julilili42/papers huggingface dataset:
Visualization and quantification of disease progression in multiple system atrophy
2006-07-07

Abstract To visualize and quantify disease progression in multiple system atrophy (MSA) from cerebellar type (MSA‐C), we combined two magnetic resonance imaging (MRI) techniques, voxel‐based morphometry (VBM) and 3D‐based volumetry. Patients suffering from MSA‐C (n = 14) were imaged twice with an interval of 2.0 ± 0.2 years. We first applied VBM to map brain morphology changes between MSA patients and controls and to identify brain areas that showed a significant amount of atrophy. Using 3D‐based volumetry, we confirmed that in MSA‐C patients, the brainstem including medulla and pons, vermis and cerebellar hemispheres, caudate nucleus and putamen showed significant atrophy compared with controls. Next, we used 3D‐based volumetry to analyze the atrophy rates. Atrophy rates in patients with MSA were significantly different from controls for putamen (−11.4% ± 2.6%/year), vermis (−12.3% ± 2.9%/year), and cerebellar hemispheres (−6.6% ± 1.1%/year). The results show that 3D‐based MRI volumetry is a tool that allows the disease progression of MSA to be followed over a time period of 2 years and suggest that it may serve as a surrogate marker in clinical trials to measure disease progression. © 2006 Movement Disorder Society
Identification of genes involved in siderophore transport inStreptomyces coelicolorA3(2)
2006-07-07

The potential iron siderophore transporter genes have been determined from the genome sequence of Streptomyces coelicolor A3(2). One of these gene clusters, cdtABC, was disrupted and characterized to determine its role in the uptake of the siderophores produced by S. coelicolor. Resistance to the siderophore-like antibiotics, salmycin and albomycin, was tested in the parent and cdtABC mutant, showing that the parent, but not the mutant, was sensitive to salmycin, while both were resistant to albomycin. Ferrioxamine competition assays against salmycin suggest that the uptake of salmycin is via a ferrioxamine transport system. However, Fe-55 ferrioxamine B uptake experiments did not reveal any difference between the parent and mutant. This suggests that CdtABC specifically transports salmycin, while ferrioxamine uptake maybe substituted by another transport system.
Mutations in TITF1 are not relevant to sporadic and familial chorea of unknown cause
2006-07-07

Abstract Benign hereditary chorea (BHC; OMIM 118700) is an autosomal dominant movement disorder. Mutations in the thyroid transcription factor 1 (TITF1) gene have been linked with BHC. The phenotype for BHC is highly variable and may include atypical features such as dystonia, slow saccades, and even cognitive deficits. Although BHC is commonly transmitted in a dominant manner, assessment of TITF1 mutations in familial or sporadic patients with late‐onset nonprogressive or early‐onset progressive chorea is of practical relevance in order to evaluate diagnostic strategies in single patients. In this study, 18 patients with chorea of unknown cause including index patients of three families with autosomal dominantly inherited nonprogressive chorea have been screened for TITF1 mutations by means of denaturating high‐pressure liquid chromatography (dHPLC). No sequence variations were detected for the complete open reading frame, suggesting that TITF1 mutations are not a common cause of sporadic or familial chorea of unknown cause. Additionally, linkage analysis excluded TITF1 mutations in a large family with benign hereditary chorea. © 2006 Movement Disorder Society
Impaired intestinal NHE3 activity in the PDK1 hypomorphic mouse
2006-07-07

