julilili42/papers huggingface dataset:
Probabilistic Consensus Scoring Improves Tandem Mass Spectrometry Peptide Identification
2011-06-06

Database search is a standard technique for identifying peptides from their tandem mass spectra. To increase the number of correctly identified peptides, we suggest a probabilistic framework that allows the combination of scores from different search engines into a joint consensus score. Central to the approach is a novel method to estimate scores for peptides not found by an individual search engine. This approach allows the estimation of p-values for each candidate peptide and their combination across all search engines. The consensus approach works better than any single search engine across all different instrument types considered in this study. Improvements vary strongly from platform to platform and from search engine to search engine. Compared to the industry standard MASCOT, our approach can identify up to 60% more peptides. The software for consensus predictions is implemented in C++ as part of OpenMS, a software framework for mass spectrometry. The source code is available in the current development version of OpenMS and can easily be used as a command line application or via a graphical pipeline designer TOPPAS.
A Potent Trivalent Sialic Acid Inhibitor of Adenovirus Type 37 Infection of Human Corneal Cells
2011-06-06

Wouldn′t it be useful to have three arms? It came in handy for a trivalent sialic acid inhibitor, which blocked all three binding pockets of a trimeric adenoviral fiber-knob protein and thus prevented cell attachment and the subsequent infection of human corneal epithelial cells. The picture shows the terminal sialic acid moietes of the inhibitor bound to the top of the fiber head (C yellow, O red, N blue; the spacers and scaffold are not shown).
A Potent Trivalent Sialic Acid Inhibitor of Adenovirus Type 37 Infection of Human Corneal Cells
2011-06-06

Graphical Abstract Wie wär's mit einem dritten Arm? Geschadet hat Ähnliches einem Inhibitor mit drei Sialinsäuregruppen auf jeden Fall nicht: Er blockierte alle drei Bindetaschen eines trimeren adenoviralen Fiber-Knob-Proteins und verhinderte dadurch die Anlagerung und anschließende Infektion bei menschlichen Corneaepithelzellen. Das Bild zeigt die terminalen Sialinsäure-Einheiten des Inhibitors gebunden an das Peptid (C gelb, O rot, N blau; das Molekülgerüst ist nicht abgebildet).
Propagators in lattice Coulomb gauge and confinement mechanisms
2011-06-06

We discuss the gluon propagator in 3- and 4-dimensional Yang-Mills theories in Coulomb gauge and compare it with the corresponding Landau gauge propagator, showing that for both the relevant IR mass scale coincides. We also report preliminary results on Coulomb gauge ghost form factor and quark propagators and give a comment on the gluon propagator’s strong coupling limit.
Real-Time fMRI
2011-06-07

Real-time fMRI permits simultaneous measurement and observation of brain activity during an ongoing task. One of the most challenging applications of real-time fMRI in neuroscientific and clinical research is the possibility of acquiring volitional control of localized brain activity using real-time fMRI–based neurofeedback protocols. Real-time fMRI allows the experimenter to noninvasively manipulate brain activity as an independent variable to observe the effects on behavior. Real-time fMRI neurofeedback studies demonstrated that learned control of the local brain activity leads to specific changes in behavior. Here, the authors describe the implementation and application of real-time fMRI with particular emphasis on the self-regulation of local brain activity and the investigation of brain-function relationships. Real-time fMRI represents a promising new approach to cognitive neuroscience that could complement traditional neuroimaging techniques by providing more causal insights into the functional role of circumscribed brain regions in behavior.
Novel approach to controlled protein crystallization through ligandation of yttrium cations
2011-06-07

Crystal structure determination of macromolecules is often hampered by the lack of crystals suitable for diffraction experiments. This article describes a protocol to crystallize the acidic protein bovine β-lactoglobulin in the presence of yttrium to yield high-quality crystals that belong to a new space group. The yttrium ions not only are used to engineer the crystallization, but are an integral part of the crystal lattice and can therefore be used to solve the phase problem using anomalous dispersion methods. Protein crystallization conditions were first optimized using an experimental phase diagram in the protein and salt concentration plane. Crystal growth strongly depends on the position in the phase diagram, and the best crystals grow near the phase transition boundaries. The structure analysis demonstrates the specific binding of yttrium ions to surface-exposed glutamate and aspartate side chains contributed by different molecules in the crystal lattice. By bridging molecules in this manner, contacts between molecules are formed that enable the formation of a stable crystal lattice. The potential application of this strategy to the crystallization of other acidic proteins is discussed on the basis of the universal features of the phase behavior of these proteins and the interactions induced by multivalent ions.
Thalamus segmentation based on the local diffusion direction: A group study
2011-06-07

