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Field-resolved infrared spectroscopy of biological systems 期刊论文
NATURE, 2020, 577 (7788) : 52-+
作者:  Pupeza, Ioachim;  Huber, Marinus;  Trubetskov, Michael;  Schweinberger, Wolfgang;  Hussain, Syed A.;  Hofer, Christina;  Fritsch, Kilian;  Poetzlberger, Markus;  Vamos, Lenard;  Fill, Ernst;  Amotchkina, Tatiana;  Kepesidis, Kosmas V.;  Apolonski, Alexander;  Karpowicz, Nicholas;  Pervak, Vladimir;  Pronin, Oleg;  Fleischmann, Frank;  Azzeer, Abdallah;  Zigman, Mihaela;  Krausz, Ferenc
收藏  |  浏览/下载:14/0  |  提交时间:2020/07/03

The proper functioning of living systems and physiological phenotypes depends on molecular composition. Yet simultaneous quantitative detection of a wide variety of molecules remains a challenge(1-8). Here we show how broadband optical coherence opens up opportunities for fingerprinting complex molecular ensembles in their natural environment. Vibrationally excited molecules emit a coherent electric field following few-cycle infrared laser excitation(9-12), and this field is specific to the sample'  s molecular composition. Employing electro-optic sampling(10,12-15), we directly measure this global molecular fingerprint down to field strengths 10(7) times weaker than that of the excitation. This enables transillumination of intact living systems with thicknesses of the order of 0.1 millimetres, permitting broadband infrared spectroscopic probing of human cells and plant leaves. In a proof-of-concept analysis of human blood serum, temporal isolation of the infrared electric-field fingerprint from its excitation along with its sampling with attosecond timing precision results in detection sensitivity of submicrograms per millilitre of blood serum and a detectable dynamic range of molecular concentration exceeding 10(5). This technique promises improved molecular sensitivity and molecular coverage for probing complex, real-world biological and medical settings.


  
Entanglement-based secure quantum cryptography over 1,120 kilometres 期刊论文
NATURE, 2020
作者:  Paldi, Flora;  Alver, Bonnie;  Robertson, Daniel;  Schalbetter, Stephanie A.;  Kerr, Alastair;  Kelly, David A.;  Baxter, Jonathan;  Neale, Matthew J.;  Marston, Adele L.
收藏  |  浏览/下载:48/0  |  提交时间:2020/07/03

An efficient entanglement-based quantum key distribution is sent from the Micius satellite to two ground observatories 1,120 kilometres apart to establish secure quantum cryptography for the exchange ofquantum keys.


Quantum key distribution (QKD)(1-3)is a theoretically secure way of sharing secret keys between remote users. It has been demonstrated in a laboratory over a coiled optical fibre up to 404 kilometres long(4-7). In the field, point-to-point QKD has been achieved from a satellite to a ground station up to 1,200 kilometres away(8-10). However, real-world QKD-based cryptography targets physically separated users on the Earth, for which the maximum distance has been about 100 kilometres(11,12). The use of trusted relays can extend these distances from across a typical metropolitan area(13-16)to intercity(17)and even intercontinental distances(18). However, relays pose security risks, which can be avoided by using entanglement-based QKD, which has inherent source-independent security(19,20). Long-distance entanglement distribution can be realized using quantum repeaters(21), but the related technology is still immature for practical implementations(22). The obvious alternative for extending the range of quantum communication without compromising its security is satellite-based QKD, but so far satellite-based entanglement distribution has not been efficient(23)enough to support QKD. Here we demonstrate entanglement-based QKD between two ground stations separated by 1,120 kilometres at a finite secret-key rate of 0.12 bits per second, without the need for trusted relays. Entangled photon pairs were distributed via two bidirectional downlinks from the Micius satellite to two ground observatories in Delingha and Nanshan in China. The development of a high-efficiency telescope and follow-up optics crucially improved the link efficiency. The generated keys are secure for realistic devices, because our ground receivers were carefully designed to guarantee fair sampling and immunity to all known side channels(24,25). Our method not only increases the secure distance on the ground tenfold but also increases the practical security of QKD to an unprecedented level.


