social issues and understand public institutions based on framing provided by political elites, these findings raise implications for state educational policies and the public purposes of education.
Overcoming Language Variation in Sentiment Analysis with Social Attention

Variation in language is ubiquitous, particularly in newer forms of writing such as social media. Fortunately, variation is not random; it is often linked to social properties of the author. In this paper, we show how to exploit social networks to make sentiment analysis more robust to social language variation. The key idea is linguistic homophily: the tendency of socially linked individuals to use language in similar ways. We formalize this idea in a novel attention-based neural network architecture, in which attention is divided among several basis models, depending on the author’s position in the social network. This has the effect of smoothing the classification function across the social network, and makes it possible to induce personalized classifiers even for authors for whom there is no labeled data or demographic metadata. This model significantly improves the accuracies of sentiment analysis on Twitter and on review data.
LoWPANs Meet Service-Oriented Architecture

The Low-Power Wireless Personal Area Networks (LoWPANs) have been recognized as a promising technology for ubiquitous and pervasive computing systems. However, LoWPAN technology is still open to being adapted to existing interoperability mechanisms defined for the Internet. Service-Oriented-Architecture (SOA) is one of the key paradigms that enables the deployment of services at large-scale over the Internet domain and its integration with LoWPANs has opened new pathways for novel applications and research. Despite the need to integrate SOA with LoWPANs, only a handful efforts are underway to achieve the goal. In this paper, we discuss the integration of LoWPANs with ServiceOriented-Architecture (SOA) for seamless provisioning of services in LoWPANs, especially considering the future of LoWPANs, i.e., IPv6-enabled LoWPANs (6LoWPANs). We first present an overview about the general concepts of SOA and its applicability onto low-power devices. Then, we discuss 6LoWPAN, a milestone protocol that bridged the gap between low-power devices and the IP world and discuss the advantages, challenges and opportunities for porting SOA over LoWPANs. We also present the main research efforts that contributed to featuring the integration LoWPANs with SOA and we draw a research roadmap on potential research directions and challenges for achieving an efficient coupling among LoWPANs and SOA.
An interdisciplinary perspective: The value that instructors place on giving written feedback

Students need feedback from instructors to learn from their mistakes and improve their academic skills. Responding to student writing is a central and necessary component of the instructor–student feedback loop. There are many forms of feedback on written assignments, and not all of them have the same role in supporting student learning. For example, as for written feedback, one primary distinction is between comments made in the margins and comments at the end of the written work. Work has focused on practices of instructor feedback among instructors, and other studies have focused on practices of feedback within a single discipline. Although there have been many studies on the topic of instructor feedback, no studies were found that explored possible differences of feedback across disciplines. The purpose of the study described here was to explore what instructors consider to be the purpose(s)/value of writing feedback (whether it is in the margins or at the end) on written assignments, as well as how instructors from different disciplines conceive of using comments in the margins and end of essays/written work, that is, whether or not they would conceive of them differently, and therefore provide different feedback, according to discipline. Nearly half of the instructors valued the use of written feedback on written assignments as fostering future improvements. In contrast, when analyzing responses across disciplines, identifying specific errors seemed to be more important in making comments in the margins. Further analysis and recommendations are provided.
Local Organization and Business Ontology (LOBO)

In the advent of globalization and increasing tourism local companies and business get more and more attention from people in different parts of the world. In this paper the authors outline an approach which leads to a description of organizations and business, i.e. non-profit and profit organizations, with an emphasis on local or regional basis. For this, publicly available upper ontologies and business area and e-tourism ontologies are studied and used as appropriate, added by an ontology describing the concepts of locality, forming a Local Organizations and Business Ontology system (LOBO). As an example the authors set up an ontology for organizations and enterprises in Phitsanulok Province (Thailand). The system aims at establishing web based dynamic yellow pages as well as company and organizational histories with the help of the semantic web. Therefore the authors do not only use a spatial (regional, local) but also a temporal ontology. The ontology is implemented with Protege (OWL).
A stable robust adaptive controller for a class of nonlinear systems

