Gig1, a novel antiviral effector involved in fish interferon response

Vertebrate interferon (IFN) response defenses against viral infection through the induction of hundreds of IFN-stimulated genes (ISGs). Most ISGs are conserved across vertebrates; however, little is known about the species-specific ISGs. In this study, we reported that grass carp reovirus (GCRV)-induced gene 1 (Gig1), previously screened as a virus-induced gene from UV-inactivated GCRV-infected crucian carp (Carassius auratus) blastulae embryonic (CAB) cells, was a typical fish ISG, which was significantly induced by intracellular poly(I:C) through retinoic acid-inducible gene I (RIG-I)-like receptors-triggered IFN signaling pathway. Transient or stable overexpression of Gig1 prevented GCRV replication efficiently in cultured fish cells. Strikingly, Gig1 homologs were found exclusively in fish species forming a novel gene family. These results illustrate that there exists a Gig1 gene family unique to fish species and the founding gene mediates a novel fish IFN antiviral pathway. (C) 2013 Elsevier Inc. All rights reserved.Vertebrate interferon (IFN) response defenses against viral infection through the induction of hundreds of IFN-stimulated genes (ISGs). Most ISGs are conserved across vertebrates; however, little is known about the species-specific ISGs. In this study, we reported that grass carp reovirus (GCRV)-induced gene 1 (Gig1), previously screened as a virus-induced gene from UV-inactivated GCRV-infected crucian carp (Carassius auratus) blastulae embryonic (CAB) cells, was a typical fish ISG, which was significantly induced by intracellular poly(I:C) through retinoic acid-inducible gene I (RIG-I)-like receptors-triggered IFN signaling pathway. Transient or stable overexpression of Gig1 prevented GCRV replication efficiently in cultured fish cells. Strikingly, Gig1 homologs were found exclusively in fish species forming a novel gene family. These results illustrate that there exists a Gig1 gene family unique to fish species and the founding gene mediates a novel fish IFN antiviral pathway. (C) 2013 Elsevier Inc. All rights reserved

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

Research Note: Near-surface layer replacement for sparse data: Is interpolation needed?

Near-surface problem is a common challenge faced by land seismic data processing, where often, due to near-surface anomalies, events of interest are obscured. One method to handle this challenge is near-surface layer replacement, which is a wavefield reconstruction process based on downward wavefield extrapolation with the near-surface velocity model and upward wavefield extrapolation with a replacement velocity model. This requires, in theory, that the original wavefield should be densely sampled. In reality, data acquisition is always sparse due to economic reasons, and as a result in the near-surface layer replacement data interpolation should be resorted to. For datasets with near-surface challenges, because of the complex event behaviour, a suitable interpolation scheme by itself is a challenging problem, and this, in turn, makes it difficult to carry out the near-surface layer replacement. In this research note, we first point out that the final objective of the near-surface layer replacement is not to obtain a newly reconstructed wavefield but to obtain a better final image. Next, based upon this finding, we propose a new thinking, interpolation-free near-surface layer replacement, which can handle complex datasets without any interpolation. Data volume expansion is the key idea, and with its help, the interpolation-free near-surface layer replacement is capable of preserving the valuable information of areas of interest in the original dataset. Two datasets, i.e., a two-dimensional synthetic dataset and a three-dimensional field dataset, are used to demonstrate this idea. One conclusion that can be drawn is that an attempt to interpolate data before layer replacement may deteriorate the final image after layer replacement, whereas interpolation-free near-surface layer replacement preserves all image details in the subsurface.ImPhys/Acoustical Wavefield Imagin

[[alternative]]A Semantic and Pedagogical Study of DOU in Mandarin Chinese

[[abstract]]本論文主要是探討華語副詞「都」的語義及其教學語法。長期以來語言學家對「都」的語義有不少的研究，我們將整理分析這些研究的內涵，綜合歸納並建立本論文對「都」的語義解釋及分類。再者，有鑑於華語教學與漢語語言學之間一直存在著鴻溝，我們還要透過教學語法來作為兩者間的橋樑，所以以本文對「都」的語義及語用分析成果為基礎，加上考量教與學這個實際面所做的調整，我們嘗試為教學及學習架構一套「都」的教學語法，內容包含教學排序以及語法規則的編寫。 本論文的章節及其內容如下： 第一章 介紹研究目的與動機、研究範圍以及研究架構； 第二章 是關於「都」的文獻探討； 第三章 探討「都」的語義並分析相關的語用問題； 第四章 從英語的‘all’與「都」的比較談起，進而解釋 ‘所有 NP’、‘每NP’、‘任何NP’等不同指稱方式與 「都」 的搭配關係； 第五章 結合平衡語料庫、中介語語料庫、語法等級大綱等分析的結 果，為「都」的相關用法建議一套教學排序，並編寫「都」的 處方式教學語法。 第六章 為本論文的研究結果提出總結，並提出研究限制及對後續研究 的建議。

[[alternative]]Measuring Behavior And Temperament Traits in Pet Dogs：Factors Contributing to Aggressive And Fearful Behavior of Pet Dogs in Taiwan

