Individual Template Research Articles

Single-step fronto-orbital resection and reconstruction with individual resection template and corresponding titanium implant: a new method of computer-aided surgery

In the cranio-maxillofacial field, computer-aided surgery based on computed tomography (CT) data is becoming more and more important. Navigation systems, which allow the precise intraoperative orientation of surgical instruments, can be used for greater accuracy in determining resection margins of tumours. These techniques support ablative procedures very well, but defect reconstruction still remains a problem. In contrast, computer-aided design (CAD) and computer-aided manufacturing (CAM) systems allow the construction and fabrication of individual templates for bone resection based on coherent numerical 3-D models. The template determines the exact pathway of an oscillating saw so that the planned extent of the resection and, if necessary, also the orientation of the cutting plane are verified. An individual titanium implant is prefabricated with a geometry fitting to that of the template. This implant closes the bone defect so that the contour is reconstructed precisely and individually. This new method was used for the first time for a single-step resection of a meningioma and defect-reconstruction. The tumour which had infiltrated the frontal bone resulting in a protrusion. Fronto-orbital resection and insertion of the titanium implant worked precisely as planned, so that this method offers promising new applications in the field of computer-aided surgery.

Computer-assisted bone segment navigation

Computer-assisted bone segment navigation is defined as the precise 3-D positioning of geometrically mapped and mathematically described skeletal segments. These bone segments are osteotomized, fractured or prefabricated according to a surgical plan. The high-precision positioning should have an accuracy of 1 mm or better. Segment navigation should be prepared with plain computed tomography (CT) without the implantation of registration markers before CT in order to reduce the number of CTs and operations. The Surgical Segment Navigator (SSN) was developed at the University of Regensburg with the support of Carl Zeiss. This is the first system to meet these criteria. The SSN is based on an infrared positioning device which is connected to a Hewlett Packard LD Pro Workstation. Infrared transmitters are connected to individual templates which are fixed to the bone segment by osteosynthesis screws. Intraoperative correlation between surgical planning and surgical site is achieved by use of a surface-pattern of the bone segment which fits equally well to the laboratory model and the conditions encountered in the patient. The concept of the SSN was submitted by Carl Zeiss as German Patent DE 19747427 A1 in 1997. The SSN system presented here has already been applied clinically and its precision has been evaluated by bone segment navigation in human cadavers.

In vitro method for the generation of protein libraries using PCR amplification of a single DNA molecule and coupled transcription/translation.

A novel in vitro method for the generation of a protein library has been developed using the polymerase chain reaction (PCR) amplification of a single DNA molecule followed by in vitro coupled transcription/translation. DNA template encoding green fluorescent protein of a jellyfish Aequorea victoria was extensively diluted to one molecule per well, and then amplified by a total of 80 cycles of PCR with nested primers. The exact number of origins in the amplified DNA fragment was then estimated by directly sequencing a part of the fragment, at which an individual template molecule was marked by PCR with a primer containing three randomized bases. Since the sequences obtained in 91 independent amplifications were diversified statistically, each amplified fragment was likely originated from a single DNA molecule. In addition, the amplified fragments served as a template for in vitro coupled transcription/translation using T7 RNA polymerase and Escherichia coli S30 extract. These results suggest that the library obtained by the PCR amplification of a single DNA molecule diluted from a variety of DNA pools is potentially useful in high-throughput generation of protein libraries.

Computer assisted orthopaedic surgery with image based individual templates.

Recent developments in computer assisted surgery offer promising solutions for the translation of the high accuracy of the preoperative imaging and planning into precise intraoperative surgery. Broad clinical application is hindered by high costs, additional time during intervention, problems of intraoperative man and machine interaction, and the spatially constrained arrangement of additional equipment within the operating theater. An alternative technique for computerized tomographic image based preoperative three-dimensional planning and precise surgery on bone structures using individual templates has been developed. For the preoperative customization of these mechanical tool guides, a desktop computer controlled milling device is used as a three-dimensional printer to mold the shape of small reference areas of the bone surface automatically into the body of the template. Thus, the planned position and orientation of the tool guide in spatial relation to bone is stored in a structural way and can be reproduced intraoperatively by adjusting the position of the customized contact faces of the template until the location of exact fit to the bone is found. No additional computerized equipment or time is needed during surgery. The feasibility of this approach has been shown in spine, hip, and knee surgery, and it has been applied clinically for pelvic repositioning osteotomies in acetabular dysplasia therapy.

