| 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. |
- Wang, Hongyu, et al.
(författare)
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Exploration of selective copper ion separation from wastewater via capacitive deionization with highly effective 3D carbon framework-anchored Co(PO3)2 electrode
- 2024
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Ingår i: Separation and Purification Technology. - : ELSEVIER. - 1383-5866 .- 1873-3794. ; 336
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Tidskriftsartikel (refereegranskat)abstract
- The increasing amount of heavy metal copper ions (Cu2+) in industrial emissions, poses a serious threat to human health, biological environment, and resource scarcity. Capacitive deionization (CDI) is considered as a green and efficient method for desalination. It is crucial to develop high-performance electrodes for efficient operation of CDI that go beyond conventional carbon and yield considerable environmental benefits. Here, metal organic frameworks (MOFs) derived carbon-loaded cobalt metaphosphate (NC-Co(PO3)2) was prepared by lowtemperature gas-solid phosphating for Cu2+ removal as CDI electrode for the first time. NC-Co(PO3)2 demonstrated superior electrode structure and function due to the synergistic effects of electric double layer coupling PO bonds, the binding tendency of metaphosphate groups with Cu2+, and interfacial redox reactions induced by the labile valence state of cobalt. The optimal electrosorption capacity of NC-Co(PO3)2 was 95.41 mg g-1 at 1 V in 50 mL Cu2+ solution with splendid cyclic regeneration capability. Moreover, NC-Co(PO3)2 exhibited excellent selectivity and outstanding electrosorption performance in the presence of multiple coexisting ions and this CDI system realized the purification of actual copper-containing wastewater. A series of characterizations further revealed the specific mechanism of Cu2+ in adsorption-desorption process. Our finding strongly supported NCCo(PO3)2 electrode can extend the CDI platform's capability for effectively removing and retrieving Cu2+ from wastewater.
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| 3. |
- 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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| 4. |
- Blanton, Michael R., et al.
(författare)
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Sloan Digital Sky Survey IV : Mapping the Milky Way, Nearby Galaxies, and the Distant Universe
- 2017
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Ingår i: Astronomical Journal. - : IOP Publishing Ltd. - 0004-6256 .- 1538-3881. ; 154:1
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Tidskriftsartikel (refereegranskat)abstract
- We describe the Sloan Digital Sky Survey IV (SDSS-IV), a project encompassing three major spectroscopic programs. The Apache Point Observatory Galactic Evolution Experiment 2 (APOGEE-2) is observing hundreds of thousands of Milky Way stars at high resolution and. high signal-to-noise ratios in the near-infrared. The Mapping Nearby Galaxies at Apache Point Observatory (MaNGA) survey is obtaining spatially resolved spectroscopy for thousands of nearby galaxies (median z similar to 0.03). The extended Baryon Oscillation Spectroscopic Survey (eBOSS) is mapping the galaxy, quasar, and neutral gas distributions between z similar to 0.6 and 3.5 to constrain cosmology using baryon acoustic oscillations, redshift space distortions, and the shape of the power spectrum. Within eBOSS, we are conducting two major subprograms: the SPectroscopic IDentification of eROSITA Sources (SPIDERS), investigating X-ray AGNs. and galaxies in X-ray clusters, and the Time Domain Spectroscopic Survey (TDSS), obtaining spectra of variable sources. All programs use the 2.5 m Sloan Foundation Telescope at the. Apache Point Observatory; observations there began in Summer 2014. APOGEE-2 also operates a second near-infrared spectrograph at the 2.5 m du Pont Telescope at Las Campanas Observatory, with observations beginning in early 2017. Observations at both facilities are scheduled to continue through 2020. In keeping with previous SDSS policy, SDSS-IV provides regularly scheduled public data releases; the first one, Data Release 13, was made available in 2016 July.
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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. |
- Dai, Qile, et al.
(författare)
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OTTERS: a powerful TWAS framework leveraging summary-level reference data
- 2023
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Ingår i: Nature Communications. - : Springer Nature. - 2041-1723. ; 14:1
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Tidskriftsartikel (refereegranskat)abstract
- Most existing TWAS tools require individual-level eQTL reference data and thus are not applicable to summary-level reference eQTL datasets. The development of TWAS methods that can harness summary-level reference data is valuable to enable TWAS in broader settings and enhance power due to increased reference sample size. Thus, we develop a TWAS framework called OTTERS (Omnibus Transcriptome Test using Expression Reference Summary data) that adapts multiple polygenic risk score (PRS) methods to estimate eQTL weights from summary-level eQTL reference data and conducts an omnibus TWAS. We show that OTTERS is a practical and powerful TWAS tool by both simulations and application studies.
