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  • 1
    Online Resource
    Online Resource
    De novo mutations across 1,465 diverse genomes reveal mutational insights and reductions in the Amish founder population
    Proceedings of the National Academy of Sciences ; 2020
    In:  Proceedings of the National Academy of Sciences Vol. 117, No. 5 ( 2020-02-04), p. 2560-2569
    Details
    In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 117, No. 5 ( 2020-02-04), p. 2560-2569
    Abstract: De novo mutations (DNMs), or mutations that appear in an individual despite not being seen in their parents, are an important source of genetic variation whose impact is relevant to studies of human evolution, genetics, and disease. Utilizing high-coverage whole-genome sequencing data as part of the Trans-Omics for Precision Medicine (TOPMed) Program, we called 93,325 single-nucleotide DNMs across 1,465 trios from an array of diverse human populations, and used them to directly estimate and analyze DNM counts, rates, and spectra. We find a significant positive correlation between local recombination rate and local DNM rate, and that DNM rate explains a substantial portion (8.98 to 34.92%, depending on the model) of the genome-wide variation in population-level genetic variation from 41K unrelated TOPMed samples. Genome-wide heterozygosity does correlate with DNM rate, but only explains 〈 1% of variation. While we are underpowered to see small differences, we do not find significant differences in DNM rate between individuals of European, African, and Latino ancestry, nor across ancestrally distinct segments within admixed individuals. However, we did find significantly fewer DNMs in Amish individuals, even when compared with other Europeans, and even after accounting for parental age and sequencing center. Specifically, we found significant reductions in the number of C→A and T→C mutations in the Amish, which seem to underpin their overall reduction in DNMs. Finally, we calculated near-zero estimates of narrow sense heritability ( h 2 ), which suggest that variation in DNM rate is significantly shaped by nonadditive genetic effects and the environment.
    Type of Medium: Online Resource
    ISSN: 0027-8424 , 1091-6490
    URL: Article
    DOI: 10.1073/pnas.1902766117
    RVK:
    TA 1000
    RVK:
    WA 15000
    Language: English
    Publisher: Proceedings of the National Academy of Sciences
    Publication Date: 2020
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  • 2
    Online Resource
    Online Resource
    Human-specific tandem repeat expansion and differential gene expression during primate evolution
    Proceedings of the National Academy of Sciences ; 2019
    In:  Proceedings of the National Academy of Sciences Vol. 116, No. 46 ( 2019-11-12), p. 23243-23253
    Details
    In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 116, No. 46 ( 2019-11-12), p. 23243-23253
    Abstract: Short tandem repeats (STRs) and variable number tandem repeats (VNTRs) are important sources of natural and disease-causing variation, yet they have been problematic to resolve in reference genomes and genotype with short-read technology. We created a framework to model the evolution and instability of STRs and VNTRs in apes. We phased and assembled 3 ape genomes (chimpanzee, gorilla, and orangutan) using long-read and 10x Genomics linked-read sequence data for 21,442 human tandem repeats discovered in 6 haplotype-resolved assemblies of Yoruban, Chinese, and Puerto Rican origin. We define a set of 1,584 STRs/VNTRs expanded specifically in humans, including large tandem repeats affecting coding and noncoding portions of genes (e.g., MUC3A , CACNA1C ). We show that short interspersed nuclear element–VNTR– Alu (SVA) retrotransposition is the main mechanism for distributing GC-rich human-specific tandem repeat expansions throughout the genome but with a bias against genes. In contrast, we observe that VNTRs not originating from retrotransposons have a propensity to cluster near genes, especially in the subtelomere. Using tissue-specific expression from human and chimpanzee brains, we identify genes where transcript isoform usage differs significantly, likely caused by cryptic splicing variation within VNTRs. Using single-cell expression from cerebral organoids, we observe a strong effect for genes associated with transcription profiles analogous to intermediate progenitor cells. Finally, we compare the sequence composition of some of the largest human-specific repeat expansions and identify 52 STRs/VNTRs with at least 40 uninterrupted pure tracts as candidates for genetically unstable regions associated with disease.
