julilili42/papers huggingface dataset:
Acclimatory responses of the Daphnia pulex proteome to environmental changes. I. Chronic exposure to hypoxia affects the oxygen transport system and carbohydrate metabolism
2009-04-21

Abstract Background Freshwater planktonic crustaceans of the genus Daphnia show a remarkable plasticity to cope with environmental changes in oxygen concentration and temperature. One of the key proteins of adaptive gene control in Daphnia pulex under hypoxia is hemoglobin (Hb), which increases in hemolymph concentration by an order of magnitude and shows an enhanced oxygen affinity due to changes in subunit composition. To explore the full spectrum of adaptive protein expression in response to low-oxygen conditions, two-dimensional gel electrophoresis and mass spectrometry were used to analyze the proteome composition of animals acclimated to normoxia (oxygen partial pressure [ P o 2 ]: 20 kPa) and hypoxia ( P o 2 : 3 kPa), respectively. Results The comparative proteome analysis showed an up-regulation of more than 50 protein spots under hypoxia. Identification of a major share of these spots revealed acclimatory changes for Hb, glycolytic enzymes (enolase), and enzymes involved in the degradation of storage and structural carbohydrates (e.g. cellubiohydrolase). Proteolytic enzymes remained constitutively expressed on a high level. Conclusion Acclimatory adjustments of the D. pulex proteome to hypoxia included a strong induction of Hb and carbohydrate-degrading enzymes. The scenario of adaptive protein expression under environmental hypoxia can be interpreted as a process to improve oxygen transport and carbohydrate provision for the maintenance of ATP production, even during short episodes of tissue hypoxia requiring support from anaerobic metabolism.
The ethical dimension of terahertz and millimeter-wave imaging technologies: security, privacy, and acceptability
2009-04-21

Terahertz and millimeter-wave imaging technologies, wherever they are applied to human beings, generate problems with the "naked" body. Security issues thus inevitably lead to ethical questions of privacy and intimacy. Less apparent but no less important are other issues such as discrimination and the question of reducing this problem through post processing of data; scalability; questions of controlling the controllers; questions of proliferation. Ethical research alone can not provide acceptability. However, ultimately innovative technologies will not achieve widespread and sustainable acceptance without a fundamental clarification of the ethically relevant issues.
Outcome of Transanal Endorectal Pull-through in Patients with Hirschsprung's Disease
2009-04-22

The functional outcome in most patients after TERPT is satisfactory. We suggest that routine rectal digital examination and anal calibration under anaesthesia 6 weeks postoperatively might detect occult anodermal stenosis and allow early initiation of an anorectal dilatation program, which could decrease the incidence of enterocolitis, persistent constipation and the necessity for further surgical intervention.
Asset pricing with a reference level of consumption: New evidence from the cross‐section of stock returns
2009-04-22

Abstract This paper presents an empirical evaluation of recently proposed asset pricing models which extend the standard preference specification by a reference level of consumption. We motivate an alternative model that accounts for the return on human capital as a determinant of the reference level. Our analysis is based on a broad cross‐section of test assets, which provides a level playing field for a comparison to established benchmark models. The reference level model extended by human capital does a good job in explaining size and value premia. Estimated on Fama and French's size and book‐to‐market sorted portfolios, it outperforms Lettau and Ludvigson's scaled CCAPM and delivers average pricing errors comparable to the Fama–French three‐factor model.
KIRMES: kernel-based identification of regulatory modules in euchromatic sequences
2009-04-23

Abstract Motivation: Understanding transcriptional regulation is one of the main challenges in computational biology. An important problem is the identification of transcription factor (TF) binding sites in promoter regions of potential TF target genes. It is typically approached by position weight matrix-based motif identification algorithms using Gibbs sampling, or heuristics to extend seed oligos. Such algorithms succeed in identifying single, relatively well-conserved binding sites, but tend to fail when it comes to the identification of combinations of several degenerate binding sites, as those often found in cis-regulatory modules. Results: We propose a new algorithm that combines the benefits of existing motif finding with the ones of support vector machines (SVMs) to find degenerate motifs in order to improve the modeling of regulatory modules. In experiments on microarray data from Arabidopsis thaliana, we were able to show that the newly developed strategy significantly improves the recognition of TF targets. Availability: The python source code (open source-licensed under GPL), the data for the experiments and a Galaxy-based web service are available at http://www.fml.mpg.de/raetsch/suppl/kirmes/ Contact: sebi@tuebingen.mpg.de Supplementary information: Supplementary data are available at Bioinformatics online.
Triggering of suicidal erythrocyte death by radiocontrast agents
2009-04-23

