| 1. |
- Mahajan, Anubha, et al.
(författare)
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Refining the accuracy of validated target identification through coding variant fine-mapping in type 2 diabetes
- 2018
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Ingår i: Nature Genetics. - : Nature Publishing Group. - 1061-4036 .- 1546-1718. ; 50:4, s. 559-571
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Tidskriftsartikel (refereegranskat)abstract
- We aggregated coding variant data for 81,412 type 2 diabetes cases and 370,832 controls of diverse ancestry, identifying 40 coding variant association signals (P < 2.2 × 10−7); of these, 16 map outside known risk-associated loci. We make two important observations. First, only five of these signals are driven by low-frequency variants: even for these, effect sizes are modest (odds ratio ≤1.29). Second, when we used large-scale genome-wide association data to fine-map the associated variants in their regional context, accounting for the global enrichment of complex trait associations in coding sequence, compelling evidence for coding variant causality was obtained for only 16 signals. At 13 others, the associated coding variants clearly represent ‘false leads’ with potential to generate erroneous mechanistic inference. Coding variant associations offer a direct route to biological insight for complex diseases and identification of validated therapeutic targets; however, appropriate mechanistic inference requires careful specification of their causal contribution to disease predisposition.
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| 2. |
- Beal, Jacob, et al.
(författare)
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Robust estimation of bacterial cell count from optical density
- 2020
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Ingår i: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
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Tidskriftsartikel (refereegranskat)abstract
- Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data.
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| 3. |
- Brout, Dillon, et al.
(författare)
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The Pantheon+ analysis : cosmological constraints
- 2022
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Ingår i: Astrophysical Journal. - : Institute of Physics (IOP). - 0004-637X .- 1538-4357. ; 938:2
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Tidskriftsartikel (refereegranskat)abstract
- We present constraints on cosmological parameters from the Pantheon+ analysis of 1701 light curves of 1550 distinct Type Ia supernovae (SNe Ia) ranging in redshift from z = 0.001 to 2.26. This work features an increased sample size from the addition of multiple cross-calibrated photometric systems of SNe covering an increased redshift span, and improved treatments of systematic uncertainties in comparison to the original Pantheon analysis, which together result in a factor of 2 improvement in cosmological constraining power. For a flat ΛCDM model, we find ΩM = 0.334 ± 0.018 from SNe Ia alone. For a flat w0CDM model, we measure w0 = −0.90 ± 0.14 from SNe Ia alone, H0 = 73.5 ± 1.1 km s−1 Mpc−1 when including the Cepheid host distances and covariance (SH0ES), and w0 = -0.978-+0.0310.024 when combining the SN likelihood with Planck constraints from the cosmic microwave background (CMB) and baryon acoustic oscillations (BAO); both w0 values are consistent with a cosmological constant. We also present the most precise measurements to date on the evolution of dark energy in a flat w0waCDM universe, and measure wa = -0.1-+2.00.9 from Pantheon+ SNe Ia alone, H0 = 73.3 ± 1.1 km s−1 Mpc−1 when including SH0ES Cepheid distances, and wa = -0.65-+0.320.28 when combining Pantheon+ SNe Ia with CMB and BAO data. Finally, we find that systematic uncertainties in the use of SNe Ia along the distance ladder comprise less than one-third of the total uncertainty in the measurement of H0 and cannot explain the present “Hubble tension” between local measurements and early universe predictions from the cosmological model.
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| 4. |
- Chettiyam Thodi, Muhamed Fasil, et al.
(författare)
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Using RS and GIS Techniques to Assess and Monitor Coastal Changes of Coastal Islands in the Marine Environment of a Humid Tropical Region
- 2023
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Ingår i: Water. - : MDPI. - 2073-4441. ; 15:21
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Tidskriftsartikel (refereegranskat)abstract
- Vypin, Vallarpadam, and Bolgatty are significant tropical coastal islands situated in the humid tropical Kerala region of India, notable for their environmental sensitivity. This study conducted a comprehensive assessment of shoreline alterations on these islands by integrating Remote Sensing (RS) and Geographic Information Systems (GIS) techniques. Utilizing satellite imagery from the LANDSAT series with a spatial resolution of 30 m, the analysis spanned the years from 1973 to 2019. The Digital Shoreline Analysis System (DSAS) tool, integrated into the ArcGIS software, was employed to monitor and analyze shoreline shifts, encompassing erosion and accretion. Various statistical parameters, including Net Shoreline Movement (NSM), End Point Rate (EPR), and Linear Regression Rate (LRR), were utilized to evaluate these changes. Additionally, the study aimed to discern the root causes of shoreline modifications in the study area, encompassing disturbances and the construction of new structures on these islands. The results conclusively demonstrated the substantial impact endured by these coastal islands, with accretion on both sides leading to the creation of new landmasses. This manuscript effectively illustrates that these islands have experienced marine transgression, notably evidenced by accretion. Anthropogenic activities were identified as the primary drivers behind the observed shoreline changes, underscoring the need for careful management and sustainable practices in these fragile coastal ecosystems.
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| 5. |
- Melaibari, Ammar A., et al.
