| 1. |
- Brownstein, Catherine A., et al.
(författare)
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An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge
- 2014
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Ingår i: Genome Biology. - : Springer Science and Business Media LLC. - 1465-6906 .- 1474-760X. ; 15:3, s. R53-
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Tidskriftsartikel (refereegranskat)abstract
- Background: There is tremendous potential for genome sequencing to improve clinical diagnosis and care once it becomes routinely accessible, but this will require formalizing research methods into clinical best practices in the areas of sequence data generation, analysis, interpretation and reporting. The CLARITY Challenge was designed to spur convergence in methods for diagnosing genetic disease starting from clinical case history and genome sequencing data. DNA samples were obtained from three families with heritable genetic disorders and genomic sequence data were donated by sequencing platform vendors. The challenge was to analyze and interpret these data with the goals of identifying disease-causing variants and reporting the findings in a clinically useful format. Participating contestant groups were solicited broadly, and an independent panel of judges evaluated their performance. Results: A total of 30 international groups were engaged. The entries reveal a general convergence of practices on most elements of the analysis and interpretation process. However, even given this commonality of approach, only two groups identified the consensus candidate variants in all disease cases, demonstrating a need for consistent fine-tuning of the generally accepted methods. There was greater diversity of the final clinical report content and in the patient consenting process, demonstrating that these areas require additional exploration and standardization. Conclusions: The CLARITY Challenge provides a comprehensive assessment of current practices for using genome sequencing to diagnose and report genetic diseases. There is remarkable convergence in bioinformatic techniques, but medical interpretation and reporting are areas that require further development by many groups.
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| 2. |
- Lin, Yuanyuan, et al.
(författare)
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Investigation of the Reynolds number independence of cavity flow in 2D street canyons by wind tunnel experiments and numerical simulations
- 2021
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Ingår i: Building and Environment. - : Elsevier. - 0360-1323 .- 1873-684X. ; 201
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Tidskriftsartikel (refereegranskat)abstract
- The Reynolds number independence (Re independence) criterion of Re > 11,000 is widely adopted to fulfill the dynamic similarity between the urban flow modeling and the down-scale measurements. However, for 2D street canyons with H/W ≥ 1.5, experiments, numerical simulations, and in-situ observations have reported different vortex-flow regimes with similar building configurations but at different scales. This study uses both wind tunnel experiments and numerical simulations to revisit the Re-independent flow regimes and Re independence criteria with an extensive Re range for idealized 2D street canyons with various aspect ratios (H/W = 1.1, 2.4, 3, 4, and 5). We introduced an optimized ratio of relative changes (RRCs) to evaluate the flow regimes’ similarity. The wind tunnel experiment confirms that the cavity flow with H/W = 1.1 meets the Re independence when reference building Re (Reref) exceeds 11,000. Simulations validated by the experiment results are conducted to investigate detailed flow regimes and the critical Re (Rec) range for each aspect ratio. The canyons with H/W = 2.4, 3, and 4 are dominated by a single asymmetric vortex when the Re independence is satisfied, while there are two vertically-stacked counter-rotating vortices in the canyon with H/W = 5. The value range of Rec increases with aspect ratio from 1.9 × 104–2.6 × 104 (H/W = 2.4) to 1.3 × 105–2.1 × 105 (H/W = 3), and 2.1 × 106–6.4 × 106 (H/W = 4 and 5). Our results indicate that the fully Re-independent flow regimes in deep canyons have fewer vortices than the literature value with down-scale experiments and simulations. The variant Rec with different aspect ratios suggests the requirement to conduct the Re-independence test for different model configurations.
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| 3. |
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| 4. |
- Abolfathi, Bela, et al.
