Miracle-dz/UniFAR-FTUs huggingface dataset:
MODBASE: a database of annotated comparative protein structure models and associated resources

MODBASE () is a database of annotated comparative protein structure models for all available protein sequences that can be matched to at least one known protein structure. The models are calculated by MODPIPE, an automated modeling pipeline that relies on MODELLER for fold assignment, sequence–structure alignment, model building and model assessment (). MODBASE is updated regularly to reflect the growth in protein sequence and structure databases, and improvements in the software for calculating the models. MODBASE currently contains 3 094 524 reliable models for domains in 1 094 750 out of 1 817 889 unique protein sequences in the UniProt database (July 5, 2005); only models based on statistically significant alignments and models assessed to have the correct fold despite insignificant alignments are included. MODBASE also allows users to generate comparative models for proteins of interest with the automated modeling server MODWEB (). Our other resources integrated with MODBASE include comprehensive databases of multiple protein structure alignments (DBAli, ), structurally defined ligand binding sites and structurally defined binary domain interfaces (PIBASE, ) as well as predictions of ligand binding sites, interactions between yeast proteins, and functional consequences of human nsSNPs (LS-SNP, ).
Altered neurovascular coupling during information‐processing states

Brain imaging techniques rely on changes in blood flow, volume and oxygenation to infer the loci and magnitude of changes in activity. Although progress has been made in understanding the link between stimulus‐evoked neural activity and haemodynamics, the extent to which neurovascular‐coupling relationships remain constant during different states of baseline cortical activity is poorly understood. Optical imaging spectroscopy, laser Doppler flowmetry and electrophysiology were used to measure haemodynamics and neural activity in the barrel cortex of anaesthetized rats. The responses to stimulation of the whisker pad were recorded during quiescence and cortical desynchronization produced by stimulation of the brainstem. Cortical desynchronization was accompanied by increases in baseline blood flow, volume and oxygenation. Haemodynamic responses to low‐frequency whisker stimuli (1 Hz) were attenuated during arousal compared with that observed during quiescence. During arousal it was possible to increase stimulus‐evoked haemodynamics by increasing the frequency of the stimulus. Neural responses to low‐frequency stimuli were also attenuated but to a far lesser extent than the reduction in the accompanying haemodynamics. In contrast, neuronal activity evoked by high‐frequency stimuli (40 Hz) was enhanced during arousal, but induced haemodynamic responses of a similar magnitude compared with that observed for the same high‐frequency stimulus presented during quiescence. These data suggest that there may be differences in stimulus‐evoked neural activity and accompanying haemodynamics during different information‐processing states.
A system based on hierarchical fuzzy clustering for web users profiling

In this paper, we present a system based on an Unsupervised Fuzzy Divisive Hierarchical Clustering (UFDHC) algorithm to determine a hierarchy of profiles of web site typical users from the web access log. These profiles can be extremely useful, for instance, to customize the web site, or to send personalized advertisements. After eliminating categories that have not been accessed by a significant percentage of users and removing the occasional users, the access log data are input to the UFDHC algorithm which clusters the users of the web site into a hierarchy of groups characterized by a set of common interests and represented by a prototype, which defines the profile of the group typical member. To show the effectiveness of our system, we describe how the profiles determined by the UFDHC algorithm from access log data collected along a period of 15 days allow classifying approximately 95% of the users defined by access log data collected during subsequent 60 days.
Encirclement of multiple targets using model predictive control

Two teams of Unmanned Aerial Vehicles (UAVs) are used in the encirclement of two targets at the same time. Encirclement is defined as the situation in which a target is isolated and surrounded by a group of UAVs. It is a tactic that can be employed by a team of UAVs to neutralize a target by restricting its movement due to a containment motion near the target while maintaining a formation around it. In this paper, the problem of choosing the correct target to create a dynamic circular formation is considered and a Decentralized Model Predictive Control (DMPC) policy is formulated. From simulation results the derived Model Predictive Control (MPC) policy is effective for the case of two teams of UAVs encircling two stationary targets, and two teams of UAVs encircling two moving targets. The contributions of this paper are the application of MPC to the problem of encirclement, the explicit objective of a dynamic circular formation around the target, and the ability of each team to choose its correct target.
VLSI implementation of shape-adaptive discrete wavelet transform

