julilili42/papers huggingface dataset:
Embryonal rhabdomyosarcoma with metastases confined to the lungs: Report from the CWS Study Group
2010-11-08

Abstract Background Embryonal rhabdomyosarcoma [RME] is the most common pediatric soft tissue sarcoma. Whereas the prognosis of localized rhabdomyosarcoma has improved, it remains poor for metastatic disease. Methods We analyzed RME‐patients with isolated pulmonary metastases [PRME] treated in four consecutive CWS‐trials. Treatment included multiagent chemotherapy and local treatment of the primary tumor. Therapy of lung metastases after induction chemotherapy depended on response and individual decisions. Results Twenty‐nine patients &lt;21 years had PRME. Their median age was six years, the median follow‐up nine years. Twenty‐eight children had their primary tumor located in an unfavorable site and 22 of the primaries were &gt;5 cm. In addition to conventional chemotherapy, seven patients received high‐dose treatment and eight patients oral metronomic chemotherapy. The lung metastases were in remission after induction chemotherapy in 22 individuals. 19 patients received no local treatment of metastases; 3 patients had pulmonary metastasectomy and lung radiation was administered to 9 individuals. In total, 24/29 patients achieved a complete remission [CR]. Actuarial 5‐year event‐free and overall survival for all patients was 37.9 ± 18% and 48.7 ± 18%, respectively; it was 45.8 ± 20% and 58.3 ± 20% for the 24 patients who achieved a CR. Local treatment of metastases had no impact on the failure pattern. Younger age, good response, achievement of CR and maintenance‐treatment were favorable prognostic factors in univariate analysis. Conclusions Children with PRME have a fair prognosis. Local treatment of metastases did not improve outcome in our sample. Metronomic treatment may be an attractive option for PREM‐patients. [correction made here after initial online publication]. Pediatr Blood Cancer 2011;56:725–732. © 2010 Wiley‐Liss, Inc.
Acquired coagulopathy caused by intoxication with the superwarfarin-type anticoagulant rodenticide flocoumafen
2010-11-08

A 28 year-old heretofore healthy woman was transferred to our hospital with a two-month history of recurring episodes of bleeding. Administration of vitamin K and prothrombin complex concentrates in the transferring hospital had only temporarily corrected both the markedly elevated international normalized ratio (INR) and the prolonged activated partial thromboplastin time (aPTT). The patient's medical and family history revealed no reason for these abnormalities. Our laboratory analyses revealed a sustained deficiency of vitamin K-dependent clotting factors. Presence of an acquired inhibitor of clotting factors was excluded. Thus we suspected, intoxication with an anticoagulant rodenticide. Liquid chromatography-mass spectrometry (LC-MS/MS) revealed pharmacologically active concentrations of flocoumafen, a rodenticide belonging to the superwarfarin family, in the patient's serum. While the long elimination half-life of superwarfarins is well described in rodents, information on pharmacokinetics in humans is not yet available. Therefore, patient management was not limited to prolonged administration of vitamin K, but also included repeated measurements of flocoumafen serum levels. During follow-up visits, clotting tests remained normal and flocoumafen levels gradually decreased, reaching the limit of quantification after 48 days. Based on the repeated measurements of flocoumafen serum levels, a half-life of 6.7 days was estimated in our patient, which is in clear contrast to the 220 days reported in rodents. Thus, monitoring flocoumafen serum concentrations in affected patients may provide a rational basis for the duration of vitamin K substitution and adequate follow-up intervals.
Radiative properties of highly magnetized isolated neutron star surfaces and approximate treatment of absorption features in their spectra
2010-11-09