In this paper, a robust adaptive control is proposed for a class of nonlinear systems subject to unmodeled dynamics and bounded disturbances. The nonlinear systems are represented by their input-output maps. The e1-modification scheme is proposed to achieve robustness and enhance the convergence properties of the tracking error in the absence of disturbances. The stability of the closed-loop system is shown by Lyapunov's direct method. Simulation results demonstrate the improved performance of the proposed controller as compared with the previously reported adaptive controllers in the literature.
The role of isoforms in the evolution of cryptic coloration in Peromyscus mice

A central goal of evolutionary biology is to understand the molecular mechanisms underlying phenotypic adaptation. While the contribution of protein-coding and cis-regulatory mutations to adaptive traits have been well documented, additional sources of variation—such as the production of alternative RNA transcripts from a single gene, or isoforms—have been understudied. Here, we focus on the pigmentation gene Agouti, known to express multiple alternative transcripts, to investigate the role of isoform usage in the evolution of cryptic color phenotypes in deer mice (genus Peromyscus). We first characterize the Agouti isoforms expressed in the Peromyscus skin and find two novel isoforms not previously identified in Mus. Next, we show that a locally adapted light-colored population of P. maniculatus living on the Nebraska Sand Hills shows an up-regulation of a single Agouti isoform, termed 1C, compared to their ancestral dark-colored conspecifics. Using in vitro assays, we show that this preference for isoform 1C may be driven by isoform-specific differences in translation. In addition, using an admixed population of wild-caught mice, we find that variation in overall Agouti expression maps to a region near exon 1C, which also has patterns of nucleotide variation consistent with strong positive selection. Finally, we show that the independent evolution of cryptic light pigmentation in a different species, P. polionotus, has been driven by a preference for the same Agouti isoform. Together, these findings present an example of the role of alternative transcript processing in adaptation and demonstrate molecular convergence at the level of isoform regulation.
STEM Uygulamaları Öğretmen Öz-yeterlik Ölçeğinin Geliştirilmesi: Bir Geçerlik ve Güvenirlik Çalışması

Bu calismanin amaci, STEM yaklasimi ile ilgili STEM Uygulamalari Ogretmen Ozyeterlik Olcegi’ni gelistirmektir. Bu nedenle, calisma icin 55 maddelik bir STEM Uygulamalari Ogretmen Ozyeterlik Olcegi soru havuzu hazirlanmistir. Hazirlanan olcek maddeleri Turkiye’nin bati bolgesinde bulunan bir kamu universitesinin egitim fakultesinde ogrenim gormekte olan 219 ogretmen adayina uygulanmis, gecerlik ve guvenirlik calismalari yapilmistir. Olcegin Cronbach’s Alpha ic tutarlik katsayisi . 97 olarak hesaplanmistir. Olcek tek boyutlu olup, toplam varyansin % 68.2’sini aciklamaktadir. Yapilan analizler sonucunda STEM Uygulamalari Ogretmen Ozyeterlik Olcegi 55 maddeden 18 maddeye dusurulmustur. Dogrulayici faktor analizi sonuclarina gore olcegin tek faktorlu yapisina ait uyum indeksleri oldukca iyi duzeydedir (RMSEA= .05, NFI= .99, CFI= 1.00, IFI= 1.00, RFI= .98, GFI= .90 ve SRMR= .025). Ayrica gecerlige katki saglamak icin de STEM egitim programina katilan ve katilmayan, STEM hakkinda bilgisi olan ve olmayan ogrencilerin STEM ozyeterlik puanlari karsilastirilmistir. Yapilan analizler sonucunda STEM hakkinda bilgisi olan ogrenciler ve STEM etkinligi yapan ogrenciler lehine anlamli farklar bulunmustur.
Note-level Music Transcription by Maximum Likelihood Sampling

Note-level music transcription, which aims to transcribe note events (often represented by pitch, onset and offset times) from music audio, is an important intermediate step towards complete music transcription. In this paper, we present a note-level music transcription system, which is built on a state-of-the-art frame-level multi-pitch estimation (MPE) system. Preliminary note-level transcription achieved by connecting pitch estimates into notes often lead to many spurious notes due to MPE errors. In this paper, we propose to address this problem by randomly sampling notes in the preliminary note-level transcription. Each sample is a subset of all notes and is viewed as a notelevel transcription candidate. We evaluate the likelihood of each candidate using the MPE model, and select the one with the highest likelihood as the final transcription. The likelihood treats notes in a transcription as a whole and favors transcriptions with less spurious notes. Experiments conducted on 110 pieces of J.S. Bach chorales with polyphony from 2 to 4 show that the proposed sampling scheme significantly improves the transcription performance from the preliminary approach. The proposed system also significantly outperforms two other state-of-the-art systems in both frame-level and note-level transcriptions.
Fingerprint enhancement based on edge-directed diffusion

