julilili42/papers huggingface dataset:
Cell Nucleus Directed 2,3,5-triiodobenzoic Acid Conjugates
2009-07-01

Triiodobenzoic acid (TIBA) represents the core structure of most clinically used contrast agents for computed tomography and other X-ray procedures. To construct an intracellular radiopaque contrast agent, TIBA was coupled to various different positively and negatively charged fluorescein iothiocyanate (FITC)-labelled peptides. TIBA coupled to the SV40 T Antigen nuclear localization sequence (NLS) stained 80% of human glioma cells and caused cell death. This occurred with C- or N-terminal binding of TIBA and with the correct or mutant NLS. No cell death and only small numbers of stained cells (below 3 %) were observed after incubation with NLS conjugates lacking TIBA or after incubation with TIBA-conjugates containing a negatively charged polyglutamic acid stretch. TIBA-conjugates containing the Antennapedia-derived cell-penetrating peptide penetratin were only nuclearly taken up when TIBA and FITC were coupled to lysines outside the 16-amino acid peptide sequence. The study shows that intracellular TIBA may have potential as a chemotherapeutic agent rather than a contrast agent.
A Framework to Structure CSCL for Pupils with Cognitive Disabilities
2009-07-01

Verbal communication is a key not only for learning but also for every day life. Since one goal of schools for pupils with cognitive disabilities is to prepare pupils to manage their every day life on their own, we expect that teaching pupils how to learn and work collaboratively by sharing tasks, give directions to each other and understand them, will support this process. In this paper we will present an environment which supports implicit scripted collaborative task solving without increasing cognitive load.
A new emulsifier-free w/o system based on a triterpene extract from the outer bark of birch
2009-07-01

Surfactants are critically seen due to their impairment of skin barrier function. Therefore surfactant-free emulsions become more and more important. Here we present a new w/o emulsion system based on a triterpene dry extract from the outer bark of birch (TE) that is supposed to be emulsifier-free. Beside the galenic properties the TE display various pharmacological activities also important for dermatology [1]. 80% of TE is betulin, a pentacyclic triterpene with a polar group (alcohol) on each side of the molecule, respectively [1].
Effects of STW 5 and its single extracts on ileal oxygen radical production induced by histamine
2009-07-01

STW 5 (Iberogast®) is a well established mixture prepared from nine plant extracts (angelika root, bitter candy tuft, camomile flowers, caraway fruits, greater celandine herb, liquorice root, milk thistle fruits, lemon balm leafs, peppermint leafs) with clinically proven efficacy in several digestive diseases, especially in therapy of Irritable Bowel Syndrome (IBS). Recent findings favour that inflammation seems to play an important role in IBS, suggesting that oxidative stress could be involved in the pathogenesis. Here we could show by luminol-enhanced chemiluminescence that histamine was able to increase oxygen free radical production of incubated samples of mouse intestine. In addition, the antioxidative effects of STW 5 and its constituent extracts were studied.
Parametrization of integrated hydrological model of Nam Co lake catchment on Tibetan Plateau using synergy of SAR and optical data
2009-07-01

Understanding of exchange processes over Tibetan Plateau including hydrological cycle is becoming increasingly important since their influence on the formation of the Asian monsoon system is known. Tibetan Plateau is source area for main Asian rivers that are of crucial importance for downstream communities of China, India, Bangladesh, Pakistan and SE Asia. Accurate and up-to date information of the characteristics and the current trend of these changes, provided by modern satellite systems like TerraSAR-X, are thus needed. The study area is delimited by the watershed of Nam Co basin on Tibetan Plateau in Tibet Autonomous Region of China approximately 100 km NNW from Lhasa. The no-outlet basin of the lake offers an excellent example of landscape unit characteristic for Tibetan Plateau where all exchange processes between land and atmosphere can be studied. Hydrologic modeling of Nam Co basin will be supported by complex interpretation of TerraSAR-X data that will provide whole set of hydrologic parameters. The TerraSAR data will be processed in synergy with other available microwave and optical remote sensing data sets. Basic extracted variables will be thus transformed into meaningful hydrological parameters. Data evaluation will take into account various aspects of landscape qualities with respect to water cycle. Variability of lake level, seasonal changes of soil moisture, influence of wetlands, lake icing and snow melt will be estimated. The synergetic approach to interpretation of TerraSAR-X data will benefit from major advantages of the high spatial resolution, the fast repetition cycle and the full-polarimetric capabilities in combination with high resolution optical data (RapidEye, QuickBird, Kompsat-2, ASTER. Landsat etc.) and digital elevation models.
Spectrum and variability of the Galactic center VHE γ-ray source HESS J1745–290
2009-07-02

