julilili42/papers huggingface dataset:
Biotinylated fluorescent peptide substrates for the sensitive and specific determination of cathepsin D activity
2004-10-11

Cathepsin D (CatD) is a member of the mammalian aspartic protease family and is involved in cellular protein degradation and in several pathological processes. A sensitive and specific assay for the determination of CatD activity in biological samples was developed. The peptide amide substrates Amca-EDKPILF downward arrowFRLGK(biotin)-CONH2 (I), Amca-EEKPIC(Acm)F downward arrowFRLGK(biotin)-CONH2 (II) and Amca-EEKPISF downward arrowFRLGK(biotin)-CONH2 (III) contain a CatD cleavage site (F downward arrowF) flanked by a N-terminal Amca-fluorophore (7-amino-4-methylcoumarin-3-acetic acid) and a C-terminal biotin moiety. Substrates II and III proved to be specific substrates containing only one cleavage site for CatD. After cleavage of the Phe-Phe bond by CatD all biotin conjugated peptides were removed with streptavidin-coated magnetic beads. The remaining fluorescent peptides in solution represent the amount of digested substrate. The versatility of this CatD digest and pull down assay was demonstrated by measuring the activity of CatD in different subcellular fractions of human EBV-transformed B cells and human monocytes. The described method based on the designed CatD substrates represents a valuable tool for routine assays.
Detection of non-radial g-mode pulsations in the newly discovered PG 1159 star HE 1429-1209
2004-10-11

We performed time-series photometry of the PG1159-type star HE 1429-1209, which was recently discovered in the ESO SPY survey. We show that the star is a low-amplitude (about 0.05 mag) non-radial g-mode pulsator with a period of 919s. HE 1429-1209 is among the hottest known post-AGB stars (Teff=160000 K) and, together with the known pulsator RX J2117.1+3412, it defines empirically the blue edge of the GW Vir instability strip in the HRD at high luminosities.
Imaging of μm wavelength collective cavity resonances in Bi2Sr2CaCu2O8+x intrinsic Josephson junction stacks under microwave irradiation
2004-10-11

We have used low-temperature scanning electron microscopy to image the electromagnetic field distribution in microstructured Bi2Sr2CaCu2O8+x intrinsic Josephson junction stacks under microwave irradiation. Even for microwave frequencies below 10GHz, standing waves along the stack with wavelengths of order 10μm can be observed. The data, together with numerical simulations based on coupled sine-Gordon equations, strongly indicate that the standing waves are due to collective Josephson plasma cavity resonances, with a large number of junctions oscillating in phase. The resonance frequencies are estimated to be of order 100–500GHz, that is, much higher than the drive frequency. We suggest that, under the low-frequency microwave irradiation, fluxon∕antifluxon pairs form, in turn exciting the high-frequency collective cavity resonances.
Improving XMM-Newton EPIC pn data at low energies: method and application to the Vela SNR
2004-10-11

High quantum efficiency over a broad spectral range is one of the main properties of the EPIC pn camera on-board XMM-Newton. The quantum efficiency rises from ~75% at 0.2 keV to ~100% at 1 keV, stays close to 100% until 8 keV, and is still ~90% at 10 keV. The EPIC pn camera is attached to an X-ray telescope which has the highest collecting area currently available, in particular at low energies (more than 1400 cm2 between 0.1 and 2.0 keV). Thus, this instrument is very sensitive to the low-energy X-ray emission. However, X-ray data at energies below ~0.2 keV are considerably affected by detector effects, which become more and more important towards the lowest transmitted energies. In addition to that, pixels which have received incorrect offsets during the calculation of the offset map at the beginning of each observation, show up as bright patches in low-energy images. Here we describe a method which is not only capable of suppressing the contaminations found at low energies, but which also improves the data quality throughout the whole EPIC pn spectral range. This method is then applied to data from the Vela supernova remnant.
Bright source x-ray spectroscopy with XMM-Newton: a modified EPIC-pn timing mode
2004-10-11

