Showing papers by "University of Tübingen published in 2004"

BCI2000: a general-purpose brain-computer interface (BCI) system

Abstract: Many laboratories have begun to develop brain-computer interface (BCI) systems that provide communication and control capabilities to people with severe motor disabilities. Further progress and realization of practical applications depends on systematic evaluations and comparisons of different brain signals, recording methods, processing algorithms, output formats, and operating protocols. However, the typical BCI system is designed specifically for one particular BCI method and is, therefore, not suited to the systematic studies that are essential for continued progress. In response to this problem, we have developed a documented general-purpose BCI research and development platform called BCI2000. BCI2000 can incorporate alone or in combination any brain signals, signal processing methods, output devices, and operating protocols. This report is intended to describe to investigators, biomedical engineers, and computer scientists the concepts that the BCI2000 system is based upon and gives examples of successful BCI implementations using this system. To date, we have used BCI2000 to create BCI systems for a variety of brain signals, processing methods, and applications. The data show that these systems function well in online operation and that BCI2000 satisfies the stringent real-time requirements of BCI systems. By substantially reducing labor and cost, BCI2000 facilitates the implementation of different BCI systems and other psychophysiological experiments. It is available with full documentation and free of charge for research or educational purposes and is currently being used in a variety of studies by many research groups.

Visualization of protein interactions in living plant cells using bimolecular fluorescence complementation.

Abstract: Dynamic networks of protein-protein interactions regulate numerous cellular processes and determine the ability to respond appropriately to environmental stimuli. However, the investigation of protein complex formation in living plant cells by methods such as fluorescence resonance energy transfer has remained experimentally difficult, time consuming and requires sophisticated technical equipment. Here, we report the implementation of a bimolecular fluorescence complementation (BiFC) technique for visualization of protein-protein interactions in plant cells. This approach relies on the formation of a fluorescent complex by two non-fluorescent fragments of the yellow fluorescent protein brought together by association of interacting proteins fused to these fragments (Hu et al., 2002). To enable BiFC analyses in plant cells, we generated different complementary sets of expression vectors, which enable protein interaction studies in transiently or stably transformed cells. These vectors were used to investigate and visualize homodimerization of the basic leucine zipper (bZIP) transcription factor bZIP63 and the zinc finger protein lesion simulating disease 1 (LSD1) from Arabidopsis as well as the dimer formation of the tobacco 14-3-3 protein T14-3c. The interaction analyses of these model proteins established the feasibility of BiFC analyses for efficient visualization of structurally distinct proteins in different cellular compartments. Our investigations revealed a remarkable signal fluorescence intensity of interacting protein complexes as well as a high reproducibility and technical simplicity of the method in different plant systems. Consequently, the BiFC approach should significantly facilitate the visualization of the subcellular sites of protein interactions under conditions that closely reflect the normal physiological environment.

Further characterisation of the 91500 zircon crystal

Abstract: This paper reports the results from a second characterisation of the 91500 zircon, including data from electron probe microanalysis, laser ablation inductively coupled plasma-mass spectrometry (LA-ICP-MS), secondary ion mass spectrometry (SIMS) and laser fluorination analyses. The focus of this initiative was to establish the suitability of this large single zircon crystal for calibrating in situ analyses of the rare earth elements and oxygen isotopes, as well as to provide working values for key geochemical systems. In addition to extensive testing of the chemical and structural homogeneity of this sample, the occurrence of banding in 91500 in both backscattered electron and cathodoluminescence images is described in detail. Blind intercomparison data reported by both LA-ICP-MS and SIMS laboratories indicate that only small systematic differences exist between the data sets provided by these two techniques. Furthermore, the use of NIST SRM 610 glass as the calibrant for SIMS analyses was found to introduce little or no systematic error into the results for zircon. Based on both laser fluorination and SIMS data, zircon 91500 seems to be very well suited for calibrating in situ oxygen isotopic analyses.

Autosomal dominant cerebellar ataxias: clinical features, genetics, and pathogenesis.

Abstract: Summary Autosomal dominant cerebellar ataxias are hereditary neurodegenerative disorders that are known as spinocerebellar ataxias (SCA) in genetic nomenclature. In the pregenomic era, ataxias were some of the most poorly understood neurological disorders; the unravelling of their molecular basis enabled precise diagnosis in vivo and explained many clinical phenomena such as anticipation and variable phenotypes even within one family. However, the discovery of many ataxia genes and loci in the past decade threatens to cause more confusion than optimism among clinicians. Therefore, the provision of guidance for genetic testing according to clinical findings and frequencies of SCA subtypes in different ethnic groups is a major challenge. The identification of ataxia genes raises hope that essential pathogenetic mechanisms causing SCA will become more and more apparent. Elucidation of the pathogenesis of SCA hopefully will enable the development of rational therapies for this group of disorders, which currently can only be treated symptomatically.

