julilili42/papers huggingface dataset:
Bis(trifluoromethyl)phosphinous Acid (CF3)2P‐O‐H: An Example of a Thermally Stable Phosphinous Acid—Synthesis, Gas‐Phase Structure, and Rotational Isomers
2006-02-21

Abstract The bis(trifluoromethyl)phosphinous acid, (CF 3 ) 2 POH, is the only known example of a thermally stable phosphinous acid. Although this compound has been known since 1960, little is known about the chemistry of this extraordinary compound; this might be due to the tedious, and in some part risky, synthesis that was originally published. An improved, simple, and safe synthesis that is based on the treatment of the easily accessible (CF 3 ) 2 PNEt 2 , with at least three equivalents of p ‐toluene sulfonic acid, is presented. The reaction results in a complete conversion to the phosphinous acid, which is isolated in almost 90 % yield. The compound exists in an equilibrium of two POH rotational isomers, a fact which is supported by quantum chemical calculations. The relative enthalpy difference of 6.4 kJ mol −1 , calculated at the B3PW91/6‐311G(3d,p) level, is in excellent agreement with the experimental value of 5.9 kJ mol −1 , which was determined from the temperature dependence of the (OH) bands of the two rotational isomers. The complete experimental vibrational spectra of both rotamers, their predicted vibrational spectra obtained by using quantum chemical calculations, and an attempt at photoinduced isomerization of matrix‐isolated (CF 3 ) 2 POH is presented. The experimental structure, obtained from an electron‐diffraction study in the gas phase, is reproduced very well by ab initio and density functional theory (DFT) methods.
The Blue Obelisk—Interoperability in Chemical Informatics
2006-02-22

The Blue Obelisk Movement (http://www.blueobelisk.org/) is the name used by a diverse Internet group promoting reusable chemistry via open source software development, consistent and complimentary chemoinformatics research, open data, and open standards. We outline recent examples of cooperation in the Blue Obelisk group: a shared dictionary of algorithms and implementations in chemoinformatics algorithms drawing from our various software projects; a shared repository of chemoinformatics data including elemental properties, atomic radii, isotopes, atom typing rules, and so forth; and Web services for the platform-independent use of chemoinformatics programs.
Zonal gene expression in murine liver: Lessons from tumors
2006-02-22

Gene expression in hepatocytes within the liver lobule is differentially regulated along the portal to central axis; however, the mechanisms governing the processes of zonation within the lobule are unknown. A model for zonal heterogeneity in normal liver is proposed, based on observations of differential expression of genes in liver tumors from mice that harbor activating mutations in either Catnb (which codes for β-catenin) or Ha-ras . According to the model, the regulatory control consists of two opposing signals, one delivered by endothelial cells of the central veins activating a β-catenin–dependent pathway (retrograde signal), the other by blood-borne molecules activating Ras-dependent downstream cascades (anterograde signal). In conclusion , gradients of opposing signaling molecules along the portocentral axis determine the pattern of enzymes and other proteins expressed in hepatocytes of the periportal and pericentral domains of the liver lobule. (Hepatology 2006;43:407–414.)
HDAC inhibitor treatment of hepatoma cells induces both TRAIL-independent apoptosis and restoration of sensitivity to TRAIL
2006-02-22

Hepatocellular carcinoma (HCC) displays a striking resistance to chemotherapeutic drugs or innovative tumor cell apoptosis–inducing agents such as tumor necrosis factor–related apoptosis-inducing ligand (TRAIL). Recently, we found 2 histone deacetylase inhibitors (HDAC-I), valproic acid and ITF2357, exhibiting inherent therapeutic activity against HCC. In TRAIL-sensitive cancer cells, the mechanism of HDAC-I–induced cell death has been identified to be TRAIL-dependent by inducing apoptosis in an autocrine fashion. In contrast, in HCC-derived cells, a prototype of TRAIL-resistant tumor cells, we found a HDAC-I-mediated apoptosis that works independently of TRAIL and upregulation of death receptors or their cognate ligands. Interestingly, TRAIL resistance could be overcome by a combinatorial application of HDAC-I and TRAIL, increasing the fraction of apoptotic cells two- to threefold compared with HDAC-I treatment alone, whereas any premature HDAC-I withdrawal rapidly restored TRAIL resistance. Furthermore, a tumor cell–specific downregulation of the FLICE inhibitory protein (FLIP) was observed, constituting a new mechanism of TRAIL sensitivity restoration by HDAC-I. In contrast, FLIP levels in primary human hepatocytes (PHH) from different donors were upregulated by HDAC-I. Importantly, combination HDAC-I/TRAIL treatment did not induce any cytotoxicity in nonmalignant PHH. In conclusion , HDAC-I compounds, exhibiting a favorable in vivo profile and inherent activity against HCC cells, are able to selectively overcome the resistance of HCC cells toward TRAIL. Specific upregulation of intracellular FLIP protein levels in nonmalignant hepatocytes could enhance the therapeutic window for clinical applications of TRAIL, opening up a highly specific new treatment option for advanced HCC. (Hepatology 2006;43:425–434.)
Visual Navigation in Adolescents with Early Periventricular Lesions: Knowing Where, but Not Getting There
2006-02-22

