julilili42/papers huggingface dataset:
Frequency and syndrome specificity of antibodies to aquaporin-4 in neurological patients with rheumatic disorders
2011-05-04

Background: A new autoantibody (termed NMO-IgG, or AQP4-Ab) has recently been described in patients with neuromyelitis optica (NMO) and its formes frustes, longitudinally extensive transverse myelitis (LETM) and recurrent optic neuritis (rON). However, AQP4-Ab has been found also in patients with co-existing rheumatic diseases such as systemic lupus erythematosus (SLE) or Sjögren’s syndrome (SS), conditions which are characterized by broad, polyspecific B cell activation. Objectives: In this study, we aimed at evaluating the syndrome specificity and frequency of AQP4-Ab in patients with rheumatic diseases and neurological symptoms. Methods: For this purpose, serum samples from 109 neurological patients with established connective tissue disorders (CTD) ( n = 54), possible CTD ( n = 42), or vasculitis ( n = 13) were analysed for the presence of AQP4-Ab by a cell-based assay employing recombinant human AQP4. Results: AQP4-Ab was detectable in 31/40 (78%) patients with CTD and NMO spectrum disorders (median titre, 1:1000) but in none of the samples obtained from patients with CTD or vasculitis and neurological disorders other than NMO, LETM, or rON ( n = 69). Conclusion: The high syndrome specificity of the antibody for neuromyelitis optica spectrum disorders (NMOSDs) in patients with CTD supports the concept of AQP4-Ab being involved in the pathogenesis of these neurological conditions, and argues against AQP4-Ab simply being part of the polyclonal B cell activation generally associated with rheumatic diseases. Moreover, the finding that AQP4-Ab is present in patients with CTD and co-existing NMOSD with approximately the same frequency as in patients without CTD strengthens the case of CTD and AQP4-Ab positive NMOSD representing two co-existing yet distinct entities in the majority of patients.
Intraperitoneal adhesions—an ongoing challenge between biomedical engineering and the life sciences
2011-05-04

Abstract Peritoneal adhesions remain a relevant clinical problem despite the currently available prophylactic barrier materials. So far, the physical separation of traumatized serosa areas using barriers represents the most important clinical strategy for adhesion prevention. However, the optimal material has not yet been found. Further optimization or pharmacological functionalization of these barriers could give an innovative input for peritoneal adhesion prevention. Therefore, a more complete understanding of pathogenesis is required. On the basis of the pathophysiology of adhesion formation the main barriers currently in clinical practice as well as new innovations are discussed in the present review. Physiologically, mesothelial cells play a decisive role in providing a frictionless gliding surface on the serosa. Adhesion formation results from a cascade of events and is regulated by a variety of cellular and humoral factors. The main clinically applied strategy for adhesion prevention is based on the use of liquid or solid adhesion barriers to separate physically any denuded tissue. Both animal and human trials have not yet been able to identify the optimal barrier to prevent adhesion formation in a sustainable way. Therefore, further developments are required for effective prevention of postoperative adhesion formation. To reach this goal the combination of structural modification and pharmacological functionalization of barrier materials should be addressed. Achieving this aim requires the interaction between basic research, materials science and clinical expertise. © 2011 Wiley Periodicals, Inc. J Biomed Mater Res Part A:, 2011.
Evolution of inclined planets in three-dimensional radiative\\n discs
2011-05-05

