Miracle-dz/UniFAR-FTUs huggingface dataset:
Global Analyses of Small Interfering RNAs Derived from Bamboo mosaic virus and Its Associated Satellite RNAs in Different Plants

Background Satellite RNAs (satRNAs), virus parasites, are exclusively associated with plant virus infection and have attracted much interest over the last 3 decades. Upon virus infection, virus-specific small interfering RNAs (vsiRNAs) are produced by dicer-like (DCL) endoribonucleases for anti-viral defense. The composition of vsiRNAs has been studied extensively; however, studies of satRNA-derived siRNAs (satsiRNAs) or siRNA profiles after satRNA co-infection are limited. Here, we report on the small RNA profiles associated with infection with Bamboo mosaic virus (BaMV) and its two satellite RNAs (satBaMVs) in Nicotiana benthamiana and Arabidopsis thaliana. Methodology/Principal Findings Leaves of N. benthamiana or A. thaliana inoculated with water, BaMV alone or co-inoculated with interfering or noninterfering satBaMV were collected for RNA extraction, then large-scale Solexa sequencing. Up to about 20% of total siRNAs as BaMV-specific siRNAs were accumulated in highly susceptible N. benthamiana leaves inoculated with BaMV alone or co-inoculated with noninterfering satBaMV; however, only about 0.1% of vsiRNAs were produced in plants co-infected with interfering satBaMV. The abundant region of siRNA distribution along BaMV and satBaMV genomes differed by host but not by co-infection with satBaMV. Most of the BaMV and satBaMV siRNAs were 21 or 22 nt, of both (+) and (−) polarities; however, a higher proportion of 22-nt BaMV and satBaMV siRNAs were generated in N. benthamiana than in A. thaliana. Furthermore, the proportion of non-viral 24-nt siRNAs was greatly increased in N. benthamiana after virus infection. Conclusions/Significance The overall composition of vsiRNAs and satsiRNAs in the infected plants reflect the combined action of virus, satRNA and different DCLs in host plants. Our findings suggest that the structure and/or sequence demands of various DCLs in different hosts may result in differential susceptibility to the same virus. DCL2 producing 24-nt siRNAs under biotic stresses may play a vital role in the antiviral mechanism in N. benthamiana.
Being Proactive: Where Action Research Meets Design Research

Information systems research has been criticized for having little influence on practice. One approach to achieving more relevance is to conduct research using appropriate research methods that balance the interests of both researchers and practitioners. This paper examines the similarities between two methods that address this mandate by adopting a proactive stance to investigating information systems in organizations. These two approaches, action research and design research, both directly intervene in real-world domains and effect changes in these domains. We investigate these similarities by examining exemplars of each type of research according to the criteria of the other. Our analysis reveals interesting parallels and similarities between the two, suggesting that the two approaches have much to learn from each other. Based on our analysis, we propose ways to facilitate cross-fertilization between the two approaches that we believe will be useful for both and for IS research in general.
Footing in human-robot conversations: How robots might shape participant roles using gaze cues

During conversations, speakers establish their and others' participant roles (who participates in the conversation and in what capacity)-or “footing” as termed by Goffman-using gaze cues. In this paper, we study how a robot can establish the participant roles of its conversational partners using these cues. We designed a set of gaze behaviors for Robovie to signal three kinds of participant roles: addressee, bystander, and overhearer. We evaluated our design in a controlled laboratory experiment with 72 subjects in 36 trials. In three conditions, the robot signaled to two subjects, only by means of gaze, the roles of (1) two addressees, (2) an addressee and a bystander, or (3) an addressee and an overhearer. Behavioral measures showed that subjects' participation behavior conformed to the roles that the robot communicated to them. In subjective evaluations, significant differences were observed in feelings of groupness between addressees and others and liking between overhearers and others. Participation in the conversation did not affect task performance-measured by recall of information presented by the robot-but affected subjects' ratings of how much they attended to the task.
The Virtual Reality Responsive Workbench: Applications and Experiences

