julilili42/papers huggingface dataset:
Melanoma patients respond to a new HLA‐A*01‐presented antigenic ligand derived from a multi‐epitope region of melanoma antigen TRP‐2
2005-04-26

Abstract Tyrosinase‐related protein‐2 (TRP‐2) is a known target antigen of spontaneous cytotoxic T cell responses in melanoma patients. Its frequent expression in metastatic tumors suggests that it might be an ideal candidate antigen for T cell‐based immunotherapy. To provide knowledge about TRP‐2‐derived T cell epitopes useful for immunotherapy we applied a “reverse immunology strategy” based on repeated in vitro peptide stimulation of peripheral blood lymphocytes (PBL) from normal donors with predicted HLA‐A*01 ligands. This led to the identification of TRP‐2 181–190 as the first HLA‐A*01‐presented TRP‐2‐derived epitope. T‐cell lines specific for peptide TRP‐2 181–190 could be established from PBL of 50% of the normal HLA‐A*01 + donors tested. Such T cells responded specifically to autologous dendritic cells transduced virally with TRP‐2, as well as to HLA‐A*01 + , TRP‐2 + melanoma cells, although tumor cells had to be pretreated with IFN‐γ to become susceptible to T cell recognition. Interestingly, short‐term in vitro peptide stimulation of PBL from HLA‐A*01 + melanoma patients showed the presence of TRP‐2 181–190 ‐reactive CD8 + T cells in some donors, suggesting their in vivo sensitization. Because TRP‐2 181–190 overlaps with the known HLA‐A*0201‐presented epitope TRP‐2 180–188 , an 11mer peptide encompassing both epitopes might be of specific value for vaccination of a broad population of melanoma patients. © 2005 Wiley‐Liss, Inc.
Cognitive functions correlate with white matter architecture in a normal pediatric population: A diffusion tensor MRI study
2005-04-27

Abstract A possible relationship between cognitive abilities and white matter structure as assessed by magnetic resonance diffusion tensor imaging (DTI) was investigated in the pediatric population. DTI was performed on 47 normal children ages 5–18. Using a voxelwise analysis technique, the fractional anisotropy (FA) and mean diffusivity (MD) were tested for significant correlations with Wechsler full‐scale IQ scores, with subject age and gender used as covariates. Regions displaying significant positive correlations of IQ scores with FA were found bilaterally in white matter association areas, including frontal and occipito‐parietal areas. No regions were found exhibiting correlations of IQ with MD except for one frontal area significantly overlapping a region containing a significant correlation with FA. The positive direction of the correlation with FA is the same as that found previously with age, and indicates a positive relationship between fiber organization and/or density with cognitive function. The results are consistent with the hypothesis that regionally specific increased fiber organization is a mechanism responsible for the normal development of white matter tracts. Hum Brain Mapp, 2005. © 2005 Wiley‐Liss, Inc.
A kinetic model for dynamic [18F]-Fmiso PET data to analyse tumour hypoxia
2005-04-27

A method is presented to identify and quantify hypoxia in human head-and-neck tumours based on dynamic [18F]-Fmiso PET patient data, using a model for the tracer transport. A compartmental model was developed, inspired by recent immunohistochemical investigations with the tracer pimonidazole. In order to take the trapping of the tracer and the diffusion in interstitial space into account, the kinetic model consists of two compartments and a specific input function. This voxel-based data analysis allows us to decompose the time-activity curves (TACs) into their perfusion, diffusion and hypoxia-induced retention components. This characterization ranges from well perfused tumours over diffusion limited hypoxia to strong hypoxia and necrosis. The overall shape of the TAC and the model parameters may point at the structural architecture of the tissue sample. The model addresses the two main problems associated with hypoxia imaging with PET. Firstly, the hypoxic areas are spatially separated from well perfused vessels, causing long diffusion times of the tracer. Secondly, tracer uptake occurs only in viable hypoxic cells, which constitute only a small subpopulation in the presence of necrosis. The resulting parameters such as the concentration of hypoxic cells and the perfusion are displayed in parameter plots ('hypoxia map'). Quantification of hypoxia performed with the presented kinetic model is more reliable than a criterion based on static standardized uptake values (SUV) at an early timepoint, because severely hypoxic/necrotic tissues show low uptake and are thus overlooked by SUV threshold identification. The derived independent measures for perfusion and hypoxia may provide a basis for individually adapted treatment planning.
Measurement of Helicity-Dependent Photoabsorption Cross Sections on the Neutron from 815 to 1825 MeV
2005-04-28

