Miracle-dz/UniFAR-FTUs huggingface dataset:
Retinoic Acid Signaling Regulates Differential Expression of the Tandemly-Duplicated Long Wavelength-Sensitive Cone Opsin Genes in Zebrafish

The signaling molecule retinoic acid (RA) regulates rod and cone photoreceptor fate, differentiation, and survival. Here we elucidate the role of RA in differential regulation of the tandemly-duplicated long wavelength-sensitive (LWS) cone opsin genes. Zebrafish embryos were treated with RA from 48 hours post-fertilization (hpf) to 75 hpf, and RNA was isolated from eyes for microarray analysis. ~170 genes showed significantly altered expression, including several transcription factors and components of cellular signaling pathways. Of interest, the LWS1 opsin gene was strongly upregulated by RA. LWS1 is the upstream member of the tandemly duplicated LWS opsin array and is normally not expressed embryonically. Embryos treated with RA 48 hpf to 100 hpf or beyond showed significant reductions in LWS2-expressing cones in favor of LWS1-expressing cones. The LWS reporter line, LWS-PAC(H) provided evidence that individual LWS cones switched from LWS2 to LWS1 expression in response to RA. The RA signaling reporter line, RARE:YFP indicated that increased RA signaling in cones was associated with this opsin switch, and experimental reduction of RA signaling in larvae at the normal time of onset of LWS1 expression significantly inhibited LWS1 expression. A role for endogenous RA signaling in regulating differential expression of the LWS genes in postmitotic cones was further supported by the presence of an RA signaling domain in ventral retina of juvenile zebrafish that coincided with a ventral zone of LWS1 expression. This is the first evidence that an extracellular signal may regulate differential expression of opsin genes in a tandemly duplicated array.
Pro-neurotrophins, sortilin, and nociception

Nerve growth factor (NGF) signaling is important in the development and functional maintenance of nociceptors, but it also plays a central role in initiating and sustaining heat and mechanical hyperalgesia following inflammation. NGF signaling in pain has traditionally been thought of as primarily engaging the classic high‐affinity receptor tyrosine kinase receptor TrkA to initiate sensitization events. However, the discovery that secreted proforms of nerve NGF have biological functions distinct from the processed mature factors raised the possibility that these proneurotrophins (proNTs) may have distinct function in painful conditions. ProNTs engage a novel receptor system that is distinct from that of mature neurotrophins, consisting of sortilin, a type I membrane protein belonging to the VPS10p family, and its co‐receptor, the classic low‐affinity neurotrophin receptor p75NTR. Here, we review how this new receptor system may itself function with or independently of the classic TrkA system in regulating inflammatory or neuropathic pain.
Speaking while monitoring addressees for understanding q

Speakers monitor their own speech and, when they discover problems, make repairs. In the proposal examined here, speakers also monitor addressees for understanding and, when necessary, alter their utterances in progress. Addressees cooperate by displaying and signaling their understanding in progress. Pairs of participants were videotaped as a director instructed a builder in assembling 10 Lego models. In one group, directors could see the builders workspace; in a second, they could not; in a third, they gave instructions by audiotape. Two partners were much slower when directors could not see the builders workspace, and they made many more errors when the instructions were audiotaped. When their workspace was visible, builders communicated with directors by exhibiting, poising, pointing at, placing, and orienting blocks, and by eye gaze, head nods, and head shakes, all timed with precision. Directors often responded by altering their utterances midcourse, also timed with precision. 2003 Elsevier Inc. All rights reserved.
The Performing State: Reflection on an Idea Whose Time Has Come but Whose Implementation Has Not

The contemporary nation-state exists to perform, to provide financial assistance, public services and other benefits to its people. How well the government performs influences the economic and social well-being of citizens, the mindset that voters take into the election booth, the programs and behavior of politicians and bureaucrats, and the relationship between government and the governed.
Systematic Validation of Protein Force Fields against Experimental Data

Molecular dynamics simulations provide a vehicle for capturing the structures, motions, and interactions of biological macromolecules in full atomic detail. The accuracy of such simulations, however, is critically dependent on the force field—the mathematical model used to approximate the atomic-level forces acting on the simulated molecular system. Here we present a systematic and extensive evaluation of eight different protein force fields based on comparisons of experimental data with molecular dynamics simulations that reach a previously inaccessible timescale. First, through extensive comparisons with experimental NMR data, we examined the force fields' abilities to describe the structure and fluctuations of folded proteins. Second, we quantified potential biases towards different secondary structure types by comparing experimental and simulation data for small peptides that preferentially populate either helical or sheet-like structures. Third, we tested the force fields' abilities to fold two small proteins—one α-helical, the other with β-sheet structure. The results suggest that force fields have improved over time, and that the most recent versions, while not perfect, provide an accurate description of many structural and dynamical properties of proteins.
Anticipation of future food: suppression and facilitation of saccharin intake depending on the delay and type of future food.

