| 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. |
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| 3. |
- Aad, G, et al.
(författare)
-
- 2015
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swepub:Mat__t
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| 4. |
- Liu, Hui, et al.
(författare)
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Centromere-Specific Retrotransposons and Very-Long-Chain Fatty Acid Biosynthesis in the Genome of Yellowhorn (Xanthoceras sorbifolium, Sapindaceae), an Oil-Producing Tree With Significant Drought Resistance
- 2021
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Ingår i: Frontiers in Plant Science. - : Frontiers Media S.A.. - 1664-462X. ; 12
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Tidskriftsartikel (refereegranskat)abstract
- In-depth genome characterization is still lacking for most of biofuel crops, especially for centromeres, which play a fundamental role during nuclear division and in the maintenance of genome stability. This study applied long-read sequencing technologies to assemble a highly contiguous genome for yellowhorn (Xanthoceras sorbifolium), an oil-producing tree, and conducted extensive comparative analyses to understand centromere structure and evolution, and fatty acid biosynthesis. We produced a reference-level genome of yellowhorn, ∼470 Mb in length with ∼95% of contigs anchored onto 15 chromosomes. Genome annotation identified 22,049 protein-coding genes and 65.7% of the genome sequence as repetitive elements. Long terminal repeat retrotransposons (LTR-RTs) account for ∼30% of the yellowhorn genome, which is maintained by a moderate birth rate and a low removal rate. We identified the centromeric regions on each chromosome and found enrichment of centromere-specific retrotransposons of LINE1 and Gypsy in these regions, which have evolved recently (∼0.7 MYA). We compared the genomes of three cultivars and found frequent inversions. We analyzed the transcriptomes from different tissues and identified the candidate genes involved in very-long-chain fatty acid biosynthesis and their expression profiles. Collinear block analysis showed that yellowhorn shared the gamma (γ) hexaploidy event with Vitis vinifera but did not undergo any further whole-genome duplication. This study provides excellent genomic resources for understanding centromere structure and evolution and for functional studies in this important oil-producing plant.
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| 5. |
- Liu, Kui, et al.
(författare)
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Kallikrein genes are associated with lupus and glomerular basement membrane-specific antibody-induced nephritis in mice and humans
- 2009
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Ingår i: Journal of Clinical Investigation. - 0021-9738 .- 1558-8238. ; 119:4, s. 911-923
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Tidskriftsartikel (refereegranskat)abstract
- Immune-mediated nephritis contributes to disease in systemic lupus erythematosus, Goodpasture syndrome (caused by antibodies specific for glomerular basement membrane [anti-GBM antibodies]), and spontaneous lupus nephritis. Inbred mouse strains differ in susceptibility to anti-GBM antibody-induced and spontaneous lupus nephritis. This study sought to clarify the genetic and molecular factors that maybe responsible for enhanced immune-mediated renal disease in these models. When the kidneys of 3 mouse strains sensitive to anti-GBM antibody-induced nephritis were compared with those of 2 control strains using microarray analysis, one-fifth of the underexpressed genes belonged to the kallikrein gene family,which encodes serine esterases. Mouse strains that upregulated renal and urinary kallikreins exhibited less evidence of disease. Antagonizing the kallikrein pathway augmented disease, while agonists dampened the severity of anti-GBM antibody-induced nephritis. In addition, nephritis-sensitive mouse strains had kallikrein haplotypes that were distinct from those of control strains, including several regulatory polymorphisms,some of which were associated with functional consequences. Indeed, increased susceptibility to anti-GBM antibody-induced nephritis and spontaneous lupus nephritis was achieved by breeding mice with a genetic interval harboring the kallikrein genes onto a disease-resistant background. Finally, both human SLE and spontaneous lupus nephritis were found to be associated with kallikrein genes, particularly KLK1 and the KLK3 promoter, when DNA SNPs from independent cohorts of SLE patients and controls were compared. Collectively, these studies suggest that kallikreins are protective disease-associated genes in anti-GBM antibody-induced nephritis and lupus.
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| 6. |
- Pan, Qinying, et al.
(författare)
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Ultrafast charge transfer dynamics in 2D covalent organic frameworks/Re-complex hybrid photocatalyst
- 2022
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Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 13:1
-
Tidskriftsartikel (refereegranskat)abstract
- Rhenium(I)-carbonyl-diimine complexes have emerged as promising photocatalysts for carbon dioxide reduction with covalent organic frameworks recognized as perfect sensitizers and scaffold support. Such Re complexes/covalent organic frameworks hybrid catalysts have demonstrated high carbon dioxide reduction activities but with strong excitation energy-dependence. In this paper, we rationalize this behavior by the excitation energy-dependent pathways of internal photo-induced charge transfer studied via transient optical spectroscopies and time-dependent density-functional theory calculation. Under band-edge excitation, the excited electrons are quickly injected from covalent organic frameworks moiety into catalytic RheniumI center within picosecond but followed by fast backward geminate recombination. While under excitation with high-energy photon, the injected electrons are located at high-energy levels in RheniumI centers with longer lifetime. Besides those injected electrons to RheniumI center, there still remain some long-lived electrons in covalent organic frameworks moiety which is transferred back from RheniumI. This facilitates the two-electron reaction of carbon dioxide conversion to carbon monoxide.
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| 7. |
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| 8. |
- Quan, Zhou, et al.
(författare)
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Face Recognition Using Dense SIFT Feature Alignment
- 2016
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Ingår i: Chinese journal of electronics. - : Institution of Engineering and Technology (IET). - 1022-4653 .- 2075-5597. ; 25:6, s. 1034-1039
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Tidskriftsartikel (refereegranskat)abstract
- This paper addresses face recognition problem in a more challenging scenario where the training and test samples are both subject to the visual variations of poses, expressions and misalignments. We employ dense Scale-invariant feature transform (SIFT) feature matching as a generic transformation to roughly align training samples; and then identify input facial images via an improved sparse representation model based on the aligned training samples. Compared with previous methods, the extensive experimental results demonstrate the effectiveness of our method for the task of face recognition on three benchmark datasets.
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| 9. |
- Yu, Wenjin, et al.
