Browsing by Author "Zhang, Y."

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Open Access
1/f Noise characteristics of SEJ Y-Ba-Cu-O Rf-SQUIDs on LaAlO3 substrate and the step structure, film, and temperature dependence
(IEEE, 2001-03) Fardmanesh, M.; Schubert, J.; Akram, R.; Bick, M.; Zhang, Y.; Banzet, M.; Zander, W.; Krause, H. J.; Burkhart, H.; Schilling, M.
Step edge junction (SEJ) rf-SQUID magnetometers and gradiometers were fabricated using PLD Y-Ea-Cu-0 films on LaA10,(100) and SrTi0,(100) substrates. Effects of different step structure and the film properties on the yield, optimal operating temperature, and the l/f noise of the SQUIDs were investigated. The step structure was controlled using various IBE processes. The devices on LaAIO, showed higher sensitivity to the step structure compared to those on SrTiO,. This was due to re-deposition of substrate material at the steps prepared using the conventional IBE process resulting in a very low yield of unstable SQUIDs. High yield of low l/f noise stable SQUIDs was obtained on LaAIO, substrates with sharp steps prepared using an optimized IBE process. A typical l/f noise corner frequency of about lOHz at 77K with two major temperature dependencies was obtained. The temperature dependencies of the l/f noise could be correlated to the junction and the film of washer area of the SQUIDS. The white noise of our devices showed a dependency mainly on the amplitude of the flux to voltage transfer function signal. The operating temperature range of the SQUIDs could be controlled by the step structure and narrowed when the optimal operating temperature range was increased. All the measured junctions of our devices on the modified steps showed RSJ type behavior with a moderate decrease of the R, versus temperature.
Open Access
Adaptive prefetching for shared cache based chip multiprocessors
(IEEE, 2009-04) Kandemir, M.; Zhang, Y.; Öztürk, Özcan
Chip multiprocessors (CMPs) present a unique scenario for software data prefetching with subtle tradeoffs between memory bandwidth and performance. In a shared L2 based CMP, multiple cores compete for the shared on-chip cache space and limited off-chip pin bandwidth. Purely software based prefetching techniques tend to increase this contention, leading to degradation in performance. In some cases, prefetches can become harmful by kicking out useful data from the shared cache whose next usage is earlier than the prefetched data, and the fraction of such harmful prefetches usually increases when we increase the number of cores used for executing a multi-threaded application code. In this paper, we propose two complementary techniques to address the problem of harmful prefetches in the context of shared L2 based CMPs. These techniques, namely, suppressing select data prefetches (if they are found to be harmful) and pinning select data in the L2 cache (if they are found to be frequent victim of harmful prefetches), are evaluated in this paper using two embedded application codes. Our experiments demonstrate that these two techniques are very effective in mitigating the impact of harmful prefetches, and as a result, we extract significant benefits from software prefetching even with large core counts. © 2009 EDAA.
Open Access
Alignment controlled growth of single-walled carbon nanotubes on quartz substrates
(American Chemical Society, 2009-09-11) Xiao, J.; Dunham, S.; Liu, P.; Zhang, Y.; Kocabaş, Coşkun; Moh, L.; Huang, Y.; Hwang, K. -C.; Lu, C.; Huang, W.; Rogers, J. A.
Single-walled carbon nanotubes (SWNTs) possess extraordinary electrical properties, with many possible applications in electronics. Dense, horizonally aligned arrays of linearly configured SWNTs represent perhaps the most attractive and scalable way to implement this class of nanomaterial in practical systems. Recent work shows that templated growth of tubes on certain crystalline substrates yields arrays with the necessary levels of perfection, as demonstrated by the formation of devices and full systems on quartz. This paper examines advanced implementations of this process on crystalline quartz substrates with different orientations, to yield strategies for forming diverse, but welldefined horizontal configurations of SWNTs. Combined experimental and theoretical studies indicate that angle-dependent van der Waals interactions can account for nearly all aspects of alignment on quartz with X, Y, Z, and ST cuts, as well as quartz with disordered surface layers. These findings provide important insights into methods for guided growth of SWNTs, and possibly other classes of nanomaterials, for applications in electronics, sensing, photodetection, light emission, and other areas.
Open Access
Analysis of electrical characteristics and magnetic field dependences of YBCO step edge and bicrystal grain boundary junctions for rf-SQUID applications
(Institute of Physics, 2004) Fardmanesh, M.; Schubert, J.; Akram, R.; Bick, M.; Banzet, M.; Zander, W.; Zhang, Y.; Krause, H-J.
The dc characteristics and magnetic field dependences of Y-Ba-Cu-O bicrystal grain boundary junctions (BGBJs) and step edge junctions (SEJs) were investigated for fabrication of rf-SQUIDs. Test junctions with up to 8 μm widths as well as the junctions of the two types of junction-based rf-SQUID were studied. The SEJs typically showed lower Jc and higher ρN as compared to the BGBJs, resulting in close IcRN products. All the BGBJs showed classical field dependent Ic following their junction width, resembling Fraunhofer patterns. The field sensitivity of the BGBJs' Uc led to low yield submicron BGBJ rf-SQUIDs partially impaired by the Earth's magnetic field. Two major behaviours of low and high field dependences of Ic were observed for the SEJs. Only the low field-sensitive SEJs resulted in micron size junction rf-SQUIDs not impaired by the Earth's magnetic field. The low field-sensitive SEJs led to low I/f noise magnetically stable rf-SQUIDs appropriate for applications in unshielded environments at 77 K.
Open Access
Autoantibodies against type I IFNs in patients with life-threatening COVID-19
(2020) Bastard, P.; Rosen, L. B.; Zhang, Q.; Michailidis, E.; Hoffmann, H.-H.; Zhang, Y.; Dorgham, K.; Philippot, Q.; Rosain, J.; Béziat, V.; Manry, J.; Shaw, E.; Haljasmägi, L.; Peterson, P.; Lorenzo, L.; Bizien, L.; Trouillet-Assant, S.; Dobbs, K.; Almeida de Jesus, A.; Belot, A.; Kallaste, A.; Catherinot, E.; Tandjaoui-Lambiotte, Y.; Le Pen, J.; Kerner, G.; Bigio, B.; Seeleuthner, Y.; Yang, R.; Bolze, A.; Spaan, A. N.; Delmonte, O. M.; Abers, M. S.; Aiuti, A.; Casari, G.; Lampasona, V.; Piemonti, L.; Ciceri, F.; Bilguvar, K.; Lifton, R. P.; Vasse, M.; Smadja, D. M.; Migaud, M.; Hadjadj, J.; Terrier, B.; Duffy, D.; Quintana-Murci, L.; van de Beek, D.; Roussel, L.; Vinh, D. C.; Tangye, S. G.; Haerynck, F.; Dalmau, D.; Martinez-Picado, J.; Brodin, P.; Nussenzweig, M. C.; Boisson-Dupuis, S.; Rodríguez-Gallego, C.; Vogt, G.; Mogensen, T. H.; Oler, A. J.; Gu, J.; Burbelo, P. D.; Cohen, J. I.; Biondi, A.; Bettini, L. R.; D'Angio, M.; Bonfanti, P.; Rossignol, P.; Mayaux, J.; Rieux-Laucat, F.; Husebye, E. S.; Fusco, F.; Ursini, M. V.; Imberti, L.; Sottini, A.; Paghera, S.; Quiros-Roldan, E.; Rossi, C.; Castagnoli, R.; Montagna, D.; Özçelik, Tayfun; Licari, A.; Marseglia, G. L.; Duval, X.; Ghosn, J.; Tsang, J. S.; Goldbach-Mansky, R.; Kisand, K.; Lionakis, M. S.; Puel, A.; Zhang, S.- Y.; Holland, S. M.; Gorochov, G.; Jouanguy, E.; Rice, C. M.; Cobat, A.; Notarangelo, L. D.; Abel, L.; Su, H. C.; Casanova, J. L.; HGID Lab; NIAID-USUHS Immune Response to COVID Group; COVID Clinicians; COVID-STORM Clinicians; Imagine COVID Group; French COVID Cohort Study Group; Milieu Intérieur Consortium; CoV-Contact Cohort; Amsterdam UMC Covid-19 Biobank; COVID Human Genetic Effort
Interindividual clinical variability in the course of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is vast. We report that at least 101 of 987 patients with life-threatening coronavirus disease 2019 (COVID-19) pneumonia had neutralizing immunoglobulin G (IgG) autoantibodies (auto-Abs) against interferon-ω (IFN-ω) (13 patients), against the 13 types of IFN-α (36), or against both (52) at the onset of critical disease; a few also had auto-Abs against the other three type I IFNs. The auto-Abs neutralize the ability of the corresponding type I IFNs to block SARS-CoV-2 infection in vitro. These auto-Abs were not found in 663 individuals with asymptomatic or mild SARS-CoV-2 infection and were present in only 4 of 1227 healthy individuals. Patients with auto-Abs were aged 25 to 87 years and 95 of the 101 were men. A B cell autoimmune phenocopy of inborn errors of type I IFN immunity accounts for life-threatening COVID-19 pneumonia in at least 2.6% of women and 12.5% of men.