In vitro experiments have demonstrated the stimulating effect of serum- and glucocorticoid-inducible kinase (SGK)1 on the activity of the Na + /H + exchanger (NHE3). SGK1 requires activation by phosphoinositide-dependent kinase (PDK)1, which may thus similarly play a role in the regulation of NHE3-dependent epithelial electrolyte transport. The present study was performed to explore the role of PDK1 in the regulation of NHE3 activity. Because mice completely lacking functional PDK1 are not viable, hypomorphic mice expressing ∼20% of PDK1 ( pdk1 hm ) were compared with their wild-type littermates ( pdk1 wt ). NHE3 activity in the intestine and PDK1-overexpressing HEK-293 cells was estimated by utilizing 2′,7′-bis(2-carboxyethyl)-5(6)-carboxyfluorescein fluorescence for the determination of intracellular pH. NHE activity was reflected by the Na + -dependent pH recovery from an ammonium prepulse (ΔpH NHE ). The pH changes after an ammonium pulse allowed the calculation of cellular buffer capacity, which was not significantly different between pdk1 hm and pdk1 wt mice. ΔpH NHE was in pdk1 hm mice, only 30 ± 6% of the value obtained in pdk1 wt mice. Conversely, ΔpH NHE was 32 ± 7% larger in PDK1-overexpressing HEK-293 cells than in HEK-293 cells expressing the empty vector. The difference between pdk1 hm and pdk1 wt mice and between PDK1-overexpressing and empty vector-transfected HEK cells, respectively, was completely abolished in the presence of the NHE3 inhibitor S3226 (10 μM). In conclusion, defective PDK1 expression leads to significant impairment of NHE3 activity in the intestine, pointing to a role of PDK1-dependent signaling in the regulation of NHE-mediated electrolyte transport.
Cardiac Cine Imaging at 3 Tesla
2006-07-07

This study shows that cardiac cine imaging at 3 T using a 32-element body-array coil is feasible in healthy volunteers. Using a large number of coil elements with a favorable sensitivity profile supports faster image acquisition, with high diagnostic image quality even for high parallel imaging factors.
3D Surveillance A Distributed Network of Smart Cameras for Real-Time Tracking and its Visualization in 3D
2006-07-10

The demand for surveillance systems has increased extremely over recent times. We present a system consisting of a distributed network of cameras that allows for tracking and handover of multiple persons in real time. The intercamera tracking results are embedded as live textures in an integrated 3D world model which is available ubiquitously and can be viewed from arbitrary perspectives independent of the persons' movements. We mainly concentrate on our implementation of embedded camera nodes in the form of smart cameras and discuss the benefits of such a distributed surveillance network compared to a host centralized approach. We also briefly describe our way of hassle free 3D model acquisition to cover the complete system from setup to operation and finally show some results of both an indoor and an outdoor system in operation.
Indicators of Gas Source Proximity using Metal Oxide Sensors in a Turbulent Environment
2006-07-10

This paper addresses the problem of estimating proximity to a gas source using concentration measurements. In particular, we consider the problem of gas source declaration by a mobile robot equipped with metal oxide sensors in a turbulent indoor environment. While previous work has shown that machine learning classifiers can be trained to detect close proximity to a gas source, it is difficult to interpret the learned models. This paper investigates possible underlying indicators of gas source proximity, comparing three different statistics derived from the sensor measurements of the robot. A correlation analysis of 1056 trials showed that response variance (measured as standard deviation) was a better indicator than average response. An improved result was obtained when the standard deviation was normalized to the average response for each trial, a strategy that also reduces calibration problems.
nScan-matching: simultaneous matching of multiple scans and application to SLAM
2006-07-10

Scan matching is a popular way of recovering a mobile robot's motion and constitutes the basis of many localization and mapping approaches. Consequently, a variety of scan matching algorithms have been proposed in the past. All these algorithms share one common attribute: They match pairs of scans to obtain spatial relations between two robot poses. In this paper we present a method for matching multiple scans simultaneously. We discuss the need for such a method and describe how the result of such a multi-scan matching can be incorporated into relation-based SLAM in the Lu and Milios style
Spectral analyses of eighteen hot H-deficient (pre-) white dwarfs from the Sloan Digital Sky Survey Data Release 4
2006-07-11

\\n Context.The Sloan Digital Sky Survey Data Release 4 has provided spectra of\\n several new PG 1159 stars and DO white dwarfs. This increase in\\n known hot H-deficient compact objects significantly improves the statistics\\n and helps to investigate late stages of stellar evolution.\\n Aims.From the optical SDSS spectra, effective temperatures and surface\\n gravities are derived in order to place the observed objects in an\\n evolutionary context. Especially the connection between PG 1159 stars\\n and DO white dwarfs shall be investigated.\\n Methods.Using our non-LTE model atmospheres and applying -fitting\\n techniques, we determine stellar parameters and their\\n errors. We derive total stellar masses for the DO white dwarfs using\\n model evolutionary tracks.\\n Results.We confirm three PG 1159 stars, with one showing ultra-high\\n excitation ion features, and one sdO which we originally classified\\n as a PG 1159 star. Additionally, we re-analysed the known PG 1159\\n star, PG 1424+535, with our new models. Furthermore, we present\\n the first spectral analyses of thirteen DO white dwarfs, three of which\\n show M-star features in their spectra, while two display ultra-high\\n excitation ion features.\\n
Correlations and effective interactions in nuclear matter
2006-07-11

