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PubMed2003

P systems with deadlock.

Rewriting P systems with parallel application of evolution rules, as defined in Besozzi et al. [Parallel rewriting P systems with deadlock. In: Hagiya, M., Ohuchi, A. (Eds.), Pre-Proceedings of DNA8 Conference, Hokkaido University, Japan, June 2002a, pp. 171-183], are considered here. Different kinds of parallelism methods are defined for string rewriting. The notion of deadlock is then introduced to describe situations where rules with mixed target indications are simultaneously applied to a common string. The generative power of parallel P systems with deadlock is analyzed, with respect to Lindenmayer systems, and some relations among different types of parallel P systems with or without deadlock, allowing to rewrite all occurrences of a single symbol, or all the symbols applying either any of the rules or only those belonging to a specific set (table) of rules are studied. Some open problems are also formulated.

Algorithms↗
PubMed2005

Methods of translating NMR proton distances into their corresponding heavy atom distances for protein structure prediction with limited experimental data.

This paper proposes a strategy to translate experimental 1H NMR proton distance restraints into their corresponding heavy atom distance restraints for the purpose of protein structure prediction. The relationships between interproton distances and the corresponding heavy atom distances are determined by studying well-resolved X-ray protein structures. The data from the interproton distances of amide protons, alpha-protons, beta-protons and side chain methyl protons are plotted against the corresponding heavy atoms in scatter plots and then fitted with linear equations for lower bounds, upper bounds and optimal fits. We also transform the scatter plots into two-dimensional heat maps and three-dimensional histograms, which identify the regions where data points concentrate. The common interproton distances between amide protons, alpha-protons, beta-protons in alpha-helices, anti-parallel beta-sheets and parallel beta-sheets are also tabulated. We have found several patterns emerging from the distance relationships between heavy atom pairs and their corresponding proton pairs. All our upper bound, lower bound and optimal fit results for translating the interproton distance into their corresponding heavy atom distances are tabulated.

Algorithms↗
PubMed2005

Precise robot-assisted guide positioning for distal locking of intramedullary nails.

This paper presents a novel image-guided robot-based system to assist orthopedic surgeons in performing distal locking of long bone intramedullary nails. The system consists of a bone-mounted miniature robot fitted with a drill guide that provides rigid mechanical guidance for hand-held drilling of the distal screws' pilot holes. The robot is automatically positioned so that the drill guide and nail distal locking axes coincide, using a single fluoroscopic X-ray image. Since the robot is rigidly attached to the intramedullary nail or bone, no leg immobilization or real-time tracking is required. We describe the system and protocol and present a method for accurate and robust drill guide and nail hole localization and registration. The in vitro system accuracy experiments for fronto-parallel viewing show a mean angular error of 1.3 degrees (std = 0.4 degrees ) between the computed drill guide axes and the actual locking holes axes, and a mean 3.0 mm error (std = 1.1 mm) in the entry and exit drill point, which is adequate for successfully locking the nail.

Algorithms↗
PubMed2004

Ancestral inference on gene trees under selection.

The extent to which natural selection shapes diversity within populations is a key question for population genetics. Thus, there is considerable interest in quantifying the strength of selection. A full likelihood approach for inference about selection at a single site within an otherwise neutral fully linked sequence of sites is described here. A coalescent model of evolution is used to model the ancestry of a sample of DNA sequences which have the selected site segregating. The mutation model, for the selected and neutral sites, is the infinitely many-sites model where there is no back or parallel mutation at sites. A unique perfect phylogeny, a gene tree, can be constructed from the configuration of mutations on the sample sequences under this model of mutation. The approach is general and can be used for any bi-allelic selection scheme. Selection is incorporated through modelling the frequency of the selected and neutral allelic classes stochastically back in time, then using a subdivided population model considering the population frequencies through time as variable population sizes. An importance sampling algorithm is then used to explore over coalescent tree space consistent with the data. The method is applied to a simulated data set and the gene tree presented in Verrelli et al. (2002).

