CiteULike: Author Brugger

Automatic Cluster Detection in Kohonen's SOM

D Brugger — 2008-03-17T02:08:56-00:00

Neural Networks, IEEE Transactions on, Vol. 19, No. 3. (2008), pp. 442-459.

<para> Kohonen's self-organizing map (SOM) is a popular neural network architecture for solving problems in the field of explorative data analysis, clustering, and data visualization. One of the major drawbacks of the SOM algorithm is the difficulty for nonexpert users to interpret the information contained in a trained SOM. In this paper, this problem is addressed by introducing an enhanced version of the Clusot algorithm. This algorithm consists of two main steps: 1) the computation of the Clusot surface utilizing the information contained in a trained SOM and 2) the automatic detection of clusters in this surface. In the Clusot surface, clusters present in the underlying SOM are indicated by the local maxima of the surface. For SOMs with 2-D topology, the Clusot surface can, therefore, be considered as a convenient visualization technique. Yet, the presented approach is not restricted to a certain type of 2-D SOM topology and it is also applicable for SOMs having an <formula formulatype="inline"><tex>$n$</tex></formula>-dimensional grid topology. </para>

Is graphene on Ru(0001) a nanomesh?

Thomas Brugger — 2008-07-30T20:16:32-00:00

(27 Jul 2008)

The electronic structure of a single layer graphene on Ru(0001) is compared with that of a single layer hexagonal boron nitride nanomesh on Ru(0001). Both are corrugated sp2 networks and display a pi-band gap at the K point of their 1 x 1 Brillouin zone. Graphene has a distinct Fermi surface which indicates that 0.1 electrons are transferred per 1 x 1 unit cell. Photoemission from adsorbed xenon identifies two distinct Xe 5p1/2 lines, separated by 240 meV, which reveals a corrugated electrostatic potential energy surface. These two Xe species are related to the topography of the system and have different desorption energies.

Pharmacokinetics and pharmacodynamics of rocuronium bromide in adult patients.

JA Alvarez-Gomez — 2008-06-14T11:21:16-00:00

European journal of anaesthesiology. Supplement, Vol. 9 (1994), pp. 53-56.

In seven patients (M/F: 4:3) rocuronium 0.6 mg kg-1 was given after the induction of anaesthesia with propofol, and during maintenance with N2O/O2, halothane 0.5% and alfentanil 60-90 micrograms kg-1 h-1. Intubation conditions were scored at 60 s and lag time, onset time, maximal block achieved, recovery to 25% of T1, and Recovery Index, were measured using a Relaxograph. Blood samples were taken over a 300 min period and analysed for rocuronium. Intubating conditions at 60 s were excellent in all patients. Mean clearance was 5.2 ml kg-1 min-1, the terminal half-life was 69 min and distribution volume at steady state was 0.22 litre kg-1. Cumulative urinary excretion was around 18% within 24 h.

Evaluation of a standardized internet-based and telephone-based patient monitoring system for pain therapy with transdermal fentanyl.

R Theiler — 2008-06-05T14:23:35-00:00

The Clinical journal of pain, Vol. 23, No. 9. (c 2007), pp. 804-811.

The aim of the present observational 4-week study was to document the feasibility and utility of telephone-based or Internet-based pain monitoring in patients with chronic cancer or noncancer pain, such as nociceptive or neuropathic pain, using transdermal fentanyl. Pain intensity, treatment tolerability, activities of daily living, quality of life, and patient and physician satisfaction were evaluated in 60 (60% women, 42% opioid-naive) chronic pain patients who were switched from oral pain therapy to transdermal fentanyl therapy because of persisting severe pain. When the total dataset of all patient entries was analyzed, treatment with transdermal fentanyl led to decreases in maximal and mean pain scores as reported by the patients (-14% and -19%, respectively, last observation carried forward vs. baseline). Pain reduction was more pronounced in opioid-naive than in opioid-experienced patients (-35% and -25% vs. baseline, respectively; P=0.03). Overall, impairment of daily activities was reduced by 23% with transdermal fentanyl. No effect was observed with regard to quality of life and use of rescue pain medication. Transdermal fentanyl was generally well tolerated. Most patients (60%) preferred the telephone-based to the Internet-based or Internet combined with telephone questionnaires. Patient preference was driven by age, whereby younger patients tended to prefer the Internet and older patients the telephone (mean age, 45 and 54 y, respectively; difference n.s.). Internet-based and telephone-based monitoring of the efficacy and tolerability of opioid treatment for chronic pain was feasible in daily practice and generally well accepted by patients and physicians. Future research will determine the relative contribution of these 2 new options for patient-physician interaction and delineate their role in improving chronic pain control.