Open Access
Autoantibodies neutralizing type I IFNs are present in ~4% of uninfected individuals over 70 years old and account for ~20% of COVID-19 deaths
(American Association for the Advancement of Science (AAAS), 2021-08-20) Bastard, P.; Gervais, A.; Le Voyer, T.; Rosain, J.; Philippot, Q.; Manry, J.; Michailidis, E.; Hoffmann, H. H.; Eto, S.; Garcia-Prat, M.; Bizien, L.; Parra-Martinez, A.; Yang, R.; Haljasmagi, L.; Migaud, M.; Sarekannu, K.; Maslovskaja, J.; de Prost, N.; Tandjaoui-Lambiotte, Y.; Luyt, C. E.; Amador-Borrero, B.; Gaudet, A.; Poissy, J.; Morel, P.; Richard, P.; Cognasse, F.; Troya, J.; Trouillet-Assant, S.; Belot, A.; Saker, K.; Garcon, P.; Riviere, J. G.; Lagier, J. C.; Gentile, S.; Rosen, L. B.; Shaw, E.; Morio, T.; Tanaka, J.; Dalmau, D.; Tharaux, PL.; Sene, D.; Stepanian, A.; Megarbane, B.; Triantafyllia, V.; Fekkar, A.; Heath, J. R.; Franco, JL.; Anaya, J. M.; Sole-Violan, J.; Imberti, L.; Biondi, A.; Bonfanti, P.; Castagnoli, R.; Delmonte, O. M.; Zhang, Y.; Snow, A. L.; Holland, S. M.; Biggs, C. M.; Moncada-Velez, M.; Arias, A. A.; Lorenzo, L.; Boucherit, S.; Coulibaly, B.; Anglicheau, D.; Planas, A. M.; Haerynck, F.; Duvlis, S.; Nussbaum, R. L.; Özçelik, Tayfun; Keles, S.; Bousfiha, A. A.; El Bakkouri, J.; Ramirez-Santana, C.; Paul, S.; Pan-Hammarstrom, Q.; Hammarstrom, L.; Dupont, A.; Kurolap, A.; Metz, CN.; Aiuti, A.; Casari, G.; Lampasona, V.; Ciceri, F.; Barreiros, L. A.; Dominguez-Garrido, E.; Vidigal, M.; Zatz, M.; van de Beek, D.; Sahanic, S.; Tancevski, I.; Stepanovskyy, Y.; Boyarchuk, O.; Nukui, Y.; Tsumura, M.; Vidaur, L.; Tangye, S. G.; Burrel, S.; Duffy, D.; Quintana-Murci, L.; Klocperk, A.; Kann, N. Y.; Shcherbina, A.; Lau, Y. L.; Leung, D.; Coulongeat, M.; Marlet, J.; Koning, R.; Reyes, L. F.; Chauvineau-Grenier, A.; Venet, F.; Monneret, G.; Nussenzweig, MC.; Arrestier, R.; Boudhabhay, I.; Baris-Feldman, H.; Hagin, D.; Wauters, J.; Meyts, I.; Dyer, A. H.; Kennelly, SP.; Bourke, N. M.; Halwani, R.; Sharif-Askari, N. S.; Dorgham, K.; Sallette, J.; Sedkaoui, S. M.; AlKhater, S.; Rigo-Bonnin, R.; Morandeira, F.; Roussel, L.; Vinh, DC.; Ostrowski, SR.; Condino-Neto, A.; Prando, C.; Bondarenko, A.; Spaan, A. N.; Gilardin, L.; Fellay, J.; Lyonnet, S.; Bilguvar, K.; Lifton, R. P.; Mane, S.; Anderson, M. S.; Boisson, B.; Beziat, V.; Zhang, SY.; Andreakos, E.; Hermine, O.; Pujol, A.; Peterson, P.; Mogensen, T. H.; Rowen, L.; Mond, J.; Debette, S.; de Lamballerie, X.; Duval, X.; Mentre, F.; Zins, M.; Soler-Palacin, P.; Colobran, R.; Gorochov, G.; Solanich, X.; Susen, S.; Martinez-Picado, J.; Raoult, D.; Vasse, M.; Gregersen, P. K.; Piemonti, L.; Rodriguez-Gallego, C.; Notarangelo, LD.; Su, H. C.; Kisand, K.; Okada, S.; Puel, A.; Jouanguy, E.; Rice, C. M.; Tiberghien, P.; Zhang, Q.; Cobat, A.; Abel, L.; Casanova, J. L.
Circulating autoantibodies (auto-Abs) neutralizing high concentrations (10 ng/ml; in plasma diluted 1:10) of IFN-α and/or IFN-ω are found in about 10% of patients with critical COVID-19 (coronavirus disease 2019) pneumonia but not in individuals with asymptomatic infections. We detect auto-Abs neutralizing 100-fold lower, more physiological, concentrations of IFN-α and/or IFN-ω (100 pg/ml; in 1:10 dilutions of plasma) in 13.6% of 3595 patients with critical COVID-19, including 21% of 374 patients >80 years, and 6.5% of 522 patients with severe COVID-19. These antibodies are also detected in 18% of the 1124 deceased patients (aged 20 days to 99 years; mean: 70 years). Moreover, another 1.3% of patients with critical COVID-19 and 0.9% of the deceased patients have auto-Abs neutralizing high concentrations of IFN-β. We also show, in a sample of 34,159 uninfected individuals from the general population, that auto-Abs neutralizing high concentrations of IFN-α and/or IFN-ω are present in 0.18% of individuals between 18 and 69 years, 1.1% between 70 and 79 years, and 3.4% >80 years. Moreover, the proportion of individuals carrying auto-Abs neutralizing lower concentrations is greater in a subsample of 10,778 uninfected individuals: 1% of individuals <70 years, 2.3% between 70 and 80 years, and 6.3% >80 years. By contrast, auto-Abs neutralizing IFN-β do not become more frequent with age. Auto-Abs neutralizing type I IFNs predate SARS-CoV-2 infection and sharply increase in prevalence after the age of 70 years. They account for about 20% of both critical COVID-19 cases in the over 80s and total fatal COVID-19 cases.
Open Access
A charge inverter for III-nitride light-emitting diodes
(American Institute of Physics Inc., 2016) Zhang Z.-H.; Zhang, Y.; Bi, W.; Geng, C.; Xu S.; Demir, Hilmi Volkan; Sun, X. W.
