| 1. |
- 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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| 2. |
- Mahapatra, Sayanta, et al.
(författare)
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Substoichiometric Hsp104 regulates the genesis and persistence of self-replicable amyloid seeds of Sup35 prion domain
- 2022
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Ingår i: Journal of Biological Chemistry. - : Elsevier. - 0021-9258 .- 1083-351X. ; 298:8
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Tidskriftsartikel (refereegranskat)abstract
- Prion-like self-perpetuating conformational conversion of proteins is involved in both transmissible neurodegenerative diseases in mammals and non-Mendelian inheritance in yeast. The transmissibility of amyloid-like aggregates is dependent on the stoichiometry of chaperones such as heat shock proteins (Hsps), including disaggregases. To provide the mechanistic underpinnings of the formation and persistence of prefibrillar amyloid seeds, we investigated the role of substoichiometric Hsp104 on the in vitro amyloid aggregation of the prion domain (NM-domain) of Saccharomyces cerevisiae Sup35. At low substoichiometric concentrations, we show Hsp104 exhibits a dual role: it considerably accelerates the formation of prefibrillar species by shortening the lag phase but also prolongs their persistence by introducing unusual kinetic halts and delaying their conversion into mature amyloid fibers. Additionally, Hsp104-modulated amyloid species displayed a better seeding capability compared to NM-only amyloids. Using biochemical and biophysical tools coupled with site-specific dynamic readouts, we characterized the distinct structural and dynamical signatures of these amyloids. We reveal that Hsp104-remodeled amyloidogenic species are compositionally diverse in prefibrillar aggregates and are packed in a more ordered fashion compared to NM-only amyloids. Finally, we show these Hsp104-remodeled, conformationally distinct NM aggregates display an enhanced autocatalytic self-templating ability that might be crucial for phenotypic outcomes. Taken together, our results demonstrate that substoichiometric Hsp104 promotes compositional diversity and conformational modulations during amyloid formation, yielding effective prefibrillar seeds that are capable of driving prion-like Sup35 propagation. Our findings underscore the key functional and pathological roles of substoichiometric chaperones in prion-like propagation.
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| 3. |
- Das, Rasel, et al.
(författare)
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Nanocellulose for Sustainable Water Purification
- 2022
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Ingår i: Chemical Reviews. - : American Chemical Society (ACS). - 0009-2665 .- 1520-6890. ; 122:9, s. 8936-9031
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Forskningsöversikt (refereegranskat)abstract
- Nanocelluloses (NC) are nature-based sustainable biomaterials, which not only possess cellulosic properties but also have the important hallmarks of nanomaterials, such as large surface area, versatile reactive sites or functionalities, and scaffolding stability to host inorganic nanoparticles. This class of nanomaterials offers new opportunities for a broad spectrum of applications for clean water production that were once thought impractical. This Review covers substantial discussions based on evaluative judgments of the recent literature and technical advancements in the fields of coagulation/flocculation, adsorption, photocatalysis, and membrane filtration for water decontamination through proper understanding of fundamental knowledge of NC, such as purity, crystallinity, surface chemistry and charge, suspension rheology, morphology, mechanical properties, and film stability. To supplement these, discussions on low-cost and scalable NC extraction, new characterizations including solution small-angle X-ray scattering evaluation, and structure-property relationships of NC are also reviewed. Identifying knowledge gaps and drawing perspectives could generate guidance to overcome uncertainties associated with the adaptation of NC-enabled water purification technologies. Furthermore, the topics of simultaneous removal of multipollutants disposal and proper handling of post/spent NC are discussed. We believe NC-enabled remediation nanomaterials can be integrated into a broad range of water treatments, greatly improving the cost-effectiveness and sustainability of water purification.
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| 4. |
- Khandelwal, Akanksha, et al.