\\n Context. While planets in the solar system only have a low inclination\\n with respect to the ecliptic there is mounting evidence that in extrasolar systems the\\n inclination can be very high, at least for close-in planets. One process to alter the\\n inclination of a planet is through planet-disc interactions. Recent simulations\\n considering radiative transport have shown that the evolution of migration and\\n eccentricity can strongly depend on the thermodynamic state of the disc. So far, this\\n process has only been studied for a few selected planet masses using isothermal discs.\\n Aims. We extend previous studies to investigate the planet-disc\\n interactions of fixed and moving planets on inclined and eccentric orbits. We also analyse\\n the effect of the disc’s thermodynamic properties on the orbital evolution of embedded\\n planets in detail.\\n Methods. The protoplanetary disc is modelled as a viscous gas where the\\n internally produced dissipation is transported by radiation. To solve the equations we use\\n an explicit three-dimensional (3D) hydrodynamical code NIRVANA that includes full tensor\\n viscosity, as well as implicit radiation transport in the flux-limited diffusion\\n approximation. To speed up the simulations we apply the FARGO-algorithm in\\n a 3D context.\\n Results. For locally isothermal discs, we confirm previous results and\\n find inclination damping and inward migration for planetary cores. For low inclinations\\n (i ≲ 2H/r), the damping is\\n exponential, while it follows\\n di/dt ∝ i-2 for\\n larger i. For radiative discs, the planetary migration is very limited,\\n as long as their inclination exceeds a certain threshold. If the inclination is damped\\n below this threshold, planetary cores with a mass up to\\n ≈33 MEarth start to migrate outwards, while larger cores\\n migrate inwards right from the start. The inclination is damped for all analysed planet\\n masses. \\n Conclusions. In a viscous disc an initial inclination of embedded\\n planets will be damped for all planet masses. This damping occurs on timescales that are\\n shorter than the migration time. If the inclination lies beneath a certain threshold,\\n the outward migration in radiative discs is not handicapped. However, only planets with a\\n mass up to ≈33 MEarth are prone to this outward migration.\\n Outward migration is strongest for circular and non-inclined orbits.\\n
Methodological and ethical aspects of randomized controlled clinical trials in minors with malignant diseases
2011-05-05

Abstract Background Due to the new European regulations for pediatric medications, future clinical trials will include an increasing number of minors. It is therefore important to reconsider and evaluate recent methodological and ethical aspects of clinical trials in minors. Procedure The following questions were investigated: How are randomized controlled clinical trials (RCTs) performed in practice? Do investigators take into consideration biomedical ethical principles, explicated for example by Beauchamp and Childress, when planning and conducting a trial? The study was conducted in a descriptive manner. A systematic, algorithm‐guided search focusing on RCTs in minors with malignant diseases was carried out in PubMed. One‐thousand‐nine‐hundred‐sixty‐two publications from 2001 to 2005 were randomized in sequence. The first 1,000 publications were screened according to a priori defined inclusion criteria. One hundred seventy‐five publications met the criteria and were reviewed using the SIGN methodological checklist (2004), the CONSORT Statement (2001, section Methods, items 3–12) and indicators for ethical aspects. Seventeen publications were checked by two raters. Results Information on randomization and blinding was often equivocal. The publications were mainly rated positive for the criteria of the SIGN checklist, and mostly rated negative for the additional items of the CONSORT Statement. Regarding the ethical principles, only few contributions were found in the publications. Inter‐rater reliability was good. Conclusions In the publications analyzed, we found only limited information concerning methods and reflections on ethical principles of the trials. Improvements are thus necessary and possible. We suggest how such trials and their respective publications can be optimized for these aspects. Pediatr Blood Cancer 2011; 57: 599–605. © 2011 Wiley‐Liss, Inc.
Structures of the Major Capsid Proteins of the Human Karolinska Institutet and Washington University Polyomaviruses
2011-05-05

ABSTRACT The Karolinska Institutet and Washington University polyomaviruses (KIPyV and WUPyV, respectively) are recently discovered human viruses that infect the respiratory tract. Although they have not yet been linked to disease, they are prevalent in populations worldwide, with initial infection occurring in early childhood. Polyomavirus capsids consist of 72 pentamers of the major capsid protein viral protein 1 (VP1), which determines antigenicity and receptor specificity. The WUPyV and KIPyV VP1 proteins are distant in evolution from VP1 proteins of known structure such as simian virus 40 or murine polyomavirus. We present here the crystal structures of unassembled recombinant WUPyV and KIPyV VP1 pentamers at resolutions of 2.9 and 2.55 Å, respectively. The WUPyV and KIPyV VP1 core structures fold into the same β-sandwich that is a hallmark of all polyomavirus VP1 proteins crystallized to date. However, differences in sequence translate into profoundly different surface loop structures in KIPyV and WUPyV VP1 proteins. Such loop structures have not been observed for other polyomaviruses, and they provide initial clues about the possible interactions of these viruses with cell surface receptors.
Adjectival Conversion of Unaccusatives in German
2011-05-06