Abstract : Virtual Reality (VR) is a complex and challenging field [Earnshaw and Rosenblum, 1995; Rosenblum and Cross, 1997], and several distinct types of systems have been developed for displaying and interacting with virtual environments. One of the newest is the Virtual Reality Responsive Workbench [Kreuger and Froehlich, 1994; Kreuger et al., 1995; Rosenblum, Bryson, and Feiner, 1995]. The Workbench is an interactive VR environment designed to support a team of end users such as military and civilian command and control specialists, designers, engineers, and doctors. The Virtual Workbench creates a match for the real work environment of persons who would typically stand over a table or a workbench as part of their professional routine. For example, the Workbench could be used to represent fluid flow over a ship's hull while supporting a design team in interactive visualization. Perhaps the greatest strength of the VR Responsive Workbench is the ease of natural interaction with virtual objects. Current interactive methods emphasize gesture recognition, speech recognition, and a simulated laser pointer to identify and manipulate objects. This paper classifies VR systems into three categories: immersive head-mounted displays (HMDs), immersive non-HMD systems, and partially immersive tabletop systems. We discuss the utility of each classification. Several applications that we have developed in the Virtual Reality Laboratory of the Information Technology Division (ITD), Naval Research Laboratory (NRL) are examined, and we discuss our experiences with VR Responsive Workbench interfaces and software architecture.
Improving the treatment for depressive symptoms and major depression with anti-inflammatory drugs

ABSTRACT FROM: Kohler O, Benros ME, Nordentoft M, et al. Effect of anti-inflammatory treatment on depression, depressive symptoms, and adverse effects: a systematic review and meta-analysis of randomized clinical trials. JAMA Psychiatry 2014;71:1381–91. Major depression and depressive symptoms may be associated with an inflammatory state: subgroups of depressed patients show elevated levels of cytokines,1 ,2 autoimmune diseases and infections are known risk factors for mood disorders3 and treatment with proinflammatory agents induces symptoms of depression.4 This study investigated the promising effects of anti-inflammatory drugs used in addition or instead of traditional antidepressants, which have shown to improve symptoms but where possible adverse side effects are a concern. This systematic review evaluated 14 randomised placebo-controlled trials assessing the efficacy and adverse effects of pharmacological anti-inflammatory treatment in 6262 adults with major depression or depressive symptoms. The study included papers published prior to 31 December 2013 and were …
Fc receptor biology.

This review deals with membrane Fc receptors (FcR) of the immunoglobulin superfamily. It is focused on the mechanisms by which FcR trigger and regulate biological responses of cells on which they are expressed. FcR deliver signals when they are aggregated at the cell surface. The aggregation of FcR having immunoreceptor tyrosine-based activation motifs (ITAMs) activates sequentially src family tyrosine kinases and syk family tyrosine kinases that connect transduced signals to common activation pathways shared with other receptors. FcR with ITAMs elicit cell activation, endocytosis, and phagocytosis. The nature of responses depends primarily on the cell type. The aggregation of FcR without ITAM does not trigger cell activation. Most of these FcR internalize their ligands, which can be endocytosed, phagocytosed, or transcytosed. The fate of internalized receptor-ligand complexes depends on defined sequences in the intracytoplasmic domain of the receptors. The coaggregation of different FcR results in positive or negative cooperation. Some FcR without ITAM use FcR with ITAM as signal transduction subunits. The coaggregation of antigen receptors or of FcR having ITAMs with FcR having immunoreceptor tyrosine-based inhibition motifs (ITIMs) negatively regulates cell activation. FcR therefore appear as the subunits of multichain receptors whose constitution is not predetermined and which deliver adaptative messages as a function of the environment.
Applying critical realism in qualitative research: methodology meets method

Abstract Critical realism (CR) is a useful philosophical framework for social science; however, little guidance is available on which precise methods – including methods of data collection, coding, and analysis – are best suited to applied CR research. This article provides a concrete example of applied qualitative research using CR as a philosophical and methodological framework. Drawing examples from a study of Canadian farm women’s experiences with agricultural policy, I suggest a flexible deductive process of coding and data analysis that is consistent with CR ontology and epistemology. The paper follows the typical stages of qualitative research while demonstrating the application of methods informed by CR at each stage. Important considerations CR ontology and epistemology raise, such as the use of existing theory and critical engagement with participants’ knowledge and experience, are discussed throughout. Ultimately, I identify two key causal mechanisms shaping the lives of farm women and suggest a future direction for feminist political economy theory to more effectively analyze women’s work in agricultural contexts.
A model for prediction of cisplatin induced nephrotoxicity by kidney weight in experimental rats

