julilili42/papers huggingface dataset:
TOPPView: An Open-Source Viewer for Mass Spectrometry Data
2009-05-08

Visualization of complex mass spectrometric data sets is becoming increasingly important in proteomics and metabolomics. We present TOPPView, an integrated data visualization and analysis tool for mass spectrometric data sets. TOPPView allows the visualization and comparison of individual mass spectra, two-dimensional LC-MS data sets and their accompanying metadata. By supporting standardized XML-based data exchange formats, data import is possible from any type of mass spectrometer. The integrated analysis tools of the OpenMS Proteomics Pipeline (TOPP) allow efficient data analysis from within TOPPView through a convenient graphical user interface. TOPPView runs on all major operating systems and is available free of charge under an open-source license at http://www.openms.de.
Suppression of dissipation in Nb thin films with triangular antidot arrays by random removal of pinning sites
2009-05-08

The depinning current Ic versus applied magnetic field B close to the\\ntransition temperature Tc of Nb thin films with randomly diluted triangular\\narrays of antidots is investigated. % Our experiments confirm essential\\nfeatures in Ic(B) as predicted by Reichhardt and Olson Reichhardt [Phys.Rev. B\\n76, 094512 (2007)]. % We show that, by introducing disorder into periodic\\npinning arrays, Ic can be enhanced. % In particular, for arrays with fixed\\ndensity n_p of antidots, an increase in dilution Pd induces an increase in Ic\\nand decrease of the flux-flow voltage for B&gt;Bp=n_p Phi_0.\\n
Combined rock slope stability and shallow landslide susceptibility assessment of the Jasmund cliff area (Rügen Island, Germany)
2009-05-08

Abstract. In this contribution we evaluated both the structurally-controlled failure susceptibility of the fractured Cretaceous chalk rocks and the topographically-controlled shallow landslide susceptibility of the overlying glacial sediments for the Jasmund cliff area on Rügen Island, Germany. We employed a combined methodology involving spatially distributed kinematical rock slope failure testing with tectonic fabric data, and both physically- and inventory-based shallow landslide susceptibility analysis. The rock slope failure susceptibility model identifies areas of recent cliff collapses, confirming its value in predicting the locations of future failures. The model reveals that toppling is the most important failure type in the Cretaceous chalk rocks of the area. The shallow landslide susceptibility analysis involves a physically-based slope stability evaluation which utilizes material strength and hydraulic conductivity data, and a bivariate landslide susceptibility analysis exploiting landslide inventory data and thematic information on ground conditioning factors. Both models show reasonable success rates when evaluated with the available inventory data, and an attempt was made to combine the individual models to prepare a map displaying both terrain instability and landslide susceptibility. This combination highlights unstable cliff portions lacking discrete landslide areas as well as cliff sections highly affected by past landslide events. Through a spatial integration of the rock slope failure susceptibility model with the combined shallow landslide assessment we produced a comprehensive landslide susceptibility map for the Jasmund cliff area.
Wall Teichoic Acid Protects Staphylococcus aureus against Antimicrobial Fatty Acids from Human Skin
2009-05-09

ABSTRACT Skin-colonizing gram-positive bacteria produce wall teichoic acids (WTAs) or related glycopolymers for unclear reasons. Using a WTA-deficient Staphylococcus aureus mutant, we demonstrated that WTA confers resistance to antimicrobial fatty acids from human sebaceous glands by preventing fatty acid binding. Thus, WTA is probably important for bacterial skin colonization.
Angiogenesis drives psoriasis pathogenesis
2009-05-11

Summary Psoriasis pathogenesis is closely associated with disease‐inducing Th1 and Th17 cells. Yet, several studies suggest that aberrant keratinocyte or endothelial cell signalling significantly contributes to disease manifestation. Histological hallmarks of psoriatic skin include the infiltration of multiple immune cells, keratinocyte proliferation and increased dermal vascularity. Formation of new blood vessels starts with early psoriatic changes and disappears with disease clearance. Several angiogenic mediators like vascular endothelial growth factor, hypoxia‐inducible factors, angiopoietins and pro‐angiogenic cytokines, such as tumour necrosis factor (TNF), interleukin (IL)‐8 and IL‐17, are up‐regulated in psoriasis development. Contact‐ and mediator‐dependent factors derived from keratinocytes, mast cells and immune cells may contribute to the strong blood vessel formation of psoriasis. New technologies and experimental models provide new insights into the role of angiogenesis in psoriasis pathogenesis. Interestingly, many therapies target not only immune cells, but also protein structures of endothelial cells. Here we summarize the role of pro‐angiogenic factors in psoriasis development and discuss angiogenesis as a potential target of novel therapies.
Clock Test Deficits Are Associated With Semantic Memory Impairment in Alzheimer Disease
2009-05-11