Helicity-dependent total photoabsorption cross sections on the deuteron have been measured for the first time at ELSA (Bonn) in the photon energy range from 815 to 1825 MeV. Circularly polarized tagged photons impinging on a longitudinally polarized LiD target have been used together with a highly efficient 4pi detector system. The data around 1 GeV are not compatible with predictions from existing multipole analyses. From the measured energy range an experimental contribution to the GDH integral on the neutron of [33.9 +/- 5.5(stat) +/- 4.5(syst)] microb is extracted.
Hydrophobically Assisted Switching Phase Synthesis:  The Flexible Combination of Solid-Phase and Solution-Phase Reactions Employed for Oligosaccharide Preparation
2005-04-28

Hydrophobically assisted switching phase (HASP) synthesis is a concept that allows the choice between the advantages of solid-supported chemistry and those of solution-phase synthesis. Starting from the examination of adsorption and desorption properties of hydrophobic molecules to and from reversed-phase silica, we designed a dilipid as a quantitative and fully reversible HASP anchor, permitting final product release. The utility of this new tool in synthetic organic chemistry was demonstrated on oligosaccharide preparation. The synthesis of a pentarhamnoside was accomplished by repetitive glycosylation reactions. Glycosylations were conducted preferably in solution, whereas all protecting group manipulations were performed on solid support. Without the need for chromatographic purification of intermediates, the HASP system furnished the final product after 12 linear steps with average yields of 94% per step at a scale of 0.1 mmol, thus overcoming several of the limitations encountered in the solid-phase synthesis of complex carbohydrates.
Rubidium spectroscopy with 778- to 780-nm distributed feedback laser diodes
2005-04-28

Distributed feedback (DFB) laser chips have recently become available at wavelengths that match the D1 and D2 resonance transitions of alkaline atoms. We investigated the spectral properties, tuning characteristics and modulation behavior of continuous wave, single-mode DFB diodes at 778-780 nm and performed high-resolution spectroscopy of Rubidium vapor. The mode-hop free tuning range of the DFB diodes was as large as 2.4 nm (1186 GHz). The line width of the laser diodes was examined both with a heterodyne beat experiment and with high-resolution Doppler-free two photon spectroscopy, yielding a half width of 2-2.5 MHz. The saturation spectra of the D2-line of <sup>85</sup>Rb and <sup>87</sup>Rb were recorded with a resolution close to the natural line width. The emission frequency was actively stabilized to Doppler-free transitions with a relative accuracy of better than 4 parts in 10<sup>9</sup> using commercially available servo devices only. The output power of 80 mW was sufficient to allow for two photon spectroscopy of the 5S-5D-transition of <sup>87</sup>Rb. We conclude that the performance of the DFB laser equals that of grating-stabilized external-cavity diode lasers (ECDLs), without the mechanical complexity of the latter systems. The DFB diode is thus well-suited to high-resolution applications in alkaline spectroscopy, including laser cooling and optical manipulation of ultra-cold atoms.
Infection of human CD34+ progenitor cells with Bartonella henselae results in intraerythrocytic presence of B henselae
2005-04-29

