julilili42/papers huggingface dataset:
Regulation of Nitric Oxide Synthesis in Wounds by IFN-γ Depends on TNF-α
2006-01-01

Macrophage-derived nitric oxide is a critical mediator in wound healing. Its regulation in vivo, however, remains unclear. We hypothesized that interferon (IFN)-gamma plays an important role in the regulation of nitric oxide in wounds. Groups of 12 male IFN-gamma -knockout mice and wild-type controls underwent dorsal skin incision and polyvinyl alcohol sponges were inserted subcutaneously. Mice were sacrificed 10 days later to determine wound breaking strength and reparative collagen deposition. Synthesis of nitric oxide (NO), tumor necrosis factor (TNF)-alpha, and IFN-gamma was measured in the wound. Wound-derived macrophages were tested for NO synthesis in the presence or absence of IFN-gamma, TNF-alpha, and anti-TNF-alpha antibody. In a separate experiment, IFN-gamma -knockout mice and wild-type controls were treated with molsidomine, a nitric oxide donor. It was found that wound collagen deposition and wound breaking strength were impaired in IFN-gamma-knockout mice (p < .05). Impaired healing was reflected in diminished synthesis of TNF-alpha and NO in wounds (p < .05). In vivo treatment with molsidomine reversed impaired healing in IFN-gamma-deficient mice. Ex vivo, addition of IFN-gamma stimulated the synthesis of TNF-alpha and NO in wound-derived macrophages. IFN-gamma -induced NO synthesis by wound-derived macrophages was abolished by anti-TNF-alpha-antibody-treatment, which could be fully reversed by exogenous TNF-alpha. Thus we conclude that IFN-gamma-deficiency impairs wound healing and diminishes NO synthesis in wound-derived macrophages. The stimulatory effect of IFN-gamma on macrophage NO production depends on endogenous TNF-alpha synthesis.
Air pollution-associated fly ash particles induce fibrotic mechanisms in primary fibroblasts
2006-01-01

Air pollution is associated with a variety of respiratory and cardiovascular disorders, including fibrosis. To understand the possible molecular mechanisms underlying this observation, we examined the effect of particulate matter on primary fibroblasts, the key regulators of the extracellular matrix. Fly ash collected in an experimental waste incinerator was used as model particles for fine and ultrafine pollution components. Brief treatment of fibroblasts isolated from adult male Wistar rat hearts with fly ash triggered the immediate formation of intracellular reactive oxygen species (ROS). Using phospho-specific antibodies we observed activation of p38 MAP kinase, p44/42 MAP kinase (ERK1/2) and p70(S6) kinase. Prolonged incubation with fly ash increased the expression of collagen 1 and TGF-beta1, but decreased mRNA levels of MMP9 and TNF-alpha. Cell proliferation was inhibited at high concentrations of fly ash. An increase in the level of advanced glycation endproduct (AGE) modification of various cellular proteins after long-term treatment of cultured fibroblasts with fly ash was observed. The results of our study demonstrate that direct activation of fibroblasts by combustion-derived particles is a mechanism that may contribute to the adverse health effects of particulate air pollution.
Defining Insulin-Like Growth Factor-I Deficiency
2006-01-01

• The GH-IGF system should be viewed like other endocrine systems, with a central, trophic hormone (GH) and a peripherally active hormone (IGF-I). • A decrease in IGF-I production, without a concomitant impairment in GH secretion, should be termed 'Primary IGF deficiency'. • IGF-I and IGFBP-3 measurements should be given precedence in the work-up of children with suspected defects of the GH-IGF axis. • The terms 'GH insensitivity' and 'IGF-I deficiency' are not identical terms. To define a disease condition in terms of its lack of response to treatment is conceptually misleading.
Atypical Teratoid-Rhabdoid Tumor Spreading along the Trigeminal Nerve
2006-01-01