Based on previous findings, we hypothesized that Clock Test deficits in patients with Alzheimer disease (AD) are associated primarily with the impairment of semantic memory regarding the appearance and functionality of a clock. To scrutinize this hypothesis, we developed a Clock Questionnaire that examined the semantic knowledge of the concept of a ‘‘Clock’’ and correlated scores from the questionnaire with performance in Clock Drawing, Clock Setting, and Clock Reading by healthy control participants and patients with mild cognitive impairment, early AD, and progressed AD. The Rey-Osterrieth-Complex-Figure is known to measure both visuospatial abilities and executive functions, and was chosen as a control variable. We found that deteriorated semantic memory best predicted Clock Test performance. In progressed AD, degraded knowledge regarding the appearance of a clock can explain the reduced ability to draw a clock face, while in early AD, impaired access to semantic knowledge about the minute hand might explain observed difficulties in drawing, setting, and reading the minute hand.
Akt2 and SGK3 are both determinants of postnatal hair follicle development
2009-05-11

ABSTRACT SGK3, which previously has been shown to play a key role in hair follicle development in mice, is a member of the AGC family of serine‐threonine kinases. Mice lacking SGK3 have abnormal follicle cycling, which begins shortly after birth and ameliorates substantially with age. However, this developmental abnormality is not recapitulated in mice lacking closely related kinases Aktl, Akt2, or Akt3. To examine whether Akt2 interacts with SGK3 in postnatal hair development, we have generated and characterized Akt2/SGK3 double knockouts (DKOs). We find that the DKO mice have a defect in hair growth that is markedly worse than that of SGK3 −/− mice and does not ameliorate with age. Morphologically, this defect is characterized by accelerated entry into catagen and through anagen, irregular hair follicle orientation, and increased expression of sebaceous glands. The defect is preceded by a profound failure to increase follicle matrix cell nuclear β‐catenin accumulation and proliferation at the onset of morphogenesis. Furthermore, in cultured keratinocytes, transfected Akt2 and SGK3 both stimulate transcription of a β‐catenin‐LEF1‐depen‐dent reporter gene. Thus, SGK3 and Akt2 both appear to play important roles in postnatal hair follicle morphogenesis, likely because of their redundant regulation of β‐catenin‐dependent transcriptional processes, which control hair follicle cell proliferation.—Mauro, T. M., McCormick, J. A., Wang, J., Boini, K. M., Ray, L., Monks, B., Birnbaum, M. J., Lang, F., and Pearce, D. Akt2 and SGK3 are both determinants of postnatal hair follicle development. FASEB J. 23, 3193–3202 (2009). www.fasebj.org
Haplotype specific-sequencing reveals MBL2 association with asymptomatic Plasmodium falciparum infection
2009-05-11