Abstract Although there is evidence that endothelial cells are important targets for human pathogenic Bartonella species, the primary niche of infection is unknown. Here we elucidated whether human CD34+ hematopoietic progenitor cells (HPCs) internalize B henselae and may serve as a potential niche of the pathogen. We showed that B henselae does not adhere to or invade human erythrocytes. In contrast, B henselae invades and persists in HPCs as shown by gentamicin protection assays, confocal laser scanning microscopy (CLSM), and electron microscopy (EM). Fluorescence-activated cell sorting (FACS) analysis of glycophorin A expression revealed that erythroid differentiation of HPCs was unaffected following infection with B henselae. The number of intracellular B henselae continuously increased over a 13-day period. When HPCs were infected with B henselae immediately after isolation, intracellular bacteria were subsequently detectable in differentiated erythroid cells on day 9 and day 13 after infection, as shown by CLSM, EM, and FACS analysis. Our data provide, for the first time, evidence that a bacterial pathogen is able to infect and persist in differentiating HPCs, and suggest that HPCs might serve as a potential primary niche in Bartonella infections.
Stereospecific Synthesis of Chiral Tetrahydroquinoxaline, 2,3- Dihydrobenzo[ 1,4]dioxin and 2,3-Dihydro-naphtho[2,3-b][1,4]-dioxin Derivatives
2005-04-29

In this communication a convenient and novel method for the stereospecific synthesis of chiral tetrahydroquinoxaline, 2,3-dihydro-benzo[1,4]dioxin and 2,3-dihydro-naphtho[2,3-b][1,4]dioxin derivatives from anhydro sugars is described. Keywords: stereospecific synthesis, anhydro sugars, dioxin derivatives
Differential Gene Expression Profiling of Staphylococcus aureus Cultivated under Biofilm and Planktonic Conditions
2005-05-01

ABSTRACT It is well known that biofilm formation by pathogenic staphylococci on implanted medical devices leads to “chronic polymer-associated infections.” Bacteria in these biofilms are more resistant to antibiotics and the immune defense system than their planktonic counterparts, which suggests that the cells in a biofilm have altered metabolic activity. To determine which genes are up-regulated in Staphylococcus aureus biofilm cells, we carried out a comparative transcriptome analysis. Biofilm growth was simulated on dialysis membranes laid on agar plates. Staphylococci were cultivated planktonically in Erlenmeyer flasks with shaking. mRNA was isolated at five time points from cells grown under both conditions and used for hybridization with DNA microarrays. The gene expression patterns of several gene groups differed under the two growth conditions. In biofilm cells, the cell envelope appeared to be a very active compartment since genes encoding binding proteins, proteins involved in the synthesis of murein and glucosaminoglycan polysaccharide intercellular adhesin, and other enzymes involved in cell envelope synthesis and function were significantly up-regulated. In addition, evidence was obtained that formate fermentation, urease activity, the response to oxidative stress, and, as a consequence thereof, acid and ammonium production are up-regulated in a biofilm. These factors might contribute to survival, persistence, and growth in a biofilm environment. Interestingly, toxins and proteases were up-regulated under planktonic growth conditions. Physiological and biochemical tests for the up-regulation of urease, formate dehydrogenase, proteases, and the synthesis of staphyloxanthin confirmed the microarray data.
Neuroimaging of Gender Differences in Alcohol Dependence: Are Women More Vulnerable?
2005-05-01

Gender-specific differences in the onset of alcohol dependence were confirmed. This is in line with the telescoping effect, where a later onset and a more rapid development of dependence in women were described. Under the assumption of a gradual development of consequential organ damage, brain atrophy seems to develop faster in women. As shown in other organs (i.e., heart, muscle, liver), this may confirm a higher vulnerability to alcohol among women.
Overproduction, purification and characterization of FgaPT2, a dimethylallyltryptophan synthase from Aspergillus fumigatus
2005-05-01

