| 1. |
- Abazov, V. M., et al.
(author)
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The upgraded DO detector
- 2006
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In: Nuclear Instruments and Methods in Physics Research Section A. - : Elsevier BV. - 0168-9002 .- 1872-9576. ; 565:2, s. 463-537
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Journal article (peer-reviewed)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.
(author)
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Quantum Chemistry Common Driver and Databases (QCDB) and Quantum Chemistry Engine (QCEngine) : Automation and interoperability among computational chemistry programs
- 2021
-
In: Journal of Chemical Physics. - : American Institute of Physics (AIP). - 0021-9606 .- 1089-7690. ; 155:20
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Journal article (peer-reviewed)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.
(author)
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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
-
In: Circulation. - 1524-4539.
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Journal article (peer-reviewed)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.
(author)
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Guidelines for thermodynamic sorption modelling in the context of radioactive waste disposal
- 2013
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In: Environmental Modelling and Software. - : Elsevier BV. - 1364-8152. ; 42, s. 143-156
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Journal article (peer-reviewed)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.
(author)
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Pressure-induced reentrant transition in NbS3 phases : Combined Raman scattering and x-ray diffraction study
- 2019
-
In: Physical Review B. - : AMER PHYSICAL SOC. - 2469-9950 .- 2469-9969. ; 99:23
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Journal article (peer-reviewed)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.
(author)
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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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In: European journal of cardio-thoracic surgery : official journal of the European Association for Cardio-thoracic Surgery. - 1873-734X.
-
Journal article (peer-reviewed)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.
(author)
-
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
-
In: Applied Physics Letters. - : AIP Publishing. - 0003-6951 .- 1077-3118. ; 105:3
-
Journal article (peer-reviewed)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.
(author)
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Biotransformation-coupled mutasynthesis for the generation of novel pristinamycin derivatives by engineering the phenylglycine residue
- 2023
-
In: Rsc Chemical Biology. - 2633-0679. ; 4:12, s. 1050-1063
-
Journal article (peer-reviewed)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.
(author)
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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
-
In: Photosynthesis Research. - : SPRINGER. - 0166-8595 .- 1573-5079. ; 84:1-3, s. 347-353
-
Journal article (peer-reviewed)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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| 10. |
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| 11. |
- Kulik, L V, et al.
(author)
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Electron spin-lattice relaxation of the so state of the oxygen-evolving complex in photosystem II and of dinuclear manganese model complexes
- 2005
-
In: Biochemistry. - : AMER CHEMICAL SOC. - 0006-2960 .- 1520-4995. ; 44:26, s. 9368-9374
-
Journal article (peer-reviewed)abstract
- The temperature dependence of the electron spin-lattice relaxation time T, was measured for the So state of the oxygen-evolving complex (OEC) in photosystem II and for two dinuclear manganese model complexes by pulse EPR using the inversion-recovery method. For [Mn(III)Mn(IV)(mu-O)(2)bipy(4)]ClO4, the Raman relaxation process dominates at temperatures below 50 K. In contrast, Orbach type relaxation was found for [Mn(II)Mn(III)(mu-OH)(mu-piv)(2)(Me(3)tacn)(2)](ClO4)(2) between 4.3 and 9 K. For the latter complex, an energy separation of 24.7-28.0 cm(-1) between the ground and the first excited electronic state was determined. In the So state of photosystem II, the T-1 relaxation times were measured in the range of 4.3-6.5 K. A comparison with the relaxation data (rate and pre-exponential factor) of the two model complexes and of the S-2 state of photosystem II indicates that the Orbach relaxation process is dominant for the So state and that its first excited state lies 21.7 +/- 0.4 cm(-1) above its ground state. The results are discussed with respect to the structure of the OEC in photosystem II.
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| 12. |
- Mackenbach, J. P., et al.
