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Nearest neighbours reveal fast and slow components of motor learning 期刊论文
NATURE, 2020, 577 (7791) : 526-+
作者:  Kollmorgen, Sepp;  Hahnloser, Richard H. R.;  Mante, Valerio
收藏  |  浏览/下载:4/0  |  提交时间:2020/07/03

A new method for analysing change in high-dimensional data is based on nearest-neighbour statistics and is applied here to song dynamics during vocal learning in zebra finches, but could potentially be applied to other biological and artificial behaviours.


Changes in behaviour resulting from environmental influences, development and learning(1-5) are commonly quantified on the basis of a few hand-picked features(2-4,6,7) (for example, the average pitch of acoustic vocalizations(3)), assuming discrete classes of behaviours (such as distinct vocal syllables)(2,3,8-10). However, such methods generalize poorly across different behaviours and model systems and may miss important components of change. Here we present a more-general account of behavioural change that is based on nearest-neighbour statistics(11-13), and apply it to song development in a songbird, the zebra finch(3). First, we introduce the concept of '  repertoire dating'  , whereby each rendition of a behaviour (for example, each vocalization) is assigned a repertoire time, reflecting when similar renditions were typical in the behavioural repertoire. Repertoire time isolates the components of vocal variability that are congruent with long-term changes due to vocal learning and development, and stratifies the behavioural repertoire into '  regressions'  , '  anticipations'  and '  typical renditions'  . Second, we obtain a holistic, yet low-dimensional, description of vocal change in terms of a stratified '  behavioural trajectory'  , revealing numerous previously unrecognized components of behavioural change on fast and slow timescales, as well as distinct patterns of overnight consolidation(1,2,4,14,15) across the behavioral repertoire. We find that diurnal changes in regressions undergo only weak consolidation, whereas anticipations and typical renditions consolidate fully. Because of its generality, our nonparametric description of how behaviour evolves relative to itself-rather than to a potentially arbitrary, experimenter-defined goal(2,3,14,16)-appears well suited for comparing learning and change across behaviours and species(17,18), as well as biological and artificial systems(5).


  
Variability in the analysis of a single neuroimaging dataset by many teams 期刊论文
NATURE, 2020
作者:  Liu, Jifeng;  Soria, Roberto;  Zheng, Zheng;  Zhang, Haotong;  Lu, Youjun;  Wang, Song;  Yuan, Hailong
收藏  |  浏览/下载:22/0  |  提交时间:2020/07/03

Data analysis workflows in many scientific domains have become increasingly complex and flexible. Here we assess the effect of this flexibility on the results of functional magnetic resonance imaging by asking 70 independent teams to analyse the same dataset, testing the same 9 ex-ante hypotheses(1). The flexibility of analytical approaches is exemplified by the fact that no two teams chose identical workflows to analyse the data. This flexibility resulted in sizeable variation in the results of hypothesis tests, even for teams whose statistical maps were highly correlated at intermediate stages of the analysis pipeline. Variation in reported results was related to several aspects of analysis methodology. Notably, a meta-analytical approach that aggregated information across teams yielded a significant consensus in activated regions. Furthermore, prediction markets of researchers in the field revealed an overestimation of the likelihood of significant findings, even by researchers with direct knowledge of the dataset(2-5). Our findings show that analytical flexibility can have substantial effects on scientific conclusions, and identify factors that may be related to variability in the analysis of functional magnetic resonance imaging. The results emphasize the importance of validating and sharing complex analysis workflows, and demonstrate the need for performing and reporting multiple analyses of the same data. Potential approaches that could be used to mitigate issues related to analytical variability are discussed.


The results obtained by seventy different teams analysing the same functional magnetic resonance imaging dataset show substantial variation, highlighting the influence of analytical choices and the importance of sharing workflows publicly and performing multiple analyses.


  
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.


  
B cells are associated with survival and immunotherapy response in sarcoma 期刊论文
NATURE, 2020, 577 (7791) : 556-+
作者:  Willis, J. P.;  Canning, R. E. A.;  Noordeh, E. S.;  Allen, S. W.;  King, A. L.;  Mantz, A.;  Morris, R. G.;  Stanford, S. A.;  Brammer, G.
收藏  |  浏览/下载:15/0  |  提交时间:2020/07/03