Background: Cisplatin (cis-diamminedichloroplatinum II; CP) is used widely as an antitumor drug in clinics, but is accompanied with renal toxicity. Cisplatin induced nephrotoxicity consists of change in kidney weight, histological changes in kidney and increase in serum creatinine (Cr) and blood urea nitrogen (BUN). This study was designed to find out a model for prediction of cisplatin induced nephrotoxicity. Materials and Methods: Pathological damage score, kidney weight, BUN, and Cr of 227 rats that were involved in different projects were determined. A total of 187 rats were treated with 7 mg/kg cisplatin and sacrificed 1 week later. Results: There was a good significant correlation between normalized kidney weight and logarithmic scale of BUN and Cr. Relationship between BUN, Cr or normalized kidney weight and pathology damage score was significant. Conclusion: Normalized kidney weight and pathology damage score is a good predictor of renal function in cisplatin induced nephrotoxicity in experimental rats.
Antimicrobial Peptides for Therapeutic Applications: A Review

Antimicrobial peptides (AMPs) have been considered as potential therapeutic sources of future antibiotics because of their broad-spectrum activities and different mechanisms of action compared to conventional antibiotics. Although AMPs possess considerable benefits as new generation antibiotics, their clinical and commercial development still have some limitations, such as potential toxicity, susceptibility to proteases, and high cost of peptide production. In order to overcome those obstacles, extensive efforts have been carried out. For instance, unusual amino acids or peptido-mimetics are introduced to avoid the proteolytic degradation and the design of short peptides retaining antimicrobial activities is proposed as a solution for the cost issue. In this review, we focus on small peptides, especially those with less than twelve amino acids, and provide an overview of the relationships between their three-dimensional structures and antimicrobial activities. The efforts to develop highly active AMPs with shorter sequences are also described.
Towards optimization-safe systems: analyzing the impact of undefined behavior

This paper studies an emerging class of software bugs called optimization-unstable code: code that is unexpectedly discarded by compiler optimizations due to undefined behavior in the program. Unstable code is present in many systems, including the Linux kernel and the Postgres database. The consequences of unstable code range from incorrect functionality to missing security checks. To reason about unstable code, this paper proposes a novel model, which views unstable code in terms of optimizations that leverage undefined behavior. Using this model, we introduce a new static checker called Stack that precisely identifies unstable code. Applying Stack to widely used systems has uncovered 160 new bugs that have been confirmed and fixed by developers.
Sleep in Adults with Attention-deficit/Hyperactivity Disorder of the Predominantly Inattentive and Combined Subtypes

ii! PREFACE . iv! ACKNOWLEDGMENTS . vi! TABLE OF CONTENTS . vii! LIST OF TABLES. xiii! LIST OF FIGURES. xiv! LIST OF APPENDICES . xv! LIST OF ABBREVIATIONS. xvi! Chapter,1,INTRODUCTION.1! 1.1! Preamble. 1! 1.2! ADHD. 3! 1.2.1! A! historical! account! of! ADHD . 3! 1.2.2! Clinical! features! of! adult! ADHD . 7! 1.2.2.1! Differences! between! the! Inattentive! and! Combined! subtypes! of! ADHD.8! 1.2.2. 2! Changes! introduced! in! the! DSM0V! and! implications . 10! 1.2. 3! Neurobiology! of! ADHD . 12! 1.2. 3.1! Brain! structure . 13! 1.2. 3.2! Brain! function . 15! 1.2. 3.3! Signaling . 16! 1.2. 3.3.1! Regulation! of! DA! and! NE! signaling. 17! 1.2. 3.3.2! Pharmacodynamics! of! ADHD! medications . 18! 1.2. 3.3.3! ADHD:! excess! or! deficit! of! catecholamines? 19! 1.2. 4! Etiological! factors . 22! 1.2. 4.1! Genes. 22! 1.2. 4.2! Environmental! factors. 25! 1.2. 4.3! Gene0environment! interactions . 26! 1.2. 5! Co0morbidities! of! ADHD . 27! 1.3! Sleep . 28!
Serial Addition: Locally Connected Architectures

