Miracle-dz/UniFAR-FTUs huggingface dataset:
PSI-Search: iterative HOE-reduced profile SSEARCH searching

Summary: Iterative similarity searches with PSI-BLAST position-specific score matrices (PSSMs) find many more homologs than single searches, but PSSMs can be contaminated when homologous alignments are extended into unrelated protein domains—homologous over-extension (HOE). PSI-Search combines an optimal Smith–Waterman local alignment sequence search, using SSEARCH, with the PSI-BLAST profile construction strategy. An optional sequence boundary-masking procedure, which prevents alignments from being extended after they are initially included, can reduce HOE errors in the PSSM profile. Preventing HOE improves selectivity for both PSI-BLAST and PSI-Search, but PSI-Search has ~4-fold better selectivity than PSI-BLAST and similar sensitivity at 50% and 60% family coverage. PSI-Search is also produces 2- for 4-fold fewer false-positives than JackHMMER, but is ~5% less sensitive. Availability and implementation: PSI-Search is available from the authors as a standalone implementation written in Perl for Linux-compatible platforms. It is also available through a web interface (www.ebi.ac.uk/Tools/sss/psisearch) and SOAP and REST Web Services (www.ebi.ac.uk/Tools/webservices). Contact: pearson@virginia.edu; rodrigo.lopez@ebi.ac.uk
Optimizations for faster execution of Esterel programs

Several efficient compilation techniques have been recently proposed for the generation of sequential (C) code from Esterel programs. Consisting essentially in direct simulation of the reactive features of the language, these techniques need now to be accommodated with traditional issues of Esterel - the definition of formal semantics, the constructive causality, and the design of efficient and correct methods for analysis and optimization. We address some of these problems by defining a new intermediate model for the representation of Esterel programs. The new representation level preserves much of the initial program structure while making the control flow pattern and the hierarchical state structure explicit. It supports the full Esterel semantics, and it is a good support for efficient analysis, optimization, and code generation algorithms based on static analysis.
Terbium-doped colloidal photonic crystal

Sol-gel process is shown as a promising synthetic route to develop the 3D photonic crystals doped with the optically active terbium. Using silica and Tb-doped titania sols the colloidal crystal with photonic stop band ranging from 480 to 550 nm have been developed, thus fitting the 5D4 yields 7F6 and 5D4 yields 7F5 transition of Tb3+ ions. Pronounced inhibition of optical transitions of Tb3+ ions was observed. The structures fabricated are considered as promising probes to examine the influence of photonic stop band on modification of the spontaneous emission spectra of phosphors.
Root hydraulic conductivity and adjustments in stomatal conductance: hydraulic strategy in response to salt stress in a halotolerant species

In plants, the total hydraulic resistance adjustment is a crucial trait in tolerance. We explored the link between root and shoot by means of simultaneously characterizing root hydraulic conductivity and stomatal conductance in a halotolerant model (Beta vulgaris). Under salt stress, B. vulgaris triggers a hydraulic strategy tuning the root and shoot in a coupled process. After halting the stress, the profile of root efficiency at transporting water differed from that of shoot adjustment, underlining the relevance of the root for the overall hydraulic response: root capability allows recovery of water flow before the aerial water demand is restored.
Psychological Foundations of Incentives

During the last two decades economists have made much progress in understanding incentives, contracts and organizations. Yet, they constrained their attention to a very narrow and empirically questionable view of human motivation. The purpose of this paper is to show that this narrow view of human motivation may severely limit understanding the determinants and e0ects of incentives. Economists may fail to understand the levels and the changes in behaviour if they neglect motives like the desire to reciprocate or the desire to avoid social disapproval. We show that monetary incentives may back2re and reduce the performance of agents or their compliance with rules. In addition, these motives may generate very powerful incentives themselves. c
Dynamic Coding of Taste Stimuli in the Brainstem: Effects of Brief Pulses of Taste Stimuli on Subsequent Taste Responses

Recent studies have suggested that the response profiles of taste-responsive cells in the brainstem may be modulated by inhibitory interactions, potentially originating from activity in peripheral taste nerves. This idea was explored by testing the hypothesis that brief (100 msec) pulses of taste stimuli would alter the responses to subsequently presented tastants in the nucleus of the solitary tract (NTS) of urethane-anesthetized rats. Pulses of taste stimuli, called prepulses, were followed by a 3 sec presentation of the same or different taste stimulus. The prepulse-stimulus interval was either 1 or 5 sec, during which the tongue was rinsed with distilled water. Taste stimuli consisted of 0.1 m NaCl, 0.5 m sucrose, 0.01 m quinine HCl, and 0.01 m HCl. Taste prepulses suppressed (or enhanced) subsequent taste responses in 30 of 49 (61%) units when the prepulse-stimulus interval was 1 sec but were ineffective when this interval was 5 sec. Most commonly, NaCl or HCl prepulses attenuated the response to quinine. Control experiments showed that these effects were not attributable to adaptation, mixture effects, or response variability. In 19 (39%) of the units tested, effects of prepulses were large enough to change the order of effectiveness of the taste stimuli. Taste responses in these cells were “dynamically tuned” in that the magnitude of response was a function of the taste stimulus that immediately preceded it. Dynamic tuning may be the result of inhibitory interactions within the NTS; cells that show dynamic tuning may have a unique function in taste coding.
SWAN: a mobile multimedia wireless network