Visual navigation in familiar and unfamiliar surroundings is an essential ingredient of adaptive daily life behavior. Recent brain imaging work helps to recognize that establishing connectivity between brain regions is of importance for successful navigation. Here, we ask whether the ability to navigate is impaired in adolescents who were born premature and suffer congenital bilateral periventricular brain damage that might affect the pathways interconnecting subcortical structures with cortex. Performance on a set of visual labyrinth tasks was significantly worse in patients with periventricular leukomalacia (PVL) as compared with premature-born controls without lesions and term-born adolescents. The ability for visual navigation inversely relates to the severity of motor disability, leg-dominated bilateral spastic cerebral palsy. This agrees with the view that navigation ability substantially improves with practice and might be compromised in individuals with restrictions in active spatial exploration. Visual navigation is negatively linked to the volumetric extent of lesions over the right parietal and frontal periventricular regions. Whereas impairments of visual processing of point-light biological motion are associated in patients with PVL with bilateral parietal periventricular lesions, navigation ability is specifically linked to the frontal lesions in the right hemisphere. We suggest that more anterior periventricular lesions impair the interrelations between the right hippocampus and cortical areas leading to disintegration of neural networks engaged in visual navigation. For the first time, we show that the severity of right frontal periventricular damage and leg-dominated motor disorders can serve as independent predictors of the visual navigation disability.
Heterologous expression of a plant uracil transporter in yeast: Improvement of plasma membrane targeting in mutants of the Rsp5p ubiquitin protein ligase
2006-02-22

Abstract Plasma membrane proteins involved in transport processes play a crucial role in cell physiology. On account of these properties, these molecules are ideal targets for development of new therapeutic and agronomic agents. However, these proteins are of low abundance, which limits their study. Although yeast seems ideal for expressing heterologous transporters, plasma membrane proteins are often retained in intracellular compartments. We tried to find yeast mutants potentially able to improve functional expression of a whole set of heterologous transporters. We focused on Arabidopsis thaliana ureide transporter 1 (AtUPS1), previously cloned by functional complementation in yeast. Tagged versions of AtUPS1 remain mostly trapped in the endoplasmic reticulum and were able to reach slowly the plasma membrane. In contrast, untagged AtUPS1 is rapidly delivered to plasma membrane, where it remains in stable form. Tagged and untagged versions of AtUPS1 were expressed in cells deficient in the ubiquitin ligase Rsp5p, involved in various stages of the intracellular trafficking of membrane‐bound proteins. rsp5 mutants displayed improved steady state amounts of untagged and tagged versions of AtUPS1. rsp5 cells are thus powerful tools to solve the many problems inherent to heterologous expression of membrane proteins in yeast, including ER retention.
Molecular phylogeny and taxonomic revision of the sportive lemurs (Lepilemur, Primates)
2006-02-23