(författare)
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Discovery of an inflated hot Jupiter around a slightly evolved star TOI-1789
- 2022
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Ingår i: Monthly Notices of the Royal Astronomical Society. - : Oxford University Press (OUP). - 0035-8711 .- 1365-2966. ; 509:3, s. 3339-3354
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Tidskriftsartikel (refereegranskat)abstract
- We report here the discovery of a hot Jupiter at an orbital period of 3.208664 ± 0.000015 d around TOI-1789 (TYC 1962-00303-1, TESSmag = 9.1) based on the TESS photometry, ground-based photometry, and high-precision radial velocity (RV) observations. The high-precision RV observations were obtained from the high-resolution spectrographs, PARAS at Physical Research Laboratory (PRL), India, and TCES at Thüringer Landessternwarte Tautenburg (TLS), Germany, and the ground-based transit observations were obtained using the 0.43-m telescope at PRL with the Bessel-R filter. The host star is a slightly evolved (log g∗ = 3.943+0.023-0.043), late F-type (Teff= 5991 ± 55 K), metal-rich star ([Fe/H] = 0.373+0.071-0.086 dex) with a radius of R ∗ = 2.168+0.036}-0.034 R located at a distance of 223.53+0.91-0.90} pc. The simultaneous fitting of the multiple light curves and the RV data of TOI-1789 reveals that TOI-1789 b has a mass of MP = 0.70 ± 0.16 MJ, a radius of RP = 1.44+0.24-0.14, RJ, and a bulk density of ρP = 0.28+0.14-0.12 g cm-3 with an orbital separation of a = 0.04882+0.00063-0.0016 au. This puts TOI-1789 b in the category of inflated hot Jupiters. It is one of the few nearby evolved stars with a close-in planet. The detection of such systems will contribute to our understanding of mechanisms responsible for inflation in hot Jupiters and also provide an opportunity to understand the evolution of planets around stars leaving the main-sequence branch.
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| 5. |
- Mueller, Stefanie H., et al.
(författare)
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Aggregation tests identify new gene associations with breast cancer in populations with diverse ancestry
- 2023
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Ingår i: Genome Medicine. - : BioMed Central (BMC). - 1756-994X. ; 15
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Tidskriftsartikel (refereegranskat)abstract
- Background: Low-frequency variants play an important role in breast cancer (BC) susceptibility. Gene-based methods can increase power by combining multiple variants in the same gene and help identify target genes.Methods: We evaluated the potential of gene-based aggregation in the Breast Cancer Association Consortium cohorts including 83,471 cases and 59,199 controls. Low-frequency variants were aggregated for individual genes' coding and regulatory regions. Association results in European ancestry samples were compared to single-marker association results in the same cohort. Gene-based associations were also combined in meta-analysis across individuals with European, Asian, African, and Latin American and Hispanic ancestry.Results: In European ancestry samples, 14 genes were significantly associated (q < 0.05) with BC. Of those, two genes, FMNL3 (P = 6.11 x 10(-6)) and AC058822.1 (P = 1.47 x 10(-4)), represent new associations. High FMNL3 expression has previously been linked to poor prognosis in several other cancers. Meta-analysis of samples with diverse ancestry discovered further associations including established candidate genes ESR1 and CBLB. Furthermore, literature review and database query found further support for a biologically plausible link with cancer for genes CBLB, FMNL3, FGFR2, LSP1, MAP3K1, and SRGAP2C.Conclusions: Using extended gene-based aggregation tests including coding and regulatory variation, we report identification of plausible target genes for previously identified single-marker associations with BC as well as the discovery of novel genes implicated in BC development. Including multi ancestral cohorts in this study enabled the identification of otherwise missed disease associations as ESR1 (P = 1.31 x 10(-5)), demonstrating the importance of diversifying study cohorts.
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| 6. |
- Panchal, Vaidik, et al.