The SWAN (Seamless Wireless ATM Network) is an experimental indoor wireless network that instigates the combination of wireless access with multimedia networked computing in an indoor setting. It is based on room-sized pico-cells and mobile multimedia endpoints. It enables users carrying multimedia endpoints, such as personal digital assistants (PDAs), laptops, and portable multimedia terminals, to seamlessly roam while accessing multimedia data resident in a backbone wired network. The network model of SWAN consists of base stations connected by a wired asynchronous transfer mode (ATM) backbone network, and wireless ATM last hops to the mobile hosts. SWAN is one of the first systems to realize the concept of a wireless and mobile ATM network. Mobile hosts as well as base stations are embedded with custom-designed ATM adapter cards called FAWN (Flexible Adapter for Wireless Networking). FAWN uses off-the-shelf 2.4 GHz industrial, scientific, and medical (ISM) band radios. After giving an overview of the SWAN network model, and discussing the challenges in making ATM wireless and mobile, the article describes the first phase implementation of SWAN hardware and software. This initial implementation provides connectivity over the wireless last hop. We have investigated both native-mode end-to-end ATM communication across the wired ATM backbone and wireless ATM links, and transmission control protocol (TCP) and user datagram protocol (UDP) communication using Internet protocol (IP) over wireless ATM in the wireless link with IP forwarding and segmentation and reassemble modules at the base stations.
Distributed Function Calculation via Linear Iterative Strategies in the Presence of Malicious Agents

Given a network of interconnected nodes, each with its own value (such as a measurement, position, vote, or other data), we develop a distributed strategy that enables some or all of the nodes to calculate any arbitrary function of the node values, despite the actions of malicious nodes in the network. Our scheme assumes a broadcast model of communication (where all nodes transmit the same value to all of their neighbors) and utilizes a linear iteration where, at each time-step, each node updates its value to be a weighted average of its own previous value and those of its neighbors. We consider a node to be malicious or faulty if, instead of following the predefined linear strategy, it updates its value arbitrarily at each time-step (perhaps conspiring with other malicious nodes in the process). We show that the topology of the network completely characterizes the resilience of linear iterative strategies to this kind of malicious behavior. First, when the network contains 2f or fewer vertex-disjoint paths from some node xj to another node xi , we provide an explicit strategy for f malicious nodes to follow in order to prevent node xi from receiving any information about xj's value. Next, if node xi has at least 2f+1 vertex-disjoint paths from every other (non-neighboring) node, we show that xi is guaranteed to be able to calculate any arbitrary function of all node values when the number of malicious nodes is f or less. Furthermore, we show that this function can be calculated after running the linear iteration for a finite number of time-steps (upper bounded by the number of nodes in the network) with almost any set of weights (i.e., for all weights except for a set of measure zero).
A Unified Tagging Approach to Text Normalization

This paper addresses the issue of text normalization, an important yet often overlooked problem in natural language processing. By text normalization, we mean converting ‘informally inputted’ text into the canonical form, by eliminating ‘noises’ in the text and detecting paragraph and sentence boundaries in the text. Previously, text normalization issues were often undertaken in an ad-hoc fashion or studied separately. This paper first gives a formalization of the entire problem. It then proposes a unified tagging approach to perform the task using Conditional Random Fields (CRF). The paper shows that with the introduction of a small set of tags, most of the text normalization tasks can be performed within the approach. The accuracy of the proposed method is high, because the subtasks of normalization are interdependent and should be performed together. Experimental results on email data cleaning show that the proposed method significantly outperforms the approach of using cascaded models and that of employing independent models.
Evidence for Two Concurrent Inhibitory Mechanisms during Response Preparation