(författare)
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Deep Learning-Based Classification of Cancer Cell in Leptomeningeal Metastasis on Cytomorphologic Features of Cerebrospinal Fluid
- 2022
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Ingår i: Frontiers in Oncology. - : Frontiers Media SA. - 2234-943X. ; 12, s. 1-11
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Tidskriftsartikel (refereegranskat)abstract
- Background: It is a critical challenge to diagnose leptomeningeal metastasis (LM), given its technical difficulty and the lack of typical symptoms. The existing gold standard of diagnosing LM is to use positive cerebrospinal fluid (CSF) cytology, which consumes significantly more time to classify cells under a microscope.Objective: This study aims to establish a deep learning model to classify cancer cells in CSF, thus facilitating doctors to achieve an accurate and fast diagnosis of LM in an early stage.Method: The cerebrospinal fluid laboratory of Xijing Hospital provides 53,255 cells from 90 LM patients in the research. We used two deep convolutional neural networks (CNN) models to classify cells in the CSF. A five-way cell classification model (CNN1) consists of lymphocytes, monocytes, neutrophils, erythrocytes, and cancer cells. A four-way cancer cell classification model (CNN2) consists of lung cancer cells, gastric cancer cells, breast cancer cells, and pancreatic cancer cells. Here, the CNN models were constructed by Resnet-inception-V2. We evaluated the performance of the proposed models on two external datasets and compared them with the results from 42 doctors of various levels of experience in the human-machine tests. Furthermore, we develop a computer-aided diagnosis (CAD) software to generate cytology diagnosis reports in the research rapidly.Results: With respect to the validation set, the mean average precision (mAP) of CNN1 is over 95% and that of CNN2 is close to 80%. Hence, the proposed deep learning model effectively classifies cells in CSF to facilitate the screening of cancer cells. In the human-machine tests, the accuracy of CNN1 is similar to the results from experts, with higher accuracy than doctors in other levels. Moreover, the overall accuracy of CNN2 is 10% higher than that of experts, with a time consumption of only one-third of that consumed by an expert. Using the CAD software saves 90% working time of cytologists.Conclusion: A deep learning method has been developed to assist the LM diagnosis with high accuracy and low time consumption effectively. Thanks to labeled data and step-by-step training, our proposed method can successfully classify cancer cells in the CSF to assist LM diagnosis early. In addition, this unique research can predict cancer’s primary source of LM, which relies on cytomorphologic features without immunohistochemistry. Our results show that deep learning can be widely used in medical images to classify cerebrospinal fluid cells. For complex cancer classification tasks, the accuracy of the proposed method is significantly higher than that of specialist doctors, and its performance is better than that of junior doctors and interns. The application of CNNs and CAD software may ultimately aid in expediting the diagnosis and overcoming the shortage of experienced cytologists, thereby facilitating earlier treatment and improving the prognosis of LM.
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| 10. |
- Zhou, Guang-Quan, et al.
(författare)
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A Single-Shot Region-Adaptive Network for Myotendinous Junction Segmentation in Muscular Ultrasound Images
- 2020
-
Ingår i: IEEE Transactions on Ultrasonics, Ferroelectrics and Frequency Control. - : Institute of Electrical and Electronics Engineers (IEEE). - 0885-3010 .- 1525-8955. ; 67:12, s. 2531-2542
-
Tidskriftsartikel (refereegranskat)abstract
- Tracking the myotendinous junction (MTJ) in consecutive ultrasound images is crucial for understanding the mechanics and pathological conditions of the muscletendon unit. However, the lack of reliable and efficient identification of MTJ due to poor image quality and boundary ambiguity restricts its application in motion analysis. In recent years, with the rapid development of deep learning, the region-based convolution neural network (RCNN) has shown great potential in the field of simultaneous objection detection and instance segmentation in medical images. This article proposes a region-adaptive network (RAN) to localize MTJ region and to segment it in a single shot. Our model learns about the salient information of MTJ with the help of a composite architecture. Herein, a region-based multitask learning network explores the region containing MTJ, while a parallel end-to-end U-shaped path extracts the MTJ structure from the adaptively selected region for combating data imbalance and boundary ambiguity. By demonstrating the ultrasound images of the gastrocnemius, we showed that the RAN achieves superior segmentation performance when compared with the state-of-the-art Mask RCNN method with an average Dice score of 80.1. Our proposed method is robust and reliable for advanced muscle and tendon function examinations obtained by ultrasound imaging.
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| 11. |
- Zhou, Guang-Quan, et al.
(författare)
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Automatic Myotendinous Junction Identification in Ultrasound Images Based on Junction-Based Template Measurements
- 2023
-
Ingår i: IEEE transactions on neural systems and rehabilitation engineering. - : Institute of Electrical and Electronics Engineers (IEEE). - 1534-4320 .- 1558-0210. ; 31, s. 851-862
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Tidskriftsartikel (refereegranskat)abstract
- Tracking the myotendinous junction (MTJ) motion in consecutive ultrasound images is essential to assess muscle and tendon interaction and understand the mechanics' muscle-tendon unit and its pathological conditions during motion. However, the inherent speckle noises and ambiguous boundaries deter the reliable identification of MTJ, thus restricting their usage in human motion analysis. This study advances a fully automatic displacement measurement method for MTJ using prior shape knowledge on the Y-shape MTJ, precluding the influence of irregular and complicated hyperechoic structures in muscular ultrasound images. Our proposed method first adopts the junction candidate points using a combined measure of Hessian matrix and phase congruency, followed by a hierarchical clustering technique to refine the candidates approximating the position of the MTJ. Then, based on the prior knowledge of Y-shape MTJ, we finally identify the best matching junction points according to intensity distributions and directions of their branches using multiscale Gaussian templates and a Kalman filter. We evaluated our proposed method using the ultrasound scans of the gastrocnemius from 8 young, healthy volunteers. Our results present more consistent with the manual method in the MTJ tracking method than existing optical flow tracking methods, suggesting its potential in facilitating muscle and tendon function examinations with in vivo ultrasound imaging.
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| 12. |
- Zhou, Guang-Quan, et al.
(författare)
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Automatic Myotendinous Junction Tracking in Ultrasound Images with Phase-Based Segmentation.
- 2018
-
Ingår i: BioMed Research International. - : Hindawi Limited. - 2314-6133 .- 2314-6141.
