Miracle-dz/UniFAR-FTUs huggingface dataset:
Analysis of Ribosome-Associated mRNAs in Rice Reveals the Importance of Transcript Size and GC Content in Translation

Gene expression is controlled at transcriptional and post-transcriptional levels including decoding of messenger RNA (mRNA) into polypeptides via ribosome-mediated translation. Translational regulation has been intensively studied in the model dicot plant Arabidopsis thaliana, and in this study, we assessed the translational status [proportion of steady-state mRNA associated with ribosomes] of mRNAs by Translating Ribosome Affinity Purification followed by mRNA-sequencing (TRAP-seq) in rice (Oryza sativa), a model monocot plant and the most important food crop. A survey of three tissues found that most transcribed rice genes are translated whereas few transposable elements are associated with ribosomes. Genes with short and GC-rich coding regions are overrepresented in ribosome-associated mRNAs, suggesting that the GC-richness characteristic of coding sequences in grasses may be an adaptation that favors efficient translation. Transcripts with retained introns and extended 5′ untranslated regions are underrepresented on ribosomes, and rice genes belonging to different evolutionary lineages exhibited differential enrichment on the ribosomes that was associated with GC content. Genes involved in photosynthesis and stress responses are preferentially associated with ribosomes, whereas genes in epigenetic regulation pathways are the least enriched on ribosomes. Such variation is more dramatic in rice than that in Arabidopsis and is correlated with the wide variation of GC content of transcripts in rice. Taken together, variation in the translation status of individual transcripts reflects important mechanisms of gene regulation, which may have a role in evolution and diversification.
The SRI EduSpeak System: Recognition and Pronunciation Scoring for Language Learning

The EduSpeak system is a software development toolkit that enables developers of interactive language education software to use state-of-the-art speech recognition and pronunciation scoring technology. We first report results on the application of adaptation techniques to recognize both native and nonnative speech in a speaker-independent manner. We discuss our pronunciation scoring paradigm and show experimental results in the form of correlations between the pronunciation quality estimators included in the toolkit and grades given by human listeners. We review phone-level pronunciation estimation schemes and describe the phone-level mispronunciation detection functionality that we have incorporated in the toolkit. Finally, we mention some of the EduSpeak toolkit system features that facilitate the creation and deployment of computer-assisted language learning (CALL) applications.
Distributed Systems Diagnosis Using Belief Propagation

In this paper, we focus on diagnosis in distributed computer systems using end-to-end transactions, or probes. Diagnostic problem is formulated as a probabilistic inference in a bipartite noisy-OR Bayesian network. Due to general intractability of exact inference in such networks, we apply belief propagation (BP), a popular approximation technique proven successful in various applications, from image analysis to probabilistic decoding. Another attractive property of BP for our application is it natural parallelism that allows a distributed implementation of diagnosis in a distributed system to improve diagnostic speed and robustness. We derive lower bounds for diagnostic error in bipartite Bayesian networks, and particularly in noisy-OR networks, and provide promising empirical results for belief propagation on both randomly generated and realistic noisy-OR problems.
Some experiments with array data collected in actual urban and suburban environments

We compare the performance of several algorithms for signal separation based on actual mobile cellular radio data. The data were collected by base stations in two different environments: using an eight element linear array on a hillside overlooking a suburban area, and using a four element square array at the top of a ten story building in a dense urban area. Calibration data were available for one of the arrays used for the suburban data, allowing for performance comparisons between DOA-based and blind signal separators. Experiments were conducted with three different types of signal waveforms: sinewaves, simple FM waveforms, and /spl pi//4-DQPSK signals, each of which necessitated the use of a different performance metric. We focus on the results obtained for cases where the data were approximately low rank, with little delay spread (although not all data sets from the urban environment were of this type).
Mental State Recognition via Wearable EEG

The increasing quality and affordability of consumer electroencephalogram (EEG) headsets make them attractive for situations where medical grade devices are impractical. Predicting and tracking cognitive states is possible for tasks that were previously not conducive to EEG monitoring. For instance, monitoring operators for states inappropriate to the task (e.g. drowsy drivers), tracking mental health (e.g. anxiety) and productivity (e.g. tiredness) are among possible applications for the technology. Consumer grade EEG headsets are affordable and relatively easy to use, but they lack the resolution and quality of signal that can be achieved using medical grade EEG devices. Thus, the key questions remain: to what extent are wearable EEG devices capable of mental state recognition, and what kind of mental states can be accurately recognized with these devices? In this work, we examined responses to two different types of input: instructional (logical) versus recreational (emotional) videos, using a range of machine-learning methods. We tried SVMs, sparse logistic regression, and Deep Belief Networks, to discriminate between the states of mind induced by different types of video input, that can be roughly labeled as logical vs. emotional. Our results demonstrate a significant potential of wearable EEG devices in differentiating cognitive states between situations with large contextual but subtle apparent differences.
Pad: an alternative approach to the computer interface

