1,521 research outputs found

    From data to analysis: linking NWChem and Avogadro with the syntax and semantics of Chemical Markup Language

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    Background: Multidisciplinary integrated research requires the ability to couple the diverse sets of data obtained from a range of complex experiments and computer simulations. Integrating data requires semantically rich information. In this paper an end-to-end use of semantically rich data in computational chemistry is demonstrated utilizing the Chemical Markup Language (CML) framework. Semantically rich data is generated by the NWChem computational chemistry software with the FoX library and utilized by the Avogadro molecular editor for analysis and visualization. Results: The NWChem computational chemistry software has been modified and coupled to the FoX library to write CML compliant XML data files. The FoX library was expanded to represent the lexical input files and molecular orbitals used by the computational chemistry software. Draft dictionary entries and a format for molecular orbitals within CML CompChem were developed. The Avogadro application was extended to read in CML data, and display molecular geometry and electronic structure in the GUI allowing for an end-to-end solution where Avogadro can create input structures, generate input files, NWChem can run the calculation and Avogadro can then read in and analyse the CML output produced. The developments outlined in this paper will be made available in future releases of NWChem, FoX, and Avogadro. Conclusions: The production of CML compliant XML files for computational chemistry software such as NWChem can be accomplished relatively easily using the FoX library. The CML data can be read in by a newly developed reader in Avogadro and analysed or visualized in various ways. A community-based effort is needed to further develop the CML CompChem convention and dictionary. This will enable the long-term goal of allowing a researcher to run simple "Google-style" searches of chemistry and physics and have the results of computational calculations returned in a comprehensible form alongside articles from the published literature

    Three-body decay of the d* dibaryon

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    Under certain circumstances, a three-body decay width can be approximated by an integral involving a product of two off-shell two-body decay widths. This ``angle-average'' approximation is used to calculate the πNN\pi NN decay width of the d(Jπ=3+,T=0)d^*(J^\pi=3^+, T=0) dibaryon in a simple Δ2\Delta^2 model for the most important Feynman diagrams describing pion emissions with baryon-baryon recoil and meson retardation. The decay width is found to be about 0.006 (0.07, 0.5) MeV at the dd^* mass of 2065 (2100, 2150) MeV for input dynamics derived from the Full Bonn potential. The smallness of this width is qualitatively understood as the result of the three-body decay being ``third forbidden''. The concept of \ell forbiddenness and the threshold behavior of a three-body decay are further studied in connection with the πNN\pi NN decay of the dibaryon d(Jπ=0,T=0or2)d'(J^\pi=0^-, T=0 or 2) where the idea of unfavorness has to be introduced. The implications of these results are briefly discussed.Comment: 15 pages, RevTeX, two-column journal style, six figure

    Tailored or Routine Addition of an Antireflux Fundoplication in Laparoscopic Large Hiatal Hernia Repair: A Comparative Cohort Study

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    Contains fulltext : 98394.pdf (publisher's version ) (Open Access)BACKGROUND: There is controversy about the tailored or routine addition of an antireflux fundoplication in large hiatal hernia (type II-IV) repair. We investigated the strategy of selective addition of a fundoplication in patients with a large hiatal hernia and concomitant gastroesophageal reflux disease. METHODS: Between 2002 and 2008, 60 patients with a large hiatal hernia were evaluated preoperatively and 12 months after surgery by reflux-related symptoms, upper endoscopy, and esophageal 24-h pH monitoring. In patients with preoperatively documented gastroesophageal reflux disease, an antireflux fundoplication was added during hiatal hernia repair. RESULTS: An antireflux procedure was added in 35 patients and 25 patients underwent hiatal hernia repair only. Preoperative symptoms were improved or resolved in 31 patients (88.6%) in the group who had fundoplication and in 20 patients (87.0%) in the group who did not have fundoplication. In patients with fundoplication, esophagitis was present in 6 patients (22.2%) after surgery and abnormal esophageal acid exposure persisted in 11 (39.3%). Seven patients (38.9%) with hernia repair only developed abnormal esophageal acid exposure, and esophagitis was postoperatively generated in five (27.8%). In neither group did patients have new onset of daily heartburn or dysphagia. CONCLUSIONS: In patients with a large hiatal hernia associated with gastroesophageal reflux disease, addition of a fundoplication during hernia repair yields acceptable reduction of symptoms and does not generate symptomatic side effects. Objective control of reflux, however, is only moderate. Omission of an antireflux procedure in the absence of gastroesophageal reflux disease induced esophagitis in 28% and abnormal esophageal acid exposure in 39% of patients. Therefore, routine addition of an antireflux fundoplication should be recommended

    Dose-response effect of Gelofusine on renal uptake and retention of radiolabelled octreotate in rats with CA20948 tumours

