julilili42/papers huggingface dataset:
Gene expression analysis after exercise stress using microarrays
2004-05-01

0593 PURPOSE: Microarray analyses in exercise physiology will provide new insights into the complex molecular mechanisms of the exercise-induced stress response. METHODS: Blood samples before (T0), directly (T1) and 24 h (T2) after a half marathon were investigated using a specifically designed ‘stress chip’ (Sirs-Lab, Jena, Germany). This chip includes over 480 genes for the analyses of inflammatory, stress response and related processes which code for cell-surface proteins and receptors, signal transduction, cell cycle and apoptosis, transcription and translation factors, cytokines, chemokines, growth hormones, interleukins, heat shock proteins and further molecules of stress response. Whole blood RNA was isolated, reverse transcribed and thereby labeled with cyanine fluorescent dyes. Each athlete sample (Cy3) was hybridized on one chip against universal-RNA (Cy5). The chips were scanned by an Axon scanner using the AIDA software for data processing (Raytest, Germany). Thresholds were determined (0.66 and 1.5) which allow significant discrimination of the analyzed gene expression. The aim was to compare the post-exercise gene expression with the pre-exercise data. RESULTS: The comparison revealed 115 genes which were significantly changed after exercise in one subject. These genes could be clustered into six gene groups which behaved in a similar manner: cluster 1 (15 genes): T1 < T0, T2 < T0; cluster 2 (14 genes): T1 < T0 but not T2; cluster 3 (17 genes): T2 <T0 but not T1; cluster 4 (19 genes): T1 > T0 but not T2; cluster 5 (16 genes): T2 > T0 but not T1; cluster 6 (34 genes): T1 > T0, T2 > T0. A more detailed interpretation of the results is not given here because this first experiment needs further evaluation with additional subjects to verify these modified genes and clusters. CONCLUSION: Primary analyses of gene expression post exercise may suggest that the inflammatory response is directed to monocyte and macrophage recruitment and function. The upregulation of specific mRNA is extremely sensitive, short lived and provide a number of individual response patterns. Genes which were upregulated for at least 24h have a broader effect on immune function and intracellular trafficking. These first data may be useful to demonstrate the kind of information that can be obtained from microarray analysis.
Endurance Training In Women
2004-05-01

1487 Most aggressive for the formation of the atheromatic plaque is oxidized LDL. Endurance training leads to a protection of the arteries by an elevation of HDL and a reduction of LDL. PURPOSE: To determine the effect of endurance training on the oxidation of LDL in vitro and to correlate possible effects to changes in cholesterol, triglycerides, lipoproteins and lipoprotein (a). METHODS: 20 untrained women and 10 controls agreed to participate in an 8-week running program, performed 3 times a week for 30 min at an intensity of the 4 mmol/l lactate threshold. The intensity was derived from a stepwise spiroergometric test before the start of the program. Venous blood was taken 30 min before and 3 min after the test. The test was repeated after the training. The oxidation of LDL in vitro, the products of lipidperoxidation malondialdehyd and conjugated diens were measured as well as cholesterol, triglycerides and lipoproteins. RESULTS: With a compliance of 97%, the running speed was increased by 1.5 km/h and the VO2max from 38 to 41 ml•min−1•kg−1 at the same maximum lactate. The submaximum running speed increased by 1.8 km/h. Training induced differences between the training and control groups in LDL and HDL2, but not for lagtime of LDL, malondialdehyd and conjugated diens, HDL3, VLDL, triglycerides, total cholesterol and lipoprotein (a). LDL was reduced from 122 to 105 mg/dl and HDL2 rose from 18.4 to 21.2 mg/dl (p<0.01). CONCLUSIONS: In young women, the antioxidative protection for LDL may not be improved by endurance training of eight weeks. Only the lipoproteins HDL2 and LDL showed beneficial changes.
Depletion of MLL-AF4 fusion gene by RNAi inhibits proliferation and induces apoptosis in t(4;11)-positive SEM cells
2004-05-01

The t(4;11)(q21;23) translocation is diagnosed in more than 50% of infant high-risk acute lymphoblastic leukemias and is associated with very poor prognosis. Using RNAi, we have silenced the expression of MLL-AF4 fusion gene in the SEM cells carrying t(4;11)(q21;23) translocation. Down-regulation of MLL-AF4 mRNA expression by specific siRNAs caused more than two-fold transient decrease in mRNA levels, reduced 10-fold the clonogenic capacity of siRNA-treated cells. Two transfections of SEM cells with the MLL-AF4 siRNAs also reduced the proliferation, inhibited G1-S transition in cell cycle and induced apoptosis. We conclude that siRNA specific against MLL-AF4 are promising agents for novel treatment concept of t(4;11)(q21;q23) leukemias.
A Multi-Modal Documentation System for Warao
2004-05-01