German Cancer Society Neuro-Oncology Working Group NOA-03 multicenter trial of single-agent high-dose methotrexate for primary central nervous system lymphoma.

U Herrlinger — 2008-05-26T10:26:24-00:00

Annals of neurology, Vol. 51, No. 2. (February 2002), pp. 247-252.

The prospective multicenter NOA-03 trial, conducted by the Neuro-Oncology Working Group (NOA) of the German Cancer Society, was initiated to define the feasibility and efficacy of single-agent high-dose methotrexate therapy without concomitant radiotherapy in immunocompetent patients with primary central nervous system lymphoma. Thirty-seven patients (median age, 60 years) received 179 biweekly courses of 8 g/m2 methotrexate. Response was assessed after 3 and 6 courses. We had planned to enter 105 patients into the trial. Since fewer than the projected 18 of 37 patients achieved a complete response after an intermediate analysis, the trial was closed. In intention-to-treat analysis, 11 of 37 patients (29.7%) achieved complete response, whereas 14 of 37 patients (37.8%) were found to have progressive disease. The median relapse-free survival among complete response patients was 13.7 months. Multivariate logistic regression analysis revealed that corticosteroid application during the first methotrexate course was associated with complete response. The regimen was well tolerated, but, unlike previously reported results, the activity of high-dose methotrexate was only moderate.

Muscle spindles and Golgi tendon organs in bovine calf extraocular muscle studied by means of double-fluorescent labeling, electron microscopy, and three-dimensional reconstruction.

R Blumer — 2008-05-23T11:35:17-00:00

Experimental eye research, Vol. 77, No. 4. (October 2003), pp. 447-462.

In the present study muscle spindles (MSps) and Golgi tendon organs (GTOs) in bovine extraocular muscles (EOMs) were analyzed in detail. The innervation pattern of these proprioceptors was investigated with transmission electron microscope and confocal laser scanning microscope after double-fluorescent labeling. Three-dimensional (3D) reconstructions were performed of GTOs.Muscle spindles. MSps are numerous, each containing two nuclear bag fibers and up to eight nuclear chain fibers. In the equatorial region and paraequatorial region thin axons enwrapping the intrafusal muscle fibers form numerous nerve contacts on the muscle fiber surface. Double staining of such nerve terminals with synaptophysin and alpha-bungarotoxin and their fine structural features confirm their sensory nature. In the encapsulated part of the polar region neuromuscular contacts have structural features of motor nerve terminals and stain positively with alpha-bungarotoxin. Golgi tendon organs. GTOs are numerous in bovine EOMs. Each GTO contains collagen bundles but frequently also intracapsular muscle fibers. Intracapsular muscle fibers either terminate inside the GTO in collagen bundles or pass through the proprioceptor. GTOs are richly supplied with sensory nerve terminals which intermingle with the collagen bundles. Nerve terminals on intracapsular muscle fibers exhibit fine structural characteristics of motor nerve terminals and are alpha-bungarotoxin positive. The 3D images of GTOs show the detailed spatial arrangement of the GTO tissue components. These new insights in the complex and specific morphology of MSps and GTOs in bovine EOMs indicate that we deal with highly developed proprioceptors. These are supposed to provide important information for EOM innervation.