We here describe the case of a boy with an atypical teratoid-rhabdoid tumor (ATRT) of the 4th ventricle at 1 year of age and a local tumor recurrence at 19 months of age. Due to brainstem infiltration, only incomplete tumor resection was possible each time. High-dose chemotherapy, stem cell transplantation and irradiation resulted in complete tumor remission on a control MRI. At 8 years of age, another tumor appeared extending from the cerebellopontine angle along the right trigeminal nerve through Meckel’s cave into the cavernous sinus. The trigeminal tumor was not in continuity with the primary ATRT but was located within the field of prior irradiation, neuroradiologically mimicking a schwannoma or a meningioma. The origin of the trigeminal tumor as a late metastasis of the former ATRT or as a less likely irradiation-induced secondary ATRT and the operative approach are discussed.
Modeling Familial British Dementia in Transgenic Mice
2006-01-01

The chromosome 13 linked amyloidopathies familial British dementia (FBD) and familial Danish dementia (FDD) are caused by mutations in the C-terminus of the BRI2 gene. In both diseases, novel peptides are deposited in amyloid plaques in the brain. Several laboratories have attempted to model these diseases in BRI2 transgenic mice with limited success. While high expression levels of BRI protein were achieved in transgenic lines, no ABri-amyloidosis was observed in aged mice. This review discusses the strategies chosen and problems experienced with the development of FBD/FDD models and suggests novel approaches to model the diseases in murine models.
Parallel Support Vector Machines
2006-01-01

The Support Vector Machine (SVM) is a supervised algorithm for the solution of classification and regression problems. SVMs have gained widespread use in recent years because of successful applications like character recognition and the profound theoretical underpinnings concerning generalization performance. Yet, one of the remaining drawbacks of the SVM algorithm is its high computational demands during the training and testing phase. This article describes how to efficiently parallelize SVM training in order to cut down execution times. The parallelization technique employed is based on a decomposition approach, where the inner quadratic program (QP) is solved using Sequential Minimal Optimization (SMO). Thus all types of SVM formulations can be solved in parallel, including C-SVC and ν-SVC for classification as well as ε-SVR and ν-SVR for regression. Practical results show, that on most problems linear or even superlinear speedups can be attained. 1
How Does the Inner Ear Generate Distortion Product Otoacoustic Emissions?
2006-01-01

There is general agreement that distortion product (DP) otoacoustic emissions elicited by stimuli up to 80–90 dB SPL originate from the saturating nonlinearity of the cochlear amplifier at the basilar membrane site, S, where the responses to the two primary tones overlap. There are, however, different interpretations of how the inner ear transmits the effects of this process to the stapes. The supporters of transmission line models assert that the phenomenon depends upon two main mechanisms: (1) the generation of forward and backward traveling waves (TWs) by DP oscillations at S; (2) the backward propagation of wave components reflected by ‘micromechanical impedance perturbations’ at the sites where the DP TWs peak. However, quantitative predictions based on this view are still lacking. In contrast, here we show, using a nonlinear hydrodynamic model, that the emissions are propagated almost instantaneously through the fluid.
Ontogeny and homology of the claustra in Otophysan Ostariophysi (Teleostei)
2006-01-01

We studied the ontogeny of the claustrum comparatively in representatives of all otophysan subgroups. The claustrum of cypriniforms has a cartilaginous precursor, the claustral cartilage, which subsequently ossifies perichondrally at its anterior face and develops an extensive lamina of membrane bone. The membrane bone component of the claustrum and its close association with the atrium sinus imparis, a perilymphatic space of the Weberian apparatus, are both synapomorphies of cypriniforms. The characiform claustrum is not preformed in cartilage and originates as a membrane bone ossification, a putative synapomorphy of that taxon. Among siluriforms, the claustrum is present only in more basal groups and originates as an elongate cartilage that ossifies in a characteristic ventrodorsal direction, possibly a synapomorphy of catfishes. Gymnotiforms lack the claustral cartilage and claustrum. We review all previous hypothesis of claustrum homology in light of the above findings and conclude that the most plausible hypothesis is the one originally proposed by Bloch ([1900] Jen Z Naturw 34:1-64) that claustra are homologs of the supradorsals of the first vertebra.
Pattern matching for arc-annotated sequences
2006-01-01