Abstract Background The number of species within the Malagasy genus Lepilemur and their phylogenetic relationships is disputed and controversial. In order to establish their evolutionary relationships, a comparative cytogenetic and molecular study was performed. We sequenced the complete mitochondrial cytochrome b gene (1140 bp) from 68 individuals representing all eight sportive lemur species and most major populations, and compared the results with those obtained from cytogenetic studies derived from 99 specimens. Results Interspecific genetic variation, diagnostic characters and significantly supported phylogenetic relationships were obtained from the mitochondrial sequence data and are in agreement with cytogenetic information. The results confirm the distinctiveness of Lepilemur ankaranensis , L. dorsalis , L. edwardsi , L. leucopus , L. microdon , L. mustelinus , L. ruficaudatus and L. septentrionalis on species level. Additionally, within L. ruficaudatus large genetic differences were observed among different geographic populations. L. dorsalis from Sahamalaza Peninsula and from the Ambanja/Nosy Be region are paraphyletic, with the latter forming a sister group to L. ankaranensis . Conclusion Our results support the classification of the eight major sportive lemur taxa as independent species. Moreover, our data indicate further cryptic speciation events within L. ruficaudatus and L. dorsalis . Based on molecular data we propose to recognize the sportive lemur populations from north of the Tsiribihina River, south of the Betsiboka River, and from the Sahamalaza Peninsula, as distinct species.
First detection of a VHE gamma-ray spectral maximum from a cosmic source: HESS discovery of the Vela X nebula
2006-02-24

The Vela supernova remnant (SNR) is a complex region containing a number of sources of non-thermal radiation. The inner section of this SNR, within 2 degrees of the pulsar PSR B0833-45 , has been observed by the HESS -ray atmospheric Cherenkov detector in 2004 and 2005. A strong signal is seen from an extended region to the south of the pulsar, within an integration region of radius around the position ( , J2000.0). The excess coincides with a region of hard X-ray emission seen by the ROSAT and ASCA satellites. The observed energy spectrum of the source between 550 GeV and 65 TeV is well fit by a power law function with photon index and an exponential cutoff at an energy of TeV. The integral flux above 1 TeV is . This result is the first clear measurement of a peak in the spectral energy distribution from a VHE -ray source, likely related to inverse Compton emission. A fit of an Inverse Compton model to the HESS spectral energy distribution gives a total energy in non-thermal electrons of ~ erg between 5 TeV and 100 TeV, assuming a distance of 290 parsec to the pulsar. The best fit electron power law index is 2.0, with a spectral break at 67 TeV.
Mayday-a microarray data analysis workbench
2006-02-24

Abstract Mayday is a workbench for visualization, analysis and storage of microarray data. It features a graphical user interface and supports the development and integration of existing and new analysis methods. Besides the infrastructural core functionality, Mayday offers a variety of plug-ins, such as various interactive viewers, a connection to the R statistical environment, a connection to SQL-based databases and different data mining methods, including WEKA-library based methods for classification and various clustering methods. In addition, so-called meta information objects are provided for annotation of the microarray data allowing integration of data from different sources, which is a feature that, for instance, is employed in the enhanced heatmap visualization. Contact: nieselt@informatik.uni-tuebingen.de Supplementary information: The software and more detailed information including screenshots and a user guide as well as test data can be found on the Mayday home page . The core is published under the GPL (GNU Public License) and the associated plug-ins under the LGPL (Lesser GNU Public License).
Importance and intensity of competition along a fertility gradient and across species
2006-02-24

Abstract Questions: 1. Can the importance and the intensity of competition vary independently along a nutrient gradient? 2. Are these variations species dependent? Location: Sub‐alpine pastures of the northern French Alps. Methods: Competition intensity measures how much competition decreases the performances of an organism. Competition importance measures how much competition contributes to affect performance, among other processes (such as environmental stress or disturbance). Competition intensity and importance were measured on three co‐occurring species: Festuca rubra , a perennial grass, and two forbs of contrasting basal area, Chaerophyllum hirsutum and Alchemilla xantho‐chlora. A neighbour removal experiment was performed on Festuca rubra in three sub‐alpine grassland communities differing in fertility and on Chaerophyllum hirsutum and Alchemilla xanthochlora in the two more fertile of these communities. The importance of competition was quantified using an index proposed by Brooker et al. (2005). Results: Competition intensity and importance showed different patterns of variation along the fertility gradient for Festuca rubra : competition importance decreased with decreasing fertility whereas competition intensity did not change. The largest forb was the least affected by competition. Our results suggest that the importance of competition for all three species depended on their individual tolerance to low nutrient availability. Conclusions: 1. The distinction between the importance and the intensity of competition is helpful to explain conflicting results obtained on the variations of competition indices along productivity gradients. 2. The choice of a phytometer can affect the conclusions drawn from empirical studies.
The neutron electric dipole form factor in the perturbative chiral quark model
2006-02-24