-
Tidskriftsartikel (refereegranskat)abstract
- Displacement of the myotendinous junction (MTJ) obtained by ultrasound imaging is crucial to quantify the interactive length changes of muscles and tendons for understanding the mechanics and pathological conditions of the muscle-tendon unit during motion. However, the lack of a reliable automatic measurement method restricts its application in human motion analysis. This paper presents an automated measurement of MTJ displacement using prior knowledge on tendinous tissues and MTJ, precluding the influence of nontendinous components on the estimation of MTJ displacement. It is based on the perception of tendinous features from musculoskeletal ultrasound images using Radon transform and thresholding methods, with information about the symmetric measures obtained from phase congruency. The displacement of MTJ is achieved by tracking manually marked points on tendinous tissues with the Lucas-Kanade optical flow algorithm applied over the segmented MTJ region. The performance of this method was evaluated on ultrasound images of the gastrocnemius obtained from 10 healthy subjects (26.0±2.9 years of age). Waveform similarity between the manual and automatic measurements was assessed by calculating the overall similarity with the coefficient of multiple correlation (CMC). In vivo experiments demonstrated that MTJ tracking with the proposed method (CMC = 0.97±0.02) was more consistent with the manual measurements than existing optical flow tracking methods (CMC = 0.79±0.11). This study demonstrated that the proposed method was robust to the interference of nontendinous components, resulting in a more reliable measurement of MTJ displacement, which may facilitate further research and applications related to the architectural change of muscles and tendons. [ABSTRACT FROM AUTHOR]
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| 13. |
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| 14. |
- Abuimara, Tareq, et al.
(författare)
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Detailed Case Studies
- 2023
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Ingår i: Occupant-Centric Simulation-Aided Building Design. - 9781000865752 ; , s. 257-367
-
Bokkapitel (övrigt vetenskapligt/konstnärligt)abstract
- Wireless body area networks (WBANs) are one of the key technologies that support the development of pervasive health monitoring (remote patient monitoring systems), which has attracted more attention in recent years. These WBAN applications requires stringent security requirements as they are concerned with human lives. In the recent scenario of the corona pandemic, where most of the healthcare providers are giving online services for treatment, DDoS attacks become the major threats over the internet. This chapter particularly focusses on detection of DDoS attack using machine learning algorithms over the healthcare environment. In the process of attack detection, the dataset is preprocessed. After preprocessing the dataset, the cleaned dataset is given to the popular classification algorithms in the area of machine learning namely, AdaBoost, J48, k-NN, JRip, Random Committee and Random Forest classifiers. Those algorithms are evaluated independently and the results are recorded. Results concluded that J48 outperform with accuracy of 99.98% with CICIDS dataset and random forest outperform with accuracy of 99.917, but it takes the longest model building time. Depending on the evaluation performance the appropriate classifier is selected for further DDoS detection at real-time.
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| 15. |
- Abuimara, Tareq, et al.
(författare)
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Understanding the Needs and Challenges of Occupant-centric Building Design among Stakeholders: A Review
- 2019
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Ingår i: ZEMCH International Conference. - 2652-2926. ; , s. 348-354
-
Konferensbidrag (refereegranskat)abstract
- Designing high-performance buildings is a complex process that involves several stakeholders at different stages of design development. Design stakeholders need to work together to achieve design objectives and overcome the challenge that arises from inefficient collaboration and coordination. Among these challenges are occupant-related assumptions which are made throughout the design process, including schematic design, energy modelling, construction, and even operation. Accuracy of these assumptions is highly dependent on the design stakeholders' objectives and the time that they are engaged in the design process. Differences in occupant-related assumptions can lead to a considerable level of uncertainty, which probably leads to suboptimal design decisions. To this end, the current practice, including the challenges and the barriers, needs to be documented and understood in order to develop an improved occupant modelling approach during building design. Therefore, this paper highlights the current practices of communicating occupant-related assumptions in the building design process. In this paper, we also argue the need for in-depth consideration of communication among design stakeholders.
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| 16. |
- Chang, Bo, et al.
(författare)
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Capillary Self-Alignment of Microchips on Soft Substrates
- 2016
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Ingår i: Micromachines. - : MDPI AG. - 2072-666X. ; 7:3
-
Tidskriftsartikel (refereegranskat)abstract
- Soft micro devices and stretchable electronics have attracted great interest for their potential applications in sensory skins and wearable bio-integrated devices. One of the most important steps in building printed circuits is the alignment of assembled micro objects. Previously, the capillary self-alignment of microchips driven by surface tension effects has been shown to be able to achieve high-throughput and high-precision in the integration of micro parts on rigid hydrophilic/superhydrophobic patterned surfaces. In this paper, the self-alignment of microchips on a patterned soft and stretchable substrate, which consists of hydrophilic pads surrounded by a superhydrophobic polydimethylsiloxane (PDMS) background, is demonstrated for the first time. A simple process has been developed for making superhydrophobic soft surface by replicating nanostructures of black silicon onto a PDMS surface. Different kinds of PDMS have been investigated, and the parameters for fabricating superhydrophobic PDMS have been optimized. A self-alignment strategy has been proposed that can result in reliable self-alignment on a soft PDMS substrate. Our results show that capillary self-alignment has great potential for building soft printed circuits.
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| 17. |
- Chang, Bo, et al.
(författare)
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HYDROPHILIC-SUPERHYDROPHOBIC PATTERNED SURFACE FOR PARALLEL MICROASSEMBLY
- 2014
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Ingår i: Technical Digest of the 25th Micromechanics and Microsystems Europe Conference (MME 2014), Istanbul, Turkey, 2014.
-
Konferensbidrag (refereegranskat)abstract
- In this paper, a hydrophilic-superhydrophobic patterned surface is investigated for parallel microassembly of 200 µm × 200 µm chips with receptor sites of the same dimensions, allowing for correction of significant error as compared to the state-of-the-art. The hydrophilic-superhydrophobic pattered surface consists of 200 µm × 200 µm silicondioxide receptor sites with black silicon substrate coated with fluorocarbon polymer. The measured contact angle of water on the silicon dioxide padsand the background are 50° and 170°, respectively.The water mist-induced hybrid microassembly technique is used to carry out the experimental studies on hydrophilic-superhydrophobic pattered surface for parallel microassembly. The experimental results show that the parallel microassembly of chips can not only be achieved on hydrophilic-superhydrophobic patterned surface, but also demonstrate significant error correction capability. With extreme large initial placement error, where achip is placed next to a receptor site and has zero overlapping with the receptor site, the chip is still able to align with the receptor site. The results also indicate that the reliability of the microassembly process can be greatly enhanced using hydrophilic patterns with super-hydrophobic background.
