julilili42/papers huggingface dataset:
3D imaging of the whole spine at 3T compared to 1.5T: initial experiences
2006-06-01

Purpose: To describe our first experiences with a recently introduced 3T system for T2-weighted isotropic 3D whole-spine imaging. Material and Methods: Magnetic resonance imaging of the whole spine was performed by implementing an isotropic 3D fast spin-echo sequence with variable flip-angle refocusing pulses at 3T and 1.5T. Signal-to-noise ratio (SNR) was compared on both systems in eight subjects. Results: Mean values for SNR were significantly higher at 3T (346±214) for 1.0 mm voxel size compared to 1.5T (202±41), but showed considerably higher variability at 3T. At 3T, measurements with 0.9 mm voxel size were possible with similar SNR as with 1.0 mm voxel size at 1.5T. Conclusion: High-resolution 3D imaging of the whole spine is feasible at 3T with an increased SNR compared to 1.5T. Signal gain at 3T can be used to further increase spatial resolution. Pronounced interpatient variability of SNR at 3T may be a result of inhomogeneous RF deposition due to dielectric effects.
Can conductivity and stable isotope tracers determine water sources during flooding? An example from the Elbe River in 2002
2006-06-01

Abstract Despite drastic runoff variations, stable isotope data of water in the upstream part of the Elbe River showed remarkable similarity during, and two months after the flood of 2002. This homogeneity indicates that water sources remained the same and most likely represents dominant groundwater input regardless of the flood. While the latter remains the most plausible explanation, it was difficult to prove with water stable isotopes for the upstream part of the river. Overlapping isotope compositions of long‐term average precipitation data (as a proxy for the groundwater end member) and of the weighted average from precipitation events in August 2002 did not allow quantification of the groundwater component during flooding. This shows that better spatial and temporal sample resolution is necessary for enhanced understanding of water sources and mass balances during floods. Such mass balances were only possible in the estuary where conductivity and stable isotope tracers both revealed much stronger freshwater fluxes to the estuary during the flooding event of 2002 when compared to those of two months after the flood. Conductivity was also a good indicator for additions of more saline waters from the Saale River when the system was not affected by flooding. However, during the flood in August 2002, large volumes of low‐saline waters, most likely from shallow groundwater, masked these usually high conductivity values. This indicates that conductivity better reveals input of dissolved constituents, while the stable isotopes can better indicate sources of water input. Both tracers become most powerful when applied in combination for better understanding of water sources and river basin management.
Catalytic Efficiencies of Alkaline Proteinases from Microorganisms
2006-06-01

Catalytic efficiencies of proteinase K and mesentericopeptidase were determined using series of peptide-4-nitroanilide substrates and compared with those of subtilisin DY, savinase and esperase. For each enzyme the subsites S1-S4 were characterized. The data for the enzyme specificities were related to our high resolution X-ray models of the five enzymes and their complexes with peptides. The catalytic efficiencies of the alkaline proteinases are modulated by the hydrophobicity, solvent accessibility, flexibility and electrostatic effects in the substrate binding sites. The longer and nonpolar S1 loop offers more possibilities for hydrophobic interactions and increases the enzyme efficiency. S2 is a small narrow cleft which limits the possibilities for effective substitutions in P2. The wide specificity of S3 is due to its location on the protein surface of all investigated proteinases. The affinity of S4 for aromatic groups depends on the nature of the residues building the hydrophobic cavity.
BCI meeting 2005-workshop on technology: hardware and software
2006-06-01

This paper describes the outcome of discussions held during the Third International BCI Meeting at a workshop to review and evaluate the current state of BCI-related hardware and software. Technical requirements and current technologies, standardization procedures and future trends are covered. The main conclusion was recognition of the need to focus technical requirements on the users' needs and the need for consistent standards in BCI research.
GENETIC STUDY: The polymorphism GABABR1 T1974C[rs29230] of the GABAB receptor gene is not associated with the diagnosis of alcoholism or alcohol withdrawal seizures
2006-06-01