Abstract Background According to in vitro observations, gadolinium‐containing magnetic resonance (MRT) contrast agents stimulate suicidal cell death or apoptosis. Similar to nucleated cells, erythrocytes may undergo suicidal death or eryptosis, characterized by cell shrinkage and cell membrane scrambling with phosphatidylserine (PS) exposure at the erythrocyte surface. Eryptosis is triggered by increased cytosolic Ca 2+ ‐activity. This study explored whether gadolinium‐containing MRT contrast agents stimulate eryptosis. Materials and methods Annexin V‐binding reflecting PS exposure and forward scatter reflecting cell volume were determined in erythrocytes within freshly drawn blood from patients (8♀, 3♂, 29–72 years) prior to and 10 min after administration of gadoterate meglumine (0·1 mmol kg −1 b.w. Dotarem ® ; six patients) or gadobenate dimeglumine (0·05 mmol kg −1 bw Multi Hance ® ; five patients). In a separate series, eryptosis was determined prior to and following in vitro incubation of erythrocytes from 16 blood donors for 4 h with gadoterate meglumine (5 mM Dotarem ® ) or gadobenate dimeglumine (5 mM Multi Hance ® ). Finally, eryptosis and Fluo3 fluorescence reflecting cytosolic Ca 2+ were determined in vitro following exposure to Gd 3+ . Data were analysed using paired t ‐test or anova with Tukey’s test as post‐test. Results The MRT contrast agents such as gadoterate meglumine (Dotarem ® ) and gadobenate dimeglumine (Multi Hance ® ) significantly increased the percentage of eryptotic cells. Moreover, in vitro exposure to gadoterate meglumine (5 mM), gadobenate dimeglumine (5 mM) or Gd 3+ (1·9 μM) stimulated eryptosis in vitro . The effect of Gd 3+ was paralleled by increase in cytosolic Ca 2+ ‐activity. Conclusions MRT contrast agents may stimulate suicidal erythrocyte death or eryptosis in vitro and in vivo .
Cyclo‐oxygenase‐2 expression in photon‐radiated and non‐radiated uveal melanomas
2009-04-23

ABSTRACT. Purpose: To determine and compare cyclo‐oxygenase‐2 (COX‐2) expression in photon‐radiated and non‐radiated malignant uveal melanomas and to analyse the correlation between COX‐2 expression and prognosis. Methods: Immunohistochemical staining for COX‐2 was performed on 21 uveal melanomas that were endoresected after prior stereotactic radiotherapy with photons and on 22 tumours that were treated by endoresection without prior radiotherapy. COX‐2 staining was further analysed in respect to cell type, maximal prominence, time interval between radiotherapy and surgery, apoptotic index (AI), proliferative index (PI) and the development of metastatic disease. Results: There was no difference in COX‐2 expression between radiated and non‐radiated melanomas ( P &gt; 0.15). COX‐2 staining correlated with neither the tumour prominence ( P &gt; 0.40) nor the AI or the PI (both P &gt; 0.35). Tumours with high COX‐2 expression were significantly more likely to develop metastasis ( P = 0.022). Conclusion: Radiotherapy with photons does not induce COX‐2 expression in malignant melanomas of the uvea. But high COX‐2 expression may be a marker for poor prognosis.
SIMULTANEOUS OBSERVATIONS OF PKS 2155–304 WITH HESS, FERMI , RXTE , AND ATOM: SPECTRAL ENERGY DISTRIBUTIONS AND VARIABILITY IN A LOW STATE
2009-04-24