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| 18. |
- Chang, Bo, et al.
(författare)
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Self-transport and self-alignment of microchips using microscopic rain
- 2015
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Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 5
-
Tidskriftsartikel (refereegranskat)abstract
- Alignment of microchips with receptors is an important process step in the construction of integrated micro- and nanosystems for emerging technologies, and facilitating alignment by spontaneous self-assembly processes is highly desired. Previously, capillary self-alignment of microchips driven by surface tension effects on patterned surfaces has been reported, where it was essential for microchips to have sufficient overlap with receptor sites. Here we demonstrate for the first time capillary self-transport and self-alignment of microchips, where microchips are initially placed outside the corresponding receptor sites and can be self-transported by capillary force to the receptor sites followed by self-alignment. The surface consists of hydrophilic silicon receptor sites surrounded by superhydrophobic black silicon. Rain-induced microscopic droplets are used to form the meniscus for the self-transport and self-alignment. The boundary conditions for the self-transport have been explored by modeling and confirmed experimentally. The maximum permitted gap between a microchip and a receptor site is determined by the volume of the liquid and by the wetting contrast between receptor site and substrate. Microscopic rain applied on hydrophilic-superhydrophobic patterned surfaces greatly improves the capability, reliability and error-tolerance of the process, avoiding the need for accurate initial placement of microchips, and thereby greatly simplifying the alignment process.
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| 19. |
- Chang, Bo, et al.
(författare)
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Sliding droplets on hydrophilic/superhydrophobic patterned surfaces for liquid deposition
- 2016
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Ingår i: Applied Physics Letters. - : AIP Publishing. - 0003-6951 .- 1077-3118. ; 108:15
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Tidskriftsartikel (refereegranskat)abstract
- A facile gravity-induced sliding droplets method is reported for deposition of nanoliter sized droplets on hydrophilic/superhydrophobic patterned surface. The deposition process is parallel where multiple different liquids can be deposited simultaneously. The process is also high-throughput, having a great potential to be scaled up by increasing the size of the substrate.
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| 20. |
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| 21. |
- Chen, Mei-Qin, et al.
(författare)
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Arabidopsis NMD3 is required for nuclear export of 60S ribosomal subunits and affects secondary cell wall thickening
- 2012
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Ingår i: PLoS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 7:4, s. 35904-35904
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Tidskriftsartikel (refereegranskat)abstract
- NMD3 is required for nuclear export of the 60S ribosomal subunit in yeast and vertebrate cells, but no corresponding function of NMD3 has been reported in plants. Here we report that Arabidopsis thaliana NMD3 (AtNMD3) showed a similar function in the nuclear export of the 60S ribosomal subunit. Interference with AtNMD3 function by overexpressing a truncated dominant negative form of the protein lacking the nuclear export signal sequence caused retainment of the 60S ribosomal subunits in the nuclei. More interestingly, the transgenic Arabidopsis with dominant negative interference of AtNMD3 function showed a striking failure of secondary cell wall thickening, consistent with the altered expression of related genes and composition of cell wall components. Observation of a significant decrease of rough endoplasmic reticulum (RER) in the differentiating interfascicular fiber cells of the transgenic plant stems suggested a link between the defective nuclear export of 60S ribosomal subunits and the abnormal formation of the secondary cell wall. These findings not only clarified the evolutionary conservation of NMD3 functions in the nuclear export of 60S ribosomal subunits in yeast, animals and plants, but also revealed a new facet of the regulatory mechanism underlying secondary cell wall thickening in Arabidopsis. This new facet is that the nuclear export of 60S ribosomal subunits and the formation of RER may play regulatory roles in coordinating protein synthesis in cytoplasm and transcription in nuclei.
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| 22. |
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| 23. |
- Cheng, Shi-Ping, et al.
(författare)
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Haplotype-resolved genome assembly and allele-specific gene expression in cultivated ginger
- 2021
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Ingår i: Horticulture Research. - : Springer Nature. - 2052-7276. ; 8:1
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Tidskriftsartikel (refereegranskat)abstract
- Ginger (Zingiber officinale) is one of the most valued spice plants worldwide; it is prized for its culinary and folk medicinal applications and is therefore of high economic and cultural importance. Here, we present a haplotype-resolved, chromosome-scale assembly for diploid ginger anchored to 11 pseudochromosome pairs with a total length of 3.1 Gb. Remarkable structural variation was identified between haplotypes, and two inversions larger than 15 Mb on chromosome 4 may be associated with ginger infertility. We performed a comprehensive, spatiotemporal, genome-wide analysis of allelic expression patterns, revealing that most alleles are coordinately expressed. The alleles that exhibited the largest differences in expression showed closer proximity to transposable elements, greater coding sequence divergence, more relaxed selection pressure, and more transcription factor binding site differences. We also predicted the transcription factors potentially regulating 6-gingerol biosynthesis. Our allele-aware assembly provides a powerful platform for future functional genomics, molecular breeding, and genome editing in ginger.
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| 24. |
- Dong, Yi-Min, et al.
(författare)
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Development and Validation of a Nomogram for Assessing Survival in Patients With COVID-19 Pneumonia
- 2021
-
Ingår i: Clinical Infectious Diseases. - : Oxford University Press. - 1058-4838 .- 1537-6591. ; 72:4, s. 652-660
-
Tidskriftsartikel (refereegranskat)abstract
- Background. The outbreak of coronavirus disease 2019 (COVID-19) has spread worldwide and continues to threaten peoples' health as well as put pressure on the accessibility of medical systems. Early prediction of survival of hospitalized patients will help in the clinical management of COVID-19, but a prediction model that is reliable and valid is still lacking. Methods. We retrospectively enrolled 628 confirmed cases of COVID-19 using positive RT-PCR tests for SARS-CoV-2 in Tongji Hospital, Wuhan, China. These patients were randomly grouped into a training (60%) and a validation (40%) cohort. In the training cohort, LASSO regression analysis and multivariate Cox regression analysis were utilized to identify prognostic factors for in-hospital survival of patients with COVID-19. A nomogram based on the 3 variables was built for clinical use. AUCs, concordance indexes (C-index), and calibration curves were used to evaluate the efficiency of the nomogram in both training and validation cohorts. Results. Hypertension, higher neutrophil-to-lymphocyte ratio, and increased NT-proBNP values were found to be significantly associated with poorer prognosis in hospitalized patients with COVID-19. The 3 predictors were further used to build a prediction nomogram. The C-indexes of the nomogram in the training and validation cohorts were 0.901 and 0.892, respectively. The AUC in the training cohort was 0.922 for 14-day and 0.919 for 21-day probability of in-hospital survival, while in the validation cohort this was 0.922 and 0.881, respectively. Moreover, the calibration curve for 14- and 21-day survival also showed high coherence between the predicted and actual probability of survival. Conclusions. We built a predictive model and constructed a nomogram for predicting in-hospital survival of patients with COVID-19. This model has good performance and might be utilized clinically in management of COVID-19.