A Conformational Change in the -subunit of Coatomer Induced by Ligand Binding to -COP Revealed by Single-pair FRET

Langer — 2008-03-10T16:25:09-00:00

Traffic, Vol. 9, No. 4. (April 2008), pp. 597-607.

The HIV lipidome: A raft with an unusual composition

Britta Brugger — 2008-05-13T13:06:12-00:00

Proceedings of the National Academy of Sciences, Vol. 103, No. 8. (21 February 2006), pp. 2641-2646.

The lipids of enveloped viruses play critical roles in viral morphogenesis and infectivity. They are derived from the host membranes from which virus budding occurs, but the precise lipid composition has not been determined for any virus. Employing mass spectrometry, this study provides a quantitative analysis of the lipid constituents of HIV and a comprehensive comparison with its host membranes. Both a substantial enrichment of the unusual sphingolipid dihydrosphingomyelin and a loss of viral infectivity upon inhibition of sphingolipid biosynthesis in host cells are reported, establishing a critical role for this lipid class in the HIV replication cycle. Intriguingly, the overall lipid composition of native HIV membranes resembles detergent-resistant membrane microdomains and is strikingly different from that of host cell membranes. With this composition, the HIV lipidome provides strong evidence for the existence of lipid rafts in living cells. 10.1073/pnas.0511136103

Preservation of motor programs in paraplegics as demonstrated by attempted and imagined foot movements

Sabina Hotz-Boendermaker — 2008-03-07T10:45:49-00:00

NeuroImage, Vol. 39, No. 1. (1 January 2008), pp. 383-394.

Execution and imagination of movement activate distinct neural circuits, partially overlapping in premotor and parietal areas, basal ganglia and cerebellum. Can long-term deafferented/deefferented patients still differentiate attempted from imagined movements The attempted execution and motor imagery network of foot movements have been investigated in nine chronic complete spinal cord-injured (SCI) patients using fMRI. Thorough behavioral assessment showed that these patients were able to differentiate between attempted execution and motor imagery. Supporting the outcome of the behavioral assessment, fMRI disclosed specific patterns of activation for movement attempt and for motor imagery. Compared with motor execution data of healthy controls, movement attempt in SCI patients revealed reduced primary motor cortex activation at the group level, although activation was found in all single subjects with a high variability. Further comparisons with healthy subjects revealed that during attempt and motor imagery, SCI patients show enhanced activation and recruitment of additional regions in the parietal lobe and cerebellum that are important in sensorimotor integration. These findings reflect central plastic changes due to altered input and output and suggest that SCI patients may require additional cognitive resources to perform these tasks that may be one and the same phenomenon, or two versions of the same phenomenon, with quantitative differences between the two. Nevertheless, the retained integrity of movement attempt and motor imagery networks in SCI patients demonstrates that chronic paraplegics can still dispose of the full motor programs for foot movements and that therefore, attempted and imagined movements should be integrated in rehabilitative strategies.

Head turns bias the brain's internal random generator

Tobias Loetscher — 2008-01-30T14:47:28-00:00

Current Biology, Vol. 18, No. 2. (22 January 2008), pp. R60-R62.

Summary Numerical and spatial cognition rely on common functional circuits in the parietal lobes of the brain [1]. While previous work has established that the mere perception of numbers can bias a subject's attention in space [2], the method of random digit generation has only recently been introduced to a rapidly growing literature exploring asymmetries in number space [3]. Here we show that human subjects' attempts to generate numbers `at random' are systematically influenced by lateral head turns, which are known to reallocate spatial attention in the outside world. Specifically, while facing left, subjects produced relatively small numbers, whereas while facing right they tended to produce larger numbers. These results support current concepts of parietal cortex as mediating the interplay between spatial attention and abstract thought [4].

www.rnaworkbench.com: A new program for analyzing RNA interference.