The large collecting area of XMM-Newton combined with the good energy resolution of the EPIC-pn CCDs allows the study, with unprecedented detail, of accretion processes onto neutron stars and black holes. The EPIC-pn CCD camera in Timing mode, in which data are read out continuously, is among the fastest X-ray CCD camera available; however, telemetry constraints do not allow full use of these capabilities for many sources because currently randomly distributed data gaps are introduced by the on-board data handling electronics. As an alternative, we have proposed to implement a modification of the Timing mode in which data from soft X-ray events are not transmitted to Earth. Here we discuss the properties of this modified Timing mode, which will first be used in simultaneous XMM-Newton, RXTE, and INTEGRAL observations of the Galactic black hole binary Cygnus X-1 in autumn 2004. We discuss the predicted performance of this new mode based upon laboratory measurements, Monte Carlo simulations, and data from existing Timing mode observations.
Detection of non-radial g-mode pulsations in the newly discovered PG 1159 star HE 1429-1209
2004-10-11

\\n We performed time-series photometry of the PG 1159-type star\\n <ext-link ext-link-type="aoi">HE 1429-1209</ext-link>, which was recently discovered in the ESO SPY survey. We show that\\n the star is a low-amplitude (≈0.05 mag) non-radial g-mode pulsator\\n with a period of 919 s. <ext-link ext-link-type="aoi">HE 1429-1209</ext-link> is among the hottest known post-AGB\\n stars ( T_\\\\mathrm{eff} K) and, together with the known pulsator <ext-link ext-link-type="aoi">RX J2117.1+3412</ext-link>, it\\n defines empirically the blue edge of the GW Vir instability strip in the HRD\\n at high luminosities. \\n\\n\\n
The Dark Universe Observatory (DUO): telescope concept
2004-10-11

What is the nature of the Dark Energy that is driving the universe apart? Clusters of galaxies offer an ideal probe of cosmology because they are the best tracers of Dark Matter and their distribution on very large scales which is dominated by the Dark Energy. DUO will measure 10.000 clusters of galaxies, the power spectrum of density fluctuations of clusters and their number density as a function of cosmic time. Although designed long before the existence of Dark Energy was claimed, the ABRIXAS type X-ray telescope turns out to be ideally suited for this task: DUO is, in essence, a re-flight of the ABRIXAS X-ray telescope which some modifications of the focal plane instrumentation. First of all, we will use new CCDs which are improved versions of the pn-CCDs successfully flown on XMM-Newton. A modular concept having seven individual cameras in the foci of the seven mirror systems allows us to design the orientation of the seven telescopes with respect to each other matching the scientific needs of the DUO mission. Details of the concept including mechanical, electrical and thermal aspects are given.
Fast timing instrument for XEUS: scientific expectations
2004-10-11

X-ray timing with musec time resolution can be used to probe strong gravity fields around collapsed objects and to constrain the equation of state of dense matter in neutron stars. With its large collecting area, XEUS will be ideally suited for very high signal to noise studies of such objects. An instrument dedicated to X-ray timing of bright Galactic sources has thus been foreseen as part of the XEUS instrumentation. In this contribution we present numerical simulations for silicon based detectors (silicon drift detectors and pixel based sensors) for a variety of astrophysical sources such as neutron star power spectra (including kHz quasi-periodic oscillations) and black hole lightcurves to illustrate the expected scientific capabilities of the fast timing mode instrument.
MIRAX: the galactic bulge transient monitor mission
2004-10-11

Monitor e Imageador de RAios-X (MIRAX) is a Brazilian high energy astronomy mission dedicated to monitoring the central 1000 sq. deg. of the Galactic plane to observe unpredictable transient phenomena from compact objects in the 2-200 keV range through nearly continuous imaging with good spatial/temporal/energy resolution. The strength of MIRAX lies in the departure of its observing strategy from traditional pointed programs and scanning monitors. MIRAX will achieve two major advantages over previous and existing missions. First, it will detect, localize, and study transient phenomena, which last on all timescales from milliseconds to years, and are very likely to be missed by traditional observing strategies. Second, MIRAX will study longer lived phenomena in exquisite detail. The mission elements and science will be presented.
Crystal Structure of F-93 from Sulfolobus Spindle-Shaped Virus 1, a Winged-Helix DNA Binding Protein
2004-10-12