Inhibitory mechanisms are critically involved in goal-directed behaviors. To gain further insight into how such mechanisms shape motor representations during response preparation, motor evoked potentials (MEPs) elicited by transcranial magnetic stimulation (TMS) and H-reflexes were recorded from left hand muscles during choice reaction time tasks. The imperative signal, which indicated the required response, was always preceded by a preparatory cue. During the postcue delay period, left MEPs were suppressed when the left hand had been cued for the forthcoming response, suggestive of a form of inhibition specifically directed at selected response representations. H-reflexes were also suppressed on these trials, indicating that the effects of this inhibition extend to spinal circuits. In addition, left MEPs were suppressed when the right hand was cued, but only when left hand movements were a possible response option before the onset of the cue. Notably, left hand H-reflexes were not modulated on these trials, consistent with a cortical locus of inhibition that lowers the activation of task-relevant, but nonselected responses. These results suggest the concurrent operation of two inhibitory mechanisms during response preparation: one decreases the activation of selected responses at the spinal level, helping to control when selected movements should be initiated by preventing their premature release; a second, upstream mechanism helps to determine what response to make during a competitive selection process.
Coding joint formation of endogenous T cell receptor genes in lymphoid cells from scid mice: unusual P‐nucleotide additions in VJ‐coding joints

The mouse mutation scid adversely affects the process of VDJ recombination. Attempts to form coding joints, that is, to join V or D to J gene segments generally fail in developing scid lymphocytes. It has been proposed that the scid mutation results a defective VDJ recombinase system. Here we describe five scid T cell lymphomas containing one or two TcRγ coding joints each, even though the majority of the multiple TcRγ chain gene rearrangements and all TcRβ rearrangements in these cells were abnormal with the deletions typically found in scid lymphoid cells. One of the five T cell lymphomas was shown to have an active VDJ recombinase system; however, this activity was defective indicating that the scid phenotype has been retained. We conclude that the scid VDJ recombinase system has not completely lost the ability to form coding joints. P‐nucleotide additions of unusual length or composition were found at the junctional border in five of the eight TcRγ coding joints. This might reflect a defect in the activity of a component of the VDJ recombinase system involved in the generation of P‐nucleotide additions. In one of the observed rearrangements, a Vγ5‐Jγ3 coding joint was formed. This establishes the transcriptional orientation of Jγ3‐Cγ3 and confirms a previously proposed organization of the TcRγ genes.
Business Process Reengineering and Customer Satisfaction with reference to Indian Telecommunication sector

Intention of the study was to quantitatively analyze the factors based on which telecom service providers can formulate strategy to satisfy customers to get an edge over the competitors. And we will see how Business Process Management and Re-engineering might play the role of a weapon to Indian Telco service providers. The elements of the business processes of the Telecom domain, which affect customer satisfaction level and how BPR can impact the level of customer satisfaction in the telecom sector in India was investigated in this study. Mainly three categories of research findings have been deduced from the study. The first category dealing with the customer's perception on different areas of Indian Telecom processes exposed the need for a fast cycle capability and competitiveness of the Telco system. The second category analyzes customer's satisfaction with the existing service facilities of Indian Telco services and shows an average figure of their present satisfaction level. The third category describes customer's perception on Indian telecom service providers for enhancement of the level of satisfaction revealing a strong need for strategic planning and implementation of IT-enabled reengineered business process. The findings will be useful to increase customer value, customer satisfaction and retention and can guide the strategic business planners to introduce better, innovative and customized products to the consumers.
A New Collaborative Knowledge-Based Approach for Wireless Sensor Networks

This work presents a new approach for collaboration among sensors in Wireless Sensor Networks. These networks are composed of a large number of sensor nodes with constrained resources: limited computational capability, memory, power sources, etc. Nowadays, there is a growing interest in the integration of Soft Computing technologies into Wireless Sensor Networks. However, little attention has been paid to integrating Fuzzy Rule-Based Systems into collaborative Wireless Sensor Networks. The objective of this work is to design a collaborative knowledge-based network, in which each sensor executes an adapted Fuzzy Rule-Based System, which presents significant advantages such as: experts can define interpretable knowledge with uncertainty and imprecision, collaborative knowledge can be separated from control or modeling knowledge and the collaborative approach may support neighbor sensor failures and communication errors. As a real-world application of this approach, we demonstrate a collaborative modeling system for pests, in which an alarm about the development of olive tree fly is inferred. The results show that knowledge-based sensors are suitable for a wide range of applications and that the behavior of a knowledge-based sensor may be modified by inferences and knowledge of neighbor sensors in order to obtain a more accurate and reliable output.
Thermic Effects of Tocolytic Agents: Decreased Temperature With Magnesium Sulfate

The effect of the tocolytic agents terbutaline and magnesium sulfate on patients' temperatures was examined. Fifty-two women admitted for preterm labor were randomized to a treatment protocol for one of the two agents. Oral temperatures were measured intially and every two hours during treatment. There was no significant difference between the initial temperature and the lowest temperature recorded during treatment in the terbutaline group, but temperature decreased significantly during treatment with magnesium sulfate. This decrease in maternal temperature may have importance in the treatment of preterm labor with magnesium sulfate in patients with an infectious etiology for uterine activity.
Particle Swarm as a Model for Community Formation in Social Networks