In this work, we propose a charge inverter that substantially increases the hole injection efficiency for InGaN/GaN light-emitting diodes (LEDs). The charge inverter consists of a metal/electrode, an insulator, and a semiconductor, making an Electrode-Insulator-Semiconductor (EIS) structure, which is formed by depositing an extremely thin SiO2 insulator layer on the p+-GaN surface of a LED structure before growing the p-electrode. When the LED is forward-biased, a weak inversion layer can be obtained at the interface between the p+-GaN and SiO2 insulator. The weak inversion region can shorten the carrier tunnel distance. Meanwhile, the smaller dielectric constant of the thin SiO2 layer increases the local electric field within the tunnel region, and this is effective in promoting the hole transport from the p-electrode into the p+-GaN layer. Due to the improved hole injection, the external quantum efficiency is increased by 20% at 20 mA for the 350 × 350 μm2 LED chip. Thus, the proposed EIS holds great promise for high efficiency LEDs.
Open Access
Decoupling contact and mirror: an effective way to improve the reflector for flip-chip InGaN/GaN-based light-emitting diodes
(Institute of Physics Publishing, 2016) Zhu B.; Liu W.; Lu S.; Zhang, Y.; Hasanov N.; Zhang X.; Ji Y.; Zhang Z.-H.; Tan S.T.; Liu, H.; Demir, Hilmi Volkan
In the conventional fabrication process of the widely-adopted Ni/Ag/Ti/Au reflector for InGaN/GaN-based flip-chip light-emitting diodes (LEDs), the contact and the mirror are entangled together with contrary processing conditions which set constraints to the device performance severely. Here we first report the concept and its effectiveness of decoupling the contact formation and the mirror construction. The ohmic contact is first formed by depositing and annealing an extremely thin layer of Ni/Ag on top of p-GaN. The mirror construction is then carried out by depositing thick layer of Ag/Ti/Au without any annealing. Compared with the conventional fabrication method of the reflector, by which the whole stack of Ni/Ag/Ti/Au is deposited and annealed together, the optical output power is improved by more than 70% at 350 mA without compromising the electrical performance. The mechanism of decoupling the contact and the mirror is analyzed with the assistance of contactless sheet resistance measurement and secondary ion mass spectrometry (SIMS) depth profile analysis. © 2016 IOP Publishing Ltd.
Unknown
Dependence of the substrate structure and the film growth at the junction of YBCO SEJ rf-SQUIDs on the IBE process and effects on the SQUID's characteristics
(Elsevier, 2002) Fardmanesh, Mehdi; Schubert, J.; Akram, Rizwan; Banzet, M.; Zander, W.; Zhang, Y.; Schilling, M.; Krause, H-J.
Step edge junction (SEJ) rf-SQUIDs were made of 200 nm thick YBCO films on LaAlO3(100) substrates using pulsed laser deposition technique. The steps on the substrates were developed using a combination of stationary and rotating angled argon ion beams with different beam energies and intensities. While sharp clean steps with heights up to 300 nm were obtained on the substrates using the combinatorial ion beam etching (IBE) process, very shallow ramp-type surfaces were found developing on the bottom of the trench, close to the steps. The ramp-type surfaces were found to be a source of hole-type defects in the films grown at the step edges. High quality films could be obtained on the flat regions away from the steps. Higher defect densities in the films close to the SEJs resulted in devices with higher 1/f noise and wider spread of the junction parameters. The 1/f noise of such devices increased with decreasing temperature. High quality films on sharp clean steps with flat substrate surfaces, developed using optimized combinatorial IBE process, resulted in higher yield of low 1/f noise SQUIDs. The Ic of the junctions and hence the working temperature of the SQUID could also be controlled by the junction width and the step height.
Open Access
Dynamic environment at the Zr6 oxo cluster surface is key for the catalytic formation of amide bonds
(Royal Society of Chemistry, 2022-10-22) Zhang, Y.; Kökçüler, İsmail Yaşar; Azambuja, F.; Parac-Vogt, T.N.
Zirconium compounds are an attractive alternative to costly, low abundant metals for the development of inexpensive, readily available, and robust catalysts. The air and moisture stable Zr oxo clusters such as the Zr6O8 species, are of particular interest as they are key building blocks of several Zr-based metal–organic framework (Zr-MOF) catalysts. However, broader use of these cluster-based materials as catalysts is still hampered by the modest understanding of their fundamental reactivity. To bridge this gap, we report on the activity of a soluble Zr6O8 cluster, [Zr6(OH)4O4(OMc)12] (OMc = methacrylate) (Zr6), as a discrete molecular catalyst for the atom-economic formation of amide bonds. This reaction demands two completely different substrates interacting with the Zr6 catalyst, a key step rarely addressed in MOF catalyzed reactions. Remarkably, Zr6 catalyzes the formation of amide bonds directly from non-activated carboxylic acid and amine substrates in ethanol, without requiring anhydrous conditions or water scavenging to achieve good yields. As shown by a series of kinetic, and mechanistic experiments, this promising reactivity arises from a dynamic environment at the cluster surface, where the essential coordination of both substrates requires an excess of amine to enhance the reaction output. Strikingly, Zr6 catalyst tolerates a range of substrates, including (hetero)aromatic, aliphatic, and α-branched acids, even though their nature directly impacts the reaction efficiency. Further, insights for the future design of catalysts based on Zr oxo cluster are discussed through a detailed comparison of Zr6 reactivity with a related Zr12 cluster, and Zr-MOF catalysts. Considering the advantages of zirconium, and the relevance of discrete Zr oxo clusters as building blocks of several MOF materials of varied utility, the molecular level understanding disclosed here contributes at large to the development of novel catalytic entities, and sustainable approaches to synthetic chemistry.
Open Access
Effect of Mg doping in the barriers on the electrical performance of InGaN/GaN-based light-emitting diodes
(Elsevier B. V., 2018-04) Zhu, B.; Zhang, Z.; Tan, S. T.; Lu, S.; Zhang, Y.; Kang, X.; Wang, N.; Hasanov, N.; Demir, Hilmi Volkan
In this work, we report how the Mg doping in the barriers affects the electrical performance of InGaN/GaN-based light-emitting diodes. When compared with the reference device that does not have Mg doped quantum barriers, the turn-on voltage for the proposed device is reduced and the electrical thermal stability is improved. The superior electrical performance is analyzed through the temperature dependent current-voltage and capacitance-voltage characteristics. Meanwhile a reduced depletion length and increased acceptor concentration are achieved in the control devices which is consistent with the simulated results.
Open Access
Effects of the step structure on the yield, operating temperature, and the noise in step-edge Josephson junction rf-SQUID magnetometers and gradiometers
(Elsevier, 2001) Fardmanesh, M.; Schubert, J.; Banzet, M.; Zander, W.; Zhang, Y.; Krause, H. J.
Step-edge Josephson junction rf-SQUID magnetometers and gradiometers were made using YBCO films on LaAlO3(1 0 0) and SrTiO3(1 0 0) substrates. Designs with 150×150 μm2 loop and 3.6 mm diameter washer area for the magnetometers (230 pH), and 1.5 mm baseline and 1.5 mm diameter washer areas with a loop of 75×75 μm2 for the Gradiometers (490 pH) were used. Effects of the step structure on the yield, optimal operating temperature range, and the 1/f noise of the devices were investigated. The step structure was controlled using different ion beam etching (IBE) processes. The devices on LaAlO3 showed high sensitivity to the IBE parameters and the step structure while this was much less for the SrTiO3 substrate samples. This is mainly due to a considerable re-deposition of the substrate material on the step during the IBE process, in particular for LaAlO3, resulting in very low yield and high 1/f noise devices. The film structure at the step was also found to be essentially dependent on the step structure strongly affecting the 1/f noise of the devices. Using an optimized “combinational IBE” process, surface modified sharp steps were prepared resulting in high yield of low 1/f noise devices when combined with high quality YBCO film. A typical 1/f noise corner frequency of less than about 10 Hz with a white noise level of about 20 μΦo/Hz at liquid nitrogen temperature was obtained for these devices. The devices have shown stability over many thermal cycles and the time (over half a year since their fabrication) while kept at the room temperature environment. The operating temperature range of the devices was found to be controllable by the step depth and the film thickness for the steps.