    Type of Medium: Online Resource
    ISSN: 0027-8424 , 1091-6490
    URL: Article
    DOI: 10.1073/pnas.1912175116
    RVK:
    TA 1000
    RVK:
    WA 15000
    Language: English
    Publisher: Proceedings of the National Academy of Sciences
    Publication Date: 2019
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    SSG: 11
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  • 3
    Online Resource
    Online Resource
    Infrared spectroscopy of neutral water clusters at finite temperature: Evidence for a noncyclic pentamer
    Proceedings of the National Academy of Sciences ; 2020
    In:  Proceedings of the National Academy of Sciences Vol. 117, No. 27 ( 2020-07-07), p. 15423-15428
    Details
    In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 117, No. 27 ( 2020-07-07), p. 15423-15428
    Abstract: Infrared spectroscopic study of neutral water clusters is crucial to understanding of the hydrogen-bonding networks in liquid water and ice. Here we report infrared spectra of size-selected neutral water clusters, (H 2 O) n ( n = 3−6), in the OH stretching vibration region, based on threshold photoionization using a tunable vacuum ultraviolet free-electron laser. Distinct OH stretch vibrational fundamentals observed in the 3,500−3,600-cm −1 region of (H 2 O) 5 provide unique spectral signatures for the formation of a noncyclic pentamer, which coexists with the global-minimum cyclic structure previously identified in the gas phase. The main features of infrared spectra of the pentamer and hexamer, (H 2 O) n ( n = 5 and 6), span the entire OH stretching band of liquid water, suggesting that they start to exhibit the richness and diversity of hydrogen-bonding networks in bulk water.
    Type of Medium: Online Resource
    ISSN: 0027-8424 , 1091-6490
    URL: Article
    DOI: 10.1073/pnas.2000601117
    RVK:
    TA 1000
    RVK:
    WA 15000
    Language: English
    Publisher: Proceedings of the National Academy of Sciences
    Publication Date: 2020
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  • 4
    Online Resource
    Online Resource
    Global COVID-19 pandemic demands joint interventions for the suppression of future waves
    Proceedings of the National Academy of Sciences ; 2020
    In:  Proceedings of the National Academy of Sciences Vol. 117, No. 42 ( 2020-10-20), p. 26151-26157
    Details
    In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 117, No. 42 ( 2020-10-20), p. 26151-26157
    Abstract: Emerging evidence suggests a resurgence of COVID-19 in the coming years. It is thus critical to optimize emergency response planning from a broad, integrated perspective. We developed a mathematical model incorporating climate-driven variation in community transmissions and movement-modulated spatial diffusions of COVID-19 into various intervention scenarios. We find that an intensive 8-wk intervention targeting the reduction of local transmissibility and international travel is efficient and effective. Practically, we suggest a tiered implementation of this strategy where interventions are first implemented at locations in what we call the Global Intervention Hub, followed by timely interventions in secondary high-risk locations. We argue that thinking globally, categorizing locations in a hub-and-spoke intervention network, and acting locally, applying interventions at high-risk areas, is a functional strategy to avert the tremendous burden that would otherwise be placed on public health and society.
    Type of Medium: Online Resource
    ISSN: 0027-8424 , 1091-6490
    URL: Article
    DOI: 10.1073/pnas.2012002117
    RVK:
    TA 1000
    RVK:
    WA 15000
    Language: English
    Publisher: Proceedings of the National Academy of Sciences
    Publication Date: 2020
    detail.hit.zdb_id: 209104-5
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  • 5
    Online Resource
    Online Resource
    Hierarchically buckled sheath-core fibers for superelastic electronics, sensors, and muscles
    American Association for the Advancement of Science (AAAS) ; 2015
    In:  Science Vol. 349, No. 6246 ( 2015-07-24), p. 400-404
    Details
    In: Science, American Association for the Advancement of Science (AAAS), Vol. 349, No. 6246 ( 2015-07-24), p. 400-404
    Abstract: Superelastic conducting fibers with improved properties and functionalities are needed for diverse applications. Here we report the fabrication of highly stretchable (up to 1320%) sheath-core conducting fibers created by wrapping carbon nanotube sheets oriented in the fiber direction on stretched rubber fiber cores. The resulting structure exhibited distinct short- and long-period sheath buckling that occurred reversibly out of phase in the axial and belt directions, enabling a resistance change of less than 5% for a 1000% stretch. By including other rubber and carbon nanotube sheath layers, we demonstrated strain sensors generating an 860% capacitance change and electrically powered torsional muscles operating reversibly by a coupled tension-to-torsion actuation mechanism. Using theory, we quantitatively explain the complementary effects of an increase in muscle length and a large positive Poisson’s ratio on torsional actuation and electronic properties.
