julilili42/papers huggingface dataset:
Properties of asymmetric nuclear matter in different approaches
2009-02-13

Properties of asymmetric nuclear matter are derived from various many-body approaches. This includes phenomenological ones like the Skyrme Hartree-Fock and relativistic mean field approaches, which are adjusted to fit properties of nuclei, as well as more microscopic attempts like the Brueckner-Hartree-Fock approximation, a self-consistent Greens function method and the so-called approach, which are based on realistic nucleon-nucleon interactions which reproduce the nucleon-nucleon phase shifts. These microscopic approaches are supplemented by a density-dependent contact interaction to achieve the empirical saturation property of symmetric nuclear matter. The predictions of all these approaches are discussed for nuclear matter at high densities in -equilibrium. Special attention is paid to behavior of the isovector component of the effective mass in neutron-rich matter.
Resolving temporal Gribov copies in Coulomb gauge Yang-Mills theory
2009-02-13

The continuum Yang-Mills functional integral within the first order formalism and in Coulomb gauge is studied. In particular, the temporal zero-modes of the Faddeev-Popov operator are explicitly accounted for. It is shown that the treatment of these zero-modes results in the constraint that the total color charge of the system vanishes at all times. Further, it is argued that the functional integral is effectively fully gauge-fixed once Gauss' law has been resolved in Coulomb gauge.
Genetic Variants of Wnt Transcription Factor TCF-4 (TCF7L2) Putative Promoter Region Are Associated with Small Intestinal Crohn's Disease
2009-02-14

Reduced expression of Paneth cell antimicrobial alpha-defensins, human defensin (HD)-5 and -6, characterizes Crohn's disease (CD) of the ileum. TCF-4 (also named TCF7L2), a Wnt signalling pathway transcription factor, orchestrates Paneth cell differentiation, directly regulates the expression of HD-5 and -6, and was previously associated with the decrease of these antimicrobial peptides in a subset of ileal CD. To investigate a potential genetic association of TCF-4 with ileal CD, we sequenced 2.1 kb of the 5' flanking region of TCF-4 in a small group of ileal CD patients and controls (n = 10 each). We identified eight single nucleotide polymorphisms (SNPs), of which three (rs3814570, rs10885394, rs10885395) were in linkage disequilibrium and found more frequently in patients; one (rs3814570) was thereby located in a predicted regulatory region. We carried out high-throughput analysis of this SNP in three cohorts of inflammatory bowel disease (IBD) patients and controls. Overall 1399 healthy individuals, 785 ulcerative colitis (UC) patients, 225 CD patients with colonic disease only and 784 CD patients with ileal involvement were used to determine frequency distributions. We found an association of rs3814570 with ileal CD but neither with colonic CD or UC, in a combined analysis (allele positivity: OR 1.27, 95% CI 1.07 to 1.52, p = 0.00737), which was the strongest in ileal CD patients with stricturing behaviour (allele frequency: OR 1.32, 95% CI 1.08 to1.62, p = 0.00686) or an additional involvement of the upper GIT (allele frequency: OR 1.38, 95% CI 1.03 to1.84, p = 0.02882). The newly identified genetic association of TCF-4 with ileal CD provides evidence that the decrease in Paneth cell alpha-defensins is a primary factor in disease pathogenesis.
Aberrant expression of the homeobox gene CDX2 in pediatric acute lymphoblastic leukemia
2009-02-14

Abstract Members of the caudal (cdx) family of homeobox proteins are essential regulators of embryonic blood development in zebrafish. Previously, we reported that the murine homologues (Cdx1, Cdx2, and Cdx4) affect formation and differentiation of embryonic stem cell (ESC)–derived hematopoietic progenitor cells. Consistent with the notion that embryonic pathways can reactivate during adult oncogenesis, recent studies suggest involvement of CDX2 in human acute myeloid leukemia (AML). Here we study CDX2 in healthy and leukemic human lymphoid cells, and show that a majority of leukemic samples display various degrees of aberrant CDX2 expression. Analysis of a cohort of 37 childhood acute lymphoblastic leukemia (ALL) patients treated in our hospital reveals that high CDX2 expression levels at diagnosis correlate with persistence of minimal residual disease (MRD) during the course of treatment. Thus, CDX2 expression levels may serve as a marker for adverse prognosis in pediatric ALL.
Modular Synthesis of a New Type of Chiral Bis(carbene) Ligand from L‐Valinol and Iridium(I) and Rhodium(I) Complexes Thereof
2009-02-17