A series of studies examined the (Sprague-Dawley) rat's tendency to suppress intake of . 15% saccharin when it was followed by a second food after 4-, 16-, or 32-min delays. The second foods examined were 32% sucrose, 64% sucrose, lab chow, a Nutrasweet solution, skim milk, and chocolate milk. Saccharin intake was influenced by both the delay and the specific food available. Subsequent analysis showed that saccharin intake before the 4-min delay was an inverse function of the caloric value of the second food. However, saccharin intake before the 16-min delay was better predicted as an inverse function of the hedonic value of the second food. The results suggest that the caloric and hedonic values of a food may influence food selection across different time courses, and that the effective time horizon for the sequential comparison of foods depends on the specific foods that are compared.
What is a device bend gesture really good for?

Device deformation allows new types of gestures to be used in interaction. We identify that the gesture/use-case pairings proposed by interaction designers are often driven by factors relating improved tangibility, spatial directionality and strong metaphorical bonds. With this starting point, we argue that some of the designs may not make use of the full potential of deformation gestures as continuous, bipolar input techniques. In two user studies, we revisited the basics of deformation input by taking a new systematic look at the question of matching gestures with use cases. We observed comparable levels of UX when using bend input in different continuous bipolar interactions, irrespective of the choice of tangibility, directionality and metaphor. We concluded that device bend gestures use their full potential when used to control continuous bipolar parameters, and when quick reactions are needed. From our studies, we also identify relative strengths of absolute and relative mappings, and report a Fitts' law study for device bending input.
Comparing the application of classification and association rule mining techniques of data mining in an Indian university to uncover hidden patterns

The Untouched data of the University can be used to achieve the competitive advantage by having data analysis using Data Mining Techniques. Comparing Application of Classification and Association Rule Mining Techniques to identify fitness of the technique in education domain is an attempt towards uncovering hidden patterns in an Indian University. By experimental results authors have found the Classification comparatively brings more clear and straight pictures of hidden patterns subject to the dataset chosen.
Discovering Social Photo Navigation Patterns

In general, user browsing behavior has been examined within specific tasks (e.g., search), or in the context of particular web sites or services ( e.g., in shopping sites). However, with the growth of social networks and the proliferation of many different types of web services ( e.g., news aggregators, blogs, forums, etc.), the web can be viewed as an ecosystem in which a user's actions in a particular web service may be influenced by the service she arrived from ( e.g., are users browsing patterns similar if they arrive at a website via search or via links in aggregators? ). In particular, since photos in services like Flickr are used extensively throughout the web, it is common for visitors to the site to arrive via links in many different types of web sites. In this paper, we depart from the hypothesis that visitors to social sites such as Flickr behave differently depending on where they come from. For this purpose, we analyze a large sample of Flickr user logs to discover social photo navigation patterns. More specifically, we classify pages within Flickr into different categories ( e.g., "add a friend page", "single photo page," etc.), and by clustering sessions discover important differences in social photo navigation that manifest themselves depending on the type of site users visit before visiting Flickr. Our work examines photo navigation patterns in Flickr for the first time taking into account the referrer domain. Our analysis is useful in that it can contribute to a better understanding of how people use photo services like Flickr, and it can be used to inform the design of user modeling and recommendation algorithms, among others.
DSGE-Modelling: When Agents are Imperfectly Informed

DSGE-models have become important tools of analysis not only in academia but increasingly in the board rooms of central banks. The success of these models has much to do with the coherence of the intellectual framework it provides. The limitations of these models come from the fact that they make very strong assumptions about the cognitive abilities of agents in understanding the underlying model. In this paper we relax this strong assumption. We develop a stylized DSGE-model in which individuals use simple rules of thumb (heuristics) to forecast the future inflation and output gap. We compare this model with the rational expectations version of the same underlying model. We find that the dynamics predicted by the heuristic model differs from the rational expectations version in some important respects, in particular in their capacity to produce endogenous economic cycles. JEL Classification: E10, E32, D83
Necessary Optimality Conditions for Two-Stage Stochastic Programs with Equilibrium Constraints