Open Access
A global reference for human genetic variation
(Nature Publishing Group, 2015) Auton, A.; Abecasis, G. R.; Altshuler, D. M.; Durbin, R. M.; Bentley, D. R.; Chakravarti, A.; Clark, A. G.; Donnelly, P.; Eichler, E. E.; Flicek, P.; Gabriel, S. B.; Gibbs, R. A.; Green, E. D.; Hurles, M. E.; Knoppers, B. M.; Korbel, J. O.; Lander, E. S.; Lee, C.; Lehrach, H.; Mardis, E. R.; Marth, G. T.; McVean, G. A.; Nickerson, D. A.; Schmidt, J. P.; Sherry, S. T.; Wang, J.; Wilson, R. K.; Boerwinkle, E.; Doddapaneni, H.; Han, Y.; Korchina, V.; Kovar, C.; Lee, S.; Muzny, D.; Reid, J. G.; Zhu, Y.; Chang, Y.; Feng, Q.; Fang, X.; Guo, X.; Jian, M.; Jiang, H.; Jin, X.; Lan, T.; Li, G.; Li, J.; Li, Y.; Liu, S.; Liu, X.; Lu, Y.; Ma, X.; Tang, M.; Wang, B.; Wang, G.; Wu, H.; Wu, R.; Xu, X.; Yin, Y.; Zhang, D.; Zhang, W.; Zhao, J.; Zhao, M.; Zheng, X.; Gupta, N.; Gharani, N.; Toji, L. H.; Gerry, N. P.; Resch, A. M.; Barker, J.; Clarke, L.; Gil, L.; Hunt, S. E.; Kelman, G.; Kulesha, E.; Leinonen, R.; McLaren, W. M.; Radhakrishnan, R.; Roa, A.; Smirnov, D.; Smith, R. E.; Streeter, I.; Thormann, A.; Toneva, I.; Vaughan, B.; Zheng-Bradley, X.; Grocock, R.; Humphray, S.; James, T.; Kingsbury, Z.; Sudbrak, R.; Albrecht, M. W.; Amstislavskiy, V. S.; Borodina, T. A.; Lienhard, M.; Mertes, F.; Sultan, M.; Timmermann, B.; Yaspo, Marie-Laure; Fulton, L.; Ananiev, V.; Belaia, Z.; Beloslyudtsev, D.; Bouk, N.; Chen, C.; Church, D.; Cohen, R.; Cook, C.; Garner, J.; Hefferon, T.; Kimelman, M.; Liu, C.; Lopez, J.; Meric, P.; O'Sullivan, C.; Ostapchuk, Y.; Phan, L.; Ponomarov, S.; Schneider, V.; Shekhtman, E.; Sirotkin, K.; Slotta, D.; Zhang, H.; Balasubramaniam, S.; Burton, J.; Danecek, P.; Keane, T. M.; Kolb-Kokocinski, A.; McCarthy, S.; Stalker, J.; Quail, M.; Davies, C. J.; Gollub, J.; Webster, T.; Wong, B.; Zhan, Y.; Campbell, C. L.; Kong, Y.; Marcketta, A.; Yu, F.; Antunes, L.; Bainbridge, M.; Sabo, A.; Huang, Z.; Coin, L. J. M.; Fang, L.; Li, Q.; Li, Z.; Lin, H.; Liu, B.; Luo, R.; Shao, H.; Xie, Y.; Ye, C.; Yu, C.; Zhang, F.; Zheng, H.; Zhu, H.; Alkan, C.; Dal, E.; Kahveci, F.; Garrison, E. P.; Kural, D.; Lee, W. P.; Leong, W. F.; Stromberg, M.; Ward, A. N.; Wu, J.; Zhang, M.; Daly, M. J.; DePristo, M. A.; Handsaker, R. E.; Banks, E.; Bhatia, G.; Del Angel, G.; Genovese, G.; Li, H.; Kashin, S.; McCarroll, S. A.; Nemesh, J. C.; Poplin, R. E.; Yoon, S. C.; Lihm, J.; Makarov, V.; Gottipati, S.; Keinan, A.; Rodriguez-Flores, J. L.; Rausch, T.; Fritz, M. H.; Stütz, A. M.; Beal, K.; Datta, A.; Herrero, J.; Ritchie, G. R. S.; Zerbino, D.; Sabeti, P. C.; Shlyakhter, I.; Schaffner, S. F.; Vitti, J.; Cooper, D. N.; Ball, E. V.; Stenson, P. D.; Barnes, B.; Bauer, M.; Cheetham, R. K.; Cox, A.; Eberle, M.; Kahn, S.; Murray, L.; Peden, J.; Shaw, R.; Kenny, E. E.; Batzer, M. A.; Konkel, M. K.; Walker, J. A.; MacArthur, D. G.; Lek, M.; Herwig, R.; Ding, L.; Koboldt, D. C.; Larson, D.; Ye, K.; Gravel, S.; Swaroop, A.; Chew, E.; Lappalainen, T.; Erlich, Y.; Gymrek, M.; Willems, T. F.; Simpson, J. T.; Shriver, M. D.; Rosenfeld, J. A.; Bustamante, C. D.; Montgomery, S. B.; De La Vega, F. M.; Byrnes, J. K.; Carroll, A. W.; DeGorter, M. K.; Lacroute, P.; Maples, B. K.; Martin, A. R.; Moreno-Estrada, A.; Shringarpure, S. S.; Zakharia, F.; Halperin, E.; Baran, Y.; Cerveira, E.; Hwang, J.; Malhotra, A.; Plewczynski, D.; Radew, K.; Romanovitch, M.; Zhang, C.; Hyland, F. C. L.; Craig, D. W.; Christoforides, A.; Homer, N.; Izatt, T.; Kurdoglu, A. A.; Sinari, S. A.; Squire, K.; Xiao, C.; Sebat, J.; Antaki, D.; Gujral, M.; Noor, A.; Ye, K.; Burchard, E. G.; Hernandez, R. D.; Gignoux, C. R.; Haussler, D.; Katzman, S. J.; Kent, W. J.; Howie, B.; Ruiz-Linares, A.; Dermitzakis, E. T.; Devine, S. E.; Kang, H. M.; Kidd, J. M.; Blackwell, T.; Caron, S.; Chen, W.; Emery, S.; Fritsche, L.; Fuchsberger, C.; Jun, G.; Li, B.; Lyons, R.; Scheller, C.; Sidore, C.; Song, S.; Sliwerska, E.; Taliun, D.; Tan, A.; Welch, R.; Wing, M. K.; Zhan, X.; Awadalla, P.; Hodgkinson, A.; Li, Y.; Shi, X.; Quitadamo, A.; Lunter, G.; Marchini, J. L.; Myers, S.; Churchhouse, C.; Delaneau, O.; Gupta-Hinch, A.; Kretzschmar, W.; Iqbal, Z.; Mathieson, I.; Menelaou, A.; Rimmer, A.; Xifara, D. K.; Oleksyk, T. K.; Fu, Y.; Liu, X.; Xiong, M.; Jorde, L.; Witherspoon, D.; Xing, J.; Browning, B. L.; Browning, S. R.; Hormozdiari, F.; Sudmant, P. H.; Khurana, E.; Tyler-Smith, C.; Albers, C. A.; Ayub, Q.; Chen, Y.; Colonna, V.; Jostins, L.; Walter, K.; Xue, Y.; Gerstein, M. B.; Abyzov, A.; Balasubramanian, S.; Chen, J.; Clarke, D.; Fu, Y.; Harmanci, A. O.; Jin, M.; Lee, D.; Liu, J.; Mu, X. J.; Zhang, J.; Zhang, Y.; Hartl, C.; Shakir, K.; Degenhardt, J.; Meiers, S.; Raeder, B.; Casale, F. P.; Stegle, O.; Lameijer, E. W.; Hall, I.; Bafna, V.; Michaelson, J.; Gardner, E. J.; Mills, R. E.; Dayama, G.; Chen, K.; Fan, X.; Chong, Z.; Chen, T.; Chaisson, M. J.; Huddleston, J.; Malig, M.; Nelson, B. J.; Parrish, N. F.; Blackburne, B.; Lindsay, S. J.; Ning, Z.; Zhang, Y.; Lam, H.; Sisu, C.; Challis, D.; Evani, U. S.; Lu, J.; Nagaswamy, U.; Yu, J.; Li, W.; Habegger, L.; Yu, H.; Cunningham, F.; Dunham, I.; Lage, K.; Jespersen, J. B.; Horn, H.; Kim, D.; Desalle, R.; Narechania, A.; Sayres, M. A. W.; Mendez, F. L.; Poznik, G. D.; Underhill, P. A.; Mittelman, D.; Banerjee, R.; Cerezo, M.; Fitzgerald, T. W.; Louzada, S.; Massaia, A.; Yang, F.; Kalra, D.; Hale, W.; Dan, X.; Barnes, K. C.; Beiswanger, C.; Cai, H.; Cao, H.; Henn, B.; Jones, D.; Kaye, J. S.; Kent, A.; Kerasidou, A.; Mathias, R.; Ossorio, P. N.; Parker, M.; Rotimi, C. N.; Royal, C. D.; Sandoval, K.; Su, Y.; Tian, Z.; Tishkoff, S.; Via, M.; Wang, Y.; Yang, H.; Yang, L.; Zhu, J.; Bodmer, W.; Bedoya, G.; Cai, Z.; Gao, Y.; Chu, J.; Peltonen, L.; Garcia-Montero, A.; Orfao, A.; Dutil, J.; Martinez-Cruzado, J. C.; Mathias, R. A.; Hennis, A.; Watson, H.; McKenzie, C.; Qadri, F.; LaRocque, R.; Deng, X.; Asogun, D.; Folarin, O.; Happi, C.; Omoniwa, O.; Stremlau, M.; Tariyal, R.; Jallow, M.; Joof, F. S.; Corrah, T.; Rockett, K.; Kwiatkowski, D.; Kooner, J.; Hien, T. T.; Dunstan, S. J.; ThuyHang, N.; Fonnie, R.; Garry, R.; Kanneh, L.; Moses, L.; Schieffelin, J.; Grant, D. S.; Gallo, C.; Poletti, G.; Saleheen, D.; Rasheed, A.; Brooks, L. D.; Felsenfeld, A. L.; McEwen, J. E.; Vaydylevich, Y.; Duncanson, A.; Dunn, M.; Schloss, J. A.
