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Systematic Functional Annotation of Somatic Mutations in Cancer
Ng, Patrick Kwok-Shing,Li, Jun,Jeong, Kang Jin,Shao, Shan,Chen, Hu,Tsang, Yiu Huen,Sengupta, Sohini,Wang, Zixing,Bhavana, Venkata Hemanjani,Tran, Richard,Soewito, Stephanie,Minussi, Darlan Conterno,Mo Cell Press 2018 CANCER CELL Vol. No.
<P><B>Summary</B></P> <P>The functional impact of the vast majority of cancer somatic mutations remains unknown, representing a critical knowledge gap for implementing precision oncology. Here, we report the development of a moderate-throughput functional genomic platform consisting of efficient mutant generation, sensitive viability assays using two growth factor-dependent cell models, and functional proteomic profiling of signaling effects for select aberrations. We apply the platform to annotate >1,000 genomic aberrations, including gene amplifications, point mutations, indels, and gene fusions, potentially doubling the number of driver mutations characterized in clinically actionable genes. Further, the platform is sufficiently sensitive to identify weak drivers. Our data are accessible through a user-friendly, public data portal. Our study will facilitate biomarker discovery, prediction algorithm improvement, and drug development.</P> <P><B>Highlights</B></P> <P> <UL> <LI> Developed a versatile functional genomic platform for somatic mutation annotation </LI> <LI> Annotated >1,000 genomic aberrations, doubling the number of known driver mutations </LI> <LI> Assessed performance of existing algorithms for mutation functional predictions </LI> <LI> Built a user-friendly, open-access data portal for community-based investigation </LI> </UL> </P> <P><B>Graphical Abstract</B></P> <P>[DISPLAY OMISSION]</P>
Development of the ASHRAE Global Thermal Comfort Database II
Fö,ldvá,ry Lič,ina, Veronika,Cheung, Toby,Zhang, Hui,de Dear, Richard,Parkinson, Thomas,Arens, Edward,Chun, Chungyoon,Schiavon, Stefano,Luo, Maohui,Brager, Gail,Li, Peixian,Kaam, Soazig Elsevier 2018 Building and environment Vol.142 No.-
<P><B>Abstract</B></P> <P>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 “<I>right-here-right-now</I>” 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.</P> <P><B>Highlights</B></P> <P> <UL> <LI> The scope, development, contents, and accessibility of the Comfort Database is documented. </LI> <LI> The Comfort Database II includes approximately 76,000 complete sets of thermal comfort data. </LI> <LI> The Comfort Database provides access to the collected raw data. </LI> <LI> Web-based interactive visualization tool was developed that allows end-users to interactively explore the data. </LI> </UL> </P>
Li Yan Michael,Frisch Richard Francis,Huang Zheng,Towner James Edward,Li Yan Icy,Edsall Amber Lynn,Ledonio Charles 대한척추외과학회 2021 Asian Spine Journal Vol.15 No.1
Study Design: Retrospective chart review.Purpose: This study compared the clinical and radiographic outcomes of patients treated with expandable and static interbody spacers following minimally invasive lateral lumbar interbody fusion (MIS-LLIF) with 12-month follow-up.Overview of Literature: A common surgical option for the treatment of degenerative disk disease (DDD) is MIS-LLIF using static or expandable spacers to restore disk height (DH), neuroforaminal height (NH), and segmental lordosis. Static spacers may require excessive trialing and aggressive impaction, potentially leading to endplate disruption and subsidence. Expandable spacers allow for in situ expansion to help address complications associated with static spacers.Methods: This is an Institutional Review Board-exempt review of 69 patients (static, n=32; expandable, n=37) diagnosed with DDD who underwent MIS-LLIF at 1–2 contiguous level(s) using static or expandable spacers. Radiographic and clinical outcomes were collected and compared at pre- and postoperative time points up to 12 months.Results: The expandable group had a significantly higher mean change in Visual Analog Scale (VAS) scores at 6 weeks, 6 months, and 12 months vs. static (∆VAS at 12 months: expandable, 6.7±1.3; static, 5.1±2.6). Mean improvement of Oswestry Disability Index (ODI) scores at 3, 6, and 12 months were significantly better for the expandable group vs. static (∆ODI at 12 months: expandable, 63.2±13.2; static, 29.8±23.4). Mean DH and NH significantly increased at final follow-up for both groups, with no significant difference in DH improvement between groups. The expandable mean NH improvement at 6 weeks and 6 months was significantly greater vs. static. Segmental lordosis significantly improved in the expandable group at all time intervals vs static. Subsidence rate at 12 months was significantly lower in the expandable group (1/46, 2.2%) vs. static (12/37, 32.4%).Conclusions: Expandable spacers resulted in a significantly lower subsidence rate, improve segmental lordosis, and VAS and ODI outcomes at 12 months vs. static.
