Miracle-dz/UniFAR-FTUs huggingface dataset:
Generalized macro level models of amino acid sequences using passive electrical circuits

In this paper, we discuss four types of electrical network circuits have been used for modeling amino acid sequences at the gross molecular level. The standard 20 amino acids have been partitioned into mutually exclusive parti- tions based on their chemical and structural properties and each partition is as- signed a distinct electrical circuit. This enables the construction of electrical networks for representing any amino acid sequence. These networks have been analyzed to establish putative relationships between a network's electrical re- sponse and known behavior of protein sequences. To aid in the analysis of cir- cuit response, we have also developed a unique visualization technique. Similar circuits have been used to model DNA/RNA sequences as well as non- biological strings which have applications in message encryption and computer security.
Structure of an Hsp 90-Cdc 37-Cdk 4 complex

This document is made available in accordance with publisher policies and may differ from the published version or from the version of record. If you wish to cite this item you are advised to consult the publisher's version. Please see the URL above for details on accessing the published version. Copyright and all moral rights to the version of the paper presented here belong to the individual author(s) and/or other copyright owners. To the extent reasonable and practicable, the material made available in SRO has been checked for eligibility before being made available. Copies of full text items generally can be reproduced, displayed or performed and given to third parties in any format or medium for personal research or study, educational, or not-for-profit purposes without prior permission or charge, provided that the authors, title and full bibliographic details are credited, a hyperlink and/or URL is given for the original metadata page and the content is not changed in any way. Summary Activation of many protein kinases depends on their interaction with the Hsp90 molecular chaperone system. Recruitment of protein kinase clients to the Hsp90 chaperone system is mediated by the cochaperone adaptor protein Cdc37, which acts as a scaffold, simultaneously binding protein kinases and Hsp90. We have now expressed and purified an Hsp90-Cdc37-Cdk4 complex, defined its stoichiometry, and determined its 3D structure by single-particle electron microscopy. Comparison with the crystal structure of Hsp90 allows us to identify the locations of Cdc37 and Cdk4 in the complex and suggests a mechanism by which confor-mational changes in the kinase are coupled to the Hsp90 ATPase cycle.
Summarizing gene-expression-based classifiers by meta-mining comprehensible relational patterns

We propose a methodology for predictive classification from gene expression data, able to combine the robustness of high-dimensional statistical classification methods with the comprehensibility and interpretability of simple logic-based models. We first construct a robust classifier combining contributions of a large number of gene expression values, and then (meta)-mine the classifier for compact summarizations of subgroups among genes associated with a given class therein. The subgroups are described by means of relational logic features extracted from publicly available gene ontology information. The curse of dimensionality pertaining to the gene expression based classification problem due to the large number of attributes (genes) is turned into an advantage in the secondary, meta-mining task as here the original attributes become learning examples. We cross-validate the proposed method on two classification problems: (i) acute lymphoblastic leukemia (ALL) vs. acute myeloid leukemia (AML), (ii) seven subclasses of ALL.
Low-Loss Frequency-Agile Bandpass Filters With Controllable Bandwidth and Suppressed Second Harmonic

This paper presents a novel approach to design frequency-agile bandpass filters with constant absolute bandwidth and passband shape, as well as a suppressed second harmonic. A novel mixed electric and magnetic coupling scheme is proposed to control the coupling coefficient variation. Theoretical analysis indicates that it is able to achieve desired coupling coefficients between the proposed resonators at various frequencies so as to obtain constant absolute bandwidth. Moreover, this half-wavelength resonator has a Q higher than the quarter- and half-wavelength counterparts, thus resulting in low insertion loss. A filter of this type is designed to validate the proposed idea. To remove the spurious responses of the filter, a method is then introduced to suppress the second harmonic without degrading the passband performance. For demonstration, two frequency-agile filters with 60- and 80-MHz constant absolute bandwidth are implemented with the frequency tuning range from 680 to 1000 MHz. Comparisons of experimental and simulated results are presented to verify the theoretical predications.
The third-level agenda-setting study: an examination of media, implicit, and explicit public agendas in China

ABSTRACT Through two separate studies in the context of Hong Kong, a Chinese society, this research tests the third-level agenda-setting effects and examines the differences between the explicit and implicit public agendas based on the attributes consciously and unconsciously reported by the public. A total of 1667 news reports and 680 responses to a public survey are collected for analysis. Evidence from both studies shows strong attribute agenda-setting effects at the third level, no matter the focus of the issue is obtrusive or unobtrusive. Results also demonstrate that the media agenda is positively associated at a higher level with the implicit public agenda than the explicit one. Findings well extend the network agenda-setting research.
Learning Control for Air Hockey Striking Using Deep Reinforcement Learning