(author)
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Variations in the relation between education and cause-specific mortality in 19 European populations : A test of the "fundamental causes" theory of social inequalities in health
- 2015
-
In: Social Science and Medicine. - : Elsevier BV. - 0277-9536 .- 1873-5347. ; 127, s. 51-62
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Journal article (peer-reviewed)abstract
- Link and Phelan have proposed to explain the persistence of health inequalities from the fact that socioeconomic status is a "fundamental cause" which embodies an array of resources that can be used to avoid disease risks no matter what mechanisms are relevant at any given time. To test this theory we compared the magnitude of inequalities in mortality between more and less preventable causes of death in 19 European populations, and assessed whether inequalities in mortality from preventable causes are larger in countries with larger resource inequalities.We collected and harmonized mortality data by educational level on 19 national and regional populations from 16 European countries in the first decade of the 21st century. We calculated age-adjusted Relative Risks of mortality among men and women aged 30-79 for 24 causes of death, which were classified into four groups: amenable to behavior change, amenable to medical intervention, amenable to injury prevention, and non-preventable.Although an overwhelming majority of Relative Risks indicate higher mortality risks among the lower educated, the strength of the education-mortality relation is highly variable between causes of death and populations. Inequalities in mortality are generally larger for causes amenable to behavior change, medical intervention and injury prevention than for non-preventable causes. The contrast between preventable and non-preventable causes is large for causes amenable to behavior change, but absent for causes amenable to injury prevention among women. The contrast between preventable and non-preventable causes is larger in Central & Eastern Europe, where resource inequalities are substantial, than in the Nordic countries and continental Europe, where resource inequalities are relatively small, but they are absent or small in Southern Europe, where resource inequalities are also large.In conclusion, our results provide some further support for the theory of "fundamental causes". However, the absence of larger inequalities for preventable causes in Southern Europe and for injury mortality among women indicate that further empirical and theoretical analysis is necessary to understand when and why the additional resources that a higher socioeconomic status provides, do and do not protect against prevailing health risks.
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| 13. |
- Pelling, S., et al.
(author)
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Point contact readout for a quantum dot terahertz sensor
- 2008
-
In: Applied Physics Letters. - 0003-6951 .- 1077-3118. ; 93:7, s. 073501-
-
Journal article (peer-reviewed)abstract
- We introduce a terahertz radiation sensor in which the photon-induced ionization state of a quantum dot is monitored by a point contact formed in the same semiconductor heterostructure. For comparison we used a readout based on a single electron transistor coupled to the same quantum dot. The experiments prove functionality of the point contact-based device with additional practical advantage of a higher operation temperature up to 1.5 K and ease of nanofabrication
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| 14. |
- Pogorily, A. N., et al.
(author)
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Magnetic anisotropy of epitaxial Co2Fe-Ge Heusler alloy films on MgO (100) substrates
- 2017
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In: AIP Advances. - : American Institute of Physics Inc.. - 2158-3226. ; 7:5
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Journal article (peer-reviewed)abstract
- Films of Co2Fe-Ge Heusler alloy with variable Ge concentration deposited on monocrystalline MgO (100) substrates by magnetron co-sputtering are investigated using microstructural, morphological, magnetometric, and magnetic resonance methods. The films were found to grow epitaxially, with island-like or continuous-layer morphology depending the Ge-content. The ferromagnetic resonance data versus out-of-plane and in-plane angle indicate the presence of easy plane and 4-fold in-plane anisotropy. The magnetometry data indicate additional weak 2-fold in-plane anisotropy and pronounced at low fields rotatable anisotropy. The observed magnetic anisotropy properties discussed in correlation with the microstructure and morphology of the films.
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| 15. |
- Spasov, S., et al.
