Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “process mapping”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 523 records · Page 29Linked to original sources
PubMed2005

Variations in soil N cycling and trace gas emissions in wet tropical forests.

We used a previously described precipitation gradient in a tropical montane ecosystem of Hawai'i to evaluate how changes in mean annual precipitation (MAP) affect the processes resulting in the loss of N via trace gases. We evaluated three Hawaiian forests ranging from 2200 to 4050 mm year-1 MAP with constant temperature, parent material, ecosystem age, and vegetation. In situ fluxes of N2O and NO, soil inorganic nitrogen pools (NH4+ and NO3-), net nitrification, and net mineralization were quantified four times over 2 years. In addition, we performed 15N-labeling experiments to partition sources of N2O between nitrification and denitrification, along with assays of nitrification potential and denitrification enzyme activity (DEA). Mean NO and N2O emissions were highest at the mesic end of the gradient (8.7+/-4.6 and 1.1+/-0.3 ng N cm-2 h-1, respectively) and total oxidized N emitted decreased with increased MAP. At the wettest site, mean trace gas fluxes were at or below detection limit (<or=0.2 ng N cm-2 h-1). Isotopic labeling showed that with increasing MAP, the source of N2O changed from predominately nitrification to predominately denitrification. There was an increase in extractible NH4+ and decline in NO3- , while mean net mineralization and nitrification did not change from the mesic to intermediate sites but decreased dramatically at the wettest site. Nitrification potential and DEA were highest at the mesic site and lowest at the wet site. MAP exerts strong control N cycling processes and the magnitude and source of N trace gas flux from soil through soil redox conditions and the supply of electron donors and acceptors.

Ammonia↗
PubMed2006

Activity-independent prespecification of synaptic partners in the visual map of Drosophila.

Specifying synaptic partners and regulating synaptic numbers are at least partly activity-dependent processes during visual map formation in all systems investigated to date . In Drosophila, six photoreceptors that view the same point in visual space have to be sorted into synaptic modules called cartridges in order to form a visuotopically correct map . Synapse numbers per photoreceptor terminal and cartridge are both precisely regulated . However, it is unknown whether an activity-dependent mechanism or a genetically encoded developmental program regulates synapse numbers. We performed a large-scale quantitative ultrastructural analysis of photoreceptor synapses in mutants affecting the generation of electrical potentials (norpA, trp;trpl), neurotransmitter release (hdc, syt), vesicle endocytosis (synj), the trafficking of specific guidance molecules during photoreceptor targeting (sec15), a specific guidance receptor required for visual map formation (Dlar), and 57 other novel synaptic mutants affecting 43 genes. Remarkably, in all these mutants, individual photoreceptors form the correct number of synapses per presynaptic terminal independently of cartridge composition. Hence, our data show that each photoreceptor forms a precise and constant number of afferent synapses independently of neuronal activity and partner accuracy. Our data suggest cell-autonomous control of synapse numbers as part of a developmental program of activity-independent steps that lead to a "hard-wired" visual map in the fly brain.

Animals↗
PubMed2006

Dynamics and topographic organization of recursive self-organizing maps.

Recently there has been an outburst of interest in extending topographic maps of vectorial data to more general data structures, such as sequences or trees. However, there is no general consensus as to how best to process sequences using topographic maps, and this topic remains an active focus of neurocomputational research. The representational capabilities and internal representations of the models are not well understood. Here, we rigorously analyze a generalization of the self-organizing map (SOM) for processing sequential data, recursive SOM(RecSOM) (Voegtlin, 2002), as a nonautonomous dynamical system consisting of a set of fixed input maps. We argue that contractive fixed-input maps are likely to produce Markovian organizations of receptive fields on the RecSOM map. We derive bounds on parameter beta (weighting the importance of importing past information when processing sequences) under which contractiveness of the fixed-input maps is guaranteed. Some generalizations of SOM contain a dynamic module responsible for processing temporal contexts as an integral part of the model. We show that Markovian topographic maps of sequential data can be produced using a simple fixed (nonadaptable) dynamic module externally feeding a standard topographic model designed to process static vectorial data of fixed dimensionality (e.g., SOM). However, by allowing trainable feedback connections, one can obtain Markovian maps with superior memory depth and topography preservation. We elaborate on the importance of non-Markovian organizations in topographic maps of sequential data.