Is There a “Trochaic Bias” in Early Word Learning? Evidence from Infant Production in English and French

Studies of speech perception and segmentation in the prelinguistic period, early word production, and patterns of function word omission in early syntax have all recently emphasized the role of the trochaic accentual pattern in English, sometimes positing a universal trochaic bias. We make use of perceptual and acoustic analyses of words and babble from 9 children acquiring English and 5 acquiring French in the late single-word period (13-20 months) to provide a direct test for the existence of such a bias. Neither English nor French infant vocalizations were exclusively trochaic. The iambic productions of American infants were traced to the presence of iambic phrases in the input. Differences between English and French in the acoustic realization of accent in infant vocalizations were also traceable to adult patterns. However, the almost bipolar distribution of trochaic and iambic patterns in the data from English-learning infants was ultimately traceable to the integration of prosodic and segmental patterning in individual child word production templates, themselves arguably the product of an earlier acting articulatory filter.

Rho-dependent termination within the trp t' terminator. I. Effects of rho loading and template sequence.

About one-half of the terminators of the Escherichia coli genome require transcription termination factor rho to function. Here we use the very "diffuse" trp t' terminator of E. coli to show that both template sequence and transcript secondary structure are involved in controlling the template positions and efficiencies of rho-dependent termination. Termination begins in the wild-type trp t' terminator sequence approximately 97 bps downstream of the promoter under our standard reaction conditions, and termination efficiencies for individual positions on three related templates have been determined in the form of quantitative patterns of rho-dependent RNA release. Comparison of these patterns shows that the rho-dependent termination efficiency at individual template positions depends primarily on the nucleotide sequence at and near the putative 3' end of the transcript, although these efficiencies can also be influenced by RNA sequence elements located further upstream. The amplitudes of the peaks of the RNA release patterns at specific template positions are controlled primarily by the effectiveness of the binding of the rho hexamer to the "rho loading site" of the transcript. Introduction of a stable element of secondary structure into the nascent RNA within the loading site both shifts the position of initial rho-dependent termination downstream and decreases the amplitudes of the peaks of the RNA release pattern at the corresponding sequences. These results and others are consistent with the view that rho-dependent terminators contain two essential components: (i) an upstream rho loading site on the RNA that is 70-80 nucleotide residues in length, essentially devoid of secondary structure, and which contains sufficient numbers of rC residues to activate the RNA-dependent ATPase of rho; and (ii) a downstream sequence within which termination actually occurs. In this study we use the trp t' terminator to characterize the involvement of each of these sequence components in detail in order to provide the parameters required to define a quantitative mechanistic model for the function of rho in transcript termination.

Modelling Crack Propagation in Anisotropic Media

Based on the asymptotic crack tip characteristics of anisotropic elasticity, a moving template finite element simulation scheme is developed to establish the stress intensity factors of multiple cracks in materials with directionally dependent mechanical properties. This is achieved from a hierarchical point of view wherein a global finite element model is recursively used to obtain the boundary condition information (deflections/forces) for the templates, i.e. 2nd level finite element mesh attached to the various cracks associated with a given structure. The many crack wakes in the global model are defined through the use of birth and death elements which are themselves handled hierarchically. The individual templates are solved separately so that their associated embedded singularities can be employed to determine local crack tip physics. The procedure provides the capability to handle both directional stiffness, strength and fatigue property variations. This is achieved by reinterpreting the tip physics from a probabilistic point of view. The result is a new scheme to define cracking directionality. Overall, the procedure provides such information as the mean cracking direction, as well as higher order probabilistic properties, the standard deviation, skewness, multimodality, kurtosis, i.e. lepto/platekurticity and so on. Due to the generality of the moving scheme, propagating multiple cracks can be simulated along with their joint interactions/shading effects. To demonstrate the scheme, several example problems are included. These both illustrate the effects of material anisotropy, as well as benchmark the procedures overall accuracy in correlations with available simulations.