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| 25. |
- Dong, Yi-Min, et al.
(författare)
-
Reply to Collins et al
- 2021
-
Ingår i: Clinical Infectious Diseases. - : Oxford University Press. - 1058-4838 .- 1537-6591. ; 73:3, s. 558-559
-
Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)
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| 26. |
- Földváry Ličina, Veronika, et al.
(författare)
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Development of the ASHRAE Global Thermal Comfort Database II
- 2018
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Ingår i: Building and Environment. - : Elsevier BV. - 0360-1323. ; 142, s. 502-512
-
Tidskriftsartikel (refereegranskat)abstract
- Recognizing the value of open-source research databases in advancing the art and science of HVAC, in 2014 the ASHRAE Global Thermal Comfort Database II project was launched under the leadership of University of California at Berkeley's Center for the Built Environment and The University of Sydney's Indoor Environmental Quality (IEQ) Laboratory. The exercise began with a systematic collection and harmonization of raw data from the last two decades of thermal comfort field studies around the world. The ASHRAE Global Thermal Comfort Database II (Comfort Database), now an online, open-source database, includes approximately 81,846 complete sets of objective indoor climatic observations with accompanying “right-here-right-now” subjective evaluations by the building occupants who were exposed to them. The database is intended to support diverse inquiries about thermal comfort in field settings. A simple web-based interface to the database enables filtering on multiple criteria, including building typology, occupancy type, subjects' demographic variables, subjective thermal comfort states, indoor thermal environmental criteria, calculated comfort indices, environmental control criteria and outdoor meteorological information. Furthermore, a web-based interactive thermal comfort visualization tool has been developed that allows end-users to quickly and interactively explore the data.
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| 27. |
- Han, Yong, et al.
(författare)
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Comparison of the landing kinematics of pedestrians and cyclists during ground impact determined from vehicle collision video records
- 2018
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Ingår i: International Journal of Vehicle Safety. - 1479-3105 .- 1479-3113. ; 10:3-4, s. 212-234
-
Tidskriftsartikel (refereegranskat)abstract
- The purpose of this study was to investigate the landing kinematics (LK) of pedestrians and cyclists and to provide an analysis of the influencing factors. A total of 112 pedestrian cases and 51 cyclist cases with video information were analysed. The results showed that the pedestrians' and cyclists' landing kinematics depends on the vehicle front-end shape and impact velocity. In this LK1, the pedestrian/cyclist body had a clear rotation speed during ground contact. In this case, 71% of the cyclists and 39% of the pedestrians were found head firstly contact to the ground. In the most frequent LK2, the pedestrian/cyclist was thrown upward-forward and then landed without rotational speed (46% of all pedestrian and 49% of all cyclist cases). Research on the relation between the vehicle front shape and the LK of pedestrians/ cyclists can guide the safety design of a motor vehicle for reducing head injury risk
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| 28. |
- He, Lei, et al.
(författare)
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Asymmetric Hydrogenation of Imines Using NHC-Phosphine Iridium Complexes
- 2023
-
Ingår i: Asian Journal of Organic Chemistry. - 2193-5807 .- 2193-5815. ; 12:6
-
Tidskriftsartikel (refereegranskat)abstract
- α-Chiral amines represent a frequently observed functional group in pharmaceuticals. Here, the synthesis of such motifs (up to 91% ee) is described by asymmetric hydrogenation of imines catalyzed by NHC,P-iridium complexes. The hydrogenation proceeded smoothly, even under balloon pressure of hydrogen atmosphere. Mechanistic experiments indicated that the reduction most likely advances by a combination of direct hydrogenation and a hydrogen transfer process using either H2 or iPrOH as the reductant, respectively.
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| 29. |
- Hensgens, Geert, et al.
(författare)
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The role of the understory in litter DOC and nutrient leaching in boreal forests
- 2020
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Ingår i: Biogeochemistry. - : Springer Science and Business Media LLC. - 0168-2563 .- 1573-515X. ; 149:1, s. 87-103
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Tidskriftsartikel (refereegranskat)abstract
- Dissolved organic carbon (DOC) derived from plant litter plays an important role in the ecosystem carbon balance and soil biogeochemistry. However, in boreal coniferous forests no integrated understanding exists of how understory vegetation contributes to litter leaching of DOC, nitrogen (N) and phosphorus (P) with different bioavailability at the forest stand level. We characterized water extractable leachates from fresh and decayed litter of dominant canopy and understory sources in a boreal coniferous forest, in order to explore the contribution of understory vegetation as a source of both total and bioavailable forms of DOC, N and P. Recently produced litter from deciduous species (including Vaccinium myrtillus) yielded the highest amounts of DOC. However, this leaching potential decreased exponentially with mass loss through litter decay. The DOC lability generally showed little interspecific variation, although wood derived DOC was more recalcitrant. Lability decreased progressively with litter aging. Water extractable nutrients increased proportionally with DOC, and roughly a quarter (N) or half (P) had directly bioavailable inorganic forms. Scaled to annual litterfall at the forest stand, understory vegetation contributed ~ 80% of the water extractable DOC and nutrients from fresh litter, with > 60% coming from Vaccinium myrtillus alone. However, as litter decomposes, the data suggest a lower leaching potential is maintained with a larger contribution from needle, wood and moss litter. Our study shows that understory vegetation, especially V. myrtillus, is a key driver of litter DOC and nutrient leaching in boreal coniferous forests.
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| 30. |
- Klionsky, Daniel J., et al.
(författare)
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Guidelines for the use and interpretation of assays for monitoring autophagy
- 2012
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Ingår i: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
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Forskningsöversikt (refereegranskat)abstract
- In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.
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| 31. |
- Li, Xingyu, et al.
