julilili42/papers huggingface dataset:
GLUT1 mutations are a cause of paroxysmal exertion-induced dyskinesias and induce hemolytic anemia by a cation leak
2008-04-30

Paroxysmal dyskinesias are episodic movement disorders that can be inherited or are sporadic in nature. The pathophysiology underlying these disorders remains largely unknown but may involve disrupted ion homeostasis due to defects in cell-surface channels or nutrient transporters. In this study, we describe a family with paroxysmal exertion-induced dyskinesia (PED) over 3 generations. Their PED was accompanied by epilepsy, mild developmental delay, reduced CSF glucose levels, hemolytic anemia with echinocytosis, and altered erythrocyte ion concentrations. Using a candidate gene approach, we identified a causative deletion of 4 highly conserved amino acids (Q282_S285del) in the pore region of the glucose transporter 1 (GLUT1). Functional studies in Xenopus oocytes and human erythrocytes revealed that this mutation decreased glucose transport and caused a cation leak that alters intracellular concentrations of sodium, potassium, and calcium. We screened 4 additional families, in which PED is combined with epilepsy, developmental delay, or migraine, but not with hemolysis or echinocytosis, and identified 2 additional GLUT1 mutations (A275T, G314S) that decreased glucose transport but did not affect cation permeability. Combining these data with brain imaging studies, we propose that the dyskinesias result from an exertion-induced energy deficit that may cause episodic dysfunction of the basal ganglia, and that the hemolysis with echinocytosis may result from alterations in intracellular electrolytes caused by a cation leak through mutant GLUT1.
SBMLsqueezer: A CellDesigner plug-in to generate kinetic rate equations for biochemical networks
2008-04-30

SBMLsqueezer considers the annotation of all participating reactants, products and regulators when generating rate laws for reactions. Thus, for each reaction, only applicable kinetic formulas are considered. This modeling scheme creates kinetics in accordance with the diagrammatic representation. In contrast most previously published tools have relied on the stoichiometry and generic modulators of a reaction, thus ignoring and potentially conflicting with the information expressed through the process diagram. Additional material and the source code can be found at the project homepage (URL found in the Availability and requirements section).
Three-dimensional constructive interference in steady-state magnetic resonance imaging in syringomyelia: advantages over conventional imaging
2008-04-30

Object Neuroradiology has become indispensable in detecting the pathophysiology in syringomyelia. Constructive interference in steady-state (CISS) magnetic resonance (MR) imaging can provide superior contrast at the sub-arachnoid tissue borders. As this region is critical in preoperative evaluation, the authors hypothesized that CISS imaging would provide superior assessment of syrinx pathology and surgical planning. Methods Based on records collected from a database of 130 patients with syringomyelia treated at the authors' institution, 59 patients were prospectively evaluated with complete neuroradiological examinations. In addition to routine acquisitions with FLAIR, T1- and T2-weighted, and contrast-enhanced MR imaging series, the authors obtained sagittal cardiac-gated sequences to visualize cerebrospinal fluid (CSF) pulsations and axial 3D CISS MR sequences to detect focal arachnoid webs. Statistical qualitative and quantitative evaluations of spinal cord/CSF contrast, spinal cord/CSF delineation, motion artifacts, and artifacts induced by pulsatile CSF flow were performed. Results The 3D CISS MR sequences demonstrated a contrast-to-noise ratio significantly better than any other routine imaging sequence (p &lt; 0.001). Moreover, 3D CISS imaging can detect more subarachnoid webs and cavitations in the syrinx than T2-weighted MR imaging with less flow-void artifact. The limitation of 3D CISS imaging is a susceptibility to motion artifacts that can cause reduced spatial resolution. Lengthy acquisition times for axial segments can be reduced with multiplanar reconstruction of 3D CISS–generated sagittal images. Conclusions Constructive interference in steady-state imaging is the MR sequence of choice in the preoperative evaluation of syringomyelia, allowing significantly higher detection rates of focal subarachnoid webs, whereas standard T2-weighted MR imaging shows turbulent CSF flow voids. Constructive interference in steady-state MR imaging enables the neurosurgeon to accurately identify cases requiring decompression for obstructed CSF. Motion artifacts can be eliminated with technical variations.
Comparison of imaging techniques in the diagnosis of bridging bronchus
2008-04-30