(författare)
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The Fourteenth Data Release of the Sloan Digital Sky Survey : First Spectroscopic Data from the Extended Baryon Oscillation Spectroscopic Survey and from the Second Phase of the Apache Point Observatory Galactic Evolution Experiment
- 2018
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Ingår i: Astrophysical Journal Supplement Series. - : IOP Publishing Ltd. - 0067-0049 .- 1538-4365. ; 235:2
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Tidskriftsartikel (refereegranskat)abstract
- The fourth generation of the Sloan Digital Sky Survey (SDSS-IV) has been in operation since 2014 July. This paper describes the second data release from this phase, and the 14th from SDSS overall (making this Data Release Fourteen or DR14). This release makes the data taken by SDSS-IV in its first two years of operation (2014-2016 July) public. Like all previous SDSS releases, DR14 is cumulative, including the most recent reductions and calibrations of all data taken by SDSS since the first phase began operations in 2000. New in DR14 is the first public release of data from the extended Baryon Oscillation Spectroscopic Survey; the first data from the second phase of the Apache Point Observatory (APO) Galactic Evolution Experiment (APOGEE-2), including stellar parameter estimates from an innovative data-driven machine-learning algorithm known as "The Cannon"; and almost twice as many data cubes from the Mapping Nearby Galaxies at APO (MaNGA) survey as were in the previous release (N = 2812 in total). This paper describes the location and format of the publicly available data from the SDSS-IV surveys. We provide references to the important technical papers describing how these data have been taken (both targeting and observation details) and processed for scientific use. The SDSS web site (www.sdss.org) has been updated for this release and provides links to data downloads, as well as tutorials and examples of data use. SDSS-IV is planning to continue to collect astronomical data until 2020 and will be followed by SDSS-V.
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| 5. |
- Chen, Hongyu, et al.
(författare)
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Effects of microbial culture and chicken manure biochar on compost maturity and greenhouse gas emissions during chicken manure composting
- 2020
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Ingår i: Journal of Hazardous Materials. - : Elsevier. - 0304-3894 .- 1873-3336. ; 389
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Tidskriftsartikel (refereegranskat)abstract
- The effects of chicken manure biochar (CMB) and chicken manure integrated microbial consortium (CMMC) as co-amendments were assessed on compost maturity and reduction of greenhouse gases and ammonia (NH3) emissions during chicken manure composting. Composting was conducted using six combinations of CMB and CMCC (0 % CMB + 0 % CMMC, 0 % CMB + 10 % CMMC, 2 % CMB + 10 % CMMC, 4 % CMB + 10 % CMMC, 6 % CMB + 10 % CMMC, 10 % CMB + 10 % CMMC added on a dry weight basis) in six polyvinyl chloride composting reactors for 42 days under an aerobic environment. Co-amendment of CMB and CMMC extended the thermophilic stage and promoted compost maturity. The release of greenhouse gases [nitrous oxide (N2O) and methane (CH4)] and NH3 from treatments co-amended by CMB and CMMC were reduced by 19.0-27.4 %, 9.3-55.9 % and 24.2-56.9 %, respectively, compared with the control. In addition, a redundancy analysis showed that the C/N ratio and temperature had a significant relationship with greenhouse gases and NH3 emissions among all physiochemical characteristics.
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| 6. |
- Chen, Zhishan, et al.
(författare)
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Fine-mapping analysis including over 254 000 East Asian and European descendants identifies 136 putative colorectal cancer susceptibility genes
- 2024
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Ingår i: Nature Communications. - : Springer Nature. - 2041-1723. ; 15:1
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Tidskriftsartikel (refereegranskat)abstract
- Genome-wide association studies (GWAS) have identified more than 200 common genetic variants independently associated with colorectal cancer (CRC) risk, but the causal variants and target genes are mostly unknown. We sought to fine-map all known CRC risk loci using GWAS data from 100,204 cases and 154,587 controls of East Asian and European ancestry. Our stepwise conditional analyses revealed 238 independent association signals of CRC risk, each with a set of credible causal variants (CCVs), of which 28 signals had a single CCV. Our cis-eQTL/mQTL and colocalization analyses using colorectal tissue-specific transcriptome and methylome data separately from 1299 and 321 individuals, along with functional genomic investigation, uncovered 136 putative CRC susceptibility genes, including 56 genes not previously reported. Analyses of single-cell RNA-seq data from colorectal tissues revealed 17 putative CRC susceptibility genes with distinct expression patterns in specific cell types. Analyses of whole exome sequencing data provided additional support for several target genes identified in this study as CRC susceptibility genes. Enrichment analyses of the 136 genes uncover pathways not previously linked to CRC risk. Our study substantially expanded association signals for CRC and provided additional insight into the biological mechanisms underlying CRC development.
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| 7. |
- Hou, Qiong, et al.