In this paper, several VLSI architectures and implementations of Shape-Adaptive Discrete Wavelet Transform (SA-DWT) with odd symmetric biorthogonal filters are presented. The hardware implementation issues of SA-DWT algorithm are first addressed, and one lifting scheme together with some appropriate shape information processing units is introduced for the 1-D SA-DWT architectures. These architectures can efficiently perform 1-D length-adaptive DWT on continuous line segments and solve the corresponding boundary extension and subsampling problems without any overhead. In addition to 1-D architectures, two 2-D SA-DWT architectures are also proposed. One is the direct method, which uses the 1-D SA-DWT architectures as basis to extend to 2-D SA-DWT by direct row-column approach. The other is the line-based method, which is an efficient and feasible architecture that uses internal line buffers rather than external frame memory. These two 2-D SA-DWT architectures are both VLSI implemented by using cell-based chip design flow. The Daubechies (9,7) filter is used for the implementation by direct method, and the Daubechies (9,3) filter is used for the line-based implementation. The proposed architectures can be applied both in arbitrarily shaped visual objects coding such as MPEG-4 still texture coding and rectangular region image coding such as JPEG2000 still image coding.
Digital implementation of a constant frequency hysteresis controller for dual mode operation of an inverter acting as a PV-grid interface and STATCOM

This paper presents a new constant frequency hysteresis current controller for the grid interface of a PVfed three-phase voltage source inverter (VSI) for a dual mode operation, feeding real power during the daytime and reactive power alone during nights, thereby acting as a STATCOM. The constant frequency is inherently achieved by means of digital implementation in a simplified manner without any complex manipulations to choose a variable band width; rather the hysteresis band varies as a natural consequence of selecting appropriate constant sampling frequency. Analytical proof is presented for the switching frequency to remain constant, without compromising on the performance indices. The design of the proposed controller for a grid-connected inverter operating in dual mode is presented, along with simulation results. The proposed controller is successfully implemented using a 1.1 kW PV array-fed inverter. The hardware results presented show the grid current harmonics complies with IEEE 1547 and has been achieved in a simpler means when compared to other existing techniques. The proposed controller is expected to be an attractive solution for grid-connected inverter applications including distributed generation, power quality, and drive applications
Physiological and Molecular Determinants of Insulin Action in the Baboon

OBJECTIVE—To quantitate insulin sensitivity in lean and obese nondiabetic baboons and examine the underlying cellular/molecular mechanisms responsible for impaired insulin action to characterize a baboon model of insulin resistance. RESEARCH DESIGN AND METHODS—Twenty baboons received a hyperinsulinemic-euglycemic clamp with skeletal muscle and visceral adipose tissue biopsies at baseline and at 30 and 120 min after insulin. Genes and protein expression of key molecules involved in the insulin signaling cascade (insulin receptor, insulin receptor substrate-1, p85, phosphatidylinositol 3-kinase, Akt, and AS160) were sequenced, and insulin-mediated changes were analyzed. RESULTS—Overall, baboons show a wide range of insulin sensitivity (6.2 ± 4.8 mg · kg−1 · min−1), and there is a strong inverse correlation between indexes of adiposity and insulin sensitivity (r = −0.946, P < 0.001 for % body fat; r = −0.72, P < 0.001 for waist circumference). The genes and protein sequences analyzed were found to have ∼98% identity to those of man. Insulin-mediated changes in key signaling molecules were impaired both in muscle and adipose tissue in obese insulin-resistant compared with lean insulin-sensitive baboons. CONCLUSIONS—The obese baboon is a pertinent nonhuman primate model to examine the underlying cellular/molecular mechanisms responsible for insulin resistance and eventual development of type 2 diabetes.
Hacking the Nintendo Wii Remote inside the Wii Remote

Johnny Chung Lee Carnegie Mellon University I n November 2006, Nintendo released its fifth home videogame console, the Nintendo Wii. The company’s previous game console, the Gamecube, hadn’t fared well in terms of market share against the much higher-powered alternatives released by its competitors, Microsoft and Sony. At first the Wii also seemed significantly underpowered relative to its competitors. However, one year later it became the market leader of its console generation, selling over 20 million units worldwide.1 This success is largely attributable to the innovative interactive technology and game-play capabilities introduced by the console’s game controller, the Wii remote, shown in Figure 1. The Nintendo Wii remote, or Wiimote, is a handheld device resembling a television remote, but in addition to buttons, it contains a 3-axis accelerometer, a high-resolution highspeed IR camera, a speaker, a vibration motor, and wireless Bluetooth connectivity. This technology makes the Wii remote one of the most sophisticated PC-compatible input devices available today; together with the game console’s market success, it’s also one of most common. At a suggested retail price of US$40, the Wii remote is an impressively cost-effective and capable platform for exploring interaction research. Software applications developed for it have the additional advantage of being readily usable by millions of individuals around the world who already own the hardware. I’ve recently begun using Internet video tutorials to demonstrate interaction techniques supported or enabled by the Wii remote. In just a few weeks, these tutorials have received over six million unique views and generated over 700,000 software downloads. In this article, I will talk about the Wii remote’s technology, cover what’s involved in developing custom applications, describe intended and unintended interaction techniques, and outline additional uses of the device.
FACIT PD: a framework for analysis and creation of intergenerational techniques for participatory design