This contribution presents a multi-modal documentation system for the Amerindian culture and language of the Venezuelan Warao. The project has two main tasks: the documentation of language and culture of the Warao and the development of a documentation system. Our key aim is to allow the integration of different media and data types (photos, drawings, file cards, and audio data) in such a fashion that all of them would be first class objects. Furthermore the system has to be usable by ethnolinguistic field workers who are not trained computer scientists and has to guarantee integrability into larger documentation projects as well as data exchange. We therefore opted to use Microsoft Access as the underlying database system and XML as the annotation standard for corpora. One of the key features of the documentation system is an open concept space that allows the free definition of linguistic and cultural concepts and their relations and thus goes beyond the expression of hierarchical relations between concepts. 1.
Surgery of cavoatrial tumor thrombus in nephroblastoma: A report of the SIOP/GPOH study
2004-05-03

Abstract Background Resection of a Wilms tumor extending through the inferior vena cava into the right atrium represents a challenge to the pediatric surgeon. Exact preoperative diagnosis is essential to identify the tumor and its in travascular extension. To achieve a complete excision of the tumor cardiopulmonary bypass and hypothermia may be required. The feasibility of a complete resection is important as it guides subsequent therapy such as chemotherapy and radiation. Procedure In order to define these issues, we reviewed the records of 33 of 1,151. Patients enrolled in the SIOP 93‐01/GPOH Study and the SIOP 2001/GPOH Study who had a tumor thrombus into the inferior venacava and into the right atrium. Results The median age at diagnosis was 3.73 years. Twenty‐four patients had a tumor thrombus into the inferior vena cava, in nine patients the thrombus reached into the right atrium. All patients were operated on; cardiopulmonary bypass was used in nine patients. There were no deaths intraoperatively. Twenty‐nine children are still alive; four patients died, one patient due to aspiration and failed resuscitation, two patients died from a recurrent tumor, and one child due to an unresectable primary tumor. Conclusion Our report suggests that Wilms tumor extending to the inferior vena cava and the right atrium is technical challenging, but with adequate preoperative diagnosis and a multidisciplinary surgical approach including cardiopulmonary bypass and hypothermia, the prognosis is favorable. © 2004 Wiley‐Liss, Inc.
Regulated expression of pathogen-associated molecular pattern molecules in Staphylococcus epidermidis: quorum-sensing determines pro-inflammatory capacity and production of phenol-soluble modulins
2004-05-04

Phenol-soluble modulin (PSM) is a peptide complex produced by the nosocomial pathogen Staphylococcus epidermidis that has a strong capacity to activate the human innate immune response. We developed a novel method based on liquid chromatography-mass spectrometry (LC-MS) to quantify the production of the individual PSM components. Each PSM peptide was abundant in most of the 76 S epidermidis strains tested. Importantly, none of the PSM components were secreted by an agr mutant strain, indicating that PSM synthesis is regulated strictly by the agr quorum-sensing system. Furthermore, the agr mutant strain failed to elicit production of TNFalpha by human myeloid cells and induced significantly less neutrophil chemotaxis compared with the wild-type strain. Thus, quorum-sensing in S. epidermidis dramatically influenced activation of human host defence. We propose that an agr quorum-sensing mechanism facilitates growth and survival in infected hosts by adapting production of the pro-inflammatory PSMs to the stage of infection.
Degeneration of the central vestibular system in spinocerebellar ataxia type 3 (SCA3) patients and its possible clinical significance
2004-05-04

