Search Template Research Articles

Novel σ F-dependent genes of Escherichia coli found using a specified promoter consensus

Availability of whole genome information opens new bioinformatics approaches to study global regulation. We developed a program, named ScanProm, that allows to search a genome database for promoter consensus elements. The program uses a multiple alignment of previously identified components of a regulon as an input and generates a consensus profile. The profile is then optimized by adjusting the cutoff value for position-specific similarity assessment and used for a genome scan to search for unknown members of the regulon. The candidates obtained are scored by their similarity to the consensus profile. The ScanProm program was applied to search for novel members of the class III flagellar regulon of Escherichia coli. The search template included the previously defined 4 bp (−35) and 8 bp (−10) promoter elements, presumably recognized by the flagellar-specific σ F, with additional 4 bp at the 3′ of the −35 consensus. The majority of highly scoring candidates obtained from the whole genome sequence scan were known class III genes, although several new genes were also identified. We tested 10 novel highly scoring candidate class III genes by cloning their promoter fragments into a fusion vector designed to monitor the transcriptional activity with lacZ. Two of these genes, b2737( ygbK) and ppdAB, were found to be dependent on FlhDC, the master regulator of the flagellar genes. The regulation of these genes by σ F was further confirmed by comparing their expression in the wild-type and fliA backgrounds. An overproduction or inactivation of these genes did not exhibit any notable phenotypes in motility or chemotaxis.

Less accurate but more efficient family of search templates for detection of gravitational waves from inspiraling compact binaries

The network of interferometric detectors that is under construction at various locations on Earth is expected to start searching for gravitational waves in a few years. The number of search templates that is needed to be cross correlated with the noisy output of the detectors is a major issue since computing power capabilities are restricted. By choosing higher and higher post-Newtonian order expansions for the family of search templates we make sure that our filters are more accurate copies of the real waves that hit our detectors. However, this is not the only criterion for choosing a family of search templates. To make the process of detection as efficient as possible, one needs a family of templates with a relatively small number of members that manages to pick up any detectable signal with only a tiny reduction in signal-to-noise ratio. Evidently, one family is better than another if it accomplishes its goal with a smaller number of templates. Following the geometric language of Owen, we have studied the performance of the ${\mathrm{post}}^{1.5}\ensuremath{-}\mathrm{N}\mathrm{e}\mathrm{w}\mathrm{t}\mathrm{o}\mathrm{n}\mathrm{i}\mathrm{a}\mathrm{n}$ family of templates on detecting ${\mathrm{post}}^{2}\ensuremath{-}\mathrm{N}\mathrm{e}\mathrm{w}\mathrm{t}\mathrm{o}\mathrm{n}\mathrm{i}\mathrm{a}\mathrm{n}$ signals for binaries. Several technical issues arise from the fact that the two types of waveforms cannot be made to coincide by a suitable choice of parameters. In general, the parameter space of the signals is not identical with the parameter space of the templates, although in our case they are of the same dimension, and one has to take into account all such peculiarities before drawing any conclusion. An interesting result we have obtained is that the ${\mathrm{post}}^{1.5}\ensuremath{-}\mathrm{N}\mathrm{e}\mathrm{w}\mathrm{t}\mathrm{o}\mathrm{n}\mathrm{i}\mathrm{a}\mathrm{n}$ family of templates happens to be more economical for detecting ${\mathrm{post}}^{2}\ensuremath{-}\mathrm{N}\mathrm{e}\mathrm{w}\mathrm{t}\mathrm{o}\mathrm{n}\mathrm{i}\mathrm{a}\mathrm{n}$ signals than the perfectly accurate ${\mathrm{post}}^{2}\ensuremath{-}\mathrm{N}\mathrm{e}\mathrm{w}\mathrm{t}\mathrm{o}\mathrm{n}\mathrm{i}\mathrm{a}\mathrm{n}$ family of templates itself. The number of templates is reduced by $20\ensuremath{-}30%,$ depending on the acceptable level of reduction in signal-to-noise ratio due to discretization of the family of templates. This makes the ${\mathrm{post}}^{1.5}\ensuremath{-}\mathrm{N}\mathrm{e}\mathrm{w}\mathrm{t}\mathrm{o}\mathrm{n}\mathrm{i}\mathrm{a}\mathrm{n}$ family of templates more favorable for detecting gravitational waves from inspiraling, compact, nonspinning, binaries. Apart from this useful quantitative result, this study constitutes an application of the template-numbering technique, introduced by Owen, for families of templates that are not described by the same mathematical expression as the assumed signals. For example, this analysis will be very useful when constructing sufficiently simple templates for detecting precessing spinning binaries.