\\n Context. In the X-ray spectra of most X-ray dim isolated neutron stars (XDINSs), absorption features with equivalent widths (EWs) of 50–200 eV are observed. These features are usually connected with the proton cyclotron line, but their nature is not yet well known. \\n Aims. We theoretically investigate different models to explain these absorption features and compare their properties with observations to obtain a clearer understanding of the radiation properties of magnetized neutron star surfaces. Based on these models, we create a fast and flexible code to fit observed spectra of isolated neutron stars. \\n Methods. We consider various theoretical models of the magnetized neutron star surface, including naked condensed iron surfaces and partially ionized hydrogen model atmospheres, with semi-infinite and thin atmospheres above a condensed surface. Spectra of condensed iron surfaces are represented by a simple analytical approximation. The condensed surface radiation properties are considered as the inner atmosphere boundary condition for the thin atmosphere. The properties of the absorption features (especially equivalent widths) and the angular distributions of the emergent radiation are described for all models. A code for computing light curves and integral emergent spectra of magnetized neutron stars is developed. We assume a dipole surface magnetic field distribution with a possible toroidal component and corresponding temperature distribution. A model with two uniform hot spots at the magnetic poles may also be employed. \\n Results. Light curves and spectra of highly magnetized neutron stars with parameters typical of XDINSs are computed using different surface temperature distributions and various local surface models. Spectra of magnetized model atmospheres are approximated by diluted black-body spectra with one or two Gaussian lines having parameters, which allow us to describe the model absorption features. The EWs of the absorption features in the integral spectra cannot significantly exceed 100 eV, if a local surface model assumes either a semi-infinite magnetic atmosphere or a naked condensed surface. A thin atmosphere above a condensed surface can have an absorption feature whose EW exceeds 200 eV in the integrated spectrum. If the toroidal component of the magnetic field on the neutron star atmosphere is 3–7 times higher than the poloidal component, the absorption feature in the integral spectrum is too wide and shallow to be detectable.\\n Conclusions. To explain the prominent absorption features in the soft X-ray spectra of XDINSs, we infer that a thin atmosphere above the condensed surface must be present, whereas a strong toroidal magnetic field component on the XDINS surfaces can be excluded. \\n
Arthroscopic Treatment of Osteochondral Lesions of the Ankle With Matrix-Associated Chondrocyte Implantation
2010-11-10

Background: Conventional autologous chondrocyte transplantation in the ankle often requires tibial or fibular osteotomies with potential morbidity for the patient. Advances in biotechnology and surgical techniques have resulted in the development of matrix-associated chondrocyte implantation (MACI). As the chondrocyte-loaded scaffold can be applied arthroscopically, this procedure is especially useful for the treatment of osteochondral defects in the ankle. Hypothesis: Arthroscopic MACI is a safe procedure in the ankle with good clinical and magnetic resonance imaging results. Study Design: Case series; Level of evidence, 4. Methods: The authors reviewed all patients (n = 18) who had arthroscopic MACI for osteochondral lesions of the ankle (n = 19) between February 2006 and May 2008 clinically and with magnetic resonance imaging. The pain and disability module of the Foot Function Index (FFI), the American Orthopaedic Foot &amp; Ankle Society (AOFAS) clinical rating system, the Core Scale of the Foot and Ankle Module of the American Academy of Orthopaedic Surgeons (AAOS) Lower Limb Outcomes Assessment Instruments, and the Magnetic Resonance Observation of Cartilage Repair Tissue (MOCART) score were used. The clinical results up to 3 years after MACI (mean follow-up, 24.5 months) were compared with preoperative data for 14 cases and the magnetic resonance imaging data for all 19. Results: A significant improvement (50.3% ± 13.2%) in all clinical scores was noted (FFI pain before MACI: 5.5 ± 2.0, after MACI: 2.8 ± 2.2; FFI disability before MACI: 5.0 ± 2.3, after MACI: 2.6 ± 2.2; AOFAS before MACI: 58.6 ± 16.1, after MACI: 80.4 ± 14.1; AAOS standardized mean before MACI: 59.9 ± 16.0, after MACI: 83.5 ± 13.2; AAOS normative score before MACI: 23.0 ± 13.0, after MACI: 42.2 ± 10.7). According to the AOFAS Hindfoot score, 64% were rated as excellent and good, whereas 36% were rated fair and poor. The results correlated with the age of the patient and the duration of symptoms, but not with the size of the lesion. Sixteen patients (89%) reported regular sports activities before the onset of symptoms; 13 of them (81%) returned to sports after the MACI, 56% (n = 9) to the same level. The mean MOCART score was 62.4 ± 15.8 points. In general, there was no relation between MOCART score and clinical outcome, although the filling of the defect showed some correlation with the AAOS score. Conclusion: Arthroscopic MACI is a safe procedure for the treatment of osteochondral lesions in the ankle with overall good clinical and magnetic resonance imaging results.
External quality assurance of circulating tumor cell enumeration using the CellSearch® system: A feasibility study
2010-11-10