Genetic Variation↗
PubMed1998

Measurement-based evaluation of optical pathlength distributions reconstructed from simulated differential interference contrast images.

Recently a method was presented for reconstructing optical pathlength distributions (OPDs) from images of weak phase objects obtained by a conventional differential interference contrast (DIC) microscope. A potential application of this technique is the determination of the mass of biological objects: by integrating the optical pathlength over the projected surface of the image of an object, a measure of the dry mass, i.e. the total mass of all solid constituents present in the object, is obtained. To assess the possibilities of DIC microscopy for this application, simulations were performed on computer-generated DIC images of objects of various sizes, shapes and orientation angles. After reconstructing the OPDs from these images, the integrated optical pathlength of each of the test objects was determined, and compared with the expected results. The parameter settings used in the reconstruction algorithm were found to be very important in obtaining a reliable measurement. Using optimal parameter settings, errors in the integrated OPD could be limited to a few per cent for circular objects within the investigated size range. For non-circular objects, however, the orientation angle of the object relative to the lateral shift was found to influence the measured values. Ellipses with their long axes perpendicular to the shift direction had a significantly higher integrated OPD than ellipses orientated parallel to the shift. By adjusting the reconstruction parameters the effect could be limited, but complete elimination of the artefact was not possible within the parameter range investigated.

Journal Article↗
PubMed2003

Deep brain stimulation of the subthalamic nucleus in Parkinson's disease: evaluation of active electrode contacts.

BACKGROUND: The subthalamic nucleus is the preferred target for deep brain stimulation in patients with advanced Parkinson's disease. The site of permanent stimulation is the subject of ongoing debate, as stimulation both within and adjacent to the subthalamic nucleus may be effective. OBJECTIVE: To assess the position of active electrode contacts in relation to the dorsal margin of the subthalamic nucleus as determined by intraoperative microrecordings and magnetic resonance imaging (MRI). METHODS: In 25 patients suffering from severe levodopa sensitive parkinsonism, deep brain stimulating electrodes (n = 49) were implanted following mapping of the subthalamic nucleus by microrecording and microstimulation along five parallel tracks. Postoperative stereotactic radiography and fusion of pre- and postoperative MRI studies were used to determine the stereotactic position relative to the midcommissural point of the most effective electrode contacts selected for permanent stimulation (n = 49). Intraoperative microrecordings were analysed retrospectively to define the dorsal margin of the subthalamic nucleus. In cases where the dorsal margin could be defined in at least three microrecording tracks (n = 37) it was correlated with the position of the active contact using an algorithm developed for direct three dimensional comparisons. RESULTS: Stimulation of the subthalamic nucleus resulted in marked improvement in levodopa sensitive parkinsonian symptoms and levodopa induced dyskinesias, with significant improvement in UPDRS III scores. In several instances, projection of the electrode artefacts onto the T2 weighted MRI visualised subthalamic nucleus of individual patients suggested that the electrodes had passed through the subthalamic nucleus. When the actual position of active electrode contacts (n = 35) was correlated with the dorsal margin of the subthalamic nucleus as defined neurophysiologically, most contacts were located either in proximity (+/- 1.0 mm) to the dorsal border of the subthalamic nucleus (32.4%) or further dorsal within the subthalamic region (37.8%). The other active contacts (29.7%) were detected within the dorsal (sensorimotor) subthalamic nucleus. The average position of all active contacts (n = 49) was 12.8 mm (+/- 1.0) lateral, 1.9 mm (+/- 1.4) posterior, and 1.6 mm (+/- 2.1) ventral to the midcommissural point. CONCLUSIONS: Subthalamic nucleus stimulation appears to be most effective in the border area between the upper subthalamic nucleus (sensorimotor part) and the subthalamic area containing the zona incerta, fields of Forel, and subthalamic nucleus projections.

Aged↗
PubMed2006

Revisiting the metabolic syndrome.