Automatic Redshift Determination by Use of Principal Component Analysis. I. Fundamentals

With the advent of very large redshift surveys of tens to hundreds of thousands of galaxies reliable techniques for automatically determining galaxy redshifts are becoming increasingly important. The most common technique currently in common use is the cross-correlation of a galactic spectrum with a set of templates. This series of papers presents a new method based on Principal Component Analysis. The method generalizes the cross-correlation approach by replacing the individual templates by a simultaneous linear combination of orthogonal templates. This effectively eliminates the mismatch between templates and data and provides for the possibility of better error estimates. In this paper, the first of a series, the basic mathematics are presented along with a simple demonstration of the application.

Spectral envelope and context effects in the tritone paradox.

In previous studies of the 'tritone paradox' Deutsch has suggested that, when listeners are presented with pairs of octave-complex tones that are equal in average log frequency but differ in chroma by 6 semitones (a tritone), they perceive the direction of the chroma difference according to an individual pitch-class template. However, it has also been found that the perceived direction changes for many listeners when the spectral envelope of the tones is shifted along the frequency axis. Reanalysis of these data indicates a strong tendency to perceive the pitch class corresponding to the frequency on which the spectral envelope is centered as subjectively lowest. In experiment 1 this spectral-envelope effect was replicated with tone pairs presented in isolation, at the rate of one a day, which rules out artifacts of test format. In experiment 2, involving another context-free format, envelope center frequency was varied over a wide range and it was shown that some individuals are totally envelope dependent, whereas others rely more on pitch class, and yet others show mixed patterns. Experiment 3 demonstrated that listeners' judgments of tritone pairs can be swayed easily by preceding context. Finally, experiment 4 showed that strong envelope effects are also obtained with Deutsch's own tritone test (issued on CD). The subjective relative pitch height of octave-complex tones thus depends on several competing factors, only one of which is pitch class.

Individual prostheses and resection templates for mandibular resection and reconstruction — Introduction of a new technique

Individual prostheses and resection templates for mandibular resection and reconstruction — Introduction of a new technique

In situ isolation of mRNA from individual plant cells: creation of cell-specific cDNA libraries.

A method for isolating and cloning mRNA populations from individual cells in living, intact plant tissues is described. The contents of individual cells were aspirated into micropipette tips filled with RNA extraction buffer. The mRNA from these cells was purified by binding to oligo(dT)-linked magnetic beads and amplified on the beads using reverse transcription and PCR. The cell-specific nature of the isolated mRNA was verified by creating cDNA libraries from individual tomato leaf epidermal and guard cell mRNA preparations. In testing the reproducibility of the method, we discovered an inherent limitation of PCR amplification from small amounts of any complex template. This phenomenon, which we have termed the "Monte Carlo" effect, is created by small and random differences in amplification efficiency between individual templates in an amplifying cDNA population. The Monte Carlo effect is dependent upon template concentration: the lower the abundance of any template, the less likely its true abundance will be reflected in the amplified library. Quantitative assessment of the Monte Carlo effect revealed that only rare mRNAs (< or = 0.04% of polyadenylylated mRNA) exhibited significant variation in amplification at the single-cell level. The cDNA cloning approach we describe should be useful for a broad range of cell-specific biological applications.