Abstract Fast and accurate segmentation of deep gray matter regions in the brain is important for clinical applications such as surgical planning for the placement of deep brain stimulation implants. Mapping anatomy from stereotactic atlases to patient data is problematic because of individual differences in subject anatomy that are not accounted for by commonly used atlases. We present a segmentation method for individual subject diffusion tensor MR data that is based on local diffusion information to identify subregions of the thalamus. We show the correspondence of our segmentation results to anatomy by comparison with stereotactic atlas data. Importantly, we verify the consistency of our segmentation by evaluating the method on 63 healthy volunteers. Our method is fast, reliable, and independent of any segmentation before the classification of regions within the thalamus. It should, therefore, be useful in clinical applications. Magn Reson Med, 2011. © 2011 Wiley‐Liss, Inc.
N-terminal ataxin-3 causes neurological symptoms with inclusions, endoplasmic reticulum stress and ribosomal dislocation
2011-06-07

Mutant ataxin-3 is aberrantly folded and proteolytically cleaved in spinocerebellar ataxia type 3. The C-terminal region of the protein includes a polyglutamine stretch that is expanded in spinocerebellar ataxia type 3. Here, we report on the analysis of an ataxin-3 mutant mouse that has been obtained by gene trap integration. The ataxin-3 fusion protein encompasses 259 N-terminal amino acids including the Josephin domain and an ubiquitin-interacting motif but lacks the C-terminus with the polyglutamine stretch, the valosin-containing protein binding region and part of the ubiquitin-interacting motif 2. Homozygous ataxin-3 mutant mice were viable and showed no apparent anatomical defects at birth. However, at the age of 9 months, homozygous and heterozygous mutant mice revealed significantly altered behaviour and progressing deficits of motor coordination followed by premature death at ∼12 months. At this time, prominent extranuclear protein aggregates and neuronal cell death was found in mutant mice. This was associated with disturbances of the endoplasmic reticulum-mediated unfolded protein response, consistent with the normal role of ataxin-3 in endoplasmic reticulum homeostasis. Thus, the ataxin-3 gene trap model provides evidence for a contribution of the non-polyglutamine containing ataxin-3 N-terminus, which mimics a calpain fragment that has been observed in spinocerebellar ataxia type 3. Consistent with the disease in humans, gene trap mice develop cytoplasmic inclusion bodies and implicate impaired unfolded protein response in the pathogenesis of spinocerebellar ataxia type 3.
Templating Effect for Organic Heterostructure Film Growth: Perfluoropentacene on Diindenoperylene
2011-06-07

We present a systematic study of templating effects in organic heterostructure growth, that is, where the growth behavior of the top layer is significantly influenced by the structural and morphological properties of the bottom layer. We prepared thin films of the donor material diindenoperylene (DIP) differing in crystal structure, grain size, and grain orientation on indium tin oxide (ITO). The acceptor material perfluoropentacene (PFP) was chosen to be evaporated on DIP to form the heterostructure. We employed X-ray reflectivity and grazing incidence X-ray diffraction as well as atomic force microscopy to investigate the heterostructures. The structure and morphology of the PFP layers depend on the properties of the DIP layer underneath. Two main effects were observed: PFP molecules in the top layer tend to adopt the orientation of the DIP molecules in the bottom layer and the crystalline quality of the PFP layer correlates with the crystalline quality of the DIP layer underneath in terms of the in-plane coherent crystal size.
Tritium and rhenium as a probe of cosmic neutrino background
2011-06-07

Abstract\\nWe analyze the possibility of detection of cosmological relic neutrinos via neutrino capture on beta decaying nuclei. This reaction has no threshold in neutrino energy, which is crucial for searching for relic neutrinos possessing very low energies. We focus on tritium (3 H) and rhenium (187 Re) beta radioactive isotopes to be used in the Karlsruhe tritium neutrino mass (KATRIN) experiment and project, called the " Microcalorimeter Arrays for a Rhenium Experiment " (MARE), dedicated to measurement of the electron neutrino mass at sub-eV scale. We examine these experiments from the viewpoint of searching for the cosmological neutrinos via neutrino capture. We conclude that even with possible gravitational clustering of relic neutrinos the prospects for their detection in these and other similar experiments are not optimistic. Nevertheless KATRIN and MARE experiments could establish some useful constraints on density of relic neutrinos.
The 2-(Triphenylsilyl)ethoxycarbonyl-(“Tpseoc”-) Group: A New Silicon-Based, Fluoride Cleavable Oxycarbonyl Protecting Group Highly Orthogonal to the Boc-, Fmoc- and Cbz-Groups
2011-06-07