Metabolic syndrome (MS) refers to the clustering of cardiometabolic risk factors - including abdominal obesity, hyperglycaemia, dyslipidaemia and elevated blood pressure - that are thought to be linked to insulin resistance. MS is associated with increased risk of cardiovascular disease and type 2 diabetes. MS is common, affecting a quarter to a third of adults, and its prevalence is rising, in parallel with increasing obesity and population ageing. Operational definitions of MS have been proposed by the World Health Organization and the National Cholesterol Education Program. Recently, the International Diabetes Federation proposed a global definition that emphasised the importance of central adiposity. In cardiovascular risk assessment, MS encapsulates the contribution of non-traditional risk factors and provides a clinically useful framework for early identification of people at increased long-term risk. It should be used in conjunction with standard algorithms based on conventional risk factors, which better predict short-term risk. Management of MS should emphasise lifestyle interventions (eg, physical activity, healthy diet and weight reduction) to reduce long-term risk of cardiovascular disease and diabetes. Those at increased short-term risk should also have individual risk factors treated according to established guidelines.

Cardiovascular Diseases↗
PubMed2005

Focused, eight-element transceive phased array coil for parallel magnetic resonance imaging of the chest--theoretical considerations.

A new transceive system for chest imaging for MRI applications is presented. A focused, eight-element transceive torso phased array coil is designed to investigate transmitting a focused radiofrequency field deep within the torso and to enhance signal homogeneity in the heart region. The system is used in conjunction with the SENSE reconstruction technique to enable focused parallel imaging. A hybrid finite-difference-time-domain/method-of-moments method is used to accurately predict the radiofrequency behavior inside the human torso. The simulation results reported herein demonstrate the feasibility of the design concept, which shows that radiofrequency field focusing with SENSE reconstruction is theoretically achievable.

Algorithms↗
PubMed1996

Analysis of domain structural class using an automated class assignment protocol.

The extent to which the contemporary dataset of protein structures can be segregated into four structural "classes" as originally defined by Levitt & Chothia in 1976 is examined and a simple method presented for the assignment of protein domains into these classes. Assignments are based on known three-dimensional structures, and for successful assignment it was found that helix/sheet content, contacts between secondary structures and their sequential order had to be used. The procedure attempts to maximise the automatic separation into classes for a dataset of 197 manually classified, non-homologous domains. It was found that approximately 90% of the structures were classified automatically; the remainder were borderline and were left for manual inspection. The method was then applied to a test set of 43 protein domains with similar results. The data support the concept of distinct classes of protein structure, although a few intermediate structures are found, demonstrating that it is possible to define relatively simple parameters complying with commonly accepted nomenclature that automatically define 90% of protein domains with essentially 100% accuracy. However, re-examination of the data also suggested that the previously separate alpha/beta and alpha + beta classes show considerable overlap and are more naturally represented as a single alpha beta class. This large alpha beta class can then be most easily subdivided by consideration of whether the sheets are mainly parallel, antiparallel or mixed. The correlation between structural class and function is discussed, together with the conservation of class within a sequence superfamily. This represents the first step in an automated phenetic description of protein structure complementing the usual phylogenetic approach to protein structure classification.

Algorithms↗
PubMed2003

Acetan:glucomannan interactions--a molecular modeling study.

X-ray fiber diffraction patterns from deacylated acetan and glucomannan (konjac mannan) blends are diagnostic of good orientation and modest polycrystallinity. The meridional reflection on the sixth layer line suggests that the binary complex is a 6-fold helix of pitch 55.4 A. A molecular modeling study incorporating this information reveals that a double helix in which one strand is acetan and the other glucomannan is stereochemically feasible. While the backbone and side groups are sufficiently flexible to allow the chains to associate with the same or opposite polarity, the parallel model is superior in terms of unit cell packing. The results are compatible with the observed synergy; namely the weak gelation behavior of the complex. The molecular model can be generalized for the binary system when acetan is replaced by xanthan or glucomannan by galactomannan.