ABSTRACT As the inhibitory neurotransmitter gamma aminobutyric acid (GABA) modulates ethanol consumption, alcohol withdrawal symptoms and seizure generation by interacting with the GABA B receptor, the genes encoding for the GABA B receptor can be considered as candidate genes for alcoholism and alcohol withdrawal seizures (AWS). As the polymorphism GABA B R1 T1974C [rs29230] of the GABA B receptor gene had been associated with alcoholism and EEG abnormalities in prior studies, the present examination investigated if the polymorphism is associated with the diagnosis of alcoholism or AWS. After genotyping the allele and genotype frequencies of a group of alcoholics with a history of AWS ( n = 69) were compared with the results of a group of alcoholics with only mild withdrawal symptoms ( n = 97). Additionally a group of healthy controls ( n = 101) was compared with individuals with the diagnosis of alcoholism ( n = 220). As no significant differences were found between the compared groups, this study gave no further evidence for GABA B R1 T1974C [rs29230] as a candidate for alcoholism or AWS.
Emx2 in the developing hippocampal fissure region
2006-06-01

Abstract Mice deficient in transcription factor gene Emx2 show developmental alterations in the hippocampal dentate gyrus. Emx2 , however, is also expressed in the region around the developing hippocampal fissure. The developing fissure contains a radial glial scaffolding, and is surrounded by the outer marginal zone and the dentate marginal zone, which become specifically colonized by neurons and differentiate into stratum lacunosum‐moleculare and molecular layer of the dentate, respectively. In this study we show that the Emx2 mutant lacks the glial scaffolding of the fissure and has an outer marginal zone (precursor of the stratum lacunosum‐moleculare), as well as a dentate marginal zone severely reduced in size while most of the reelin (Reln) ‐expressing cells that should occupy it fail to be generated. We have also identified a subpopulation of hippocampal Reln ‐expressing cells of the marginal zone, probably born in the hem, expressing a specific combination of markers, and for which Emx2 is not essentially required. Additionally, we show differential mutant phenotypes of both Emx2 and Pax6 in neocortical vs. hippocampal Reln ‐expressing cells, indicating differential development of both subpopulations.
Comparison of Flexible Grasping Forceps and Stone Basket for Removal of Retracted Ureteral Stents
2006-06-01

Using a stone basket instead of grasping forceps in difficult cases of dislocated stents opens new possibilities for their cystoscopic and ureteroscopic removal. Because the superiority of the basket is counterbalanced by its higher costs, we suggest the basket extraction method only in difficult cases.
BCR-ABL Is Not an Immunodominant Antigen in Chronic Myelogenous Leukemia
2006-06-01

Abstract In the present study, we analyzed the involvement of the BCR-ABL protein in the induction of antigen-specific CTL in order to develop an immunotherapeutic approach in patients with chronic myelogenous leukemia (CML). To accomplish this, we generated dendritic cells (DC) in vitro and electroporated them with various sources of RNA harboring the chimeric bcr-abl transcript. These genetically engineered DCs were used as antigen-presenting cells for the induction of CTLs. By applying this approach, we found that the CTLs induced by DCs transfected with RNA extracted from bcr-abl–positive K-562 cells or CML blasts lysed DCs transfected with the corresponding RNA, but failed to recognize epitopes derived from the chimeric BCR-ABL fusion protein in 51Cr-release assays. In contrast, they were able to lyse autologous DCs electroporated with RNA isolated from patients with acute myeloid leukemia, indicating that antigens shared among these malignant cells are involved and recognized by these CTLs. In patients with CML in complete cytogenetic remission during IFN-α treatment, we detected some reactivity of CD8+ T cells against BCR-ABL in IFN-γ ELISPOT assays, which was weaker as compared with proteinase 3 (PR3)- or prame-directed responses, suggesting that the BCR-ABL protein is less immunogenic as compared with other CML-derived antigens. (Cancer Res 2006; 66(11): 5892-900)
Laparoscopic Splenectomy in an Adipose Elderly Patient With Symptomatic Non-Hodgkin Lymphoma-related Splenomegaly and Traumatic Central Splenic Hematoma
2006-06-01

During recent years, laparoscopic splenectomy has shown to be a safe and effective surgical approach in patients with hematologic disorders requiring spleen removal. Especially in cases with splenomegaly, the laparoscopic approach results in a shorter hospital stay and faster recovery of the patients. Due to the increasing experience in laparoscopy, this approach also is emerging to be a therapeutic option in patients with blunt abdominal trauma with splenic rupture or hematoma. We report the case of an 80-year-old female patient who underwent laparoscopic splenectomy for symptomatic splenomegaly due to non-hodgkin Lymphoma in combination with stable traumatic splenic hematoma after blunt abdominal trauma.
Visualization Aided Performance Tuning of Irregular Task-Parallel Computations
2006-06-01