The 1000 Genomes Project set out to provide a comprehensive description of common human genetic variation by applying whole-genome sequencing to a diverse set of individuals from multiple populations. Here we report completion of the project, having reconstructed the genomes of 2,504 individuals from 26 populations using a combination of low-coverage whole-genome sequencing, deep exome sequencing, and dense microarray genotyping. We characterized a broad spectrum of genetic variation, in total over 88 million variants (84.7 million single nucleotide polymorphisms (SNPs), 3.6 million short insertions/deletions (indels), and 60,000 structural variants), all phased onto high-quality haplotypes. This resource includes >99% of SNP variants with a frequency of >1% for a variety of ancestries. We describe the distribution of genetic variation across the global sample, and discuss the implications for common disease studies. © 2015 Macmillan Publishers Limited. All rights reserved.
Open Access
High-performance triangular miniaturized-LEDs for high current and power density applications
(American Chemical Society, 2021-08-18) Lu, S.; Zhang, Y.; Zhang, Zi-H.; Zhu, B.; Zheng, H.; Tan, S. T.; Demir, Hilmi Volkan
This work proposes an effective electrode length model and reveals for the first time the relationship between this model and the mesa shape effect. On the basis of this model, we demonstrate high-performance triangular miniaturized-LEDs (mini-LEDs) and benchmark to the conventional square, and circular shapes of the same mesa area. Here, we systematically study the impact of shaping in mini-LEDs both theoretically and experimentally, which is fundamentally different than that of the conventional regular-sized LEDs. We find that, at the current level of 200 mA, the triangular mini-LEDs deliver an enhancement of 36.4% in the optical output power and a decrease of 9.6% for the forward voltage compared to the commonly used square ones, and also an enhancement of 24.6% in the optical output power and a decrease of 14.3% for the forward voltage compared to the circular ones. The superior optical performance is proved to result from longer effective n-electrode length in the case of the triangular mini-LEDs, which suppresses the self-heating effect and thus well preserves the internal quantum efficiency, whereas the light extraction efficiency and the heat dissipation for the triangular shape are not significantly increased for such small mesa sizes, unlike conventional broad-area LEDs. Meanwhile, the reduced voltage is revealed to stem from the decreased n-GaN resistance. Different than conventional LEDs, these findings therefore indicate that the effective n-electrode length matters substantially for the miniaturized-LEDs.
Open Access
A hole accelerator for InGaN/GaN light-emitting diodes
(AIP Publishing, 2014) Zhang, Z. H.; Liu, W.; Tan, S. T.; Ji, Y.; Wang, L.; Zhu, B.; Zhang, Y.; Lu, S.; Zhang, X.; Hasanov, N.; Sun, X. W.; Demir, Hilmi Volkan
The quantum efficiency of InGaN/GaN light-emitting diodes (LEDs) has been significantly limited by the insufficient hole injection, and this is caused by the inefficient p-type doping and the low hole mobility. The low hole mobility makes the holes less energetic, which hinders the hole injection into the multiple quantum wells (MQWs) especially when a p-type AlGaN electron blocking layer (EBL) is adopted. In this work, we report a hole accelerator to accelerate the holes so that the holes can obtain adequate kinetic energy, travel across the p-type EBL, and then enter the MQWs more efficiently and smoothly. In addition to the numerical study, the effectiveness of the hole accelerator is experimentally shown through achieving improved optical output power and reduced efficiency droop for the proposed InGaN/GaN LED. (C) 2014 AIP Publishing LLC.
Open Access
Inborn errors of OAS–RNase L in SARS-CoV-2–related multisystem inflammatory syndrome in children
(American Association for the Advancement of Science (AAAS), 2022-12-20) Lee, D.; Pen, J. L.; Yatim, A.; Dong, B.; Aquino, Y.; Ogishi, M.; Pescarmona, R.; Talouarn, E.; Rinchai, D.; Zhang, P.; Perret, M.; Liu, Z.; Jordan, L.; Bozdemir, S. E.; Bayhan, G. I.; Beaufils, C.; Bizien, L.; Bisiaux, A.; Lei, W.; Hasan, M.; Chen, J.; Gaughan, C.; Asthana, A.; Libri, V.; Luna, Joseph M.; Jaffré, Fabrice; Hoffmann, H.; Michailidis, E.; Moreews, M.; Seeleuthner, Y.; Bilguvar, K.; Mane, S.; Flores, C.; Zhang, Y.; Arias, A. A.; Bailey, R.; Schlüter, A.; Milisavljevic, B.; Bigio, B.; Voyer, T. L.; Materna, M.; Gervais, A.; Moncada-Velez, M.; Pala, F.; Lazarov, T.; Levy, R.; Neehus, A.; Rosain, J.; Peel, J.; Chan, Y.; Morin, M.; Pino-Ramirez, R. M.; Belkaya, Serkan; Lorenzo, L.; Anton, J.; Delafontaine, S.; Toubiana, J.; Bajolle, F.; Fumadó, V.; DeDiego, M. L.; Fidouh, N.; Rozenberg, F.; Pérez-Tur, J.; Chen, S.; Evans, T.; Geissmann, F.; Lebon, P.; Weiss, S. R.; Bonnet, D.; Duval, X.; Cohort§, C.; Effort, C.; Pan-Hammarström, Q.; Planas, A. M.; Meyts, I.; Haerynck, F.; Pujol, A.; Sancho-Shimizu, V.; Dalgard, C.; Bustamante, J.; Puel, A.; Boisson-Dupuis, S.; Boisson, B.; Maniatis, T.; Zhang, Q.; Bastard, P.; Notarangelo, L.; Béziat, V.; Diego, R.; Rodriguez-Gallego, C.; Su, H. C.; Lifton, R. P.; Jouanguy, E.; Cobat, A.; Alsina, L.; Keles, S.; Haddad, E.; Abel, L.; Belot, A.; Quintana-Murci, L.; Rice, C. M.; Silverman, R. H.; Zhang, S.; Casanova, J.