We performed Self-Consistent Greens Function (SCGF) calculations for symmetric nuclear matter using realistic nucleon-nucleon (NN) interactions and effective low-momentum interactions ( ), which are derived from such realistic NN interactions. We compare the spectral distributions resulting from such calculations. We also introduce a density-dependent effective low-momentum interaction which accounts for the dispersive effects in the single-particle propagator in the medium.
Mannan-binding lectin plasma levels in leprosy: deficiency confers protection against the lepromatous but not the tuberculoid forms
2006-07-12

Summary Mannan-binding lectin (MBL) is an important component of the first-line defence against infections. Evidence has shown that MBL deficiency, reducing phagocytosis and internalization of intracellular pathogens may protect the host against intracellular infections such as leprosy. In this study, we speculated whether genetically determined low MBL serum levels confer protection against Mycobacterium leprae infection. One hundred and ninety-one patients with leprosy, presenting lepromatous (n = 118), tuberculoid (n = 31), dimorph (n = 30) and indeterminate (n = 12) clinical forms and 110 healthy controls matched with the patients according to sex, age and ethnic background were investigated. MBL concentrations were measured in a double-antibody enzyme immune assay and C-reactive protein (CRP) serum levels by nephelometry. A significant negative association of MBL low values (&amp;lt; 100 ng/ml) was observed with lepromatous patients when comparing with controls and tuberculoid patients [10/118, 8.47%versus 21/110, 19.09%P = 0.03 χ2 with Yates’ correction, odds ratio (OR) 0.39, confidence interval (CI) 0.18–0.88 and 8/31, 25.81%, P = 0.02, OR 0.27, CI 0.09–0.75, respectively]. There was no significant difference in the distribution of MBL levels between patients and controls or among the clinical forms. The concentration of CRP was significantly increased in the patients (P = 0.0002) and in the lepromatous form (P = 0.0001) when compared to controls. A weak positive correlation between MBL and CRP levels was observed in the patients (P = 0.010, R = 0.255). These data suggest a protective role for MBL deficiency against the development of the most severe and multi-bacillary form of leprosy.
Irradiation and hypoxia promote homing of haematopoietic progenitor cells towards gliomas by TGF- -dependent HIF-1 -mediated induction of CXCL12
2006-07-12

Previously we defined a pathway of transforming growth factor beta (TGF-beta) and stromal cell-derived factor-1/CXC chemokine ligand 12 (SDF-1alpha/CXCL12) dependent migration of adult haematopoietic stem and progenitor cells (HPC) towards glioma cells in vitro and their homing to experimental gliomas in vivo. Hypoxia is a critical aspect of the microenvironment of gliomas and irradiation is an essential part of the standard therapy. To evaluate the therapeutic potential of HPC as vectors for a cell-based therapy of gliomas, we investigated the impact of hypoxia and irradiation on the attraction of HPC by glioma cells. Temozolomide (TMZ) treatment and hyperthermia served as controls. Supernatants of irradiated or hypoxic LNT-229 glioma cells promote HPC migration in vitro. Reporter assays reveal that the CXCL12 promoter activity is enhanced in LNT-229 cells at 24 h after irradiation at 8 Gy or after exposure to 1% oxygen for 12 h. The irradiation- and hypoxia-induced release of CXCL12 depends on hypoxia inducible factor-1 alpha (HIF-1alpha), but not on p53. Induction of transcriptional activity of HIF-1alpha by hypoxia or irradiation requires an intact TGF-beta signalling cascade. This delineates a novel stress signalling cascade in glioma cells involving TGF-beta, HIF-1alpha and CXCL12. Stress stimuli can be irradiation, hypoxia or TMZ, but not hyperthermia. Cerebral irradiation of nude mice at 21 days after intracerebral implantation of LNT-229 glioma induces tumour satellite formation and enhances the glioma tropism of HPC to the tumour bulk and even to these satellites in vivo. These data suggest that the use of HPC as cellular vectors in the treatment of glioblastoma may well be combined with irradiation or other anti-angiogenic therapies that induce tumour hypoxia.
Language lateralization in magnetoencephalography: two tasks to investigate hemispheric dominance
2006-07-12

