1. |
- Abazov, V. M., et al.
(författare)
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The upgraded DO detector
- 2006
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Ingår i: Nuclear Instruments and Methods in Physics Research Section A. - : Elsevier BV. - 0168-9002 .- 1872-9576. ; 565:2, s. 463-537
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Tidskriftsartikel (refereegranskat)abstract
- The DO experiment enjoyed a very successful data-collection run at the Fermilab Tevatron collider between 1992 and 1996. Since then, the detector has been upgraded to take advantage of improvements to the Tevatron and to enhance its physics capabilities. We describe the new elements of the detector, including the silicon microstrip tracker, central fiber tracker, solenoidal magnet, preshower detectors, forward muon detector, and forward proton detector. The uranium/liquid -argon calorimeters and central muon detector, remaining from Run 1, are discussed briefly. We also present the associated electronics, triggering, and data acquisition systems, along with the design and implementation of software specific to DO.
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2. |
- Smith, Daniel G. A., et al.
(författare)
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Quantum Chemistry Common Driver and Databases (QCDB) and Quantum Chemistry Engine (QCEngine) : Automation and interoperability among computational chemistry programs
- 2021
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Ingår i: Journal of Chemical Physics. - : American Institute of Physics (AIP). - 0021-9606 .- 1089-7690. ; 155:20
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Tidskriftsartikel (refereegranskat)abstract
- Community efforts in the computational molecular sciences (CMS) are evolving toward modular, open, and interoperable interfaces that work with existing community codes to provide more functionality and composability than could be achieved with a single program. The Quantum Chemistry Common Driver and Databases (QCDB) project provides such capability through an application programming interface (API) that facilitates interoperability across multiple quantum chemistry software packages. In tandem with the Molecular Sciences Software Institute and their Quantum Chemistry Archive ecosystem, the unique functionalities of several CMS programs are integrated, including CFOUR, GAMESS, NWChem, OpenMM, Psi4, Qcore, TeraChem, and Turbomole, to provide common computational functions, i.e., energy, gradient, and Hessian computations as well as molecular properties such as atomic charges and vibrational frequency analysis. Both standard users and power users benefit from adopting these APIs as they lower the language barrier of input styles and enable a standard layout of variables and data. These designs allow end-to-end interoperable programming of complex computations and provide best practices options by default.
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3. |
- Gaudino, Mario, et al.
(författare)
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Graft Failure After Coronary Artery Bypass Grafting and Its Association With Patient Characteristics and Clinical Events: A Pooled Individual Patient Data Analysis of Clinical Trials With Imaging Follow-Up.
- 2023
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Ingår i: Circulation. - 1524-4539.
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Tidskriftsartikel (refereegranskat)abstract
- Graft patency is the postulated mechanism for the benefits of coronary artery bypass grafting (CABG). However, systematic graft imaging assessment after CABG is rare, and there is a lack of contemporary data on the factors associated with graft failure and on the association between graft failure and clinical events after CABG.We pooled individual patient data from randomized clinical trials with systematic CABG graft imaging to assess the incidence of graft failure and its association with clinical risk factors. The primary outcome was the composite of myocardial infarction or repeat revascularization occurring after CABG and before imaging. A 2-stage meta-analytic approach was used to evaluate the association between graft failure and the primary outcome. We also assessed the association between graft failure and myocardial infarction, repeat revascularization, or all-cause death occurring after imaging.Seven trials were included comprising 4413 patients (mean age, 64.4±9.1 years; 777 [17.6%] women; 3636 [82.4%] men) and 13163 grafts (8740 saphenous vein grafts and 4423 arterial grafts). The median time to imaging was 1.02 years (Q1;Q3: 1.00;1.03). Graft failure occurred in 1487 (33.7%) patients and in 2190 (16.6%) grafts. Age (adjusted odds ratio [aOR], 1.08 [per 10-year increment] [95% CI, 1.01-1.15]; P=0.03), female sex (aOR, 1.27 [95% CI, 1.08-1.50]; P=0.004), and smoking (aOR, 1.20 [95% CI, 1.04-1.38]; P=0.01) were independently associated with graft failure, whereas statins were associated with a protective effect (aOR, 0.74 [95% CI, 0.63-0.88]; P<0.001). Graft failure was associated with an increased risk of myocardial infarction or repeat revascularization occurring between CABG and imaging assessment (8.0% in patients with graft failure versus 1.7% in patients without graft failure; aOR, 3.98 [95% CI, 3.54-4.47]; P<0.001). Graft failure was also associated with an increased risk of myocardial infarction or repeat revascularization occurring after imaging (7.8% versus 2.0%; aOR, 2.59 [95% CI, 1.86-3.62]; P<0.001). All-cause death after imaging occurred more frequently in patients with graft failure compared with patients without graft failure (11.0% versus 2.1%; aOR, 2.79 [95% CI, 2.01-3.89]; P<0.001).In contemporary practice, graft failure remains common among patients undergoing CABG and is strongly associated with adverse cardiac events.