Radka Svobodová Vařeková — 2008-01-22T12:48:30-00:00

Comput Methods Programs Biomed (18 January 2008)

RNA interference (RNAi) has become an important tool to study and utilize gene silencing by introducing short interfering RNA (siRNA). In order to predict the most efficient siRNAs, a new software tool, RNA Workbench (RNAWB), has been designed and is freely available (after registration) on http://www.rnaworkbench.com. In addition to the standard selection rules, RNAWB includes the possibility of statistical analyses of the applied selection rules (criteria). The role of RNA secondary structures in the RNA interference process as well as the application of sequence rules are discussed to show the applicability of the software.

The Rap GTPases Regulate B Cell Morphology, Immune-Synapse Formation, and Signaling by Particulate B Cell Receptor Ligands.

Kevin B L Lin — 2008-01-17T18:02:45-00:00

Immunity (9 January 2008)

B lymphocytes spread and extend membrane processes when searching for antigens and form immune synapses upon contacting cells that display antigens on their surface. Although these dynamic morphological changes facilitate B cell activation, the signaling pathways underlying these processes are not fully understood. We found that activation of the Rap GTPases was essential for these changes in B cell morphology. Rap activation was important for B cell receptor (BCR)- and lymphocyte-function-associated antigen-1 (LFA-1)-induced spreading, for BCR-induced immune-synapse formation, and for particulate BCR ligands to induce localized F-actin assembly and membrane-process extension. Rap activation and F-actin assembly were also required for optimal BCR signaling in response to particulate antigens but not soluble antigens. Thus by controlling B cell morphology and cytoskeletal organization, Rap might play a key role in the activation of B cells by particulate and cell-associated antigens.

Investigation of normal organ development with fetal MRI.

D Prayer — 2007-12-11T14:43:07-00:00

Eur Radiol, Vol. 17, No. 10. (October 2007), pp. 2458-2471.

The understanding of the presentation of normal organ development on fetal MRI forms the basis for recognition of pathological states. During the second and third trimesters, maturational processes include changes in size, shape and signal intensities of organs. Visualization of these developmental processes requires tailored MR protocols. Further prerequisites for recognition of normal maturational states are unequivocal intrauterine orientation with respect to left and right body halves, fetal proportions, and knowledge about the MR presentation of extrafetal/intrauterine organs. Emphasis is laid on the demonstration of normal MR appearance of organs that are frequently involved in malformation syndromes. In addition, examples of time-dependent contrast enhancement of intrauterine structures are given.

Variables that influence the generation of random sequences: an update.

P Brugger — 2007-08-23T17:36:42-00:00

Percept Mot Skills, Vol. 84, No. 2. (April 1997), pp. 627-661.

This article updates Tune's 1964 review of variables influencing human subjects' attempts at generating random sequences of alternatives. It also covers aspects not included in the original review such as randomization behavior by patients with neurological and psychiatric disorders. Relevant work from animal research (spontaneous alternation paradigm) is considered as well. It is conjectured that Tune's explanation of sequential nonrandomness in terms of a limited capacity of short-term memory can no longer be maintained. Rather, interdependence among consecutive choices is considered a consequence of an organism's natural susceptibility to interference. Random generation is thus a complex action which demands complete suppression of any rule-governed behavior. It possibly relies on functions of the frontal lobes but cannot otherwise be "localized" to restricted regions of the brain. Possible developments in the field are briefly discussed, both with respect to basic experiments regarding the nature of behavioral nonrandomness and to potential applications of random-generation tasks.

Determination of Third-Order Elastic Coefficients in Crystals

K Brugger — 2007-08-23T15:45:08-00:00

Journal of Applied Physics, Vol. 36, No. 3. (1965), pp. 768-773.

Third-order elastic coefficients can be derived from sound speed measurements in statically stressed crystals. The necessary relations between experimental data and elastic coefficients are here presented for orthorhombic, tetragonal, cubic, rhombohedral, and hexagonal crystal classes. For each symmetry a sufficient number of wave modes and stress systems is selected to determine all third-order coefficients and to allow experimental cross checks. All the modes considered are pure longitudinal or transverse. They are selected so as to minimize the number of specimen orientations required, and following experimental procedures for uniaxial static stress, only wave modes propagating at right angles to the stress direction are considered. ©1965 The American Institute of Physics

Pure Modes for Elastic Waves in Crystals

K Brugger — 2007-08-23T15:41:38-00:00

Journal of Applied Physics, Vol. 36, No. 3. (1965), pp. 759-768.