Bridging bronchus (BB) is a rare, congenital bronchial anomaly that is frequently associated with congenital cardiac malformations, especially left pulmonary artery sling. It represents an anomalous bronchus to the right originating from the left main bronchus. Discrimination from other bronchial anomalies is important, since BB is frequently associated with bronchial stenoses due to abnormal cartilage rings. This case study describes the findings of bronchoscopy, bronchography and multidetector computed tomography (MDCT) in three patients. Bronchoscopy was helpful in the description of the severity and length of bronchial stenoses. However, it was not possible to establish a diagnosis of BB based on this method in two patients, since it is difficult or even impossible to differentiate the bifurcation from the pseudocarina. It was not possible to establish the correct diagnosis in all patients based on bronchography or MDCT. MDCT was able to depict the relationship of bronchial and vascular structures, which is particularly important in patients with pulmonary artery sling. Multidetector computed tomography is preferable to bronchography as it is less invasive and due to its short acquisition time it can be performed in children with severe respiratory disease. In the current authors’ experience, detection of cartilage rings still requires flexible bronchoscopy.
Combinatorial Biosynthesis, Metabolic Engineering and Mutasynthesis for the Generation of New Aminocoumarin Antibiotics
2008-04-30

The aminocoumarin antibiotics novobiocin, clorobiocin and coumermycin A1 are produced by different Streptomyces strains. They are potent inhibitors of bacterial gyrase and topoisomerase IV, and novobiocin has been licensed as antibiotic for clinical use (Albamycin). They also have potential applications in oncology. The biosynthetic gene clusters of all three antibiotics have been cloned and sequenced, and the function of nearly all genes contained therein has been elucidated. Rapid and versatile methods have been developed for the heterologous expression of these biosynthetic gene clusters, and in Streptomyces coelicolor M512 as heterologous host these antibiotics were produced in yields comparable to those in the natural producer strains. lambda RED-mediated homologous recombination was used for genetic modification of the gene clusters in Escherichia coli. The phage PhiC31 attachment site and integrase functions were introduced into the cosmid backbones and employed for stable integration of the clusters into the genome of the heterologous hosts. Modification of the clusters by single or multiple gene replacements or gene deletions resulted in the formation of numerous new aminocoumarin derivatives, providing an efficient tool for the rational generation of antibiotics with modified structure. Additionally, many new antibiotics were generated by mutasynthesis experiments, i.e. the targeted deletion of genes required for the biosynthesis of a certain structural moiety of the antibiotic, and the replacement of this moiety by structural analogs which were added to the culture broth. The diversity of new structures obtained by this approach could be expanded by further genetic modifications of the gene deletion mutants, especially by expression of heterologous biosynthetic enzymes with appropriate substrate specificity.
A comparative molecular force spectroscopy study of homophilic JAM‐A interactions and JAM‐A interactions with reovirus attachment protein σ1
2008-04-30

Abstract JAM‐A belongs to a family of immunoglobulin‐like proteins called junctional adhesion molecules (JAMs) that localize at epithelial and endothelial intercellular tight junctions. JAM‐A is also expressed on dendritic cells, neutrophils, and platelets. Homophilic JAM‐A interactions play an important role in regulating paracellular permeability and leukocyte transmigration across epithelial monolayers and endothelial cell junctions, respectively. In addition, JAM‐A is a receptor for the reovirus attachment protein, σ1. In this study, we used single molecular force spectroscopy to compare the kinetics of JAM‐A interactions with itself and σ1. A chimeric murine JAM‐A/Fc fusion protein and the purified σ1 head domain were used to probe murine L929 cells, which express JAM‐A and are susceptible to reovirus infection. The bond half‐life ( t 1/2 ) of homophilic JAM‐A interactions was found to be shorter ( ) than that of σ1/JAM‐A interactions ( ). These results are in accordance with the physiological functions of JAM‐A and σ1. A short bond lifetime imparts a highly dynamic nature to homophilic JAM‐A interactions for regulating tight junction permeability while stable interactions between σ1 and JAM‐A likely anchor the virus to the cell surface and facilitate viral entry. Copyright © 2008 John Wiley &amp; Sons, Ltd.
An Exocyst Complex Functions in Plant Cell Growth inArabidopsisand Tobacco
2008-05-01