Hemispheric specialization for language has been the focus of many studies, mainly using functional magnetic resonance imaging. Here, we used magnetoencephalography to investigate hemispheric dominance and time-dependent aspects of cortical language processing. We implemented a verb generation task and a newly designed vowel identification task. Eleven healthy adults were investigated. By using oscillatory magnetoencephalography spectral analysis, significant hemispheric differences were found for both tasks in cerebral language areas. Robust left-lateralization in frontal brain regions was observed with the verb generation task, confirming previous functional magnetic resonance imaging and magnetoencephalography studies. Our new vowel identification task yields significant left-lateralization in posterior language regions, making this silent and child-friendly task a valuable alternative for non-invasive language assessment in difficult populations.
Effects of Electrically Coupled Inhibitory Networks on Local Neuronal Responses to Intracortical Microstimulation
2006-07-13

Using in vivo multielectrode electrophysiology in mice, we investigated the underpinnings of a local, long-lasting firing rate suppression evoked by intracortical microstimulation. Synaptic inhibition contributes to this suppression as it was reduced by pharmacological blockade of γ-aminobutyric acid type B (GABA B ) receptors. Blockade of GABA B receptors also abolished the known sublinear addition of inhibitory response duration after repetitive electrical stimulation. Furthermore, evoked inhibition was weaker and longer in connexin 36 knockout (KO) mice that feature decoupled cortical inhibitory networks. In supragranular layers of KO mice even an unusually long excitatory response (≤50 ms) appeared that was never observed in wild-type (WT) mice. Furthermore, the spread and duration of very fast oscillations (&gt;200 Hz) evoked by microstimulation at a short latency were strongly enhanced in KO mice. In the spatial domain, lack of connexin 36 unmasked a strong anisotropy of inhibitory spread. Although its reach along layers was almost the same as that in WT mice, the spread across cortical depth was severely hampered. In summary, the present data suggest that connexin 36–coupled networks significantly shape the electrically evoked cortical inhibitory response. Electrical coupling renders evoked cortical inhibition more precise and strong and ensures a uniform spread along the two cardinal axes of neocortical geometry.
Structure of A197 from Sulfolobus Turreted Icosahedral Virus: a Crenarchaeal Viral Glycosyltransferase Exhibiting the GT-A Fold
2006-07-13

ABSTRACT Sulfolobus turreted icosahedral virus (STIV) was the first icosahedral virus characterized from an archaeal host. It infects Sulfolobus species that thrive in the acidic hot springs (pH 2.9 to 3.9 and 72 to 92°C) of Yellowstone National Park. The overall capsid architecture and the structure of its major capsid protein are very similar to those of the bacteriophage PRD1 and eukaryotic viruses Paramecium bursaria Chlorella virus 1 and adenovirus, suggesting a viral lineage that predates the three domains of life. The 17,663-base-pair, circular, double-stranded DNA genome contains 36 potential open reading frames, whose sequences generally show little similarity to other genes in the sequence databases. However, functional and evolutionary information may be suggested by a protein's three-dimensional structure. To this end, we have undertaken structural studies of the STIV proteome. Here we report our work on A197, the product of an STIV open reading frame. The structure of A197 reveals a GT-A fold that is common to many members of the glycosyltransferase superfamily. A197 possesses a canonical DXD motif and a putative catalytic base that are hallmarks of this family of enzymes, strongly suggesting a glycosyltransferase activity for A197. Potential roles for the putative glycosyltransferase activity of A197 and their evolutionary implications are discussed.
Human Cytomegalovirus Subverts the Functions of Monocytes, Impairing Chemokine-Mediated Migration and Leukocyte Recruitment
2006-07-13