Multisystem inflammatory syndrome in children (MIS-C) is a rare and severe condition that follows benign COVID-19. We report autosomal recessive deficiencies of OAS1, OAS2, or RNASEL in five unrelated children with MIS-C. The cytosolic double-stranded RNA (dsRNA)-sensing OAS1 and OAS2 generate 2'-5'-linked oligoadenylates (2-5A) that activate the single-stranded RNA-degrading ribonuclease L (RNase L). Monocytic cell lines and primary myeloid cells with OAS1, OAS2, or RNase L deficiencies produce excessive amounts of inflammatory cytokines upon dsRNA or severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) stimulation. Exogenous 2-5A suppresses cytokine production in OAS1-deficient but not RNase L-deficient cells. Cytokine production in RNase L-deficient cells is impaired by MDA5 or RIG-I deficiency and abolished by mitochondrial antiviral-signaling protein (MAVS) deficiency. Recessive OAS-RNase L deficiencies in these patients unleash the production of SARS-CoV-2-triggered, MAVS-mediated inflammatory cytokines by mononuclear phagocytes, thereby underlying MIS-C.
Open Access
An integrated map of genetic variation from 1,092 human genomes
(Nature Publishing Group, 2012) Altshuler, D.M.; Durbin, R.M.; Abecasis G.R.; Bentley, D.R.; Chakravarti, A.; Clark, A.G.; Donnelly P.; Eichler, E.E.; Flicek P.; Gabriel, S.B.; Gibbs, R.A.; Green, E.D.; Hurles, M.E.; Knoppers, B.M.; Korbel J.O.; Lander, E.S.; Lee, C.; Lehrach H.; Mardis, E.R.; Marth G.T.; McVean G.A.; Nickerson, D.A.; Schmidt J.P.; Sherry, S.T.; Wang, J.; Wilson, R.K.; Dinh H.; Kovar, C.; Lee, S.; Lewis L.; Muzny, D.; Reid J.; Wang, M.; Fang X.; Guo X.; Jian, M.; Jiang H.; Jin X.; Li G.; Li J.; Li Y.; Li, Z.; Liu X.; Lu, Y.; Ma X.; Su, Z.; Tai, S.; Tang, M.; Wang, B.; Wang G.; Wu H.; Wu, R.; Yin, Y.; Zhang W.; Zhao J.; Zhao, M.; Zheng X.; Zhou, Y.; Gupta, N.; Clarke L.; Leinonen, R.; Smith, R.E.; Zheng-Bradley X.; Grocock, R.; Humphray, S.; James, T.; Kingsbury, Z.; Sudbrak, R.; Albrecht, M.W.; Amstislavskiy V.S.; Borodina, T.A.; Lienhard, M.; Mertes F.; Sultan, M.; Timmermann, B.; Yaspo, M.-L.; Fulton L.; Fulton, R.; Weinstock G.M.; Balasubramaniam, S.; Burton J.; Danecek P.; Keane, T.M.; Kolb-Kokocinski, A.; McCarthy, S.; Stalker J.; Quail, M.; Davies, C.J.; Gollub J.; Webster, T.; Wong, B.; Zhan, Y.; Auton, A.; Yu F.; Bainbridge, M.; Challis, D.; Evani, U.S.; Lu J.; Nagaswamy, U.; Sabo, A.; Wang Y.; Yu J.; Coin L.J.M.; Fang L.; Li Q.; Li, Z.; Lin H.; Liu, B.; Luo, R.; Qin, N.; Shao H.; Wang, B.; Xie, Y.; Ye, C.; Yu, C.; Zhang F.; Zheng H.; Zhu H.; Garrison, E.P.; Kural, D.; Lee W.-P.; Fung Leong W.; Ward, A.N.; Wu J.; Zhang, M.; Griffin L.; Hsieh, C.-H.; Mills, R.E.; Shi X.; Von Grotthuss, M.; Zhang, C.; Daly, M.J.; Depristo, M.A.; Banks, E.; Bhatia G.; Carneiro, M.O.; Del Angel G.; Genovese G.; Handsaker, R.E.; Hartl, C.; McCarroll, S.A.; Nemesh J.C.; Poplin, R.E.; Schaffner, S.F.; Shakir, K.; Yoon, S.C.; Lihm J.; Makarov V.; Jin H.; Kim W.; Cheol Kim, K.; Rausch, T.; Beal, K.; Cunningham F.; Herrero J.; McLaren W.M.; Ritchie G.R.S.; Gottipati, S.; Keinan, A.; Rodriguez-Flores J.L.; Sabeti P.C.; Grossman, S.R.; Tabrizi, S.; Tariyal, R.; Cooper, D.N.; Ball, E.V.; Stenson P.D.; Barnes, B.; Bauer, M.; Keira Cheetham, R.; Cox, T.; Eberle, M.; Kahn, S.; Murray L.; Peden J.; Shaw, R.; Ye, K.; Batzer, M.A.; Konkel, M.K.; Walker J.A.; MacArthur, D.G.; Lek, M.; Herwig, R.; Shriver, M.D.; Bustamante, C.D.; Byrnes J.K.; De La Vega F.M.; Gravel, S.; Kenny, E.E.; Kidd J.M.; Maples, B.K.; Moreno-Estrada, A.; Zakharia F.; Halperin, E.; Baran, Y.; Craig, D.W.; Christoforides, A.; Homer, N.; Izatt, T.; Kurdoglu, A.A.; Sinari, S.A.; Squire, K.; Xiao, C.; Sebat J.; Bafna V.; Ye, K.; Burchard, E.G.; Hernandez, R.D.; Gignoux, C.R.; Haussler, D.; Katzman, S.J.; James Kent W.; Howie, B.; Ruiz-Linares, A.; Dermitzakis, E.T.; Lappalainen, T.; Devine, S.E.; Liu X.; Maroo, A.; Tallon L.J.; Rosenfeld J.A.; Michelson L.P.; Min Kang H.; Anderson P.; Angius, A.; Bigham, A.; Blackwell, T.; Busonero F.; Cucca F.; Fuchsberger, C.; Jones, C.; Jun G.; Li Y.; Lyons, R.; Maschio, A.; Porcu, E.; Reinier F.; Sanna, S.; Schlessinger, D.; Sidore, C.; Tan, A.; Kate Trost, M.; Awadalla P.; Hodgkinson, A.; Lunter G.; Marchini J.L.; Myers, S.; Churchhouse, C.; Delaneau O.; Gupta-Hinch, A.; Iqbal, Z.; Mathieson I.; Rimmer, A.; Xifara, D.K.; Oleksyk, T.K.; Fu, Y.; Liu X.; Xiong, M.; Jorde L.; Witherspoon, D.; Xing J.; Browning, B.L.; Alkan C.; Hajirasouliha I.; Hormozdiari F.; Ko, A.; Sudmant P.H.; Chen, K.; Chinwalla, A.; Ding L.; Dooling, D.; Koboldt, D.C.; McLellan, M.D.; Wallis J.W.; Wendl, M.C.; Zhang Q.; Tyler-Smith, C.; Albers, C.A.; Ayub Q.; Chen, Y.; Coffey, A.J.; Colonna V.; Huang, N.; Jostins L.; Li H.; Scally, A.; Walter, K.; Xue, Y.; Zhang, Y.; Gerstein, M.B.; Abyzov, A.; Balasubramanian, S.; Chen J.; Clarke, D.; Fu, Y.; Habegger L.; Harmanci, A.O.; Jin, M.; Khurana, E.; Jasmine Mu X.; Sisu, C.; Degenhardt J.; Stütz, A.M.; Keira Cheetham, R.; Church, D.; Michaelson J.J.; Blackburne, B.; Lindsay, S.J.; Ning, Z.; Frankish, A.; Harrow J.; Mu X.J.; Fowler G.; Hale W.; Kalra, D.; Barker J.; Kelman G.; Kulesha, E.; Radhakrishnan, R.; Roa, A.; Smirnov, D.; Streeter I.; Toneva I.; Vaughan, B.; Ananiev V.; Belaia, Z.; Beloslyudtsev, D.; Bouk, N.; Chen, C.; Cohen, R.; Cook, C.; Garner J.; Hefferon, T.; Kimelman, M.; Liu, C.; Lopez J.; Meric P.; O'Sullivan, C.; Ostapchuk, Y.; Phan L.; Ponomarov, S.; Schneider V.; Shekhtman, E.; Sirotkin, K.; Slotta, D.; Zhang H.; Barnes, K.C.; Beiswanger, C.; Cai H.; Cao H.; Gharani, N.; Henn, B.; Jones, D.; Kaye J.S.; Kent, A.; Kerasidou, A.; Mathias, R.; Ossorio P.N.; Parker, M.; Reich, D.; Rotimi, C.N.; Royal, C.D.; Sandoval, K.; Su, Y.; Tian, Z.; Tishkoff, S.; Toji L.H.; Via, M.; Wang Y.; Yang H.; Yang L.; Zhu J.; Bodmer W.; Bedoya G.; Ming, C.Z.; Yang G.; Jia You, C.; Peltonen L.; Garcia-Montero, A.; Orfao, A.; Dutil J.; Martinez-Cruzado J.C.; Brooks L.D.; Felsenfeld, A.L.; McEwen J.E.; Clemm, N.C.; Duncanson, A.; Dunn, M.; Guyer, M.S.; Peterson J.L.; Lacroute P.
