Miracle-dz/UniFAR-FTUs huggingface dataset:
Structure of a low-population binding intermediate in protein-RNA recognition

Significance All biochemical reactions in living organisms require molecular recognition events. In particular, the interactions between protein and RNA molecules are crucial in the regulation of gene expression. However, the transient nature of the conformations populated during the recognition process has prevented a detailed characterization of the mechanisms by which these interactions take place. To address this problem, we report a high-resolution structure of an intermediate state in protein-RNA recognition. We determined this structure by using NMR measurements as ensemble-averaged structural restraints in metadynamics simulations, and validated it by performing a structure-based design of two mutants with rationally modified binding rates. The interaction of the HIV-1 protein transactivator of transcription (Tat) and its cognate transactivation response element (TAR) RNA transactivates viral transcription and represents a paradigm for the widespread occurrence of conformational rearrangements in protein-RNA recognition. Although the structures of free and bound forms of TAR are well characterized, the conformations of the intermediates in the binding process are still unknown. By determining the free energy landscape of the complex using NMR residual dipolar couplings in replica-averaged metadynamics simulations, we observe two low-population intermediates. We then rationally design two mutants, one in the protein and another in the RNA, that weaken specific nonnative interactions that stabilize one of the intermediates. By using surface plasmon resonance, we show that these mutations lower the release rate of Tat, as predicted. These results identify the structure of an intermediate for RNA-protein binding and illustrate a general strategy to achieve this goal with high resolution.
A 1.2-GHz comparator with adaptable offset in 0.35-μm CMOS

We apply the technique of floating-gate differential injection to a 1.2-GHz CMOS comparator to achieve arbitrary, accurate, and adaptable offsets. The comparator uses nonvolatile charge storage on floating-gate nodes for either offset nulling or automatic programming of a desired offset. We utilize impact-ionized pFET hot-electron injection to achieve fully automatic offset programming. The design has been fabricated in a commercially available 4-metal, 2-poly 0.35-mum CMOS process. Experimental results confirm the ability to reduce the variance of comparator offset by 3600times and to accurately program a desired offset with maximum observed residual offset of 469 muV and standard deviation of 199 mu V. We achieve controlled injection to accurately program the input offset to voltages uniformly distributed from -1 to 1 V. The comparator operates at 1.2 GHz with a power consumption of 3.3 mW.
Adaptive multi-task learning for fine-grained categorization

Multi-task learning has been proposed to improve the generalization performance by learning multiple tasks jointly. One challenge for this learning paradigm is to effectively seek the shared information across multiple tasks. In this paper, we propose a novel multi-task learning method to adaptively share information. Unlike many existing multi-task learning methods which impose strong assumptions on task related-ness, our method captures the relationships among tasks and identifies the disparities of each task simultaneously, thus can flexibly exploit the shared information. Moreover, we apply it to fine-grained categorization problem, which usually suffers from the difficulties of insufficient training data and high inter-class similarity. The experimental results on two widely used datasets show the superiority of our method compared with some state-of-the-art methods.
Generating a Context-Aware Sentiment Lexicon for Aspect-Based Product Review Mining

A great share of current sentiment analysis techniques is based on special purpose lexicons providing information about the semantic orientation (e.g. positive, negative, neutral) of its entries. Due to the high labor costs of manually assembling such resources, recent work has focused on automatically inducing the polarity of given terms. We follow this line of work while focusing on the domain of user-generated product reviews, a main field of application for sentiment analysis. In this domain, a major observation is that the semantic orientation of terms is often context-dependent which poses an additional challenge to the automatic construction of such lexicons (e.g. positive: “longbattery life” vs. negative: “long shutter lag time”). We propose a novel unsupervised method to induce a context-aware sentiment lexicon by utilizing the semi-structuredness of user-generated product reviews.
A MAC Protocol for Opportunistic Spectrum Access in Cognitive Radio Networks

We present a MAC protocol for opportunistic spectrum access (OSA-MAC) in cognitive wireless networks. The proposed MAC protocol works in a multi-channel environment which is capable of performing channel sensing to discover spectrum opportunities. For this MAC protocol, two channel selection methods are considered which trade the implementation complexity with throughput improvement. We then analyze the saturation throughput performance of the proposed MAC protocol under scenarios where the probabilities for each channel to be available to different secondary flows are the same or different. We then derive analytically the probability of collision of secondary users with primary users due to sensing errors. This analysis can be used, for example, to determine the requirement of sensing accuracy for secondary users, and to design an admission control method. We present numerical results to demonstrate the throughput performance of the OSA-MAC protocol and applications of the proposed analytical model.
Survivable and impairment-aware virtual topologies for reconfigurable optical networks: A cognitive approach