Circulating tumor cells in patients with breast cancer dormancy

Abstract: Purpose: The purpose of this study was to test the hypothesis that circulating tumor cells (CTCs) are present in patients many years after mastectomy without evidence of disease and that these CTCs are shed from persisting tumor in patients with breast cancer dormancy. Experimental Design: We searched for CTCs in 36 dormancy candidate patients and 26 age-matched controls using stringent criteria for cytomorphology, immunophenotype, and aneusomy. Results: Thirteen of 36 dormancy candidates, 7 to 22 years after mastectomy and without evidence of clinical disease, had CTCs, usually on more than one occasion. Only 1 of 26 controls had a possible CTC (no aneusomy). The statistical difference of these two distributions was significant (exact P = 0.0043). The CTCs in patients whose primary breast cancer was just removed had a half-life measured in 1 to 2.4 hours. Conclusions: The CTCs that are dying must be replenished every few hours by replicating tumor cells somewhere in the tissues. Hence, there appears to be a balance between tumor replication and cell death for as long as 22 years in dormancy candidates. We conclude that this is one mechanism underlying tumor dormancy.

Magnetic phase control by an electric field

Abstract: The quest for higher data density in information storage is motivating investigations into approaches for manipulating magnetization by means other than magnetic fields. This is evidenced by the recent boom in magnetoelectronics and 'spintronics', where phenomena such as carrier effects in magnetic semiconductors and high-correlation effects in colossal magnetoresistive compounds are studied for their device potential. The linear magnetoelectric effect-the induction of polarization by a magnetic field and of magnetization by an electric field-provides another route for linking magnetic and electric properties. It was recently discovered that composite materials and magnetic ferroelectrics exhibit magnetoelectric effects that exceed previously known effects by orders of magnitude, with the potential to trigger magnetic or electric phase transitions. Here we report a system whose magnetic phase can be controlled by an external electric field: ferromagnetic ordering in hexagonal HoMnO3 is reversibly switched on and off by the applied field via magnetoelectric interactions. We monitor this process using magneto-optical techniques and reveal its microscopic origin by neutron and X-ray diffraction. From our results, we identify basic requirements for other candidate materials to exhibit magnetoelectric phase control.

Molecular and neuronal substrates for general anaesthetics.

Abstract: Although general anaesthesia has been of tremendous importance for the development of surgery, the underlying mechanisms by which this state is achieved are only just beginning to be understood in detail. In this review, we describe the neuronal systems that are thought to be involved in mediating clinically relevant actions of general anaesthetics, and we go on to discuss how the function of individual drug targets, in particular GABA(A)-receptor subtypes, can be revealed by genetic studies in vivo.

The BCI competition 2003: progress and perspectives in detection and discrimination of EEG single trials

Abstract: Interest in developing a new method of man-to-machine communication-a brain-computer interface (BCI)-has grown steadily over the past few decades. BCIs create a new communication channel between the brain and an output device by bypassing conventional motor output pathways of nerves and muscles. These systems use signals recorded from the scalp, the surface of the cortex, or from inside the brain to enable users to control a variety of applications including simple word-processing software and orthotics. BCI technology could therefore provide a new communication and control option for individuals who cannot otherwise express their wishes to the outside world. Signal processing and classification methods are essential tools in the development of improved BCI technology. We organized the BCI Competition 2003 to evaluate the current state of the art of these tools. Four laboratories well versed in EEG-based BCI research provided six data sets in a documented format. We made these data sets (i.e., labeled training sets and unlabeled test sets) and their descriptions available on the Internet. The goal in the competition was to maximize the performance measure for the test labels. Researchers worldwide tested their algorithms and competed for the best classification results. This paper describes the six data sets and the results and function of the most successful algorithms.

Using human brain lesions to infer function: a relic from a past era in the fMRI age?

Abstract: Recent technological advances, such as functional imaging techniques, allow neuroscientists to measure and localize brain activity in healthy individuals. These techniques avoid many of the limitations of the traditional method for inferring brain function, which relies on examining patients with brain lesions. This has fueled the zeitgeist that the classical lesion method is an inferior and perhaps obsolescent technique. However, although the lesion method has important weaknesses, we argue that it complements the newer activation methods (and their weaknesses). Furthermore, recent developments can address many of the criticisms of the lesion method. Patients with brain lesions provide a unique window into brain function, and this approach will fill an important niche in future research.