In this paper, we present a framework that describes commonly used design techniques for Participatory Design with children. Although there are many currently used techniques for designing with children, researchers working in differing contexts and in a changing technological landscape find themselves facing difficult design situations. The FACIT PD framework presented in this paper can aid in choosing existing design techniques or in developing new techniques regardless of the stage in the design cycle, the technology being developed, or philosophical approach to design method. The framework consists of eight dimensions, concerning the design partners, the design goal, and the design technique. The partner dimensions are partner experience and need for accommodation. The design goal dimensions are design space and maturity of design. The technique dimensions include: cost, portability, technology and physical interaction. Three cases will be presented which describe new techniques developed using the framework and two cases will describe existing techniques.
ISP Service Tier Design

Internet Service Provider design of service tiers are modeled and analyzed, based on demand for web browsing and video streaming. A basic model that considers user willingness to pay, network capacity, and application performance is formulated to determine when multiple tiers maximize profit. An extended model that also considers the time that users devote to each application is formulated to determine the optimal network capacity, tier rates, and tier prices. We show that an Internet Service Provider may simplify tier and capacity design by allowing its engineering department to set network capacity, its marketing department to set tier prices, and both to jointly set tier rates. Numerical results are presented to illustrate the magnitude of the decrease in profit compared to the optimal profit resulting from such a simplified design.
A Unified Multicarrier Modulation Framework

Orthogonal frequency division multiplexing (OFDM) has been recently recognized as inadequate to meet the increased requirements of the next generation of communication systems. A number of alternative modulation solutions, based on the use of filter banks, have thus been proposed and are currently being considered as candidate waveforms for the envisaged air interface of the future networks. A unified view of these schemes would largely facilitate a systematic comparison of their pros and cons as well as the study of methods for related signal processing problems. To this end, a generic modulator is developed in this paper, following a structured matrix formulation. With appropriate parameter settings, existing modulation schemes can result as special cases. Three such popular examples are presented in detail.
Assignment of Different-Sized Inputs in MapReduce

A MapReduce algorithm can be described by a mapping schema, which assigns inputs to a set of reducers, such that for each required output there exists a reducer that receives all the inputs that participate in the computation of this output. Reducers have a capacity, which limits the sets of inputs that they can be assigned. However, individual inputs may vary in terms of size. We consider, for the first time, mapping schemas where input sizes are part of the considerations and restrictions. One of the significant parameters to optimize in any MapReduce job is communication cost between the map and reduce phases. The communication cost can be optimized by minimizing the number of copies of inputs sent to the reducers. The communication cost is closely related to the number of reducers of constrained capacity that are used to accommodate appropriately the inputs, so that the requirement of how the inputs must meet in a reducer is satisfied. In this work, we consider a family of problems where it is required that each input meets with each other input in at least one reducer. We also consider a slightly different family of problems in which, each input of a set, X, is required to meet each input of another set, Y, in at least one reducer. We prove that finding an optimal mapping schema for these families of problem is NP-hard, and present several approximation algorithms for finding a near optimal mapping schema.
A Linear Performance-Breakdown Model for GPU Programming Optimization Guidance

The use Graphic Processing Units (GPU) as computing accelerators has been. Nevertheless, writing efficient GPU programs is a difficult and time consuming task. In this paper we present the Linear Performance Breakdown Model (LBPM), an analytic model that is used to extract the breakdown of GPU kernel programs execution time into the three major components that affect its running time. The model can be used as a tool to provide guidelines to detect the performance bottlenecks. Our approach is the incorporation of three elements, the Global-to-Shared Memory Time slice, Shared-to-Private Time slice and Processing Units Time slice. These three factors are integrated into a performance model formula by applying the Normalized Least Squares Method (NLSM). The resulting coefficients are used to construct a performance breakdown graph that reveals the effects of each element in the total execution time of the kernel program. We demonstrate the results obtained with our proposed model with two common numeric routines: Single-Precision General Matrix Multiplication (SGMM) and Fast Fourier Transform (FFT), and apply the model to the results obtained from two GPU devices: A8-3870 AMD Accelerated Processing Unit (APU) and a GTX 660 Nvidia GPU.
The Gene Ontology (GO) project in 2006