By characterizing the geographic and functional spectrum of human genetic variation, the 1000 Genomes Project aims to build a resource to help to understand the genetic contribution to disease. Here we describe the genomes of 1,092 individuals from 14 populations, constructed using a combination of low-coverage whole-genome and exome sequencing. By developing methods to integrate information across several algorithms and diverse data sources, we provide a validated haplotype map of 38 million single nucleotide polymorphisms, 1.4 million short insertions and deletions, and more than 14,000 larger deletions. We show that individuals from different populations carry different profiles of rare and common variants, and that low-frequency variants show substantial geographic differentiation, which is further increased by the action of purifying selection. We show that evolutionary conservation and coding consequence are key determinants of the strength of purifying selection, that rare-variant load varies substantially across biological pathways, and that each individual contains hundreds of rare non-coding variants at conserved sites, such as motif-disrupting changes in transcription-factor-binding sites. This resource, which captures up to 98% of accessible single nucleotide polymorphisms at a frequency of 1% in related populations, enables analysis of common and low-frequency variants in individuals from diverse, including admixed, populations. © 2012 Macmillan Publishers Limited. All rights reserved.
Open Access
An integrated map of structural variation in 2,504 human genomes
(Nature Publishing Group, 2015) Sudmant, P. H.; Rausch, T.; Gardner, E. J.; Handsaker, R. E.; Abyzov, A.; Huddleston, J.; Zhang, Y.; Ye, K.; Jun, G.; Fritz, M. Hsi-Yang; Konkel, M. K.; Malhotra, A.; Stütz, A. M.; Shi, X.; Casale, F. P.; Chen, J.; Hormozdiari, F.; Dayama, G.; Chen, K.; Malig, M.; Chaisson, M. J. P.; Walter, K.; Meiers, S.; Kashin, S.; Garrison, E.; Auton, A.; Lam, H. Y. K.; Mu, X. J.; Alkan, C.; Antaki, D.; Bae, T.; Cerveira, E.; Chines, P.; Chong, Z.; Clarke, L.; Dal, E.; Ding, L.; Emery, S.; Fan, X.; Gujral, M.; Kahveci, F.; Kidd, J. M.; Kong, Y.; Lameijer, Eric-Wubbo; McCarthy, S.; Flicek, P.; Gibbs, R. A.; Marth, G.; Mason, C. E.; Menelaou, A.; Muzny, D. M.; Nelson, B. J.; Noor, A.; Parrish, N. F.; Pendleton, M.; Quitadamo, A.; Raeder, B.; Schadt, E. E.; Romanovitch, M.; Schlattl, A.; Sebra, R.; Shabalin, A. A.; Untergasser, A.; Walker J. A.; Wang, M.; Yu, F.; Zhang, C.; Zhang, J.; Zheng-Bradley, X.; Zhou, W.; Zichner, T.; Sebat, J.; Batzer, M. A.; McCarroll, S. A.; Mills, R. E.; Gerstein, M. B.; Bashir, A.; Stegle, O.; Devine, S. E.; Lee, C.; Eichler, E. E.; Korbel, J. O.
Structural variants are implicated in numerous diseases and make up the majority of varying nucleotides among human genomes. Here we describe an integrated set of eight structural variant classes comprising both balanced and unbalanced variants, which we constructed using short-read DNA sequencing data and statistically phased onto haplotype blocks in 26 human populations. Analysing this set, we identify numerous gene-intersecting structural variants exhibiting population stratification and describe naturally occurring homozygous gene knockouts that suggest the dispensability of a variety of human genes. We demonstrate that structural variants are enriched on haplotypes identified by genome-wide association studies and exhibit enrichment for expression quantitative trait loci. Additionally, we uncover appreciable levels of structural variant complexity at different scales, including genic loci subject to clusters of repeated rearrangement and complex structural variants with multiple breakpoints likely to have formed through individual mutational events. Our catalogue will enhance future studies into structural variant demography, functional impact and disease association.