(författare)
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FPGA implementation of proposed number plate localization algorithm based on YOLOv2 (You Only Look Once)
- 2023
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Ingår i: Microsystem Technologies. - : Springer Nature. - 0946-7076 .- 1432-1858. ; 29:10, s. 1501-1513
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Tidskriftsartikel (refereegranskat)abstract
- Many algorithms used in machine learning and artificial intelligence rely on exact object identification and recognition as their foundation for efficiency and accuracy. Hardware implementation of such methods, when implemented, serves to boost the reliability and productivity of object detection in a wide range of contexts. Hardware implementation of such an algorithm takes a lot of resources and a huge amount of calculation time. The object detection and recognition process require a collection of complex algorithms and a series of filtering approaches to work beyond the boundary conditions. The YOLOv2 network is superior to filters and complicated algorithms for this problem. The authors of this study propose an enhanced YOLOv2 Network for object recognition and a novel approach for optimising the existing YOLOv2 Network for localization to pinpoint the ROI that can be used to scale down and contain the object's original area. The network is proposed by configuring the existing YOLOv2 with additional convolution layers and dropout layers. The dropout layers are added to reduce the dependency on a single neuron and is an effective way of preventing overfitting of the network. Also, instead of ReLU as the activation function, we are using the Swish activation function which tends to provide better results. By isolating and producing the region of interest (ROI) from the original image, the algorithm was able to significantly cut down on both the number of resources needed and the time needed to complete the task. The proposed work is implemented on an FPGA board (Xilinx Zynq-Z7010 FPGA board), and the dataset is collected and prepared by the authors. Data augmentation is done to enhance the training data to enhance the training data, which results in better trained network. MATLAB is used to demonstrate the feasibility of the work and provide a thorough evaluation of its merits. The results show that the accuracy of the conventional algorithm approach drops to 20–30% once you move outside the boundaries, whereas the accuracy of the proposed work increases to 60–70% and a 15–20% increase in efficiency with proposed network based on YOLOv2. The proposed algorithm is three times as fast as the standard method while using only 35 percent as much technology.
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| 7. |
- Rajput, Kunwar Pritiraj, et al.
(författare)
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Robust Linear Hybrid Beamforming Designs Relying on Imperfect CSI in mmWave MIMO IoT Networks
- 2023
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Ingår i: IEEE Internet of Things Journal. - : Institute of Electrical and Electronics Engineers (IEEE). - 2327-4662 .- 2372-2541. ; 10:10, s. 8893-8906
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Tidskriftsartikel (refereegranskat)abstract
- Linear hybrid beamformer designs are conceived for the decentralized estimation of a vector parameter in a millimeter wave (mmWave) multiple-input multiple-output (MIMO) Internet of Things network (IoTNe). The proposed designs incorporate both total IoTNe and individual IoTNo power constraints, while also eliminating the need for a baseband receiver combiner at the fusion center (FC). To circumvent the non-convexity of the hybrid beamformer design problem, the proposed approach initially determines the minimum mean square error (MMSE) digital transmit precoder (TPC) weights followed by a simultaneous orthogonal matching pursuit (SOMP)-based framework for obtaining the analog RF and digital baseband TPCs. Robust hybrid beamformers are also derived for the realistic imperfect channel state information (CSI) scenario, utilizing both the stochastic and norm-ball CSI uncertainty frameworks. The centralized MMSE bound derived in this work serves as a lower bound for the estimation performance of the proposed hybrid TPC designs. Finally, our simulation results quantify the benefits of the various designs developed.
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| 8. |
- Sharma, Priyanka, et al.