Abstract Background: Circulating tumor cells (CTCs) are cells that have detached from solid tumors and entered the blood. CTCs can be detected, among others, by semi‐automated immunomagnetic enrichment and image cytometry using CellSearch® (Veridex, Raritan, NJ). We studied the feasibility of external quality assurance (EQA) of the entire CellSearch procedure from blood draw to interpretation of results in multiple laboratories. Methods: Blood samples from six cancer patients and controls were distributed to 14 independent laboratories to test between‐laboratory, between‐assay, and between‐instrument variation. Additionally, between‐operator variability was assessed through the interpretation of blinded images of all blood samples on a website. Results: Shipment and storage of samples had no influence on CTC values. Between‐instrument (coefficient of variation (CV) &lt; 12%) and between‐assay variation was low (CV ≤ 20%), indicating high reproducibility. However, between‐laboratory CV ranged from 45 to 64%. Although inter‐operator agreement on image interpretation (Fleiss' κ statistics) ranged from “substantial” to “almost perfect,” image interpretation, particularly of samples containing high numbers of apoptotic cells, was the main contributor to between‐laboratory variation. Conclusions: This multicenter study shows the feasibility of an EQA program for CTC detection in patient samples, and the importance of continuation of such a program for the harmonization of CTC enumeration. © 2010 International International Clinical Cytometry Society
High Fill Factor and Open Circuit Voltage in Organic Photovoltaic Cells with Diindenoperylene as Donor Material
2010-11-11

Abstract Small‐molecule photovoltaic cells using diindenoperylene (DIP) as a new donor material in combination with the fullerene C 60 as an electron acceptor are demonstrated. In addition to the successful application in planar and bulk heterojunction devices, a comprehensive analysis including structural studies, the determination of the energy level alignment and electrical transport investigations is given, stressing the correlation between growth conditions, film morphology, and device performance. Due to pronounced crystallinity and a large surface area of DIP films grown at elevated temperature, exceptionally high fill factors of almost 75% are achieved in planar heterojunction cells. Bulk heterojunctions exhibit large‐scale phase separation forming a bicontinuous network of both molecular species, which enables efficient exciton dissociation and charge carrier transport. The high ionization potential of DIP and the favorable energy level alignment with the fullerene C 60 yield large open circuit voltages close to 1 V and comparable power conversion efficiencies of about 4% in both cell architectures.
Specificity and rate of human and mouse liver and plasma phosphatidylcholine synthesis analyzed in vivo
2010-11-11

Phosphatidylcholine (PC) synthesis by the direct cytidine diphosphate choline (CDP-choline) pathway in rat liver generates predominantly mono- and di-unsaturated molecular species, while polyunsaturated PC species are synthesized largely by the phosphatidylethanolamine-N-methyltransferase (PEMT) pathway. Although altered PC synthesis has been suggested to contribute to development of hepatocarcinoma and nonalcoholic steatohepatitis, analysis of the specificity of hepatic PC metabolism in human patients has been limited by the lack of sensitive and safe methodologies. Here we incorporated a deuterated methyl-D(9)-labled choline chloride, to quantify biosynthesis fluxes through both of the PC synthetic pathways in vivo in human volunteers and compared these fluxes with those in mice. Rates and molecular specificities of label incorporated into mouse liver and plasma PC were very similar and strongly suggest that label incorporation into human plasma PC can provide a direct measure of hepatic PC synthesis in human subjects. Importantly, we demonstrate for the first time that the PEMT pathway in human liver is selective for polyunsaturated PC species, especially those containing docosahexaenoic acid. Finally, we present a multiple isotopomer distribution analysis approach, based on transfer of deuterated methyl groups to S-adenosylmethionine and subsequent sequential methylations of PE, to quantify absolute flux rates through the PEMT pathway that are applicable to studies of liver dysfunction in clinical studies.
Human Neurocysticercosis: Comparison of Different Diagnostic Tests Using Cerebrospinal Fluid
2010-11-11

