| 1. |
- Kootte, R. S., et al.
(author)
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Improvement of Insulin Sensitivity after Lean Donor Feces in Metabolic Syndrome Is Driven by Baseline Intestinal Microbiota Composition
- 2017
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In: Cell Metabolism. - : Elsevier BV. - 1550-4131. ; 26:4, s. 611-619
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Journal article (peer-reviewed)abstract
- The intestinal microbiota has been implicated in insulin resistance, although evidence regarding causality in humans is scarce. We therefore studied the effect of lean donor (allogenic) versus own (autologous) fecal microbiota transplantation (FMT) to male recipients with the metabolic syndrome. Whereas we did not observe metabolic changes at 18 weeks after FMT, insulin sensitivity at 6 weeks after allogenic FMT was significantly improved, accompanied by altered microbiota composition. We also observed changes in plasma metabolites such as gamma-aminobutyric acid and show that metabolic response upon allogenic FMT (defined as improved insulin sensitivity 6 weeks after FMT) is dependent on decreased fecal microbial diversity at baseline. In conclusion, the beneficial effects of lean donor FMT on glucose metabolism are associated with changes in intestinal microbiota and plasma metabolites and can be predicted based on baseline fecal microbiota composition.
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| 2. |
- Kupfer, Thomas, et al.
(author)
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Year 1 of the ZTF high-cadence Galactic plane survey : strategy, goals, and early results on new single-mode hot subdwarf B-star pulsatos
- 2021
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In: Monthly notices of the Royal Astronomical Society. - : Oxford University Press (OUP). - 0035-8711 .- 1365-2966. ; 505:1, s. 1254-1267
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Journal article (peer-reviewed)abstract
- We present the goals, strategy, and first results of the high-cadence Galactic plane survey using the Zwicky Transient Facility (ZTF). The goal of the survey is to unveil the Galactic population of short-period variable stars, including short-period binaries, and stellar pulsators with periods less than a few hours. Between 2018 June and 2019 January, we observed 64 ZTF fields resulting in 2990 deg2 of high stellar density in the ZTF-r band along the Galactic plane. Each field was observed continuously for 1.5 to 6 h with a cadence of 40 sec. Most fields have between 200 and 400 observations obtained over 2–3 continuous nights. As part of this survey, we extract a total of ≈230 million individual objects with at least 80 epochs obtained during the high-cadence Galactic plane survey reaching an average depth of ZTF–r ≈ 20.5 mag. For four selected fields with 2–10 million individual objects per field, we calculate different variability statistics and find that ≈1–2 per cent of the objects are astrophysically variable over the observed period. We present a progress report on recent discoveries, including a new class of compact pulsators, the first members of a new class of Roche lobe filling hot subdwarf binaries as well as new ultracompact double white dwarfs and flaring stars. Finally, we present a sample of 12 new single-mode hot subdwarf B-star pulsators with pulsation amplitudes between ZTF–r = 20–76 mmag and pulsation periods between P = 5.8–16 min with a strong cluster of systems with periods ≈6 min. All of the data have now been released in either ZTF Data Release 3 or Data Release 4.
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| 3. |
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| 4. |
- Cronin, M. F., et al.
(author)
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Developing an Observing Air-Sea Interactions Strategy (OASIS) for the global ocean
- 2022
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In: Ices Journal of Marine Science. - : Oxford University Press (OUP). - 1054-3139 .- 1095-9289. ; 80:2, s. 367-73
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Journal article (peer-reviewed)abstract
- The Observing Air-Sea Interactions Strategy (OASIS) is a new United Nations Decade of Ocean Science for Sustainable Development programme working to develop a practical, integrated approach for observing air-sea interactions globally for improved Earth system (including ecosystem) forecasts, CO2 uptake assessments called for by the Paris Agreement, and invaluable surface ocean information for decision makers. Our "Theory of Change" relies upon leveraged multi-disciplinary activities, partnerships, and capacity strengthening. Recommendations from >40 OceanObs'19 community papers and a series of workshops have been consolidated into three interlinked Grand Ideas for creating #1: a globally distributed network of mobile air-sea observing platforms built around an expanded array of long-term time-series stations; #2: a satellite network, with high spatial and temporal resolution, optimized for measuring air-sea fluxes; and #3: improved representation of air-sea coupling in a hierarchy of Earth system models. OASIS activities are organized across five Theme Teams: (1) Observing Network Design & Model Improvement; (2) Partnership & Capacity Strengthening; (3) UN Decade OASIS Actions; (4) Best Practices & Interoperability Experiments; and (5) Findable-Accessible-Interoperable-Reusable (FAIR) models, data, and OASIS products. Stakeholders, including researchers, are actively recruited to participate in Theme Teams to help promote a predicted, safe, clean, healthy, resilient, and productive ocean.
