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| 2. |
- Pathan, M., et al.
(författare)
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A novel community driven software for functional enrichment analysis of extracellular vesicles data
- 2017
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Ingår i: Journal of Extracellular Vesicles. - : Wiley. - 2001-3078. ; 6:1
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Tidskriftsartikel (refereegranskat)abstract
- Bioinformatics tools are imperative for the in depth analysis of heterogeneous high-throughput data. Most of the software tools are developed by specific laboratories or groups or companies wherein they are designed to perform the required analysis for the group. However, such software tools may fail to capture "what the community needs in a tool". Here, we describe a novel community-driven approach to build a comprehensive functional enrichment analysis tool. Using the existing FunRich tool as a template, we invited researchers to request additional features and/or changes. Remarkably, with the enthusiastic participation of the community, we were able to implement 90% of the requested features. FunRich enables plugin for extracellular vesicles wherein users can download and analyse data from Vesiclepedia database. By involving researchers early through community needs software development, we believe that comprehensive analysis tools can be developed in various scientific disciplines.
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| 3. |
- Kanungo, J, et al.
(författare)
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Surface treatment of nanoporous silicon with noble metal ions and characterizations
- 2010
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Ingår i: APPLIED SURFACE SCIENCE. - : Elsevier Science B.V., Amsterdam.. - 0169-4332. ; 256:13, s. 4231-4240
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Tidskriftsartikel (refereegranskat)abstract
- A very large surface to volume ratio of nanoporous silicon (PS) produces a high density of surface states, which are responsible for uncontrolled oxidation of the PS surface. Hence it disturbs the stability of the material and also creates difficulties in the formation of a reliable electrical contact. To passivate the surface states of the nanoporous silicon, noble metals (Pd, Ru, and Pt) were dispersed on the PS surface by an electroless chemical method. GIXRD (glancing incidence X-ray diffraction) proved the crystallinity of PS and the presence of noble metals on its surface. While FESEM (field emission scanning electron microscopy) showed the morphology, the EDX (energy dispersive X-ray) line scans and digital X-ray image mapping indicated the formation of the noble metal islands on the PS surface. Dynamic SIMS (secondary ion mass spectroscopy) further confirmed the presence of noble metals and other impurities near the surface of the modified PS. The variation of the surface roughness after the noble metal modification was exhibited by AFM (atomic force microscopy). The formation of a thin oxide layer on the modified PS surface was verified by XPS (X-ray photoelectron spectroscopy).
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| 4. |
- Linden, S. T., et al.
(författare)
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Star Cluster Formation and Evolution in M101 : An Investigation with the Legacy Extragalactic UV Survey
- 2022
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Ingår i: Astrophysical Journal. - : American Astronomical Society. - 0004-637X .- 1538-4357. ; 935:2
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Tidskriftsartikel (refereegranskat)abstract
- We present Hubble Space Telescope WFC3/UVIS (F275W, F336W) and ACS/WFC optical (F435W, F555W, and F814W) observations of the nearby grand-design spiral galaxy M101 as part of the Legacy Extragalactic UV Survey (LEGUS). Compact sources detected in at least four bands were classified by both human experts and the convolutional neural network StarcNet. Human experts classified the 2351 brightest sources, retrieving N-c = 965 star clusters. StarcNet, trained on LEGUS data not including M101, classified all 4725 sources detected in four bands, retrieving N-c = 2270 star clusters. The combined catalog represents the most complete census to date of compact star clusters in M101. We find that for the 2351 sources with both a visual- and machine-learning classification StarcNet is able to reproduce the human classifications at high levels of accuracy (similar to 80%-90%), which is equivalent to the level of agreement between human classifiers in LEGUS. The derived cluster age distribution implies a disruption rate of dN/d tau proportional to tau(-0.45 +/- 0.14) over 10(7) < tau < 10(8.5) yr for cluster masses >= 10(3.55) M-circle dot for the central region of M101 and dN/d tau proportional to tau(-0.02 +/- 0.15) for cluster masses >= 10(3.38) M-circle dot in the northwest region of the galaxy. The trends we recover are weaker than those of other nearby spirals (e.g., M51) and starbursts, consistent with the M101 environment having a lower-density interstellar medium, and providing evidence in favor of environmentally dependent cluster disruption in the central, southeast, and northwest regions of M101.