Aims: A detailed study of the spectrum and variability of the source HESS J1745−290 in the Galactic Center (GC) region using new data from the H.E.S.S. array of Cherenkov telescopes is presented. Flaring activity and quasi periodic oscillations (QPO) of HESS J1745−290 are investigated. Methods: The image analysis is performed with a combination of a semi-analytical shower model and the statistical moment-based Hillas technique. The spectrum and lightcurves of HESS J1745−290 are derived with a likelihood method based on a spectral shape hypothesis. Rayleigh tests and Fourier analysis of the H.E.S.S. GC signal are used to study the periodicity of the source. Results: With a three-fold increase in statistics compared to previous work, a deviation from a simple power law spectrum is detected for the first time. The measured energy spectrum over the three years 2004, 2005 and 2006 of data taking is compatible with both a power law spectrum with an exponential cut-off and a broken power law spectrum. The curvature of the energy spectrum is likely to be intrinsic to the photon source, as opposed to effects of interstellar absorption. The power law spectrum with an exponential cut-off is characterized by a photon index of 2.10 ± 0.04stat ± 0.10syst and a cut-off energy at 15.7 ± 3.4stat ± 2.5syst TeV. The broken power law spectrum exhibits spectral indices of 2.02 ± 0.08stat ± 0.10syst and 2.63 ± 0.14stat ± 0.10syst with a break energy at 2.57 ± 0.19stat ± 0.44syst TeV. No significant flux variation is found. Increases in the γ-ray flux of HESS J1745−290 by at least a factor of two would be required for a 3σ detection of a flare with time scales of an hour. Investigation of possible QPO activity at periods claimed to be detected in X-rays does not show any periodicities in the H.E.S.S. signal.
Spillovers from Multinationals to Heterogeneous Domestic Firms: Evidence from Hungary
2009-07-02

Abstract Firms cluster their economic activities to exploit technological and informational spillovers from other firms. Spillovers from multinational firms can be particularly beneficial to firms in less developed economies, because technological superiority and management expertise of foreign multinational firms yield various opportunities for learning. Yet, the importance of foreign firms’ spillovers might vary with respect to two key features of domestic firms: their productivity level and their export status. In line with theories on the absorptive capacity of firms, we argue on the basis of an empirical analysis of Hungarian firms that larger and more productive firms are more able than smaller firms to reap spillovers from multinationals. However, the export status is found to be of minor importance once higher productivity is controlled for.
What a Plant Sounds Like: The Statistics of Vegetation Echoes as Received by Echolocating Bats
2009-07-02

A critical step on the way to understanding a sensory system is the analysis of the input it receives. In this work we examine the statistics of natural complex echoes, focusing on vegetation echoes. Vegetation echoes constitute a major part of the sensory world of more than 800 species of echolocating bats and play an important role in several of their daily tasks. Our statistical analysis is based on a large collection of plant echoes acquired by a biomimetic sonar system. We explore the relation between the physical world (the structure of the plant) and the characteristics of its echo. Finally, we complete the story by analyzing the effect of the sensory processing of both the echolocation and the auditory systems on the echoes and interpret them in the light of information maximization. The echoes of all different plant species we examined share a surprisingly robust pattern that was also reproduced by a simple Poisson model of the spatial reflector arrangement. The fine differences observed between the echoes of different plant species can be explained by the spatial characteristics of the plants. The bat's emitted signal enhances the most informative spatial frequency range where the species-specific information is large. The auditory system filtering affects the echoes in a similar way, thus enhancing the most informative spatial frequency range even more. These findings suggest how the bat's sensory system could have evolved to deal with complex natural echoes.
Arsenic Binding to Iron(II) Minerals Produced by An Iron(III)-Reducing Aeromonas Strain Isolated from Paddy Soil
2009-07-02