This paper will briefly review nanoelectronic challenges while focusing on reliability. We shall present and analyze a series of CMOS-based examples for addition starting from the device level and moving up to the gate, the circuit, and the block level. Our analysis, backed by simulation results, on comparing parallel and serial addition shows that serial adders are more reliable while also dissipating less. Their reliability can be improved by using reliability-enhanced gates and/or other redundancy techniques (like e.g., multiplexing). Additionally, the architectural technique of short-circuiting the outputs (of several redundant devices/gates/blocks) exhibits "vanishing" voting and an inherent fault detection mechanism, as both transient and permanent faults could be detected based on current changes. The choice of CMOS is due to the broad design base available (but the ideas can be applied to other technologies), while addition was chosen due to its very solid background (both theoretical and practical). The design approach will constantly be geared towards enhancing reliability as much as possible at all the levels. Theory and simulations will support the claim that a serial adder is a very serious candidate for highly reliable and low power operations. Finally, our simulations will identify the VDD range where the power-delay-product and energy-delay-product are minimized. All of these suggest that a reliable (redundant) solution can also be a low power one if using serial architectures, while speed could still be traded for power (e.g., by dynamically varying the supply voltage both above and below Vth).
MATLAB/Simulink Based Transmission Line Automation Using Multiagent System

This study presents MATLAB/Simulink model of multiagent system for the automation of transmission utility to suppress the outage of grids. The traditional fault diagnosis methods like SCADA systems, digital fault recorders, travelling wave fault locators and other monitoring devices are haggard upon to inform the engineers of incidents, problems and fault. In the recent complex power system network scenario there is a delay in the action to be taken due to the lack of data available in the centralized system. The proposed system is implemented in MATLAB/Simulink software platform. The simulation results indicates that the use of multiagent system provides intelligence and has self healing characteristics for the transmission utility.
Oral rehydration for viral gastroenteritis in adults: a randomized, controlled trial of 3 solutions.

BACKGROUND Pedialyte and Gatorade are advocated for the treatment of dehydration in viral gastroenteritis, but there is limited evidence to support their use. We examine the efficacy, safety, and palatability of Pedialyte, Gatorade, and a New Oral Rehydration Solution (N-ORS). This was a randomized double-blind trial conducted in an inpatient, community hospital. Seventy-five consecutive adult patients (male, 42; female, 33) admitted with viral gastroenteritis were randomized to receive Gatorade, Pedialyte, or N-ORS for 48 hours. A yogurt/rice diet was allowed ad libitum. Stool and urine output, electrolytes, fluid intake, body weight, hematocrit, and palatability of solutions were measured. RESULTS Sixty completed the study. Stool frequency, consistency, and body weight improved (p < .001) in all 3 groups, but there was no difference between groups. Likewise, urine output, hematocrit, and correlations between fluid ingested, stool weight, or urine output were similar. At admission and 24 and 48 hours later, hypokalemia was observed in 7, 10, and 8 patients with Gatorade; 3, 2, and 1 with N-ORS; and 2, 2, and 1 with Pedialyte, respectively. Similarly, hyponatremia was observed in 6, 9, and 3 patients with Gatorade; 5, 3, and 4 with N-ORS; and 4, 5, and 4 with Pedialyte. Tastewise, Gatorade and N-ORS were rated higher (p < .05) than Pedialyte. Limitations were a smaller sample size and higher dropout (20%). CONCLUSIONS Gatorade and N-ORS seem to be as effective as Pedialyte in correcting dehydration and in improving bowel symptoms. All 3 solutions were safe. Unlike other groups, hypokalemia persisted in the Gatorade group. Gatorade and N-ORS may be effective in the treatment of dehydration associated with mild viral gastroenteritis.
HMM-based approach for automatic chord detection using refined acoustic features