Although the vestibular complex represents an important component of the neural circuits crucial for the maintenance of truncal and postural stability, and it is integrated into specialized oculomotor circuits, knowledge regarding the extent of the involvement of its nuclei and associated fibre tracts in cases with spinocerebellar ataxia type 3 (SCA3) is incomplete. Accordingly, we performed a pathoanatomical analysis of the vestibular complex and its associated fibre tracts in four clinically diagnosed and genetically confirmed SCA3 patients with the aim of providing more exact information as to the involvement of the vestibular system in this disorder. By means of unconventionally thick serial sections through the vestibular nuclei stained for lipofuscin pigment and Nissl material, we could show that all five nuclei of this complex (interstitial, lateral, medial, spinal, and superior vestibular nuclei) are subject to neurodegenerative processes in SCA3, whereby examination of thick serial sections stained for myelin revealed that all associated fibre tracts (ascending tract of Deiters, juxtarestiform body, lateral and medial vestibulospinal tracts, medial longitudinal fascicle, vestibular portion of the eighth cranial nerve) underwent atrophy and demyelinization in all four of the patients studied. The reported lesions can help to explain the truncal and postural instability as well as the impaired optokinetic nystagmus, vestibulo‐ocular reaction, and horizontal gaze‐holding present in SCA3 cases.
GJB2mutations in patients with non-syndromic hearing loss from Northeastern Hungary
2004-05-05

Mutations in the GJB2 gene encoding the gap-junction protein connexin 26 have been identified in many patients with childhood hearing impairment (HI). One single mutation, c.35delG, accounts for the majority of mutations in Caucasian patients with HI. In the present study we screened 500 healthy control individuals and a group of patients with HI from Northeastern Hungary for GJB2 mutations. The patients' group consisted of 102 familial from 28 families and 92 non-familial cases. The most common mutation in the Hungarian population is the c.35delG, followed by the c.71G>A (p.W24X) mutation. 34.3% of the patients in the familial group were homozygous, and 17.6% heterozygous for 35delG. In the non-familial group the respective values were 37% and 18% (allele frequency: 46.2%). In the general population an allele frequency of 2.4% was determined. Several patients were identified with additional, already described or new GJB2 mutations, mostly in heterozygous state. The mutation c.380G>A (p.R127H) was formerly found only in heterozygous state and its disease relation was controversial. We demonstrated the presence of this mutation in a family with three homozygous patients and 4 heterozygous unaffected family members, a clear indication of recessively inherited HI. Furthermore, we provided evidence for the pathogenic role of two new mutations, c.51C>A (p.S17Y) and c.177G>T (p.G59V), detected in the present study. In the latter case the pattern of inheritance might be dominant. Our results confirm the importance of GJB2 mutations in the Hungarian population displaying mutation frequencies that are comparable with those in the Mediterranean area.
Inhibition of erythrocyte phosphatidylserine exposure by urea and Cl−
2004-05-06

Osmotic shock by addition of sucrose to the medium stimulates erythrocyte sphingomyelinase with subsequent ceramide formation and triggers Ca 2+ entry through stimulation of cation channels. Both ceramide and Ca 2+ activate an erythrocyte scramblase, leading to breakdown of phosphatidylserine asymmetry, a typical feature of apoptosis. Because erythrocytes are regularly exposed to osmotic shock during passage of kidney medulla, the present study explored the influence of NaCl and urea on erythrocyte phosphatidylserine exposure as determined by annexin binding. The percentage of annexin-binding erythrocytes increased from &lt;5 to 80 ± 4% ( n = 4) upon addition of 650 mM sucrose, an effect paralleled by activation of the cation channel and stimulation of ceramide formation. The number of annexin-binding erythrocytes increased only to 18% after addition of 325 mM NaCl and was not increased by addition of 650 mM urea. According to whole cell patch-clamp experiments, the cation conductance was activated by replacement of extracellular Cl − with gluconate at isotonic conditions or by addition of hypertonic sucrose or urea. Although stimulating the cation conductance, urea abrogated the annexin binding and concomitant increase of ceramide levels induced by osmotic cell shrinkage. In vitro sphingomyelinase assays demonstrated a direct inhibitory effect of urea on sphingomyelinase activity. Urea did not significantly interfere with annexin binding after addition of ceramide. In conclusion, both Cl − and urea blunt erythrocyte phosphatidylserine exposure after osmotic shock. Whereas Cl − is effective through inhibition of the cation conductance, urea exerts its effect through inhibition of sphingomyelinase, thus blunting formation of ceramide.
Oscillations of Bose-Einstein condensates with vortex lattices: Finite temperatures
2004-05-06