Abstract The exocyst, an octameric tethering complex and effector of Rho and Rab GTPases, facilitates polarized secretion in yeast and animals. Recent evidence implicates three plant homologs of exocyst subunits (SEC3, SEC8, and EXO70A1) in plant cell morphogenesis. Here, we provide genetic, cell biological, and biochemical evidence that these and other predicted subunits function together in vivo in Arabidopsis thaliana. Double mutants in exocyst subunits (sec5 exo70A1 and sec8 exo70A1) show a synergistic defect in etiolated hypocotyl elongation. Mutants in exocyst subunits SEC5, SEC6, SEC8, and SEC15a show defective pollen germination and pollen tube growth phenotypes. Using antibodies directed against SEC6, SEC8, and EXO70A1, we demonstrate colocalization of these proteins at the apex of growing tobacco pollen tubes. The SEC3, SEC5, SEC6, SEC8, SEC10, SEC15a, and EXO70 subunits copurify in a high molecular mass fraction of 900 kD after chromatographic fractionation of an Arabidopsis cell suspension extract. Blue native electrophoresis confirmed the presence of SEC3, SEC6, SEC8, and EXO70 in high molecular mass complexes. Finally, use of the yeast two-hybrid system revealed interaction of Arabidopsis SEC3a with EXO70A1, SEC10 with SEC15b, and SEC6 with SEC8. We conclude that the exocyst functions as a complex in plant cells, where it plays important roles in morphogenesis.
BART: A modular toolkit for coreference resolution
2008-05-01

Developing a full coreference system able to run all the way from raw text to semantic interpretation is a considerable engineering effort. Accordingly, there is very limited availability of off-the shelf tools for researchers whose interests are not primarily in coreference or others who want to concentrate on a specific aspect of the problem. We present BART, a highly modular toolkit for developing coreference applications. In the Johns Hopkins workshop on using lexical and encyclopedic knowledge for entity disambiguation, the toolkit was used to extend a reimplementation of the Soon et al. (2001) proposal with a variety of additional syntactic and knowledge-based features, and experiment with alternative resolution processes, preprocessing tools, and classifiers. 1.
Interplay of conjugating enzymes with OATP uptake transporters and ABCC/MRP efflux pumps in the elimination of drugs
2008-05-01

OATP uptake transporters, conjugating enzymes, and ABCC2/MRP2 work in concert to enable the hepatobiliary elimination of anionic drugs and their metabolites. It is increasingly important to understand how genetic variants of these transporters and enzymes influence the interindividual variability of drug elimination.
Neural correlates of verbal episodic memory in patients with MCI and Alzheimer's disease––a VBM study
2008-05-01

Abstract Objective The hippocampus is a key area for episodic memory processes. Hippocampal atrophy is a hallmark feature of Alzheimer's disease (AD). We used a new and automatized morphometric technique to better characterize brain atrophy in subjects with different levels of cognitive deficit. Methods In this study 21 participants with Mild Cognitive Impairment (MCI), 12 patients with early AD and 29 elderly control subjects were subjected to high resolution MRI and a neuropsychological test battery. Brain volume across participants, measured by voxel‐based morphometry (VBM), was correlated with verbal memory capacity, measured with a verbal memory test (VLMT). Results Atrophy in the anterior hippocampus, the ento‐ and perirhinal cortex as well as the parahippocampal gyrus, middle temporal gyrus and anterior cingulate cortex correlated closely with episodic memory performance. Conclusions These brain areas are known to subserve episodic encoding of verbal material. The data contribute to a better understanding of atrophic brain processes in subjects at risk for AD. A combination of neuropsychological testing and voxel‐based morphometry may serve as a diagnostic tool in the future. Copyright © 2008 John Wiley &amp; Sons, Ltd.
Quantification of Pancreatic Lipomatosis and Liver Steatosis by MRI: Comparison of In/Opposed-Phase and Spectral-Spatial Excitation Techniques
2008-05-01