We study pattern matching for arc-annotated sequences. An O ( nm ) time algorithm is given for the problem to determine whether a length m sequence with nested arc annotation is an arc-preserving subsequence (aps) of a length n sequence with nested arc annotation, called APS(NESTED,NESTED). Arc-annotated sequences and, in particular, those with nested arc annotation are motivated by applications in RNA structure comparison. Our algorithm generalizes results for ordered tree inclusion problems and it is useful for recent fixed-parameter algorithms for LAPCS(NESTED,NESTED), which is the problem of computing a longest arc-preserving common subsequence of two sequences with nested arc annotations. In particular, the presented dynamic programming methodology implies a quadratic-time algorithm for an open problem posed by Vialette.
Femoral Subsidence Assessment After Hip Replacement
2006-01-01

The main error of subsidence measurement is caused by tilt of the femur for standard methods and partly can be reduced by EBRA-FCA. EBRA-FCA is more reliable than standard methods but might underestimate the actual subsidence in a clinical situation.
Radioimmunotherapy as non-myeloablative conditioning for allogeneic marrow transplantation
2006-01-01

Radioimmunotherapy (RIT) combines the advantages of specific immunotherapy with the cytotoxicity of radionuclides resulting in targeted radiation therapy. In the setting of allogeneic hematopoietic cell transplantation (HCT), RIT can be used to both target tumor cells and to suppress immunocompetent recipient cells. RIT with beta-emitters has been successfully used for further dose intensification of myeloablative conditioning regimens for HCT. Alpha-emitters with their short path length and high linear energy transfer bear certain advantages over beta-emitters if used to target hematopoietic cells. Using a canine model of non-myeloablative HCT, one could demonstrate that pre-transplant RIT with the alpha-emitter bismuth-213 (213Bi) coupled to anti-CD45 or anti-TCRalphabeta monoclonal antibodies (mAb) together with post-grafting immunosuppression with mycophenolate mofetil and cyclosporine can achieve stable engraftment and long-term mixed chimerism. The two mAbs may allow a tailored approach to RIT in non-myeloablative conditioning with 213Bi-anti-CD45 used for patients with hematologic malignancies and 213Bi-anti-TCRalphabeta for non-malignant diseases. Extensive studies of biodistribution, dose de-escalation and toxicity provide the basis for the conception of clinical trials using RIT for non-myeloablative HCT.
Regulation of immediate early gene expression by exercise: short cuts for the adaptation of immune function.
2006-01-01

Onset of physical activity induces a wide variety of rapid biophysical and biochemical responses that act on cells and lead to a wide range of phenotypic adaptations. Here we elucidate the role of immediate early gene (IEG) expression as a first line of transcriptional response that mediates protein neosynthesis and leads to adaptation of immune function. New posttranscriptional mechanisms have been described that speed up transcriptional responses. These include RNA-RNA interactions such as those exploited by miRNAs and stimulus-dependent cytoplasmic polyadenylation. We describe these shortcuts that modulate expression and discuss the challenges of accurately measuring them using various transcriptomic screening and quantification approaches. Although there is high complexity of the upstream as well as the downstream pathways that lead to IEG expression, IEG expression itself may only show a limited number of response patterns. Focusing transcriptomic approaches in exercise immunology at the IEG-level may facilitate the discovery of exercise-specific transcriptional signatures.
Max-tolerance graphs as intersection graphs
2006-01-01

Max-tolerance graphs can be regarded as generalized interval graphs, where two intervals Ii and Ij only induce an edge in the corresponding graph iff they overlap for an amount of at least max{ti, tj} where ti is an individual tolerance parameter associated to each interval Ii. A new geometric characterization of max-tolerance graphs as intersection graphs of isosceles right triangles, shortly called semi-squares, leverages the solution of various graph-theoretic problems in connection with max-tolerance graphs. First, we solve the maximal and maximum cliques problem. It arises naturally in DNA sequence analysis where the maximal cliques might be interpreted as functional domains carrying biologically meaningful information. We prove an upper bound of O(n3) for the number of maximal cliques in max-tolerance graphs and give an efficient O(n3) algorithm for their computation. In the same vein, the semi-square representation yields a simple proof for the fact that this bound is asymptotically tight, i.e., a class of max-tolerance graphs is presented where the instances have Ω(n3) maximal cliques. Additionally, we answer an open question posed in [8] by showing that max-tolerance graphs do not contain complements of cycles Cn for n > 9. By exploiting the new representation more deeply, we can go even further and prove that the recognition problem for max-tolerance graphs is NP-hard.
Comparative proteomic analysis of neoplastic and non-neoplastic germ cell tissue
2006-01-01