Pedestrian level wind speeds in downtown Auckland
Richards, P.J.,Mallinson, G.D.,McMillan, D.,Li, Y.F. Techno-Press 2002 Wind and Structures, An International Journal (WAS Vol.5 No.2
Predictions of the pedestrian level wind speeds for the downtown area of Auckland that have been obtained by wind tunnel and computational fluid dynamic (CFD) modelling are presented. The wind tunnel method involves the observation of erosion patterns as the wind speed is progressively increased. The computational solutions are mean flow calculations, which were obtained by using the finite volume code PHOENICS and the $k-{\varepsilon}$ turbulence model. The results for a variety of wind directions are compared, and it is observed that while the patterns are similar there are noticeable differences. A possible explanation for these differences arises because the tunnel prediction technique is sensitivity to gust wind speeds while the CFD method predicts mean wind speeds. It is shown that in many cases the computational model indicates high mean wind speeds near the corner of a building while the erosion patterns are consistent with eddies being shed from the edge of the building and swept downstream.
Li, Faqiang,Chung, Taijoon,Vierstra, Richard D. American Society of Plant Biologists 2014 The Plant cell Vol.26 No.2
<P>The ATG1/13 kinase complex that regulates autophagy also includes ATG11 and ATG101, with ATG11 helping regulate the phosphorylation and turnover of ATG1 and ATG13, tether the complex to developing autophagic structures, and promote the delivery of autophagic vesicles to the vacuole. ATG11 and other autophagy factors also direct the elimination of mitochondria via a vacuolar mitophagic process.</P>
Li, Yuan,Heng, Wee-Kuan,Lee, Byung Sun,Aratani, Naoki,Zafra, José,L.,Bao, Nina,Lee, Richmond,Sung, Young Mo,Sun, Zhe,Huang, Kuo-Wei,Webster, Richard D.,Ló,pez Navarrete, Juan T.,Kim, Dongh American Chemical Society 2012 JOURNAL OF THE AMERICAN CHEMICAL SOCIETY - Vol.134 No.36
<P>Polycyclic aromatic hydrocarbons with an open-shell singlet biradical ground state are of fundamental interest and have potential applications in materials science. However, the inherent high reactivity makes their synthesis and characterization very challenging. In this work, a convenient synthetic route was developed to synthesize two kinetically blocked heptazethrene (<B>HZ-TIPS</B>) and octazethrene (<B>OZ-TIPS</B>) compounds with good stability. Their ground-state electronic structures were systematically investigated by a combination of different experimental methods, including steady-state and transient absorption spectroscopy, variable temperature NMR, electron spin resonance (ESR), superconducting quantum interfering device (SQUID), FT Raman, and X-ray crystallographic analysis, assisted by unrestricted symmetry-broken density functional theory (DFT) calculations. All these demonstrated that the heptazethrene derivative <B>HZ-TIPS</B> has a closed-shell ground state while its octazethrene analogue <B>OZ-TIPS</B> with a smaller energy gap exists as an open-shell singlet biradical with a large measured biradical character (<I>y</I> = 0.56). Large two-photon absorption (TPA) cross sections (σ<SUP>(2)</SUP>) were determined for <B>HZ-TIPS</B> (σ<SUP>(2)</SUP><SUB>max</SUB> = 920 GM at 1250 nm) and <B>OZ-TIPS</B> (σ<SUP>(2)</SUP><SUB>max</SUB> = 1200 GM at 1250 nm). In addition, <B>HZ-TIPS</B> and <B>OZ-TIPS</B> show a closely stacked 1D polymer chain in single crystals.</P><P><B>Graphic Abstract</B> <IMG SRC='http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jacsat/2012/jacsat.2012.134.issue-36/ja304618v/production/images/medium/ja-2012-04618v_0015.gif'></P><P><A href='http://pubs.acs.org/doi/suppl/10.1021/ja304618v'>ACS Electronic Supporting Info</A></P>
Lu, Li Ping,Finlayson, Chris E.,Kabra, Dinesh,Albert‐,Seifried, Sebastian,Song, Myoung Hoon,Havenith, Remco W. A.,Tu, Guoli,Huck, Wilhelm T. S.,Friend, Richard H. WILEY‐VCH Verlag 2013 Macromolecular chemistry and physics Vol.214 No.9
<P><B>Abstract</B></P><P>A study of the organic semiconductor F8TBT is presented, directly comparing a conventional form (F8TBT‐out) with a form with varied alkyl side‐chain position (F8TBT‐in), in terms of optical properties and device performance in light‐emitting‐diodes (LEDs). Computational simulations of the side‐chain position with respect to the TBT unit reveal geometrical differences between F8TBT‐out and F8TBT‐in. π–π conjugation on the backbone of F8TBT‐in is interrupted by a distortion of the benzothiadiazole ring, leading to a blue‐shift of the absorption spectrum and increased photoluminescence quantum efficiency. Both conventional and hybrid LEDs demonstrate that devices with F8TBT‐in show improved performance, as compared to F8TBT‐out, illustrating how tuning the optoelectronic properties of conjugated polymers by varying the placement of side chains has an important role in device optimization.</P>