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| 6. |
- Strawn, Clayton, et al.
(författare)
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The AGORA High-resolution Galaxy Simulations Comparison Project. VI. Similarities and Differences in the Circumgalactic Medium
- 2024
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Ingår i: Astrophysical Journal. - 0004-637X. ; 962:1
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Tidskriftsartikel (refereegranskat)abstract
- We analyze the circumgalactic medium (CGM) for eight commonly-used cosmological codes in the AGORA collaboration. The codes are calibrated to use identical initial conditions, cosmology, heating and cooling, and star formation thresholds, but each evolves with its own unique code architecture and stellar feedback implementation. Here, we analyze the results of these simulations in terms of the structure, composition, and phase dynamics of the CGM. We show properties such as metal distribution, ionization levels, and kinematics are effective tracers of the effects of the different code feedback and implementation methods, and as such they can be highly divergent between simulations. This is merely a fiducial set of models, against which we will in the future compare multiple feedback recipes for each code. Nevertheless, we find that the large parameter space these simulations establish can help disentangle the different variables that affect observable quantities in the CGM, e.g., showing that abundances for ions with higher ionization energy are more strongly determined by the simulation’s metallicity, while abundances for ions with lower ionization energy are more strongly determined by the gas density and temperature.
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| 7. |
- Jung, Christian, et al.
(författare)
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A comparison of very old patients admitted to intensive care unit after acute versus elective surgery or intervention
- 2019
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Ingår i: Journal of critical care. - : W B SAUNDERS CO-ELSEVIER INC. - 0883-9441 .- 1557-8615. ; 52, s. 141-148
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Tidskriftsartikel (refereegranskat)abstract
- Background: We aimed to evaluate differences in outcome between patients admitted to intensive care unit (ICU) after elective versus acute surgery in a multinational cohort of very old patients (80 years; VIP). Predictors of mortality, with special emphasis on frailty, were assessed.Methods: In total, 5063 VIPs were induded in this analysis, 922 were admitted after elective surgery or intervention, 4141 acutely, with 402 after acute surgery. Differences were calculated using Mann-Whitney-U test and Wilcoxon test. Univariate and multivariable logistic regression were used to assess associations with mortality.Results: Compared patients admitted after acute surgery, patients admitted after elective surgery suffered less often from frailty as defined as CFS (28% vs 46%; p < 0.001), evidenced lower SOFA scores (4 +/- 5 vs 7 +/- 7; p < 0.001). Presence of frailty (CFS >4) was associated with significantly increased mortality both in elective surgery patients (7% vs 12%; p = 0.01), in acute surgery (7% vs 12%; p = 0.02).Conclusions: VIPs admitted to ICU after elective surgery evidenced favorable outcome over patients after acute surgery even after correction for relevant confounders. Frailty might be used to guide clinicians in risk stratification in both patients admitted after elective and acute surgery.
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| 8. |
- Maji, Samir K, et al.
(författare)
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Functional Amyloids As Natural Storage of Peptide Hormones in Pituitary Secretory Granules
- 2009
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Ingår i: SCIENCE. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 325:5938, s. 328-332
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Tidskriftsartikel (refereegranskat)abstract
- Amyloids are highly organized cross-beta-sheet-rich protein or peptide aggregates that are associated with pathological conditions including Alzheimers disease and type II diabetes. However, amyloids may also have a normal biological function, as demonstrated by fungal prions, which are involved in prion replication, and the amyloid protein Pmel17, which is involved in mammalian skin pigmentation. We found that peptide and protein hormones in secretory granules of the endocrine system are stored in an amyloid-like cross-beta-sheet-rich conformation. Thus, functional amyloids in the pituitary and other organs can contribute to normal cell and tissue physiology.
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