We consider the task of learning control policies for a robotic mechanism striking a puck in an air hockey game. The control signal is a direct command to the robot's motors. We employ a model free deep reinforcement learning framework to learn the motoric skills of striking the puck accurately in order to score. We propose certain improvements to the standard learning scheme which make the deep Q-learning algorithm feasible when it might otherwise fail. Our improvements include integrating prior knowledge into the learning scheme, and accounting for the changing distribution of samples in the experience replay buffer. Finally we present our simulation results for aimed striking which demonstrate the successful learning of this task, and the improvement in algorithm stability due to the proposed modifications.
An explanatory and “argumentative” interface for a model-based diagnostic system

That intelligent systems need an explanatory capability if they are to aid or support human users has long been understood. A system which can justify its decisions generally obtains improved user trust, greater accuracy in use and offers embedded training potential. Extensive work has been done to provide rule-based systems with explanatory interfaces, but little has been done to provide the same benefits for model-based systems. We develop an approach to organizing the presentation of large amounts of model-based data in an interactive format patterned after a model of human-human explanatory and argumentative discourse. Portions of this interface were implemented for Honeywell's model-based Flight Control Maintenance and Diagnostic System (FCMDS). We conclude that sufficient information exists in a model-based system to provide a wide range of explanation types, and that, the discourse approach is a convenient, powerful and broadly applicable method of organizing and controlling information exchange involving this data.
A new buffer management scheme for multimedia terminals in broadband satellite networks

We propose a novel head of line priority cell discard (HoL-PCD) buffer management mechanism at the Earth terminal buffers of broadband satellite networks. It preserves QoS for compliant traffic at the expense of non compliant traffic, and improves the overall delay performance of the network. Our simulation model includes a GEO satellite with onboard bandwidth scheduler, with multimedia earth terminals accessing the satellite by means of multiple frequency time division multiple access (MFTDMA) with combined free/demand assignment (CFDAMA). Results verify the effectiveness of the HoL-PCD scheme in increasing the amount of compliant traffic accommodated by the network while maintaining the QoS guarantees required by the users.
Prediction and measurement of delay spread, fading statistics, and receiving quality in indoor wireless networks

| A new model for the prediction of the field strength, the delay spread and the fast fading for mobile communication networks inside buildings is presented in this paper. In the first part of the paper, the equipment for the measurements is described. Some measurement results are shown to illustrate the performance of the measurement equipment. Based on the measurements a new parameter for the description of the bit error rate (BER) and the quality of service (QoS) is introduced. The model for the prediction of the field strength, the delay spread and the fast fading is based on the new dominant path model, presented in [14]. This new model leads to very accurate results, even in buildings not used for the calibration of the model.
Automatic classification of speech and music using neural networks

The importance of automatic discrimination between speech signals and music signals has evolved as a research topic over recent years. The need to classify audio into categories such as speech or music is an important aspect of many multimedia document retrieval systems. Several approaches have been previously used to discriminate between speech and music data. In this paper, we propose the use of the mean and variance of the discrete wavelet transform in addition to other features that have been used previously for audio classification. We have used Multi-Layer Perceptron (MLP) Neural Networks as a classifier. Our initial tests have shown encouraging results that indicate the viability of our approach.
Building Japanese-English Dictionary based on Ontology for Machine Translation

This paper describes a semi-automatic method for associating a Japanese lexicon with a semantic concept taxonomy called an ontology, using a Japanese-English bilingual dictionary as a "bridge". The ontology supports semantic processing in a knowledge-based machine translation system by providing a set of language-neutral symbols and semantic information. To put the ontology to practical use, lexical items of each language of interest must be linked to appropriate ontology items. The association of ontology items with lexical items of various languages is a process fraught with difficulty: since much of this work depends on the subjective decisions of human workers, large MT dictionaries tend to be subject to some dispersion and inconsistency. The problem we focus on here is how to associate concepts in the ontology with Japanese lexical entities by automatic methods, since it is too difficult to define adequately many concepts manually. We have designed three algorithms to associate a Japanese lexicon with the concepts of the ontology automatically: the equivalent-word match, the argument match, and the example match. We simulated these algorithms for 980 nouns, 860 verbs and 520 adjectives as preliminary experiments. The algorithms are found to be effective for more than 80% of the words.
Assessing the relevance of node features for network structure