This paper puts forward a new edge-directed forward and backward anisotropic diffusion model for texture enhancement and edge sharpening of image. Since forward and backward diffusion cannot hold flow-like edges, and coherence enhancement diffusion cannot sharpen edges, our new model gets a new diffusivity, which combine the merits of these two methods. The new model adapts an image structure tensor like coherence enhancement diffusion for edge orientation, and defines eigenvalues based on edge orientation such that the new tensor has positive diffusivity in edge direction and negative diffusivity in gradient direction. Both theory analysis and numerical results show that the new model has better enhancement result than coherence enhancing diffusion and forward and backward diffusion.
The Schooling Costs of Teenage Out-of-Wedlock Childbearing: Analysis with a Within-School Propensity-Score-Matching Estimator

Teen out-of-wedlock mothers have lower education and earnings than do peers who have children later. This study uses the National Educational Longitudinal Survey of 1988 to examine the extent to which the apparent effects of out-of-wedlock teen childbearing are due to preexisting disadvantages of the young women and their families. We use a novel method that matches teen mothers to similar young women in their junior high school (that is, prior to pregnancy). We find that out-of-wedlock fertility reduces education substantially, although far less than the cross-sectional comparisons of means suggest. We further find that this effect is larger among those with lower probabilities of having a child out of wedlock.
On generalized gradients and optimization ∗

There exists a calculus for general nondifferentiable functions that englobes a large part of the familiar subdifferential calculus for convex nondifferentiable functions [1]. This development started with F.H. Clarke, who introduced a generalized gradient for functions that are locally Lipschitz, but (possibly) nondifferentiable. Generalized gradients turn out to be the subdifferentials, in the sense of convex analysis [1], of generalized directional derivative functions that are canonically associated to the locally Lipschitz functions under consideration. The key point to note is that such generalized directional derivative functions are automatically convex, even when the original locally Lipschitz functions are not convex. Two important special cases of functions f that are locally Lipschitz near some point x0 ∈ R and their generalized gradients, denoted by ∂̄f(x0), are as follows: (i) f is continuously differentiable at x0 and (ii) f is convex on R and x0 ∈ int dom f . Then
Batesian mimics influence the evolution of conspicuousness in an aposematic salamander

Conspicuousness, or having high contrast relative to the surrounding background, is a common feature of unpalatable species. Several hypotheses have been proposed to explain the occurrence of conspicuousness, and while most involve the role of conspicuousness as a direct signal of unpalatability to potential predators, one hypothesis suggests that exaggerated conspicuousness may evolve in unpalatable species to reduce predator confusion with palatable species (potential Batesian mimics). This hypothesis of antagonistic coevolution between palatable and unpalatable species hinges on the ‘cost of conspicuousness’, in which conspicuousness increases the likelihood of predation more in palatable species than in unpalatable species. Under this mimicry scenario, four patterns are expected: (i) mimics will more closely resemble local models than models from other localities, (ii) there will be a positive relationship between mimic and model conspicuousness, (iii) models will be more conspicuous in the presence of mimics, and (iv) when models and mimics differ in conspicuousness, mimics will be less conspicuous than models. We tested these predictions in the salamander mimicry system involving Notophthalmus viridescens (model) and one colour morph of Plethodon cinereus (mimic). All predictions were supported, indicating that selection for Batesian mimicry not only influences the evolution of mimics, but also the evolution of the models they resemble. These findings indicate that mimicry plays a large role in the evolution of model warning signals, particularly influencing the evolution of conspicuousness.
An Active Queue Management Algorithm Based on DiffServ Model

DiffServ model is a main model that guarantees QoS in modern-Large-scale network. , On the basis of RIO-C, the paper introduces an Active Queue Management algorithm -- PFRIO that is suitable for DiffServ model. The algorithm increases the fair for bandwidth allocation and the network’s capacity to hand of sudden data flow, and improves the overall performance of DiffServ model effectively.
How should meta‐regression analyses be undertaken and interpreted?