In an anisotropic medium there are only certain directions along which elastic waves can propagate in pure longitudinal and transverse modes. For the determination of third-order elastic coefficients from sound speed measurements in stressed crystals it is desirable to know these modes. Using a method due to Borgnis the pure mode directions are determined for all crystal point groups belonging to the orthorhombic, tetragonal, cubic, rhombohedral, and hexagonal systems. The eigenvalue problem is solved for each of these directions, and the polarization vectors and the wave speeds are tabulated. ©1965 The American Institute of Physics

Thermodynamic Definition of Higher Order Elastic Coefficients

K Brugger — 2007-08-23T14:33:52-00:00

Physical Review, Vol. 133, No. 6A. (16 March 1964), A1611.

General thermodynamic definitions of the higher order elastic coefficients of thermoelastic media are presented in tensor and engineering notation. They are natural generalizations of the customary definitions of second-order coefficients; they retain the usual conventions relating tensor and engineering stresses and strains; and they simplify thermodynamic calculations.

Identification of novel non-coding RNAs as potential antisense regulators in the archaeon Sulfolobus solfataricus

Thean-Hock Tang — 2005-01-13T07:48:04-00:00

Molecular Microbiology, Vol. 55, No. 2., 469.

Vestibular stimulation affects dichotic lexical decision performance.

H Schüeli — 2007-06-13T21:02:11-00:00

Neuropsychologia, Vol. 37, No. 6. (June 1999), pp. 653-659.

We report an experimental attempt to shift, by vestibular stimulation, healthy subjects' right ear advantage (REA) in a dichotic listening (DL) task with words and nonwords as stimuli. Forty right-handed men performed the task under two different conditions, once while sitting in a stationary turning chair (baseline) and once during sinusoidal rotation. In this latter condition, every other stimulation was received during maximal left-to-right (i.e., clockwise), every other during maximal right-to-left (i.e., counterclockwise) acceleration. There was a reliable REA for lexical decision accuracy in the baseline and right-to-left trials but not during left-to-right rotation. While right ear performance was unaffected by rotation, there were more correct lexical decisions to left ear targets exclusively during left-to-right turns (one-tailed P = 0.05). Since there were no parallel shifts in auditory thresholds under the different conditions, this effect is not due to any hypothetical auditory-vestibular interactions on a primary sensory level. The improvement in left ear DL performance, although small in our study, is comparable to the symptom-alleviating effect of caloric vestibular stimulation in patients with left-sided hemispatial neglect and interpreted as a consequence of a rotation-induced attentional shift towards the left hemispace.

The Sur7p Family Defines Novel Cortical Domains in Saccharomyces cerevisiae, Affects Sphingolipid Metabolism, and Is Involved in Sporulation

Michael Young — 2007-05-20T14:42:41-00:00

Mol. Cell. Biol., Vol. 22, No. 3. (1 February 2002), pp. 927-934.

We have discovered a novel cortical patch structure in Saccharomyces cerevisiae defined by a family of integral plasma membrane proteins, including Sur7p, Ynl194p, and Ydl222p. Sur7p-family patches localized as cortical patches that were immobile and stable. These patches were polarized to regions of the cell with a mature cell wall; they were absent from small buds and the tips of many medium-sized buds. These patches were distinct from other known cortical structures. Digestion of the cell wall caused Sur7p patches to disassemble, indicating that Sur7p requires cell wall-dependent extracellular interactions for its localization as patches. sur7Delta, ydl222Delta, and ynl194Delta mutants had reduced sporulation efficiencies. SUR7 was originally described as a multicopy suppressor of rvs167, whose product is an actin patch component. This suppression is probably mediated by sphingolipids, since deletion of SUR7, YDL222, and YNL194 altered the sphingolipid content of the yeast plasma membrane, and other SUR genes suppress rvs167 via effects on sphingolipid synthesis. In particular, the sphingoid base length and number of hydroxyl groups in inositolphosphorylceramides were altered in sur7Delta, ydl222Delta, and yne194Delta strains. 10.1128/MCB.22.3.927-934.2002