Networks describe a variety of interacting complex systems in social science, biology, and information technology. Usually the nodes of real networks are identified not only by their connections but also by some other characteristics. Examples of characteristics of nodes can be age, gender, or nationality of a person in a social network, the abundance of proteins in the cell taking part in protein-interaction networks, or the geographical position of airports that are connected by directed flights. Integrating the information on the connections of each node with the information about its characteristics is crucial to discriminating between the essential and negligible characteristics of nodes for the structure of the network. In this paper we propose a general indicator Θ, based on entropy measures, to quantify the dependence of a network's structure on a given set of features. We apply this method to social networks of friendships in U.S. schools, to the protein-interaction network of Saccharomyces cerevisiae and to the U.S. airport network, showing that the proposed measure provides information that complements other known measures.
On the selection of tags for tag clouds

We examine the creation of a tag cloud for exploring and understanding a set of objects (e.g., web pages, documents). In the first part of our work, we present a formal system model for reasoning about tag clouds. We then present metrics that capture the structural properties of a tag cloud, and we briefly present a set of tag selection algorithms that are used in current sites (e.g., del.icio.us, Flickr, Technorati) or that have been described in recent work. In order to evaluate the results of these algorithms, we devise a novel synthetic user model. This user model is specifically tailored for tag cloud evaluation and assumes an "ideal" user. We evaluate the algorithms under this user model, as well as the model itself, using two datasets: CourseRank (a Stanford social tool containing information about courses) and del.icio. us (a social bookmarking site). The results yield insights as to when and why certain selection schemes work best.
Author ' s personal copy Phonological knowledge guides 2-year-olds ’ and adults ’ interpretation of salient pitch contours in word learning

Phonology provides a system by which a limited number of types of phonetic variation can signal communicative intentions at multiple levels of linguistic analysis. Because phonologies vary from language to language, acquiring the phonology of a language demands learning to attribute phonetic variation appropriately. Here, we studied the case of pitch-contour variation. In English, pitch contour does not differentiate words, but serves other functions, like marking yes/no questions and conveying emotions. We show that, in accordance with their phonology, English-speaking adults and 2-year-olds do not interpret salient pitch contours as inherent to novel words. We taught participants a new word with consistent segmental and pitch characteristics, and then tested word recognition for trained and deviant pronunciations using an eyegaze-based procedure. Vowel-quality mispronunciations impaired recognition, but large changes in pitch contour did not. By age 2, children already apply their knowledge of English phonology to interpret phonetic consistencies in their experience with words. 2009 Elsevier Inc. All rights reserved.
Coulomb and Overlap Self-Similarities: A Comparative Selectivity Analysis of Structure-Function Relationships for Auxin-like Molecules

Auxins are defined mainly by a set of physiological actions, but the structure-effect relationship still is based on chemical intuition. Currently a well-defined auxin molecular structure is not available. The existence of different auxin binding proteins and mechanisms of auxin action, the wide diversity of the auxin molecules, and the pleiotropic effects of auxin imply a completely different mechanism as described for the animal hormone concept. Here, we present a computational approach dealing with semiempirical optimizations of the auxin molecules themselves, which represent a number of about 250 different chemical structures. Our approach uses molecular quantum similarity measures and additional quantum variables for the analysis of auxin-like molecules. The finding of similarities in molecules by focusing basically on their electron structure results in new insights in the relationship of the different auxin groups. Additional statistical analysis allows the identification of relationships between similarity groups and their biological activity, respectively. It is postulated that the auxin-like molecular recognition depends more on specific molecular assembling states than on a specific ring system or side chain.
Generalized Thresholding of Large Covariance Matrices

We propose a new class of generalized thresholding operators that combine thresholding with shrinkage, and study generalized thresholding of the sample covariance matrix in high dimensions. Generalized thresholding of the covariance matrix has good theoretical properties and carries almost no computational burden. We obtain an explicit convergence rate in the operator norm that shows the tradeoff between the sparsity of the true model, dimension, and the sample size, and shows that generalized thresholding is consistent over a large class of models as long as the dimension p and the sample size n satisfy log p/n → 0. In addition, we show that generalized thresholding has the “sparsistency” property, meaning it estimates true zeros as zeros with probability tending to 1, and, under an additional mild condition, is sign consistent for nonzero elements. We show that generalized thresholding covers, as special cases, hard and soft thresholding, smoothly clipped absolute deviation, and adaptive lasso, and compare different types of generalized thresholding in a simulation study and in an example of gene clustering from a microarray experiment with tumor tissues.
Two Novel Particle Swarm Optimization Algorithm Models

