Pan-cancer analysis of whole genomes

Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale(1-3). Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4-5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter(4); identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation(5,6); analyses timings and patterns of tumour evolution(7); describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity(8,9); and evaluates a range of more-specialized features of cancer genomes(8,10-18).Peer reviewe

Erratum to: 36th International Symposium on Intensive Care and Emergency Medicine

[This corrects the article DOI: 10.1186/s13054-016-1208-6.]

Sparsity-based Human Activity Recognition with PointNet using a Portable FMCW Radar

Radar-based solutions have attracted great attention in human activity recognition (HAR) for their advantages in accuracy, robustness, and privacy protection. The conventional approaches transform radar signals into feature maps and then directly process them as visual images. While effective, these image-based methods may not be the best solutions in terms of representation efficiency to encode the relevant information for classification. This article proposes a novel HAR method combining sparse theory and PointNet network, with both operations in the time-Doppler (TD) and range-Doppler (RD) domains. First, sparsity-based feature extraction is introduced to use a limited number of sparse solutions to characterize human activities in the form of TD sparse point clouds (TDSP) or dynamic RD sparse point clouds (DRDSP). This new representation is validated by comparing the reconstructed and original signals. Then, PointNet networks are adopted to summarize multidomain features and predict human activity labels by a sparse set of input point clouds. Comprehensive experiments were conducted to demonstrate that the proposed method can yield a higher representation efficiency, classification accuracy, and better generalization capability than existing ones.Green Open Access added to TU Delft Institutional Repository ‘You share, we take care!’ – Taverne project https://www.openaccess.nl/en/you-share-we-take-care Otherwise as indicated in the copyright section: the publisher is the copyright holder of this work and the author uses the Dutch legislation to make this work public.Microwave Sensing, Signals & System

教師A型行為組型和外顯行為與班級氣氛、學生成就動機、測試焦慮之關係

[[abstract]]本研究旨在探討教師A 型行為組型、教師行為與班級氣氛、學生成就動動、測試焦慮 之關係。 以40位國小六年級女教師(20 位為A 型，20位為B 型) 及其所任教班級學生1733名為 受試。使用工具有：中國人A 型量表、教師行為評量表、班級氣氛問卷、學校生活經 驗問卷、兒童測試焦慮量表及兒童A 型量表。以Hotelling T 、二因子多變項變異 數分析、皮爾遜積差相關分析、典型相關分析及徑路分析等統計法進行資料處理。 研究結果發現： ( 一)A型教師比B 型教師更常使用「間接影響行為」，至於「直接影響行為」，兩類 型教師無顯著差異存在。 ( 二)A型教師所領導的學生對班級之滿意度較高，班級較有凝聚力，但是較常有互相 爭吵、搗蛋不合作、不服從班長管理等衝突情形發生，而且班級秩序較差。 ( 三)A型教師班上學生的成就動機、測試焦慮比B 型教師班上的學生高；女生的成就 動機、測試焦慮比男生高。 ( 四)A型學生的成就動機比B 型學生高。 ( 五) 教師的「間接影響行為」與班級氣氛呈正相關；教師的「直接影響行為」與班 級氣氛呈負相關，與學生的測試焦慮呈正相關。 ( 六) 教師的A 型行為組型、教師行為與班級氣氛、成就動機、測試焦慮之間有典型 相關存在。 ( 七) 本研究所提的徑路模式不能完全成立，只有「努力競爭與成就」影響「教師間 接影響行為」再影響「班級氣氛」的徑路得到支持。 #50008962.abs #50008962.abs

Microphysical processes of super typhoon Lekima (2019) and their impacts on polarimetric radar remote sensing of precipitation

The complex precipitation microphysics associated with super typhoon Lekima (2019) and its potential impacts on the consistency of multi-source datasets and radar quantitative precipitation estimation were disentangled using a suite of in situ and remote sensing observations around the waterlogged area in the groove windward slope (GWS) of Yandang Mountain (YDM) and Kuocang Mountain, China. The main findings include the following: (i) the quality control processing for radar and disdrometers, which collect raindrop size distribution (DSD) data, effectively enhances the self-consistency between radar measurements, such as radar reflectivity (ZH), differential reflectivity (ZDR), and the specific differential phase (KDP), as well as the consistency between radar, disdrometers, and gauges. (ii) The microphysical processes, in which breakup overwhelms coalescence in the coalescence-breakup balance of precipitation particles, noticeably make radar measurements prone to be breakup-dominated in radar volume gates, which accounts for the phenomenon where the high number concentration rather than the large size of drops contributes more to a given attenuation-corrected ZH (ZHC) and the significant deviation of attenuation-corrected ZDR (ZDRC) from its expected values (ẐDR) estimated by DSD-simulated ZDR-ZH relationships. (iii) The twin-parameter radar rainfall estimates based on measured ZH (ZHM) and ZDR (ZDRM), and their corrected counterparts ZHC and ZDRC, i.e., R(ZHM, ZDRM) and R(ZHC, ZDRC), both tend to overestimate rainfall around the GWS of YDM, mainly ascribed to the unique microphysical process in which the breakup-dominated small-sized drops above transition to the coalescence-dominated large-sized drops falling near the surface. (iv) The improved performance of R(ZHC, ẐDR) is attributed to the utilization of ẐDR, which equals physically converting breakup-dominated measurements in radar volume gates to their coalescence-dominated counterparts, and this also benefits from the better self-consistency between ZHC, Z¯DR, and KDP, as well as their consistency with the surface counterparts.Atmospheric Remote Sensin