  
Massively parallel coherent laser ranging using a soliton microcomb 期刊论文
NATURE, 2020, 581 (7807) : 164-+
作者:  Casanova, Emmanuelle;  Knowles, Timothy D. J.;  Bayliss, Alex;  Dunne, Julie;  Baranski, Marek Z.;  Denaire, Anthony;  Lefranc, Philippe;  di Lernia, Savino;  Roffet-Salque, Melanie;  Smyth, Jessica;  Barclay, Alistair;  Gillard, Toby;  Classen, Erich;  Coles, Bryony;  Ilett, Michael;  Jeunesse, Christian;  Krueger, Marta;  Marciniak, Arkadiusz;  Minnitt, Steve;  Rotunno, Rocco;  van de Velde, Pieter;  van Wijk, Ivo;  Cotton, Jonathan;  Daykin, Andy;  Evershed, Richard P.
收藏  |  浏览/下载:45/0  |  提交时间:2020/07/03

Coherent ranging, also known as frequency-modulated continuous-wave (FMCW) laser-based light detection and ranging (lidar)(1) is used for long-range three-dimensional distance and velocimetry in autonomous driving(2,3). FMCW lidar maps distance to frequency(4,5) using frequency-chirped waveforms and simultaneously measures the Doppler shift of the reflected laser light, similar to sonar or radar(6,7) and coherent detection prevents interference from sunlight and other lidar systems. However, coherent ranging has a lower acquisition speed and requires precisely chirped(8) and highly coherent(5) laser sources, hindering widespread use of the lidar system and impeding parallelization, compared to modern time-of-flight ranging systems that use arrays of individual lasers. Here we demonstrate a massively parallel coherent lidar scheme using an ultra-low-loss photonic chip-based soliton microcomb(9). By fast chirping of the pump laser in the soliton existence range(10) of a microcomb with amplitudes of up to several gigahertz and a sweep rate of up to ten megahertz, a rapid frequency change occurs in the underlying carrier waveform of the soliton pulse stream, but the pulse-to-pulse repetition rate of the soliton pulse stream is retained. As a result, the chirp from a single narrow-linewidth pump laser is transferred to all spectral comb teeth of the soliton at once, thus enabling parallelism in the FMCW lidar. Using this approach we generate 30 distinct channels, demonstrating both parallel distance and velocity measurements at an equivalent rate of three megapixels per second, with the potential to improve sampling rates beyond 150 megapixels per second and to increase the image refresh rate of the FMCW lidar by up to two orders of magnitude without deterioration of eye safety. This approach, when combined with photonic phase arrays(11) based on nanophotonic gratings(12), provides a technological basis for compact, massively parallel and ultrahigh-frame-rate coherent lidar systems.


  
Surface Solar Irradiance in Continental Shallow Cumulus Fields: Observations and Large-Eddy Simulation 期刊论文
JOURNAL OF THE ATMOSPHERIC SCIENCES, 2020, 77 (3) : 1065-1080
作者:  Gristey, Jake J.;  Feingold, Graham;  Glenn, Ian B.;  Schmidt, K. Sebastian;  Chen, Hong
收藏  |  浏览/下载:5/0  |  提交时间:2020/07/02
Cloud radiative effects  Cumulus clouds  Shortwave radiation  Sampling  Surface observations  Large eddy simulations  
Video-based AI for beat-to-beat assessment of cardiac function 期刊论文
NATURE, 2020, 580 (7802) : 252-+
作者:  Pleguezuelos-Manzano, Cayetano;  Puschhof, Jens;  Huber, Axel Rosendahl;  van Hoeck, Arne;  Wood, Henry M.;  Nomburg, Jason;  Gurjao, Carino;  Manders, Freek;  Dalmasso, Guillaume;  Stege, Paul B.;  Paganelli, Fernanda L.;  Geurts, Maarten H.;  Beumer, Joep;  Mizutani, Tomohiro;  Miao, Yi;  van der Linden, Reinier;  van der Elst, Stefan;  Garcia, K. Christopher;  Top, Janetta;  Willems, Rob J. L.;  Giannakis, Marios;  Bonnet, Richard;  Quirke, Phil;  Meyerson, Matthew;  Cuppen, Edwin;  van Boxtel, Ruben;  Clevers, Hans
收藏  |  浏览/下载:117/0  |  提交时间:2020/07/03

