julilili42/papers huggingface dataset:
Discovery of gamma- and X-ray pulsations from the young and energetic PSR J1357−6429 withFermiandXMM-Newton
2011-08-03

Context. Since the launch of the Fermi satellite, the number of known gamma-ray pulsars has increased tenfold. Most gamma-ray detected pulsars are young and energetic, and many are associated with TeV sources. PSR J1357-6429 is a high spin-down power pulsar (È = 3.1 × 1036 erg s&lt;sup&gt;-1&lt;/sup&gt;), discovered during the Parkes multibeam survey of the Galactic plane, with significant timing noise typical of very young pulsars. In the very-high-energy domain (E &gt; 100 GeV), H.E.S.S. has reported the detection of the extended source HESS J1356-645 (intrinsic Gaussian width of 12') whose centroid lies 7' from PSR J1357-6429. Aims. We search for gamma- and X-ray pulsations from this pulsar, characterize the neutron star emission and explore the environment of PSR J1357-6429. Methods. Using a rotational ephemeris obtained with 74 observations made with the Parkes telescope at 1.4 GHz, we phase-fold more than two years of gamma-ray data acquired by the Large Area Telescope on-board Fermi as well as those collected with XMM-Newton, and perform gamma-ray spectral modeling. Results. Significant gamma- and X-ray pulsations are detected from PSR J1357-6429. The light curve in both bands shows one broad peak. Gamma-ray spectral analysis of the pulsed emission suggests that it is well described by a simple power-law of index 1.5 ± 0.3&lt;sub&gt;stat&lt;/sub&gt; ± 0.3&lt;sub&gt;syst&lt;/sub&gt; with an exponential cut-off at 0.8 ± 0.3&lt;sub&gt;stat&lt;/sub&gt; ± 0.3&lt;sub&gt;syst&lt;/sub&gt; GeV and an integral photon flux above 100 MeV of (6.5 ± 1.6&lt;sub&gt;stat&lt;/sub&gt; ± 2.3&lt;sub&gt;syst&lt;/sub&gt;) × 10&lt;sup&gt;-8&lt;/sup&gt; cm&lt;sup&gt;-2&lt;/sup&gt; s&lt;sup&gt;-1&lt;/sup&gt;. The X-ray spectra obtained from the new data provide results consistent with previous work. Upper limits on the gamma-ray emission from its potential pulsar wind nebula (PWN) are also reported. Conclusions. Assuming a distance of 2.4 kpc, the Fermi LAT energy flux yields a gamma-ray luminosity for PSR J1357-6429 of L&lt;sub&gt;γ&lt;/sub&gt; = (2.13 ± 0.25&lt;sub&gt;stat&lt;/sub&gt; ± 0.83&lt;sub&gt;syst&lt;/sub&gt;) × 1034 erg s&lt;sup&gt;-1&lt;/sup&gt;, consistent with an relationship. The Fermi non-detection of the pulsar wind nebula associated with HESS J1356-645 provides new constraints on the electron population responsible for the extended TeV emission.
The Complexity of Finding Multiple Solutions to Betweenness and Quartet Compatibility
2011-08-03

We show that two important problems that have applications in computational biology are ASP-complete, which implies that, given a solution to a problem, it is NP-complete to decide if another solution exists. We show first that a variation of BETWEENNESS, which is the underlying problem of questions related to radiation hybrid mapping, is ASP-complete. Subsequently, we use that result to show that QUARTET COMPATIBILITY, a fundamental problem in phylogenetics that asks whether a set of quartets can be represented by a parent tree, is also ASP-complete. The latter result shows that Steel’s QUARTET CHALLENGE, which asks whether a solution to QUARTET COMPATIBILITY is unique, is coNP-complete.
Infection with cytomegalovirus but not herpes simplex virus induces the accumulation of late-differentiated CD4+ and CD8+ T-cells in humans
2011-08-04

