| 1. |
- Abe, K., et al.
(författare)
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J-PARC Neutrino Beamline Upgrade Technical Design Report
- 2019
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Rapport (refereegranskat)abstract
- In this document, technical details of the upgrade plan of the J-PARC neutrino beamline for the extension of the T2K experiment are described. T2K has proposed to accumulate data corresponding to 2×1022 protons-on-target in the next decade, aiming at an initial observation of CP violation with 3σ or higher significance in the case of maximal CP violation. Methods to increase the neutrino beam intensity, which are necessary to achieve the proposed data increase, are described.
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| 2. |
- Nakamoto, T, et al.
(författare)
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Dental panoramic radiograph as a tool to detect postmenopausal women with low bone mineral density : untrained general dental practitioners’ diagnostic performance
- 2003
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Ingår i: Osteoporosis International. - : Springer Science and Business Media LLC. - 0937-941X .- 1433-2965. ; 14:8, s. 659-664
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- The detection of postmenopausal women with low bone mineral density (BMD) is an important strategy to reduce the incidence of osteoporotic fracture. Recent studies suggested that incidental findings on dental panoramic radiographs may be used as a tool to detect women with low BMD. However, little is known whether this finding is sufficiently assessed by untrained general dental practitioners (GDPs). The purpose of this study was to investigate: (1) the observer agreement and (2) the diagnostic efficacy in detecting women with low BMD, when untrained GDPs assess the appearance (normal or eroded) of the mandibular inferior cortex on dental panoramic radiographs of postmenopausal women. Twenty-seven GDPs were asked to classify the appearance of the mandibular inferior cortex on dental panoramic radiographs of 100 postmenopausal women who had completed BMD assessments of the lumbar spine and of the femoral neck. Intra- and inter-observer agreements were analyzed with kappa statistics. The diagnostic efficacy (sensitivity, specificity and predictive values) was analyzed by comparing two groups classified by the mandibular inferior cortex (women with normal and women with eroded mandibular inferior cortex) with those classified by BMD (women with normal BMD and women with osteopenia or osteoporosis). The mean sensitivity and specificity were 77 % and 40 %, respectively, when BMD of the lumbar spine was used as standard and 75 % and 39 %, respectively, when BMD of the femoral neck comprised the standard. Nineteen untrained GDPs (70 %) presented a moderate to almost perfect intra-observer agreement. We conclude that dental panoramic radiograph may be used in clinical dental practice to identify postmenopausal women who have undetected low BMD and should undergo further testing with bone densitometry.
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| 3. |
- Latallo, M. J., et al.
(författare)
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Predicting allosteric mutants that increase activity of a major antibiotic resistance enzyme
- 2017
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Ingår i: Chemical Science. - Cambridge : Royal Soc Chemistry. - 2041-6520 .- 2041-6539. ; 8:9, s. 6484-6492
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Tidskriftsartikel (refereegranskat)abstract
- The CTX-M family of beta lactamases mediate broad-spectrum antibiotic resistance and are present in the majority of drug-resistant Gram-negative bacterial infections worldwide. Allosteric mutations that increase catalytic rates of these drug resistance enzymes have been identified in clinical isolates but are challenging to predict prospectively. We have used molecular dynamics simulations to predict allosteric mutants increasing CTX-M9 drug resistance, experimentally testing top mutants using multiple antibiotics. Purified enzymes show an increase in catalytic rate and efficiency, while mutant crystal structures show no detectable changes from wild-type CTX-M9. We hypothesize that increased drug resistance results from changes in the conformational ensemble of an acyl intermediate in hydrolysis. Machine-learning analyses on the three top mutants identify changes to the binding-pocket conformational ensemble by which these allosteric mutations transmit their effect. These findings show how molecular simulation can predict how allosteric mutations alter active-site conformational equilibria to increase catalytic rates and thus resistance against common clinically used antibiotics.
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| 4. |
- Ni, P., et al.
(författare)
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A kinetic model on oxygen transfer at a steel/slag interface under effect of interfacial tension
- 2018
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Ingår i: ISIJ International. - : Iron and Steel Institute of Japan. - 0915-1559 .- 1347-5460. ; 58:11, s. 1979-1988
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Tidskriftsartikel (refereegranskat)abstract
- A kinetic model was developed to predict the dynamic change of the oxygen content in the sub-interface region as well as the dynamic change of the interfacial tension between molten steel and slag. The dynamic steel/slag interfacial phenomena are very complex, where the combined effect of thermodynamics and kinetics on the interfacial tension needs to be accounted for. As a first step, the current model only considers the SiO2 decomposition, oxygen adsorption and desorption at the steel/slag interface to realize the modeling of the dynamic change of the steel/slag interface phenomena. The oxygen desorption rate was derived based on the slope of the interfacial tension change over oxygen content. Specifically, the oxygen change with time in a sub-interface was predicted by the current model. The oxygen desorption rate was found to have an important influence on the dynamic change of the oxygen content in the sub-interface region. Furthermore, a low slag viscosity was found to increase the oxygen content at the interface due to the fast supply of SiO2 from the slag bulk to the interface. In addition, the equilibrium constant for the oxygen adsorption at an interface due to the interfacial tension effect increases the oxygen content in the sub-interface region.
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| 5. |
- Feron, Romain, et al.