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| 5. |
- Manni, Giovanni Li, et al.
(author)
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The OpenMolcas Web : A Community-Driven Approach to Advancing Computational Chemistry
- 2023
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In: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 19:20, s. 6933-6991
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Journal article (peer-reviewed)abstract
- The developments of the open-source OpenMolcas chemistry software environment since spring 2020 are described, with a focus on novel functionalities accessible in the stable branch of the package or via interfaces with other packages. These developments span a wide range of topics in computational chemistry and are presented in thematic sections: electronic structure theory, electronic spectroscopy simulations, analytic gradients and molecular structure optimizations, ab initio molecular dynamics, and other new features. This report offers an overview of the chemical phenomena and processes OpenMolcas can address, while showing that OpenMolcas is an attractive platform for state-of-the-art atomistic computer simulations.
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| 6. |
- Tang, Xiaoqin, et al.
(author)
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Segmentation-Driven Optimization For Iterative Reconstruction in Optical Projection Tomography : An Exploration
- 2020
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In: IEEE Transactions on Computational Imaging. - 2573-0436 .- 2333-9403. ; 6, s. 1537-1547
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Journal article (peer-reviewed)abstract
- Three-dimensional reconstruction of tomograms from optical projection microscopy is confronted with several drawbacks. In this paper we employ iterative reconstruction algorithms to avoid streak artefacts in the reconstruction and explore possible ways to optimize two parameters of the algorithms, i.e., iteration number and initialization, in order to improve the reconstruction performance. As benchmarks for direct reconstruction evaluation in optical projection tomography are absent, we consider the assessment through the performance of the segmentation on the 3D reconstruction. In our explorative experiments we use the zebrafish model system which is a typical specimen for use in optical projection tomography system; and as such frequently used. In this manner data can be easily obtained from which a benchmark set can be built. For the segmentation approach we apply a two-dimensional U-net convolutional neural network because it is recognized to have a good performance in biomedical image segmentation. In order to prevent the training from getting stuck in local minima, a novel learning rate schema is proposed. This optimization achieves a lower training loss during the training process, as compared to an optimal constant learning rate. Our experiments demonstrate that the approach to the benchmarking of iterative reconstruction via results of segmentation is very useful. It contributes an important tool to the development of computational tools for optical projection tomography.
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| 7. |
- Tremblay, P. -E, et al.
(author)
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3D Model Atmospheres for Extremely Low-Mass White Dwarfs
- 2015
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In: Astrophysical Journal. - 0004-637X .- 1538-4357. ; 809:2
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Journal article (peer-reviewed)abstract
- We present an extended grid of mean three-dimensional (3D) spectra for low-mass, pure-hydrogen atmosphere DA white dwarfs (WDs). We use CO5BOLD radiation-hydrodynamics 3D simulations covering T-eff = 6000-11,500 K and log g = 5-6.5 (g in cm s(-2)) to derive analytical functions to convert spectroscopically determined 1D temperatures and surface gravities to 3D atmospheric parameters. Along with the previously published 3D models, the 1D to 3D corrections are now available for essentially all known convective DA WDs (i.e., log g - 5-9). For low-mass WDs, the correction in temperature is relatively small (a few percent at the most), but the surface gravities measured from the 3D models are lower by as much as 0.35 dex. We revisit the spectroscopic analysis of the extremely low-mass (ELM) WDs, and demonstrate that the 3D models largely resolve the discrepancies seen in the radius and mass measurements for relatively cool ELM WDs in eclipsing double WD and WD + millisecond pulsar binary systems. We also use the 3D corrections to revise the boundaries of the ZZ Ceti instability strip, including the recently found ELM pulsators.