The paper presents an in-depth study of the conditions under which unaccusative verbs in German take part in the formation of so-called ADJECTIVAL PASSIVES. It provides corpus-linguistic as well as psycho-linguistic evidence arguing that combinations of sein ‘to be’ with the participle of an unaccusative verb are systematically ambiguous between a present perfect reading (with sein as auxiliary) and an adjectival reading (with sein as copula). The first part of the paper highlights the adjectival character of the construction in question. The second part presents the results of three rating studies that help unravel the pragmatic conditions that govern the adjectival conversion of unaccusatives. This leads to the conclusion that what has become known as the “adjectival passive” construction is a rather general, broadly available word formation process that is characteristically shaped and controlled by pragmatic factors. *
Lexicalized Non-Local MCTAG with Dominance Links is NP-Complete
2011-05-07

An NP-hardness proof for non-local Multicomponent Tree Adjoining Grammar (MCTAG) by Rambow and Satta (1st International Workshop on Tree Adjoining Grammers 1992), based on Dahlhaus and Warmuth (in J Comput Syst Sci 33:456–472, 1986), is extended to some linguistically relevant restrictions of that formalism. It is found that there are NP-hard grammars among non-local MCTAGs even if any or all of the following restrictions are imposed: (i) lexicalization: every tree in the grammar contains a terminal; (ii) dominance links: every tree set contains at most two trees, and in every such tree set, there is a link between the foot node of one tree and the root node of the other tree, indicating that the former node must dominate the latter in the derived tree. This is the version of MCTAG proposed in Becker et al. (Proceedings of the 5th conference of the European chapter of the Association for Computational Linguistics 1991) to account for German long-distance scrambling. This result restricts the field of possible candidates for an extension of Tree Adjoining Grammar that would be both mildly context-sensitive and linguistically adequate.
NRPSpredictor2—a web server for predicting NRPS adenylation domain specificity
2011-05-09

The products of many bacterial non-ribosomal peptide synthetases (NRPS) are highly important secondary metabolites, including vancomycin and other antibiotics. The ability to predict substrate specificity of newly detected NRPS Adenylation (A-) domains by genome sequencing efforts is of great importance to identify and annotate new gene clusters that produce secondary metabolites. Prediction of A-domain specificity based on the sequence alone can be achieved through sequence signatures or, more accurately, through machine learning methods. We present an improved predictor, based on previous work (NRPSpredictor), that predicts A-domain specificity using Support Vector Machines on four hierarchical levels, ranging from gross physicochemical properties of an A-domain's substrates down to single amino acid substrates. The three more general levels are predicted with an F-measure better than 0.89 and the most detailed level with an average F-measure of 0.80. We also modeled the applicability domain of our predictor to estimate for new A-domains whether they lie in the applicability domain. Finally, since there are also NRPS that play an important role in natural products chemistry of fungi, such as peptaibols and cephalosporins, we added a predictor for fungal A-domains, which predicts gross physicochemical properties with an F-measure of 0.84. The service is available at http://nrps.informatik.uni-tuebingen.de/.
Impact of structural imperfections on the energy-level alignment in organic films
2011-05-09

This paper reports that structural imperfection in an organic thin film modulates the electronic structure to result in a serious band bending and change in the energy-level alignment (ELA) at the organic-conductor interface. Ultraviolet photoelectron spectroscopy (UPS) and metastable atom electron spectroscopy (MAES) were adopted to investigate thickness dependences of the electronic structure of polar phthalocyanine (chlorogallium phthalocyanine) thin films grown on graphite with respect to the film structure. We observed a large band-bending-like shift of occupied molecular-orbital bands toward the Fermi level and a continuous increase in the vacuum level for the as-grown film, whereas these phenomena were considerably suppressed by annealing the film. Both the as-grown and annealed films were characterized as essentially the same stacked bilayer film structure; however, high-resolution UPS and MAES measurements evidenced that there are structural defects in the as-grown film but not clearly in the annealed film, indicating that the defects are the origin of the modulation of the ELA and the band bending. Controlling the structural imperfections is a key issue for the desired ELA in organic devices.
A new SNR with TeV shell-type morphology: HESS J1731-347
2011-05-10