We derive the finite temperature oscillation modes of a harmonically confined\\nBose-Einstein condensed gas undergoing rigid body rotation supported by a\\nvortex lattice in the condensate. The hydrodynamic modes separate into two\\nclasses corresponding to in-phase (center-of-mass) and counter-phase (relative)\\noscillations of the thermal cloud and the condensate. The in- and counter-phase\\noscillations are independent of each other in the case where the thermal cloud\\nis inviscid for all modes studied, except the radial pulsations which couple\\nthem because the pressure perturbations of the condensate and the thermal cloud\\nare governed by different adiabatic indices. If the thermal cloud is viscous,\\nthe two classes of oscillations are coupled, i.e. each type of motion involves\\nsimultaneously mass and entropy currents. The counter-phase oscillations are\\ndamped by the mutual friction between the condensate and the thermal cloud\\nmediated by the vortex lattice. The damping is large for the values of the\\ndrag-to-lift ratio of the order of unity and becomes increasingly ineffective\\nin either limit of small or large friction. An experimental measurement of a\\nsubset of these oscillation modes and their damping rates can provide\\ninformation on the values of the phenomenological mutual friction coefficients,\\nand hence the quasiparticle-vortex scattering processes in dilute atomic Bose\\ngases.\\n
Para-aortic irradiation for stage I testicular seminoma: results of a prospective study in 675 patients. A trial of the German testicular cancer study group (GTCSG)
2004-05-11

A prospective nonrandomised trial was performed in order to evaluate tumour control and toxicity of low-dose adjuvant radiotherapy in stage I seminoma with treatment portals confined to the para-aortic lymph nodes. Between April 1991 and March 1994, 721 patients were enrolled for the trial by 48 centres in Germany. Patients with pure seminoma and no evidence of lymph node involvement or distant metastases received 26 Gy prophylactic limited para-aortic radiotherapy. Disease-free survival at 5 years was the primary end point. With a median follow-up of 61 months, 675 patients with follow-up investigations were evaluable for this analysis. Kaplan-Meier estimates of disease-free and disease-specific survival were 95.8% (95% CI: 94.2-97.4) and 99.6% (95% CI: 99.2-100%) at 5 years and 94.9% (95% CI: 92.5-97.4%) and 99.6% (95% CI: 99.2-100%) at 8 years, respectively. A total of 26 patients relapsed. All except two were salvaged from relapse. In all, 21 recurrences were located in infradiaphragmatic lymph nodes without any 'in-field' relapse. Nausea and diarrhoea grade 3 were observed in 4.0 and 1.0% of the patients, respectively. Grade 3 late effects have not been observed so far. The results of our trial lend further support to the concept of limited para-aortic irradiation as the recently defined new standard of radiotherapy in stage I seminoma. There is no obvious compromise in disease-specific or disease-free survival compared to more extensive hockey-stick portals, which were used as standard portals at the time this study was initiated.
Improving occlusion query efficiency with occupancy maps
2004-05-13

Image space occlusion culling is an useful approach to reduce the rendering load of large polygonal models. Like most large model techniques, it trades overhead costs with the rendering costs of the possibly occluded geometry. Meanwhile, modern graphics hardware supports occlusion culling, whereas they associate a significant query overhead, which hurts in particular, if the occlusion culling query itself was unsuccessful. We propose the occupancy map - a compact, cache-optimized representation of coverage information - to reduce the number of costly but unsuccessful occlusion culling queries and to arrange multiple occlusion queries. The information of the occupancy map is used to skip an occlusion query, if the respective map area is not yet set $the respective area has not yet received rendered pixels -, hence an occlusion query would always return not occluded. The remaining occlusion information is efficiently determined by asynchronous multiple occlusion queries with hardware-supported query functionality. To avoid redundant results, we arrange these multiple occlusion queries according to the information of several occupancy maps. Our presented technique is conservative and benefits from a partial depth order of the geometry.
Ruthenium(II) Octaphenylporphyrazine Complexes with Mixed Axial Ligands: Peculiarities of Their Formation and Spectral Properties
2004-05-13