ABSTRACT Despite their role in innate and adaptive immunity, during human cytomegalovirus (HCMV) infection, monocytes are considered to be an important target of infection, a site of latency, and vehicles for virus dissemination. Since chemokine receptors play crucial roles in monocyte activation and trafficking, we investigated the effects of HCMV on their expression and function. By using endotheliotropic strains of HCMV, we obtained high rates (roughly 50%) of in vitro-infected monocytes but only restricted viral gene expression. At 24 h after infection, while the chemokine receptors CX3CR and CCR7 were unaffected, CCR1, CCR2, CCR5, and CXCR4 were downmodulated on the cell surface and retained intracellularly. Structural components of the viral particles, but not viral gene expression or soluble factors released from infected cells, accounted for the changed localization of the receptor molecules and for the block of chemokine-driven migration. HCMV-infected monocytes indeed became unresponsive to inflammatory and homeostatic chemokines, although the basal cell motility and responsiveness to N -formyl-Met-Leu-Phe were unaffected or slightly increased. The production of inflammatory mediators responsible for the recruitment of other immune cells was also hampered by HCMV. Whereas endothelial and fibroblast cells infected by HCMV efficiently recruited leukocytes, infected monocytes were unable to recruit lymphocytes, monocytes, and neutrophils. Our data further highlight the complex level of interference exerted by HCMV on the host immune system.
In Vitro Synthesis of Cross-linked Murein and Its Attachment to Sacculi by PBP1A from Escherichia coli
2006-07-14

The penicillin-binding protein (PBP) 1A is a major murein (peptidoglycan) synthase in Escherichia coli. The murein synthesis activity of PBP1A was studied in vitro with radioactive lipid II substrate. PBP1A produced murein glycan strands by transglycosylation and formed peptide cross-links by transpeptidation. Time course experiments revealed that PBP1A, unlike PBP1B, required the presence of polymerized glycan strands carrying monomeric peptides for cross-linking activity. PBP1A was capable of attaching nascent murein synthesized from radioactive lipid II to nonlabeled murein sacculi. The attachment of the new material occurred by transpeptidation reactions in which monomeric triand tetrapeptides in the sacculi were the acceptors.
Unexpected Abundance of HLA Class II Presented Peptides in Primary Renal Cell Carcinomas
2006-07-15

Abstract Purpose: To elicit a long-lasting antitumor immune response, CD8+ and CD4+ T cells should be activated. We attempted to isolate HLA-DR–presented peptides directly from dissected solid tumors, in particular from renal cell carcinoma, to identify MHC class II ligands from tumor-associated antigens (TAA) for their use in peptide-based immunotherapy. Experimental Design: Tumor specimens were analyzed by immunohistochemical staining for their HLA class II expression. HLA class II peptides were subsequently isolated and identified by mass spectrometry. Gene expression analysis was done to detect genes overexpressed in tumor tissue. Peptides from identified TAAs were used to induce peptide-specific CD4+ T-cell responses in healthy donors and in tumor patients. Results: In the absence of inflammation, expression of MHC class II molecules is mainly restricted to cells of the immune system. To our surprise, we were able to isolate and characterize hundreds of class II peptides directly from primary dissected solid tumors, especially from renal cell carcinomas, and from colorectal carcinomas and transitional cell carcinomas. Infiltrating leukocytes expressed MHC class II molecules and tumor cells, very likely under the influence of IFNγ. Our list of identified peptides contains ligands from several TAAs, including insulin-like growth factor binding protein 3 and matrix metalloproteinase 7. The latter bound promiscuously to HLA-DR molecules and were able to elicit CD4+ T-cell responses. Conclusions: Thus, our direct approach will rapidly expand the limited number of T-helper epitopes from TAAs for their use in clinical vaccination protocols.
Proceedings of the Eighth International Workshop on Tree Adjoining Grammar and Related Formalisms
2006-07-15

As at previous TAG+ conferences, the topics addressed by the presentations belong to diverse areas of research, namely the mathematics of grammar formalisms and parsing, the syntax and semantics of natural languages, compact grammar representations and grammar engineering, the relation between TAG and other grammar formalisms, and applications to computational biology. By bringing together these different topics under the common theme of Tree Adjoining Grammars, the workshop promises to be an inspiring and fruitful event.