This paper deals with a visualization-based approach to performance analyzing and tuning of highly irregular task-parallel applications. At its core lies a novel automatic layout algorithm for execution graphs which is based on Sugiyama's framework. Our visualization enables the application designer to reliably detect manifestations of parallel overhead and to investigate on their individual root causes. We particularly focus on structural properties of task-parallel computations which are hard to detect in a more analytical way, for example, false sharing and false parallelism. In addition, we discuss embedding our visualization into an integrated development environment, realizing a seamless work-flow for implementation, execution, analysis, and tuning of parallel programs.
Combined X-ray and electron microscopy study of MgB2powders, wires and tapes
2006-06-01

MgB2 wires, tapes and bulk samples produced within the EU-funded HIPERMAG project have been studied by a combination of X-ray diffraction and electron microscopy. The reaction layers forming at the interface between the ceramic core and Fe or Ni sheaths can be studied with both methods. The complementary techniques enable to study both the microstructure and the formation kinetics of the interface layers. Grain sizes can be determined either by direct observation or by analysis of the shape of X-ray diffraction peaks. Electron microscopy can detect B-rich secondary phases and phases present in small fractions that are not accessible by x-ray diffraction. On the other hand, synchrotron diffraction provides a fast and non-destructive method for the study of the main phases and their development during in-situ, high-temperature investigations. The combination of the two techniques is a very valuable tool for the optimisation of MgB2-based superconducting material.
Clinical outcome after cystectomy in patients with lymph node-positive bladder cancer
2006-06-01

Whereas radical cystectomy is the standard of care in high-grade, invasive bladder tumors, the extent of lymphadenectomy and its diagnostic and/or therapeutic potential is controversial. Independent predictors for lymph node involvement are T-stage, histological grading and lymphovascular invasion. Preoperative assessment, including 3D magnetic resonance imaging and sentinel node detection, are promising concepts for the future. The extension of lymphadenectomy is not yet defined, although prospective data regarding the absence of skipped lesions in the case of pelvic lymphadenectomy and the damage of autonomic nerves in the case of extensive lymphadenectomy are arguments for a limited or stepwise approach. Outcome of N1 patients appears to be nearly equivalent to N0 patients in organ-confined tumors, whereas the outcome of N3 patients is poor in all studies presented to date. Therefore, it has been suggested that a meticulous lymphadenectomy in N1 patients, with positive lymph nodes almost exclusively localized within the endopelvic region, has a long-term therapeutic impact in terms of an improvement in the patient's clinical prognosis. For N2 patients, a long-term survival benefit from extensive lymphadenectomy remains to be demonstrated. Recognizing the inevitably poor clinical prognosis in cases with gross nodal involvement (N3), the clinical value of an extended lymph node dissection in these patients is very questionable.
Al-alloyed MgB2: correlation of superconducting properties, microstructure and chemical composition
2006-06-01

Al-alloyed MgB2 was prepared by solid state reaction of Mg1-xAlx alloy and crystalline B powder particles. The nominal composition of the samples was Mg1-xAlxB2, with x = 0, 0.1, 0.2, 0.3. Residual resistivity (ρ0) of the samples measured by four-probe technique is comparable to the single crystals, indicating the excellent quality of these samples. The lattice parameters c and a decrease at a rate of 1.15 pm and 0.17 pm per at.% Al, respectively. Superconducting transition temperature (Tc) determined by measuring the resistive superconducting transition, decreases with increasing Al alloying at a rate of 1.56 K/at.% Al. Microstructure and chemical composition have been investigated by scanning electron microscopy (SEM), electron probe microanalysis (EPMA), and transmission electron microscopy (TEM). Al is incorporated into MgB2 grains of ∼1 μm size by substitution of Mg lattice sites with Al. Al was found to be distributed inhomogenously which partially explains the broadening of the superconducting transition width (ΔTc) with increasing Al mole fraction. Al alloyed samples contain large (∼15 μm) and small (∼ 2 μm ) secondary phases embedded in the (Mg, Al)B2 matrix. The composition of large secondary phases is found to be (Mg, Al)B7+δ, with the mole fraction of excess boron (δ) increasing from 0.99 at.% in pure sample to 4.14 at.% in highest alloyed sample. The Al to Mg mole fraction ratio in these large secondary phases is about half of that in the matrix. The size and density of the large secondary phases increased with increase in Al mole fraction. The secondary phases constitute less than 4% of the total sample volume and are thus not likely to affect the bulk superconductivity.
TU‐C‐ValB‐04: Margin‐Less Prostate IMRT Plans, Directly Optimized for TCP and NTCP Including Geometric Uncertainties
2006-06-01