ABSTRACT Sulfolobus spindle-shaped viruses (SSVs), or Fuselloviridae , are ubiquitous crenarchaeal viruses found in high-temperature acidic hot springs around the world (pH ≤4.0; temperature of ≥70°C). Because they are relatively easy to isolate, they represent the best studied of the crenarchaeal viruses. This is particularly true for the type virus, SSV1, which contains a double-stranded DNA genome of 15.5 kilobases, encoding 34 putative open reading frames. Interestingly, the genome shows little sequence similarity to organisms other than its SSV homologues. Together, sequence similarity and biochemical analyses have suggested functions for only 6 of the 34 open reading frames. Thus, even though SSV1 is the best-studied crenarchaeal virus, functions for most (28) of its open reading frames remain unknown. We have undertaken biochemical and structural studies for the gene product of open reading frame F-93. We find that F-93 exists as a homodimer in solution and that a tight dimer is also present in the 2.7-Å crystal structure. Further, the crystal structure reveals a fold that is homologous to the SlyA and MarR subfamilies of winged-helix DNA binding proteins. This strongly suggests that F-93 functions as a transcription factor that recognizes a (pseudo-)palindromic DNA target sequence.
Dynamical Role of Anyonic Excitation Statistics in Rapidly Rotating Bose Gases
2004-10-12

We show that for rotating harmonically trapped Bose gases in a fractional quantum Hall state, the anyonic excitation statistics in the rotating gas can effectively play a dynamical role. For particular values of the two-dimensional coupling constant g=-2pih2(2k-1)/m, where k is a positive integer, the system becomes a noninteracting gas of anyons, with exactly obtainable solutions satisfying Bogomol'nyi self-dual order parameter equations. Attractive Bose gases under rapid rotation thus can be stabilized in the thermodynamic limit due to the anyonic statistics of their quasiparticle excitations.
Murein (Peptidoglycan) Binding Property of the Essential Cell Division Protein FtsN from Escherichia coli
2004-10-13

ABSTRACT The binding of the essential cell division protein FtsN of Escherichia coli to the murein (peptidoglycan) sacculus was studied. Soluble truncated variants of FtsN, including the complete periplasmic part of the protein as well as a variant containing only the C-terminal 77 amino acids, did bind to purified murein sacculi isolated from wild-type cells. FtsN variants lacking this C-terminal region showed reduced or no binding to murein. Binding of FtsN was severely reduced when tested against sacculi isolated either from filamentous cells with blocked cell division or from chain-forming cells of a triple amidase mutant. Binding experiments with radioactively labeled murein digestion products revealed that the longer murein glycan strands (&gt;25 disaccharide units) showed a specific affinity to FtsN, but neither muropeptides, peptides, nor short glycan fragments bound to FtsN. In vivo FtsN could be cross-linked to murein with the soluble disulfide bridge containing cross-linker DTSSP. Less FtsN, but similar amounts of OmpA, was cross-linked to murein of filamentous or of chain-forming cells compared to levels in wild-type cells. Expression of truncated FtsN variants in cells depleted in full-length FtsN revealed that the presence of the C-terminal murein-binding domain was not required for cell division under laboratory conditions. FtsN was present in 3,000 to 6,000 copies per cell in exponentially growing wild-type E. coli MC1061. We discuss the possibilities that the binding of FtsN to murein during cell division might either stabilize the septal region or might have a function unrelated to cell division.
Propagators in Coulomb gauge from SU(2) lattice gauge theory
2004-10-13

A thorough study of 4-dimensional SU(2) Yang-Mills theory in Coulomb gauge is\\nperformed using large scale lattice simulations. The (equal-time) transverse\\ngluon propagator, the ghost form factor d(p) and the Coulomb potential V_{coul}\\n(p) ~ d^2(p) f(p)/p^2 are calculated. For large momenta p, the gluon propagator\\ndecreases like 1/p^{1+\\\\eta} with \\\\eta =0.5(1). At low momentum, the propagator\\nis weakly momentum dependent. The small momentum behavior of the Coulomb\\npotential is consistent with linear confinement. We find that the inequality\\n\\\\sigma_{coul} \\\\ge \\\\sigma comes close to be saturated. Finally, we provide\\nevidence that the ghost form factor d(p) and f(p) acquire IR singularities,\\ni.e., d(p) \\\\propto 1/\\\\sqrt{p} and f(p) \\\\propto 1/p, respectively. It turns out\\nthat the combination g_0^2 d_0(p) of the bare gauge coupling g_0 and the bare\\nghost form factor d_0(p) is finite and therefore renormalization group\\ninvariant.\\n
Five‐year follow‐up study of hyperechogenicity of the substantia nigra in Parkinson's disease
2004-10-14