Searching for actions

Suppose that you are searching for a teapot in your kitchen, which is crowded with objects. Current theories of attention assume that it is the perceptual properties of the sought-for object (such as its shape, colour or texture), which are stored in long-term memory and temporarily retrieved in working memory, that guide your selection. However, in a recent report, Humphreys and Riddoch 1xDetection by action: neuropsychological evidence for action-defined templates in search. Humphreys, G.W and Riddoch, M.J. Nat. Neurosci. 2001; 4: 84–88Crossref | PubMed | Scopus (85)See all References1 suggest that the potential action an object affords might also provide an effective memory template for attentional selection. They used a visual search task to compare perceptual versus action cues (‘affordances’) in a patient, ‘MP’, with hemispatial neglect following damage to the right hemisphere. Results were clear-cut. Across the different experiments, MP was significantly faster and more accurate in detecting contralesional targets defined by the action they afforded (e.g. ‘an object you would use to pour from’) than detecting targets cued by colour (‘a brown item’) or name (‘a teapot’). This held regardless of whether the action cue was given through a verbal description or a gesture made by the experimenter. The effect disappeared, however, if words instead of objects were used as targets (words do not afford a limb action), or when objects were oriented so as to make them less suited for action (handles faced away from the patient).Interestingly though, two other patients with neglect showed the opposite pattern of results, being better at detecting targets defined by their names. This suggests that action-based and perceptual-based selections may depend on functionally separated neural mechanisms. Facilitation of visual processing by action cues could operate through top-down priming signals from a network of areas in the dorsal stream, in particular the ventral premotor cortex and inferior parietal cortex. Neurons in these areas encode the relationship between visual objects and the appropriate movements required to grasp them, rather than the perceptual properties of objects per se.This study confirms the importance of action in visual processing and the highly integrated nature of visual and motor representations. As such, it fits nicely with Duncan's integrated-competition hypothesis 2xCompetitive brain activity in visual attention. Duncan, J et al. Curr. Opin. Neurobiol. 1997; 7: 255–261Crossref | PubMed | Scopus (339)See all References2, which suggests that many different biases, both visual and non-visual, influence hemispatial neglect, and with Rizzolatti et al.'s premotor theory of attention 3xReorienting attention across the horizontal and vertical meridians: evidence in favor of a premotor theory of attention. Rizzolatti, G et al. Neuropsychologia. 1987; 25: 31–40Crossref | PubMed | Scopus (989)See all References3, which maintains that preparation to act on an object enhances perceptual processing of that object. Experiments like these bring the understanding of the relationship between perception and action a step closer.

Comparison of search templates for gravitational waves from binary inspiral

We compare the performances of the templates defined by three different types of approaches: traditional post-Newtonian templates (Taylor approximants), “resummed” post-Newtonian templates assuming the adiabatic approximation and stopping before the plunge (P approximants), and further “resummed” post-Newtonian templates going beyond the adiabatic approximation and incorporating the plunge with its transition from the inspiral (effective-one-body approximants). The signal to noise ratio is significantly enhanced (mainly because of the inclusion of the plunge signal) by using these new effective-one-body templates relative to the usual post-Newtonian ones for a total binary mass m≳30M⊙, and reaches a maximum around m∼80M⊙. Independently of the question of the plunge signal, the comparison of the various templates confirms the usefulness of using resummation methods. The paper also summarizes the key elements of the construction of various templates and thus can serve as a resource for those involved in writing inspiral search software. © 2001 The American Physical Society

Detection by action: neuropsychological evidence for action-defined templates in search

How do we detect a target in a cluttered environment? Here we present neuropsychological evidence that detection can be based on the action afforded by a target. A patient showing symptoms of unilateral neglect following damage to the right fronto-temporal-parietal region was slow and sometimes unable to find targets when they were defined by their name or even by a salient visual property (such as their color). In contrast, he was relatively efficient at finding a target defined by the action it afforded. Two other patients with neglect showed an opposite pattern; they were better at finding a target defined by its name. The data suggest that affordances can be effective even when a brain lesion limits the use of other properties in search tasks. The findings give evidence for a direct pragmatic route from vision to action in the brain.