We calculate the electric dipole form factor of the neutron in a perturbative chiral quark model, parameterizing CP-violation of generic origin by means of effective electric dipole moments of the constituent quarks and their CP-violating couplings to the chiral fields. We discuss the relation of these effective parameters to more fundamental ones such as the intrinsic electric and chromoelectric dipole moments of quarks and the Weinberg parameter. From the existing experimental upper limits on the neutron EDM we derive constraints on these CP-violating parameters.
Age and immunity
2006-02-24

Longitudinal studies are defining progressive alterations to the immune system associated with increased mortality in the very elderly. Many of these changes are exacerbated by or even caused by chronic T cell stimulation by persistent antigen, particularly from Cytomegalovirus. The composition of T cell subsets, their functional integrity and representation in the repertoire are all markedly influenced by age and by CMV. How these findings relate to epidemiological, functional, genetic, genomic and proteomic studies of human T cell immunosenescence was the subject of intense debate at an international conference held just before Christmas 2005 in the Black Forest.
SDSS J212531.92–010745.9 – the first definite PG 1159 close binary system
2006-02-24

Aims. The archival spectrum of SDSS J212531.92−010745.9 shows not only the typical signature of a PG1159 star, but also indicates the&#13;\\npresence of a companion. Our aim was the proof of the binary nature of this object and the determination of its orbital period.&#13;\\nMethods. We performed time-series photometry of SDSS J212531.92−010745.9. We observed the object during 10 nights, spread over&#13;\\none month, with the Tübingen 80 cm and the Göttingen 50 cm telescopes. We fitted the observed light curve with a sine and simulated&#13;\\nthe light curve of this system with the nightfall program. Furthermore, we compared the spectrum of SDSS J212531.92−010745.9 with&#13;\\nNLTE models, the results of which also constrain the light curve solution.&#13;\\nResults. An orbital period of 6.95616(33) h with an amplitude of 0.354(3) mag is derived from our observations. A pulsation period could&#13;\\nnot be detected. For the PG1159 star we found, as preliminary results from comparison with our NLTE models, Teff ∼ 90 000 K, log g ∼ 7.60,&#13;\\nand the abundance ratio C/He ∼ 0.05 by number fraction. For the companion we obtained with a mean radius of 0.4 ± 0.1 R , amass of 0.4 ±&#13;\\n0.1 M , and a temperature of 8200 K on the irradiated side, good agreement between the observed light curve and the nightfall simulation,&#13;\\nbut we do not regard those values as final.
SDSS J212531.92–010745.9 – the first definite PG 1159 close binary system
2006-02-24

\\n Aims.The archival spectrum of SDSS J212531.92-010745.9 shows not\\n only the typical signature of a PG 1159 star, but also indicates the\\n presence of a companion. Our aim was the proof of the binary nature of\\n this object and the determination of its orbital period.Methods.We performed time-series photometry of SDSS J212531.92-010745.9. We\\n observed the object during 10 nights, spread over one month, with the \\n Tübingen 80 cm and the Göttingen 50 cm telescopes. We fitted the\\n observed light curve with a sine and simulated the light curve of this\\n system with the <monospace>nightfall</monospace> program. Furthermore, we compared the\\n spectrum of SDSS J212531.92-010745.9 with NLTE models, the results of which \\n also constrain the light curve solution. Results.An orbital period of 6.95616(33) h with an amplitude of 0.354(3) mag is derived from our observations. A pulsation period could not be detected. For the\\n PG 1159 star we found, as preliminary results from comparison with our NLTE models, Teff ~ 90 000 K, ~ 7.60, and the abundance ratio\\n C/He ~ 0.05 by number fraction. For the companion we obtained with a mean radius of\\n 0.4 ± , a mass of 0.4 ± , and a temperature of 8200 K on the irradiated side, good agreement between\\n the observed light curve and the <monospace>nightfall</monospace> simulation, but we\\n do not regard those values as final. \\n
Hepatic lipid accumulation in healthy subjects: A comparative study using spectral fat‐selective MRI and volume‐localized 1H‐MR spectroscopy
2006-02-27