Open Access
Integrating sequence and array data to create an improved 1000 Genomes Project haplotype reference panel
(Nature Publishing Group, 2014) Delaneau O.; Marchini J.; McVeanh G.A.; Donnelly P.; Lunter G.; Marchini J.L.; Myers, S.; Gupta-Hinch, A.; Iqbal, Z.; Mathieson I.; Rimmer, A.; Xifara, D.K.; Kerasidou, A.; Churchhouse, C.; Altshuler, D.M.; Gabriel, S.B.; Lander, E.S.; Gupta, N.; Daly, M.J.; DePristo, M.A.; Banks, E.; Bhatia G.; Carneiro, M.O.; Del Angel G.; Genovese G.; Handsaker, R.E.; Hartl, C.; McCarroll, S.A.; Nemesh J.C.; Poplin, R.E.; Schaffner, S.F.; Shakir, K.; Sabeti P.C.; Grossman, S.R.; Tabrizi, S.; Tariyal, R.; Li H.; Reich, D.; Durbin, R.M.; Hurles, M.E.; Balasubramaniam, S.; Burton J.; Danecek P.; Keane, T.M.; Kolb-Kokocinski, A.; McCarthy, S.; Stalker J.; Quail, M.; Ayub Q.; Chen, Y.; Coffey, A.J.; Colonna V.; Huang, N.; Jostins L.; Scally, A.; Walter, K.; Xue, Y.; Zhang, Y.; Blackburne, B.; Lindsay, S.J.; Ning, Z.; Frankish, A.; Harrow J.; Chris, T.-S.; Abecasis G.R.; Kang H.M.; Anderson P.; Blackwell, T.; Busonero F.; Fuchsberger, C.; Jun G.; Maschio, A.; Porcu, E.; Sidore, C.; Tan, A.; Trost, M.K.; Bentley, D.R.; Grocock, R.; Humphray, S.; James, T.; Kingsbury, Z.; Bauer, M.; Cheetham, R.K.; Cox, T.; Eberle, M.; Murray L.; Shaw, R.; Chakravarti, A.; Clark, A.G.; Keinan, A.; Rodriguez-Flores J.L.; De LaVega F.M.; Degenhardt J.; Eichler, E.E.; Flicek P.; Clarke L.; Leinonen, R.; Smith, R.E.; Zheng-Bradley X.; Beal, K.; Cunningham F.; Herrero J.; McLaren W.M.; Ritchie G.R.S.; Barker J.; Kelman G.; Kulesha, E.; Radhakrishnan, R.; Roa, A.; Smirnov, D.; Streeter I.; Toneva I.; Gibbs, R.A.; Dinh H.; Kovar, C.; Lee, S.; Lewis L.; Muzny, D.; Reid J.; Wang, M.; Yu F.; Bainbridge, M.; Challis, D.; Evani, U.S.; Lu J.; Nagaswamy, U.; Sabo, A.; Wang, Y.; Yu J.; Fowler G.; Hale W.; Kalra, D.; Green, E.D.; Knoppers, B.M.; Korbel J.O.; Rausch, T.; Sttz, A.M.; Lee, C.; Griffin L.; Hsieh, C.-H.; Mills, R.E.; Von Grotthuss, M.; Zhang, C.; Shi X.; Lehrach H.; Sudbrak, R.; Amstislavskiy V.S.; Lienhard, M.; Mertes F.; Sultan, M.; Timmermann, B.; Yaspo, M.L.; Herwig, S.R.; Mardis, E.R.; Wilson, R.K.; Fulton L.; Fulton, R.; Weinstock G.M.; Chinwalla, A.; Ding L.; Dooling, D.; Koboldt, D.C.; McLellan, M.D.; Wallis J.W.; Wendl, M.C.; Zhang Q.; Marth G.T.; Garrison, E.P.; Kural, D.; Lee W.-P.; Leong W.F.; Ward, A.N.; Wu J.; Zhang, M.; Nickerson, D.A.; Alkan, C.; Hormozdiari F.; Ko, A.; Sudmant P.H.; Schmidt J.P.; Davies, C.J.; Gollub J.; Webster, T.; Wong, B.; Zhan, Y.; Sherry, S.T.; Xiao, C.; Church, D.; Ananiev V.; Belaia, Z.; Beloslyudtsev, D.; Bouk, N.; Chen, C.; Cohen, R.; Cook, C.; Garner J.; Hefferon, T.; Kimelman, M.; Liu, C.; Lopez J.; Meric P.; Ostapchuk, Y.; Phan L.; Ponomarov, S.; Schneider V.; Shekhtman, E.; Sirotkin, K.; Slotta, D.; Zhang H.; Wang J.; Fang X.; Guo X.; Jian, M.; Jiang H.; Jin X.; Li G.; Li J.; Li, Y.; Liu X.; Lu, Y.; Ma X.; Tai, S.; Tang, M.; Wang, B.; Wang G.; Wu H.; Wu, R.; Yin, Y.; Zhang W.; Zhao J.; Zhao, M.; Zheng X.; Lachlan H.; Fang L.; Li Q.; Li, Z.; Lin H.; Liu, B.; Luo, R.; Shao H.; Wang, B.; Xie, Y.; Ye, C.; Yu, C.; Zheng H.; Zhu H.; Cai H.; Cao H.; Su, Y.; Tian, Z.; Yang H.; Yang L.; Zhu J.; Cai, Z.; Wang J.; Albrecht, M.W.; Borodina, T.A.; Auton, A.; Yoon, S.C.; Lihm J.; Makarov V.; Jin H.; Kim W.; Kim, K.C.; Gottipati, S.; Jones, D.; Cooper, D.N.; Ball, E.V.; Stenson P.D.; Barnes, B.; Kahn, S.; Ye, K.; Batzer, M.A.; Konkel, M.K.; Walker J.A.; MacArthur, D.G.; Lek, M.; Shriver, M.D.; Bustamante, C.D.; Gravel, S.; Kenny, E.E.; Kidd J.M.; Lacroute P.; Maples, B.K.; Moreno-Estrada, A.; Zakharia F.; Henn, B.; Sandoval, K.; Byrnes J.K.; Halperin, E.; Baran, Y.; Craig, D.W.; Christoforides, A.; Izatt, T.; Kurdoglu, A.A.; Sinari, S.A.; Homer, N.; Squire, K.; Sebat J.; Bafna V.; Ye, K.; Burchard, E.G.; Hernandez, R.D.; Gignoux, C.R.; Haussler, D.; Katzman, S.J.; Kent W.J.; Howie, B.; Ruiz-Linares, A.; Dermitzakis, E.T.; Lappalainen, T.; Devine, S.E.; Liu X.; Maroo, A.; Tallon L.J.; Rosenfeld J.A.; Michelson L.P.; Angius, A.; Cucca F.; Sanna, S.; Bigham, A.; Jones, C.; Reinier F.; Li, Y.; Lyons, R.; Schlessinger, D.; Awadalla P.; Hodgkinson, A.; Oleksyk, T.K.; Martinez-Cruzado J.C.; Fu, Y.; Liu X.; Xiong, M.; Jorde L.; Witherspoon, D.; Xing J.; Browning, B.L.; Hajirasouliha I.; Chen, K.; Albers, C.A.; Gerstein, M.B.; Abyzov, A.; Chen J.; Fu, Y.; Habegger L.; Harmanci, A.O.; Mu X.J.; Sisu, C.; Balasubramanian, S.; Jin, M.; Khurana, E.; Clarke, D.; Michaelson J.J.; OSullivan, C.; Barnes, K.C.; Gharani, N.; Toji L.H.; Gerry, N.; Kaye J.S.; Kent, A.; Mathias, R.; Ossorio P.N.; Parker, M.; Rotimi, C.N.; Royal, C.D.; Tishkoff, S.; Via, M.; Bodmer W.; Bedoya G.; Yang G.; You, C.J.; Garcia-Montero, A.; Orfao, A.; Dutil J.; Brooks L.D.; Felsenfeld, A.L.; McEwen J.E.; Clemm, N.C.; Guyer, M.S.; Peterson J.L.; Duncanson, A.; Dunn, M.; Peltonen L.
A major use of the 1000 Genomes Project (1000GP) data is genotype imputation in genome-wide association studies (GWAS). Here we develop a method to estimate haplotypes from low-coverage sequencing data that can take advantage of single-nucleotide polymorphism (SNP) microarray genotypes on the same samples. First the SNP array data are phased to build a backbone (or 'scaffold') of haplotypes across each chromosome. We then phase the sequence data 'onto' this haplotype scaffold. This approach can take advantage of relatedness between sequenced and non-sequenced samples to improve accuracy. We use this method to create a new 1000GP haplotype reference set for use by the human genetic community. Using a set of validation genotypes at SNP and bi-allelic indels we show that these haplotypes have lower genotype discordance and improved imputation performance into downstream GWAS samples, especially at low-frequency variants. © 2014 Macmillan Publishers Limited. All rights reserved.
Open Access
Investigation of p-type depletion doping for InGaN/GaN-based light-emitting diodes
(American Institute of Physics Inc., 2017) Zhang, Y.; Zhang Z.-H.; Tan S.T.; Hernandez-Martinez, P. L.; Zhu B.; Lu S.; Kang, X. J.; Sun, X. W.; Demir, Hilmi Volkan
Due to the limitation of the hole injection, p-type doping is essential to improve the performance of InGaN/GaN multiple quantum well light-emitting diodes (LEDs). In this work, we propose and show a depletion-region Mg-doping method. Here we systematically analyze the effectiveness of different Mg-doping profiles ranging from the electron blocking layer to the active region. Numerical computations show that the Mg-doping decreases the valence band barrier for holes and thus enhances the hole transportation. The proposed depletion-region Mg-doping approach also increases the barrier height for electrons, which leads to a reduced electron overflow, while increasing the hole concentration in the p-GaN layer. Experimentally measured external quantum efficiency indicates that Mg-doping position is vitally important. The doping in or adjacent to the quantum well degrades the LED performance due to Mg diffusion, increasing the corresponding nonradiative recombination, which is well supported by the measured carrier lifetimes. The experimental results are well numerically reproduced by modifying the nonradiative recombination lifetimes, which further validate the effectiveness of our approach.