We report on the first simultaneous observations that cover the optical, X-ray, and high-energy gamma-ray bands of the BL Lac object PKS 2155–304. The gamma-ray bands were observed for 11 days, between 2008 August 25 and 2008 September 6 (MJD 54704–54715), jointly with the Fermi Gamma-ray Space Telescope and the HESS atmospheric Cherenkov array, providing the first simultaneous MeV-TeV spectral energy distribution (SED) with the new generation of γ-ray telescopes. The ATOM telescope and the RXTE and Swift observatories provided optical and X-ray coverage of the low-energy component over the same time period. The object was close to the lowest archival X-ray and very high energy (VHE; &gt;100 GeV) state, whereas the optical flux was much higher. The light curves show relatively little (~30%) variability overall when compared to past flaring episodes, but we find a clear optical/VHE correlation and evidence for a correlation of the X-rays with the high-energy spectral index. Contrary to previous observations in the flaring state, we do not find any correlation between the X-ray and VHE components. Although synchrotron self-Compton models are often invoked to explain the SEDs of BL Lac objects, the most common versions of these models are at odds with the correlated variability we find in the various bands for PKS 2155–304.
Self-Healing of Gold Nanoparticles in the Presence of Zinc Phthalocyanines and Their Very Efficient Nonlinear Absorption Performances
2009-04-24

We found that a gold nanoparticles (AuNP) solution shows very good nonlinear absorption properties in the nanosecond time regime at 532 nm, also at high fluences, when zinc phthalocyanines are present. The enhanced nonlinear response is due to the self-healing of gold nanoparticles, which do not undergo the fast photoinduced fragmentation usually observed during irradiation with intense laser pulses. The self-healing mechanism can be of general interest when intense laser pulses interact with plasmonic nanostructures in the presence of organic chromophores.
1H HR/MAS NMR in the suspended state: Molecular recognition processes in liquid chromatography between steroids and a silica hydride‐based cholesterol phase
2009-04-24

Abstract A mixture of eight steroids was separated by HPLC on a silica hydride‐based stationary phase modified with a moiety of cholesteryl 10‐undecanoate. Within the steroid mixture progesterone showed the longest retention time suggesting the strongest interaction with the stationary phase material. To obtain more detailed information upon the effective separation process, interaction studies were performed by high resolution/magic angle spinning (HR/MAS) NMR spectroscopy recorded in the suspended state. 1 H saturation transfer difference (STD) NMR experiments with T 1ρ suppression showed significant hydrophobic binding affinities of progesterone toward the cholesterol column material. These NMR results can be correlated directly to the chromatographic data obtained by HPLC.
Coinfections withSchistosoma haematobium, Necator americanus,andEntamoeba histolytica/Entamoeba disparin Children: Chemokine and Cytokine Responses and Changes after Antiparasite Treatment
2009-04-24

The effect of polyparasite infections on cytokine and chemokine responses as well as the effect of antiparasite treatment was studied in children without parasite infection (the G0 group), in children singly infected with Schistosoma haematobium (the G1 group), and in children multiply infected with S. haematobium/Schistosoma mansoni, Entamoeba histolytica/Entamoeba dispar, and Necator americanus (the G3+ group). Linear regression analysis disclosed a significant risk for coinfection with hookworm and Schistosoma species. Polyparasite infections detected in 23% of children before treatment were present in 5% at 15 months after treatment. Chemokine responses to S. mansoni adult worm antigen (SmAg) diminished after treatment for macrophage inflammatory chemokine (MIP)-1alpha/chemokine (C-C motif) ligand (CCL)-3 (among G3+ children, by a factor of 200 [95% confidence interval {CI}, 33-1111]) and for MIP-1beta/CCL-4 (among G3+ children, by a factor of 26 [95% CI, 6-117]) but were enhanced for thymus- and activation-regulated chemokine/CCL-17 (among G3+ children, by a factor of 10 [95% CI, 3-32]) (P < .001 for all). In response to E. histolytica antigen, interleukin (IL)-13 levels increased after treatment among G1 children by a factor of 138 (95% CI, 12-1569) and among G3+ children by a factor of 21 (95% CI, 7-64) (P < .001 for both). Cellular production of interferon (IFN)-gamma in response to SmAg decreased 4 weeks after treatment among G3+ children, whereas T helper cell type 2 (Th2) IL-13 production was enhanced among G1 and G3+ children. In summary, polyparasite infections with S. haematobium/S. mansoni, E. histolytica/E. dispar, and N. americanus generated prominent proinflammatory cytokine and chemokine responses, and, after antihelminth treatment, the inflammatory chemokine response lessened as the Th2 responsiveness in coinfected children increased.
Dysplastic nevus syndrome with development of multiple melanomas. A surgical concept for prophylaxis
2009-04-24