高中班級氣氛之研究

[[abstract]]本研究以我國公立高中三年級的學生為施測對象，就性別（男女）與地區（院轄市、 縣轄市鎮）進行分層叢集隨機取樣，共計取得樣本二十九班，一千四百三十五人。其 後，以「學習環境量表」及國文、英文、數學三科成就測驗為研究工具，蒐集所需資 料，並兼採班級與學生個人為分析單位，以曼一專特尼U 考驗、積差相關、雙因子變異數分析、逐步多元迴歸等方法，進行分析，共計得到以 下四項結論： 一、全班級級氣氛隨著性別與地區的不同而有所改變。 二、學生個人所知覺到的班級氣氛與同學所同知覺的全班班級氣氛大體一致，亦隨性 別與地區的不同而有差異。綜合言之，男生班與院轄市班級的班氣氛較為相似，都是 多系派、多衝突、教師多偏愛、學生對班級多冷淡的情形；而女生班與縣轄市鎮班級 的班級氣氛亦有共同點，即是較團結、較民主、較有班見、學生對班級較滿意、班級 速度較迅速。 三、全班班級氣氛與全班平均學業成就的關係並不很密切。 四、學生個人所知覺到的班級氣氛與其學業成就的相關亦不高。綜合言之，團結與學 業成就成負相關，派系與學業成就成正相關。 根據以上研究結果，本研究提出三項建議，以供教育決策者與學校教師參考。 一、促進良好學生同儕關係與師生關係。 二、加強團隊精神。

Experimental analysis of ballast bed state in newly constructed railways after tamping and stabilizing operation

Before the operation of newly constructed railways, tamping and stabilizing machines should be used to improve the quality of ballast beds. With the expansion of the railway network and increase of speeds and axle loads, higher quality and efficiency for tamping and stabilizing operation are required. However, previous studies did not involve the effects and parameters of three-sleeper tamping and stabilizing operation under complex working conditions. In the paper, the effect of a three-sleeper tamping and stabilizing machine on the ballast bed state has been studied by performing field experiments. The effect of important factors, including tamping modes, stabilizing frequency, and track lifting amount, are discussed in detail. The results show that the tamping operation on newly constructed railways causes a reduction of the lateral resistance by 56.5 % and a reduction of lateral resistance work by 64.9 %. After the stabilizing operation, the lateral resistance and lateral resistance work are increased by 168.6 % and 209.8 %, respectively. The tamping and stabilizing operation can significantly increase the support stiffness of ballast beds, which meets the requirements of train operation. Meanwhile, 2X tamping mode is more beneficial to improve ballast resistance. Besides, it is reasonable for a stabilizing frequency of 25 Hz to be used for newly constructed railways. The track lifting amount also has a large effect on the ballast bed quality, and it is recommended to keep the lift amount in the range of 20 mm ∼ 30 mm to achieve a better tamping quality.Green Open Access added to TU Delft Institutional Repository 'You share, we take care!' - Taverne project https://www.openaccess.nl/en/you-share-we-take-care Otherwise as indicated in the copyright section: the publisher is the copyright holder of this work and the author uses the Dutch legislation to make this work public.Mechanics and Physics of Structure

Predicting aircraft trajectory uncertainties for terminal airspace design evaluation

The terminal airspace that surrounds an airport is the area with high flight density and complex structure. Aircraft are asked to follow the standard arrival and departure routes in terminal airspace, yet the actual trajectories may deviate due to air traffic control (ATC) instructions, pilots' decisions, surveillance and flying performance variations, etc. Predicting aircraft trajectories considering such uncertainties plays a crucial role in evaluating a redesign of the standard routes. Traditional simulation approaches for generating aircraft trajectories in a terminal airspace are cumbersome to use as it requires a detailed setup for each new scenario, while most existing data-driven methods can only be used in an airspace with historical trajectories, not applicable to new structure designs or other terminal areas. To fill in gap, in this paper, we develop a new model based on Multilayer Perceptron Neural Network (MLPNN) to predict aircraft trajectories with uncertainties for terminal airspace design evaluations. A key feature of the proposed model is that it is trained on existing standard routes yet it can be applied to new standard routes to generate trajectories. The enabler of the model's transferability is a novel input-and-output construction method for feature representations of raw trajectory data based on domain knowledge, including trajectory reconstruction, feature engineering, and output designing. After the input-and-output construction, a supervised learning model based on MLPNN is built to predict the standard deviations from the extracted features using historical trajectory data of existing standard routes. Once the model is built, trajectories with uncertainty can be simulated, through applying Gaussian distribution and exponential moving average algorithms, even on newly designed standard routes, where no aircraft have flown yet. Subsequently, new terminal airspace designs could be evaluated for their safety, efficiency, and environmental implications based on the simulated trajectories. The proposed model was tested on real-world operational data. Results showed that the model can quantify the characteristics of aircraft trajectories that are transferable across standard routes, and generate trajectories for new standard routes. We also demonstrated the proposed model on evaluating deficiencies on fuel consumption of actual arrival trajectories compared with the designed arrival routes. The generated trajectories showed 23%–37% more fuel consumption on average than the standard arrival routes in the terminal airspace of Hong Kong International Airport, which was validated with actual flight data.Air Transport & Operation