A putative dimethylallyltryptophan synthase gene, fgaPT2 , was identified in the genome sequence of Aspergillus fumigatus . fgaPT2 was cloned and overexpressed in Saccharomyces cerevisiae . The protein FgaPT2 was purified to near homogeneity and characterized biochemically. This enzyme was found to convert l -tryptophan to 4-dimethylallyltryptophan, a reaction known to be the first step in ergot alkaloid biosynthesis. FgaPT2 is a soluble, dimeric protein with a subunit size of 52 kDa, and contains no putative prenyl diphosphate binding site (N/D)DXXD. K m values for l -tryptophan and dimethylallyl diphosphate (DMAPP) were determined as 8 and 4 μM, respectively. Metal ions, such as Mg 2+ and Ca 2+ , enhance the reaction velocity, but are not essential for the enzymic reaction. FgaPT2 showed a relatively strict substrate specificity for both tryptophan and DMAPP. FgaPT2 is the first enzyme in the biosynthesis of ergot alkaloids to be purified and characterized in homogeneous form after heterologous overproduction.
PREHISTORIC COPPER PRODUCTION IN THE INN VALLEY (AUSTRIA), AND THE EARLIEST COPPER IN CENTRAL EUROPE*
2005-05-01

In recent years archaeological finds and scientific analyses have provided increasing evidence for a very early beginning of copper production in the rich mining area of the Tyrolean Alps. The earliest findings derive from an excavation of a multi‐phase settlement on the Mariahilfbergl in Brixlegg, which revealed evidence that a small amount of fahlores, probably of local provenance, was at least heated if not even smelted there in the Late Neolithic Münchshöfen culture (the second half of the fifth millennium bc ). However, most copper finds of this horizon consist of low‐impurity copper that most probably derives from Majdanpek in Serbia. This long‐distance relationship is corroborated by typological features that link some aspects of the Münchshöfen culture with the Carpathian basin. Thus it is not yet clear if, at Brixlegg, actual copper production took place or, rather, an experimental treatment of the local ores. The typical fahlore composition, with arsenic and antimony in the per cent and silver and bismuth in the per mille ranges, appears in quantity only in the Early Bronze Age. Many thousands of Ösenringe are known from many central European Early Bronze Age sites, with a chemical composition typical of fahlores. At Buchberg near Brixlegg, a fortified settlement with slags from fahlore smelting proves that the local ores were indeed exploited. The lead isotope ratios of Ösenringe from the Gammersham hoard in Bavaria, which consist of fahlore copper, confirm this and suggest that copper mining and production in the Inn Valley reached a first climax during that period. In the Late Bronze Age, copper was produced at an almost industrial level.
From pedagogically relevant corpora to authentic language learning contents
2005-05-01

The potential of corpora for language learning and teaching has been widely acknowledged and their ready availability on the Web has facilitated access for a broad range of users, including language teachers and learners. However, the integration of corpora into general language learning and teaching practice has so far been disappointing. In this paper, I will argue that the shape of many existing corpora, designed with linguistic research goals in mind, clashes with pedagogic requirements for corpus design and use. Hence, a ‘pedagogic mediation of corpora’ is required (cf. Widdowson, 2003). I will also show that the realisation of this requirement touches on both the development of appropriate corpora and the ways in which they are exploited by learners and teachers. I will use a small English Interview Corpus (ELISA) to outline possible solutions for a pedagogic mediation. The major aspect of this is the combination of two approaches to the analysis and exploitation of a pedagogically relevant corpus: a corpus-based and a discourse-based approach.
Process‐based interpretation of tracer tests in carbonate aquifers
2005-05-01

Abstract A tracer test in a carbonate aquifer is analyzed using the method of moments and two analytical advection‐dispersion models (ADMs) as well as a numerical model. The numerical model is a coupled continuum‐pipe flow and transport model that accounts for two different flow components in karstified carbonate aquifers, i.e., rapid and often turbulent conduit flow and Darcian flow in the fissured porous rock. All techniques employed provide reasonable fits to the tracer breakthrough curve (TBC) measured at a spring. The resulting parameter estimates are compared to investigate how each conceptual model of flow and transport processes that forms the basis of the analyses affects the interpretation of the tracer test. Numerical modeling results suggest that the method of moments and the analytical ADMs tend to overestimate the conduit volume because part of the water discharged at the spring is wrongly attributed to the conduit system if flow in the fissured porous rock is ignored. In addition, numerical modeling suggests that mixing of the two flow components accounts for part of the dispersion apparent in the measured TBC, while the remaining part can be attributed to Taylor dispersion. These processes, however, cannot reasonably explain the tail of the TBC. Instead, retention in immobile‐fluid regions as included in a nonequilibrium ADM provides a possible explanation.
Heterologous Expression of Novobiocin and Clorobiocin Biosynthetic Gene Clusters
2005-05-01