(författare)
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Smart Reconfigurable Manufacturing: Literature Analysis
- 2024
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Ingår i: 11th CIRP Global Web Conference, CIRPe 2023. - : Elsevier B.V.. ; , s. 43-48
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Konferensbidrag (refereegranskat)abstract
- Smart manufacturing (SM) enhances the competitiveness of manufacturing companies by promoting automation and overall equipment effectiveness (OEE), targeting to produce 100% qualified products fully automatically. One of the key challenges to the SM initiatives is the continuous demand fluctuations in the specification and quantity, especially when a new product variant comes to the production line. Reconfigurable manufacturing (RM) system provides cost-effective, rapid response to abrupt market changes. It provides a solution by its flexibility in repurposing tools, adding machines, and modifying software to rapidly respond to changing demands at low unit costs. The ability of SM technologies through self-programming and cloud computation may significantly complements RM initiatives. There is increasing evidence that SM and RM may augment each other through their complementary strengths, leading to the new paradigm of smart reconfigurable manufacturing (SRM). To highlight the complementary strengths, this paper investigates the converging trend of RM and SM based on natural language processing, e.g., topic modeling and semantic embedding. Key characteristics and industrial use cases are subsequently summarized to systematically delineate the new SRM paradigm and illustrate its advantages and feasibility in practice.
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| 32. |
- Li, Yongxi, et al.
(författare)
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Non-fullerene acceptor with low energy loss and high external quantum efficiency: towards high performance polymer solar cells
- 2016
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Ingår i: Journal of Materials Chemistry A. - : Royal Society of Chemistry. - 2050-7488 .- 2050-7496. ; 4:16, s. 5890-5897
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Tidskriftsartikel (refereegranskat)abstract
- A non-fullerene electron acceptor bearing a fused 10-heterocyclic ring (indacenodithiophenoindacenodithiophene) with a narrow band gap (similar to 1.5 eV) was designed and synthesized. It possesses excellent planarity and enhanced effective conjugation length compared to previously reported fused-ring electron acceptors. When this acceptor was paired with PTB7-Th and applied in polymer solar cells, a power conversion efficiency of 6.5% was achieved with a high open circuit voltage of 0.94 V. More significantly, an energy loss as low as 0.59 eV and an external quantum efficiency as high as 63% were obtained simultaneously.
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| 33. |
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| 34. |
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| 35. |
- Liu, Wei, et al.
(författare)
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Coherent dynamics of multi-spin V-B(-) center in hexagonal boron nitride
- 2022
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Ingår i: Nature Communications. - : Nature Portfolio. - 2041-1723. ; 13:1
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Tidskriftsartikel (refereegranskat)abstract
- Hexagonal boron nitride (hBN) has recently been demonstrated to contain optically polarized and detected electron spins that can be utilized for implementing qubits and quantum sensors in nanolayered-devices. Understanding the coherent dynamics ofmicrowave driven spins in hBN is of crucial importance for advancing these emerging new technologies. Here, we demonstrate and study the Rabi oscillation and related phenomena of a negatively charged boron vacancy (V-B(-)) spin ensemble in hBN. We report on different dynamics of the V-B(-) spins at weak and strong magnetic fields. In the former case the defect behaves like a single electron spin system, while in the latter case it behaves like a multi-spin system exhibiting multiple-frequency dynamical oscillation as beat in the Ramsey fringes. We also carry out theoretical simulations for the spin dynamics of V-B(-) and reveal that the nuclear spins can be driven via the strong electron nuclear coupling existing in V-B(-) center, which can be modulated by the magnetic field and microwave field.
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| 36. |
- Liu, Zhihao, et al.
(författare)
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Robot learning towards smart robotic manufacturing : A review
- 2022
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Ingår i: Robotics and Computer-Integrated Manufacturing. - : Elsevier BV. - 0736-5845 .- 1879-2537. ; 77, s. 102360-
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Forskningsöversikt (refereegranskat)abstract
- Robotic equipment has been playing a central role since the proposal of smart manufacturing. Since the beginning of the first integration of industrial robots into production lines, industrial robots have enhanced productivity and relieved humans from heavy workloads significantly. Towards the next generation of manufacturing, this review first introduces the comprehensive background of smart robotic manufacturing within robotics, machine learning, and robot learning. Definitions and categories of robot learning are summarised. Concretely, imitation learning, policy gradient learning, value function learning, actor-critic learning, and model-based learning as the leading technologies in robot learning are reviewed. Training tools, benchmarks, and comparisons amongst different robot learning methods are delivered. Typical industrial applications in robotic grasping, assembly, process control, and industrial human-robot collaboration are listed and discussed. Finally, open problems and future research directions are summarised.
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| 37. |
- Lu, Shen-ning, et al.
(författare)
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Application of an innovative grid-based surveillance strategy to ensure elimination and prevent reintroduction of malaria in high-risk border communities in China
- 2022
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Ingår i: BMC Public Health. - : Springer Nature. - 1471-2458. ; 22:1
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Tidskriftsartikel (refereegranskat)abstract
- Grid management is a grassroots governance strategy widely implemented in China since 2004 to improve the government's efficiency to actively find and solve problems among populated regions. A grid-based strategy surveillancing high-risk groups, including mobile and migrant populations (MMPs), in the China-Myanmar border region has played an indispensable role in promoting and consolidating the malaria elimination efforts by tracking and timely identification of potential importation or re-establishment of malaria among MMPs. A sequential mixed methods was implementated to explore the operational mechanism and best practices of the grid-based strategy including through the focus group discussions (FGDs), comparison of before and after the implementation of a grid-based strategy in the field sites, and data collection from the local health system.This paper distills the implementation mechanism and highlights the role of the grid-based strategy in the elimination and prevention of re-establishment of malaria transmission.
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| 38. |
- Lu, Yahua, et al.