In this paper, we present a new version of a multiobjective genetic algorithm to design virtual topologies with the aim of reducing both the energy consumption and the network congestion. Moreover, we also propose an improved version of that algorithm, by including two cognitive techniques. Unlike the original version, the new proposals design survivable virtual topologies, as they provide shared path protection thus offering fault-tolerance capability with efficient resource utilization. Moreover, the proposed methods also take into account physical impairments in order to ensure that the survivable virtual topologies fulfill Quality of Transmission requirements in any scenario without failures or with a single cable failure. Finally, a simulation study demonstrates the advantages of the use of cognition.
ICONA: A Peer-to-Peer Approach for Software Defined Wide Area Networks Using ONOS

Several Internet Service Providers (ISP) are planning to innovate their infrastructures through a process of network softwarisation and programmability. The Software-Defined-Network (SDN) paradigm aims at improving the design, configuration, maintenance and service provisioning agility of the network through a centralised software control plane which is in charge of managing the entire system. This is easily achievable for local area networks, typical of data centres, where the benefits of having programmable access to the entire network is not restricted by latency. However, in Wide Area Networks, a centralised control plane limits the speed of responsiveness in reaction to time-constrained network events due to unavoidable latencies caused by physical distances. A logical step towards robustness in SDN is to distribute the load of the control plane between entities, each taking care of a portion of the entire geographical network and each providing an east-west communication interface to enable programmability of the entire network. Moreover, a key objective of an SDN control plane targeting an ISP networks is the east-west interface with external domains under the control of other providers. In this article we present ICONA (Inter Cluster Onos Network Application), a tool that has the objective of enabling programmable networks to span multiple clusters of controllers within either a single or multiple administrative domains. In particular, the paper describes the architecture behind ICONA and provides an initial evaluation obtained on a preliminary version of the tool, built on top of the cutting-edge network controller ONOS, Hummingbird release.
Exploring multimodal video representation for action recognition

A video contains rich perceptual information, such as visual appearance, motion and audio, which can be used for understanding the activities in videos. Recent works have shown the combination of appearance (spatial) and motion (temporal) clues can significantly improve human action recognition performance in videos. To further explore the multimodal representation of video in action recognition, We propose a framework to learn a multimodal representations from video appearance, motion as well as audio data. Convolutional Neural Networks (CNN) are trained for each modality respectively. For fusing multiple features extracted with CNNs, we propose to add a fusion layer on the top of CNNs to learn a joint video representation. In fusion phase, we investigate both early fusion and late fusion with Neural Network and Support Vector Machine. Compare to existing works, (1) our work measures the benefits of taking audio information into consideration and (2) implements sophisticated fusion methods. The effectiveness of proposed approach is evaluated on UCF101 and UCF101-50 (selected subset in which each video contains audio data) for action recognition. The experimental results show that different modalities are complementary to each other and multimodal representation can be beneficial for final prediction. Furthermore, proposed fusion approach achieves 85.1% accuracy in fusing spatial-temporal on UCF101 (split 1), which is very competitive to state-of-the-art works.
A fresh look at d-dimer in suspected pulmonary embolism

Newer imaging approaches in suspected pulmonary embolism (PE) such as the PISA-PED perfusion lung scanning criteria,1spiral computed tomography,2 and leg vein ultrasound3 are attracting widespread interest. Attempts are being made to clarify and rationalise clinical diagnosis,4 and the use of low molecular weight heparin in PE5 is increasing. However, it is often forgotten that clinical suspicion of PE turns out to be incorrect in five out of every six patients properly investigated.6 7 Since in most district general hospitals imaging tests for suspected PE cannot usually be arranged immediately, such patients have to be admitted and heparin started while awaiting an isotope lung scan which often fails to give an unequivocal answer. All this is costly in time and resources and engenders considerable anxiety in the patient. A simple cheap and accurate test to exclude PE that is also available out of hours would be of great interest to general physicians. Hopes for plasma d-dimer seemed not to have been …
Special Section—Behavioral symptoms of dementia: their measurement and intervention. Keeping wandering nursing home residents at the table: improving food intake using a behavioral communication intervention

The purpose of this multiple case design study (n = 3) with an embedded experiment was to determine the effect of the systematic use of a behavioral nursing intervention on the mealtime behavior of nursing home residents with probable Alzheimer's disease. It was hypothesized that the systematic behavioral intervention would increase time spent seated during the meal and proportion of food consumed while decreasing the frequency of table-leaving events during mealtime. The intervention was designed to impact the proximal factors of physiological need and social interaction from the Need-Driven Behavior Model. Results demonstrate that all cases were able to sit at the table longer and eat more food during the intervention, while body weight for all cases remained stable throughout the study. Two of the three cases left the table fewer times during the intervention. There were no statistically significant changes in proportion of fluids consumed in any case.
Combination of stereo SAR and InSAR for DEM generation using TanDEM-X spotlight data