    Type of Medium: Online Resource
    ISSN: 0036-8075 , 1095-9203
    URL: Article
    DOI: 10.1126/science.aaa7952
    RVK:
    TA 1000
    RVK:
    WA 15000
    Language: English
    Publisher: American Association for the Advancement of Science (AAAS)
    Publication Date: 2015
    detail.hit.zdb_id: 128410-1
    detail.hit.zdb_id: 2066996-3
    detail.hit.zdb_id: 2060783-0
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  • 6
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    Online Resource
    Real-time dissection of dynamic uncoating of individual influenza viruses
    Proceedings of the National Academy of Sciences ; 2019
    In:  Proceedings of the National Academy of Sciences Vol. 116, No. 7 ( 2019-02-12), p. 2577-2582
    Details
    In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 116, No. 7 ( 2019-02-12), p. 2577-2582
    Abstract: Uncoating is an obligatory step in the virus life cycle that serves as an antiviral target. Unfortunately, it is challenging to study viral uncoating due to methodology limitations for detecting this transient and dynamic event. The uncoating of influenza A virus (IAV), which contains an unusual genome of eight segmented RNAs, is particularly poorly understood. Here, by encapsulating quantum dot (QD)-conjugated viral ribonucleoprotein complexes (vRNPs) within infectious IAV virions and applying single-particle imaging, we tracked the uncoating process of individual IAV virions. Approximately 30% of IAV particles were found to undergo uncoating through fusion with late endosomes in the “around-nucleus” region at 30 to 90 minutes postinfection. Inhibition of viral M2 proton channels and cellular endosome acidification prevented IAV uncoating. IAV vRNPs are released separately into the cytosol after virus uncoating. Then, individual vRNPs undergo a three-stage movement to the cell nucleus and display two diffusion patterns when inside the nucleus. These findings reveal IAV uncoating and vRNP trafficking mechanisms, filling a critical gap in knowledge about influenza viral infection.
    Type of Medium: Online Resource
    ISSN: 0027-8424 , 1091-6490
    URL: Article
    DOI: 10.1073/pnas.1812632116
    RVK:
    TA 1000
    RVK:
    WA 15000
    Language: English
    Publisher: Proceedings of the National Academy of Sciences
    Publication Date: 2019
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    SSG: 11
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  • 7
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    Online Resource
    Differentiation and Characterization of Excitatory and Inhibitory Synapses by Cryo-electron Tomography and Correlative Microscopy
    Society for Neuroscience ; 2018
    In:  The Journal of Neuroscience Vol. 38, No. 6 ( 2018-02-07), p. 1493-1510
    Details
    In: The Journal of Neuroscience, Society for Neuroscience, Vol. 38, No. 6 ( 2018-02-07), p. 1493-1510
    Abstract: As key functional units in neural circuits, different types of neuronal synapses play distinct roles in brain information processing, learning, and memory. Synaptic abnormalities are believed to underlie various neurological and psychiatric disorders. Here, by combining cryo-electron tomography and cryo-correlative light and electron microscopy, we distinguished intact excitatory and inhibitory synapses of cultured hippocampal neurons, and visualized the in situ 3D organization of synaptic organelles and macromolecules in their native state. Quantitative analyses of 〉 100 synaptic tomograms reveal that excitatory synapses contain a mesh-like postsynaptic density (PSD) with thickness ranging from 20 to 50 nm. In contrast, the PSD in inhibitory synapses assumes a thin sheet-like structure ∼12 nm from the postsynaptic membrane. On the presynaptic side, spherical synaptic vesicles (SVs) of 25–60 nm diameter and discus-shaped ellipsoidal SVs of various sizes coexist in both synaptic types, with more ellipsoidal ones in inhibitory synapses. High-resolution tomograms obtained using a Volta phase plate and electron filtering and counting reveal glutamate receptor-like and GABA A receptor-like structures that interact with putative scaffolding and adhesion molecules, reflecting details of receptor anchoring and PSD organization. These results provide an updated view of the ultrastructure of excitatory and inhibitory synapses, and demonstrate the potential of our approach to gain insight into the organizational principles of cellular architecture underlying distinct synaptic functions. SIGNIFICANCE STATEMENT To understand functional properties of neuronal synapses, it is desirable to analyze their structure at molecular resolution. We have developed an integrative approach combining cryo-electron tomography and correlative fluorescence microscopy to visualize 3D ultrastructural features of intact excitatory and inhibitory synapses in their native state. Our approach shows that inhibitory synapses contain uniform thin sheet-like postsynaptic densities (PSDs), while excitatory synapses contain previously known mesh-like PSDs. We discovered “discus-shaped” ellipsoidal synaptic vesicles, and their distributions along with regular spherical vesicles in synaptic types are characterized. High-resolution tomograms further allowed identification of putative neurotransmitter receptors and their heterogeneous interaction with synaptic scaffolding proteins. The specificity and resolution of our approach enables precise in situ analysis of ultrastructural organization underlying distinct synaptic functions.