ABSTRACT Neurocysticercosis (NC), caused by the larval stage of Taenia solium , is one of the most common parasitic diseases of the central nervous system. The diagnosis of NC is mostly based on costly brain neuroimaging (computed tomography and/or nuclear magnetic resonance), which is rarely accessible in most affected areas. The most sensitive and specific tools for NC diagnosis are imagery techniques. The identification of specific antibodies and antigens is currently used only to support NC diagnosis due to their limited specificity and sensitivity. This study was performed to compare immunodiagnostic assays (antibody detection by enzyme-linked immunosorbent assay [ELISA] and enzyme-linked immunoelectrotransfer blotting [EITB] and HP10 antigen detection by ELISA) with the detection of parasite DNA by PCR amplification of a repetitive element of the parasite genome in the cerebrospinal fluid (CSF) of 121 radiologically and clinically characterized NC patients. Patients were divided into six groups according to the stage of the parasites and their localization. The CSF cellularity of each patient was also recorded. When all patients were considered, PCR exhibited the highest sensitivity (95.9%) and variable specificity (80% or 100%) depending on the controls used. The sensitivities of antibody detection by ELISA and EITB were not significantly different, and ELISA identified HP10 antigen mostly when vesicular cysticerci were located in the subarachnoideal basal cisterns. These results can help in the selection of different individual assays or combinations of assays to be used in NC diagnosis according to different requirements.
ChemInform Abstract: Reduction of Dipyrido Ureas via 6‐Alkyloxydipyrido[1,2‐c;2′,1′‐e]imidazolium Salts.
2010-11-11

Abstract Reduction of dipyrido uronium salts (VI), which are readily synthesized by alkylation of dipyrido ureas (IV) with Meerwein′s reagent, offers a new and mild synthetic route to dipyridoimidazolium salts (VII).
Contributions of different neutron pairs in different approaches for neutrinoless double-beta decay
2010-11-12

The methods used till now to calculate the neutrinoless double beta decay\\nmatrix elements are: the Quasiparticle Random Phase Approximation (QRPA), the\\nShell Model (SM), the angular momentum projected Hartee-Fock-Bogoliubov\\napproach (HFB) and the Interacting Boson Model (IBM). The different approaches\\nare compared specifically concerning the the angular momenta and parities of\\nthe neutron pairs, which are changed into two protons by the \\ndecay. The QRPA and SM involve about the same angular momentum and parity\\nneutron pairs, while the HFB is restricted to , and\\nIBM to and nucleon pairs. The differences in the seniority\\ncontributions for the QRPA and the SM are discussed.\\n
A Survey of Combinatorial Methods for Phylogenetic Networks
2010-11-15

The evolutionary history of a set of species is usually described by a rooted phylogenetic tree. Although it is generally undisputed that bifurcating speciation events and descent with modifications are major forces of evolution, there is a growing belief that reticulate events also have a role to play. Phylogenetic networks provide an alternative to phylogenetic trees and may be more suitable for data sets where evolution involves significant amounts of reticulate events, such as hybridization, horizontal gene transfer, or recombination. In this article, we give an introduction to the topic of phylogenetic networks, very briefly describing the fundamental concepts and summarizing some of the most important combinatorial methods that are available for their computation.
Magnetohydrodynamics of superfluid and superconducting neutron star cores
2010-11-15

Mature neutron stars are cold enough to contain a number of superfluid and\\nsuperconducting components. These systems are distinguished by the presence of\\nadditional dynamical degrees of freedom associated with superfluidity. In order\\nto consider models with mixtures of condensates we need to develop a multifluid\\ndescription that accounts for the presence of rotational neutron vortices and\\nmagnetic proton fluxtubes. We also need to model the forces that impede the\\nmotion of vortices and fluxtubes, and understand how these forces act on the\\ncondensates. This paper concerns the development of such a model for the outer\\ncore of a neutron star, where superfluid neutrons co-exist with a type II\\nproton superconductor and an electron gas. We discuss the hydrodynamics of this\\nsystem, focusing on the role of the entrainment effect, the magnetic field, the\\nvortex/fluxtube tension and the dissipative mutual friction forces. Out final\\nresults can be directly applied to a number of interesting astrophysical\\nscenarios, e.g. associated with neutron star oscillations or the evolution of\\nthe large scale magnetic field.\\n
Minimal information about T cell assays: the process of reaching the community of T cell immunologists in cancer and beyond
2010-11-15