We believe that navigation in information spaces is best supported by tapping into our natural spatial and geographic ways of thinking. To this end, we are developing a new computer interface model called Pad. The ongoing Pad project uses a spatial metaphor for computer interface design. It provides an intuitive base for the support of such applications as electronic marketplaces, information services, and on-line collaboration. Pad is an infinite two dimensional information plane that is shared among users, much as a network file system is shared. Objects are organized geographically; every object occupies a well defined region on the Pad surface. For navigation, Pad uses “portals” - magnifying glasses that can peer into and roam over different parts of this single infinite shared desktop; links to specific items are established and broken continually as the portal’s view changes. Portals can recursively look onto other portals. This paradigm enables the sort of peripheral activity generally found in real physical working environments. The apparent size of an object to any user determines the amount of detail it presents. Different users can share and view multiple applications while assigning each a desired degree of interaction. Documents can be visually nested and zoomed as they move back and forth between primary and secondary working attention. Things can be peripherally accessible. In this paper we describe the Pad interface. We discuss how to efficiently implement its graphical aspects, and we illustrate some of our initial applications.
An In-Depth Qualitative Examination of the Ecstasy Experience: Results of a Focus Group with Ecstasy-Using College Students

This study examined ecstasy use in 30 college students who participated in one of four 60-minute focus groups with other participants who also had a history of ecstasy use. Ten topics emerged in the sessions: 1) pill ingredients, 2) mechanism of MDMA effects, 3) reasons for initiating ecstasy use, 4) risky behaviors and ecstasy use, 5) sexual activity and ecstasy, 6) positive effects from ecstasy use, 7) negative effects related to ecstasy use, 8) ecstasy and polysubstance use, 9) perceived risks of ecstasy use, and 10) motivational factors related to quitting ecstasy use. Most participants had a basic understanding of the contents of ecstasy pills, and the effects that ecstasy has on the brain and bodily functions. Participants reported positive effects on mood, social pressure, curiosity, availability, boredom, desire for an altered state of mind, desire to escape, self-medication, desire to have fun, and the ease of use of ecstasy in comparison to other drugs as reasons for initiating ecstasy use. They were divided regarding whether ecstasy increased the likelihood of engaging in risky behaviors, including risky sexual behavior. Participants described their experiences of both the positive and negative effects (physical and psychological) that they attributed to their use of ecstasy. All participants were polysubstance users, consuming a number of other substances simultaneously and concurrently with ecstasy. The majority was unaware of specific types of problems ecstasy could potentially cause and discounted its potential harm. Participants varied in their motivation for quitting ecstasy use, including negative personal experiences while using ecstasy, health concerns, and addiction/tolerance. Implications for prevention and intervention are discussed.
Leveraging DUC

Work at the University of Ottawa on text summarization in connection with the Document Understanding Conference 2006 advanced along two tracks. We continued to refine and expand the corpus of SCU-marked documents which we created last year from materials that conference participants received from the group at Columbia University. We also developed an internal manual summary evaluation scheme based on the same responsiveness and quality criteria that NIST's evaluators apply. This scheme and a ranking procedure employing the SCU-marked corpus allowed us to evaluate various heuristics that members of our team implemented. Our DUC submission ultimately incorporated elements of three specialized research projects. This is how in 2006 we took advantage of our continuing involvement in DUC.
Aikido: A Martial Art With Mindfulness, Somatic, Relational, and Spiritual Benefits for Veterans

Aikido is a martial art that originated in Japan and incorporates meditation and breathing techniques from Zen Buddhism. Like all martial arts, it requires mindful concentration and physical exertion. In addition, it is a compassion practice that also provides a spiritual perspective and includes social touch. These components make Aikido a unique form of mindfulness that has the potential to be particularly appealing to veterans coming from a Warrior Ethos tradition who are used to rigorous somatic training. Mindfulness practices have shown efficacy with veterans, and the self-compassion, spiritual, and social touch dimensions of Aikido also offer benefits for this population, many of whom are struggling with these issues. Several pilot Aikido programs with veterans that show promise are described.
The heuristic value of the social: The effect of social quality and trust on welfare and tax attitudes

In the last decades, enhancing social trust and improving social quality have been often considered as the antidote to the problems produced by the neoliberal makeover of the social life. However, it remains unclear whether higher social quality and trust actually produce more pro-social attitudes among people. Based on a statistical analysis of a cross-national survey administered in five countries, this article shows that social quality and social trust, as empirical indicators of the social, do not always generate pro-social attitudes. It demonstrates that perceived social quality and trust on social institutions can generate both conservative and liberal attitudes toward social welfare and taxation. In order to explain the varying effects of social quality and trust, we propose a heuristic model of political cognition and motivation, which illustrates how the political variety of the social is possible. Our model highlights the contextual contingencies of the political meaning of the social.
Discovery of Blue Luminescence in the Red Rectangle: Possible Fluorescence from Neutral Polycyclic Aromatic Hydrocarbon Molecules?