ABSTRACT The objective of this work is to generate accurate digital elevation models (DEMs) from synthetic aperture radar (SAR) interferograms using the spotlight and staring spotlight modes during the TanDEM-X (TDX) science phase. We use stereo SAR with TDX or TerraSAR-X (TSX) to estimate absolute heights of natural or man-made reflectors for input to the unwrapped interferograms. The accuracy of the absolute heights in the DEMs was a few decimetres in flat regions and a few metres in the hilly and rugged terrain.
The driving forces in the virtual society

traffic jam? The definition of “virtual” was extended by Grenier and Metes [2] to include significant enhanced effects or actions, physical behavior of non-physical entities, and the supporting use of telecommunications and computing technologies. A culture once based exclusively on physical contact is in the process of being transformed to a culture where goods and services are accessible without the need for face-to-face contact with other people. Technology enables this transformation toward a virtual society and is the glue that makes virtual societies plausible. However, technology alone does not guarantee the viability of the virtual society; the technical power must be used intelligently and deliberately by an informed population. The virtual society is a compilation of leadingedge computer, communications, and information technologies and the impact of these technologies on individuals, groups, organizations, and societies. As the number of implementations of the newly formed virtual societies increases, societies face new challenges to cope with their social structure. Limited research has been conducted to study issues related to the virtual society phenomenon. Although there has been a fair amount of research on the virtual workplace or telecommuting, this research is usually focused on the individual. It does not consider global issues and models for virtual organizations, communities, and nations. Existing research also espouses the positive aspects of interactive communication in a business environment. It ignores the negative elements, is descriptive, and does not consider consumers, politics, and the culture as a whole. An intellectual comprehension of the entire domain of the virtual society—individual, group, organization, community, and world—is an imperative for studying this impending societal form. The purpose of this article is to review existing articles in academic and business journals within the fields of information science, social science, economics, and management for the purpose of derivThe term virtual society refers to all components that are part of a society’s culture based on
Risk-aware organizational design

Operational risk is an important, complex, and difficult, criterion to consider during any form of organizational decision making. In practice (1) complexity typically arises from: the use of a variety of risk related indicators; the use of multiple heterogeneous measurement scales; measurement uncertainty; varying levels of measurement precision; and, the widespread effect of each measurement; (2) difficulties arise due to the: time bound nature of the decision making process; and, the availability and interpretation of risk-related measurements. To help address these issues, we propose a conceptual framework to support and minimize the level of analyst involvement during the management of operational risk specified in organizational models. This is achieved by propagating/analyzing risk-related evaluations across descriptions of distributed, inter-dependant and mission critical work activities.
Super MBox: an efficient/effective content-based music retrieval system

This demo presents an implementation of a content-based music retrieval system that can take a user's acoustic input (8-second clip of singing or humming) via a microphone and then retrieve the intended song from a database containing 13,000 candidate songs. The system, known as Super MBox, demonstrates the feasibility of real-time music retrieval with a high recognition rate, which can be used for music search engines over the Internet and/or query engines in digital music libraries or karaoke machines.
Reuse and optimization of testbenches and properties in a TLM-to-RTL design flow

In transaction-level modeling (TLM), verification methodologies based on transactions allow testbenches, properties, and IP cores in mixed TL-RTL designs to be reused. However, no papers in the literature analyze the effectiveness of transaction-based verification (TBV) in comparison to the more traditional RTL approach. The first contribution of this article is the introduction of a functional-fault-model-based methodology for demonstrating the effectiveness of reuse through TBV. A second contribution is the introduction of a similar methodology for efficient property checking which identifies and removes redundant properties prior to assertion-based verification or model checking.
HOLSR: a hierarchical proactive routing mechanism for mobile ad hoc networks

This article reviews the hierarchical optimized link state routing (HOLSR) mechanism for heterogeneous mobile ad hoc networks. In this work a heterogeneous mobile ad hoc network is defined as a network of mobile nodes that are characterized by different communications capabilities, such as multiple radio interfaces. The article focuses on proposing the HOLSR protocol. The HOLSR mechanism is derived from the OLSR protocol; however, unlike OLSR, the HOLSR protocol takes advantage of different mobile node capabilities to reduce the routing control overhead in large heterogeneous ad hoc networks, thus improving the performance of the routing mechanism.
Functional Near-Infrared Spectroscopy (fNIRS): Principles and Neuroscientific Applications