(författare)
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Ultrahard boron nitride material through a hybrid laser/waterjet based surface treatment
- 2016
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Ingår i: Acta Materialia. - : Elsevier BV. - 1873-2453 .- 1359-6454. ; 102, s. 315-322
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Tidskriftsartikel (refereegranskat)abstract
- We report a dual phase boron nitride (BN) material composed of 50% cubic and 50% wurtzite phases that has the same level of hardness as polycrystalline diamond. The dual phase BN material was initially synthesized from high pressure and high temperature consolidation of powder materials and subsequently, a laser/waterjet heat treatment (LWH) was applied to the material surface. The LWH process consisted of heating the sample surface using a continuous wave CO2 laser beam followed by tandem waterjet quenching of the laser irradiated material. The indentation hardness of the as-synthesized material was measured to be nominally 37 GPa. After the heat treatment the indentation hardness increased to nominal values of 75 GPa reaching the hardness of polycrystalline diamond 65-80 GPa. Dispersive Raman spectroscopy, high-resolution scanning electron microscope (HRSEM) and surface grazing XRD were used to characterize the BN phase signatures, grain size changes and phase transitions in both as-synthesized and heat treated material. Comparison of the as-synthesized and heat treated material microstructure revealed that heat treatment resulted in microstructure that consists of large grains; surrounded with regions of nano-grains between larger grains and; formation of solid interlayer along the grain boundaries. The increase in hardness was observed for LWH processing at laser fluence below 35 J/mm(2), and LWH processing above this value resulted in spallation of BN material from the surface. Raman spectrums of the material processed below the laser fluence of 35 J/mm(2) indicated that there are minimal phase transitions in the material; however, above that fluence, BN transformed into hexagonal phase resulting in surface damage through spallation. A combination of amorphous phase formation at the grain boundaries and grain size refinement are suggested as the mechanisms responsible for the LWH processing induced hardness increase. (C) 2015 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.
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| 6. |
- Ovalle, Anaelia, et al.
(författare)
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Queer In AI : A Case Study in Community-Led Participatory AI
- 2023
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Ingår i: FAccT '23. - : Association for Computing Machinery (ACM). - 9798400701924 ; , s. 1882-1895
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Konferensbidrag (refereegranskat)abstract
- Queerness and queer people face an uncertain future in the face of ever more widely deployed and invasive artificial intelligence (AI). These technologies have caused numerous harms to queer people, including privacy violations, censoring and downranking queer content, exposing queer people and spaces to harassment by making them hypervisible, deadnaming and outing queer people. More broadly, they have violated core tenets of queerness by classifying and controlling queer identities. In response to this, the queer community in AI has organized Queer in AI, a global, decentralized, volunteer-run grassroots organization that employs intersectional and community-led participatory design to build an inclusive and equitable AI future. In this paper, we present Queer in AI as a case study for community-led participatory design in AI. We examine how participatory design and intersectional tenets started and shaped this community's programs over the years. We discuss different challenges that emerged in the process, look at ways this organization has fallen short of operationalizing participatory and intersectional principles, and then assess the organization's impact. Queer in AI provides important lessons and insights for practitioners and theorists of participatory methods broadly through its rejection of hierarchy in favor of decentralization, success at building aid and programs by and for the queer community, and effort to change actors and institutions outside of the queer community. Finally, we theorize how communities like Queer in AI contribute to the participatory design in AI more broadly by fostering cultures of participation in AI, welcoming and empowering marginalized participants, critiquing poor or exploitative participatory practices, and bringing participation to institutions outside of individual research projects. Queer in AI's work serves as a case study of grassroots activism and participatory methods within AI, demonstrating the potential of community-led participatory methods and intersectional praxis, while also providing challenges, case studies, and nuanced insights to researchers developing and using participatory methods.
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| 7. |
- Scolnic, Dan, et al.
(författare)
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The Pantheon+ analysis : the full data set and light-curve release
- 2022
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Ingår i: Astrophysical Journal. - : Institute of Physics (IOP). - 0004-637X .- 1538-4357. ; 938:2
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Tidskriftsartikel (refereegranskat)abstract
- Here we present 1701 light curves of 1550 unique, spectroscopically confirmed Type Ia supernovae (SNe Ia) that will be used to infer cosmological parameters as part of the Pantheon+ SN analysis and the Supernovae and H0 for the Equation of State of dark energy distance-ladder analysis. This effort is one part of a series of works that perform an extensive review of redshifts, peculiar velocities, photometric calibration, and intrinsic-scatter models of SNe Ia. The total number of light curves, which are compiled across 18 different surveys, is a significant increase from the first Pantheon analysis (1048 SNe), particularly at low redshift (z). Furthermore, unlike in the Pantheon analysis, we include light curves for SNe with z < 0.01 such that SN systematic covariance can be included in a joint measurement of the Hubble constant (H0) and the dark energy equation-of-state parameter (w). We use the large sample to compare properties of 151 SNe Ia observed by multiple surveys and 12 pairs/triplets of “SN siblings”—SNe found in the same host galaxy. Distance measurements, application of bias corrections, and inference of cosmological parameters are discussed in the companion paper by Brout et al., and the determination of H0 is discussed by Riess et al. These analyses will measure w with ∼3% precision and H0 with ∼1 km s−1 Mpc−1 precision.
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