(författare)
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RADSex : A computational workflow to study sex determination using restriction site-associated DNA sequencing data
- 2021
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Ingår i: Molecular Ecology Resources. - : John Wiley & Sons. - 1755-098X .- 1755-0998. ; 21:5, s. 1715-1731
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Tidskriftsartikel (refereegranskat)abstract
- The study of sex determination and sex chromosome organization in nonmodel species has long been technically challenging, but new sequencing methodologies now enable precise and high-throughput identification of sex-specific genomic sequences. In particular, restriction site-associated DNA sequencing (RAD-Seq) is being extensively applied to explore sex determination systems in many plant and animal species. However, software specifically designed to search for and visualize sex-biased markers using RAD-Seq data is lacking. Here, we present RADSex, a computational analysis workflow designed to study the genetic basis of sex determination using RAD-Seq data. RADSex is simple to use, requires few computational resources, makes no prior assumptions about the type of sex-determination system or structure of the sex locus, and offers convenient visualization through a dedicated R package. To demonstrate the functionality of RADSex, we re-analysed a published data set of Japanese medaka, Oryzias latipes, where we uncovered a previously unknown Y chromosome polymorphism. We then used RADSex to analyse new RAD-Seq data sets from 15 fish species spanning multiple taxonomic orders. We identified the sex determination system and sex-specific markers in six of these species, five of which had no known sex-markers prior to this study. We show that RADSex greatly facilitates the study of sex determination systems in nonmodel species thanks to its speed of analyses, low resource usage, ease of application and visualization options. Furthermore, our analysis of new data sets from 15 species provides new insights on sex determination in fish.
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| 6. |
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| 7. |
- Premeaux, Thomas A, et al.
(författare)
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Elevated cerebrospinal fluid Galectin-9 is associated with central nervous system immune activation and poor cognitive performance in older HIV-infected individuals.
- 2019
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Ingår i: Journal of neurovirology. - : Springer Science and Business Media LLC. - 1538-2443 .- 1355-0284. ; 25:2, s. 150-161
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Tidskriftsartikel (refereegranskat)abstract
- We previously reported that galectin-9 (Gal-9), a soluble lectin with immunomodulatory properties, is elevated in plasma during HIV infection and induces HIV transcription. The link between Gal-9 and compromised neuronal function is becoming increasingly evident; however, the association with neuroHIV remains unknown. We measured Gal-9 levels by ELISA in cerebrospinal fluid (CSF) and plasma of 70 HIV-infected (HIV+) adults stratified by age (older >40years and younger <40years) either ART suppressed or with detectable CSF HIV RNA, including a subgroup with cognitive assessments, and 18 HIV uninfected (HIV-) controls. Gal-9 tissue expression was compared in necropsy brain specimens from HIV- and HIV+ donors using gene datasets and immunohistochemistry. Among older HIV+ adults, CSF Gal-9 was elevated in the ART suppressed and CSF viremic groups compared to controls, whereas in the younger group, Gal-9 levels were elevated only in the CSF viremic group (p<0.05). CSF Gal-9 positively correlated with age in all groups (p<0.05). CSF Gal-9 tracked with CSF HIV RNA irrespective of age (β=0.33; p<0.05). Higher CSF Gal-9 in the older viremic HIV+ group correlated with worse neuropsychological test performance scores independently of age and CSF HIV RNA (p<0.05). Furthermore, CSF Gal-9 directly correlated with myeloid activation (CSF-soluble CD163 and neopterin) in both HIV+ older groups (p<0.05). Among HIV+ necropsy specimens, Gal-9 expression was increased in select brain regions compared to controls (p<0.05). Gal-9 may serve as a novel neuroimmuno-modulatory protein that is involved in driving cognitive deficits in those aging with HIV and may be valuable in tracking cognitive abnormalities.
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| 8. |
- Taguchi, Akira, et al.
(författare)
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Visual assessment of non-eroded thin cortex on panoramic radiographs in identifying women with osteoporosis : Osteoporosis Screening Project in Dentistry (OSPD)
- 2009
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Ingår i: Programme and abstract book. ; , s. 65-65
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- Introduction The presence of an eroded or thinned cortex of the mandible on panoramic radiographs may be useful in identifying women with osteoporosis. However, little is known as to whether a non-eroded thin cortex predicts osteoporosis. Objective To clarify whether visual assessment of non-eroded thin cortex increases the diagnostic efficacy of identifying women with osteoporosis. Materials and methods Of 60 observers who participated in OSPD (Taguchi et al., Bone, 2008), 41 observers visually assessed non-eroded thin cortex in addition to Klemetti’s index (KI) for 100 panoramic radiographs on the OSPD website via the Internet twice with approximately a two-week interval. The area under the receiver operating characteristics curves (AUROC) in identifying women with osteoporosis by both KI and non-eroded thin cortex was calculated on two occasions; non-eroded thin cortex was included in “class 1 of KI (decreased probability of osteoporosis)” or “class 3 of KI (increased probability of osteoporosis)”. Mean AUROC was compared between these two occasions with paired ttest. Results In the first series of observations, the mean AUROC significantly increased when noneroded thin cortex was considered as a sign of increased probability of osteoporosis (mean +/- SD, 0.68 +/- 0.08 vs. 0.70 +/- 0.07, P=0.011). In the second set of observations, the result was unchanged (0.68 +/- 0.09 vs. 0.71 +/- 0.08, P<0.001). Conclusions and discussion Visual identification of a non-eroded thin cortex on panoramic radiographs may increase the diagnostic efficacy of identifying women with osteoporosis.
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