Developing first order optimality conditions for two-stage stochastic mathematical programs with equilibrium constraints (SMPECs) whose second stage problem has multiple equilibria/solutions is a challenging undone work. In this paper we take this challenge by considering a general class of two-stage SMPECs whose equilibrium constraints are represented by a parametric variational inequality (where the first stage decision vector and a random vector are treated as parameters). We use the sensitivity analysis on deterministic mathematical programs with equilibrium constraints (MPECs) as a tool to deal with the challenge: First, we extend a well-known theorem in nonsmooth analysis about the exchange of the subdifferential operator with Aumann's integration from a nonatomic probability space to a general setting; second, we apply the extended result together with the existing sensitivity analysis results on the value function of the deterministic MPEC and the bilevel programming to the value function of our second stage problem; third, we develop various optimality conditions in terms of the subdifferential of the value function of the second stage problem and its relaxations which are constructed through the gradients of the underlying function at the second stage; finally we analyze special cases when the variational inequality constraint reduces to a complementarity problem and further to a system of nonlinear equalities and inequalities. The subdifferential to be used in this paper is the limiting (Mordukhovich) subdifferential, and the probability space is not necessarily nonatomic which means that Aumann's integral of the limiting subdifferential of a random function may be strictly smaller than that of Clarke's.
Finite-difference methods for simulation models incorporating nonconservative forces

We discuss algorithms applicable to the numerical solution of second-order ordinary differential equations by finite differences. We make particular reference to the solution of the dissipative particle dynamics fluid model, and present extensive results comparing one of the algorithms discussed with the standard method of solution. These results show the successful modeling of phase separation and surface tension in a binary immiscible fluid mixture.
Toward a new stakeholders’ identification: a redefinition of stakeholders through the legitimacy

The stakeholders’ theory (SHT) has generated a lot of interest from both academics and professionals (Cazal & Dietrich, 2005; Schlange, 2006). And it has also an ultimate objective, which is to allow the leaders to identify and to understand their stakeholders. In this research, we will try to define the stakeholders of the company through the analysis, more in-depth, of the process of their identification and by basing ourselves on the crossing of the components of the legitimacy with the other attributes of Mitchell et al. (1997) to know the power and the urgency. The choice of the bursting of the legitimacy is motivated by its ubiquity in the majority of the definitions of stakeholders presented by Mitchell et al. and the importance that it represents in their process of identification (Mitchell et al., 1997), the great status that Freeman gives him (Freeman, 1984) and the detailed analysis of its components of Santana which will enable us to highlight the role of this attribute in the process of stakeholders' identification (Santana, 2012). This crossing will enhance the stakeholders' identification whose simplicity is criticized by some authors (Schlange, 2006) and to help managers to better define their CSR strategy to adequately achieve their expectations (Freeman, 1984).
Constructing Efficient Certificateless Public Key Encryption with Pairing

Certificateless public key cryptography was introduced to overcome the key escrow limitation of the identity-based cryptography. Recently, Yum1 and Lee have proposed a generic series construction model of certificateless public key encryption (CL-PKE). However, this model pays much attention on the generic construction and neglects the properties of the pairings. In this paper we propose a CL-PKE scheme which is based on the nice algebraic properties of the pairing. The scheme breaks through the old series model and works in an efficient parallel model. Our scheme is more efficient on computation and has more compact ciphertext than the existing schemes.
Effective full-duplex Mesochronous Link Architecture for Network-on-Chip Data-Link layer

The increasing complexity of system on chip (SoC) architectures and the physical issues due to the CMOS technology scaling, led to explore new solutions to build effective on-chip interconnection and communication infrastructures. Network on chip (NoC) paradigm has been proposed as architectural solution mainly for overcoming scalability and flexibility limitations. However, advanced techniques to mitigate wire-delay effects have to be employed to reduce the impact of physical issues. Globally asynchronous locally synchronous (GALS) paradigm has been selected to this purpose as solution to implement the NoC physical layer, and many different approaches to design GALS-based NoC can be used. In this paper a full-duplex mesochronous link architecture, for which a patent has been submitted, is proposed to effectively implement the GALS paradigm in the STNoCtrade system. Such a link, exploiting the service provided by the newest mesochronous physical layer known as SKIL, effectively implements the mesochronous communication at data-link layer and enables to overcome some important issues of the previous mesochronous solutions.
Simulating from graphical models for ordinal categorical data

Multivariate ordinal categorical data is encountered in many fields of research. For analysis and data reduction the conditional independence properties of these data are studied in graphical models. However, to simulate multivariate ordinal data with a specific conditional independence structure, for use in simulation studies or computer intensive methods of inference, is non-trivial. We present a procedure to simulate data from a graphical model determined by the values of the partial gamma coefficients corresponding to the conditional dependencies in the graphical model. Implementation of the procedure is done in a standalone Pascal program, and as an R function.
A Pattern Language of Black-Box Test Design for Reactive Software Systems