The Tritone Paradox and the Pitch Range of the Speaking Voice: A Dubious Connection

Deutsch and coworkers (Deutsch, 1991; Deutsch, North, &amp; Ray, 1990) have proposed that individual differences in the perception of the "tritone paradox" derive from listeners' reference to a mental pitch template, acquired through experience with the pitch range of their own voice, as well as with the voice ranges typical of their language community. These authors have reported a correspondence between perceptual results and the upper limit of the individual voice range for a small group of selected subjects, as well as a striking difference in tritone perception between American and British listeners. The present study compared groups of Dutch, British, and American listeners on two tritone tests and also collected voice pitch data for the first two groups in a reading task. There was no within-group correlation of perceptual results with individual differences in voice range. Differences in tritone perception as a function of stimulus characteristics (spectral envelope) were much larger than reported by Deutsch, which casts doubt on the notion of stable individual pitch templates. A significant difference between British and American listeners, with the Dutch group in between, was found in one of the two tritone tests but not in the other. Although the origin of this difference remains unclear, it seems unlikely that it has anything to do with regional differences in voice pitch range.

Molecular dynamics conformational search of six cyclic peptides used in the template assembled synthetic protein approach for protein de novo design.

Six cyclic peptides, designed to act as topological templates in the TASP (template assembled synthetic protein) approach in protein de novo design, were investigated employing a 100-ps, 900-K molecular dynamics conformational search. The peptides are composed of two Lys-X-Lys (X = Gly, Ala) tripeptides connected at its N- and C-terminal end by a Pro-Gly motif and a cystine bridge (I), two Pro-Gly units (II), naphthalene derivatives (III), and tetrahydronaphthalene derivatives of different stereochemistry (IV-VI). The molecular dynamics conformational search established that template I had beta-sheet like geometry. Templates II-VI showed different preferential geometries, among them, e.g., distinct preferences for type V turns in Pro-Gly containing peptides and close spatial arrangement of hydrophobic naphthalene moieties. The orientation of the lysine side chains within preferential geometries of the individual templates is analyzed and a tentative evaluation for their potential to stabilize TASP molecules of 4-helix bundle topology is given.

Nonspecific primer and PCR generated hybridization probes for physical ordering large restriction fragments in complex genome of S. aureus

Pulsed field gel electrophoresis (PFGE) allows separation of large restriction fragments from bacterial genome. Restriction fragments obtained by digestion of Staphylococcus aureus DNA with rare cutting enzymes (Sma I, and Csp I) were separated by PFGE. To arrange the physical order of the fragments generated by digestion with one enzyme, probes were prepared by nonspecific priming and polymerase chain reaction (PCR), using individual fragments of the other enzymatic digest as a template. Probes were then used for Southern hybridization to the PFGE separated fragment distribution of the two infrequent cleaving enzymes (Sma I and Csp I). Using probes generated from four Sma I fragments and five Csp I fragments as individual templates, a partial physical order of Csp I fragments of the genome of S. aureus ISP8 has been determined in relation to a previously published Sma I map of S. aureus genome.

The dose dependence of glucocorticoid-inducible gene expression results from changes in the number of transcriptionally active templates.

Glucocorticoid hormones induce the transcription of genes having glucocorticoid response elements in a dose dependent manner. To determine whether this dose dependence represents a response of individual templates or of the mass of templates, we introduced a bacterial beta-galactosidase gene linked to the glucocorticoid-inducible enhancer/promoter of the mouse mammary tumor virus (MTV) into Ltk- cells and obtained stable transformants containing a single or a few templates per cell. Visual inspection and flow cytometry analysis by enzyme histochemistry assay for beta-galactosidase revealed that individual cells showed very heterogeneous beta-galactosidase activity after 48 h induction with dexamethasone. When the glucocorticoid concentration was increased, an increasing cell population producing beta-galactosidase was observed. These phenomena were probably not due to heterogeneity of template copy number or to a predetermined cellular state among individual cells, since cells forming a single small colony gave similar results. This was also supported by data showing that recloned cells retained both their responsiveness to the glucocorticoid hormone and their digestion pattern in Southern blotting analyses. These results indicate that the dose dependent increase of glucocorticoid-inducible gene expression is caused by an increase in the number of transcriptionally active templates.