The Anatomy of Spatial Neglect based on Voxelwise Statistical Analysis: A Study of 140 Patients

Abstract: A major challenge for any anatomical study of spatial neglect in neurological patients is that human lesions vary tremendously in extent and location between individuals. Approaches to this problem used in previous studies were to focus on subgroups of patients that are more homogeneous either with respect to the branch territory affected by the stroke or with respect to existing additional neurological symptoms (e.g. additional visual field defects). It could be argued that such strategies might bias the conclusions on the critical substrate associated with spatial neglect. The present study thus addressed the high variability inherent in naturally occurring lesions by using an unselected, but very large sample size and by comparing a neglect group with a non-neglect group using voxelwise statistical testing. We investigated an unselected 7 year sample of 140 consecutively admitted patients with right hemisphere strokes. Seventy-eight had spatial neglect, 62 did not show the disorder. The incidence of visual field defects was comparable in both groups. For assessing lesion location, in a first step, we used conventional lesion density plots together with subtraction analysis. Moreover, due to the large size of the sample voxelwise statistical testing was possible to objectively estimate which brain regions are more frequently compromised in neglect patients relative to patients without neglect. The results demonstrate that the right superior temporal cortex, the insula and subcortically putamen and caudate nucleus are the neural structures damaged significantly more often in patients with spatial neglect.

Genetic content of wild-type human cytomegalovirus

Abstract: The genetic content of wild-type human cytomegalovirus was investigated by sequencing the 235 645 bp genome of a low passage strain (Merlin). Substantial regions of the genome (genes RL1–UL11, UL105–UL112 and UL120–UL150) were also sequenced in several other strains, including two that had not been passaged in cell culture. Comparative analyses, which employed the published genome sequence of a high passage strain (AD169), indicated that Merlin accurately reflects the wild-type complement of 165 genes, containing no obvious mutations other than a single nucleotide substitution that truncates gene UL128. A sizeable subset of genes exhibits unusually high variation between strains, and comprises many, but not all, of those that encode proteins known or predicted to be secreted or membrane-associated. In contrast to unpassaged strains, all of the passaged strains analysed have visibly disabling mutations in one or both of two groups of genes that may influence cell tropism. One comprises UL128, UL130 and UL131A, which putatively encode secreted proteins, and the other contains RL5A, RL13 and UL9, which are members of the RL11 glycoprotein gene family. The case in support of a lack of protein-coding potential in the region between UL105 and UL111A was also strengthened.

Repetitive Bilateral Arm Training and Motor Cortex Activation in Chronic Stroke: A Randomized Controlled Trial

Abstract: Hemiparesis represents the dominant functionally limiting symptom in 80% of patients with acute stroke.1 Within 2 to 5 months after a stroke, patients recover a variable degree of function, depending on the magnitude of the initial deficit.1 Several studies have demonstrated that recovery is associated with reorganization of central nervous system networks.2,3 Functional brain imaging of paretic movement during the recovery period has shown recruitment of cortex immediately adjacent to the stroke cavity along with intact cortical areas within the lesioned and in the uninjured contralesional hemisphere.4,5 The pattern of recruitment depends on the severity of impairment,6 lesion location,7 and time since stroke.8 The factors that initiate and maintain cortical reorganization are not known. Imaging data suggest that circuitry in motor cortices on both sides of the brain is modified during recovery.2 Even with traditional rehabilitation therapy, 50% to 95% of stroke survivors remain impaired.9-11 For some patients, recently developed repetitive active training therapies provide additional benefit.12 Bilateral arm training with rhythmic auditory cueing (BATRAC), a rehabilitation therapy based on the concept that bilateral movement permits interhemispheric facilitation of the limbs,13 is one such intervention. We previously showed that BATRAC improves arm function in chronic stroke survivors with fixed upper extremity deficits.14 We hypothesized that BATRAC may be associated with reorganization of brain regions involved in motor control.