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    Purpose: Peptide receptor radionuclide therapy using β-emitting radiolabelled somatostatin analogues like DOTA,Tyr3-octreotate shows beneficial results in patients suffering from somatostatin receptor overexpressing tumours. However, after high-dose therapy partial renal reabsorption of radiopeptides may lead to nephrotoxicity. Co-infusion of lysine/arginine lowers renal retention of these radiopeptides without affecting tumour uptake. Recently co-administration of Gelofusine has been described to have a comparable kidney-protecting effect in rats. In the present study optimal dosing of Gelofusine co-administration was studied in tumour-bearing rats. Methods: Doses of 40, 80, 120 or 160 mg/kg Gelofusine were co-injected with 15 μg DOTA,Tyr3-octreotate, labelled with 3 MBq111In for biodistribution (24 h post-injection, n=4 per group) and with 60 MBq111In for microSPECT imaging experiments at 3, 24 and 48 h post-injection. An additional group of rats received 80 mg/kg Gelofusine plus 400 mg/kg lysine co-injection. Biodistribution studies were performed both in older (475 g) and younger (300 g) rats, the latter bearing CA20948 tumours. Results: Co-injection of 40 mg/kg Gelofusine resulted in 40-50% reduction of renal uptake and retention of111In-DOTA,Tyr3-octreotate, whereas higher doses further increased the reduction to 50-60% in both groups of rats. Combining Gelofusine and lysine caused 70% reduction of renal uptake. The uptake of radiolabelled octreotate both in somatostatin receptor-expressing normal tissues and tumours was not affected by Gelofusine co-injection. Conclusion: In rats co-injection of 80 mg/kg Gelofusine resulted in maximum reduction of renal retention of111In-DOTA,Tyr3- octreotate, which was further improved when combined with lysine. Tumour uptake of radiolabelled octreotate was not affected, resulting in an increased tumour to kidney ratio

    A standardised study to compare prostate cancer targeting efficacy of five radiolabelled bombesin analogues

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    Purpose: Prostate-specific antigen (PSA)-based screening for prostate cancer (PC) has dramatically increased early diagnosis. Current imaging techniques are not optimal to stage early PC adequately. A promising alternative to PC imaging is peptide-based scintigraphy using radiolabelled bombesin (BN) analogues that bind to gastrin-releasing peptide receptors (GRPR) being overexpressed in PC. When labelled to appropriate radionuclides BN targeting of GRPRs may also provide applications for peptide radionuclide receptor therapy (PRRT). Assessment studies under identical experimental conditions allowing a reliable comparison of the potential of such analogues are lacking. This study was performed to evaluate and directly compare five promising radiolabelled BN analogues for their targeting efficacy for PC under standardised conditions. Methods: The BN agonists [111In]DOTA-PESIN, [111In]AMBA, [111In]MP2346 and [111In]MP2653 and one antagonist [99mTc]Demobesin-1 were evaluated in GRPR-overexpressing human PC-3 tumou

    Loneliness, social support and cardiovascular reactivity to laboratory stress

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    Self-reported or explicit loneliness and social support have been inconsistently associated with cardiovascular reactivity (CVR) to stress. The present study aimed to adapt an implicit measure of loneliness, and use it alongside the measures of explicit loneliness and social support, to investigate their correlations with CVR to laboratory stress. Twenty-five female volunteers aged between 18 and 39 years completed self-reported measures of loneliness and social support, and an Implicit Association Test (IAT) of loneliness. The systolic blood pressure (SBP), diastolic blood pressure (DBP) and heart rate (HR) reactivity indices were measured in response to psychosocial stress induced in the laboratory. Functional support indices of social support were significantly correlated with CVR reactivity to stress. Interestingly, implicit, but not explicit, loneliness was significantly correlated with DBP reactivity after one of the stressors. No associations were found between structural support and CVR indices. Results are discussed in terms of validity of implicit versus explicit measures and possible factors that affect physiological outcomes

    Practice-Driven Evaluation of a Multi-layered Psychosocial Care Package for Children in Areas of Armed Conflict

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    Psychosocial and mental health service delivery frameworks for children in low-income countries are scarce. This paper presents a practice-driven evaluation of a multi-layered community-based care package in Burundi, Indonesia, Sri Lanka and Sudan, through a set of indicators; (a) perceived treatment gains; (b) treatment satisfaction; (c) therapist burden; (d) access to care; (e) care package costs. Across four settings (n = 29,292 children), beneficiaries reported high levels of client satisfaction and moderate post-treatment problem reductions. Service providers reported significant levels of distress related to service delivery. Cost analyses demonstrated mean cost per service user to vary from 3.46 to 17.32 € depending on country and specification of costs. The results suggest a multi-layered psychosocial care package appears feasible and satisfactory in reaching out to substantial populations of distressed children through different levels of care. Future replication should address therapist burden, cost reductions to increase sustainability and increase evidence for treatment efficacy
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