Algorithms↗
PubMed1995

Magnetic field tomography of cortical and deep processes: examples of "real-time mapping" of averaged and single trial MEG signals.

Magnetic field tomography (MFT) provides 3-dimensional estimates of brain activity, from non-contact, non-invasive measurements of the magnetic field generated by coherent electrical activity in the brain. MFT analysis of averaged auditory "odd-ball" data show cortical and deep activation, presumably from the amygdala and hippocampus. These results are compared with MFT estimates obtained from a patient who had undergone lobectomy which removed these structures. The variability from subject to subject is confounded by variability between trials for the same subject; the relationship between the averaged and single trials is probed by bi-hemispheric simultaneous measurements performed under the same odd-ball paradigm and by MFT analysis of auditory evoked data and interictal epileptic activity.

Acoustic Stimulation↗
PubMed2007

Rhyme processing in the brain: an ERP mapping study.

The event-related potential (ERP) N450 component has been described in rhyme detection tasks as a negative response elicited by non-rhyming words in comparison to rhyming ones. This response, which peaked around 450 ms over the midline and right hemisphere recording sites, has been subsequently suggested to start already at approximately 300 ms. Moreover, although, the phonological N450 has first been linked to the semantic N400 component, its cognitive nature and cerebral origin remained debated. In this study, we re-investigated the time course of the electrophysiological responses to rhyming and non-rhyming words and estimated their cerebral generators using source localization methods. Waveform analysis showed that, prior to the N450 response to non-rhyming, a slightly earlier negativity characterized the rhyming condition over left fronto-temporal electrodes and peaked at approximately 350 ms. The analysis of the ERP map series in terms of functional microstates revealed a specific map segment in the rhyming condition and another one in the non-rhyming condition. Source localization indicated that the rhyming-elicited microstate engaged predominantly left frontal and temporal areas while the non rhyming-specific response recruited temporal and parietal regions bilaterally. Our results suggest that, similar to the N400 component that is also induced by mismatch contexts, the N450 might rely on temporal generators.

Adult↗
PubMed1977

Genesis of body surface potential distribution in right bundle branch block.

In order to investigate the specific sites of conduction block in the three types (I, II, III) of right bundle branch block (RBBB) classified by body surface isopotential maps, the simulation of ventricular propagation process and mathematically reconstructed maps were used. Four assumptions were introduced from the results of clinical observations and animal experiments. The maps reconstructed from two of these assumptions, in which the conduction block was placed on the main stem of the right bundle branch, showed two different patterns at late stages of excitation, and these two kinds of map resembled Types I and II in clinical maps, respectively. The maps reconstructed from the other two assumptions, in which the site of the conduction block was located mainly in the Purkinje system of the right ventricular free wall, resembled Type I at the late stage of excitation in one of two assumptions and agreed with Type III through all stages of excitation in other case. Based on the above results, it is speculated that the differences of ranges and degrees of conduction block ascribed to abnormal activation in the Purkinje system of the right ventricular free wall are responsible for the genesis of clinical RBBB map patterns.

Bundle-Branch Block↗
PubMed2002

Clinical process analysis and activity-based costing at a heart center.

Cost studies, productivity, efficiency, and quality of care measures, the links between resources and patient outcomes, are fundamental issues for hospital management today. This paper describes the implementation of a model for process analysis and activity-based costing (ABC)/management at a Heart Center in Sweden as a tool for administrative cost information, strategic decision-making, quality improvement, and cost reduction. A commercial software package (QPR) containing two interrelated parts, "ProcessGuide and CostControl," was used. All processes at the Heart Center were mapped and graphically outlined. Processes and activities such as health care procedures, research, and education were identified together with their causal relationship to costs and products/services. The construction of the ABC model in CostControl was time-consuming. However, after the ABC/management system was created, it opened the way for new possibilities including process and activity analysis, simulation, and price calculations. Cost analysis showed large variations in the cost obtained for individual patients undergoing coronary artery bypass grafting (CABG) surgery. We conclude that a process-based costing system is applicable and has the potential to be useful in hospital management.