(författare)
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A triphenylamine-based four-armed molecule for solution-processed organic solar cells with high photo-voltage
- 2013
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Ingår i: JOURNAL OF MATERIALS CHEMISTRY A. - : Royal Society of Chemistry. - 2050-7488 .- 2050-7496. ; 1:16, s. 4937-4940
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Tidskriftsartikel (refereegranskat)abstract
- A new four-armed molecule Th-4(DTPAB) with a triphenylamine-benzothiadiazole-triphenylamine unit as the core and 4-hexylthiophene as arms was synthesized. Solution-processed organic solar cells based on blends of Th-4(DTPAB) and PC71BM demonstrate a power conversion efficiency of 3.18% with a high open circuit voltage of 0.96 V.
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| 8. |
- Mukesh Kumar, Awasthi, et al.
(författare)
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A critical review of organic manure biorefinery models toward sustainable circular bioeconomy: Technological challenges, advancements, innovations, and future perspectives
- 2019
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Ingår i: Renewable & sustainable energy reviews. - : Elsevier BV. - 1364-0321 .- 1879-0690. ; , s. 115-131
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Tidskriftsartikel (refereegranskat)abstract
- Total livestock emissions account for up to 14.5% of man-made greenhouse gas emissions. Counteractive measures, such as circular economy concepts and negative emission technologies are necessary to limit global warming below 1.5 °C. Possible treatment options for organic manure include anaerobic digestion, combustion, gasification, hydrothermal liquefaction and composting. The choice of treatment varies depending on the economics, the requirement of a specific product, and sociocultural factors. Commercialization of these treatments needs a blend of appropriate technology, feasible economics, policy support and agreeable socio-cultural conditions. Key findings of this study include the following: 1. Increasing scientific awareness about manure management and treatment; 2. Building a sustainable cooperative model to commercialize technologies; 3. Creating a market for manure recycling products; 4. The role of policy in supporting technologies and consumers; and 5. The codigestion of substrates for better efficacy. Current trends show minimal actions in place as opposed to the high-rate of acceleration that is necessary.
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| 9. |
- Mukesh Kumar, Awasthi, et al.
(författare)
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Metagenomics for taxonomy profiling : tools and approaches
- 2020
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Ingår i: Bioengineered. - : Taylor & Francis. - 2165-5979 .- 2165-5987. ; 11:1, s. 356-374
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Tidskriftsartikel (refereegranskat)abstract
- The study of metagenomics is an emerging field that identifies the total genetic materials in an organism along with the set of all genetic materials like deoxyribonucleic acid and ribose nucleic acid, which play a key role with the maintenance of cellular functions. The best part of this technology is that it gives more flexibility to environmental microbiologists to instantly pioneer the immense genetic variability of microbial communities. However, it is intensively complex to identify the suitable sequencing measures of any specific gene that can exclusively indicate the involvement of microbial metagenomes and be able to advance valuable results about these communities. This review provides an overview of the metagenomic advancement that has been advantageous for aggregation of more knowledge about speci?c genes, microbial communities and its metabolic pathways. More speci?c drawbacks of metagenomes technology mainly depend on sequence-based analysis. Therefore, this ‘targeted based metagenomics’ approach will give comprehensive knowledge about the ecological, evolutionary and functional sequence of significantly important genes that naturally exist in living beings either human, animal and microorganisms from distinctive ecosystems.
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| 10. |
- Qin, Shiyi, et al.
(författare)
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Resource recovery and biorefinery potential of apple orchard waste in the circular bioeconomy
- 2021
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Ingår i: Bioresource Technology. - : Elsevier BV. - 0960-8524 .- 1873-2976.
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Tidskriftsartikel (refereegranskat)abstract
- In this review investigate the apple orchard waste (AOW) is potential organic resources to produce multi-product and there sustainable interventions with biorefineries approaches to assesses the apple farm industrial bioeconomy. The thermochemical and biological processes like anaerobic digestion, composting and , etc., that generate distinctive products like bio-chemicals, biofuels, biofertilizers, animal feed and biomaterial, etc can be employed for AOW valorization. Integrating these processes can enhanced the yield and resource recovery sustainably. Thus, employing biorefinery approaches with allied different methods can link to the progression of circular bioeconomy. This review article mainly focused on the different biological processes and thermochemical that can be occupied for the production of waste to-energy and multi-bio-product in a series of reaction based on sustainability. Therefore, the biorefinery for AOW move towards identification of the serious of the reaction with each individual thermochemical and biological processes for the conversion of one-dimensional providences to circular bioeconomy.
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