Human cytomegalovirus (CMV) establishes persistent, usually asymptomatic, infection in healthy people. Because CMV infection is associated with the presence of lower proportions of peripheral naïve CD8 + T-cells and a higher fraction of late-differentiated CD8 + cells, commonly taken as biomarkers of age-associated compromised adaptive immunity (‘immunosenescence’), we asked whether chronic exposure to any persistent virus mediates these effects. Herpes simplex virus (HSV) is also a widespread herpesvirus that establishes lifelong persistence, but, unlike CMV, its impact on the distribution of T-cell subsets has not been established. Here, we analysed T-cell subsets in 93 healthy people aged 42–81 years infected or not infected with CMV and/or HSV. Individuals harbouring CMV were confirmed to possess lower frequencies of naïve CD8 + T-cells (defined as CD45RA + CCR7 + CD27 + CD28 + ) and greater proportions of late-differentiated effector memory (CD45RA − CCR7 − CD27 − CD28 − ) and so-called TEMRA (CD45RA + CCR7 − CD27 − CD28 − ) CD4 and CD8 subsets, independent of HSV seropositivity. In CMV-seronegative donors, HSV did not affect T-cell subset distribution significantly. We conclude that these hallmarks of age-associated alterations to immune signatures are indeed observed in the general population in people infected with CMV and not those infected with a different persistent herpesvirus.
Crystal Structure of Reovirus Attachment Protein σ1 in Complex with Sialylated Oligosaccharides
2011-08-04

Many viruses attach to target cells by binding to cell-surface glycans. To gain a better understanding of strategies used by viruses to engage carbohydrate receptors, we determined the crystal structures of reovirus attachment protein σ1 in complex with α-2,3-sialyllactose, α-2,6-sialyllactose, and α-2,8-di-siallylactose. All three oligosaccharides terminate in sialic acid, which serves as a receptor for the reovirus serotype studied here. The overall structure of σ1 resembles an elongated, filamentous trimer. It contains a globular head featuring a compact β-barrel, and a fibrous extension formed by seven repeating units of a triple β-spiral that is interrupted near its midpoint by a short α-helical coiled coil. The carbohydrate-binding site is located between β-spiral repeats two and three, distal from the head. In all three complexes, the terminal sialic acid forms almost all of the contacts with σ1 in an identical manner, while the remaining components of the oligosaccharides make little or no contacts. We used this structural information to guide mutagenesis studies to identify residues in σ1 that functionally engage sialic acid by assessing hemagglutination capacity and growth in murine erythroleukemia cells, which require sialic acid binding for productive infection. Our studies using σ1 mutant viruses reveal that residues 198, 202, 203, 204, and 205 are required for functional binding to sialic acid by reovirus. These findings provide insight into mechanisms of reovirus attachment to cell-surface glycans and contribute to an understanding of carbohydrate binding by viruses. They also establish a filamentous, trimeric carbohydrate-binding module that could potentially be used to endow other trimeric proteins with carbohydrate-binding properties.
The broad iron Kαline of Cygnus X-1 as seen byXMM-Newtonin the EPIC-pn modified timing mode
2011-08-04

We present the analysis of the broadened, flourescent iron Kα line in simultaneous XMM-Newton and RXTE data from the black hole Cygnus X-1. The XMM-Newton data were taken in a modified version of the timing mode of the EPIC-pn camera. In this mode the lower energy threshold of the instrument is increased to 2.8 keV to avoid telemetry drop outs due to the brightness of the source, while at the same time preserving the signal-to-noise ratio in the Fe Kα band. We find that the best-fit spectrum consists of the sum of an exponentially cutoff power-law and relativistically smeared, ionized reflection. The shape of the broadened Fe Kα feature is due to strong Compton broadening combined with relativistic broadening. Assuming a standard, thin accretion disk, the black hole is close to rotating maximally.
Pulse-amplitude-resolved spectroscopy of bright accreting pulsars: indication of two accretion regimes
2011-08-04

\\n Context. In addition to coherent pulsation, many accreting neutron stars exhibit flaring activity and strong aperiodic variability on time scales comparable to or shorter than their pulsation period. This behavior shows that the accretion flow in the vicinity of the accretor must be highly non-stationary. Observational study of this phenomenon is often problematic because it requires very high statistics of X-ray data and a specific analysis technique.\\n Aims. In our research we used high-resolution data taken with RXTE and INTEGRAL on a sample of bright transient and persistent pulsars to perform an in-depth study of their variability on time scales comparable to the pulsation period – ”pulse-to-pulse variability”.\\n Methods. The high-quality data allowed us to collect individual pulses of different amplitude and explore their X-ray spectrum as a function of pulse amplitude. The described approach allowed us for the first time to study the luminosity dependence of pulsars’ X-ray spectra in observations where the averaged (over many pulse cycles) luminosity of the source remains constant.\\n Results. In all studied pulsars we reveal significant spectral changes as a function of the pulse height both in the continuum and in the cyclotron absorption features. The sources appear to form two groups that show different dependencies of the spectrum on pulse height. We interpret this division as a manifestation of two distinct accretion regimes that are at work in different pulsars. \\n
Monocarboxylate transporter 8 deficiency: altered thyroid morphology and persistent high triiodothyronine/thyroxine ratio after thyroidectomy
2011-08-04