MARKING THE PACKAGE OR ITS CONTENTS: HOST DISCRIMINATION AND ACCEPTANCE IN THE ECTOPARASITOID DENDROCERUS CARPENTERI (HYMENOPTERA: MEGASPILIDAE)

AbstractDendrocerus carpenteri (Curtis) was reared in the laboratory on prepupae of Aphidius ervi Haliday (Hymenoptera: Braconidae, Aphidiinae) developing in pea aphid, Acyrthosiphon pisum (Harris) (Hemiptera: Aphididae). To test alternative hypotheses about host-marking behaviour and discrimination, we transferred unparasitized and previously parasitized A. ervi prepupae from donor to recipient mummies, which were either "unparasitized" or "parasitized." Females accepted already parasitized hosts within unparasitized mummies, but they rejected unparasitized hosts within previously parasitized mummies. Host discrimination was not influenced by self and conspecific parasitism. Eggs were frequently placed directly on the mummy shell, rather than on the primary parasitoid, or on dummies made from dental wax. Prepupae removed from their mummy shell were not accepted for oviposition. We propose that the "search template" of D. carpenteri is defined, primarily, by the aphid mummy, which is being marked with a contact pheromone after oviposition.

Gravitational waves from inspiraling compact binaries: Second post-Newtonian waveforms as search templates. II

We present further evidence that the second post-Newtonian (pN) approximation to the gravitational waves emitted by inspiraling compact binaries is sufficient for the detection of these systems. This is established by comparing the 2-pN wave forms to signals calculated from black hole perturbation theory. Results are presented for different detector noise curves. We also discuss the validity of this type of analysis.

Gravitational waves from inspiraling compact binaries: Second post-Newtonian waveforms as search templates

We ascertain the effectiveness of the second post-Newtonian approximation to the gravitational waves emitted during the adiabatic inspiral of a compact binary system as templates for signal searches with kilometer-scale interferometric detectors. The reference signal is obtained by solving the Teukolsky equation for a small mass moving on a circular orbit around a large nonrotating black hole. Fitting factors computed from this signal and these templates, for various types of binary systems, are all above the 90% mark. According to Apostolatos' criterion, second post-Newtonian waveforms should make acceptably effective search templates.

Construction of a template family for the detection of gravitational waves from coalescing binaries.

A discrete set of theoretical waveforms should be ready to use when searches for gravitational waves at the noisy output of the laser interferometric detectors that are presently under construction begin. In this paper we extend the method introduced by Sathyaprakash and Dhurandhar to construct such a family of templates, that was based on simple Newtonian signals, to ${\mathrm{post}}^{2}$-Newtonian signals that may be modulated due to spin-induced precession. More specifically, we show that if post-Newtonian terms of the phase are taken into account then the Newtonian templates turn out to be a rather inadequate type of search templates and other templates of higher post-Newtonian order should be used instead. This expands the number of parameters that the templates depend on, and, therefore, it leads to a required number of templates that is 2 orders of magnitude larger than it was previously thought, when precessionally modulation effects are ignored and a formidable number of templates when precessionally modulated signals are considered. From our analysis it becomes clear that a ${\mathrm{post}}^{1.5}$-Newtonian family of templates, with vanishing spin term, is a very promising family of search templates for signals coming from nonprecessing binaries. Furthermore, adding an extra oscillatory term in the phase of these ${\mathrm{post}}^{1.5}$-Newtonian templates would extend their detecting ability to signals coming from moderately precessing binaries; but, unfortunately, the number of templates then needed leaves no hope for an on-line search. This extended family of templates could be used more effectively in a hierarchical off-line search.

Influence of spin-spin coupling on inspiraling compact binaries withM1=M2andS1=S2

Searching for gravitational waves with laser-interferometer detectors requires a highly accurate knowledge of the gravitational wave forms in order to construct search templates with which to cross correlate the noisy detectors' output. In this spirit, we derive here an analytic approximate formula describing the precession of an inspiraling compact binary with equal masses and equal spins, where both the spin-orbit and the spin-spin couplings are taken into account.