Abstract Background Mannose binding lectin (MBL) has an important role in the activation of the complement system and opsonization of pathogenic microorganisms. Frequent polymorphisms found in the MBL2 gene affect the concentration and functionality of the protein and are associated with enhanced susceptibility to severe malaria in African children. Most MBL2 typing strategies were designed to the analysis of selected variants, the significance of whole haplotypes is poorly known. In this work, a new typing strategy was developed and validated in an association analysis of MBL2 with adult asymptomatic infection. Methods MBL2 allele-specific fragments of 144 healthy Gabonese adults were amplified by using haplotype-specific sequencing (HSS), a new strategy that combines sequence-specific PCR and sequence-based typing. The Gabonese were investigated for the presence of Plasmodium falciparum parasitaemia by the amplification of parasite genes, immunochromatographic antigen detection and microscopic analysis. HSS results were also compared with a previously used real-time PCR (RT-PCR) method in 72 Euro-Brazilians. Results Fourteen polymorphisms were identified beside the commonly investigated promoter ( H, L ; X, Y ; P, Q ) and exon 1 ( A, O ; O = B , C or D ) variants. The MBL2*LYPA/LYPA genotype was associated with the absence of asymptomatic infection (P = 0.017), whereas the MBL2*LYQC haplotype and YA/YO + YO/YO genotypes were associated with positive parasite counts in asymptomatic adults (P = 0.033 and 0.018, respectively). The associations were specific to LYPA (identical to the reference sequence Y16577) and LYQC (Y16578) and would not have been revealed by standard genotyping, as there was no association with LYPA and LYQC haplotypes carrying new polymorphisms defined by sequence-based typing. In contrast, HSS and RT-PCR produced very similar results in the less diverse European-derived population. Conclusion In this work, a new typing strategy for a highly polymorphic gene was developed and validated focusing on the asymptomatic status of P. falciparum- infected adults. In populations with high nucleotide diversity, it allowed for the identification of associations with fine-scaled haplotypes that would not have been found using common typing techniques. In this preliminary study, MBL2 haplotypes or SNPs linked to them were found associated with susceptibility to infection and parasitaemia control of asymptomatic adults.
Bedding, hearths, and site maintenance in the Middle Stone Age of Sibudu Cave, KwaZulu-Natal, South Africa
2009-05-12

Micromorphological analysis of sediments from the Middle Stone Age site of Sibudu Cave, KwaZulu-Natal, South Africa, provides a high-resolution sequence and evidence of site formation processes of predominantly anthropogenic deposits. This methodology allows for a detailed interpretation of individual anthropogenic activities, including the construction of hearths and bedding and the maintenance of occupational surfaces through the sweep out of hearths and the repeated burning of bedding. This analysis also provides a context for evaluating other studies at the site relating to magnetic susceptibility, paleobotany, paleozoology, anthracology, and studies of ochre.
EPISODIC RANDOM ACCRETION AND THE COSMOLOGICAL EVOLUTION OF SUPERMASSIVE BLACK HOLE SPINS
2009-05-12

The growth of supermassive black holes (BHs) located at the centers of their\\nhost galaxies comes mainly from accretion of gas, but how to fuel them remains\\nan outstanding unsolved problem in quasar evolution. This issue can be\\nelucidated by quantifying the radiative efficiency parameter ( ) as a\\nfunction of redshift, which also provides constraints on the average spin of\\nthe BHs and its possible evolution with time. We derive a formalism to link\\n with the luminosity density, BH mass density, and duty cycle of quasars,\\nquantities we can estimate from existing quasar and galaxy survey data. We find\\nthat has a strong cosmological evolution: at z~2, ,\\nand by it has decreased by an order of magnitude, to . We interpret this trend as evolution in BH spin, and we appeal to\\nepisodic, random accretion as the mechanism for reducing the spin. The\\nobservation that the fraction of radio-loud quasars decreases with increasing\\nredshift is inconsistent with the popular notion that BH spin is a critical\\nfactor for generating strong radio jets. In agreement with previous studies, we\\nshow that the derived history of BH accretion closely follows the cosmic\\nhistory of star formation, consistent with other evidence that BHs and their\\nhost galaxies coevolve.\\n
EFNS guidelines on the molecular diagnosis of neurogenetic disorders: general issues, Huntington’s disease, Parkinson’s disease and dystonias
2009-05-12

This paper provides updated guidelines for molecular diagnosis of Huntington's disease, Parkinson's disease and dystonias as well as a general introduction to the topic. Possibilities and limitations of molecular genetic diagnosis of these disorders are evaluated and recommendations are provided.
Computer modeling of the optical properties and heating of spherical gold and silica-gold nanoparticles for laser combined imaging and photothermal treatment
2009-05-12