Here we report our discovery of a band of blue luminescence (BL) in the Red Rectangle nebula. This enigmatic proto-planetary nebula is also one of the brightest known sources of extended red emission as well as of unidentified infrared (UIR) band emissions. The spectrum of this newly discovered BL is most likely fluorescence from small neutral polycyclic aromatic hydrocarbon (PAH) molecules. PAH molecules are thought to be widely present in many interstellar and circumstellar environments in our Galaxy as well as in other galaxies and are considered likely carriers of the UIR band emission. However, no specific PAH molecule has yet been identified in a source outside the solar system because the set of mid-infrared emission features attributed to these molecules between the wavelengths of 3.3 and 16.4 μm is largely insensitive to molecular sizes. In contrast, near-UV/blue fluorescence of PAHs is more specific as to size, structure, and charge state of a PAH molecule. If the carriers of this near-UV/blue fluorescence are PAHs, they are most likely neutral PAH molecules consisting of three to four aromatic rings such as anthracene (C14H10) and pyrene (C16H10). These small PAHs would then be the largest molecules specifically identified in the interstellar medium.
Teacher Experiences on the Play Based Methods and Instructional Practices Used in Half vs Full Day Kindergarten.

The purpose of this case study was to examine the play based teaching and learning methods at one particular elementary school in southeastern Massachusetts with the aim of identifying methods and practices that are seen as essential in developing the academic and social skills in kindergarten students. This school of study has been utilizing multiple approaches driven by budget, state mandates, and administrative decision making. The intrinsic case study was designed to analyze perceptions of kindergarten teachers with respect to their thoughts and believes on the most developmentally appropriate and effective way to teach academic and social skills to kindergarten students. Data were obtained through interviews, classroom observations, and a review of professional development offerings in the school district.
Practical and Provable Security against Differential and Linear Cryptanalysis for Substitution‐Permutation Networks

We examine the diffusion layers of some block ciphers referred to as substitution‐permutation networks. We investigate the practical and provable security of these diffusion layers against differential and linear cryptanalysis. First, in terms of practical security, we show that the minimum number of differentially active S‐boxes and that of linearly active S‐boxes are generally not identical and propose some special conditions in which those are identical. We also study the optimal diffusion effect for some diffusion layers according to their constraints. Second, we obtain the results that the consecutive two rounds of SPN structure provide provable security against differential and linear cryptanalysis, i.e., we prove that the probability of each differential (resp. linear hull) of the consecutive two rounds of SPN structure with a maximal diffusion layer is bounded by pn (resp. qn) and that of each differential (resp. linear hull) of the SDS function with a semi‐maximal diffusion layer is bounded by pn‐1 (resp. qn‐1), where p and q are maximum differential and linear probabilities of the substitution layer, respectively.
ON THE COMETARY ORIGIN OF THE POLONNARUWA METEORITE

The diatoms discovered in the Polonnaruwa meteorite are interpreted as originating in comets and the dust in interstellar space. The exceptionally porous structure of the Polonnaruwa meteorite points to it being a recently denuded cometary fragment. Microorganisms that were present in a freeze-dried state within pores and cavities may have survived entry to be added to the terrestrial biosphere.
Search Strategy Simulation in Constraint Booleanization

Within the recently proposed Universal Booleanization framework, we consider the CUMULATIVE constraint, for which the original Boolean encoding proves ineffective, and present a new Boolean encoding that causes the SAT solver to simulate, largely, the search strategy used by some of the best-performing native methods. Apart from providing motivation for future research in a similar direction, we obtain a significantly enhanced version of Universal Booleanization for problems containing CUMULATIVE constraints.
Two HOTs to Handle: The Concept of State Consciousness in the Higher-Order Thought Theory of Consciousness