Acetylation↗
PubMed2005

ROI-based image registration for digital subtraction radiography.

OBJECTIVE: We evaluated the influence of surrounding anatomical structures on the registration accuracy of a diagnostically important region, by varying the ROI (region of interest) window used in an automatic ROI-based digital subtraction method. STUDY DESIGN: Pairs of radiographs were taken at 2 molar regions using paralleling techniques of XCP devices (Rinn Co., Elgin, Ill) attached with and without a bite block. The global and local registration accuracies were measured by the RMS (root mean square) of subtraction images for various ROIs. RESULTS: No significant differences were found in global registration accuracies among various ROI sizes in all the paralleling techniques. The local registration accuracies decreased with extension of the ROI size. CONCLUSION: Registration using an ROI restricted to the anatomical region of diagnostic interest provides higher accuracy than using a larger ROI.

Algorithms↗
PubMed2004

Cognitive skill learning: age-related differences in strategy shifts and speed of component operations.

Younger and older adults solved novel arithmetic problems and reported the strategies used for obtaining solutions. Age deficits were demonstrated in the latencies for computing and retrieving solutions and in the shift from computation to retrieval. Rates of improvement within age groups were parallel for computations and retrievals, suggesting a single, age-attenuated mechanism that affects practice-related speedup. The age-related delay in strategy shift suggests either reluctance to use retrieval or an associative memory deficit. Experiment 1 showed that skill acquisition was unaffected by the presence and frequency of postresponse strategy probes for both age groups. Experiment 2 showed that pretraining item-learning operations facilitated subsequent item learning and that pretraining either item-learning operations or the algorithm did not alter the age trends.

Adult↗
PubMed2004

A graph-theoretic modeling on GO space for biological interpretation of gene clusters.

MOTIVATION: With the advent of DNA microarray technologies, the parallel quantification of genome-wide transcriptions has been a great opportunity to systematically understand the complicated biological phenomena. Amidst the enthusiastic investigations into the intricate gene expression data, clustering methods have been the useful tools to uncover the meaningful patterns hidden in those data. The mathematical techniques, however, entirely based on the numerical expression data, do not show biologically relevant information on the clustering results. RESULTS: We present a novel methodology for biological interpretation of gene clusters. Our graph theoretic algorithm extracts common biological attributes of the genes within a cluster or a group of interest through the modified structure of gene ontology (GO) called GO tree. After genes are annotated with GO terms, the hierarchical nature of GO terms is used to find the representative biological meanings of the gene clusters. In addition, the biological significance of gene clusters can be assessed quantitatively by defining a distance function on the GO tree. Our approach has a complementary meaning to many statistical clustering techniques; we can see clustering problems from a different viewpoint by use of biological ontology. We applied this algorithm to the well-known data set and successfully obtained the biological features of the gene clusters with the quantitative biological assessment of clustering quality through GO Biological Process.

Algorithms↗
PubMed1984

Control of complex motor gestures: orofacial muscle responses to load perturbations of lip during speech.

The contribution of ascending afferents to the control of speech movement was evaluated by applying unanticipated loads to the lower lip during the generation of combined upper lip-lower lip speech gestures. To eliminate potential contamination due to anticipation or adaptation, loads were applied randomly on only 10-15% of the trials. Physical characteristics of the perturbations were within the normal range of forces and movements involved in natural lip actions for speech. Compensatory responses in multiple facial muscles and lip movements were observed the first time a load was introduced, and achievement of the multimovement speech goals was never disrupted by these perturbations. Muscle responses were seen in the lower lip muscles, implicating corrective, feedback processes. Additionally, compensatory responses to these lower lip loads were also observed in the independently controlled muscles of the upper lip, reflecting the parallel operation of open-loop, sensorimotor mechanisms. Compensatory responses from both the upper and lower lip muscles were observed with small (1 mm) as well as large (15 mm) perturbations. The latencies of these compensatory responses were not discernible by conventional ensemble averaging. Moreover, responses at latencies of lower brain stem-mediated reflexes (i.e., 10-18 ms) were not apparent with inspection of individual records. Response latencies were determined on individual loaded trials through the use of a computer algorithm that took into account the variability of electromyograms (EMG) among the control trials. These latency measures confirmed the absence of brain stem-mediated responses and yielded response latencies that ranged from 22 to 75 ms. Response latencies appeared to be influenced by the time relation between load onset and the initiation of muscle activation. Examination of muscle activity changes for individual loaded trials revealed complementary variations in the magnitude of responses among multiple muscles contributing to a movement compensation. These observations may have implications for limb movement control if multimovement speech gestures are considered analogous to a limb action requiring coordinated movements around multiple joints. In this context, these speech motor control data might be interpreted to suggest that for complex movements, both corrective feedback and open-loop predictive processes are operating, with the latter involved in the control of coordination among multiple movement subcomponents.