Starting from 2-(triphenylsilyl)ethanol a new oxycarbonyl protecting group cleavable by fluoride ion induced Peterson-elimination has been developed. Known 2-(triphenylsilyl)ethanol has been prepared from commercially available triphenylvinyl-silane by a hydroboration-oxidation sequence using the sterically hindered borane reagent 9-BBN. The silyl alcohol was subsequently transformed into its chloroformate, imidazolylcarboxylic acid ester and p-nitrophenyl carbonate and used in standard protocols for the formation of carbamates and carbonates. The Tpseoc group proved to be highly resistant against acidic conditions applied in removal of tert-butyl esters and the t-Boc-group. It also withstood catalytic hydrogenation, treatment with morpholine, methylhydrazine and Pd-reagents/allyl-scavanger combinations, conditions required to cleave Cbz-, Fmoc-, phthalimide- and Alloc-groups. The Tpseoc-group is cleaved upon treatment with TBAF/CsF at 0 °C or r.t. with cleavage times reaching from &lt; 10 min. to 24 h. Its orthogonality, ease of cleavage and UV-detectability makes the Tpseoc-group a promising alternative to other widely used silicon based amine protecting groups like the Teoc- and SES-groups.
Reversible and Irreversible Light-Induced p-Doping of P3HT by Oxygen Studied by Photoelectron Spectroscopy (XPS/UPS)
2011-06-08

The influence of oxygen and light on the energy level alignment of poly(3-hexylthiophene) thin films (∼100 nm) is investigated quantitatively using X-ray and ultraviolet photoelectron spectroscopy (XPS/UPS) in order to probe energetic shifts and the element distribution in the film. Upon simultaneous exposure to oxygen and light a reversible shift of the occupied states of about 0.3 eV is observed together with the presence of reversibly and irreversibly bound oxygen species. Whereas the reversibly bound species correlates with the energy shifts, the latter does not alter the electronic structure. The observations are discussed in terms of light-induced p-doping of the semiconducting material by oxygen which is completely reversible upon vacuum annealing of the polymer film above the glass transition temperature of 150 °C.
H.E.S.S. OBSERVATIONS OF THE GLOBULAR CLUSTERS NGC 6388 AND M15 AND SEARCH FOR A DARK MATTER SIGNAL
2011-06-08

Observations of the globular clusters (GCs) NGC 6388 and M15 were carried out by the High Energy Stereoscopic System array of Cherenkov telescopes for a live time of 27.2 and 15.2 hr, respectively. No gamma-ray signal is found at the nominal target position of NGC 6388 and M15. In the primordial formation scenario, GCs are formed in a dark matter (DM) halo and DM could still be present in the baryon-dominated environment of GCs. This opens the possibility of observing a DM self-annihilation signal. The DM content of the GCs NGC 6388 and M15 is modeled taking into account the astrophysical processes that can be expected to influence the DM distribution during the evolution of the GC: the adiabatic contraction of DM by baryons, the adiabatic growth of a black hole in the DM halo, and the kinetic heating of DM by stars. Ninety-five percent confidence level exclusion limits on the DM particle velocity-weighted annihilation cross section are derived for these DM halos. In the TeV range, the limits on the velocity-weighted annihilation cross section are derived at the 10−25 cm3 s−1 level and a few 10−24 cm3 s−1 for NGC 6388 and M15, respectively.
Climate‐related variation of the human nasal cavity
2011-06-09

Abstract The nasal cavity is essential for humidifying and warming the air before it reaches the sensitive lungs. Because humans inhabit environments that can be seen as extreme from the perspective of respiratory function, nasal cavity shape is expected to show climatic adaptation. This study examines the relationship between modern human variation in the morphology of the nasal cavity and the climatic factors of temperature and vapor pressure, and tests the hypothesis that within increasingly demanding environments (colder and drier), nasal cavities will show features that enhance turbulence and air‐wall contact to improve conditioning of the air. We use three‐dimensional geometric morphometrics methods and multivariate statistics to model and analyze the shape of the bony nasal cavity of 10 modern human population samples from five climatic groups. We report significant correlations between nasal cavity shape and climatic variables of both temperature and humidity. Variation in nasal cavity shape is correlated with a cline from cold–dry climates to hot–humid climates, with a separate temperature and vapor pressure effect. The bony nasal cavity appears mostly associated with temperature, and the nasopharynx with humidity. The observed climate‐related shape changes are functionally consistent with an increase in contact between air and mucosal tissue in cold–dry climates through greater turbulence during inspiration and a higher surface‐to‐volume ratio in the upper nasal cavity. Am J Phys Anthropol 2011. © 2011Wiley‐Liss, Inc.
HYDROMAGNETIC INSTABILITIES IN RELATIVISTIC NEUTRON STARS
2011-06-09