Aims: The recent discovery of the radio shell-type supernova remnant (SNR), G353.6-0.7, in spatial coincidence with the unidentified TeV source HESS J1731−347 has motivated further observations of the source with the High Energy Stereoscopic System (HESS) Cherenkov telescope array to test a possible association of the γ-ray emission with the SNR. Methods: With a total of 59 h of observation, representing about four times the initial exposure available in the discovery paper of HESS J1731−347, the γ-ray morphology is investigated and compared with the radio morphology. An estimate of the distance is derived by comparing the interstellar absorption derived from X-rays and the one obtained from 12CO and HI observations. Results: The deeper γ-ray observation of the source has revealed a large shell-type structure with similar position and extension (r ~ 0.25°) as the radio SNR, thus confirming their association. By accounting for the HESS angular resolution and projection effects within a simple shell model, the radial profile is compatible with a thin, spatially unresolved, rim. Together with RX J1713.7−3946, RX J0852.0−4622 and SN 1006, HESS J1731−347 is now the fourth SNR with a significant shell morphology at TeV energies. The derived lower limit on the distance of the SNR of 3.2 kpc is used together with radio and X-ray data to discuss the possible origin of the γ-ray emission, either via inverse Compton scattering of electrons or the decay of neutral pions resulting from proton-proton interaction.
Population Structure of Staphylococcus aureus from Remote African Babongo Pygmies
2011-05-10

The high prevalence of PVL-positive isolates among Babongo Pygmies demands our attention as PVL can be associated with necrotinzing infection and may increase the risk of severe infections in remote Pygmy populations. Many S. aureus isolates from Babongo Pygmies and pandemic CA-MRSA-clones have a common genetic background. Surveillance is needed to control the development of resistance to antibiotic drugs and to assess the impact of the high prevalence of PVL in indigenous populations.
Structural and Conformational Analysis of Proanthocyanidins from Parapiptadenia rigida and Their Wound-Healing Properties
2011-05-10

Structure elucidation and conformation analysis of four proanthocyanidins isolated from the bark of Parapiptadenia rigida were performed by two-dimensional NMR spectroscopy, HRESIMS, CD, and molecular mechanics (MM+) force field calculations. The known prodelphinidin, epigallocatechin-(4β→8)-epigallocatechin-3-O-gallate (1) was accompanied by the new epigallocatechin-(4β→8)-4'-O-methylgallocatechin (2), epicatechin-(4β→8)-4'-O-methylgallocatechin (3), and (4α→8)-bis-4'-O-methylgallocatechin (4). Compound 4 was previously published but the earlier structure must presumably be revised to 4'-O-methylgallocatechin-(4α→8)-4'-O-methylepigallocatechin. Conformational studies showed the compact rotamer with B and E rings in quasi-equatorial orientations as the preferred conformation for compounds 1-3, whereas 4 consists of two stable rotamers, each with a quasi-equatorial orientation of ring B and E, respectively. The isolated compounds were studied for their wound-healing effects in a scratch assay and showed promising results.
Thermal Imaging as a Noninvasive Diagnostic Tool for Anterior Knee Pain Following Implantation of Artificial Knee Joints
2011-05-10

The variety of radiographic diagnostics used to diagnose pain localised close to metal implants is still limited.Especially magnetic resonance results can not be analysed because of artefacts.In this article we present for the first time a direct correlation between an increase in skin temperature and existent frontal (anterior) knee pain after implantation of artificial knee joints measured with thermography.In a standardised way 26 knees were analysed.Thermographic photos were taken from frontal, inner (medial) and outer (lateral) directions with a computer-assisted infrared thermograph.Temperatures in locations with pain were significantly higher compared to the reference field in inner location (median 0.95 °C, p=0.0043), as well as in outer location (median 0.5 °C, p=0.032).Median temperature difference between pain localization and localizations without pain was 0.7 °C and ranged from 0.1 °C to 1.7 °C.In the receiver operating characteristic (ROC) analysis the sensitivity of this method was 1.0 and specificity was 0.917.The evidence of a significant increase in skin temperature on the painful sites opens up the possibility to localize and assess pain more precisely in patients with joint prosthesis.We consider this novel, rapid, inexpensive and non-invasive technology to posses the potential to become a useful and objective tool for diagnosis of pain and inflammation and to generate digital data that can be stored and analysed in clinical practice.
Molecular Markers in Low-Grade Gliomas: Predictive or Prognostic?
2011-05-11