The presented results suggest that both methods are reliable tools for pancreatic and hepatic fat quantification. However, for reliable assessment of quantitative fat by the in-phase/opposed-phase technique, an additional measurement of T2* seems crucial.
Response of Dystrophic Calcification to Intravenous Immunoglobulin
2008-05-01

A 56-year-old woman with an 8-year history of CREST syndrome, a variant of scleroderma, presented with increasing calcium deposits that were causing inflammation and swelling of the index finger of her left hand (Figure 1), as well as Raynaud phenomenon, telangiectasia, and mild sclerosis of her fingers. She had intense pain and extreme morbidity and was severely handicapped in her office job. A barium swallow test revealed moderate esophageal dysmotility, and a computed tomographic scan demonstrated mild pulmonary fibrosis. Spirometry revealed normal values, particularly for carbon monoxide diffusing capacity and inspiratory vital capacity. There was no evidence of pulmonary hypertension, cardiac or renal manifestations, or systemic metabolic abnormalities in calcium regulation. Serologic tests were positive for antinuclear antibodies and anti–Scl-70 antibodies. Long-term treatment with D-penicillamine (30 weeks), warfarin sodium (13 weeks), and extracorporeal shock wave lithotripsy did not result in any improvement in the cutaneous calcifications or inflammation. The plastic surgeons refused to consider a surgical approach because of the risk of protracted and complicated wound healing.
Nonlinear optical performance of chemically tailored phthalocyanine–polymer films as solid-state optical limiting devices
2008-05-01

Linear and nonlinear optical (NLO) investigations into the material response of a selection of solid-state phthalocyanine?polymer films are reported. Using the simple method of sequentially deposited spin cast phthalocyanine doped polymer films, one can characterize the resulting NLO response by means of the Z-scan technique with 6?ns pulses at 532?nm. Effective optical coefficients are calculated with a nonlinear absorption based model and their intensity dependence is investigated. When compared with the phthalocyanine solutions, the phthalocyanine?poly(methyl methacrylate) (PMMA) films exhibit excellent nonlinear extinction effects, outperforming corresponding phthalocyanine solutions by 2?3 orders of magnitude. Molecular engineering of metallophthalocyanine compounds, through both axial and peripheral substitutes, has led to an optimization of the resulting NLO response in the nanosecond regime. Mechanistic implications of the optical dissipation for various substituted phthalocyanines are also discussed and examined.
Towards a Reference Corpus of Web Genres for the Evaluation of Genre Identification Systems
2008-05-01

We present initial results from an international and multi-disciplinary research collaboration that aims at the construction of a reference\\n\\ncorpus of web genres. The primary application scenario for which we plan to build this resource is the automatic identification of web\\n\\ngenres. Web genres are rather difficult to capture and to describe in their entirety, but we plan for the finished reference corpus to contain\\n\\nmulti-level tags of the respective genre or genres a web document or a website instantiates. As the construction of such a corpus is by no\\n\\nmeans a trivial task, we discuss several alternatives that are, for the time being, mostly based on existing collections. Furthermore, we\\n\\ndiscuss a shared set of genre categories and a multi-purpose tool as two additional prerequisites for a reference corpus of web genres.
Illustrative Hybrid Visualization and Exploration of Anatomical and Functional Brain Data
2008-05-01

Abstract Common practice in brain research and brain surgery involves the multi‐modal acquisition of brain anatomy and brain activation data. These highly complex three‐dimensional data have to be displayed simultaneously in order to convey spatial relationships. Unique challenges in information and interaction design have to be solved in order to keep the visualization sufficiently complete and uncluttered at the same time. The visualization method presented in this paper addresses these issues by using a hybrid combination of polygonal rendering of brain structures and direct volume rendering of activation data. Advanced rendering techniques including illustrative display styles and ambient occlusion calculations enhance the clarity of the visual output. The presented rendering pipeline produces real‐time frame rates and offers a high degree of configurability. Newly designed interaction and measurement tools are provided, which enable the user to explore the data at large, but also to inspect specific features closely. We demonstrate the system in the context of a cognitive neurosciences dataset. An initial informal evaluation shows that our visualization method is deemed useful for clinical research.
Registration of colored 3D point clouds with a Kernel-based extension to the normal distributions transform
2008-05-01