Purpose: To account for geometric uncertainties without the use of margins during IMRT planning such that optimal values are obtained for the population averaged TCP and NTCP functions. Methods and materials: A new method of computing cost functions was implemented within the IMRT planning tool Hyperion. Population‐averaged values of biologic score functions (TCP pop and NTCP pop ) are optimized, simulating random errors by blurring the dose, and systematic errors by displacing target and OARs relative to the dose distribution. For 19 prostate (and seminal vesicle) patients, treatment plans for a five beam setup were created, optimising TCP pop while constraining rectum NTCP pop and the maximum dose to the target. Gaussian distributions were used for the systematic and random errors (translations only, no attempt was made to model rotations or deformations). Since geometric uncertainties were accounted for within the cost functions, no CTV to PTV margin was used. For comparison, conventional plans were created using a CTV‐to‐PTV margin (M=2.5Σ+0.7σ) and a Simultaneous Integrated Boost (SIB) technique (68Gy to the above PTV, 78Gy to PTV boost with 5mm margin, 0mm towards rectum). The resulting plans were evaluated using an independent tool that simulates the effects of geometric uncertainties. Results: Compared to conventional plans, our new technique reduced the planned dose to the rectum, while increasing the volume receiving 78Gy. We ensured that TCP pop of the new technique was not smaller than for conventional techniques. The average rectum NTCP pop values were 14% (margin recipe), 8% (SIB), and 4% (new technique), for average TCP pop values of 69%, 70%, and 71%. Conclusions: The computation of TCP and NTCP including knowledge of geometric uncertainties within the inverse IMRT optimization loop is feasible (less than 1 hour optimization time), and results in robust prostate treatment plans with an improved balance between local control and rectum toxicity.
KIT mutation in mast cells and other bone marrow hematopoietic cell lineages in systemic mast cell disorders: a prospective study of the Spanish Network on Mastocytosis (REMA) in a series of 113 patients
2006-06-02

Despite the relevance of the c-kit/stem cell factor (SCF) signaling pathway in mast cell (MC) diseases, the exact frequency of KIT mutations in different compartments of bone marrow (BM) hematopoietic cells of individuals with systemic mastocytosis (SM), and its different diagnostic categories, remains unknown. In this study, we prospectively analyzed the presence of KIT mutations in fluorescence-activated cell-sorting (FACS)- purified populations of BM MCs (n = 113) and other BM cell compartments (n = 67) from adults with SM. Our results show the presence of D816V KIT mutation in virtually all adults (93%) with indolent and aggressive forms of SM, except well-differentiated SM (29%), while other KIT mutations were rarely (< 3%) detected. In around one-third of patients with mutated MCs, the KIT mutation was also detected in CD34+ hematopoietic cells and eosinophils, and, to a lesser extent, in monocytic, neutrophil-lineage BM precursor cells and lymphocytes. Most patient with poor-prognosis SM (81%) carried the KIT mutation in 2 or more BM myeloid cell populations, while this was detected in a smaller proportion (27%) of indolent cases. These results would support the notion that KIT mutation is a hallmark of adult SM where it targets a pluripotent hematopoietic stem cell, and may contribute to explaining previously observed discrepancies in the literature.
Impaired intestinal and renal glucose transport in PDK-1 hypomorphic mice
2006-06-02

The phosphoinositide-dependent kinase-1 (PDK-1) activates the serum- and glucocorticoid-inducible kinase and protein kinase B isoforms, which, in turn, are known to stimulate the renal and intestinal Na + -dependent glucose transporter 1. The present study has been performed to explore the role of PDK-1 in electrogenic glucose transport in small intestine and proximal renal tubules. To this end, mice expressing ∼20% of PDK-1 ( pdk1 hm ) were compared with their wild-type littermates ( pdk1 wt ). According to Ussing chamber experiments, electrogenic glucose transport was significantly smaller in the jejunum of pdk1 hm than of pdk1 wt mice. Similarly, proximal tubular electrogenic glucose transport in isolated, perfused renal tubule segments was decreased in pdk1 hm compared with pdk1 wt mice. Intraperitoneal injection of 3 g/kg body wt glucose resulted in a similar increase of plasma glucose concentration in pdk1 hm and in pdk1 wt mice but led to a higher increase of urinary glucose excretion in pdk1 hm mice. In conclusion, reduction of functional PDK-1 leads to impairment of electrogenic intestinal glucose absorption and renal glucose reabsorption. The experiments disclose a novel element of glucose transport regulation in kidney and small intestine.
Excellent response to apomorphine in Parkinsonism with optic atrophy unresponsive to oral antiparkinsonian medication
2006-06-05