Online communities play an important role in the world of contemporary social networks. Due to the ubiquitous availability of ICT tools individuals can easily form small, tight, dense groups around various topics and subjects of interest. These online communities share many similarities with general social networks, but they display some interesting distinguishing characteristics. In particular, online communities are usually subject-centered, require some degree of supervision and maintenance in order to continue operations, and provide higher quality user-generated content as compared with larger social networks. Many different approaches have been proposed in the past regarding methods of online community analysis and modeling. Agent-based methods have been successfully employed to simulate online community formation and evolution. However, simulation-based methods inherently suffer from the arbitrary choice of parameters that may produce radically different online community structures as the result of minuscule changes of input parameters. In this paper we examine the usability of a particular agent-based method, namely, the particle swarm model, for online community analysis. We propose a simple model that uses a swarm of particles paradigm to simulate the behavior of users and the formation of online communities and we measure the influence that changing of the swarm parameters has on the resulting online community structure.
Kinetics and Muscle Activity Patterns during Unweighting and Reloading Transition Phases in Running

Amongst reduced gravity simulators, the lower body positive pressure (LBPP) treadmill is emerging as an innovative tool for both rehabilitation and fundamental research purposes as it allows running while experiencing reduced vertical ground reaction forces. The appropriate use of such a treadmill requires an improved understanding of the associated neuromechanical changes. This study concentrates on the runner’s adjustments to LBPP-induced unweighting and reloading during running. Nine healthy males performed two running series of nine minutes at natural speed. Each series comprised three sequences of three minutes at: 100% bodyweight (BW), 60 or 80% BW, and 100% BW. The progressive unweighting and reloading transitions lasted 10 to 15 s. The LBPP-induced unweighting level, vertical ground reaction force and center of mass accelerations were analyzed together with surface electromyographic activity from 6 major lower limb muscles. The analyses of stride-to-stride adjustments during each transition established highly linear relationships between the LBPP-induced progressive changes of BW and most mechanical parameters. However, the impact peak force and the loading rate systematically presented an initial 10% increase with unweighting which could result from a passive mechanism of leg retraction. Another major insight lies in the distinct neural adjustments found amongst the recorded lower-limb muscles during the pre- and post-contact phases. The preactivation phase was characterized by an overall EMG stability, the braking phase by decreased quadriceps and soleus muscle activities, and the push-off phase by decreased activities of the shank muscles. These neural changes were mirrored during reloading. These neural adjustments can be attributed in part to the lack of visual cues on the foot touchdown. These findings highlight both the rapidity and the complexity of the neuromechanical changes associated with LBPP-induced unweighting and reloading during running. This in turn emphasizes the need for further investigation of the evolution over time of these neuromechanical changes.
Rational design and molecular effects of a new topoisomerase II inhibitor, azatoxin.

Azatoxin [NSC 640737-M; 5.R,11aS-1H,6H,3-one-5,4,11,11a-tetrahydro-5-(3,5-dimethoxy-4-hydr oxyphenyl) oxazolo (3',4':1,6)pyrido-(3,4-b)indole] was rationally designed from a model for the pharmacophore of drugs with topoisomerase II inhibition activity. This pharmacophore has at least 2 domains: a quasiplanar polycyclic ring system proposed to bind between the DNA base pairs and a pendant substituent proposed to interact with the enzyme and/or to the DNA grooves. The present study shows that, in cell free systems, azatoxin induces a large number of double strand-breaks in linear Simian virus 40 and human c-myc DNA. These breaks yield cleavage patterns that are different from those of well established topoisomerase II inhibitors (epipodophyllotoxins, amsacrine, mitoxantrone). Azatoxin also inhibits the catalytic activity of purified topoisomerase II, and is a nonintercalator. The structure-activity relationship of 3 isomers and 6 derivatives of azatoxin shows a stringent stereochemical requirement for activity. The effects of azatoxin pendant ring substitution on topoisomerase II mediated DNA cleavage activity were similar to the relationship observed for etoposide.
On the Discovery and Generation of Certain Heuristics

This paper explores the paradigm that heuristics are discovered by consulting simplified models of the problem domain. After describing the features of typical heuristics on some popular problems, we demonstrate that these heuristics can be obtained by the process of deleting constraints from the original problem and solving the relaxed problem which ensues. We then outline a scheme for generating such heuristics mechanically, which involves systematic refinement and deletion of constraints from the original problem specification until a semidecomposable model is identified. The solution to the latter constitutes a heuristic for the former.