Patterns have been successfully applied in software develo pment to improve the development process, by facilitating reuse, communication and documentation of sound so lutions. However, the testing domain is yet to benefit from a similar approach. This although, with the growing com plexity of test automation solutions, identifying and instrumenting patterns in test design to facilitate reu se appears to be a promising approach for shortening the development cycle and save costs. This paper presents a c ollection of patterns for designing test automation solutions for reactive software systems and reports on first experiences of applying those patterns in a case study.
Better Capitalism: Renewing the Entrepreneurial Strength of the American Economy

In the wake of the Great Recession and America's listless recovery from it, economists, policymakers, and media pundits have argued at length about what has gone wrong with the American capitalist system. Even so, few constructive remedies have emerged. This welcome book cuts through the chatter and offers a detailed, nonideological, and practical blueprint to restore the vigor of the American economy. Better Capitalism extends and significantly expands on the insights of the authors' widely praised previous book, Good Capitalism, Bad Capitalism, co-written with William Baumol. In Better Capitalism, Robert E. Litan and Carl J. Schramm focus on the huge-but often unrecognized-importance of entrepreneurship to overall economic growth. They explain how changes in seemingly unrelated policy arenas-immigration, education, finance, and federal support of university research-can accelerate America's recovery from recession and spur the nation's rate of growth in output while raising living standards. The authors also outline an innovative energy strategy and discuss the potential benefits of government belt-tightening steps. Sounding an optimistic note when gloomy predictions are the norm, Litan and Schramm show that, with wise and informed policymaking, the American entrepreneurial engine can rally and the true potential of the U.S. economy can be unlocked.
Impacts of Peer Characteristics on P2PTV Networks Scalability

A P2PTV system allows users to watch live video streams redistributed by other users via a peer-to-peer (P2P) network. In an ideal world, each peer in a P2P network would be able to redistribute more bytes than it receives. A P2PTV system built from such peers can support a virtually unlimited number of peers; with only a single copy of content stream injected into the network, it can redistribute the content to all peers. Two factors in the development of the Internet prevented the realization of this scenario: the deployment of asymmetric access networks and the adoption of NAT boxes. For real-time live streaming, such peer asymmetry and incompatibility is a limiting factor on the P2P network scalability. We first develop a basic formal analysis of the effect of bandwidth asymmetry on P2P network scalability. Then we present several characteristics of peer asymmetry as measured on the Zattoo P2PTV network. Our simulation results, driven by the measured peer characteristics, confirm that we cannot rely on P2P network alone to distribute live streaming content on today's Internet.
STARP: a novel routing protocol for multi-hop dynamic spectrum access networks

The technology of Dynamic Spectrum Access (DSA) can utilize unused licensed bands not being used by licensed users to improve the capacity and throughput of multi-hop wireless networks working on the ISM bands. However, DSA also brings us a new challenge: how to network the radios in multi-hop DSA networks to improve network performance, such as throughput and end-to-end delay? To address this issue, we propose a STability-Aware Routing Protocol (STARP) for multi-hop DSA networks. STARP can find the most stable path among multi paths to the destination for upper layer protocol. STARP evaluates path stability by utilizing a novel routing metric, which takes into account spectrum switching frequency, spectrum usage, and path length together. Simulation results of NS-2 show STARP is efficient and robust. In addition, STARP can achieve good improvement of TCP performance and shorten end-to-end packet delay significantly.
VLSI CAD tool protection by birthmarking design solutions

Many techniques have been proposed in the past for the protection of VLSI design IPs (intellectual property). CAD tools and algorithms are intensively used in all phases of modern VLSI designs; however, little has been done to protect them. Basically, given a problem Ρ and a solution Σ, we want to be able to determine whether Σ is obtained by a particular tool or algorithm.We propose two techniques that intentionally leave some trace or birthmark, which refers to certain easy detectable properties, in the design solutions to facilitate CAD tool tracing and protection. The pre-processing technique provides the ideal protection at the cost of losing control of solution's quality. The post-processing technique balances the level of protection and design quality.We conduct a case study on how to protect a timing-driven gate duplication algorithm. Experimental results on a large set of MCNC benchmarks confirm that the pre-processing technique results in a significant reduction (about 48%) of the optimization power of the tool, while the post-processing technique has almost no penalty (less than 2%) on the tool's performance.