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| 8. |
- Vos, Joris, et al.
(author)
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Looking into the cradle of the grave: J22564-5910, a potential young post-merger hot subdwarf
- 2021
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In: Astronomy & Astrophysics. - : EDP Sciences. - 1432-0746 .- 0004-6361. ; 655
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Journal article (peer-reviewed)abstract
- Context. We present the discovery of J22564-5910, a new type of hot subdwarf (sdB) which shows evidence of gas present in thesystem and it has shallow, multi-peaked hydrogen and helium lines which vary in shape over time. All observational evidence pointstowards J22564-5910 being observed very shortly after the merger phase that formed it.Aims. Using high-resolution, high signal-to-noise spectroscopy, combined with multi-band photometry, Gaia astrometry, and TESSlight curves, we aim to interpret these unusual spectral features.Methods. The photometry, spectra, and light curves were all analysed, and their results were combined in order to support ourinterpretation of the observations: the likely presence of a magnetic field combined with gas features around the sdB. Based onthe triple-peaked H lines, the magnetic field strength was estimated and, by using the shellspec code, qualitative models of gasconfigurations were fitted to the observations.Results. All observations can either be explained by a magnetic field of ∼650 kG, which enables the formation of a centrifugalmagnetosphere, or a non-magnetic hot subdwarf surrounded by a circumstellar gas disc or torus. Both scenarios are not mutuallyexclusive and both can be explained by a recent merger.Conclusions. J22564-5910 is the first object of its kind. It is a rapidly spinning sdB with gas still present in the system. It is thefirst post-merger star observed this early after the merger event, and as such it is very valuable system to test merger theories. If themagnetic field can be confirmed, it is not only the first magnetic sdB, but it hosts the strongest magnetic field ever found in a pre-whitedwarf object. Thus, it could represent the long sought-after immediate ancestor of strongly magnetic white dwarfs.
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| 9. |
- Bao, Jie J., et al.
(author)
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Analytic gradients for compressed multistate pair-density functional theory
- 2022
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In: Molecular Physics. - : Taylor & Francis Group. - 0026-8976 .- 1362-3028. ; 120:19-20
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Journal article (peer-reviewed)abstract
- Photochemical reactions often involve states that are closely coupled due to near degeneracies, for example by proximity to conical intersections. Therefore, a multistate method is used to accurately describe these states; for example, ordinary perturbation theory is replaced by quasidegenerate perturbation theory. Multiconfiguration pair-density functional theory (MC-PDFT) provides an efficient way to approximate the full dynamical correlation energy of strongly correlated systems, and we recently proposed compressed multistate pair-density functional theory (CMS-PDFT) to treat closely coupled states. In the present paper, we report the implementation of analytic gradients for CMS-PDFT in both OpenMolcas and PySCF, and we illustrate the use of these gradients by applying the method to the excited states of formaldehyde and phenol.
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| 10. |
- Beaugendre, F., et al.
(author)
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Accentuation boundaries in Dutch, French and Swedish
- 2001
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In: Speech Communication. - 0167-6393 .- 1872-7182. ; 33:4, s. 305-318
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Journal article (peer-reviewed)abstract
- This paper presents a comparative study investigating the relation between the timing of a rising or falling pitch movement and the temporal structure of the syllable it accentuates for three languages: Dutch, French and Swedish. In a perception experiment, the five-syllable utterances /mamamamama/ and /?a?a?a?a?a/ were provided with a relatively fast rising or falling pitch movement. The timing of the movement was systematically varied so that it accented the third or the fourth syllable, subjects were asked to indicate which syllable they perceived as accented. The accentuation boundary (AB) between the third and the fourth syllable was then defined as the moment before which more than half of the subjects indicated the third syllable as accented and after which more than half of the subjects indicated the fourth syllable. The results show that there are significant differences between the three languages as to the location of the AB. In general, for the rises, well-defined ABs were found. They were located in the middle of the vowel of the third syllable for French subjects, and later in that vowel for Dutch and swedish subjects. For the falls, a clear AB was obtained only for the Dutch and the Swedish listeners. This was located at the end of the third syllable. For the French listeners, the fall did not yield a clear AB, This corroborates the absence of accentuation by means of falls in French. By varying the duration of the pitch movement it could be shown that, in all cases in which a clear AB was found. the cue for accentuation was located at the beginning of the pitch movement.