Abstract Using transcranial sonography, an area of hyperechogenicity at the substantia nigra (SN) may be detected as a typical marker in patients with Parkinson's disease (PD) as well as in approximately 9% of healthy subjects vulnerable to nigrostriatal impairment. In this longitudinal study, we provide evidence that the area of SN hyperechogenicity does not change in the course of PD. In conjunction with earlier findings in children and adolescents, this evidence indicates that, from late adolescence onward, this ultrasound finding is a trait marker for nigrostriatal vulnerability. © 2004 Movement Disorder Society
RNA Interference Targeting Transforming Growth Factor-β Enhances NKG2D-Mediated Antiglioma Immune Response, Inhibits Glioma Cell Migration and Invasiveness, and Abrogates TumorigenicityIn vivo
2004-10-15

Abstract Transforming growth factor (TGF)-β is the key molecule implicated in impaired immune function in human patients with malignant gliomas. Here we report that patients with glioblastoma, the most common and lethal type of human glioma, show decreased expression of the activating immunoreceptor NKG2D in CD8+ T and natural killer (NK) cells. TGF-β is responsible for the down-regulation of NKG2D expression in CD8+ T and NK cells mediated by serum and cerebrospinal fluid of glioma patients in vitro. Moreover, TGF-β inhibits the transcription of the NKG2D ligand MICA. Interference with the synthesis of TGF-β1 and TGF-β2 by small interfering RNA technology prevents the down-regulation of NKG2D on immune cells mediated by LNT-229 glioma cell supernatant and strongly enhances MICA expression in the glioma cells and promotes their recognition and lysis by CD8+ T and NK cells. Furthermore, TGF-β silencing results in a less migratory and invasive glioma cell phenotype in vitro. LNT-229 glioma cells deficient in TGF-β exhibit a loss of subcutaneous and orthotopic tumorigenicity in nude mice, and NK cells isolated from these mice show an activated phenotype. RNA interference targeting TGF-β1,2 results in a glioma cell phenotype that is more sensitive to immune cell lysis and less motile in vitro and nontumorigenic in nude mice, strongly confirming TGF-β antagonism as a major therapeutic strategy for the future treatment of malignant gliomas.
Bridge verbs and V2 verbs – the same thing in spades?
2004-10-15

Abstract In this paper we investigate the quality of ‘bridgeness’, the extent to which a verb permits extraction from its complement clause. In spite of considerable study, linguists have only a limited idea of the nature of the factor involved. We address the question whether the quality of being a bridge verb is the same as the quality which permits a verb to take a verb-second complement clause in German. We report the results of two experiments using the technique of magnitude estimation, a method of eliciting grammaticality judgements with a high degree of differentiation. The data reveals that the ‘bridge’ quality and the ‘V2’ quality co-vary very closely, suggesting that they may well be facets of the same factor. We discuss the implications this finding has for the nature of the bridge quality.
Numerical Experiments into the Localization of Deformation during Recrystallization Flow
2004-10-15

The localization of deformation in recrystallizing materials is investigated via a series of two-dimensional grain-scale numerical simulations. These simulations couple a grain size and strain dependant viscous rheology with grain size reduction and grain growth processes. The simulations are able to predict the mechanical, microstructural and strain evolution of the polycrystals to high strain, and allow us to examine the nature of the time dependent feedback between mechanical and microstructural behavior. It was found that significant strain localization occurred only when the grain size dependence of the viscosity was non-linear, and was greatly enhanced by the activity of the grain size modifying processes. The intensity and location of the zone of strain localization varied spatially and temporally, with the result that the finite strain state showed a much broader, and hence less intense, zone of localized deformation than the instantaneous state.
Zircon and titanite geochronology of the Furstenstein granite massif, Bavarian Forest, NW Bohemian Massif: Pulses of the late Variscan magmatic activity
2004-10-18

The Furstenstein granite massif is the largest late Variscan granitoid body exposed in the Moldanubian basement of the Bavarian Forest. The granite massif comprises different rock types, ranging from diorite to granite in composition. This study provides precise zircon and titanite ages, obtained by the U-Pb isotopic dilution and Pb-Pb evaporation methods, and Nd-Sr isotopic data on this massif. Zircon dating constrains an intrusive sequence as following: Dioritic rocks crystallised about 334 to 332 Ma ago, earlier than the high-temperature peak stage of the Variscan metamorphism of the Moldanubian basement (325 to 320 Ma) in the Bavarian Forest. The medium- to coarse-grained Tittling granite was emplaced about 10 Ma later, between 324 and 321 Ma, while the medium-grained Eberhardsreuth granite crystallised between 316 and 312 Ma, contemporaneously with the coarse-grained porphyritic Saldenburg granite. Titanites from the dioritic rocks give U-Pb ages of about 321 ± 4 Ma, indicating thermal resetting or crystallisation due to the intrusion of the Tittling granite. The diorites have initial ε Nd values of −1.3 to −2.9 and relatively low initial 87 Sr/ 86 Sr ratios of 0.7056 to 0.7067, which suggest mantle contribution to melts or melting of young mafic lower crust. The granites have similar initial ε Nd values of −3.6 to −4.1 but show some variation in their Sr isotopic composition (initial 87 Sr/ 86 Sr ratios of 0.7063 to 0.7074), probably indicating the involvement of crustal material in their genesis.
Repetitive Bilateral Arm Training and Motor Cortex Activation in Chronic Stroke
2004-10-19