Formation of stable transcription complexes as assayed by analysis of individual templates.

Conditions were established where transient transfection of two marker genes resulted in the expression of one or the other, but not both, in individual cells as assayed by immunofluorescence. Thus, the expression from a single cell reflects the activity of single active transcription templates. Under these conditions, a vector encoding the simian virus 40 large tumor antigen (SV40 T-Ag) driven by the SV40 enhancer and early promoter was transfected into CV-1, L, or HeLa cells yielding, for all three cell types, about 10-30% T-Ag-positive cells as assayed by immunofluorescence. Similar vectors containing either mutated or deleted SV40 enhancers also gave T-Ag-positive cells, but at about 1/100 the frequency. Quantitative analysis showed that T-Ag-positive cells produced about the same amount of T-Ag whether or not an active enhancer was present. Chloramphenicol acetyltransferase-encoding vectors gave the same result. The data are consistent with the hypothesis that at a low, but finite, probability, fully functional transcription complexes can form on a given active template in the absence of enhancer DNA. Enhancers seem to increase the number of active templates. Subcloning experiments suggest that these transcription complexes can be surprisingly stable.

Talker recognition in tandem with talker-independent isolated word recognition

A talker recognition system operating in tandem with a talker-independent isolated word recognizer is described and evaluated. The word recognizer uses a small set of reference templates for each vocabulary word. Each set is intended to span and typify individual talker templates over a large population of talkers. Word recognition decisions are based on template distance scores obtained by comparing processed input utterances to each set of reference templates. The distribution of distance scores for the templates corresponding to the actual word input has been found to be reasonably consistent for individual talkers, and to vary sufficiently from talker to talker to provide the basis for a talker recognition capability. A system has been implemented to exploit this capability. An evaluation of the system, carried out using a 100-talker database of digit utterances, shows that good talker recognition performance can be obtained for input utterances consisting of sequences of seven or more digits. Identification error rates varying from 3.6 to 14.0 percent for talker populations varying from 10 to 100 talkers are obtained. When the recognizer orders the talkers as candidates for recognition, the correct talker is found, on the average, among the top 0.8 percent of the population. Tested in a talker verification mode, the average error rate is approximately 8 percent.

Stress and vowel duration effects on syllable verification

Recognition system for continuous speech must be able to deal with many sources of acoustic variation, such as variation in stress. We have examined the performance of a speaker-dependent syllable recognition task for a small group of stressed and unstressed syllables. These syllables, some containing the long vowel /æ/ and others the short vowel /I/, were excised from continuous speech and parameterized in terms of mel-scale cepstral coefficients at two levels of precision. From these data, four types of template dictionaries were formed: A contained individual templates for each stressed and unstressed syllable, B contained templates formed by warping stressed and unstressed syllables together, C contained only stressed syllables, and D contained only unstressed syllables. The recognition error rate increased when the template dictionaries were used in the order A, B, C, and D. The results indicate that training data should contain stressed and unstressed tokens, but for most syllables these may be combined into one template. Further results point out conditions for which the inclusion of stress is of importance in dictionary construction. [Work supported by NSF grant MCS-7916177.]

Speaker recognition in conjunction with speaker independent word recognition

Our method for accomplishing speaker independent word recognition is to select a small set of word templates that typify and span individual speaker reference templates obtained from a large population of speakers. An unknown utterance is processed and compared with a set of such templates for each word in the vocabulary. Word recognition decision functions are based on combinations of template distances obtained in the comparison. In this study it is hypothesized that distributions of template distance scores are reasonably consistent for individual speakers and vary characteristically from speaker to speaker. This property is exploited to provide a speaker recognition capability in conjunction with speaker independent word recognition. It is shown that good speaker identification performance is dependent on the input of a sequence of distinct words. For a 20 speaker experimental population a mean speaker identification error less than 1% is obtained over a sequence of seven distinct words. Techniques are also described for grouping individual speaker references into class references.