David Rosenthal's higher-order thought (HOT) theory is one of the most widely argued for of the higher-order accounts of consciousness. I argue that Rosenthal vacillates between two models of the HOT theory. First, I argue that these models employ different concepts of ‘state consciousness’; the two concepts each refer to mental state tokens, but in virtue of different properties. In one model, the concept of ‘state consciousness’ is more consistent with how the term is typically used, both by philosophers and scientists, and in commonsense usage. This model, however, also has its problems. In the second part of the paper, I develop a modified version of Rosenthal's transitivity principle, thereby avoiding some complications that stem from the original transitivity principle. I suggest that Rosenthal occasionally employs this modified model himself, and that the inconsistency identified in the first section of this paper might really reflect Rosenthal's vacillation between these two versions of the transitivity principle. I offer one explanation for how this equivocation may have occurred. These two versions would result if articulations of the transitivity principle employed the term ‘mental state’ inconsistently, to refer on some occasions merely to mental state types, and on others, to tokened mental states. I conclude by arguing, contrary to Rosenthal and others, that the theory is not incompatible with view that conscious states are uniquely casual efficacious.
Understanding Knowledge Management Software-Organisation Misalignments From An Institutional Perspective : A Case Study

Romano Dyerson University of London Follow this and additional works at: https://engagedscholarship.csuohio. edu/bus_facpub Part of the Business Commons How does access to this work benefit you? Let us know! Publisher's Statement NOTICE: this is the author’s version of a work that was accepted for publication in the International Journal of Information Management. Changes resulting from the publishing process, such as peer review, editing, corrections, structural formatting, and other quality control mechanisms may not be reflected in this document. Changes may have been made to this work since it was submitted for publication. A definitive version was subsequently published in the International Journal of Information Management, 34, 2, 04-01-2014, 10.1016/j.ijinfomgt. 2013.11. 003.
A Model of Postural Control in Quiet Standing: Robust Compensation of Delay-Induced Instability Using Intermittent Activation of Feedback Control

The main purpose of this study is to compare two different feedback controllers for the stabilization of quiet standing in humans, taking into account that the intrinsic ankle stiffness is insufficient and that there is a large delay inducing instability in the feedback loop: 1) a standard linear, continuous-time PD controller and 2) an intermittent PD controller characterized by a switching function defined in the phase plane, with or without a dead zone around the nominal equilibrium state. The stability analysis of the first controller is carried out by using the standard tools of linear control systems, whereas the analysis of the intermittent controllers is based on the use of Poincaré maps defined in the phase plane. When the PD-control is off, the dynamics of the system is characterized by a saddle-like equilibrium, with a stable and an unstable manifold. The switching function of the intermittent controller is implemented in such a way that PD-control is ‘off’ when the state vector is near the stable manifold of the saddle and is ‘on’ otherwise. A theoretical analysis and a related simulation study show that the intermittent control model is much more robust than the standard model because the size of the region in the parameter space of the feedback control gains (P vs. D) that characterizes stable behavior is much larger in the latter case than in the former one. Moreover, the intermittent controller can use feedback parameters that are much smaller than the standard model. Typical sway patterns generated by the intermittent controller are the result of an alternation between slow motion along the stable manifold of the saddle, when the PD-control is off, and spiral motion away from the upright equilibrium determined by the activation of the PD-control with low feedback gains. Remarkably, overall dynamic stability can be achieved by combining in a smart way two unstable regimes: a saddle and an unstable spiral. The intermittent controller exploits the stabilizing effect of one part of the saddle, letting the system evolve by alone when it slides on or near the stable manifold; when the state vector enters the strongly unstable part of the saddle it switches on a mild feedback which is not supposed to impose a strict stable regime but rather to mitigate the impending fall. The presence of a dead zone in the intermittent controller does not alter the stability properties but improves the similarity with biological sway patterns. The two types of controllers are also compared in the frequency domain by considering the power spectral density (PSD) of the sway sequences generated by the models with additive noise. Different from the standard continuous model, whose PSD function is similar to an over-damped second order system without a resonance, the intermittent control model is capable to exhibit the two power law scaling regimes that are typical of physiological sway movements in humans.
Individual Differences Related to College Students' Course Performance in Calculus II

In this study, we explore student achievement in a semester-long flipped Calculus II course, combining various predictor measures related to student attitudes (math anxiety, math confidence, math interest, math importance) and cognitive skills (spatial skills, approximate number system), as well as student engagement with the online system (discussion forum interaction, time to submission of workshop assignments, quiz attempts), in predicting final grades. Data from 85 students enrolled in a flipped Calculus II course was used in dominance analysis to determine which predictors emerged as the most important for predicting final grades. Results indicated that feelings of math importance, approximate number system (ANS) ability, total amount of discussion forum posting, and time grading peer workshop submissions was the best combination of predictors of final grade, accounting for 17% of variance in a student’s final grade. The point of this work was to determine which predictors are the most important in predicting student grade, with the end goal of building a recommendation system that could be implemented to help students in this traditionally difficult class. The methods used here could be used for any class.