These preliminary findings suggest that BATRAC induces reorganization in contralesional motor networks and provide biological plausibility for repetitive bilateral training as a potential therapy for upper extremity rehabilitation in hemiparetic stroke.
L-Type Ca 2+ Current Downregulation in Chronic Human Atrial Fibrillation Is Associated With Increased Activity of Protein Phosphatases
2004-10-19

Background— Although downregulation of L-type Ca 2+ current ( I Ca,L ) in chronic atrial fibrillation (AF) is an important determinant of electrical remodeling, the molecular mechanisms are not fully understood. Here, we tested whether reduced I Ca,L in AF is associated with alterations in phosphorylation-dependent channel regulation. Methods and Results— We used whole-cell voltage-clamp technique and biochemical assays to study regulation and expression of I Ca,L in myocytes and atrial tissue from 148 patients with sinus rhythm (SR) and chronic AF. Basal I Ca,L at +10 mV was smaller in AF than in SR (−3.8±0.3 pA/pF, n=138/37 [myocytes/patients] and −7.6±0.4 pA/pF, n=276/86, respectively; P &lt;0.001), though protein levels of the pore-forming α 1c and regulatory β 2a channel subunits were not different. In both groups, norepinephrine (0.01 to 10 μmol/L) increased I Ca,L with a similar maximum effect and comparable potency. Selective blockers of kinases revealed that basal I Ca,L was enhanced by Ca 2+ /calmodulin-dependent protein kinase II in SR but not in AF. Norepinephrine-activated I Ca,L was larger with protein kinase C block in SR only, suggesting decreased channel phosphorylation in AF. The type 1 and type 2A phosphatase inhibitor okadaic acid increased basal I Ca,L more effectively in AF than in SR, which was compatible with increased type 2A phosphatase but not type 1 phosphatase protein expression and higher phosphatase activity in AF. Conclusions— In AF, increased protein phosphatase activity contributes to impaired basal I Ca,L . We propose that protein phosphatases may be potential therapeutic targets for AF treatment.
Propofol and Sevoflurane Depress Spinal Neurons In Vitro via Different Molecular Targets
2004-10-19

Background The capacity of general anesthetics to produce immobility is primarily spinally mediated. Recently, compelling evidence has been provided that the spinal actions of propofol involve gamma-aminobutyric acid type A (GABAA) receptors, whereas the contribution of glycine receptors remains uncertain. The relevant molecular targets of the commonly used volatile anesthetic sevoflurane in the spinal cord are largely unknown, but indirect evidence suggests a mechanism of action distinct from propofol. Methods The effects of sevoflurane and propofol on spontaneous action potential firing were investigated by extracellular voltage recordings from ventral horn interneurons in cultured spinal cord tissue slices obtained from embryonic rats (embryonic days 14-15). Results Propofol and sevoflurane reduced spontaneous action potential firing of neurons. Concentrations causing half-maximal effects (0.11 microm propofol, 0.11 mm sevoflurane) were lower than the median effective concentration immobility (1-1.5 microm propofol, 0.35 mm sevoflurane). At higher concentrations, complete inhibition of action potential activity was observed with sevoflurane but not with propofol. Effects of sevoflurane were mediated predominantly by glycine receptors (45%) and GABAA receptors (38%), whereas propofol acted almost exclusively via GABAA receptors (96%). Conclusions The authors' results suggest that glycine and GABAA receptors are the most important molecular targets mediating depressant effects of sevoflurane in the spinal cord. They provide evidence that sevoflurane causes immobility by a mechanism distinct from the actions of the intravenous anesthetic propofol. The finding that propofol acts exclusively via GABAA receptors can explain its limited capacity to depress spinal neurons in the authors' study.