    Type of Medium: Online Resource
    ISSN: 0270-6474 , 1529-2401
    URL: Article
    URL: Article
    URL: Article
    URL: Article
    URL: Article
    URL: Article
    DOI: 10.1523/JNEUROSCI.1548-17.2017
    DOI: 10.1523/JNEUROSCI.1548-17.2017.video.1
    DOI: 10.1523/JNEUROSCI.1548-17.2017.video.2
    DOI: 10.1523/JNEUROSCI.1548-17.2017.video.3
    DOI: 10.1523/JNEUROSCI.1548-17.2017.video.4
    DOI: 10.1523/JNEUROSCI.1548-17.2017.video.5
    Language: English
    Publisher: Society for Neuroscience
    Publication Date: 2018
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  • 8
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    Nonlinear mapping between continuous- and discrete-time dynamics
    IOP Publishing ; 2022
    In:  Europhysics Letters Vol. 137, No. 6 ( 2022-03-01), p. 61002-
    Details
    In: Europhysics Letters, IOP Publishing, Vol. 137, No. 6 ( 2022-03-01), p. 61002-
    Abstract: Linear mapping is widely used in dynamic modeling and empirical data analysis, but it suffers from the serious shortcoming that it does not work in the common case of time intervals being large. The fundamental cause of the failure is that the linear mapping does not take into account the coupling effects of multiple events within a discrete time interval. Here, we develop a theoretical framework to provide a nonlinear mapping between continuous- and discrete-time dynamics by accounting for the coupling effect. We have verified the effectiveness of our mapping by exploring classical susceptible-infected-susceptible and susceptible-infected-recovered models. In particular, we give a quantitative criterion that the sum of two transition probabilities —from one state to the other and vice versa— must be strictly less than 1 for binary-state dynamics.
    Type of Medium: Online Resource
    ISSN: 0295-5075 , 1286-4854
    URL: Article
    DOI: 10.1209/0295-5075/ac5fd0
    Language: Unknown
    Publisher: IOP Publishing
    Publication Date: 2022
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    detail.hit.zdb_id: 165776-8
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  • 9
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    Online Resource
    Type-II Ising pairing in few-layer stanene
    American Association for the Advancement of Science (AAAS) ; 2020
    In:  Science Vol. 367, No. 6485 ( 2020-03-27), p. 1454-1457
    Details
    In: Science, American Association for the Advancement of Science (AAAS), Vol. 367, No. 6485 ( 2020-03-27), p. 1454-1457
    Abstract: Spin-orbit coupling has proven indispensable in the realization of topological materials and, more recently, Ising pairing in two-dimensional superconductors. This pairing mechanism relies on inversion symmetry–breaking and sustains anomalously large in-plane polarizing magnetic fields whose upper limit is predicted to diverge at low temperatures. Here, we show that the recently discovered superconductor few-layer stanene, epitaxially strained gray tin (α-Sn), exhibits a distinct type of Ising pairing between carriers residing in bands with different orbital indices near the Γ-point. The bands are split as a result of spin-orbit locking without the participation of inversion symmetry–breaking. The in-plane upper critical field is strongly enhanced at ultralow temperature and reveals the predicted upturn.
    Type of Medium: Online Resource
    ISSN: 0036-8075 , 1095-9203
    URL: Article
    DOI: 10.1126/science.aax3873
    RVK:
    TA 1000
    RVK:
    WA 15000
    Language: English
    Publisher: American Association for the Advancement of Science (AAAS)
    Publication Date: 2020
    detail.hit.zdb_id: 128410-1
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    SSG: 11
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  • 10
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    Adaptive finite-time tracking control of switched nonlinear systems
    Elsevier BV ; 2017
    In:  Information Sciences Vol. 421 ( 2017-12), p. 126-135
    Details
    In: Information Sciences, Elsevier BV, Vol. 421 ( 2017-12), p. 126-135
    Type of Medium: Online Resource
    ISSN: 0020-0255
    URL: Article
    DOI: 10.1016/j.ins.2017.08.095
    RVK:
    SA 5420
    Language: English
    Publisher: Elsevier BV
    Publication Date: 2017
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    detail.hit.zdb_id: 1478990-5
    SSG: 24,1
    SSG: 7,11
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