We discuss an HMM-based method for detecting the chord sequence from musical acoustic signals using percussion-suppressed, Fourier-transformed chroma and delta-chroma features. To reduce the interference often caused by percussive sounds in popular music, we use Harmonic/Percussive Sound Separation (HPSS) technique to suppress percussive sounds and to emphasize harmonic sound components. We also use the Fourier transform of chroma to approximately diagonalize the covariance matrix of feature parameters so as to reduce the number of model parameters without degrading performance. It is shown that HMM with the new features yields higher recognition rates (the best in MIREX 2008 audio chord detection task) than that with conventional features.
Enacting Musical Experience

I argue for an enactive account of musical experience — that is, the experience of listening 'deeply'(i.e., sensitively and under- standingly) to a piece of music. The guiding question is: what do we do when we listen 'deeply'to music? I argue that these music listening episodes are, in fact, doings. They are instances of active perceiving, robust sensorimotor engagements with and manipulations of sonic structures within musical pieces. Music is thus experiential art, and in Nietzsche's words, 'we listen to music with our muscles'. This paper attempts to explicate and defend this claim. First, I discuss enactive approaches to consciousness and cognition generally. Next, I apply an enactive model of perceptual consciousness to the experience of listening to music. To clarify what is at stake, I use Peter Kivy's 'en- hanced formalism' as a philosophical foil. I then look at how the ani- mate body shapes musical experience.
Mechanism of Heavy Metal Ion Activation of Phytochelatin (PC) Synthase

The dependence of phytochelatin synthase (γ-glutamylcysteine dipeptidyltranspeptidase (PCS), EC 2.3. 2.15) on heavy metals for activity has invariably been interpreted in terms of direct metal binding to the enzyme. Here we show, through analyses of immunopurified, recombinant PCS1 from Arabidopsis thaliana(AtPCS1), that free metal ions are not essential for catalysis. Although AtPCS1 appears to be primarily activated posttranslationally in the intact plant and purified AtPCS1 is able to bind heavy metals directly, metal binding per se is not responsible for catalytic activation. As exemplified by Cd2+- and Zn2+-dependent AtPCS1-mediated catalysis, the kinetics of PC synthesis approximate a substituted enzyme mechanism in which micromolar heavy metal glutathione thiolate (e.g.Cd·GS2 or Zn·GS2) and free glutathione act as γ-Glu-Cys acceptor and donor. Further, as demonstrated by the facility of AtPCS1 for the net synthesis of S-alkyl-PCs from S-alkylglutathiones with biphasic kinetics, consistent with the sufficiency of S-alkylglutathiones as both γ-Glu-Cys donors and acceptors in media devoid of metals, even heavy metal thiolates are dispensable. It is concluded that the dependence of AtPCS1 on the provision of heavy metal ions for activity in media containing glutathione and other thiol peptides is a reflection of this enzyme's requirement for glutathione-like peptides containing blocked thiol groups for activity.
Evolutionary model of the concepts of 'color chip' and 'color category' in Evolutionary models of color categorization based on discrimination

Komarova et al.(2007) showed that a color naming system could be evolved by combining perceptual discrimination, basic pragmatic constraints on communication, and simple learning rules. Their system relied on a flxed number of color chips and of color categories. Here, I construct an evolutionary game theory model where the equivalent concept of the former and the number of the latter are emergent properties of the learning algorithm. The solution involves not a static but a continuously evolving \perceptual space," where the continuous change is arguably a more realistic evolutionary model and echo psychological models in that it is based on a form of memory, possessing a dynamic learning feature. It is shown that such dynamic structure does lead to a stable structure of both color concepts and categories. Simulation results are aimed at replicating the major result of Komarova et al.(2007) both for individual learning and in a population of learners. The concept of icon chips is introduced whose number and stability in an icon structure are an emergent property of multiple exposures to stimuli (colors) drawn from a continuous color space. The icon chip represents a form of a memory that changes in response to novel stimuli (color) and to the distribution of those stimuli. The results replicate those of Komarova et al.(2007) using constructs they only assumed could be evolved and demonstrate that a stable macro-structures can be maintained with continuously evolving microstructures, arguably a realistic feature evolutionary learning models.