Electromyography↗
PubMed2005

Comparison of basal insulin added to oral agents versus twice-daily premixed insulin as initial insulin therapy for type 2 diabetes.

OBJECTIVE: To compare the efficacy and safety of adding once-daily basal insulin versus switching to twice-daily premixed insulin in type 2 diabetic patients insufficiently controlled by oral antidiabetic agents (OADs). RESEARCH DESIGN AND METHODS: In a 24-week, multinational, multicenter, open, parallel group clinical trial, 371 insulin-naive patients with poor glycemic control (fasting blood glucose [FBG] >/=120 mg/dl, HbA(1c) 7.5-10.5%) on OADs (sulfonylurea plus metformin) were randomized to once-daily morning insulin glargine plus glimepiride and metformin (glargine plus OAD) or to 30% regular/70% human NPH insulin (70/30) twice daily without OADs. Insulin dosage was titrated to target FBG </=100 mg/dl (both insulins) and predinner blood glucose </=100 mg/dl (70/30 only) using a weekly forced-titration algorithm. RESULTS: Mean HbA(1c) decrease from baseline was significantly more pronounced (-1.64 vs. -1.31%, P = 0.0003), and more patients reached HbA(1c) </=7.0% without confirmed nocturnal hypoglycemia (45.5 vs. 28.6%, P = 0.0013) with glargine plus OAD than with 70/30. Similarly, FBG decrease was greater with glargine plus OAD (adjusted mean difference -17 mg/dl [-0.9 mmol/l], P < 0.0001), and more patients reached target FBG </=100 mg/dl with glargine plus OAD than with 70/30 (31.6 vs. 15.0%, P = 0.0001). Glargine plus OAD patients had fewer confirmed hypoglycemic episodes than 70/30 patients (mean 4.07 vs. 9.87/patient-year, P < 0.0001). CONCLUSIONS: Initiating insulin treatment by adding basal insulin glargine once daily to glimepiride plus metformin treatment was safer and more effective than beginning twice-daily injections of 70/30 and discontinuing OADs in type 2 diabetic patients inadequately controlled with OADs.

Adult↗
PubMed2004

Convex dynamics: unavoidable difficulties in bounding some greedy algorithms.

A greedy algorithm for scheduling and digital printing with inputs in a convex polytope, and vertices of this polytope as successive outputs, has recently been proven to be bounded for any convex polytope in any dimension. This boundedness property follows readily from the existence of some invariant region for a dynamical system equivalent to the algorithm, which is what one proves. While the proof, and some constructions of invariant regions that can be made to depend on a single parameter, are reasonably simple for convex polygons in the plane, the proof of boundedness gets quite complicated in dimension three and above. We show here that such complexity is somehow justified by proving that the most natural generalization of the construction that works for polygons does not work in any dimension above two, even if we allow for as many parameters as there are faces. We first prove that some polytopes in dimension greater than two admit no invariant region to which they are combinatorially equivalent. We then modify these examples to get polytopes such that no invariant region can be obtained by pushing out the borders of the half spaces that intersect to form the polytope. We also show that another mechanism prevents some simplices (the simplest polytopes in any dimension) from admitting invariant regions to which they would be similar. By contrast in dimension two, one can always get an invariant region by pushing these borders far enough in some correlated way; for instance, pushing all borders by the same distance builds an invariant region for any polygon if the push is at a distance big enough for that polygon. To motivate the examples that we provide, we discuss briefly the bifurcations of polyhedra associated with pushing half spaces in parallel to themselves. In dimension three, the elementary codimension one bifurcation resembles the unfolding of the elementary degenerate singularity for codimension one foliations on surfaces. As the subject of this paper is new for the communities most interested in Chaos, we take some care in describing various links of our problem to classical issues (in particular linked to Diophantine approximation) as well as to various technological or commercial issues, exemplified, respectively, by digital printing and a problem in scheduling.