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4. |
- Payne, T. E., et al.
(författare)
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Guidelines for thermodynamic sorption modelling in the context of radioactive waste disposal
- 2013
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Ingår i: Environmental Modelling and Software. - : Elsevier BV. - 1364-8152. ; 42, s. 143-156
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Tidskriftsartikel (refereegranskat)abstract
- Thermodynamic sorption models (TSMs) offer the potential to improve the incorporation of sorption in environmental modelling of contaminant migration. One specific application is safety cases for radioactive waste repositories, in which radionuclide sorption on mineral surfaces is usually described using distribution coefficients (K-d values). TSMs can be utilised to provide a scientific basis for the range of K-d values included in the repository safety case, and for assessing the response of K-d to changes in chemical conditions. The development of a TSM involves a series of decisions on model features such as numbers and types of surface sites, sorption reactions and electrostatic correction factors. There has been a lack of consensus on the best ways to develop such models, and on the methods of determination of associated parameter values. The present paper therefore presents recommendations on a number of aspects of model development, which are applicable both to radioactive waste disposal and broader environmental applications.The TSM should be calibrated using a comprehensive sorption data set for the contaminant of interest, showing the impact of major geochemical parameters including pH, ionic strength, contaminant concentration, the effect of ligands, and major competing ions. Complex natural materials should be thoroughly characterised in terms of mineralogy, surface area, cation exchange capacity, and presence of impurities. During the application of numerical optimisation programs to simulate sorption data, it is often preferable that the TSM should be fitted to the experimentally determined K-d parameter, rather than to the frequently used percentage sorbed. Two different modelling approaches, the component additivity and generalised composite, can be used for modelling sorption data for complex materials such as soils. Both approaches may be coupled to the same critically reviewed aqueous thermodynamic data sets, and may incorporate the same, or similar, surface reactions and surface species. The quality of the final sorption model can be assessed against the following characteristics: an appropriate level of complexity, documented and traceable decisions, internal consistency, limitations on the number of adjustable parameter values, an adequate fit to a comprehensive calibration data set, and capability of simulating independent data sets. Key recommendations for the process of TSM development include: definition of modelling objectives, identification of major decision points, a clear decision-making rationale with reference to experimental or theoretical evidence, utilisation of a suitable consultative and iterative model development process, testing to the maximum practicable extent, and thorough documentation of key decisions. These recommendations are consistent with international benchmarks for environmental modelling.
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5. |
- Abdel-Hafiez, Mahmoud, et al.
(författare)
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Pressure-induced reentrant transition in NbS3 phases : Combined Raman scattering and x-ray diffraction study
- 2019
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Ingår i: Physical Review B. - : AMER PHYSICAL SOC. - 2469-9950 .- 2469-9969. ; 99:23
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Tidskriftsartikel (refereegranskat)abstract
- We report the evolution of charge density wave states under pressure for two NbS3 phases: triclinic (phase I) and monoclinic (phase II) at room temperature. Raman and x-ray diffraction (XRD) techniques are applied. The x-ray studies on the monoclinic phase under pressure show a compression of the lattice at different rates below and above similar to 7 GPa but without a change in space group symmetry. The Raman spectra of the two phases evolve similarly with pressure; all peaks almost disappear in the similar to 6-8 GPa range, indicating a transition from an insulating to a metallic state, and peaks at new positions appear above 8 GPa. The results suggest suppression of the ambient charge-density waves and their subsequent recovery with new orderings above 8 GPa.
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6. |
- An, Kevin R, et al.
(författare)
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Association between overweight and obesity with coronary artery bypass graft failure: an individual patient data analysis of clinical trials.
- 2024
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Ingår i: European journal of cardio-thoracic surgery : official journal of the European Association for Cardio-thoracic Surgery. - 1873-734X.
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Tidskriftsartikel (refereegranskat)abstract
- The association between obesity and graft failure after coronary artery bypass grafting has not been previously investigated.We pooled individual patient data from randomized clinical trials with systematic post-operative coronary imaging to evaluate the association between obesity and graft failure at the individual graft and patient levels. Penalized cubic regression splines and mixed-effects multivariable logistic regression models were performed.Six trials comprising 3,928 patients and 12,048 grafts were included. The median time to imaging was 1.03 (IQR, 1.00-1.09) years. By body mass index (BMI) category, 800 (20.4%) patients were normal weight (BMI 18.5-24.9), 1,668 (42.5%) were overweight (BMI 25-29.9), 983 (25.0%) were obesity class 1 (BMI 30-34.9), 344 (8.8%) were obesity class 2 (BMI 35-39.9), and 116 (2.9%) were obesity class 3 (BMI 40+). As a continuous variable, BMI was associated with reduced graft failure (adjusted odds ratio [aOR] 0.98 [95% CI, 0.97-0.99]) at the individual graft level. Compared to normal weight patients, graft failure at the individual graft level was reduced in overweight (aOR 0.79 [95% CI, 0.64-0.96]), obesity class 1 (aOR 0.81 [95% CI, 0.64-1.01]), and obesity class 2 (aOR 0.61 [95% CI, 0.45-0.83]) patients, but not different compared to obesity class 3 (aOR 0.94 [95% CI, 0.62-1.42]) patients. Findings were similar, but did not reach significance, at the patient level.In a pooled individual patient data analysis of randomized clinical trials, BMI and obesity appear to be associated with reduced graft failure at one year after coronary artery bypass grafting.