A video-based deep learning algorithm-EchoNet-Dynamic-accurately identifies subtle changes in ejection fraction and classifies heart failure with reduced ejection fraction using information from multiple cardiac cycles.


Accurate assessment of cardiac function is crucial for the diagnosis of cardiovascular disease(1), screening for cardiotoxicity(2) and decisions regarding the clinical management of patients with a critical illness(3). However, human assessment of cardiac function focuses on a limited sampling of cardiac cycles and has considerable inter-observer variability despite years of training(4,5). Here, to overcome this challenge, we present a video-based deep learning algorithm-EchoNet-Dynamic-that surpasses the performance of human experts in the critical tasks of segmenting the left ventricle, estimating ejection fraction and assessing cardiomyopathy. Trained on echocardiogram videos, our model accurately segments the left ventricle with a Dice similarity coefficient of 0.92, predicts ejection fraction with a mean absolute error of 4.1% and reliably classifies heart failure with reduced ejection fraction (area under the curve of 0.97). In an external dataset from another healthcare system, EchoNet-Dynamic predicts the ejection fraction with a mean absolute error of 6.0% and classifies heart failure with reduced ejection fraction with an area under the curve of 0.96. Prospective evaluation with repeated human measurements confirms that the model has variance that is comparable to or less than that of human experts. By leveraging information across multiple cardiac cycles, our model can rapidly identify subtle changes in ejection fraction, is more reproducible than human evaluation and lays the foundation for precise diagnosis of cardiovascular disease in real time. As a resource to promote further innovation, we also make publicly available a large dataset of 10,030 annotated echocardiogram videos.


  
Support for the habitat amount hypothesis from a global synthesis of species density studies 期刊论文
ECOLOGY LETTERS, 2020, 23 (4) : 674-681
作者:  Watling, James, I;  Arroyo-Rodriguez, Victor;  Pfeifer, Marion;  Baeten, Lander;  Banks-Leite, Cristina;  Cisneros, Laura M.;  Fang, Rebecca;  Hamel-Leigue, A. Caroli;  Lachat, Thibault;  Leal, Inara R.;  Lens, Luc;  Possingham, Hugh P.;  Raheem, Dinarzarde C.;  Ribeiro, Danilo B.;  Slade, Eleanor M.;  Urbina-Cardona, J. Nicolas;  Wood, Eric M.;  Fahrig, Lenore
收藏  |  浏览/下载:15/0  |  提交时间:2020/07/02
Forest loss  habitat amount  patch size  sampling effect  
Giant virus diversity and host interactions through global metagenomics 期刊论文
NATURE, 2020: 1-+
作者:  Su, Jie;  Morgani, Sophie M.;  David, Charles J.;  Wang, Qiong;  Er, Ekrem Emrah;  Huang, Yun-Han;  Basnet, Harihar;  Zou, Yilong;  Shu, Weiping;  Soni, Rajesh K.;  Hendrickson, Ronald C.;  Hadjantonakis, Anna-Katerina;  Massague, Joan
收藏  |  浏览/下载:20/0  |  提交时间:2020/07/03

Analysis of metagenomics data revealed that large and giant viruses are globally widely distributed and are associated with most major eukaryotic lineages.