Myocardin and ternary complex factors compete for SRF to control smooth muscle gene expression

Abstract: Smooth muscle cells switch between differentiated and proliferative phenotypes in response to extracellular cues1, but the transcriptional mechanisms that confer such phenotypic plasticity remain unclear. Serum response factor (SRF) activates genes involved in smooth muscle differentiation and proliferation by recruiting muscle-restricted cofactors, such as the transcriptional coactivator myocardin, and ternary complex factors (TCFs) of the ETS-domain family, respectively2,3,4,5,6,7,8,9. Here we show that growth signals repress smooth muscle genes by triggering the displacement of myocardin from SRF by Elk-1, a TCF that acts as a myogenic repressor. The opposing influences of myocardin and Elk-1 on smooth muscle gene expression are mediated by structurally related SRF-binding motifs that compete for a common docking site on SRF. A mutant smooth muscle promoter, retaining responsiveness to myocardin and SRF but defective in TCF binding, directs ectopic transcription in the embryonic heart, demonstrating a role for TCFs in suppression of smooth muscle gene expression in vivo. We conclude that growth and developmental signals modulate smooth muscle gene expression by regulating the association of SRF with antagonistic cofactors.

Role of teichoic acids in Staphylococcus aureus nasal colonization, a major risk factor in nosocomial infections

Abstract: Colonization of the anterior nares in approximately 37% of the population is a major risk factor for severe Staphylococcus aureus infections Here we show that wall teichoic acid (WTA), a surface-exposed staphylococcal polymer, is essential for nasal colonization and mediates interaction with human nasal epithelial cells WTA-deficient mutants were impaired in their adherence to nasal cells, and were completely unable to colonize cotton rat nares This study describes the first essential factor for S aureus nasal colonization

Chronological aging leads to apoptosis in yeast

Abstract: During the past years, yeast has been successfully established as a model to study mechanisms of apoptotic regulation. However, the beneficial effects of such a cell suicide program for a unicellular organism remained obscure. Here, we demonstrate that chronologically aged yeast cultures die exhibiting typical markers of apoptosis, accumulate oxygen radicals, and show caspase activation. Age-induced cell death is strongly delayed by overexpressing YAP1, a key transcriptional regulator in oxygen stress response. Disruption of apoptosis through deletion of yeast caspase YCA1 initially results in better survival of aged cultures. However, surviving cells lose the ability of regrowth, indicating that predamaged cells accumulate in the absence of apoptotic cell removal. Moreover, wild-type cells outlast yca1 disruptants in direct competition assays during long-term aging. We suggest that apoptosis in yeast confers a selective advantage for this unicellular organism, and demonstrate that old yeast cells release substances into the medium that stimulate survival of the clone.

HER-2 gene amplification can be acquired as breast cancer progresses.

Abstract: Amplification and overexpression of the HER-2 oncogene in breast cancer is felt to be stable over the course of disease and concordant between primary tumor and metastases. Therefore, patients with HER-2-negative primary tumors rarely will receive anti-Her-2 antibody (trastuzumab, Herceptin) therapy. A very sensitive blood test was used to capture circulating tumor cells (CTCs) and evaluate their HER-2 gene status by fluorescence in situ hybridization. The HER-2 status of the primary tumor and corresponding CTCs in 31 patients showed 97% agreement, with no false positives. In 10 patients with HER-2-positive tumors, the HER-2/chromosome enumerator probe 17 ratio in each tumor was about twice that of the corresponding CTCs (mean 6.64 +/- 2.72 vs. 2.8 +/- 0.6). Hence, the ratio of the CTCs is a reliable surrogate marker for the expected high ratio in the primary tumor. Her-2 protein expression of 10 CTCs was sufficient to make a definitive diagnosis of the HER-2 gene status of the whole population of CTCs in 19 patients with recurrent breast cancer. Nine of 24 breast cancer patients whose primary tumor was HER-2-negative each acquired HER-2 gene amplification in their CTCs during cancer progression, i.e., 37.5% (95% confidence interval of 18.8-59.4%). Four of the 9 patients were treated with Herceptin-containing therapy. One had a complete response and 2 had a partial response.

Support vector channel selection in BCI

Abstract: Designing a brain computer interface (BCI) system one can choose from a variety of features that may be useful for classifying brain activity during a mental task. For the special case of classifying electroencephalogram (EEG) signals we propose the usage of the state of the art feature selection algorithms Recursive Feature Elimination and Zero-Norm Optimization which are based on the training of support vector machines (SVM) . These algorithms can provide more accurate solutions than standard filter methods for feature selection . We adapt the methods for the purpose of selecting EEG channels. For a motor imagery paradigm we show that the number of used channels can be reduced significantly without increasing the classification error. The resulting best channels agree well with the expected underlying cortical activity patterns during the mental tasks. Furthermore we show how time dependent task specific information can be visualized.