Cardiac Care Facilities↗
PubMed1999

Inhibition of p38 MAP kinase increases okadaic acid mediated AP-1 expression and DNA binding but has no effect on TRE dependent transcription.

By performing in vitro kinase assays we found in papilloma producing 308 mouse keratinocytes that okadaic acid elevated activities of extracellular signal-regulated kinase (ERK) 1/2, c-Jun N-terminal kinases (JNKs) and p38 mitogen-activated protein kinases (MAPKs). This okadaic acid mediated activation of MAP kinases correlated with increased AP-1 binding to a consensus TPA responsive element (TRE) and elevated TRE dependent transcription. To determine the role of p38 MAP kinases in these processes we employed the specific p38 MAP kinase inhibitor SB 203580. Using orthophosphate labeling we showed a decrease in phosphorylation of MAPK activated protein kinase-2 (MAPKAP-K2) indicating reduced activity of p38 MAPKs utilizing this kinase as substrate. In contrast, we found that SB 203580 raised activities of ERK-1/2 and JNKs. Electrophoretic mobility shift assays revealed an increase in TRE binding activity in response to SB 203580 most likely resulting from increased expression of the major TRE binding components JunD and FosB as indicated by Western blot analyses. Increased TRE DNA binding failed to lead to increased transactivation correlating with the inability of SB 203580 to increase phosphorylation of these AP-1 proteins. These data indicate that SB 203580 sensitive p38 MAP kinases are not involved in okadaic acid mediated increases in TRE DNA binding and transactivation.

Animals↗
PubMed2003

A cytosolic domain of the yeast Zrt1 zinc transporter is required for its post-translational inactivation in response to zinc and cadmium.

Nutrient metals such as zinc are both essential to life and potentially toxic if overaccumulated by cells. Non-essential toxic metals like cadmium can enter cells through the uptake transporters responsible for nutrient metal acquisition. Therefore, in the face of ever changing extracellular metal levels, organisms tightly control their intracellular levels of nutrient metals and prevent accumulation of toxic metals. We show here that post-translational inactivation of the yeast Zrt1 zinc uptake transporter is important for zinc homeostasis. During the transition from zinc-limiting to zinc-replete growth conditions (i.e. zinc shock), the Zrt1 transporter is ubiquitinated, endocytosed, and subsequently degraded in the vacuole. To further understand this process at a molecular level, we mapped a region of Zrt1 required for ubiquitination and endocytosis in response to zinc to a domain located on the intracellular surface of the plasma membrane. This domain is a critical cis-acting component of the metal signaling pathway that controls Zrt1 protein trafficking. Using mutant alleles defective for metal-responsive inactivation, we also show that Zrt1 inactivation may be an important mechanism for preventing cadmium uptake and toxicity in zinc-limited cells.

Amino Acid Motifs↗
PubMed2000

Molecular mapping of the physiological cell death process. Mitochondrial events may be disordered.

The mitochondrion plays a central role in Bcl-2-inhibitable physiological cell deaths. The detailed order of mitochondrial and other events during cell death in vivo remains ambiguous, however. As part of an effort to explore this issue, we have asked whether mitochondrial dissolution during physiological cell death occurs in an orderly and concerted process. Here, we describe the characterization of two elements of mitochondrial disintegration on the level of individual cells. Using a novel cytofluorimetric approach, we have assessed simultaneously the release of cytochrome c (specifically a fluorescently tagged transfected construct) from mitochondria and the dissipation of mitochondrial membrane potential. Our results indicate that mitochondrial disintegration does not follow a strictly ordered process and is not concerted. We are extending these studies to further characterize mitochondrial events in the context of Bcl-2 family members and place them definitively within the context of the caspase cascade.

Apoptosis↗
PubMed2005

Neural network-based image reconstruction for positron emission tomography.