Abstract New, chiral bis(imidazol‐2‐ylidene) ligands, and their rhodium(I) and iridium(I) complexes, have been prepared by a simple six‐step synthesis starting from commercially available enantiomerically pure L ‐valinol. The stepwise introduction of the imidazoles makes it possible to create chiral bis(NHC) complexes with different substituents at the terminal nitrogen atoms. Formation of Ir I and Rh I complexes by a one‐pot transmetallation reaction gives the endo and exo stereoisomers in different ratios, depending on the metal and the reaction conditions. Diastereomerically pure material was obtained by crystallisation.(© Wiley‐VCH Verlag GmbH &amp; Co. KGaA, 69451 Weinheim, Germany, 2009)
Tuning the Fluorescence Emission Spectra of a Single Molecule with a Variable Optical Subwavelength Metal Microcavity
2009-02-18

We present experimental and theoretical results on changing the fluorescence emission spectrum of a single molecule by embedding it within a tunable planar microcavity with subwavelength spacing. The cavity length is changed with nanometer precision by using a piezoelectric actuator. By varying its length, the local mode structure of the electromagnetic field is changed together with the radiative coupling of the emitting molecule to the field. Because mode structure and coupling are both frequency dependent, this leads to a renormalization of the emission spectrum of the molecule. We develop a theoretical model for these spectral changes and find excellent agreement between theoretical prediction and experimental results.
Functional Characterization of the σ B -Dependent yabJ - spoVG Operon in Staphylococcus aureus : Role in Methicillin and Glycopeptide Resistance
2009-02-18

ABSTRACT The alternative sigma factor σ B of Staphylococcus aureus controls the expression of multiple genes, including virulence determinants and global regulators; promotes capsule production; and increases the resistance levels of methicillin-resistant S. aureus (MRSA) and glycopeptide-intermediate-resistant S. aureus (GISA) strains. We show here that deletion of the σ B -controlled yabJ-spoVG operon, which codes for potential downstream regulators of σ B , abolished capsule synthesis and reduced resistance in MRSA and GISA to the same extent that σ B inactivation did. Introduction of the yabJ-spoVG operon in trans restored the original phenotype. By genetic manipulations, we show that SpoVG but not YabJ is required for complementation. We therefore postulate that SpoVG is the major factor of the yabJ-spoVG operon required in S. aureus for capsule formation and antibiotic resistance.
The Akt inhibitor triciribine sensitizes prostate carcinoma cells to TRAIL‐induced apoptosis
2009-02-18

Abstract Aberrant PI3K/Akt signaling has been implicated in many human cancers, including prostate carcinomas. Currently different therapeutic strategies target the inhibition of this survival pathway. The nucleoside analog triciribine (TCN), which was initially described as a DNA synthesis inhibitor, has recently been shown to function as an inhibitor of Akt. Here, we demonstrate that TCN inhibits Akt phosphorylation at Thr308 and Ser473 and Akt activity in the human prostate cancer cell line PC‐3. In addition, TCN sensitized PC‐3 cells to TRAIL‐ and anti‐CD95‐induced apoptosis, whereas the cells remained resistant to DNA damaging chemotherapeutics. The observed sensitization essentially depended on the phosphorylation status of Akt. Thus, prostate cancer cell lines displaying constitutively active Akt, e.g. PC‐3 or LNCaP, were sensitized to death receptor‐induced apoptosis. Most importantly with respect to therapeutic application, derivatives of both TCN and TRAIL are already tested in current clinical trials. Therefore, this combinatorial treatment might open a promising therapeutic approach for the elimination of hormone‐refractory prostate cancers, which are largely resistant to conventional DNA damaging anticancer drugs or irradiation. © 2009 UICC
Reduced Efficacy of Intermittent Preventive Treatment of Malaria in Malnourished Children
2009-02-18