Algorithms↗
PubMed2006

Synthesis, crystal structure and DNA binding studies of a binuclear copper(II) complex with phenanthroline.

A new binuclear copper(II) complex, [Cu2Phen2Cl4] (Phen=1,10-phenanthroline), has been synthesized and characterized. Single crystal X-ray diffraction results suggest that this complex structure belongs to monoclinic crystal system, Cc (no. 9) with the cell dimensions: a=9.849(2)A, b=17.833(4)A, c=13.374(3)A, beta=106.61(3) degrees , V=2251.0(8)A(3), Dc=1.8569 Mgm(-3), F(000)=1256.0, Z=4. One Cu(II) central atom situated in a distorted square planar geometry is four-coordinated. The other situated in a distorted square pyramidal geometry is five-coordinated. Only one bridging Cl atom exists in the complex. Spectroscopic studies, including electronic absorption and fluorescence spectra, conductivity measurements and parallel factor analysis (PARAFAC) of fluorescence excitation-emission three-way data array, were carried out on the DNA binding behavior of the complex. All the results suggested that the breakage of DNA secondary structure took place at low molar ratio of complex to DNA (0.3 at most) and intercalation into the base pair of DNA took place at high molar ratio. Additionally, the equilibrium concentration of EB-DNA and EB (EB: ethidium bromide) could be directly obtained by PARAFAC algorithm, proved to be a convincing method for studying the interaction of complexes with DNA.

Copper↗
PubMed1995

Pruning of rat cortical taste neurons by an artificial neural network model.

1. Taste qualities are believed to be coded in the activity of ensembles of taste neurons. However, it is not clear whether all neurons are equally responsible for coding. To clarify the point, the relative contribution of each taste neuron to coding needs to be assessed. 2. We constructed simple three-layer neural networks with input units representing cortical taste neurons of the rat. The networks were trained by the back-propagation learning algorithm to classify the neural response patterns to the basic taste stimuli (sucrose, HCl, quinine hydrochloride, and NaCl). The networks had four output units representing the basic taste qualities, the values of which provide a measure for similarity of test stimuli (salts, tartaric acid, and umami substances) to the basic taste stimuli. 3. Trained networks discriminated the response patterns to the test stimuli in a plausible manner in light of previous physiological and psychological experiments. Profiles of output values of the networks paralleled those of across-neuron correlations with respect to the highest or second-highest values in the profiles. 4. We evaluated relative contributions of input units to the taste discrimination of the network by examining their significance Sj, which is defined as the sum of the absolute values of the connection weights from the jth input unit to the hidden layer. When the input units with weaker connection weights (e.g., 15 of 39 input units) were "pruned" from the trained network, the ability of the network to discriminate the basic taste qualities as well as other test stimuli was not greatly affected. On the other hand, the taste discrimination of the network progressively deteriorated much more rapidly with pruning of input units with stronger connection weights. 5. These results suggest that cortical taste neurons differentially contribute to the coding of taste qualities. The pruning technique may enable the evaluation of a given taste neuron in terms of its relative contribution to the coding, with Sj providing a quantitative measure for such evaluation.

Animals↗