ABSTRACT A method was developed for the heterologous expression of biosynthetic gene clusters in different Streptomyces strains and for the modification of these clusters by single or multiple gene replacements or gene deletions with unprecedented speed and versatility. λ-Red-mediated homologous recombination was used for genetic modification of the gene clusters, and the attachment site and integrase of phage φC31 were employed for the integration of these clusters into the heterologous hosts. This method was used to express the gene clusters of the aminocoumarin antibiotics novobiocin and clorobiocin in the well-studied strains Streptomyces coelicolor and Streptomyces lividans , which, in contrast to the natural producers, can be easily genetically manipulated. S. coelicolor M512 derivatives produced the respective antibiotic in yields comparable to those of natural producer strains, whereas S. lividans TK24 derivatives were at least five times less productive. This method could also be used to carry out functional investigations. Shortening of the cosmids' inserts showed which genes are essential for antibiotic production.
ECG-Gated 16-MDCT of the Coronary Arteries: Assessment of Image Quality and Accuracy in Detecting Stenoses
2005-05-01

In patients with no or moderate coronary calcification, MDCT of coronary arteries using 16-MDCT technology allows the reliable detection of coronary artery stenoses with high diagnostic accuracy. Obtaining an initial unenhanced scan was found to be mandatory to avoid performing useless examinations in patients with severe calcifications.
Impact of Gender on General Health-Related Quality of Life in Patients with Chronic Sinusitis
2005-05-01

Background The aim of this study was to evaluate the impact of gender on health-related quality of life (HRQOL) in patients with chronic sinusitis Methods A prospectively administered survey was performed. For measuring HRQOL, we used the German versions of the Short Form 36 (SF-36; eight subscales) and the European Quality of Life—5 Dimensions (EQ-5D) (two subscales). For all SF-36 subscales we used norm-based scoring of the general German population. Results One hundred twenty-three patients (45 women and 78 men) underwent HRQOL evaluation at baseline (preoperatively) and 3 months after endonasal sinus surgery. Compared with male patients, female patients scored a significantly worse baseline in all SF-36 and one EQ-5D subscales and 3 months later in only one SF-36 subscale. Compared with the norm-based scores, both women's and men's SF-36 scores reached normal levels in seven subscales after 3 months. Conclusion Compared with men, women assessed preoperative HRQOL as being worse. Most women's and men's SF-36 subscales reached normal levels at the 3-month follow-up.
High‐resolution magnetic resonance imaging of trabecular bone in the wrist at 3 tesla: initial results
2005-05-01

Purpose: To evaluate the feasibility of high‐resolution magnetic resonance imaging (MRI) of trabecular bone of the wrist at 3 Tesla (3T) in vivo and to assess the potential benefit of the increased resolution for clinical assessment of structural changes in spongy bone. Material and Methods: High‐resolution MRI of the wrist was performed with a whole‐body 3T MR scanner using a dedicated circularly polarized transmit–receive wrist‐coil. Two 3D‐FISP sequences with a spatial resolution of 300×300×300 μm 3 in a measuring time of T A = 7:51 min, and 200×200×200 μm 3 in T A = 9:33 min were applied. Seven young healthy volunteers and three elderly subjects with suspected osteoporosis were examined. The signal‐to‐noise ratio (SNR) in the optimized setup at 3T was compared to measurements at 1.5T. Results: The images at 3T allow microscopic analysis of the bone structure at an isotropic spatial resolution of 200 μm in examination times of &lt;10 min. Differences in the structure of the spongy bone between normal and markedly osteoporotic subjects are well depicted. The SNR at 3T was found up to 16 times higher than at 1.5T applying unchanged imaging parameters. Conclusion: The proposed high‐resolution MRI technique offers high potential in the diagnosis and follow‐up of diseases with impaired bone structure of hand and/or wrist in clinical applications.