Our current knowledge about nucleocytoplasmic large DNA viruses (NCLDVs) is largely derived from viral isolates that are co-cultivated with protists and algae. Here we reconstructed 2,074 NCLDV genomes from sampling sites across the globe by building on the rapidly increasing amount of publicly available metagenome data. This led to an 11-fold increase in phylogenetic diversity and a parallel 10-fold expansion in functional diversity. Analysis of 58,023 major capsid proteins from large and giant viruses using metagenomic data revealed the global distribution patterns and cosmopolitan nature of these viruses. The discovered viral genomes encoded a wide range of proteins with putative roles in photosynthesis and diverse substrate transport processes, indicating that host reprogramming is probably a common strategy in the NCLDVs. Furthermore, inferences of horizontal gene transfer connected viral lineages to diverse eukaryotic hosts. We anticipate that the global diversity of NCLDVs that we describe here will establish giant viruses-which are associated with most major eukaryotic lineages-as important players in ecosystems across Earth'  s biomes.


  
Improved protein structure prediction using potentials from deep learning 期刊论文
NATURE, 2020, 577 (7792) : 706-+
作者:  Ma, Runze;  Cao, Duanyun;  Zhu, Chongqin;  Tian, Ye;  Peng, Jinbo;  Guo, Jing;  Chen, Ji;  Li, Xin-Zheng;  Francisco, Joseph S.;  Zeng, Xiao Cheng;  Xu, Li-Mei;  Wang, En-Ge;  Jiang, Ying
收藏  |  浏览/下载:142/0  |  提交时间:2020/07/03

Protein structure prediction can be used to determine the three-dimensional shape of a protein from its amino acid sequence(1). This problem is of fundamental importance as the structure of a protein largely determines its function(2)  however, protein structures can be difficult to determine experimentally. Considerable progress has recently been made by leveraging genetic information. It is possible to infer which amino acid residues are in contact by analysing covariation in homologous sequences, which aids in the prediction of protein structures(3). Here we show that we can train a neural network to make accurate predictions of the distances between pairs of residues, which convey more information about the structure than contact predictions. Using this information, we construct a potential of mean force(4) that can accurately describe the shape of a protein. We find that the resulting potential can be optimized by a simple gradient descent algorithm to generate structures without complex sampling procedures. The resulting system, named AlphaFold, achieves high accuracy, even for sequences with fewer homologous sequences. In the recent Critical Assessment of Protein Structure Prediction(5) (CASP13)-a blind assessment of the state of the field-AlphaFold created high-accuracy structures (with template modelling (TM) scores(6) of 0.7 or higher) for 24 out of 43 free modelling domains, whereas the next best method, which used sampling and contact information, achieved such accuracy for only 14 out of 43 domains. AlphaFold represents a considerable advance in protein-structure prediction. We expect this increased accuracy to enable insights into the function and malfunction of proteins, especially in cases for which no structures for homologous proteins have been experimentally determined(7).


  
On the Optimal Spatial Design for Groundwater Level Monitoring Networks 期刊论文
WATER RESOURCES RESEARCH, 2019
作者:  Ohmer, M.;  Liesch, T.;  Goldscheider, N.
收藏  |  浏览/下载:8/0  |  提交时间:2020/02/16
groundwater level monitoring network  sampling design  low-discrepancy  geostatistics  spatial optimization  
Depth-Resolved Groundwater Chemistry by Longitudinal Sampling of Ambient and Pumped Flows Within Long-Screened and Open Borehole Wells 期刊论文
WATER RESOURCES RESEARCH, 2019
作者:  Poulsen, David L.;  Cook, Peter G.;  Simmons, Craig T.;  Solomon, D. Kip;  Dogramaci, Shawan
收藏  |  浏览/下载:7/0  |  提交时间:2020/02/16
sampling  chemistry  borehole flow  long-screened well  open borehole well  ambient flow