Abstract Two patients presented with the cardinal symptoms of Parkinson's disease (PD), which had developed slowly and progressively. One patient underwent brain imaging of the dopaminergic system, the results of which were compatible with PD. However, both patients showed no response to L ‐dopa or oral dopaminergic medication. They also had optic nerve atrophy of unknown etiology. The severe motor symptoms of both patients were conspicuously alleviated by apomorphine delivered subcutaneously. One patient underwent bilateral subthalamic nucleus deep brain stimulation, which also proved effective. © 2006 Movement Disorder Society
The Fumitremorgin Gene Cluster of Aspergillus fumigatus: Identification of a Gene Encoding Brevianamide F Synthetase
2006-06-06

Abstract A gene encoding a putative dimodular nonribosomal peptide synthetase (NRPS) was identified within a gene cluster of Aspergillus fumigatus , a species reported to produce fumitremorgins and other prenylated alkaloids. The gene was deleted and overexpressed in the genome reference strain Af293, and was also expressed in the naïve host Aspergillus nidulans , which lacks the equivalent gene cluster. While neither fumitremorgins nor the dipeptide brevianamide F ( cyclo ‐ L ‐Trp‐ L ‐Pro), an early intermediate, were detected in wild‐type and deletion strains of A. fumigatus , brevianamide F accumulated in fungal cultures following increased expression of the NRPS gene in both A. fumigatus and A. nidulans . We conclude that the gene Afu8g00170, named ftmA , encodes the NRPS brevianamide synthetase. Brevianamide F is the precursor of a variety of fungal prenylated alkaloids with biological activity, including fumitremorgins A, B and C and tryprostatin B.
Interaction of TLR2 and TLR4 Ligands with the N-terminal Domain of Gp96 Amplifies Innate and Adaptive Immune Responses
2006-06-06

Activation of dendritic cells by ligands for Toll-like receptors (TLR) is a crucial event in the initiation of innate and adaptive immune responses. Several classes of TLR ligands have been identified that interact with distinct members of the TLR-family. TLR4 ligands include lipopolysaccharide derived from different Gram-negative bacteria and viral proteins. Recent reports have demonstrated the TLR-mediated activation of dendritic cells by heat shock proteins (HSPs). However, doubts were raised as to what extent this effect was due to lipopolysaccharide contaminations of the HSP preparations. We re-examined this phenomenon using Gp96 or its N-terminal domain, nominally endotoxin-free (<0.5 enzyme units/mg). As described previously, innate immune cells are activated by Gp96 at high concentrations (> or =50 microg/ml) but not at lower concentrations. However, preincubation of low amounts of Gp96 with TLR2 and TLR4 ligands at concentrations unable to activate dendritic cells by themselves results in the production of high levels of proinflammatory cytokines, up-regulation of activation markers, and amplification of T cell activation. Our results provide significant new insights into the mechanism of HSP-mediated dendritic cell activation and present a new function of HSPs in the amplification of dendritic cell activation by bacterial products and induction of adaptive immune responses.
The Rift: Explaining Europe's Divergent Iraq Policies in the Run-Up of the American-Led War on Iraq
2006-06-06

Journal Article The Rift: Explaining Europe's Divergent Iraq Policies in the Run-Up of the American-Led War on Iraq Get access Jürgen Schuster, Jürgen Schuster Eberhard Karls Universität Tübingen Search for other works by this author on: Oxford Academic Google Scholar Herbert Maier Herbert Maier Universität Regensburg Search for other works by this author on: Oxford Academic Google Scholar Foreign Policy Analysis, Volume 2, Issue 3, July 2006, Pages 223–244, https://doi.org/10.1111/j.1743-8594.2006.00032.x Published: 02 June 2006