Recently, several groups of investigators (Anderson, Halas, Zharov, El-Sayed and their co-workers (Pitsillides et al 2003 Biophys. J. 84 4023-31, Zharov et al 2003 Appl. Phys. Lett. 83 4897-9, Zharov et al 2004 Proc. SPIE 5319 291-9, Loo et al 2005 Nano Lett. 5 709-11, Gobin et al 2007 Nano Lett. 7 1929-34, Fu et al 2008 Nanotechnology 19 045103, Huang et al 2006 J. Am. Chem. Soc. 128 2115-20, Jain et al 2006 J. Phys. Chem. B 110 7238-48, Jain et al 2007 Nano Today 2 18-29)) demonstrated, through pioneering results, the great potential of laser thermal therapy of cells and tissues conjugated with gold nanoparticles. It was also proposed to use combined diagnostics and therapy on the basis of nanoparticle selection for achievement of efficient contrast for laser imaging applications, as well as for photothermal therapy. However, the current understanding of the relationship between optical properties (absorption, backscattering) of nanoparticles, the efficiency of nanoparticle heating and the possibility to use them for combined imaging and therapy is limited. Here, we report the results of computer modeling of optical absorption and backscattering properties and laser heating of gold and silica-gold spherical nanoparticles for laser combined imaging and photothermal treatment of cells and tissues conjugated with nanoparticles. The efficiencies of nanoparticle heating and backscattering by nanoparticles, depending upon their radii, structure and optical properties of the metal, were investigated. This paper focuses on the analysis and determination of appropriate ranges of nanoparticle sizes for the purposes of laser combined imaging and photothermal treatment. The possibility to use spherical gold and silica-gold nanoparticles in determined ranges of radii for these purposes for laser wavelengths 532 and 800 nm is investigated.
The Role of the Monkey Dorsal Pontine Nuclei in Goal-Directed Eye and Hand Movements
2009-05-13

Prevailing concepts on the control of goal-directed hand movements (HM) have focused on a network of cortical areas whose early parieto-occipital stages are thought to extract and integrate information on target and hand location, involving subsequent stages in frontal cortex forming and executing movement plans. The substantial experimental results supporting this “cortical network” concept for hand movements notwithstanding, the concept clearly needs refinement to account for the surprisingly mild HM disturbances resulting from disconnecting the parieto-occipital from the frontal stages of the network. Clinical observations have suggested the cerebropontocerebellar projection as an alternative pathway for the sensory guidance of HM. As a first step in assessing its role, we explored the pontine nuclei (PN) of rhesus monkeys, trained to make goal-directed hand and eye movements guided by spatial memory. We were indeed able to delineate a distinct cluster of neurons in the rostrodorsal PN, activated by the preparation and the execution of hand reaches, close to but distinct from the region in which saccade-related neurons may be observed. The movement-related activity of HM-related neurons starts earlier than that of saccade-related neurons and both neuron types are usually effector specific, i.e., they respond only to the movement of the preferred effector. This is also the case when motor synergies involving both effectors are executed. Our findings support the notion of a distinct precerebellar, pontine visuomotor channel for hand reaches that is anatomically and functionally largely separated from the one serving eye movements.
Long-horizon consumption risk and the cross-section of returns: new tests and international evidence
2009-05-13

This paper investigates whether measuring consumption risk over long horizons can improve the empirical performance of the consumption-based capital asset pricing model (CCAPM) for size and value premia in international stock markets (USA, UK, and Germany). In order to account for commonalities in size and book-to-market sorted portfolios, we also include industry portfolios in our set of test assets. Our results show that, contrary to the findings of Parker and Julliard [2005. Consumption risk and the cross- section of expected returns. Journal of Political Economy 113, no. 1: 185-222], the model falls short of providing an accurate description of the cross-section of returns under our modified empirical approach. At the same time, however, measuring consumption risk over longer horizons typically yields lower risk-aversion estimates. Thus, our results suggest that more plausible parameter estimates - as opposed to lower pricing errors - can be regarded as the main achievement of the long-horizon CCAPM.
EOS at FAIR energies and the role of resonances
2009-05-13

Two microscopic models, UrQMD and QGSM, are used to extract the effective\\nequation of state (EOS) of locally equilibrated nuclear matter produced in\\nheavy-ion collisions at energies from 11.6 AGeV to 160 AGeV. Analysis is\\nperformed for the fixed central cubic cell of volume V = 125 fm**3 and for the\\nexpanding cell that followed the growth of the central area with uniformly\\ndistributed energy. For all reactions the state of local equilibrium is nearly\\napproached in both models after a certain relaxation period. The EOS has a\\nsimple linear dependence P/e = c_s**2 with 0.12 &lt; c_s**2 &lt; 0.145. Heavy\\nresonances are shown to be responsible for deviations of the c_s**2(T) and\\nc_s**2(mu_B) from linear behavior. In the T-mu_B and T-mu_S planes the EOS has\\nalso almost linear dependence and demonstrates kinks related not to the\\ndeconfinement phase transition but to inelastic freeze-out in the system.\\n
The Truth about Lying: Inhibition of the Anterior Prefrontal Cortex Improves Deceptive Behavior
2009-05-14