Summary A 58‐year‐old man presented in 2001 with dysplastic nevus syndrome with at least 300 nevi and about 100 clinically highly atypical nevi. Three melanomas had been excised by a private dermatologist within the past year. We then removed two additional melanomas. Between 2002 and 2003, 117 nevi which were atypical on dermatoscopy were removed; most by horizontal (shave) excision. Adequate clinical and dermatoscopic control was not feasible due to the large number of atypical nevi. In order to reduce the number of nevus cells, we treated test sites with both dermabrasion and split‐thickness excision. The latter proved to be more efficient and was used to completely excise the skin of the back, as well as parts of the arms and chest in two sessions under general anesthesia. Wound healing was uneventful. Following these procedures, adequate clinical and dermatoscopic monitoring of the remaining nevi was possible and only a few had to be removed. No more melanomas appeared in the treated areas.
Cu/Zn-superoxide dismutase from the fungal strain Humicola lutea 103 improves ram spermatozoa functions in vitro
2009-04-24

In this study we determined the effect of reactive oxygen species (ROS) generation during incubation in media at 39 degrees C on ram spermatozoa and the protection by exogenously added antioxidant enzyme, superoxide dismutase (SOD). A novel Cu/Zn-SOD, isolated from the fungal strain Humicola lutea 103 (HLSOD), was used. Our results point out that the levels of both, superoxide anion radicals (*O2-) and H2O2, increase approximately 8-10- and 2-3-fold, respectively, during incubation of spermatozoa. Enhanced ROS generation coincided with reduction of motility, independently of the type of diluted medium. Addition of HLSOD (30, 60 and 120 U ml(-1) sperm) improved sperm functions, maintaining almost initial percentages of motile spermatozoa and increasing the values of mean cytochemical coefficient. At the same time, a significant diminution of *O2- and H2O2 content in the presence of antioxidant enzyme was established. The results suggest that HLSOD is an effective *O2- scavenger in semen that leads to protection of sperm functions.
Ontogenetic Cycles in Pathogenic Fungi
2009-04-24

Summary The etiologic agents of mycoses of man and animals are arbitrarily characterized as “dimorphic fungi” existing in saprophytic and parasitic forms. Developmental patterns of some of the pathogenic fungi are described and illustrated. In a synoptic table, the fungi are arranged in taxonomic order. Résumé Dans cet article, les agents responsables des mycoses humaines et animales sont considérés comme »champignons dimorphiques«, existant sous forme saprophyte et parasitaire. On en trouvera des descriptions illustrées, ainsi qu'un tableau synoptique, arrangé en ordre taxino-mique. Zusammenfassung Zur Ontogenese pathogener Pilze. Um Besonderheiten der Erreger von Human- und Tiermykosen hervorzuheben, wird der Ausdruck “Dimorphismus” (saprobische und parasiti-sche Form) herangezogen, wahrend sich das Konzept desontogenetischen Zyklus“hierfür nicht eignet, und obwohl die Pilze eher als polymorph denn als dimorph zu bezeichnen sind. Ausgewählte Erreger werden vergleichend anhand von Abbildungen dargestellt und zum Überblick in einer Tabelle nach pilzsystematischen Gesichtspunkten angeordnet.
Pedogenesis, permafrost, and soil moisture as controlling factors for soil nitrogen and carbon contents across the Tibetan Plateau
2009-04-25