Modeling documents for structure recognition using generalized N-grams

R Brugger — 2007-04-15T22:23:12-00:00

Document Analysis and Recognition, 1997., Proceedings of the Fourth International Conference on, Vol. 1 (1997), pp. 56-60 vol.1.

We present and discuss a novel approach to modeling logical structures of documents, based on a statistical representation of patterns in a document class. An efficient and error tolerant recognition heuristics adapted to the model is proposed. The statistical approach permits easily automated and incremental learning of the model. The approach has been partially evaluated on a prototype. A discussion of the results achieved by the prototype is finally made

Linking Out-of-Body Experience and Self Processing to Mental Own-Body Imagery at the Temporoparietal Junction

Olaf Blanke — 2007-01-06T21:48:09-00:00

J. Neurosci., Vol. 25, No. 3. (19 January 2005), pp. 550-557.

The spatial unity of self and body is challenged by various philosophical considerations and several phenomena, perhaps most notoriously the "out-of-body experience" (OBE) during which one's visual perspective and one's self are experienced to have departed from their habitual position within one's body. Although researchers started examining isolated aspects of the self, the neurocognitive processes of OBEs have not been investigated experimentally to further our understanding of the self. With the use of evoked potential mapping, we show the selective activation of the temporoparietal junction (TPJ) at 330-400 ms after stimulus onset when healthy volunteers imagined themselves in the position and visual perspective that generally are reported by people experiencing spontaneous OBEs. Interference with the TPJ by transcranial magnetic stimulation (TMS) at this time impaired mental transformation of one's own body in healthy volunteers relative to TMS over a control site. No such TMS effect was observed for imagined spatial transformations of external objects, suggesting the selective implication of the TPJ in mental imagery of one's own body. Finally, in an epileptic patient with OBEs originating from the TPJ, we show partial activation of the seizure focus during mental transformations of her body and visual perspective mimicking her OBE perceptions. These results suggest that the TPJ is a crucial structure for the conscious experience of the normal self, mediating spatial unity of self and body, and also suggest that impaired processing at the TPJ may lead to pathological selves such as OBEs. 10.1523/JNEUROSCI.2612-04.2005

Synesthesia: When colors count

Daria Knoch — 2006-04-18T07:20:25-00:00

Cognitive Brain Research, Vol. 25, No. 1. (September 2005), pp. 372-374.

A tacitly held assumption in synesthesia research is the unidirectionality of digit-color associations. This notion is based on synesthetes' report that digits evoke a color percept, but colors do not elicit any numerical impression. In a random color generation task, we found evidence for an implicit co-activation of digits by colors, a finding that constrains neurological theories concerning cross-modal associations in general and synesthesia in particular.

Soft, entirely photoplastic probes for scanning force microscopy

G Genolet — 2006-03-15T02:07:43-00:00

Review of Scientific Instruments, Vol. 70, No. 5. (1999), pp. 2398-2401.

A new probe made entirely of plastic material has been developed for scanning probe microscopy. Using a polymer for the cantilever facilitates the realization of mechanical properties that are difficult to achieve with classical silicon technology. The new cantilever and tip presented here are made of an epoxy-based photoplastic. The fabrication process is a simple batch process in which the integrated tip and the lever are defined in one photolithography step. The simplicity of the fabrication step, the use of a polymer as material, and the ability to reuse the silicon mold lead to a soft low-cost probe for scanning force microscopy. Imaging soft condensed matter with photoplastic levers, which uses laser beam deflection sensing, exhibits a resolution that compares well with that of commercially available silicon cantilevers. ©1999 American Institute of Physics.