Abstract An iron-reducing bacterial strain was isolated from a paddy soil and identified as a member of the Aeromonas group by 16S rRNA gene sequence analysis. When the cells were growing with dissolved Fe(III) as the electron acceptor in the presence of As(V), Fe(II) minerals (siderite and vivianite) were formed and dissolved. As was removed efficiently from solution. When the cells were growing with the Fe(III) hydroxide mineral (ferrihydrite) as the electron acceptor in the presence of As(V), ferrihydrite was reduced and dissolved As(V) concentrations decreased sharply. The present study results demonstrated first that members of the Aeromonas group can reduce Fe(III) in paddy soils and second that iron reduction does not necessarily lead to arsenic mobilization. However, As immobilization can occur in environments that contain significant concentrations of counterions such as bicarbonate and phosphate.
Oscillations over long times in numerical Hamiltonian systems
2009-07-02

The numerical treatment of ordinary differential equations has continued to be a lively area of numerical analysis for more than a century, with interesting applications in various fields and rich theory. There are three main developments in the design of numerical techniques and in the analysis of the algorithms:
Effective Dynamics for Constrained Quantum Systems
2009-07-02

We consider the time dependent Schrödinger equation on a Riemannian manifold A with a potential that localizes a certain class of states close to a fixed submanifold C, the constraint manifold. When we scale the potential in the directions normal to C by a parameter ε ≪ 1, the solutions concentrate in an ε-neighborhood of the submanifold. We derive an effective Schrödinger equation on the submanifold C and show that its solutions, suitably lifted to A, approximate the solutions of the original equation on A up to errors of order ε 3 |t | at time t. Our result holds in the situation where tangential and normal energies are of the same order, and where exchange between normal and tangential energies occurs. In earlier results tangential energies were assumed to be small compared to normal energies, and rather restrictive assumptions were needed, to ensure that the separation of energies is maintained during the time evolution. Most importantly, we can now allow for constraining potentials that change their shape along the submanifold, which is the typical situation in applications like molecular dynamics and quantum waveguides.
ChemInform Abstract: Rapid and Easy Access to Indoles via Microwave‐Assisted Hemetsberger—Knittel Synthesis.
2009-07-02

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Pharmacogenomics of Tamoxifen Therapy
2009-07-03

Abstract Background: Tamoxifen is a standard endocrine therapy for the prevention and treatment of steroid hormone receptor–positive breast cancer. Content: Tamoxifen requires enzymatic activation by cytochrome P450 (CYP) enzymes for the formation of active metabolites 4-hydroxytamoxifen and endoxifen. As compared with the parent drug, both metabolites have an approximately 100-fold greater affinity for the estrogen receptor and the ability to inhibit cell proliferation. The polymorphic CYP2D6 is the key enzyme in this biotransformation, and recent mechanistic, pharmacologic, and clinical evidence suggests that genetic variants and drug interaction by CYP2D6 inhibitors influence the plasma concentrations of active tamoxifen metabolites and the outcomes of tamoxifen-treated patients. In particular, nonfunctional (poor metabolizer) and severely impaired (intermediate metabolizer) CYP2D6 alleles are associated with higher recurrence rates. Summary: Accordingly, CYP2D6 (cytochrome P450, family 2, subfamily D, polypeptide 6) genotyping before treatment to predict metabolizer status may open new avenues for individualizing endocrine treatment, with the maximum benefit being expected for extensive metabolizers. Moreover, strong CYP2D6 inhibitors such as the selective serotonin reuptake inhibitors paroxetine and fluoxetine, which are used to treat hot flashes, should be avoided because they severely impair formation of the active metabolites.
Strongly hyperbolic Hamiltonian systems in numerical relativity: formulation and symplectic integration
2009-07-03

We consider two strongly hyperbolic Hamiltonian formulations of general relativity and their numerical integration with a free and a partially constrained symplectic integrator. In those formulations we use hyperbolic drivers for the shift and in one case also for the densitized lapse. A system where the densitized lapse is an external field allows to enforce the momentum constraints in a holonomically constrained Hamiltonian system and to turn the Hamilton constraint function from a weak to a strong invariant. These schemes are tested in a perturbed Minkowski and the Schwarzschild space-time. In those examples we find advantages of the strongly hyperbolic formulations over the ADM system presented in [arXiv:0807.0734]. Furthermore we observe stabilizing effects of the partially constrained evolution in Schwarzschild space-time as long as the momentum constraints are enforced.
FRED—a framework for T-cell epitope detection
2009-07-05