ABSTRACT Intermittent preventive treatment in infants with sulfadoxine-pyrimethamine (IPTi-SP) reduces malaria episodes by 20 to 59% across Africa. This protective efficacy, however, may be affected by the high frequency of malnutrition in African infants. We analyzed the impact of malnutrition as defined by anthropometry on the incidence of malaria and on the protective efficacy of IPTi in a cohort of 1,200 children in northern Ghana, where malaria is hyperendemic. These children received IPTi-SP or placebo at 3, 9, and 15 months of age and were monitored until 24 months of age. Malnutrition was present in 32, 40, and 50% of children at ages 3, 9, and 15 months, respectively. It was associated with increased risks of severe anemia and death but not an increased risk of malaria. Although malaria slightly contributed to chronic malnutrition, IPTi did not substantially improve child growth. Importantly, the protective efficacies of IPTi in malnourished children were roughly half or even less of those observed in nonmalnourished children. In the first year of life, IPTi reduced the incidence of malaria to a significantly lesser extent in infants who received both doses in a malnourished condition (25%; 95% confidence interval [CI], −7 to 48%) compared to that of nonmalnourished children (46%; 95% CI, 30 to 58%; P = 0.049). Moreover, in contrast to nutritionally advantaged children, the rate of severe malaria appeared to be increased in malnourished children who took IPTi. IPTi might exhibit reduced efficacy in regions of abundant malnutrition. Concomitant nutrition programs may be needed in these places to achieve the desired impact.
Atomic Local Neighborhood Flexibility Incorporation into a Structured Similarity Measure for QSAR
2009-02-18

In this work, we introduce a new method to regard the geometry in a structural similarity measure by approximating the conformational space of a molecule. Our idea is to break down the molecular conformation into the local conformations of neighbor atoms with respect to core atoms. This local geometry can be implicitly accessed by the trajectories of the neighboring atoms, which are emerge by rotatable bonds. In our approach, the physicochemical atomic similarity, which can be used in structured similarity measures, is augmented by a local flexibility similarity, which gives a rough estimate of the similarity of the local conformational space. We incorporated this new type of encoding the flexibility into the optimal assignment molecular similarity approach, which can be used as a pseudokernel in support vector machines. The impact of the local flexibility was evaluated on several published QSAR data sets. This lead to an improvement of the model quality on 9 out of 10 data sets compared to the unmodified optimal assignment kernel.
Pathogen-Associated Molecular Patterns (PAMP) and PAMP-Triggered Immunity
2009-02-19

This chapter contains sections titled: The concept of plant immunity Pathogen-associated molecular patterns Damage-associated molecular patterns Pathogen-derived toxins PRRs in plant immunity Intracellular signal transduction in PTI Suppression of PTI by bacterial effectors Concluding remarks Acknowledgements References
Prion mutation D178N with highly variable disease onset and phenotype
2009-02-19

Hereditary prion disease is a fatal genetic disorder of autosomal dominant inheritance. Recent phenotype-genotype correlation studies revealed a considerable clinical and pathological overlap for patients with the D178N mutation, suggesting a continuous spectrum between fatal familial insomnia and Creutzfeldt-Jakob Disease phenotype. This report adds further evidence to this thesis from a large German prion pedigree with D178N mutation in the PRNP-gene. This pedigree shows an extensive variability in (1) age of disease onset, ranging from 19 to 72 years and including an asymptomatic 73-year-old gene carrier and (2) disease phenotype, including a Gerstmann-Straussler-Scheinker phenotype. These findings have substantial importance for genetic counselling of persons at risk.
ChemInform Abstract: Unsymmetrical Biaryls by Palladium‐Catalyzed Coupling of Aryl Halides with Internal Reduction.
2009-02-19

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.
DISCOVERY OF GAMMA-RAY EMISSION FROM THE SHELL-TYPE SUPERNOVA REMNANT RCW 86 WITH HESS
2009-02-20