Soft-tissue sarcomas represent a heterogeneous group of cancer, with more than 50 histological subtypes(1,2). The clinical presentation of patients with different subtypes is often atypical, and responses to therapies such as immune checkpoint blockade vary widely(3,4). To explain this clinical variability, here we study gene expression profiles in 608 tumours across subtypes of soft-tissue sarcoma. We establish an immune-based classification on the basis of the composition of the tumour microenvironment and identify five distinct phenotypes: immune-low (A and B), immune-high (D and E), and highly vascularized (C) groups. In situ analysis of an independent validation cohort shows that class E was characterized by the presence of tertiary lymphoid structures that contain T cells and follicular dendritic cells and are particularly rich in B cells. B cells are the strongest prognostic factor even in the context of high or low CD8(+) T cells and cytotoxic contents. The class-E group demonstrated improved survival and a high response rate to PD1 blockade with pembrolizumab in a phase 2 clinical trial. Together, this work confirms the immune subtypes in patients with soft-tissue sarcoma, and unravels the potential of B-cell-rich tertiary lymphoid structures to guide clinical decision-making and treatments, which could have broader applications in other diseases.


Immune profiling of the tumour microenvironment of soft-tissue sarcoma identifies a group of patients with high levels of B-cell infiltration and tertiary lymphoid structures that have improved survival and a high response rate to immune checkpoint blockade therapy.


  
Integrating patterns of thermal tolerance and phenotypic plasticity with population genetics to improve understanding of vulnerability to warming in a widespread copepod 期刊论文
GLOBAL CHANGE BIOLOGY, 2019
作者:  Sasaki, Matthew C.;  Dam, Hans G.
收藏  |  浏览/下载:4/0  |  提交时间:2019/11/27
climate change  climate variability hypothesis  copepod  gene flow  local adaptation  macrophysiology  phenotypic plasticity  plankton  rapid adaptation  thermal performance  
Climate change and variability impacts on grazing herds: Insights from a system dynamics approach for semi-arid Australian rangelands 期刊论文
GLOBAL CHANGE BIOLOGY, 2019, 25 (9) : 3091-3109
作者:  Godde, Cecile;  Dizyee, Kanar;  Ash, Andrew;  Thornton, Philip;  Sloat, Lindsey;  Roura, Eugeni;  Henderson, Benjamin;  Herrero, Mario
收藏  |  浏览/下载:4/0  |  提交时间:2019/11/27
climate change  climate variability  grasslands  greenhouse gas emissions  intensification  livestock modelling  system dynamics  vulnerability  
Ocean acidification refugia in variable environments 期刊论文
GLOBAL CHANGE BIOLOGY, 2019, 25 (10) : 3201-3214
作者:  Kapsenberg, Lydia;  Cyronak, Tyler
收藏  |  浏览/下载:5/0  |  提交时间:2019/11/27
adaptive capacity  biological response  management  mitigation  ocean acidification  pH variability  refugia  vulnerability  
Maximum carbon uptake rate dominates the interannual variability of global net ecosystem exchange 期刊论文
GLOBAL CHANGE BIOLOGY, 2019, 25 (10) : 3381-3394
作者:  Fu, Zheng;  Stoy, Paul C.;  Poulter, Benjamin;  Gerken, Tobias;  Zhang, Zhen;  Wakbulcho, Guta;  Niu, Shuli
收藏  |  浏览/下载:13/0  |  提交时间:2019/11/27
carbon uptake period  interannual variability  maximum carbon uptake rate  net ecosystem exchange  phenology  physiology  
Global patterns of intraspecific leaf trait responses to elevation 期刊论文
GLOBAL CHANGE BIOLOGY, 2019, 25 (7) : 2485-2498
作者:  Midolo, Gabriele;  De Frenne, Pieter;  Hoelzel, Norbert;  Wellstein, Camilla
收藏  |  浏览/下载:6/0  |  提交时间:2019/11/27
altitude  carbon isotope ratio  environmental gradient  intraspecific variability  leaf nutrient content  meta-analysis  phenotypic variability  plant functional traits  
Biochar application as a tool to decrease soil nitrogen losses (NH3 volatilization, N2O emissions, and N leaching) from croplands: Options and mitigation strength in a global perspective 期刊论文
GLOBAL CHANGE BIOLOGY, 2019, 25 (6) : 2077-2093
作者:  Liu, Qi;  Liu, Benjuan;  Zhang, Yanhui;  Hu, Tianlong;  Lin, Zhibin;  Liu, Gang;  Wang, Xiaojie;  Ma, Jing;  Wang, Hui;  Jin, Haiyang;  Ambus, Per;  Amonette, James E.;  Xie, Zubin
收藏  |  浏览/下载:8/0  |  提交时间:2019/11/26
biochar  machine learning  N leaching  N2O  NH3  spatial variability