The Gene Ontology (GO) project () develops and uses a set of structured, controlled vocabularies for community use in annotating genes, gene products and sequences (also see ). The GO Consortium continues to improve to the vocabulary content, reflecting the impact of several novel mechanisms of incorporating community input. A growing number of model organism databases and genome annotation groups contribute annotation sets using GO terms to GO's public repository. Updates to the AmiGO browser have improved access to contributed genome annotations. As the GO project continues to grow, the use of the GO vocabularies is becoming more varied as well as more widespread. The GO project provides an ontological annotation system that enables biologists to infer knowledge from large amounts of data.
Selecting Computations: Theory and Applications

Sequential decision problems are often approximately solvable by simulating possible future action sequences. Metalevel decision procedures have been developed for selecting which action sequences to simulate, based on estimating the expected improvement in decision quality that would result from any particular simulation; an example is the recent work on using bandit algorithms to control Monte Carlo tree search in the game of Go. In this paper we develop a theoretical basis for metalevel decisions in the statistical framework of Bayesian selection problems, arguing (as others have done) that this is more appropriate than the bandit framework. We derive a number of basic results applicable to Monte Carlo selection problems, including the first finite sampling bounds for optimal policies in certain cases; we also provide a simple counterexample to the intuitive conjecture that an optimal policy will necessarily reach a decision in all cases. We then derive heuristic approximations in both Bayesian and distribution-free settings and demonstrate their superiority to bandit-based heuristics in one-shot decision problems and in Go.
Ontology-Alignment Techniques: Survey and Analysis

The ontology alignment consists in generating a set of correspondences between entities. These entities can be concepts, properties or instances. The ontology alignment is an important task because it allows the joint consideration of resources described by different ontologies. This paper aims at counting all works of the ontology alignment field and analyzing the approaches according to different techniques (terminological, structural, extensional and semantic). This can clear the way and help researchers to choose the appropriate solution to their issue. They can see the insufficiency, so that they can propose new approaches for stronger alignment. They can also adapt or reuse alignment techniques for specific research issues, such as semantic annotation, maintenance of links between entities, etc.
Cholesterol activates the G-protein coupled receptor Smoothened to promote Hedgehog signaling

Cholesterol is necessary for the function of many G-protein coupled receptors (GPCRs). We find that cholesterol is not just necessary but also sufficient to activate signaling by the Hedgehog (Hh) pathway, a prominent cell-cell communication system in development. Cholesterol influences Hh signaling by directly activating Smoothened (SMO), an orphan GPCR that transmits the Hh signal across the membrane in all animals. Unlike many GPCRs, which are regulated by cholesterol through their heptahelical transmembrane domains, SMO is activated by cholesterol through its extracellular cysteine-rich domain (CRD). Residues shown to mediate cholesterol binding to the CRD in a recent structural analysis also dictate SMO activation, both in response to cholesterol and to native Hh ligands. Our results show that cholesterol can initiate signaling from the cell surface by engaging the extracellular domain of a GPCR and suggest that SMO activity may be regulated by local changes in cholesterol abundance or accessibility. DOI: http://dx.doi. org/10.7554/eLife.20304. 001
Effectiveness of Lexico-syntactic Pattern Matching for Ontology Enrichment with Clinical Documents

Summary Objective: To evaluate the effectiveness of a lexico-syntactic pattern (LSP) matching method for ontology enrichment using clinical documents. Methods: Two domains were separately studied using the same methodology. We used radiology documents to enrich RadLex and pathology documents to enrich National Cancer Institute Thesaurus (NCIT). Several known LSPs were used for semantic knowledge extraction. We first retrieved all sentences that contained LSPs across two large clinical repositories, and examined the frequency of the LSPs. From this set, we randomly sampled LSP instances which were examined by human judges. We used a twostep method to determine the utility of these patterns for enrichment. In the first step, domain experts annotated medically meaningful terms (MMTs) from each sentence within the LSP. In the second step, RadLex and NCIT curators evaluated how many of these MMTs could be added to the resource. To quantify the utility of this LSP method, we defined two evaluation metrics: suggestion rate (SR) and acceptance rate (AR). We used these measures to estimate the yield of concepts and relationships, for each of the two domains. Results: For NCIT, the concept SR was 24%, and the relationship SR was 65%. The concept AR was 21%, and the relationship AR was 14%. For RadLex, the concept SR was 37%, and the relationship SR was 55%. The concept AR was 11%, and the relationship AR was 44%. Conclusion: The LSP matching method is an effective method for concept and concept relationship discovery in biomedical domains.