Context Thyroid hormone transport across the plasma membrane depends on transmembrane transport proteins, including monocarboxylate transporter 8 (MCT8). Mutations in MCT8 (or SLC16A2 ) lead to a severe form of X-linked psychomotor retardation, which is characterised by elevated plasma triiodothyronine (T 3 ) and low/normal thyroxine (T 4 ). MCT8 contributes to hormone release from the thyroid gland. Objective To characterise the potential impact of MCT8 -deficiency on thyroid morphology in a patient and in Mct8 -deficient mice. Design Thyroid morphology in a patient carrying the A224V mutation was followed by ultrasound imaging for over 10 years. After thyroidectomy, a histopathological analysis was carried out. The findings were compared with histological analyses of mouse thyroids from the Mct8 −/y model. Results We show that an inactivating mutation in MCT8 leads to a unique, progressive thyroid follicular pathology in a patient. After thyroidectomy, histological analysis revealed gross morphological changes, including several hyperplastic nodules, microfollicular areas with stromal fibrosis and a small focus of microfollicular structures with nuclear features reminiscent of papillary thyroid carcinoma (PTC). These findings are supported by an Mct8-null mouse model in which we found massive papillary hyperplasia in 6- to 12-month-old mice and nuclear features consistent with PTC in almost 2-year-old animals. After complete thyroidectomy and substitution with levothyroxine ( l -T 4 ), the preoperative, inadequately low T 4 and free T 4 remained, while increasing the l -T 4 dosage led to T 3 serum concentrations above the normal range. Conclusions Our results implicate peripheral deiodination in the peculiar hormonal constellation of MCT8 -deficient patients. Other MCT8 -deficient patients should be closely monitored for potential thyroid abnormalities.
Runge-Kutta time discretization of parabolic differential equations on evolving surfaces
2011-08-04

Journal Article Runge–Kutta time discretization of parabolic differential equations on evolving surfaces Get access G. Dziuk, G. Dziuk Abteilung für Angewandte Mathematik, University of Freiburg, Hermann-Herder-Strasse 10, D–79104 Freiburg im Breisgau, Germany Search for other works by this author on: Oxford Academic Google Scholar Ch. Lubich, Ch. Lubich * Mathematisches Institut, University of Tübingen, Auf der Morgenstelle 10, D–72076 Tübingen, Germany *Corresponding author: lubich@na.uni-tuebingen.de Search for other works by this author on: Oxford Academic Google Scholar D. Mansour D. Mansour Mathematisches Institut, University of Tübingen, Auf der Morgenstelle 10, D–72076 Tübingen, Germany Search for other works by this author on: Oxford Academic Google Scholar IMA Journal of Numerical Analysis, Volume 32, Issue 2, April 2012, Pages 394–416, https://doi.org/10.1093/imanum/drr017 Published: 04 August 2011 Article history Received: 11 November 2010 Revision received: 04 March 2011 Published: 04 August 2011
Variational approach to Yang-Mills theory at finite temperatures
2011-08-04

We study the finite-temperature phase of a gluon ensemble in a variational\\napproximation to QCD in the Coulomb gauge. We derive and numerically solve the\\nunderlying Dyson-Schwinger equations up to one-loop order. Assuming the\\nsubcritical solution at T=0, we find a sharp transition in the infrared value\\nof the gluon energy at a critical temperature.\\n
ProDGe: investigating protein-protein interactions at the domain level
2011-08-04