Search templates for gravitational waves from inspiraling binaries: Choice of template spacing.

Gravitational waves from inspiraling, compact binaries will be searched for in the output of the LIGO-VIRGO interferometric network by the method of ``matched filtering''---i.e., by correlating the noisy output of each interferometer with a set of theoretical wave form templates. These search templates will be a discrete subset of a continuous, multiparameter family, each of which approximates a possible signal. The search might be performed hierarchically, with a first pass through the data using a low threshold and a coarsely spaced, few-parameter template set, followed by a second pass on threshold-exceeding data segments, with a higher threshold and a more finely spaced template set that might have a larger number of parameters. Alternatively, the search might involve a single pass through the data using the larger threshold and finer template set. This paper extends and generalizes the Sathyaprakash-Dhurandhar (SD) formalism for choosing the discrete, finely spaced template set used in the final (or sole) pass through the data, based on the analysis of a single interferometer. The SD formalism is rephrased in geometric language by introducing a metric on the continuous template space from which the discrete template set is drawn. This template metric is used to compute the loss of signal-to-noise ratio and reduction of event rate which result from the coarseness of the template grid. Correspondingly, the template spacing and total number N of templates are expressed, via the metric, as functions of the reduction in event rate. The theory is developed for a template family of arbitrary dimensionality (whereas the original SD formalism was restricted to a single nontrivial dimension). The theory is then applied to a simple ${\mathrm{post}}^{1}$-Newtonian template family with two nontrivial dimensions. For this family, the number of templates N in the finely spaced grid is related to the spacing-induced fractional loss L of event rate and to the minimum mass ${\mathit{M}}_{\mathrm{min}}$ of the least massive star in the binaries for which one searches by N\ensuremath{\sim}2\ifmmode\times\else\texttimes\fi{}${10}^{5}$(0.1/L)(0.2${\mathit{M}}_{\mathrm{\ensuremath{\bigodot}}}$/${\mathit{M}}_{\mathrm{min}}$${)}^{2.7}$ for the first LIGO interferometers and by N\ensuremath{\sim}8\ifmmode\times\else\texttimes\fi{}${10}^{6}$(0.1/L)(0.2${\mathit{M}}_{\mathrm{\ensuremath{\bigodot}}}$/${\mathit{M}}_{\mathrm{min}}$${)}^{2.7}$ for advanced LIGO interferometers. This is several orders of magnitude greater than one might have expected based on Sathyaprakash's discovery of a near degeneracy in the parameter space, the discrepancy being due to that paper's high choice of ${\mathit{M}}_{\mathrm{min}}$ and less stringent choice of L. The computational power P required to process the steady stream of incoming data from a single interferometer through the closely spaced set of templates is given in floating-point operations per second by P\ensuremath{\sim}3\ifmmode\times\else\texttimes\fi{}${10}^{10}$(0.1/L)(0.2${\mathit{M}}_{\mathrm{\ensuremath{\bigodot}}}$/${\mathit{M}}_{\mathrm{min}}$${)}^{2.7}$ for the first LIGO interferometers and by P\ensuremath{\sim}4\ifmmode\times\else\texttimes\fi{}${10}^{11}$(0.1/L)(0.2${\mathit{M}}_{\mathrm{\ensuremath{\bigodot}}}$/${\mathit{M}}_{\mathrm{min}}$${)}^{2.7}$ for advanced LIGO interferometers. This will be within the capabilities of LIGO-era computers, but a hierarchical search may still be desirable to reduce the required computing power. \textcopyright{} 1996 The American Physical Society.

Novel carbamates as potent histamine H3 receptor antagonists with high in vitro and oral in vivo activity.

The known histamine H3 receptor antagonists burimamide, thioperamide, clobenpropit, and a related homohistamine thioamide derivative were taken as templates in search for new leads. Novel histamine H3 receptor antagonists structurally described as carbamate derivatives of 3-(1H-imidazol-4-yl)propanol were prepared in high yields by treatment of the alcohol with corresponding isocyanates or carbamoyl chlorides and investigated for their H3 receptor antagonist activity. Different chain lengths and various substituents possessing different electronic and steric parameters were introduced and structure-activity relationships established. In different functional tests, the new antagonists showed high H3 receptor antagonist potencies in vitro (-log Ki values of 6.4-8.4) at synaptosomes of rat cerebral cortex and low activities at histamine H1 and H2 receptor subtypes. They were also screened for their central in vivo activity in mice after peroral administration. The most promising compounds (2, 16, 19) showed ED(50) values of about 1-2 mg/kg and thus are potential drugs for the therapy of H3 receptor dependent diseases. Some of the novel carbamate derivatives are H3 receptor selective compounds with high in vitro and in vivo activity.