Why are pathogenic staphylococci so lysozyme resistant? The peptidoglycan O-acetyltransferase OatA is the major determinant for lysozyme resistance of Staphylococcus aureus.

Abstract: Staphylococcus species belong to one of the few bacterial genera that are completely lysozyme resistant, which greatly contributes to their persistence and success in colonizing the skin and mucosal areas of humans and animals. In an attempt to discover the cause of lysozyme resistance, we identified a gene, oatA, in Staphylococcus aureus. The corresponding oatA deletion mutant had an increased sensitivity to lysozyme. HPLC and electrospray ionization tandem mass spectrometry analyses of the cell wall revealed that the muramic acid of peptidoglycan of the wild-type strain was O-acetylated at C6-OH, whereas the muramic acid of the oatA mutant lacked this modification. The complemented oatA mutant was lysozyme resistant. We identified the first bacterial peptidoglycan-specific O-acetyltransferase in S. aureus and showed that OatA, an integral membrane protein, is the molecular basis for the high lysozyme resistance in staphylococci.

Senataxin, the ortholog of a yeast RNA helicase, is mutant in ataxia-ocular apraxia 2

Abstract: Ataxia-ocular apraxia 2 (AOA2) was recently identified as a new autosomal recessive ataxia. We have now identified causative mutations in 15 families, which allows us to clinically define this entity by onset between 10 and 22 years, cerebellar atrophy, axonal sensorimotor neuropathy, oculomotor apraxia and elevated alpha-fetoprotein (AFP). Ten of the fifteen mutations cause premature termination of a large DEAxQ-box helicase, the human ortholog of yeast Sen1p, involved in RNA maturation and termination.

Chemotaxis Inhibitory Protein of Staphylococcus aureus, a Bacterial Antiinflammatory Agent

Abstract: Leukocyte migration is a key event both in host defense against invading pathogens as well as in inflammation. Bacteria generate chemoattractants primarily by excretion (formylated peptides), complement activation (C5a), and subsequently through activation of leukocytes (e.g., leukotriene B4, platelet-activating factor, and interleukin 8). Here we describe a new protein secreted by Staphylococcus aureus that specifically impairs the response of neutrophils and monocytes to formylated peptides and C5a. This chemotaxis inhibitory protein of S. aureus (CHIPS) is a 14.1-kD protein encoded on a bacteriophage and is found in >60% of clinical isolates. CHIPS reduces the neutrophil recruitment toward C5a in a mouse peritonitis model, even though its activity is much more potent on human than on mouse cells. These findings suggest a new immune escape mechanism of S. aureus and put forward CHIPS as a potential new antiinflammatory therapeutic compound.

Principles of a brain-computer interface (BCI) based on real-time functional magnetic resonance imaging (fMRI)

Abstract: A brain-computer interface (BCI) based on functional magnetic resonance imaging (fMRI) records noninvasively activity of the entire brain with a high spatial resolution. We present a fMRI-based BCI which performs data processing and feedback of the hemodynamic brain activity within 1.3 s. Using this technique, differential feedback and self-regulation is feasible as exemplified by the supplementary motor area (SMA) and parahippocampal place area (PPA). Technical and experimental aspects are discussed with respect to neurofeedback. The methodology now allows for studying behavioral effects and strategies of local self-regulation in healthy and diseased subjects.

Cerebellar ataxia and Purkinje cell dysfunction caused by Ca2+-activated K+ channel deficiency

Abstract: Malfunctions of potassium channels are increasingly implicated as causes of neurological disorders. However, the functional roles of the large-conductance voltage- and Ca(2+)-activated K(+) channel (BK channel), a unique calcium, and voltage-activated potassium channel type have remained elusive. Here we report that mice lacking BK channels (BK(-/-)) show cerebellar dysfunction in the form of abnormal conditioned eye-blink reflex, abnormal locomotion and pronounced deficiency in motor coordination, which are likely consequences of cerebellar learning deficiency. At the cellular level, the BK(-/-) mice showed a dramatic reduction in spontaneous activity of the BK(-/-) cerebellar Purkinje neurons, which generate the sole output of the cerebellar cortex and, in addition, enhanced short-term depression at the only output synapses of the cerebellar cortex, in the deep cerebellar nuclei. The impairing cellular effects caused by the lack of postsynaptic BK channels were found to be due to depolarization-induced inactivation of the action potential mechanism. These results identify previously unknown roles of potassium channels in mammalian cerebellar function and motor control. In addition, they provide a previously undescribed animal model of cerebellar ataxia.