(författare)
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Engineer Nanoscale Defects into Selective Channels : MOF-Enhanced Li+ Separation by Porous Layered Double Hydroxide Membrane
- 2023
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Ingår i: Nano-Micro Letters. - 2311-6706. ; 15:1
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Tidskriftsartikel (refereegranskat)abstract
- Two-dimensional (2D) membrane-based ion separation technology has been increasingly explored to address the problem of lithium resource shortage, yet it remains a sound challenge to design 2D membranes of high selectivity and permeability for ion separation applications. Zeolitic imidazolate framework functionalized modified layered double hydroxide (ZIF-8@MLDH) composite membranes with high lithium-ion (Li+) permeability and excellent operational stability were obtained in this work by in situ depositing functional ZIF-8 nanoparticles into the nanopores acting as framework defects in MLDH membranes. The defect-rich framework amplified the permeability of Li+, and the site-selective growth of ZIF-8 in the framework defects bettered its selectivity. Specifically speaking, the ZIF-8@MLDH membranes featured a high permeation rate of Li+ up to 1.73 mol m−2 h−1 and a desirable selectivity of Li+/Mg2+ up to 31.9. Simulations supported that the simultaneously enhanced selectivity and permeability of Li+ are attributed to changes in the type of mass transfer channels and the difference in the dehydration capacity of hydrated metal cations when they pass through nanochannels of ZIF-8. This study will inspire the ongoing research of high-performance 2D membranes through the engineering of defects.
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| 39. |
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| 40. |
- Manni, Giovanni Li, et al.
(författare)
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The OpenMolcas Web : A Community-Driven Approach to Advancing Computational Chemistry
- 2023
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Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 19:20, s. 6933-6991
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Tidskriftsartikel (refereegranskat)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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| 41. |
- O'Brien, William, et al.
(författare)
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An international review of occupant-related aspects of building energy codes and standards
- 2020
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Ingår i: Building and Environment. - : Elsevier BV. - 0360-1323. ; 179
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Tidskriftsartikel (refereegranskat)abstract
- In light of recent research, it is evident that occupants are playing an increasingly important role in building energy performance. Despite the important role of building energy codes and standards in design, the occupant-related aspects are typically simple and have not kept up with the leading research. This paper reviews 23 regions’ building energy codes and standards by first comparing their quantitative aspects and then analyzing their mandated rules and approaches. While the present paper focuses on offices, general recommendations are applicable to other building types as well. The review revealed a wide range of occupant-related values, approaches, and attitudes. For example, code-specified occupant density varies by nearly a factor of three between different codes. This underlines the need for development of advancement in occupant behavior modeling approaches for future occupant-centric building performance codes and standards. Moreover, occupants are often referred to only implicitly; underlying expectations about energy-saving occupant behavior from building occupants varies greatly; and, only a few codes address occupant feedback and system usability. Based on the findings of the review, a set of initial recommendations for future building energy codes is proposed.
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| 42. |
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| 43. |
- Qiao, Yingjin, et al.
(författare)
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MC1R is dispensable for the proteinuria reducing and glomerular protective effect of melanocortin therapy
- 2016
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Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 6
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Tidskriftsartikel (refereegranskat)abstract
- Melanocortin therapy by using adrenocorticotropic hormone (ACTH) or non-steroidogenic melanocortin peptides attenuates proteinuria and glomerular injury in experimental glomerular diseases and induces remission of nephrotic syndrome in patients with diverse glomerulopathies, even those resistant to steroids. The underlying mechanism remains elusive, but the role of melanocortin 1 receptor (MC1R) has been implicated and was examined here. Four patients with congenital red hair color and nephrotic syndrome caused by idiopathic membranous nephropathy or focal segmental glomerulosclerosis were confirmed by gene sequencing to bear dominant-negative MC1R mutations. Despite prior corticosteroid resistance, all patients responded to ACTH monotherapy and ultimately achieved clinical remission, inferring a steroidogenic-independent and MC1R-dispensable anti-proteinuric effect of melanocortin signaling. In confirmatory animal studies, the protective effect of [Nle4, D-Phe7 ]-α-melanocyte stimulating hormone (NDP-MSH), a potent non-steroidogenic pan-melanocortin receptor agonist, on the lipopolysaccharide elicited podocytopathy was completely preserved in MC1R-null mice, marked by reduced albuminuria and diminished histologic signs of podocyte injury. Moreover, in complementary in vitro studies, NDP-MSH attenuated the lipopolysaccharide elicited apoptosis, hypermotility and impairment of filtration barrier function equally in primary podocytes derived from MC1R-null and wild-type mice. Collectively, our findings suggest that melanocortin therapy confers a proteinuria reducing and podoprotective effect in proteinuric glomerulopathies via MC1R-independent mechanisms.
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| 44. |
- Siltala, Mikko, et al.
(författare)
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Physical and Data-Driven Models for Edge Data Center Cooling System
- 2020
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Ingår i: 2020 Swedish Workshop on Data Science, SweDS 2020. - : Institute of Electrical and Electronics Engineers Inc.. - 9781728192048
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Konferensbidrag (refereegranskat)abstract
- Edge data centers are expected to become prevalent providing low latency computing power for 5G mobile and IoT applications. This article develops two models for the complete cooling system of an edge data center: One model based on the laws of thermodynamics and one data-driven model based on LSTM neural networks. The models are validated against an actual edge data center experimental set-up showing root mean squared errors (RMSE) for most individual components below 1 °C over a simulation period of approximately 10 hours; which compares favourably to state-of-the-art models.
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| 45. |
- Sun, Xiao-dong, et al.
(författare)
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Implementing a novel capture and ligation probe-PCR method in mass screen and treatment to support malaria elimination efforts in the China-Myanmar border region
- 2023
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Ingår i: Malaria Journal. - : BioMed Central (BMC). - 1475-2875. ; 22:1
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Tidskriftsartikel (refereegranskat)abstract
- BackgroundMass screening and treatment (MSAT) for malaria elimination lacks an ideal diagnostic tool to allow sensitive and affordable test of the target population in the field. This study evaluated whether Capture and Ligation Probe-PCR (CLIP-PCR) could be used in a field MSAT in Laiza City, Myanmar.MethodsOn day 0, two dried blood spots were collected from each participant. On day 1, all samples were screened for Plasmodium in a 20 m(2) laboratory with workbench, a biosafety cabinet, a refrigerator, a benchtop shaking incubator and a qPCR machine, by four technicians using CLIP-PCR with sample pooling, at a health clinic of the Chinese bordering town of Nabang. On day 2, all positives were followed up and treated.ResultsOf 15,038 persons (65% of the total population) screened, 204 (1.36%) were CLIP-PCR positives. Among them, 188, 14, and 2 were infected with Plasmodium vivax, Plasmodium falciparum, and P. vivax/P. falciparum mix, respectively. The testing capacity was 538 persons/day, with a cost of US$0.92 /person. The proportion of submicroscopic infection was 64.7%. All positive individuals received treatment within 72 h after blood collection.ConclusionUsing CLIP-PCR in MSAT in low transmission settings can support the malaria elimination efforts in the China-Myanmar border region.