Positron emission tomography (PET) is one of the key molecular imaging modalities in medicine and biology. Penalized iterative image reconstruction algorithms frequently used in PET are based on maximum-likelihood (ML) and maximum a posterior (MAP) estimation techniques. The ML algorithm produces noisy artifacts whereas the MAP algorithm eliminates noisy artifacts by utilizing availableprior information in the reconstruction process. The MAP-based algorithms fail to determine the density class in the reconstructed image and hence penalize the pixels irrespective of the density class and irrespective of the strength of interaction between the nearest neighbors. A Hebbian neural learning scheme is proposed to model the nature of interpixel interaction to reconstruct artifact-free edge preserving reconstruction. A key motivation of the proposed approach is to avoid oversmoothing across edges that is often the case with MAP algorithms. It is assumed that local correlation plays a significant role in PET image reconstruction, and proper modeling of correlation weight (which defines the strength of interpixel interaction) is essential to generate artifact-free reconstruction. The Hebbian learning-based approach modifies the interaction weight by adding a small correction that is proportional to the product of the input signal (neighborhood pixels) and output signal. Quantitative analysis shows that the Hebbian learning-based adaptive weight adjustment approach is capable of producing better reconstructed images compared with those reconstructed by conventional ML and MAP-based algorithms in PET image reconstruction.

Algorithms↗
PubMed2005

Mapping the results of extensive surveys: the case of atmospheric biomonitoring and terrestrial mosses.

In this paper we discuss some difficulties associated with the process of constructing maps of pollution from data obtained in surveys covering extensive areas. As we show here, these problems may be wide-ranging but are seldom recognized by investigators. The origin of the problems is the existence of multiple sources of pollution in the study area, each of different intensity and affecting areas of different extent. The particular spatial structure of the pollution sources interacts with the spatial layout of the samples, resulting in data sets with distributions that are very different from the usually assumed normal distribution, and characterized by heavy tails and gross outliers. These distributions arise because of incomplete sampling of small-scale pollution processes (i.e. those occurring on a spatial scale smaller than the spatial scale of the sampling grid). After discussion of the potential problems and appropriate techniques for analyzing this kind of data, we applied the proposed techniques to a real data set of heavy metal contents in terrestrial mosses. From the exercise we concluded that a) the first step in analysis of this kind of data must be to check for the presence of spatial structure on scales larger than the sampling grid, to avoid mapping noise, and b) the map generated must not contain information about pollution sources with a spatial scale smaller than the spatial scale of the sampling grid. We present and discuss the performance of robust statistical methods of testing for spatial structure (based on robust variograms and randomization testing) and of filtering the small-scale spatial processes (using median-polishing) prior to mapping.

Atmosphere↗
PubMed1995

Self-organization as an iterative kernel smoothing process.

Kohonen's self-organizing map, when described in a batch processing mode, can be interpreted as a statistical kernel smoothing problem. The batch SOM algorithm consists of two steps. First, the training data are partitioned according to the Voronoi regions of the map unit locations. Second, the units are updated by taking weighted centroids of the data falling into the Voronoi regions, with the weighing function given by the neighborhood. Then, the neighborhood width is decreased and steps 1, 2 are repeated. The second step can be interpreted as a statistical kernel smoothing problem where the neighborhood function corresponds to the kernel and neighborhood width corresponds to kernel span. To determine the new unit locations, kernel smoothing is applied to the centroids of the Voronoi regions in the topological space. This interpretation leads to some new insights concerning the role of the neighborhood and dimensionality reduction. It also strengthens the algorithm's connection with the Principal Curve algorithm. A generalized self-organizing algorithm is proposed, where the kernel smoothing step is replaced with an arbitrary nonparametric regression method.

Algorithms↗
PubMed2001

Herpes simplex virus encodes a virion-associated protein which promotes long cellular processes in over-expressing cells.

BACKGROUND: Herpes simplex virus (HSV) possesses a number of accessory genes which are dispensable for replication in cell culture. A previous study showed that the UL21 gene product of HSV type 1 is a virion component that is not necessary for viral replication. The function of the gene product remains unknown. RESULTS: We found that the HSV-1 UL21 gene product, a capsid-associated tegument protein with an apparent molecular mass of 62 kDa, promotes the outgrowth of long cellular processes when it is over-expressed in non-neural cells. The UL21 protein co-localizes and physically associates with microtubules in the long processes. Analysis using mutant proteins implicates a proline-rich region in promotion of the processes. CONCLUSIONS: The results suggest that the UL21 protein, like tau and other MAPs, promotes the process by directly or indirectly interacting with microtubules and facilitates the intracellular transport of the virus.

Amino Acid Sequence↗