We present a new algorithm for scan registration of colored 3D point data which is an extension to the Normal Distributions Transform (NDT). The probabilistic approach of NDT is extended to a color-aware registration algorithm by modeling the point distributions as Gaussian mixture-models in color space. We discuss different point cloud registration techniques, as well as alternative variants of the proposed algorithm. Results showing improved robustness of the proposed method using real-world data acquired with a mobile robot and a time-of-flight camera are presented.
Numerical analysis of coupled hydrosystems based on an object-oriented compartment approach
2008-05-01

In this paper we present an object-oriented concept for numerical simulation of multi-field problems for coupled hydrosystem analysis. Individual (flow) processes modelled by a particular partial differential equation, i.e. overland flow by the shallow water equation, variably saturated flow by the Richards equation and saturated flow by the groundwater flow equation, are identified with their corresponding hydrologic compartments such as land surface, vadose zone and aquifers, respectively. The object-oriented framework of the compartment approach allows an uncomplicated coupling of these existing flow models. After a brief outline of the underlying mathematical models we focus on the numerical modelling and coupling of overland flow, variably saturated and groundwater flows via exchange flux terms. As each process object is associated with its own spatial discretisation mesh, temporal time-stepping scheme and appropriate numerical solution procedure. Flow processes in hydrosystems are coupled via their compartment (or process domain) boundaries without giving up the computational necessities and optimisations for the numerical solution of each individual process. However, the coupling requires a bridging of different temporal and spatial scales, which is solved here by the integration of fluxes (spatially and temporally). In closing we present three application examples: a benchmark test for overland flow on an infiltrating surface and two case studies – at the Borden site in Canada and the Beerze–Reusel drainage basin in the Netherlands.
Absorption or Adsorption? Insights from Molecular Probesn-Alkanes and Cycloalkanes into Modes of Sorption by Environmental Solid Matrices
2008-05-01

Environmental solid matrices such as soils and aerosols contain a variety of absorbents (e.g., organic matter) and adsorbents (rigid carbonaceous geosorbents, minerals) but the contribution of both modes of sorption to the overall sorption behavior is often uncertain. Absorption of a cycloalkane from air to bulk phases is generally stronger than that of the n-alkane of the same number of carbon atoms, while adsorption onto surfaces does not differ between these two compounds, or rather favors the n-alkane. The presentstudy explores this characteristic sorption behavior of alkanes and eventually claims that determination of n-alkane-to-cycloalkane sorption coefficient ratios (Kn/Kc) helps elucidate the mode of sorption by complex mixtures in the environment. Differences in sorption coefficients from air (K) between n- and cycloalkanes were explained based on the linear free energy relationship (LFER) models in the form log K = - a V+ b MR + constant, where V and MR are the molar volume and the molar refraction, respectively. The LFER models predict Kn/Kc < 1 for absorption and Kn/Kc approximately 1 for adsorption. An extensive number of experimental K values of C5--C8 alkanes for known ab- and adsorbents were evaluated. The data matched the model expectations and indeed exhibited a distinct difference in Kn/Kc, between ab- and adsorption. Steric factors due to sorbate and sorbent geometries generally favored adsorption of n-alkanes over that of cycloalkanes (Kn/Kc > 1), clarifying the contrast between the two sorption modes even more. The application to environmental solid matrices is demonstrated using sorption data for diesel soot, aerosols and snow. The results are in excellent agreement with previous discussions on the modes of sorption in these materials.
Nonlinear predictive control of an omnidirectional robot dribbling a rolling ball
2008-05-01

This paper focuses on the dribbling control problem of an omnidirectional mobile robot and a rolling ball in the RoboCup Middle Size domain. Because the ball easily slides away from the robot when the ball moves along a curve, dribbling control is more challenging than the normal mobile robot motion control problem. Based on an introduced reference point with respect to the robot body and a sophisticated planning method of robot pose, the nonlinear predictive control is used to steer the robot to follow the planned poses so as to prevent the ball from leaving the robot. Real-world experiments showed that nonlinear predictive control is capable of solving the pose following problem in a real-time application.