Abstract Summary: Over the last decade, immunoinformatics has made significant progress. Computational approaches, in particular the prediction of T-cell epitopes using machine learning methods, are at the core of modern vaccine design. Large-scale analyses and the integration or comparison of different methods become increasingly important. We have developed FRED, an extendable, open source software framework for key tasks in immunoinformatics. In this, its first version, FRED offers easily accessible prediction methods for MHC binding and antigen processing as well as general infrastructure for the handling of antigen sequence data and epitopes. FRED is implemented in Python in a modular way and allows the integration of external methods. Availability: FRED is freely available for download at http://www-bs.informatik.uni-tuebingen.de/Software/FRED. Contact: feldhahn@informatik.uni-tuebingen.de
Hidden diversity in the non‐caryophyllaceous plant‐parasitic members ofMicrobotryum(Pucciniomycotina: Microbotryales)
2009-07-06

Abstract Members of the fungal genus Microbotryum are well‐known parasites on eudicotyledonous plant hosts. However, recent studies focused exclusively on Microbotryum species being parasites in the anthers of Caryophyllaceae in which strong host‐specificity was confirmed by molecular analyses. Consequently, species numbers have risen considerably as multi‐host parasites were split up in so‐called cryptic species. We subjected three non‐caryophyllaceous Microbotryum groups to molecular phylogenetic analyses to see whether we would confirm multi‐host morphospecies or if host‐specific cryptic species in these selected groups could be revealed as well (i.e. a group of non‐caryophyllaceous anther smuts, parasites on different Fallopia species, and parasites on Polygonum bistorta and Polygonum vi‐viparum). We applied a multiple analysis strategy to correct for varying alignment effects on a two‐locus dataset (ITS and LSU rDNA). The results obtained by the different approaches are uniform; high host‐specificity exists in the non‐ caryophyllaceous anther smuts, but overlapping host ranges occur in the parasites of Fallopia species. Results for the parasites of Polygonum are similar, with Microbotryum bistortarum being separated into three lineages and M. marginale forming a lineage on P. bistorta which apparently is conspecific with M. bistortarum p.p. Our study shows that phylogenetic patterns within Microbotryum are much more complicated than deduced from morphological observations alone. Even though Microbotryum species are highly host‐specific, it is impossible to identify species based solely on host taxa affiliation. Species status is reinstated for the anther smut on Salvia pratensis.
Variable antigen uptake due to different expression of the macrophage mannose receptor by dendritic cells in various inbred mouse strains
2009-07-06

Summary Antigen uptake by dendritic cells is essential for the induction of antigen‐specific T‐cell responses. Here, we investigate the ability of dendritic cells from different mouse strains to endocytose antigens. The uptake of different fluorescently labelled soluble antigens by bone marrow‐derived dendritic cells from BALB/c, C57BL/6 and C3H/HeN mice was analysed by flow cytometry. Using transferrin as a specific marker for clathrin‐mediated endocytosis, we observed no significant differences of transferrin uptake by dendritic cells from BALB/c, C57BL/6 and C3H/HeN mice. Similar results were obtained by analysing macropinocytosis with lucifer yellow. In contrast, analysing the uptake of ovalbumin, which is predominantly mediated by clathrin‐mediated endocytosis via the macrophage mannose receptor, we found that dendritic cells from C3H/HeN mice take up three‐ to fivefold more ovalbumin than dendritic cells from BALB/c or C57BL/6 mice. Blocking the uptake of ovalbumin via the macrophage mannose receptor by using mannan led to a comparable uptake of ovalbumin by dendritic cells from all three mouse strains. Consistently, dendritic cells from C3H/HeN mice displayed significantly increased expression of the macrophage mannose receptor compared to dendritic cells from BALB/c or C57BL/6 mice. In conclusion, receptors involved in antigen uptake such as the macrophage mannose receptor may be differentially expressed and may explain variations of T‐cell responses after vaccination in different individuals.
A Novel Platform for Research on Toxins
2009-07-06