fNIRS is a device designed to detect changes in the concentration of oxygenated (oxyHb) and deoxygenated (deoxyHb) haemoglobin molecules in the blood, a method commonly used to assess cerebral activity. Over the last decade, functional near-infrared spectroscopy (fNIRS) has widely extended its applications due to its capacity to quantify oxygenation in blood and organic tissue in a continuous and non invasive manner (Chance & Leigh, 1977; Villringer & Chance, 1997). This technique is an effective, albeit ‘indirect’, optical neuroimaging method that monitors hemodynamic response to brain activation, on the basis that neural activation and vascular response are tightly coupled, so termed ‘neurovascular coupling’. Different studies show that neural activity and hemodynamic response maintain a lineal relationship (Arthurs & Boniface, 2003; Logothetis et al., 2001), suggesting that these changes in hemodynamic response could provide a good marker for assessing neural activity. In neuroscience, functional near-infrared spectroscopy (fNIRS) is used to measure cerebral functions through different chromophore mobilization (oxygenated haemoglobin, deoxygenated haemoglobin and cytochrome c-oxidase) and their timing with concrete events. Due to methodological and theoretical problems associated with cytochrome c-oxidase functioning (Cyt-Ox) (see section 3.2.), current neuroscience studies on cerebral functions only assesses and analyzes oxyHb and deoxyHb mobilizations. These chromophore mobilizations are directly related to the cerebral blood flow (CBF) associated with an event and the physiological reactions provoked by the brain’s functional state (fNIRS measures these reaction in the cerebral cortex). The assessment of these taskrelated mobilizations performed in light of a base line established by the researcher him/herself. The difference in oxyHb and deoxyHb concentrations at baseline and at task performance determines the location in the cortex of an increase or decrease in CBF. An increase in CBF is associated with cerebral activity, making the temporal and spatial correlation between CBF and task a determinant of cerebral function. This capacity to study cerebral functions, both spatial and temporal, is what gives name to the technique described in this chapter: functional near-infrared spectroscopy (fNIRS). fNIRS has become a valuable neuroimaging technique, novel in its easy application and characterized by its small size, portability, and reliability. Although relatively new to the
REARING TEMPERATURE AFFECTS THE EXPRESSION OF PROTEINS IN THE ADHESIVE OF THE STRIPED ACORN BARNACLE, BALANUS AMPHITRITE

ALL RIGHTS RESERVED iii COMMITTEE MEMBERSHIP TITLE: Rearing temperature affects the expression of proteins in the adhesive of the striped acorn barnacle, Balanus amphitrite iv ABSTRACT Rearing temperature affects the expression of proteins in the adhesive of the striped acorn barnacle, Balanus amphitrite Barnacles are dominant hard–fouling organisms in marine waters. They attach to substrates by secreting a complex proteinaceous adhesive. Understanding the chemical composition of this multi–protein underwater adhesive and how it is affected by environmental variables, such as oceanic temperatures, is critical for developing nontoxic solutions to control biofouling. Previous experiments in our lab revealed an inverse relationship between critical removal stress (CRS) and temperatures at which barnacles were reared. Further investigations showed that this correlation is not attributed to differences in physical properties such as barnacle size or short–term changes in the viscosity of adhesive. Therefore, the observed effects may be influenced by a physiological response to temperature during initial growth and development. We hypothesized that rearing temperature affects the expression of proteins found in the adhesive matrix. To elucidate the underlying mechanisms responsible for the temperature effect, we analyzed uncured barnacle adhesive using two-dimensional gel electrophoresis (2DGE) and matrix-assisted laser desorption/ionization-tandem time-of-flight (MALDI-TOF/TOF) mass spectrometry (MS). In our analysis, we 1) detected differences in protein expression at two experimental temperatures (15°C and 25°C) and 2) identified several proteins that may serve functional roles in the process of adhesion. Our data are also consistent with a model that the curing process of barnacle adhesive may be analogous to the process of wound healing in animals. v ACKNOWLEDGMENTS First and foremost, thank you to my committee for all of their support, patience and sincere guidance over the years, both inside and outside of the academic setting. Thank you for believing in me and helping me see this through to the end. Thank you to the many, many, faculty and staff members of the Biological Sciences Department, past and present. In no particular order and certainly not limited to: Chris Kitts, and special thanks to Ellen Calcagno and Melanie Gutierrez, you have all become family to me. Thank you to all of the graduate students, peers, and colleagues, who spanned the many years of my journey through this program. My sincerest gratitude goes to all of those who helped to encourage and support me, push and motivate me, and for those who were there to celebrate the seemingly small …
Pricing of barrier options by marginal functional quantization

This paper is devoted to the pricing of Barrier options by optimal quadratic quantization method. From a known useful representation of the premium of barrier options one deduces an algorithm similar to one used to estimate nonlinear filter using quadratic optimal functional quantization. Some numerical tests are fulfilled in the Black-Scholes model and in a local volatility model and a comparison to the so called Brownian Bridge method is also done.