We model the non-linear ideal magnetohydrodynamics of poloidal magnetic\\nfields in neutron stars in general relativity assuming a polytropic equation of\\nstate. We identify familiar hydromagnetic modes, in particular the\\n'sausage/varicose' mode and 'kink' instability inherent to poloidal magnetic\\nfields. The evolution is dominated by the kink instability, which causes a\\ncataclysmic reconfiguration of the magnetic field. The system subsequently\\nevolves to new, non-axisymmetric, quasi-equilibrium end-states. The existence\\nof this branch of stable quasi-equilibria may have consequences for magnetar\\nphysics, including flare generation mechanisms and interpretations of\\nquasi-periodic oscillations.\\n
Abyssomicin Biosynthesis: Formation of an Unusual Polyketide, Antibiotic‐Feeding Studies and Genetic Analysis
2011-06-09

Small wonder: Atrop-abyssomicin C is a small, yet complex spirotetronate (see scheme) that is active against Gram-positive bacteria, such as MRSA. Feeding studies and genetic manipulation of its producer, Verrucosispora maris AB-18-032, for the first time give insight into its biosynthesis and demonstrate how closely related the members of this important class of molecules are.
Threshold-resummed cross section for the Drell-Yan process in pion-nucleon collisions at COMPASS
2011-06-09

We present a study of the Drell-Yan process in pion-proton collisions\\nincluding next-to-leading-logarithmic threshold-resummed contributions. We\\nanalyze rapidity-integrated as well as rapidity-differential cross sections in\\nthe kinematic regime relevant for the COMPASS fixed target experiment. We find\\nthat resummation leads to a significant enhancement of the cross section\\ncompared to fixed-order calculations in this regime. Particularly large\\ncorrections arise at large forward and backward rapidities of the lepton pair.\\nWe also study the scale dependence of the cross section and find it to be\\nsubstantially reduced by threshold resummation.\\n
Refined Crystal Structure and Idealized Structure of Mixed-Valent Eu4F5(CN2)2: Transition Possible
2011-06-09

The new europium fluoride carbodiimide Eu(4)F(5)(CN(2))(2) was synthesized by solid state reaction from mixtures of EuF(3) and Li(2)(CN(2)) at 700 °C. The crystal structure as refined by single crystal X-ray diffraction (P ̅42(1)c, no. 114, a = 16.053(1) Å, c = 6.5150(6) Å, Z = 8) reveals three crystallographically distinct [N═C═N](2-) ions in the structure of mixed-valent Eu(4)F(5)(CN(2))(2). The presence of one Eu(3+) and three Eu(2+) per formula unit Eu(4)F(5)(CN(2))(2) is confirmed by magnetic measurements and (151)Eu-Mössbauer spectroscopy. The arrangement of Eu ions and gravity centers of [NCN](2-) ions in the structure of Eu(4)F(5)(CN(2))(2) follow the motif formed by atoms in the CuAl(2)-type structure. A possible high-symmetry structure of Eu(4)F(5)(CN(2))(2) is discussed on the basis of a group-subgroup scheme.
Synthesis, crystal structure and spectroscopic properties of Y3O2Cl[SeO3]2 : Eu3+
2011-06-09

Abstract The yttrium oxide chloride oxoselenate(IV) Y 3 O 2 Cl[SeO 3 ] 2 , doped with Eu 3+ at 3% mass percentage, can be obtained by common solid-state reactions from Y 2 O 3 , Eu 2 O 3 , YCl 3 and SeO 2 , and crystallizes isostrucäturally with the analogous terbium(III) compound Tb 3 O 2 Cl[SeO 3 ] 2 . The orthorhombic crystal structure ( Pnma , a = 548.24(4), b = 1457.92(9), c = 1102.83(7) pm and Z = 4 for undoped yttrium samples) was identified by single-crystal X-ray diffraction data and the purity of the product was checked with powder XRD methods. The presence of isolated pyramidal [SeO 3 ] 2– units could be confirmed by Raman spectroscopy. The optical band gap was determined by diffuse reflectance spectroscopy (DRS) applying the Kubelka-Munk function. Fluorescence spectroscopy measurements revealed the prominent f → f -transitions for Eu 3+ -doped compounds in both the excitation and the emission spectra of Y 3 O 2 Cl[SeO 3 ] 2 : Eu 3+ .
Ulk1-mediated phosphorylation of AMPK constitutes a negative regulatory feedback loop
2011-06-10