Appropriate methods for meta‐regression applied to a set of clinical trials, and the limitations and pitfalls in interpretation, are insufficiently recognized. Here we summarize recent research focusing on these issues, and consider three published examples of meta‐regression in the light of this work. One principal methodological issue is that meta‐regression should be weighted to take account of both within‐trial variances of treatment effects and the residual between‐trial heterogeneity (that is, heterogeneity not explained by the covariates in the regression). This corresponds to random effects meta‐regression. The associations derived from meta‐regressions are observational, and have a weaker interpretation than the causal relationships derived from randomized comparisons. This applies particularly when averages of patient characteristics in each trial are used as covariates in the regression. Data dredging is the main pitfall in reaching reliable conclusions from meta‐regression. It can only be avoided by prespecification of covariates that will be investigated as potential sources of heterogeneity. However, in practice this is not always easy to achieve. The examples considered in this paper show the tension between the scientific rationale for using meta‐regression and the difficult interpretative problems to which such analyses are prone. Copyright © 2002 John Wiley & Sons, Ltd.
Adaptive game playing using multiplicative weights

Abstract We present a simple algorithm for playing a repeated game. We show that a player using this algorithm suffers average loss that is guaranteed to come close to the minimum loss achievable by any fixed strategy. Our bounds are nonasymptotic and hold for any opponent. The algorithm, which uses the multiplicative-weight methods of Littlestone and Warmuth, is analyzed using the Kullback–Liebler divergence. This analysis yields a new, simple proof of the min–max theorem, as well as a provable method of approximately solving a game. A variant of our game-playing algorithm is proved to be optimal in a very strong sense. Journal of Economic Literature Classification Numbers: C44, C70, D83.
Metabolism of AGEs – Bacterial AGEs Are Degraded by Metallo-Proteases

Advanced Glycation End Products (AGEs) are the final products of non-enzymatic protein glycation that results in loss of protein structure and function. We have previously shown that in E. coli AGEs are continually formed as high-molecular weight protein complexes. Moreover, we showed that AGEs are removed from the cells by an active, ATP-dependent secretion and that these secreted molecules have low molecular weight. Taken together, these results indicate that E. coli contains a fraction of low molecular weight AGEs, in addition to the high-molecular weight AGEs. Here we show that the low-molecular weight AGEs originate from high-molecular weight AGEs by proteolytic degradation. Results of in-vitro and in vivo experiments indicated that this degradation is carried out not by the major ATP-dependent proteases that are responsible for the main part of bacterial protein quality control but by an alternative metal-dependent proteolysis. This proteolytic reaction is essential for the further secretion of AGEs from the cells. As the biochemical reactions involving AGEs are not yet understood, the implication of a metalloprotease in breakdown of high molecular weight AGEs and their secretion constitutes an important step in the understanding of AGEs metabolism.
Kinematics of the ultracompact helium accretor AM Canum Venaticorum

We report on the results from a five-night campaign of high-speed spectroscopy of the 17-min binary AM Canum Venaticorum (AM CVn), obtained with the 4.2-m William Herschel Telescope on La Palma. We detect a kinematic feature that appears to be entirely analogous to the 'central spike' known from the long-period, emission-line AM CVn stars GP Com, V396 Hya and SDSS J124058.03-015919.2, which has been attributed to the accreting white dwarf. Assuming that the feature indeed represents the projected velocity amplitude and phase of the accreting white dwarf, we derive a mass ratio q = 0.18 +/- 0.01 for AM CVn. This is significantly higher than the value found in previous, less direct measurements. We discuss the implications for AM CVn's evolutionary history and show that a helium star progenitor scenario is strongly favoured. We further discuss the implications for the interpretation of AM CVn's superhump behaviour, and for the detectability of its gravitational-wave signal with the Laser Interferometer Space Antenna (LISA). In addition, we demonstrate a method for measuring the circularity or eccentricity of AM CVn's accretion disc, using stroboscopic Doppler tomography. We test the predictions of an eccentric, precessing disc that are based on AM CVn's observed superhump behaviour. We limit the effective eccentricity in the outermost part of the disc, where the resonances that drive the eccentricity are thought to occur, to e = 0.04 +/- 0.01, which is smaller than previous models indicated.