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7. |
- Gluba, L., et al.
(författare)
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On the nature of the Mn-related states in the band structure of (Ga,Mn)As alloys via probing the E-1 and E-1 + Delta(1) optical transitions
- 2014
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Ingår i: Applied Physics Letters. - : AIP Publishing. - 0003-6951 .- 1077-3118. ; 105:3
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Tidskriftsartikel (refereegranskat)abstract
- The dilute (Ga,Mn)As became a model ferromagnetic semiconductor, however there is still a disagreement on the source of its magnetism. In this paper, we verify the ellipsometric results and compare them with more precise photoreflectance method, which gives an important insight into the interaction of the Mn-related states with the ones of GaAs valence band. No spectral shifts observed for the E-1 and E-1 + Delta(1) interband transitions in highly doped and annealed (Ga,Mn)As epitaxial layers indicate that the coupling between a detached Mn impurity band and the valence band does not occur. Our findings are supported by the characterizations of the (Ga,Mn)As epitaxial layers with the high resolution transmission electron microscopy and magnetization measurements. (c) 2014 AIP Publishing LLC.
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8. |
- Hennrich, O., et al.
(författare)
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Biotransformation-coupled mutasynthesis for the generation of novel pristinamycin derivatives by engineering the phenylglycine residue
- 2023
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Ingår i: Rsc Chemical Biology. - 2633-0679. ; 4:12, s. 1050-1063
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Tidskriftsartikel (refereegranskat)abstract
- Streptogramins are the last line of defense antimicrobials with pristinamycin as a representative substance used as therapeutics against highly resistant pathogenic bacteria. However, the emergence of (multi)drug-resistant pathogens renders these valuable antibiotics useless; making it necessary to derivatize compounds for new compound characteristics, which is often difficult by chemical de novo synthesis due to the complex nature of the molecules. An alternative to substance derivatization is mutasynthesis. Herein, we report about a mutasynthesis approach, targeting the phenylglycine (Phg) residue for substance derivatization, a pivotal component of streptogramin antibiotics. Mutasynthesis with halogenated Phg(-like) derivatives altogether led to the production of two new derivatized natural compounds, as there are 6-chloropristinamycin I and 6-fluoropristinamycin I based on LC-MS/MS analysis. 6-Chloropristinamycin I and 6-fluoropristinamycin I were isolated by preparative HPLC, structurally confirmed using NMR spectroscopy and tested for antimicrobial bioactivity. In a whole-cell biotransformation approach using an engineered E. coli BL21(DE3) pET28-hmo/pACYC-bcd-gdh strain, Phg derivatives were generated fermentatively. Supplementation with the E. coli biotransformation fermentation broth containing 4-fluorophenylglycine to the pristinamycin mutasynthesis strain resulted in the production of 6-fluoropristinamycin I, demonstrating an advanced level of mutasynthesis. Here, we report the development of a mutasynthesis approach for the derivatisation of pristinamycin I based on the phenylglycine residue in combination with a biotransformation process for mutasynthon provision.
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9. |
- Kulik, L, et al.
(författare)
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Pulse EPR, 55Mn-ENDOR and ELDOR-detected NMR of the S2-state of the oxygen evolving complex in Photosystem II
- 2005
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Ingår i: Photosynthesis Research. - : SPRINGER. - 0166-8595 .- 1573-5079. ; 84:1-3, s. 347-353
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Tidskriftsartikel (refereegranskat)abstract
- Pulse EPR, Mn-55-ENDOR and ELDOR-detected NMR experiments were performed on the S-2-state of the oxygen-evolving complex from spinach Photosystem II. The novel technique of random acquisition in ENDOR was used to suppress heating artefacts. Our data unambiguously shows that four Mn ions have significant hyperfine coupling constants. Numerical simulation of the Mn-55-ENDOR spectrum allowed the determination of the principal values of the hyperfine interaction tensors for all four Mn ions of the oxygen-evolving complex. The results of our Mn-55-ENDOR experiments are in good agreement with previously published data [Peloquin JM et al. (2000) J Am Chem Soc 122: 10926-10942]. For the first time ELDOR-detected NMR was applied to the S-2-state and revealed a broad peak that can be simulated numerically with the same parameters that were used for the simulation of the Mn-55-ENDOR spectrum. This provides strong independent support for the assigned hyperfine parameters.
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