Abstract Purpose: To investigate whether TP53 mutation, 1p/19q codeletions, O6-methylguanylmethyltransferase (MGMT) promoter methylation, and isocitrate dehydrogenase 1 (IDH1) mutation predict natural course of disease or response to radiotherapy or chemotherapy or both in low-grade glioma patients. Experimental Design: Cohort A consisted of 89 patients with diffuse astrocytoma World Health Organization (WHO) grade II (n = 40), oligoastrocytoma (n = 23), or oligodendroglioma (n = 26) who did not receive radiotherapy or chemotherapy after first operation and were monitored until progression [progressive disease (PD); n = 59] and beyond or until the end of follow-up (n = 30). Cohort B consisted of 50 patients with WHO grade II gliomas who received radiotherapy or chemotherapy at diagnosis. Tumors were analyzed for TP53 mutations, 1p/19q codeletions, MGMT promoter methylation, and IDH1 mutations. Results: Median progression-free survival (PFS) in cohort A was 4.1 years (95% CI: 3.1–5.1). No molecular marker was prognostic for PFS after surgery alone, using multivariate adjustment for histology, age, and extent of resection. IDH1 mutations were associated with prolonged survival from the diagnosis of PD in oligoastrocytomas (OA II)/oligodendrogliomas (O II) and with overall survival (OS) in all tumors. 1p/19q codeletion and IDH1 mutation were prognostic for PFS and OS in cohort B. Conclusions: None of the parameters are sensitive prognostic biomarkers in WHO grade II glioma patients who do not receive radiotherapy or chemotherapy after surgery. Limitations of this study include the selection of patients with favorable outcome, the nonrandomized allocation of treatment, and the insufficient sample size to distinguish between effects of radiotherapy versus chemotherapy. Regardless of histology, IDH1 mutation status is the strongest prognostic marker for OS. Clin Cancer Res; 17(13); 4588–99. ©2011 AACR.
Prefrontal Brain Activation During Emotional Processing: A Functional Near Infrared Spectroscopy Study (fNIRS)
2011-05-11

The limbic system and especially the amygdala have been identified as key structures in emotion induction and regulation. Recently research has additionally focused on the influence of prefrontal areas on emotion processing in the limbic system and the amygdala. Results from fMRI studies indicate that the prefrontal cortex (PFC) is involved not only in emotion induction but also in emotion regulation. However, studies using fNIRS only report prefrontal brain activation during emotion induction. So far it lacks the attempt to compare emotion induction and emotion regulation with regard to prefrontal activation measured with fNIRS, to exclude the possibility that the reported prefrontal brain activation in fNIRS studies are mainly caused by automatic emotion regulation processes. Therefore this work tried to distinguish emotion induction from regulation via fNIRS of the prefrontal cortex. 20 healthy women viewed neutral pictures as a baseline condition, fearful pictures as induction condition and reappraised fearful pictures as regulation condition in randomized order. As predicted, the view-fearful condition led to higher arousal ratings than the view-neutral condition with the reappraise-fearful condition in between. For the fNIRS results the induction condition showed an activation of the bilateral PFC compared to the baseline condition (viewing neutral). The regulation condition showed an activation only of the left PFC compared to the baseline condition, although the direct comparison between induction and regulation condition revealed no significant difference in brain activation. Therefore our study underscores the results of previous fNIRS studies showing prefrontal brain activation during emotion induction and rejects the hypothesis that this prefrontal brain activation might only be a result of automatic emotion regulation processes.
The Insulin-Mediated Modulation of Visually Evoked Magnetic Fields Is Reduced in Obese Subjects
2011-05-11

We demonstrated that intranasal insulin increases the cerebral processing of food pictures in lean whereas this was absent in obese subjects. This study further substantiates the presence of a "cerebral insulin resistance" in obese subjects and might be relevant in the pathogenesis of obesity.