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| 46. |
- Sun, Yu-Ping, et al.
(författare)
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Suppression of resonant auger effect with chirped x-ray free-electron laser pulse
- 2018
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Ingår i: Journal of Physics B. - : IOP PUBLISHING LTD. - 0953-4075 .- 1361-6455. ; 51:3
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Tidskriftsartikel (refereegranskat)abstract
- We study the Auger effect in the presence of strong x-ray free-electron lasers (XFELs) propagating through resonant argon vapors by solving the Maxwell-Bloch equations numerically. The simulations are based on the three-level system with the carrier frequency tuned in the 2p(3/2)-4s resonance. It is shown that the Auger branching is sensitive to the pulse area and duration. The relative Auger yield can be suppressed in the course of pulse propagation due to the interplay between the Auger decay and stimulated emission. Further suppression can be achieved by chirping the initial pulse, which is more effective for the long-pulse case. In addition, the sign and magnitude of the chirp rate play important roles in pulse reshaping and Auger emission.
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| 47. |
- Verendel, J. Johan, et al.
(författare)
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Chiral Hetero- and Carbocyclic Compounds from the Asymmetric Hydrogenation of Cyclic Alkenes
- 2012
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Ingår i: Chemistry - A European Journal. - : Wiley. - 0947-6539 .- 1521-3765. ; 18:21, s. 6507-6513
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Tidskriftsartikel (refereegranskat)abstract
- Several types of chiral hetero- and carbocyclic compounds have been synthesized by using the asymmetric hydrogenation of cyclic alkenes. N,P-Ligated iridium catalysts reduced six-membered cyclic alkenes with various substituents and heterofunctionality in good to excellent enantioselectivity, whereas the reduction of five-membered cyclic alkenes was generally less selective, giving modest enantiomeric excesses. The stereoselectivity of the hydrogenation depended more strongly on the substrate structure for the five- rather than the six-membered cyclic alkenes. The major enantiomer formed in the reduction of six-membered alkenes could be predicted from a selectivity model and isomeric alkenes had complementary enantioselectivity, giving opposite optical isomers upon hydrogenation. The utility of the reaction was demonstrated by using it as a key step in the preparation of chiral 1,3-cis-cyclohexane carboxylates.
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| 48. |
- Xu, Chao-Qun, et al.
(författare)
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Genome sequence of Malania oleifera, a tree with great value for nervonic acid production
- 2019
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Ingår i: GigaScience. - : Oxford University Press. - 2047-217X. ; 8:2
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Tidskriftsartikel (refereegranskat)abstract
- Background Malania oleifera, a member of the Olacaceae family, is an IUCN red listed tree, endemic and restricted to the Karst region of southwest China. This tree's seed is valued for its high content of precious fatty acids (especially nervonic acid). However, studies on its genetic makeup and fatty acid biogenesis are severely hampered by a lack of molecular and genetic tools. Findings We generated 51 Gb and 135Gb of raw DNA sequences, using Pacific Biosciences (PacBio) single-molecule real-time and 10x Genomics sequencing, respectively. A final genome assembly, with a scaffold N50 size of 4.65 Mb and a total length of 1.51Gb, was obtained by primary assembly based on PacBio long reads plus scaffolding with 10x Genomics reads. Identified repeats constituted approximate to 82% of the genome, and 24,064 protein-coding genes were predicted with high support. The genome has low heterozygosity and shows no evidence for recent whole genome duplication. Metabolic pathway genes relating to the accumulation of long-chain fatty acid were identified and studied in detail. Conclusions Here, we provide the first genome assembly and gene annotation for M. oleifera. The availability of these resources will be of great importance for conservation biology and for the functional genomics of nervonic acid biosynthesis.
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| 49. |
- Yang, Fu-Sheng, et al.
(författare)
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Chromosome-level genome assembly of a parent species of widely cultivated azaleas
- 2020
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Ingår i: Nature Communications. - : Nature Publishing Group. - 2041-1723. ; 11:1
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Tidskriftsartikel (refereegranskat)abstract
- Azaleas (Ericaceae) comprise one of the most diverse ornamental plants, renowned for their cultural and economic importance. We present a chromosome-scale genome assembly for Rhododendron simsii, the primary ancestor of azalea cultivars. Genome analyses unveil the remnants of an ancient whole-genome duplication preceding the radiation of most Ericaceae, likely contributing to the genomic architecture of flowering time. Small-scale gene duplications contribute to the expansion of gene families involved in azalea pigment biosynthesis. We reconstruct entire metabolic pathways for anthocyanins and carotenoids and their potential regulatory networks by detailed analysis of time-ordered gene co-expression networks. MYB, bHLH, and WD40 transcription factors may collectively regulate anthocyanin accumulation in R. simsii, particularly at the initial stages of flower coloration, and with WRKY transcription factors controlling progressive flower coloring at later stages. This work provides a cornerstone for understanding the underlying genetics governing flower timing and coloration and could accelerate selective breeding in azalea. Azaleas are one of the most diverse ornamental plants and have cultural and economic importance. Here, the authors report a chromosome-scale genome assembly for the primary ancestor of the azalea cultivar Rhododendro simsi and identify transcription factors that may function in flower coloration at different stages.
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| 50. |
- Yang, Xinping, et al.
(författare)
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Widespread Expansion of Protein Interaction Capabilities by Alternative Splicing
- 2016
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Ingår i: Cell. - : Elsevier BV. - 0092-8674 .- 1097-4172. ; 164:4, s. 805-817
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Tidskriftsartikel (refereegranskat)abstract
- While alternative splicing is known to diversify the functional characteristics of some genes, the extent to which protein isoforms globally contribute to functional complexity on a proteomic scale remains unknown. To address this systematically, we cloned full-length open reading frames of alternatively spliced transcripts for a large number of human genes and used protein-protein interaction profiling to functionally compare hundreds of protein isoform pairs. The majority of isoform pairs share less than 50% of their interactions. In the global context of interactome network maps, alternative isoforms tend to behave like distinct proteins rather than minor variants of each other. Interaction partners specific to alternative isoforms tend to be expressed in a highly tissue-specific manner and belong to distinct functional modules. Our strategy, applicable to other functional characteristics, reveals a widespread expansion of protein interaction capabilities through alternative splicing and suggests that many alternative "isoforms'' are functionally divergent (i.e., "functional alloforms'').
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