Many assays to evaluate the nature, breadth, and quality of antigen-specific T cell responses are currently applied in human medicine. In most cases, assay-related protocols are developed on an individual laboratory basis, resulting in a large number of different protocols being applied worldwide. Together with the inherent complexity of cellular assays, this leads to unnecessary limitations in the ability to compare results generated across institutions. Over the past few years a number of critical assay parameters have been identified which influence test performance irrespective of protocol, material, and reagents used. Describing these critical factors as an integral part of any published report will both facilitate the comparison of data generated across institutions and lead to improvements in the assays themselves. To this end, the Minimal Information About T Cell Assays (MIATA) project was initiated. The objective of MIATA is to achieve a broad consensus on which T cell assay parameters should be reported in scientific publications and to propose a mechanism for reporting these in a systematic manner. To add maximum value for the scientific community, a step-wise, open, and field-spanning approach has been taken to achieve technical precision, user-friendliness, adequate incorporation of concerns, and high acceptance among peers. Here, we describe the past, present, and future perspectives of the MIATA project. We suggest that the approach taken can be generically applied to projects in which a broad consensus has to be reached among scientists working in fragmented fields, such as immunology. An additional objective of this undertaking is to engage the broader scientific community to comment on MIATA and to become an active participant in the project.
Orbital evolution of eccentric planets in radiative discs
2010-11-15

\\n Context. With an average eccentricity of about 0.29, the eccentricity distribution of extrasolar planets is markedly different from the solar system. Among other scenarios considered, it has been proposed that eccentricity may grow through planet-disc interaction. Recently, it has been noticed that the thermodynamical state of the disc can significantly influence the migration properties of growing protoplanets. However, the evolution of planetary eccentricity in radiative discs has not been considered yet. \\n Aims. In this paper we study the evolution of planets on eccentric orbits that are embedded in a three-dimensional viscous disc and analyse the disc’s effect on the orbital evolution of the planet. \\n Methods. We use the three-dimensional hydrodynamical code NIRVANA that includes full tensor viscosity and implicit radiation transport in the flux-limited diffusion approximation. The code uses the FARGO-algorithm to speed up the simulations. First we measure the torque and power exerted on the planet by the disc for fixed orbits, and then we let the planet start with initial eccentricity and evolve it in the disc. \\n Results. For locally isothermal discs we confirm previous results and find eccentricity damping and inward migration for planetary cores. For low eccentricity (e ≲ 2H/r) the damping is exponential, while for higher e it follows ė ∝ e-2. In the case of radiative discs, the planets experience an inward migration as long as its eccentricity lies above a certain threshold. After the damping of eccentricity cores with masses below 33 MEarth begin to migrate outward in radiative discs, while higher mass cores always migrate inward. For all planetary masses studied (up to 200 MEarth) we find eccentricity damping.\\n Conclusions. In viscous discs the orbital eccentricity of embedded planets is damped during the evolution independent of the mass. Hence, planet-disc interaction does not seem to be a viable mechanism to explain the observed high eccentricity of exoplanets. \\n
Interaction between Cobalt Phthalocyanine and Gold Studied by X-ray Absorption and Resonant Photoemission Spectroscopy
2010-11-15

Cobalt phthalocyanine (CoPc) monolayer films evaporated on Au(100) are studied by photoexcited electron spectroscopies: X-ray absorption (XAS) and resonant photoemission spectroscopy (ResPES). According to XAS data, the Co 2p absorption spectra look different for monolayer and thicker organic films, pointing to a possible interaction of the molecules with the substrate via the Co d electrons. The contribution of Co-related states in the valence band of CoPc was observed with ResPES. The conclusions are discussed in combination with core-level X-ray photoemission spectroscopy (XPS), X-ray excited Auger electron spectroscopy (XAES), and valence band ultraviolet photoemission spectroscopy (UPS) results previously obtained.