Abstract An important goal of systems biology is the identification and investigation of known and predicted protein-protein interactions to obtain more information about new cellular pathways and processes. Proteins interact via domains, thus it is important to know which domains a protein contains and which domains interact with each other. Here we present the Java^TM^ program ProDGe (Protein Domain Gene), which visualizes existing and suggests novel domain-domain interactions and protein-protein interactions at the domain level. The comprehensive dataset behind ProDGe consists of protein, domain and interaction information for both layers, collected and combined appropriately from UniProt, Pfam, DOMINE and IntAct. Based on known domain interactions, ProDGe suggests novel protein interactions and assigns them to four confidence classes, depending on the reliability of the underlying domain interaction. Furthermore, ProDGe is able to identify potential homologous interaction partners in other species, which is particularly helpful when investigating poorly annotated species. We further evaluated and compared experimentally identified protein interactions from IntAct with domain interactions from DOMINE for six species and noticed that 31.13% of all IntAct protein interactions in all six species can be mapped to the actual interacting domains. ProDGe and a comprehensive documentation are freely available at http://www.cogsys.cs.uni-tuebingen.de/software/ProDGe.
Regulation of Cathepsin G Reduces the Activation of Proinsulin-Reactive T Cells from Type 1 Diabetes Patients
2011-08-05

Autoantigenic peptides resulting from self-proteins such as proinsulin are important players in the development of type 1 diabetes mellitus (T1D). Self-proteins can be processed by cathepsins (Cats) within endocytic compartments and loaded to major histocompatibility complex (MHC) class II molecules for CD4(+) T cell inspection. However, the processing and presentation of proinsulin by antigen-presenting cells (APC) in humans is only partially understood. Here we demonstrate that the processing of proinsulin by B cell or myeloid dendritic cell (mDC1)-derived lysosomal cathepsins resulted in several proinsulin-derived intermediates. These intermediates were similar to those obtained using purified CatG and, to a lesser extent, CatD, S, and V in vitro. Some of these intermediates polarized T cell activation in peripheral blood mononuclear cells (PBMC) from T1D patients indicative for naturally processed T cell epitopes. Furthermore, CatG activity was found to be elevated in PBMC from T1D patients and abrogation of CatG activity resulted in functional inhibition of proinsulin-reactive T cells. Our data suggested the notion that CatG plays a critical role in proinsulin processing and is important in the activation process of diabetogenic T cells.
A Role for Central Nervous Growth Hormone-Releasing Hormone Signaling in the Consolidation of Declarative Memories
2011-08-05

Contributions of somatotropic hormonal activity to memory functions in humans, which are suggested by clinical observations, have not been systematically examined. With previous experiments precluding a direct effect of systemic growth hormone (GH) on acute memory formation, we assessed the role of central nervous somatotropic signaling in declarative memory consolidation. We examined the effect of intranasally administered growth hormone releasing-hormone (GHRH; 600 μg) that has direct access to the brain and suppresses endogenous GHRH via an ultra-short negative feedback loop. Twelve healthy young men learned word-pair associates at 2030 h and were administered GHRH and placebo, respectively, at 2100 h. Retrieval was tested after 11 hours of wakefulness. Compared to placebo, intranasal GHRH blunted GH release within 3 hours after substance administration and reduced the number of correctly recalled word-pairs by ∼12% (both P<0.05). The impairment of declarative memory consolidation was directly correlated to diminished GH concentrations (P<0.05). Procedural memory consolidation as examined by the parallel assessment of finger sequence tapping performance was not affected by GHRH administration. Our findings indicate that intranasal GHRH, by counteracting endogenous GHRH release, impairs hippocampal memory processing. They provide first evidence for a critical contribution of central nervous somatotropic activity to hippocampus-dependent memory consolidation.
Exploiting Prior Information in Stochastic Knowledge Assessment
2011-08-05

Various adaptive procedures for efficiently assessing the knowledge state of an individual have been developed within the theory of knowledge structures. These procedures set out to draw a detailed picture of an individual’s knowledge in a certain field by posing a minimal number of questions. While research so far mostly emphasized theoretical issues, the present paper focuses on an empirical evaluation of probabilistic assessment. It reports on simulation data showing that both efficiency and accuracy of the assessment exhibit considerable sensitivity to the choice of parameters and prior information as captured by the initial likelihood of the knowledge states. In order to deal with problems that arise from incorrect prior information, an extension of the probabilistic assessment is proposed. Systematic simulations provide evidence for the efficiency and robustness of the proposed extension, as well as its feasibility in terms of computational costs.
Evidence for PTEN-independent Akt activation and Akt-independent p27Kip1 expression in advanced bladder cancer
2011-08-05