A comparative proteomic analysis of neoplastic versus non-neoplastic seminoma identified glutathione S-transferase M3 as a differentially expressed protein. This expression difference could also be observed at the mRNA level, implying neoplasm-associated alterations in transcriptional or post-transcriptional mechanisms.
Preparation, Characterization and Crystal Structure of Lead(II) Tricyanomethanide
2006-01-01

The so far unknown lead tricyanomethanide, Pb[C(CN) 3 ] 2 , was obtained from a saturated aqueous solution of PbCl 2 and solid AgC(CN) 3 . Its IR spectrum and thermal behaviour are described. The crystal structure was determined by single-crystal X-ray diffraction (trigonal, P31m, Z = 3, a = 1414.4(5), c = 409.02(6) pm, R 1 = 0.0249, wR 2 = 0.0527). Two crystallographically independent ninefold coordinated Pb atoms are connected by planar tricyanomethanide ions in two distinct bridging coordination modes. The Pb−N distances range between 254 and 293 pm.
Stimulation of Suicidal Erythrocyte Death by Lipoxygenase Inhibitor Bay-Y5884
2006-01-01

The prostaglandin PGE(2), a metabolite of the cyclooxygenase pathway, activates Ca(2+)-permeable cation channels in erythrocyte cell membranes leading to entry of Ca(2+) with subsequent eryptosis, i.e. cell shrinkage, breakdown of phosphatidylserine (PS) asymmetry and membrane blebbing, all features typical for apoptosis in nucleated cells. PS exposing cells are recognized by macrophages, engulfed, degraded and thus cleared from circulating blood. The present study explored whether the specific lipoxygenase inhibitor Bay-Y5884 influences eryptosis. As determined by competitive ELISA, Bay-Y5884 (20 microM) enhanced the release of PGE(2) from human erythrocytes. According to whole-cell patch-clamp, Bay-Y5884 (20 microM) activated nonselective cation channels. The effect of Bay-Y5884 on cation channels was abolished by the cyclooxygenase inhibitor diclophenac (10 microM). Bay-Y5884 (30-40 microM) significantly increased erythrocyte free Ca(2+) concentration and PS exposure as analyzed in flow cytometry by Fluo3 fluorescence and annexin-V binding, respectively. PS exposure triggered by 20 microM (but not by 40 microM) Bay-Y5884 was blunted by cyclooxygenase inhibitors acetylsalicylic acid (50 microM) and diclophenac (10 microM). In conclusion, the lipoxygenase inhibitor Bay-Y5884 enhances erythrocyte PGE(2) formation with subsequent activation of non-selective cation channels, Ca(2+) entry and phospholipid scrambling.
Analysis of Vasoreactivity of Isolated Human Radial Artery
2006-01-01

Radial artery (RA) is increasingly used as graft for coronary artery bypass grafting due to its good long-term patency. However, the mechanism of peri- and post-operative spasm is still unclear. Because of that, the aim of our study is to analyze the contractility of RA and to determine whether the presence of functional endothelium alters its contractile properties. Contractions of isolated RA rings were provoked by exogenously applied vasoconstrictors or by electrical field stimulation (EFS, 20 Hz). The order of vasoconstrictors potency based on their EC50 values was as follows: angiotensin II > phenylephrine > 5-hydroxytriptamine. Presence of endothelium increased both EC50 and maximal contraction to phenylephrine and angiotensin II, but inhibited reactivity of RA to 5-hydroxytriptamine. Spontaneous rhythmic contractions (SRC, <4 mHz) and EFS-induced contractions of RA are endothelium-independent and weaker than contractions induced by exogenously applied vasoconstrictors. Our study concludes that RA shows marked sensitivity and reactivity to angiotensin II, phenylephrine, and 5-hydroxytriptamine. Further investigations are necessary to answer why angiotensin II and phenylepehrine induce stronger contractions in the presence of endothelium. In addition, SRC as well as contractions of neurogenic origin may take part in developing vascular spasm of RA.
Annotation schemes and their influence on parsing results
2006-01-01