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| 7. |
- Dinh, Canh T., et al.
(författare)
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A New Look and Convergence Rate of Federated Multitask Learning With Laplacian Regularization
- 2024
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Ingår i: IEEE Transactions on Neural Networks and Learning Systems. - : IEEE-INST ELECTRICAL ELECTRONICS ENGINEERS INC. - 2162-237X .- 2162-2388. ; 35:6, s. 8075-8085
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Tidskriftsartikel (refereegranskat)abstract
- Non-independent and identically distributed (non-IID) data distribution among clients is considered as the key factor that degrades the performance of federated learning (FL). Several approaches to handle non-IID data, such as personalized FL and federated multitask learning (FMTL), are of great interest to research communities. In this work, first, we formulate the FMTL problem using Laplacian regularization to explicitly leverage the relationships among the models of clients for multitask learning. Then, we introduce a new view of the FMTL problem, which, for the first time, shows that the formulated FMTL problem can be used for conventional FL and personalized FL. We also propose two algorithms FedU and decentralized FedU (dFedU) to solve the formulated FMTL problem in communication-centralized and decentralized schemes, respectively. Theoretically, we prove that the convergence rates of both algorithms achieve linear speedup for strongly convex and sublinear speedup of order 1/2 for nonconvex objectives. Experimentally, we show that our algorithms outperform the conventional algorithm FedAvg, FedProx, SCAFFOLD, and AFL in FL settings, MOCHA in FMTL settings, as well as pFedMe and Per-FedAvg in personalized FL settings.
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| 8. |
- 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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| 9. |
- Li, Xinghao, et al.
(författare)
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Porous organic polycarbene nanotrap for efficient and selective gold stripping from electronic waste
- 2023
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Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 14
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Tidskriftsartikel (refereegranskat)abstract
- The role of N-heterocyclic carbene, a well-known reactive site, in chemical catalysis has long been studied. However, its unique binding and electron-donating properties have barely been explored in other research areas, such as metal capture. Herein, we report the design and preparation of a poly(ionic liquid)-derived porous organic polycarbene adsorbent with superior gold-capturing capability. With carbene sites in the porous network as the “nanotrap”, it exhibits an ultrahigh gold recovery capacity of 2.09 g/g. In-depth exploration of a complex metal ion environment in an electronic waste-extraction solution indicates that the polycarbene adsorbent possesses a significant gold recovery efficiency of 99.8%. X-ray photoelectron spectroscopy along with nuclear magnetic resonance spectroscopy reveals that the high performance of the polycarbene adsorbent results from the formation of robust metal-carbene bonds plus the ability to reduce nearby gold ions into nanoparticles. Density functional theory calculations indicate that energetically favourable multinuclear Au binding enhances adsorption as clusters. Life cycle assessment and cost analysis indicate that the synthesis of polycarbene adsorbents has potential for application in industrial-scale productions. These results reveal the potential to apply carbene chemistry to materials science and highlight porous organic polycarbene as a promising new material for precious metal recovery.
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| 10. |
- Ma, Dan, et al.
(författare)
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A global optimization-based method for the prediction of water inrush hazard from mining floor
- 2018
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Ingår i: Water. - : MDPI AG. - 2073-4441. ; 10:11
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Tidskriftsartikel (refereegranskat)abstract
- Water inrush hazards can be effectively reduced by a reasonable and accurate soft-measuring method on the water inrush quantity from the mine floor. This is quite important for safe mining. However, there is a highly nonlinear relationship between the water outburst from coal seam floors and geological structure, hydrogeology, aquifer, water pressure, water-resisting strata, mining damage, fault and other factors. Therefore, it is difficult to establish a suitable model by traditional methods to forecast the water inrush quantity from the mine floor. Modeling methods developed in other fields can provide adequate models for rock behavior on water inrush. In this study, a new forecast system, which is based on a hybrid genetic algorithm (GA) with the support vector machine (SVM) algorithm, a model structure and the related parameters are proposed simultaneously on water inrush prediction. With the advantages of powerful global optimization functions, implicit parallelism and high stability of the GA, the penalty coefficient, insensitivity coefficient and kernel function parameter of the SVM model are determined as approximately optimal automatically in the spatial dimension. All of these characteristics greatly improve the accuracy and usable range of the SVM model. Testing results show that GA has a useful ability in finding optimal parameters of a SVM model. The performance of the GA optimized SVM (GA-SVM) is superior to the SVM model. The GA-SVM enables the prediction of water inrush and provides a promising solution to the predictive problem for relevant industries.
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