(author)
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Terahertz imaging with a highly-sensitive quantum dot detector
- 2010
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In: 21st International Symposium on Space Terahertz Technology 2010, ISSTT 2010; Oxford; United Kingdom; 23 March 2010 through 25 March 2010. - 9781617823626 ; , s. 266-
-
Conference paper (peer-reviewed)abstract
- We report on an application of photon counting detector in the sub-terahertz range of electromagnetic waves for imaging of natural and stimulated radiation emitted by free standing objects. The detector is assembled from a GaAs/AlGaAs quantum dot, electron reservoir and quantum point contact (QPC). Its operation relies on photon-to-plasmon and plasmon-to-charge conversion, followed by charge measurement in a single-shot mode. Individual photons excite plasma waves in the quantum dot, with a resonance frequency determined by the shape of the QD confining potential. The plasma wave decays subsequently by single-particle electron-hole excitations, which change the electrostatic potential stepwise in the close proximity to the QD. The potential steps are probed with the QPC operating as a sensitive electrometer. A studied object is placed on a twodimensional translating stage. Its emission is projected through an optical window onto the detector attached to a 1K cold finger in a cryostat. Subsequently translating the stage in two space directions we are able to map the distribution of the emitted radiation. The presented technique has a potential for imaging of objects passively radiated in the sub-terahertz range.
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| 16. |
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| 17. |
- Yastrubchak, O., et al.
(author)
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Ferromagnetism and the electronic band structure in (Ga,Mn)(Bi,As) epitaxial layers
- 2014
-
In: Applied Physics Letters. - : AIP Publishing. - 0003-6951 .- 1077-3118. ; 105:7
-
Journal article (peer-reviewed)abstract
- Impact of Bi incorporation into (Ga,Mn)As layers on their electronic-and band-structures as well as their magnetic and structural properties has been studied. Homogenous (Ga,Mn)(Bi,As) layers of high structural perfection have been grown by the low-temperature molecular-beam epitaxy technique. Post-growth annealing treatment of the layers results in an improvement of their structural and magnetic properties and an increase in the hole concentration in the layers. The modulation photoreflectance spectroscopy results are consistent with the valence-band model of hole-mediated ferromagnetism in the layers. This material combines the properties of (Ga,Mn)As and Ga(Bi,As) ternary compounds and offers the possibility of tuning its electrical and magnetic properties by controlling the alloy composition. (C) 2014 AIP Publishing LLC.
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| 18. |
- Yastrubchak, O., et al.
(author)
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Influence of Ion Implantation on Magnetic, Structural and Optical Properties of (Ga,Mn)As Epitaxial Films
- 2008
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In: ACTA PHYSICA POLONICA A. - 0587-4246. ; 114:5, s. 1445-1450
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Conference paper (peer-reviewed)abstract
- We performed implantation experiments; applying both the chemically active oxygen ions and inactive ions of neon noble gas, to thin epitaxial films of (Ga,Mn)As ferromagnetic semiconductor. Inspection of their magnetic properties by means of a superconducting quantum interference device magnetometer revealed that the implantation with a low dose of either O or Ne ions completely suppressed ferromagnetism in the films. Both the high resolution X-ray diffraction technique and the Raman spectroscopy showed significant changes in the structural and optical properties of the films caused by oxygen and neon implantation.
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| 19. |
- Yastrubchak, O., et al.
(author)
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Ion-Implantation Control of Ferromagnetism in (Ga,Mn)As Epitaxial Layers
- 2010
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In: Journal Of Electronic Materials. - : Springer Science and Business Media LLC. - 0361-5235 .- 1543-186X. ; 39:6, s. 794-798
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Conference paper (peer-reviewed)abstract
- Epitaxial layers of (Ga,Mn)As ferromagnetic semiconductor have been subjected to low-energy ion implantation by applying a very low fluence of either chemically active, oxygen ions or inactive ions of neon noble gas. Several complementary characterization techniques have been used with the aim of studying the effect of ion implantation on the layer properties. Investigation of their electrical and magnetic properties revealed that implantation with either O or Ne ions completely suppressed both the conductivity and ferromagnetism in the layers. On the other hand, Raman spectroscopy measurements evidenced that O ion implantation influenced optical properties of the layers noticeably stronger than did Ne ion implantation. Moreover, structural modifications of the layers caused by ion implantation were investigated using high-resolution x-ray diffraction technique. A mechanism responsible for ion-implantation-induced suppression of the conductivity and ferromagnetism in (Ga,Mn)As layers, which could be applied as a method for tailoring nanostructures in the layers, is discussed in terms of defects created in the layers by the two implanted elements.
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