Abstract We investigated the main parameters [e.g. mean annual air temperature , mean annual soil temperature, mean annual precipitation, soil moisture (SM), soil chemistry, and physics] influencing soil organic carbon (C org ), soil total nitrogen (N t ) as well as plant available nitrogen (N min ) at 47 sites along a 1200 km transect across the high‐altitude and low‐latitude permafrost region of the central‐eastern Tibetan Plateau. This large‐scale survey allows testing the hypothesis that beside commonly used ecological variables, diversity of pedogenesis is another major component for assessing carbon (C) and nitrogen (N) cycling. The aim of the presented research was to evaluate consequences of permafrost degradation for C and N stocks and hence nutrient supply for plants, as the transect covers all types of permafrost including heavily degraded areas and regions without permafrost. Our results show that SM is the dominant parameter explaining 64% of C org and 60% of N variation. The extent of the effect of SM is determined by permafrost, current aeolian sedimentation occurring mostly on degraded sites, and pedogenesis. Thus, the explanatory power for C and N concentrations is significantly improved by adding CaCO 3 content ( P =0.012 for C org ; P =0.006 for N t ) and soil texture ( P =0.077 for C org ; P =0.015 for N t ) to the model. For soil temperature, no correlations were detected indicating that in high‐altitude grassland ecosystems influenced by permafrost, SM overrides soil temperature as the main driving parameter at landscape scale. It was concluded from the current study that degradation of permafrost and corresponding changes in soil hydrology combined with a shift from mature stages of pedogenesis to initial stages, have severe impact on soil C and plant available N. This may alter biodiversity patterns as well as the development and functioning of the ecosystems on the Tibetan Plateau.
Kant's Moral and Legal Philosophy
2009-04-27

This volume brings to English readers the finest postwar German-language scholarship on Kant's moral and legal philosophy. Examining Kant's relation to predecessors such as Hutcheson, Wolff, and Baumgarten, it clarifies the central issues in each of Kant's major works in practical philosophy, including The Groundwork of the Metaphysics of Morals, The Critique of Practical Reason, and The Metaphysics of Morals. It also examines the relation of Kant's philosophy to politics. Collectively, the essays in this volume provide English readers with a direct view of how leading German philosophers are now regarding Kant's revolutionary practical philosophy, one of the outstanding achievements of German thought.
Application of mycorrhizal roots improves growth of tropical tree seedlings in the nursery: a step towards reforestation with native species in the Andes of Ecuador
2009-04-27

Most tree species in tropical mountain rain forests are naturally associated with arbuscular mycorrhizal fungi. Previous studies in southern Ecuador of 115 tree species revealed that only three species were not associated with arbuscular mycorrhizal fungi. Seedlings of tropical tree species raised in the nursery may need to be associated with arbuscular mycorrhizal fungi to survive transplantation shock in higher numbers. Methods for establishing plantations with native tree species are not yet established for Ecuador. Thus, we investigated the feasibility of using mycorrhizal roots of seedlings of Inga acreana, Tabebuia chrysantha, Cedrela montana and Heliocarpus americanus that had trapped mycorrhizal fungi from forest humus in the nursery to inoculate C. montana and H. americanus with native arbuscular mycorrhizal fungi. Inoculation with either a mixture of mycorrhizal roots from the four species or only with mycorrhizal roots from the same tree species were compared with effects of moderate fertilization. Assessment of plant growth and mycorrhizal status of 6-months-old Cedrela montana and Heliocarpus americanus revealed an improvement in growth and diverse associated fungi through mycorrhizal root inoculation in comparison with moderate fertilization. Moderate fertilization did not suppress mycorrhization. © Springer Science+Business Media B.V. 2009.
Kant's Moral and Legal Philosophy
2009-04-27

This volume brings to English readers the finest postwar German-language scholarship on Kant's moral and legal philosophy. Examining Kant's relation to predecessors such as Hutcheson, Wolff, and Baumgarten, it clarifies the central issues in each of Kant's major works in practical philosophy, including The Groundwork of the Metaphysics of Morals, The Critique of Practical Reason, and The Metaphysics of Morals. It also examines the relation of Kant's philosophy to politics. Collectively, the essays in this volume provide English readers with a direct view of how leading German philosophers are now regarding Kant's revolutionary practical philosophy, one of the outstanding achievements of German thought
Convergent discretization of heat and wave map flows to spheres using approximate discrete Lagrange multipliers
2009-04-27

We propose fully discrete schemes to approximate the harmonic map heat flow and wave maps into spheres. The finite-element based schemes preserve a unit length constraint at the nodes by means of approximate discrete Lagrange multipliers, satisfy a discrete energy law, and iterates are shown to converge to weak solutions of the continuous problem. Comparative computational studies are included to motivate finite-time blow-up behavior in both cases.