Toxins are ubiquitous in nature and as such they impact our daily life. Toxins may come from a wide variety of sources and influence a myriad of biological functions. Research on toxins may address their production, structure, chemical properties, biological activity, and economic impact. On the one hand, toxins may be used to decipher biological mechanisms, to favourably influence disease or to combat unwanted organisms. On the other hand, toxins may be a hazard jeopardizing health of humans, animals or plants. [...]
Incidental prostate cancer at radical cystoprostatectomy: implications for apex‐sparing surgery
2009-07-07

Study Type – Therapy (case series) Level of Evidence 4 OBJECTIVE To analyse retrospectively the clinicopathological features of incidental prostate cancer in patients undergoing radical cystoprostatovesiculectomy (RCP) for invasive bladder cancer, as recent studies suggest that prostatic apex‐sparing surgery in patients undergoing RCP improves urinary continence and erectile function after surgery, but in those with incidental prostate cancer, leaving the apical region endangers the oncological outcome. PATIENTS AND METHODS From 2004 to 2007, at our institution, 95 men had RCP for invasive bladder cancer. We reviewed their clinicopathological variables, especially apical involvement, and the course of prostate‐specific antigen (PSA) levels before and after surgery. We compared clinically significant and insignificant prostate cancers. RESULTS Of the 95 patients, 26 had incidental prostate cancer (mean age 68 years, range 53–80) on definitive histological examination. The mean ( sd , range) preoperative PSA level in all 26 men was 3.6 (0.8, 0.2–14) ng/mL, but six of the 26 patients had preoperative PSA levels of &gt;4 ng/mL and one other had suspicious findings on a digital rectal examination. Involvement of the apex was histologically confirmed in seven of the 26 patients (27%), including four with significant prostate cancer ( P = 0.039). Preoperative PSA levels did not differ significantly between the seven patients with significant and 19 with insignificant prostate cancer, but seven patients with apical involvement had significantly higher PSA levels before RCP than the 19 who did not ( P &lt; 0.04). PSA levels after RCP remained below the limit of detection in all patients over a mean (range) follow‐up 14.3 (3–32) months. CONCLUSION In our series, preserving the apex of the prostate to decrease morbidity after RCP carried a 7.3% risk (seven of 95 patients) of leaving significant cancer in the residual prostatic tissue. No preoperative clinical value could exclude apical involvement. Therefore, our findings stress the oncological need for a careful and complete excision of the prostate during RCP.
Increase of SCF plasma concentration during donepezil treatment of patients with early Alzheimer's disease
2009-07-07

Alzheimer's disease (AD) can be treated with inhibitors of the enzyme acetylcholinesterase (AChE). There is evidence that AChE inhibitors promote neuroprotective effects and neurogenesis in the central nervous system (CNS). However, the mechanisms by which AChE inhibitors mediate these effects are still not well understood. One possible mechanism could be the up-regulation of haematopoietic growth factors (HGFs), also known to promote neuroprotective effects and to stimulate neurogenesis in the CNS. In the present study we investigated the impact of a 15-month treatment with the AChE inhibitor donepezil on blood levels of the HGFs stem cell factor (SCF), stromal cell-derived factor 1 (SDF-1), granulocyte colony- stimulating factor (G-CSF) and vascular endothelial growth factor (VEGF) in 19 patients with AD and 45 age-matched healthy controls. Before treatment with donepezil we found in AD patients significantly decreased SCF plasma concentrations (661.1+/-40.0 pg/ml) compared to healthy controls (997.7+/-33.7 pg/ml, p<0.001) but no significant differences between both groups concerning blood levels of SDF-1, G-CSF and VEGF. After 15 months' treatment SCF plasma levels increased significantly in the AD patients (764.5+/-41.5 pg/ml, p=0.016). In addition, we found a significant positive correlation between SCF plasma levels at baseline and changes of cognitive functions over the 15-month period (r=0.521, p=0.022). For the other HGFs we were unable to show a significant impact of donepezil treatment. Our findings indicate that donepezil treatment of AD patients is associated with an up-regulation of SCF plasma levels, which may contribute to neuroprotection and neurogenesis in the CNS.