On the detectability of post‐Newtonian effects in gravitational‐wave emission of a coalescing binary1

The effect of the recently obtained 2nd post-Newtonian corrections on the accuracy of estimation of parameters of the gravitational-wave signal from a coalescing binary is investigated. It is shown that addition of this correction degrades considerably the accuracy of determination of individual masses of the members of the binary. However the chirp mass and the time parameter in the sinal is still determined to a very good accuracy. The performance of the Newtonian filter is investigated and it is compared with performance of post-Newtonian search templates introduced recently. It is shown that both search templates can extract accurately useful information about the binary.

Estimation of the post-Newtonian parameters in the gravitational-wave emission of a coalescing binary.

The effect of the recently calculated second post-Newtonian correction on the accuracy of the estimation of the parameters of the gravitational-wave signal from a coalescing binary is investigated. It is shown that the addition of this correction degrades considerably the accuracy of the determination of the individual masses of the members of the binary. However the chirp mass and the time parameter in the signal are still determined to a very good accuracy. The possibility of estimating the effects of other theories of gravity is investigated. The performance of the Newtonian filter is investigated and it is compared with the performance of post-Newtonian search templates introduced recently. It is shown that both search templates can extract accurately useful information about the binary.

Search templates for gravitational waves from precessing, inspiraling binaries.

Searches for gravitational waves with the LIGO-VIRGO-GEO detector network will require families of ``search templates'' with which to cross correlate the noisy detectors' output. This paper introduces a fitting factor (FF), as a quantitative measure of how well the best template in a family ``fits'' a hypothetical gravitational waveform, in the presence of a specific detector noise spectrum. An FF0.9 corresponds to a 27% reduction in the event rate of the relevant signals; therefore a family of templates that leads to FF's below 0.9 should be considered inadequate. The FF is used to explore the adequateness of several families as search templates for gravitational waves from compact inspiraling binaries. The binaries are taken to move in circular orbits, and the ``advanced LIGO noise spectrum'' is assumed for the detectors. We first study the acceptability of the simplest three-parameter template family, the so-called ``Newtonian family.'' From previous studies by Finn, Kr\'olak, Kokotas, Sch\"afer, Dhurandar, and Balasubramanian, we infer that post-Newtonian effects in the true waveforms of binaries with vanishing spins cause the Newtonian family to have an unacceptable low FF (\ensuremath{\sim}0.6 to 0.8). We then study the influence of waveform modulations caused by spin-induced orbital precession, and we isolate the modulation effects from other post-Newtonian effects by pretending that the true signals are pure Newtonian with modulation. Many different parameters influence the precession and then the waveform modulation.A wide range of parameter values is explored, and intuition is developed into which parameters most strongly influence the FF. It is shown that the unmodulated Newtonian template family works quite well (FF>0.9 for almost all parameter values) in searches for the modulated Newtonian signal from two 1.4${\mathit{M}}_{\mathrm{\ensuremath{\bigodot}}}$ neutron stars (NS's) with one of them maximally spinning. By contrast, for a maximally spinning 10${\mathit{M}}_{\mathrm{\ensuremath{\bigodot}}}$ black hole (BH) with a nonrotating 1.4${\mathit{M}}_{\mathrm{\ensuremath{\bigodot}}}$ NS, the Newtonian template family produces FF0.9 for more than half of all the binaries' orientations, if the spin and orbital angular momenta are misaligned by 30\ifmmode^\circ\else\textdegree\fi{}. We introduce a new four-parameter template family, which has the form of the nonmodulated ${\mathrm{post}}^{1}$-Newtonian signal from a zero-spin-binary. Although, there is a substantial improvement of the FF's for a spin-modulated Newtonian signal, the FF's for nonmodulated ${\mathrm{post}}^{1.5}$-Newtonian waveforms are still very poor (\ensuremath{\sim}0.5--0.8). Therefore we propose another four-parameter template family that has the same form as a nonmodulated ${\mathrm{post}}^{1.5}$-Newtonian signal with all the spin-related parameters stripped off. This template family works ${\mathrm{post}}^{1.5}$-Newtonian modulated signals quite well. These results suggest that, in a few years, when waveforms have been computed up to ${\mathrm{post}}^{3}$-Newtonian order, a good template family will be the four-parameter ${\mathrm{post}}^{3}$-Newtonian waveforms for zero-spin binaries, augmented by some appropriate modulations to deal with misaligned, rapidly spinning BH-NS systems. Finally, we extend our investigations to the space-based low-frequency LISA detector.