Abstract Fat‐selective MRI was applied to assess the amount and spatial distribution of hepatic lipids (HL) in healthy subjects. The results were compared with those obtained by localized 1 H‐MR spectroscopy (MRS). Ninety subjects (23–63 years old) underwent single‐slice fat‐selective MRI with spatial‐spectral excitation and volume‐localized spectroscopy at 1.5 T. HLs were analyzed in ventral and dorsal regions of interest (ROIs) of the liver in fat‐selective images. Spectra were evaluated using the integral signal of methylene and methyl signals. The fat‐selective images showed smooth and homogeneous distribution of HL over the entire cross section of the liver. There was, however, a marked interindividual variability in the amount of HL. MRS revealed a lipid signal fraction between 0.5% and 39.3%. The fat content in the ROIs in images correlated well with the spectroscopic results (r ≥ 0.95). Both techniques provide sufficient sensitivity for a reliable and quantitative assessment of liver steatosis in subjects without liver disease. 1 H‐MRS has a higher sensitivity compared to MRI, especially for small amounts of HL, which may be of interest for metabolic interventions. Fat‐selective images provide more spatial information about fat distribution, which makes this technique suitable for clinical imaging of patients with liver disease. Magn Reson Med, 2006. © 2006 Wiley‐Liss, Inc.
Quiescent gemmules of the freshwater sponge, Spongilla lacustris (Linnaeus, 1759), contain remarkably high levels of Hsp70 stress protein and hsp70 stress gene mRNA
2006-02-27

Abstract With the onset of changing environmental conditions in autumn, the freshwater sponge Spongilla lacustris (Linnaeus, 1759 ) produces resistant stages (gemmules) which are in the state of quiescence. Gemmules stored at 8°C remained quiescent; however, germination occurred within 24 hr after the water temperature was increased to 22.5°C. Sponges hatched through the micropyle and subsequently built new spicules and a new canal system. The molecular and biochemical mechanisms which enable the gemmules to survive long periods of adverse conditions are not known. For the first time we focused on the role of the stress protein Hsp70 and the expression of hsp70 mRNA in S. lacustris during the development of gemmules in the state of quiescence into growing sponges. The partial sequence of hsp70 seems to be a true hsp gene since transcription could be clearly enhanced by temperature elevation. The results showed a large pool of cellular Hsp70 and hsp70 mRNA in gemmules during the state of quiescence. Within hours after a temperature trigger, the Hsp70 level decreased slowly and reached approximately the level of an adult sponge. Hsp70 presumably allows gemmules to stabilize their proteins and membranes during dormancy from autumn to spring when water temperatures change. J. Exp. Zool. 305A, 2006 . © 2006 Wiley‐Liss, Inc.
Protective Effects of Isoflurane Pretreatment in Endotoxin-induced Lung Injury
2006-02-27

Background The concept of antiinflammatory effects of volatile anesthetics is well established in vitro and in some organ systems. Their protective role in lung injury, however, remains to be elucidated. The authors hypothesized that in the lung, isoflurane pretreatment may attenuate neutrophil infiltration and reduce endotoxin-induced injury. Methods Male C57Bl/6 mice were exposed to aerosolized lipopolysaccharide. Neutrophil recruitment into the pulmonary vasculature and migration into the different lung compartments (interstitium and alveolar air space) were determined by flow cytometry. Capillary protein leakage, formation of lung edema, and concentration of the chemokines keratinocyte-derived chemokine (CXCL1) and macrophage inflammatory protein 2 (CXCL2/3) in bronchoalveolar lavage were compared in mice with or without isoflurane treatment (1.4% inspired for 30 min) at different times before and after endotoxin exposure. Results Endotoxin inhalation induced significant neutrophil migration into all lung compartments. Isoflurane pretreatment attenuated both neutrophil recruitment into lung interstitium and alveolar space when given 1 or 12 h before or 1 h after lipopolysaccharide but not at 4, 6, or 24 h before endotoxin exposure. Isoflurane pretreatment 1 or 12 h before lipopolysaccharide also reduced protein leakage and pulmonary edema. Production of CXCL1 and CXCL2/3 in the bronchoalveolar lavage was reduced when isoflurane was given 1 h but not 12 h before lipopolysaccharide, suggesting different mechanisms for early and late protection. Conclusion Isoflurane pretreatment reduces acute lung injury when given 1 or 12 h before an endotoxin challenge or within the first hour of an already established inflammation.