(författare)
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MPEG/H256 video encoder with 6T/8T hybrid memory architecture for high quality output at lower supply
- 2023
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Ingår i: Memories - Materials, Devices, Circuits and Systems. - : Elsevier. - 2773-0646. ; 4
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Tidskriftsartikel (refereegranskat)abstract
- The use of Multimedia video content is increased rapidly in the past decade, and most multimedia video content is used by mobile phone users. Multimedia video processing consumes significant power during video compression, and thus low power multimedia video compression is essential for battery operated devices. Moving Picture Experts Group (MPEG) Video encoding is giving a higher compression rate and low bandwidth requirement. Conventional MPEG Video encoding architecture uses the conventional 6T memory cells to store video frames for further compression processing. The failure probability of 6T cells is significantly large (0.0988 at 600 mV supply voltage), leading to a decrease in the output quality of the encoded video. From the hybrid memory matrix formulation, it is calculated that storing higher-order MSB bits in highly stable memory cells will provide high-quality video encoding processing as compared to the conventional technique because the human eye is more susceptible to higher-order luminance bits. Hence, in this research work instant of using conventional 6T memory cells during video encoding processing, a unique Hybrid 6T/8T memory architecture is proposed, where the 8-bit Luminance pixels are stored favourably in consonance with their effect on the output quality. The higher order luminance bits (MSB’s) require high stability and thus these bits are stored in the 8T bit cells and the remaining bits (LSB’s) are stored in the conventional 6T bit cells for high-quality video encoding processing. This research article also proposes a separate memory peripheral circuitry for hybrid memory architecture for video encoding techniques. In addition, this article proposes a unique architecture for parallel video processing with the use of a hybrid pixel memory array. The failure probability of 6T and 8T at the worst failure corner (FS corner for read and SF corner for write) is simulated for 30000 Monte-Carlo simulations points at 45 nm CMOS technology node using CADENCE EDA tool. For the simulation work here, a standard Common Intermediate Format/Quarter Common Intermediate Format (CIF/QCIF) Coastguard video sample is used and for output quality here average PSNR method is used and simulation work is performed using the MATLAB tool.The worst PSNR for conventional 6T memory array and Hybrid memory array at 600 mV supply voltage shows improvement in worst minimum PSNR as 6.43 dB is calculated. 30% less power consumption to conventional memory architecture.
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| 9. |
- Subjak, Jan, et al.
(författare)
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TOI-503: The First Known Brown-dwarf Am-star Binary from the TESS Mission
- 2020
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Ingår i: Astronomical Journal. - : American Astronomical Society. - 1538-3881 .- 0004-6256. ; 159:4
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Tidskriftsartikel (refereegranskat)abstract
- We report the discovery of an intermediate-mass transiting brown dwarf (BD), TOI-503b, from the TESS mission. TOI-503b is the first BD discovered by TESS, and it has circular orbit around a metallic-line A-type star with a period of P.=.3.6772.+/-.0.0001 days. The light curve from TESS indicates that TOI-503b transits its host star in a grazing manner, which limits the precision with which we measure the BD's radius ( = R 1.34+ R b 0.150.26 J). We obtained highresolution spectroscopic observations with the FIES, Ondr.ejov, PARAS, Tautenburg, and TRES spectrographs, and measured the mass of TOI-503b to be Mb.=.53.7.+/-.1.2 MJ. The host star has a mass of Ma.=.1.80.+/-.0.06Me, a radius of Ra.=.1.70.+/-.0.05Re, an effective temperature of Teff.=.7650.+/-.160 K, and a relatively high metallicity of 0.61.+/-.0.07 dex. We used stellar isochrones to derive the age of the system to be 180 Myr, which places its age between that of RIK 72b (a 10 Myr old BD in the Upper Scorpius stellar association) and AD 3116b (a 600 Myr old BD in the Praesepe cluster). Given the difficulty in measuring the tidal interactions between BDs and their host stars, we cannot precisely say whether this BD formed in situ or has had its orbit circularized by its host star over the relatively short age of the system. Instead, we offer an examination of plausible values for the tidal quality factor for the star and BD. TOI-503b joins a growing number of known short-period, intermediate-mass BDs orbiting mainsequence stars, and is the second such BD known to transit an A star, after HATS-70b. With the growth in the population in this regime, the driest region in the BD desert (35-55MJ sin i) is reforesting.
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