Most of the work on treebank-based statistical parsing exclusively uses the Wall-Street-Journal part of the Penn treebank for evaluation purposes. Due to the presence of this quasi-standard, the question of to which degree parsing results depend on the properties of treebanks was often ignored. In this paper, we use two similar German treebanks, TüBa-D/Z and NeGra, and investigate the role that different annotation decisions play for parsing. For these purposes, we approximate the two treebanks by gradually taking out or inserting the corresponding annotation components and test the performance of a standard PCFG parser on all treebank versions. Our results give an indication of which structures are favorable for parsing and which ones are not.
Polygon labelling of minimum leader length
2006-01-01

We study a variation of the boundary labelling prob- lem, with ∞oating sites (represented as polygons), la- bels of uniform size placed in flxed positions on the boundary of a rectangle (that encloses all sites) and special type of leaders connecting labels to sites. We seek to obtain a labelling of all sites with leaders that are non-overlapping and have
Sustainability of Linguistic Resources
2006-01-01

This paper describes a new research initiative addressing the issue of sustainability of linguistic resources. This initiative is a cooperation between three linguistic collaborative research centres in Germany, which comprise more than 40 individual research projects altogether. These projects are involved in creating manifold language resources, especially corpora, tailored to their particular needs. The aim of the project described here is to ensure an effective and sustainable access of these data by third-party researchers beyond the termination of these projects. This goal involves a number of measures, such as the definition of a common data format to completely capture the heterogeneous information encoded in the individual corpora, the development of user-friendly and sustainably usable tools for processing (e.g. querying) the data, and the specification of common inventories of metadata and terminology. Moreover, the project aims at formulating general rules of best practice for creating, accessing, and archiving linguistic resources.
Optimal Simultaneous Scheduling, Binding and Routing for Processor-Like Reconfigurable Architectures
2006-01-01

We discuss the problem of simultaneously scheduling, binding and routing a given data flow graph to a coarse-grain architecture consisting of identical processing elements (PEs) that are connected by a nearest-neighbour mesh-like interconnection network. While there are heuristics trying to solve this problem, we develop the first exact method based on integer linear programming. This allows us to achieve provably optimal solutions for two different objective functions, for small to medium instances. In addition, we describe a heuristic that seems to outperform all other known heuristics
IGF-II transgenic mice display increased aberrant colon crypt multiplicity and tumor volume after 1,2-dimethylhydrazine treatment.
2006-01-01

In colorectal cancer insulin-like growth factor II (IGF-II) is frequently overexpressed. To evaluate, whether IGF-II affects different stages of tumorigenesis, we induced neoplastic alterations in the colon of wild-type and IGF-II transgenic mice using 1,2-dimethylhydrazine (DMH). Aberrant crypt foci (ACF) served as markers of early lesions in the colonic mucosa, whereas adenomas and carcinomas characterized the endpoints of tumor development. DMH-treatment led initially to significantly more ACF in IGF-II transgenic than in wild-type mice. This increase in ACF was especially prominent for those consisting of > or =three aberrant crypts (AC). Nevertheless, adenomas and adenocarcinomas of the colon, present after 34 weeks in both genetic groups, were not found at different frequency. Tumor volumes, however, were significantly higher in IGF-II transgenic mice and correlated with serum IGF-II levels. Immunohistochemical staining for markers of proliferation and apoptosis revealed increased cell proliferation rates in tumors of IGF-II transgenic mice without significant affection of apoptosis. Increased proliferation was accompanied by elevated localization of beta-catenin in the cytosol and cell nuclei and reduced appearance at the inner plasma membrane. In conclusion, we provide evidence that IGF-II, via activation of the beta-catenin signaling cascade, promotes growth of ACF and tumors without affecting tumor numbers.