The shell-type supernova remnant (SNR) RCW 86, possibly associated with the historical supernova SN 185, with its relatively large size (about 40' in diameter) and the presence of nonthermal X-rays is a promising target for γ-ray observations. The high sensitivity, good angular resolution of a few arcminutes and the large field of view of the High Energy Stereoscopic System (HESS) make it ideally suited for the study of γ-ray morphology of such extended sources. HESS observations have indeed led to the discovery of the SNR RCW 86 in very high energy (VHE; E &amp;gt; 100 GeV) γ-rays. With 31 hr of observation time, the source is detected with a statistical significance of 8.5σ and is significantly more extended than the HESS point-spread function. Morphological studies have been performed and show that the γ-ray flux does not correlate perfectly with the X-ray emission. The flux from the remnant is ~10% of the flux from the Crab nebula, with a similar photon index of about 2.5. Possible origins of the VHE γ-ray emission, via either Inverse Compton scattering by electrons or the decay of neutral pions produced by proton interactions, are discussed on the basis of spectral features obtained both in the X-ray and γ-ray regimes.
4-[5-(4-Fluorophenyl)-1H-imidazol-4-yl]pyridine
2009-02-20

In the title compound, C(14)H(10)FN(3), the imidazole ring makes dihedral angles of 28.2 (1) and 36.60 (9)° with the pyridine ring and the 4-fluoro-phenyl ring, respectively. The pyridine ring forms a dihedral angle of 44.68 (9)° with the 4-fluoro-phenyl ring. Inter-molecular N-H⋯N hydrogen bonds are observed in the crystal structure.
Statin use and its association with musculoskeletal symptoms--a cross-sectional study in primary care settings
2009-02-22

Having a statin prescription appears to be an independent factor associated with musculoskeletal symptoms in primary care settings. Statin use may be more often associated with musculoskeletal complaints than previously assumed.
Split-liver transplantation in the high-MELD adult patient: are we being too cautious?
2009-02-23

The fear that patients with high-mathematical model for end stage liver disease (MELD) score may not be suitable candidates for segmental grafts because of their need for greater liver mass has continued to push the transplant community toward the use of whole LT (WLT) in preference to split LT (SLT). In order to define the outcome of segmental liver transplantation in a better manner in high-MELD patients (score > or =26), we queried the UNOS registry for graft and patient survival results according to MELD score in adult patients receiving WLT and SLT in the United States from the inception of MELD allocation (February 27, 2002) through March 9, 2007. A total of 316 adult patients received a SLT as compared with 20 778 WLTs. Patient and graft survival rates at 6 and 12 months were comparable for all MELD ranges, including the 'high-MELD' recipients (e.g. at MELD score 31-35, patients' and grafts' survival rates at 12 months was 87.5% in SLT group vs. 84.4% and 76.7% in WLT group respectively). The results even at higher MELD scores (i.e. >35) were more than acceptable. In conclusion, patient and graft survival rates for SLT in high-MELD adult patients are comparable to the same for WLT.
Longitudinal localization of a fluorescent bead in a tunable microcavity with an accuracy of λ/60
2009-02-23

The exact localization of a quantum emitter in a transparent dielectric medium is an important task in applications of precision confocal microscopy. Therefore we use a planar metallic subwavelength microcavity that can be reversibly tuned across the entire visible range, with the transparent medium between the cavity mirrors. By analyzing the excitation patterns resulting from the illumination of a single fluorescent bead with a radially polarized doughnut mode laser beam we can determine the longitudinal position of this bead in the microcavity with an accuracy of a few nanometers.
Comparison of clinical and pedobarographic measures in clubfeet treated with posteromedial soft-tissue release
2009-02-23

Background Many studies have evaluated the results of different therapy regimes for congenital clubfeet. Most analyzed clinical, radiographic or pedobarographic measurements alone. Few studies analyzed the correlation between foot pressure distribution and clinical outcome. Methods We evaluated the foot pressure measurements of 33 clubfeet treated with posteromedial soft-tissue release. The average age at examination was 64 months. Correlations between pedobarographic and clinical results were assessed and the McKay score was calculated. Results Significant pedobarographic differences between clubfeet and healthy feet were observed in several regions of the foot, but a correlation between pedobarographic results and clinical outcome was observed in only two regions. Longer contact time of the midfoot was observed in clubfeet, with a negative correlation of 0.53 to clinical outcome. Lower peak pressure was observed at the area under the first metatarsal bone in clubfeet, with a positive correlation of 0.33. Conclusion Foot pressure measurement is a useful tool to analyze outcomes after clubfoot treatment, but not all measured results are of clinical importance. Our study showed that especially overcorrection of cavus and recurrent supinatus are limiting factors for a good clinical outcome.
Abciximab combined with half-dose reteplase has beneficial effects on inflammatory myocardial response in patients with myocardial infarction
2009-02-23