Filtering post-Newtonian gravitational waves from coalescing binaries.

Gravitational waves from inspiralling binaries are expected to be detected using a data analysis technique known as matched filtering. This technique is applicable whenever the form of the signal is known accurately. Though we know the form of the signal precisely, we will not know a priori its parameters. Hence it is essential to filter the raw output through a host of search templates each corresponding to different values of the parameters. The number of search templates needed in detecting the Newtonian waveform characterized by three independent parameters is itself several thousands. With the inclusion of post-Newtonian corrections the inspiral waveform will have four independent parameters and this, it was thought, would lead to an increase in the number of filters by several orders of magnitude---an unfavorable feature since it would drastically slow down data analysis. In this Rapid Communication I show that by a judicious choice of signal parameters we can work, even when the first post-Newtonian corrections are included, with as many number of parameters as in the Newtonian case. In other words I demonstrate that the effective dimensionality of the signal parameter space does not change when first post-Newtonian corrections are taken into account.

The retrieval problem in photography (1932). Emanuel Goldberg (1881-1970)

A new approach to mechanized document retrieval is demonstrated using optical and photoelectric methods to retrieve indexed documents stored on microfilm. Microfilm can be used to store images of documents compactly with suitable index codes recorded on the film adjacent to the image of the document. The film can be passed through a «statistical machine» [microfilm selector] in which a combination of light source, search template, and photoeletric cell is used to scan the moving film, identify the desired index code, project or copy the associated document. The machine demonstrated can search to up to 35,000 documents per hour, which could be increased to 100,000 per hour. [Translation of «Das Registrierproblem in der Photographie», a paper presented at the VIIIth International Congress of Photography, Dresden, 1931, and published in the proceedings in 1932.]

Integration of knowledge and method in real-world discovery

An architecture which controls automated discovery of empirical knowledge must integrate a robotic component which interacts with the real world, knowledge network which accumulates knowledge, a discovery method, and the currently executed discovery tasks. We describe such an architecture implemented in the FAHRENHEIT system, concentrating on the integration and interaction between elements. The robotic component includes hardware connections to the external instruments and manipulators, operational procedures to control the hardware, and a process that controls outstanding requests for measurements and manipulations. Knowledge network describes the actual state of knowledge about the world, including all discoveries that have been made. The state of knowledge expands as the discovery process continues. Operational procedures are expanded and refined as a result of discoveries. Better procedures, in turn, allow FAHRENHEIT to collect better data and to improve its knowledge. The discovery method consists of a network of generic goals and plans for goal execution. Discovery goals require search, so most of the generic plans are solution schemes to search problems. All search problems are defined by the application of a uniform search template. Actual goals and plans executed at any given time form a recursive network of instances of generic goals and plans. The instances are selected based on the generic network of goals and plans, and the current state of knowledge. The selected plans are search instances. At any given time a number of search instances of various types may be in progress, each of them plan leading to new discoveries.

SITAR

SITAR, a low-cost interactive text handling and text analysis system for nontechnical users, is in many ways comparable to interactive bibliographical search and retrieval systems, but has several additional features. It is implemented on a PDP/11 time-sharing computer invoked by a CRT with microprogrammed editing functions. It uses a simple command language designating a function, a file, and a search template consisting of the textual string desired and strings delimiting the context in which the hit is to be delivered. Extensive experience with SITAR shows that the combined powers of simple commands, string orientation, circular file structure, a CRT with local memory, and conversational computing produce a system much more powerful than the sum of its parts.