Recent neuroimaging studies have indicated a predominant role of the anterior prefrontal cortex (aPFC) in deception and moral cognition, yet the functional contribution of the aPFC to deceptive behavior remains unknown. We hypothesized that modulating the excitability of the aPFC by transcranial direct current stimulation (tDCS) could reveal its functional contribution in generating deceitful responses. Forty-four healthy volunteers participated in a thief role-play in which they were supposed to steal money and then to attend an interrogation with the Guilty Knowledge Test. During the interrogation, participants received cathodal, anodal, or sham tDCS. Remarkably, inhibition of the aPFC by cathodal tDCS did not lead to an impairment of deceptive behavior but rather to a significant improvement. This effect manifested in faster reaction times in telling lies, but not in telling the truth, a decrease in sympathetic skin-conductance response and feelings of guilt while deceiving the interrogator and a significantly higher lying quotient reflecting skillful lying. Increasing the excitability of the aPFC by anodal tDCS did not affect deceptive behavior, confirming the specificity of the stimulation polarity. These findings give causal support to recent correlative data obtained by functional magnetic resonance imaging studies indicating a pivotal role of the aPFC in deception.
Silver ion‐induced suicidal erythrocyte death
2009-05-14

Abstract Owing to its antibiotic activity, silver is used for water purification, wound care and a wide variety of implants. Silver metal and silver compounds ionize in solution, and silver ions interfere with the function of a wide variety of proteins. In mammalian cells, silver ions may trigger apoptosis by stimulation of cytochrome c release from mitochondria. The present study explored the effect of AgNO 3 on eryptosis, the suicidal death of erythrocytes, cells devoid of mitochondria. Similar to apoptosis of nucleated cells, eryptosis is characterized by cell shrinkage and cell membrane scrambling with phosphatidylserine exposure at the cell surface. Eryptosis is triggered by energy depletion, cellular depletion of nitric oxide (NO) and activation of protein kinase C (PKC). Phosphatidylserine exposure was determined by annexin V‐binding, cell volume by forward scatter, cellular ATP by a luciferin–luciferase assay kit, and hemolysis by photometry. A 48 h exposure to AgNO 3 (≥100 n m ) but not to NaNO 3 significantly enhanced the percentage of annexin V‐binding cells, slightly but significantly decreased forward scatter and significantly decreased cytosolic ATP. Furthermore, inhibition of PKC by staurosporine and donation of NO by sodium nitroprusside significantly blunted silver‐induced eryptosis. In conclusion, AgNO 3 triggers cell membrane scrambling, an effect attributed to ATP depletion, PKC activation and decrease of cellular NO. Copyright © 2009 John Wiley &amp; Sons, Ltd.
A single nucleotide polymorphism determines protein isoform production of the human c-FLIP protein
2009-05-14

Abstract The cellular FLICE-inhibitory protein (c-FLIP) is a modulator of death receptor-mediated apoptosis and plays a major role in T- and B-cell homeostasis. Three different isoforms have been described on the protein level, including the long form c-FLIPL as well as 2 short forms, c-FLIPS and the recently identified c-FLIPR. The mechanisms controlling c-FLIP isoform production are largely unknown. Here, we identified by sequence comparison in several mammals that c-FLIPR and not the widely studied c-FLIPS is the evolutionary ancestral short c-FLIP protein. Unexpectedly, the decision for production of either c-FLIPS or c-FLIPR in humans is defined by a single nucleotide polymorphism in a 3′ splice site of the c-FLIP gene (rs10190751A/G). Whereas an intact splice site directs production of c-FLIPS, the splice-dead variant causes production of c-FLIPR. Interestingly, due to differences in protein translation rates, higher amounts of c-FLIPS protein compared with c-FLIPR are produced. Investigation of diverse human cell lines points to an increased frequency of c-FLIPR in transformed B-cell lines. A comparison of 183 patients with follicular lymphoma and 233 population controls revealed an increased lymphoma risk associated with the rs10190751 A genotype causing c-FLIPR expression.