In patients with ST-segment elevation myocardial infarction (STEMI), myocardial reperfusion is associated with an inflammatory response leading to adverse effects on further myocardial damage. Therefore, we investigated the effects of the thrombolytic regimen with half-dose reteplase (r-PA) combined with abciximab on different cytokines involved in the local and systemic inflammatory scenario in STEMI patients. Thirty-eight STEMI patients were enrolled in this study. We investigated the effects of the regimen with half-dose r-PA plus abciximab versus full-dose r-PA on interleukin-6 (IL-6), interleukin-8 (IL-8), interleukin-10 (IL-10), MCP-1 and tumor necrosis factor-alpha (TNF-alpha) up to 48 h after the start of therapy. The full-dose r-PA group had a significant IL-6 increase after 48 h compared with the combination group. Furthermore, the full-dose r-PA group showed a marked increase of IL-10 (up to 3 h after) compared with a 41% IL-10 decrease in the combination group. MCP-1 decreased significantly after 3 h in the combination group compared with patients on r-PA therapy only. The combination group showed a nonsignificant increase in IL-8 within the first 6 h. There were no differences in TNF-alpha levels between the two infarct groups. In vivo, the investigated combined thrombolytic regimen consisting of half-dose r-PA plus abciximab causes less of an IL-6 increase and marked decreases in IL-10 and MCP-1 in STEMI patients compared with the pure r-PA thrombolytic regimen. This observation suggests that besides the known beneficial effects on systemic coagulation and leukocyte-platelet aggregates, this regimen may exert a favorable influence on myocardial tissue damage and thus on cardiac repair following myocardial infarction.
Establishing wild-type levels of catalytic activity on natural and artificial (βα) 8 -barrel protein scaffolds
2009-02-24

The generation of high levels of new catalytic activities on natural and artificial protein scaffolds is a major goal of enzyme engineering. Here, we used random mutagenesis and selection in vivo to establish a sugar isomerisation reaction on both a natural (βα) 8 -barrel enzyme and a catalytically inert chimeric (βα) 8 -barrel scaffold, which was generated by the recombination of 2 (βα) 4 -half barrels. The best evolved variants show turnover numbers and substrate affinities that are similar to those of wild-type enzymes catalyzing the same reaction. The determination of the crystal structure of the most proficient variant allowed us to model the substrate sugar in the novel active site and to elucidate the mechanistic basis of the newly established activity. The results demonstrate that natural and inert artificial protein scaffolds can be converted into highly proficient enzymes in the laboratory, and provide insights into the mechanisms of enzyme evolution.
Functional maturation of the exocytotic machinery at gerbil hair cell ribbon synapses
2009-02-24

Auditory afferent fibre activity in mammals relies on neurotransmission at hair cell ribbon synapses. Developmental changes in the Ca 2+ sensitivity of the synaptic machinery allow inner hair cells (IHCs), the primary auditory receptors, to encode Ca 2+ action potentials (APs) during pre‐hearing stages and graded receptor potentials in adult animals. However, little is known about the time course of these changes or whether the kinetic properties of exocytosis differ as a function of IHC position along the immature cochlea. Furthermore, the role of afferent transmission in outer hair cells (OHCs) is not understood. Calcium currents and exocytosis (measured as membrane capacitance changes: Δ C m ) were measured with whole‐cell recordings from immature gerbil hair cells using near‐physiological conditions. The kinetics, vesicle pool depletion and Ca 2+ coupling of exocytosis were similar in apical and basal immature IHCs. This could indicate that possible differences in AP activity along the immature cochlea do not require synaptic specialization. Neurotransmission in IHCs became mature from postnatal day 20 (P20), although changes in its Ca 2+ dependence occurred at P9–P12 in basal and P12–P15 in apical cells. OHCs showed a smaller Δ C m than IHCs that was reflected by fewer active zones in OHCs. Otoferlin, the proposed Ca 2+ sensor in cochlear hair cells, was similarly distributed in both cell types despite the high‐order exocytotic Ca 2+ dependence in IHCs and the near‐linear relation in OHCs. The results presented here provide a comprehensive study of the function and development of hair cell ribbon synapses.