According to the intelligent behavior of social population, two novel particle swarm algorithm optimization models are proposed by enhancing collaboration and information sharing capabilities of individuals. Benchmark function simulation results show the new algorithms, with both a better stability and a steady convergence, not only enhance the local searching efficiency and global searching performance greatly, but also have faster convergence speed and higher precision, and can avoid the premature convergence problem effectively.
Becoming a decision-making supporter for someone with acquired cognitive disability following traumatic brain injury

Despite an increased awareness of society's obligation to ensure that people with cognitive disabilities have access to decision-making support, little is known about how this support should be provided. For people with traumatic brain injury, informal support mechanisms may provide the primary means of support but there is limited understanding of how this aids participation. As part of a larger project using constructivist grounded theory to explore processes used by adults with severe traumatic brain injury in making decisions after injury, the authors explored a single-case study, presented in this article. In particular, the study aimed to build an understanding of the evolution of decision-making support over time from multiple perspectives. Data consisted of seven in-depth, individual interviews with three participants: the central participant, Beau, and two participants whom he nominated as his decision-making supporters. Analysis of the data revealed several key themes relating to both the nature.
Localization of plastic deformation

The localization of plastic deformation into a shear band is discussed as an instability of plastic flow and a precursor to rupture. Experimental observations are reviewed, a general theoretical framework is presented, and specific calculations of critical conditions are carried out for a variety of material models. The interplay between features of inelastic constitutive description, especially deviations from normality and vertex-like yielding, and the onset of localization is emphasized.
The FIRST radio survey: Panchromatic properties of FIRST radio sources identified in the Boötes and Cetus fields

In this paper the availability of multi-wavelength optical/infrared information of FIRST (Faint Images of the Radio Sky at 20 cm) radio sources counterparts over ∼9.2 deg2 in the Bootes field and ∼2.4 deg2 in the Cetus field is exploited to infer the physical properties of the faint radio population. The radio sources optically identified have been divided into resolved galaxies and stellar-like objects finding that the faint radio population is mainly composed of early-type galaxies with very red colour (Bw – R ∼ 4.6). A total number of 57 counterparts of FIRST radio sources have extremely red colour (R – K ≥ 5). Photometric redshift from Hyperz implies that the Extremely Red Objects (EROs) counterparts to FIRST radio sources are mostly located in the range z = 0.7–2, with the bulk of the population at z ∼ 1. Taking advantage of the near infrared imaging with FLAMEX (FLAMINGOS Extragalactic Infrared Survey), the EROs counterparts to FIRST radio sources are separated into passively-evolving and dusty star-forming galaxies using their RJK colours; the relatively blue J – K of these galaxies suggest that most are old elliptical galaxies (18/25) rather than dusty starburst galaxies (7/25). A total of 15 Distant Red Galaxy (DRGs) have been identified as counterparts to FIRST radio sources in the Cetus field and 3 DRGs in the Bootes field with J – K > 2.3 (© 2009 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim)
Biodegradation of Silk Biomaterials

Silk fibroin from the silkworm, Bombyx mori, has excellent properties such as biocompatibility, biodegradation, non-toxicity, adsorption properties, etc. As a kind of ideal biomaterial, silk fibroin has been widely used since it was first utilized for sutures a long time ago. The degradation behavior of silk biomaterials is obviously important for medical applications. This article will focus on silk-based biomaterials and review the degradation behaviors of silk materials.
Relevance of Variations in the Opposing Dentition for the Functionality of Fixed and Removable Partial Dentures: A Systematic Review

The aim of this systematic review was to evaluate the functionality of fixed and removable partial dentures as test interventions in relation to variations in the opposing dentition and their prosthetic restoration. The abstracts identified in the respective databases were screened independently by two investigators. RCTs and uncontrolled studies were considered, provided the patients were included consecutively and the confounding variables were adequately monitored. Seventeen papers were included. The study and publication quality was assessed using a “biometric quality” tool showing an overall poor quality. The reported outcomes, such as survival rates, were in each case obtained from a single study. Two possible trends could be deduced for the endpoint longevity: (a) the first trend in favor of removable partial dentures, compared to fixed partial dentures, with a fully edentulous opposing arch fitted with a removable prosthesis; (b) the second trend in favor of implant-supported partial dentures, compared to conventionally fixed partial dentures, with natural opposing dentition or with a removable partial denture in the opposing arch. No evidence could be generated as to whether, and if so how, variations in the opposing dentition have a bearing on the decision to fit a partially edentulous arch with a fixed or removable partial denture.