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| 11. |
- Calio, Paul B., et al.
(author)
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Minimum-Energy Conical Intersections by Compressed Multistate Pair-Density Functional Theory
- 2024
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In: Journal of Physical Chemistry A. - : American Chemical Society (ACS). - 1089-5639 .- 1520-5215. ; 128:9, s. 1698-1706
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Journal article (peer-reviewed)abstract
- Compressed multistate pair-density functional theory (CMS-PDFT) is a multistate version of multiconfiguration pair-density functional theory that can capture the correct topology of coupled potential energy surfaces (PESs) around conical intersections. In this work, we develop interstate coupling vectors (ISCs) for CMS-PDFT in the OpenMolcas and PySCF/mrh electronic structure packages. Yet, the main focus of this work is using ISCs to calculate minimum-energy conical intersections (MECIs) by CMS-PDFT. This is performed using the projected constrained optimization method in OpenMolcas, which uses ISCs to restrain the iterations to the conical intersection seam. We optimize the S1/S0 MECIs for ethylene, butadiene, and benzene and show that CMS-PDFT gives smooth PESs in the vicinities of the MECIs. Furthermore, the CMS-PDFT MECIs are in good agreement with the MECI calculated by the more expensive XMS-CASPT2 method.
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| 12. |
- Joensuu, Heikki, et al.
(author)
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Survival Outcomes Associated with 3 Years vs 1 Year of Adjuvant Imatinib for Patients with High-Risk Gastrointestinal Stromal Tumors : An Analysis of a Randomized Clinical Trial after 10-Year Follow-up
- 2020
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In: JAMA Oncology. - : American Medical Association (AMA). - 2374-2437. ; 6:8, s. 1241-1246
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Journal article (peer-reviewed)abstract
- Importance: Adjuvant imatinib is associated with improved recurrence-free survival (RFS) when administered after surgery to patients with operable gastrointestinal stromal tumor (GIST), but its influence on overall survival (OS) has remained uncertain. Objective: To evaluate the effect of adjuvant imatinib on OS of patients who have a high estimated risk for GIST recurrence after macroscopically complete surgery. Design, Setting, and Participants: In this open-label, randomized (1:1), multicenter phase 3 clinical trial conducted in Finland, Germany, Norway, and Sweden, 400 patients who had undergone macroscopically complete surgery for GIST with a high estimated risk for recurrence according to the modified National Institutes of Health Consensus Criteria were enrolled between February 2004 and September 2008. Data for this follow-up analysis were analyzed from September to November, 2019. Interventions: Imatinib 400 mg/d administered orally for either 12 months or 36 months after surgery. Main Outcomes And Measures: The primary end point was RFS; the secondary objectives included OS and treatment safety. Results: The intention-to-treat cohort consisted of 397 patients (12-month group, 199; 36-month group, 198; 201 men and 196 women; median [IQR] age, 62 (51-69) years and 60 (51-67) years, during a median follow-up time of 119 months after the date of randomization, 194 RFS events and 96 OS events were recorded in the intention-to-treat population. Five-year and 10-year RFS was 71.4% and 52.5%, respectively, in the 36-month group and 53.0% and 41.8% in the 12-month group (hazard ratio [HR], 0.66; 95% CI, 0.49-0.87; P =.003). In the 36-month group, 5-year OS and 10-year OS rates were 92.0% and 79.0%, respectively, and in the 12-month group 85.5% and 65.3% (HR, 0.55; 95% CI, 0.37-0.83; P =.004). The results were similar in the efficacy population, from which 15 patients who did not have GIST in central pathology review and 24 patients who had intra-abdominal metastases removed at surgery were excluded (36-month group, 10-year OS 81.6%; 12-month group, 66.8%; HR, 0.50; 95% CI, 0.32-0.80; P =.003). No new safety signals were detected. Conclusions and Relevance: Three years of adjuvant imatinib is superior in efficacy compared with 1 year of imatinib. Approximately 50% of deaths may be avoided during the first 10 years of follow-up after surgery with longer adjuvant imatinib treatment. Trial Registration: ClinicalTrials.gov Identifier: NCT00116935.
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