In the treatment of advanced bladder cancer (BC), attention has recently focused on small molecule therapy concerning EGFR and the downstream Akt signalling pathway. Cellular deregulation processes are poorly understood, and biological determinants for the selection of therapy and monitoring are currently not available. The proteins PTEN, p-Akt and p27(Kip1) are suggested to be potentially significant biomarkers of Akt signalling. In this study, we investigated the expression of these proteins in advanced BC. PTEN, p-Akt and p27(Kip1) expression was determined immunohistochemically in 86 T2-4 BC specimens using a tissue microarray technique. Staining was documented with regard to intensity, cellular frequency and a multiplied staining score. Staining characteristics of the three proteins were correlated by regression analysis with the parameters of tumour stage and grade. A positive correlation was observed in the expression scores of PTEN and p-Akt, p-Akt and p27(Kip1) as well as PTEN and p27(Kip1) (p<0.02 for all combinations). The positive correlation between PTEN and p-Akt resulted mainly due to the strong correlation of PTEN intensity with p-Akt (p=0.0003 and p=0.0006 to p-Akt frequency and intensity, respectively). A positive correlation between p-Akt and p27(Kip1) was noted for p-Akt frequency as well as intensity (p<0.05 for all combinations). The positive correlation between PTEN and p27(Kip1) resulted due to the correlation of PTEN intensity alone with p27(Kip1) (p<0.03 for p27(Kip1) frequency and intensity), whereas no significance was noted for PTEN frequency. No correlation was found between T or G and expression of the proteins. However, activation of Akt in BC is known to occur independently of PTEN protein loss and appears not to cause a decrease of p27(Kip1). However, a direct regulatory impact of PTEN on p27(Kip1) was found. PTEN intensity, rather than frequency, appears to be a superior biomarker. These results may provide information to support research into protein profiling-predicted targeted therapy for BC. Correlations to benign urothelium, superficial BC specimens and follow-up data remain to be investigated.
When does regulation bite? Co-determination and nature of employment relations
2011-08-05

The German Codetermination Law grants workers of establishments with 200 or more employees the right to have a works councillor fully exempted from his regular job while still being paid his regular salary. We analyze theoretically and empirically how this de jure right to paid leave of absence translates into practice and explicitly take into account the nature of the industrial relations participation regime. We find the right of exemption to make no difference in cooperative employment relations, but to develop its bite in adversarial rela-tions, i.e. when – without legal enforcement – the legislator’s intent would not be realized.
Wet cloth simulation
2011-08-07

Both cloth and fluid simulation are important areas of research in Computer Graphics. However, only a surprisingly small amount of authors have investigated the two-way coupling of these simulations. Lenaerts et al. [2008] present a porous flow technique based on Darcy's law using a 3D particle simulation and apply their approach to textiles as well, however, their approach is computationally expensive and they use a rather simple cloth simulation system that cannot fully represent the complex effects of wet textiles. [Morimoto et al. 2007] present a technique that allows the visualization of dyeing based on diffusion terms. However, they do not consider their approach in a simulation context.
Septic arthritis of the knee: Presentation of a novel irrigation-suction system tested in a cadaver study
2011-08-07

Abstract Background The established treatment for bacterial arthritis of the knee joint is arthroscopic surgery with irrigation and debridement. The aim of this article is to summarize the relevant data in treating bacterial arthritis of the knee joint, and based on these findings to present a novel irrigation suction system, tested in a cadaver study, as an additional tool in the postoperative treatment phase of arthroscopic surgery for knee joint infections. Method The novel automated irrigation-suction system presented here was compared to conventional continuous suction irrigation in a total of six knee joints. All knee joints were filled with 80 ml methylene blue stain and rinsed by two different methods. Fluid specimens were taken after ten and twenty minutes to be compared by photometric extinction measurement at a wave length of 500 nm. Results After ten minutes, the average extinction was e 1C = 0.8 for the continuous suction irrigation and e 1N = 0.4 for the novel irrigation-suction system. After twenty minutes, we recorded an average extinction of e 2C = 0.3 for continuous suction irrigation and e 2N = 0.001 for the novel irrigation-suction system. The students t- test revealed superior results after ten and twenty minutes of washing out the knee joints with a p &lt; 0.001 for the novel irrigation-suction system. Conclusion A novel irrigation-suction system may be an effective tool for postoperative knee joint irrigation in arthroscopic therapy for bacterial arthritis of the knee. Further animal studies are needed to verify the effects in vivo.