Abstract A series of new axially bis‐coordinated (octaphenylporphyrazinato)ruthenium( II ) complexes {[(Ph 8 Pz)RuL 2 ], L = cyclohexyl isocyanide, CyNC, ( 1b ); 4,4′‐bipyridine, bpy, ( 2c ); N ‐methylimidazole, CH 3 Im, ( 3a )} was prepared and characterized. The reaction of the bis‐isocyanide adducts [(Ph 8 Pz)Ru( t BuNC) 2 ] ( 1a ) or [(Ph 8 Pz)Ru(CyNC) 2 ] ( 1b ) with monodentate N‐heterocycles gave, under certain conditions, the mixed‐ligand complexes [(Ph 8 Pz)Ru(Py)( t BuNC)] ( 4a ), [(Ph 8 Pz)Ru(Py)(CyNC)] ( 4b ) and [(Ph 8 Pz)Ru(CH 3 Im)(CyNC)] ( 3b ). The reaction of 1a or 1b with an excess of bidentate 4,4′‐bipyridine under the same conditions resulted in the formation of the corresponding dimeric species [(Ph 8 Pz)Ru( t BuNC)] 2 (μ‐bpy) ( 2a ) and [(Ph 8 Pz)Ru(CyNC)] 2 (μ‐bpy) ( 2b ) in high yield. The structures of all the complexes were unambiguously proved by 1 H NMR spectroscopy, and the possibility of their self‐assembly is discussed. All mixed‐ligand compounds were also characterized by UV/Vis and IR spectroscopy, as well as elemental analysis. The 1 H NMR spectra of these compounds are discussed in detail. (© Wiley‐VCH Verlag GmbH &amp; Co. KGaA, 69451 Weinheim, Germany, 2004)
The Gly482Ser Variant in the Peroxisome Proliferator-Activated Receptor γ Coactivator-1 is not Associated with Diabetes-Related Traits in Non-Diabetic German and Dutch Populations
2004-05-14

The peroxisome proliferator-activated receptor gamma coactivator-1 (PGC-1) is involved in regulation of fatty acid oxidation, skeletal muscle fiber type specificity, and gluconeogenesis. The prevalent Gly482Ser variant in PGC-1 was shown to be associated with type 2 diabetes in some but not all studies. Moreover, it is unclear whether it influences prediabetic subphenotypes in non-diabetic populations. We studied the association of this variant with glucose tolerance (oral glucose tolerance test), insulin sensitivity (euglycemic hyperinsulinemic clamp) of glucose disposal and antilipolysis, insulin secretion (hyperglycemic clamp, 10 mM), maximal oxygen consumption (VO(2)max, bicycle ergometry), and intramyocellular lipids (magnetic resonance spectroscopy, tibialis and soleus muscle) in a normal glucose tolerant German cohort (n = 423) and a normal (n = 65) and impaired glucose tolerant (n = 94) cohort from the Netherlands. No statistically significant association with an examined phenotype was detected in any of the study cohorts. Specifically, VO(2)max and the soleus-to-tibialis ratio of intramyocellular lipid contents as a surrogate parameter of fiber type specificity was not different between the genotype groups. We conclude, that the Gly482Ser variant in PGC-1 is not associated with diabetes-related traits or skeletal muscle fiber type composition in a non-diabetic German and Dutch population.
Sum rules and short-range correlations in nuclear matter at finite temperature
2004-05-14

The nucleon spectral function in nuclear matter fulfills an energy weighted\\nsum rule. Comparing two different realistic potential, these sum rules are\\nstudied for Green's functions that are derived self-consistently within the \\nmatrix approximation at finite temperature.\\n
Influence of Chiral Mean Field on Kaon In-plane Flow in Heavy Ion Collisions
2004-05-15

The influence of the chiral mean field on the in-plane flow in heavy ion collisions at SIS energy is investigated within covariant kaon dynamics. For the kaon mesons inside the nuclear medium a quasi-particle picture including scalar and vector fields is adopted and compared to the standard treatment with a static potential. It is confirmed that a Lorentz force from spatial component of the vector field provides an important contribution to the in-medium kaon dynamics and strongly counterbalances the influence of the vector potential on the in-plane flow. The calculated results show that the new FOPI data can be reasonably described using the Brown & Rho parametrization, which partly takes into account the correction of higher order contributions in the chiral expansion. This indicates that one can abstract the information on the kaon potential in a nuclear medium from the analysis of the in-plane flow.
Hardware accelerated per-pixel displacement mapping
2004-05-17

In this paper we present an algorithm capable of rendering a displacement mapped triangle mesh interactively on latest GPUs. The algorithm uses only pixel shaders and does not rely on adaptively adding geometry. All sampling of the displacement map takes place in the pixel shader and bi- or trilinear filtering can be applied to it, and at the same time as the calculations are done per pixel in the shader, the algorithm has automatic level of detail control. The triangles of the base mesh are extruded along the respective normal directions and then the resulting prisms are rendered by casting rays inside and intersecting them with the displaced surface. Two different implementations are discussed in detail.