Unc-51-like kinase 1 (Ulk1) plays a central role in autophagy induction. It forms a stable complex with Atg13 and focal adhesion kinase (FAK) family interacting protein of 200 kDa (FIP 200). This complex is negatively regulated by the mammalian target of rapamycin complex 1 (mTORC1) in a nutrient-dependent way. AMP-activated protein kinase (AMPK), which is activated by LKB1/Strad/Mo25 upon high AMP levels, stimulates autophagy by inhibiting mTORC1. Recently, it has been described that AMPK and Ulk1 interact and that the latter is phosphorylated by AMPK. This phosphorylation leads to the direct activation of Ulk1 by AMPK bypassing mTOR-inhibition. Here we report that Ulk1/2 in turn phosphorylates all three subunits of AMPK and thereby negatively regulates its activity. Thus, we propose that Ulk1 is not only involved in the induction of autophagy, but also in terminating signaling events that trigger autophagy. In our model, phosphorylation of AMPK by Ulk1 represents a negative feedback circuit.
Characterization of Staphylococcus aureus Cardiolipin Synthases 1 and 2 and Their Contribution to Accumulation of Cardiolipin in Stationary Phase and within Phagocytes
2011-06-10

ABSTRACT In many bacteria, including Staphylococcus aureus , progression from the logarithmic to the stationary phase is accompanied by conversion of most of bacterial membrane phosphatidylglycerol (PG) to cardiolipin (CL). Phagocytosis of S. aureus by human neutrophils also induces the conversion of most bacterial PG to CL. The genome of all sequenced strains of S. aureus contains two open reading frames (ORFs) predicting proteins encoded with ∼30% identity to the principal CL synthase ( cls ) of Escherichia coli . To test whether these ORFs ( cls1 and cls2 ) encode cardiolipin synthases and contribute to CL accumulation in S. aureus , we expressed these proteins in a cls strain of E. coli and created isogenic single and double mutants in S. aureus . The expression of either Cls1 or Cls2 in CL-deficient E. coli resulted in CL accumulation in the stationary phase. S. aureus with deletion of both cls1 and cls2 showed no detectable CL accumulation in the stationary phase or after phagocytosis by neutrophils. CL accumulation in the stationary phase was due almost solely to Cls2, whereas both Cls1 and Cls2 contributed to CL accumulation following phagocytosis by neutrophils. Differences in the relative contributions of Cls1 and Cls2 to CL accumulation under different triggering conditions suggest differences in the role and regulation of these two enzymes.
Autophagy controls plant basal immunity in a pathogenic lifestyle-dependent manner
2011-06-10

Plant genomes harbor autophagy-related (ATG) genes that encode major components of the eukaryotic autophagic machinery. Autophagy in plants has been functionally linked to senescence, oxidative stress adaptation and the nutrient starvation response. In addition, plant autophagy has been assigned negative ('anti-death') and positive ('pro-death') regulatory functions in controlling cell death programs that establish sufficient immunity to microbial infection. The role of autophagy in plant disease and basal immunity to microbial infection has, however, not been studied in detail. We have employed a series of autophagy-deficient genotypes of the genetic model plant Arabidopsis thaliana in various infection systems. Genotypes lacking ATG5, ATG10 or ATG18a develop spreading necrosis and enhanced disease susceptibility upon infection with toxin-producing pathogens preferring a necrotrophic lifestyle. These findings suggest that autophagy positively controls the containment of host tissue integrity upon infections by host-destructive microbes. In contrast, autophagy-deficient genotypes exhibit markedly increased immunity to infections by biotrophic pathogens through altered homeostasis of the plant hormone salicylic acid, thus suggesting an additional negative regulatory role of autophagy in plant basal immunity. In sum, our findings suggest that the role of plant autophagy in immunity cannot be generalized, and depends critically on the lifestyle and infection strategy of invading microbes.