[[abstract]]每隻狗的性情大不同，除了與狗本身相關的因素像是品種、性別、年齡有關之外，隨著家犬被飼養的環境與條件不同，也可能產生不同的行為表現。犬隻如果展現攻擊行為，例如：吠叫、前撲、甚至咬人或其他動物，往往會造成飼主的困擾，並會對受到攻擊的人或其他動物造成心理與生理的影響。在犬類的攻擊行為中，由恐懼而誘發的往往最為嚴重。在國外，家犬的攻擊性與恐懼程度是最常被研究與討論的犬類行為。台灣的人養狗比例雖然相當高，但是台灣對家犬行為的研究卻很少。在台灣有30%的人棄養狗是因為那些狗的行為問題。而台灣的人棄養狗時，多傾向將狗任意丟棄，而非送入收養中心，因此會衍生出一些相關的社會問題，例如流浪狗攻擊行人的事件等等。本研究使用問卷測量台灣家犬的攻擊性與恐懼程度並分析可能與其相關的一些因子。本研究分析的因子包括(一)狗本身相關的因子如性別、年齡、體型、結紮與否等等、以及(二)狗的被飼養環境與情況。本研究採用Hsu & Serpell( 2003 )所設計的問卷Canine Behavioral Assessment and Research Questionnaire( CBARQ )。CBARQ將犬隻常見的行為分成七大類，分別是(一)可訓練程度與服從性、(二)攻擊性、(三)恐懼程度、(四)易激動性、(五)分離焦慮、(六)跟隨與尋求關注傾向與(七)其它行為等共一百題。此問卷經過信度與效度的測試並被翻譯成各種語言版本在世界各地進行研究。本研究將( CBARQ )翻譯成中文( TvCBARQ )並加入與犬隻相關的問題後，透過獸醫院以及調查者，在台灣各地發放以蒐集資料。本研究藉由蒐集到的資料以測量TvCBARQ問卷的信度，再利用驗證性因素分析( Confirmatory Factor Analyses ) 將TvCBARQ與之前問卷( CBARQ )作因素結構( factor structure )的比較。最後透過順序性邏輯回歸分析( Ordinal Logistic Regression Analyses )的統計方法，分析那些因子可能與台灣家犬的攻擊性以及恐懼程度相關。 用TvCBARQ量化台灣家犬的11類行為時，其中10類行為的信度大於0.70；然而，與疼痛有關的行為之信度只有0.67。驗證性因素分析則指出台灣之TvCBARQ問卷與原始之CBARQ問卷的因素結構不完全相同。因此本研究利用探索性因素分析將TvCBARQ分成8類行為。本研究亦發現許多與台灣家犬的攻擊性與恐懼行為相關的因子。就與狗本身相關的因子來說，體型大的狗與體型為中、小型的狗比起來，對陌生人及飼主之攻擊性較弱，同時其恐懼程度也較低；年齡較大的狗、公狗、或者沒有結紮的狗，對飼主的攻擊性較強；被其他狗欺負過的家犬，對其他狗的攻擊性較強。就與家犬的飼養環境相關的因子來說，其飼主家中成員數越多，此家犬對陌生人、飼主及其他狗的攻擊性較強，恐懼程度也較高。居住在獨棟有院子的家犬比居住在公寓、電梯大樓、獨棟沒有院子的家犬，對陌生人的攻擊性較強；居住在東部的家犬比居住在北、中、南部的家犬，對其他狗的攻擊性較強；居住在鄉村的家犬比居住在城市、市郊的家犬，對其他狗的攻擊性較強；若飼主養狗的主因為看家，則其養出來的狗對陌生人及對其他狗會呈現出較高的攻擊性；非寵物店買來的狗比從寵物店買來的狗，對陌生人的攻擊性及對其他狗的攻擊性較強；飼主每天與所飼養的狗相處時間越長，其狗對飼主的攻擊性越弱；飼主每天帶其所飼養的狗外出散步的頻率若低於1次，該狗對飼主的攻擊性較強，恐懼程度也較高。 本研究建議飼主在飼養寵物狗之前，除了挑選喜歡的狗之外，也應多評估自己的飼養條件以及能給予狗的環境，並且要暸解飼養狗的義務，像是能照顧狗的時間、能帶狗散步的頻率，才不會讓所飼養的狗產生較高的攻擊或恐懼性。而本研究也顯示台灣家犬之攻擊性與恐懼程度呈顯著的正相關；因此當我們考慮台灣家犬攻擊性的議題時，也應該同時參考狗的恐懼程度。

戲劇創作與演出在華語文教學上成效研究

[[abstract]]本研究以溝通式教學觀為基礎，融合第二語言寫作歷程觀與戲劇理論，建立劇本寫作教學模式，並運用課室戲劇技巧，作為教學實務之參考，進而設計出一項完整而獨立於課室教學外的劇本寫作計畫，試圖探討戲劇活動應用在華語文教學上之可能性，期能透過從討論、寫作到演出的完整過程，帶動聽說讀寫的全面性學習。 本計畫實際進行地點在國立中央大學語言中心華語組，集合三種不同程度的十一名華語學習者，由三位教師共同指導。研究過程共分為三個部分，主要運用質性研究的參與觀察法，並搭配訪談。第一部分為前置作業：對教學設計的要素一一檢視，建立本計畫的基本架構，並訂定實施流程的階段性工作。第二部分為計畫運作：記錄計畫實施過程中，師生互動之情況，以及所運用之教學步驟與策略。第三部分為計畫評估：反映參與者觀點，評估計畫實施的成果，進行檢討與修正，並提出建議。 整體來說，本計畫完成了四大目標，即第一、學習者都嘗試將課內所學、個人經驗與作品加以結合，用最終作品自我檢視學習成果。第二、學習者直接面對個人的學習問題，並援引各種策略加以改進，成功激發出學習的自我意識。第三、學習者嘗試用目的語進行對話，解決計畫中產生的各種問題，同時也在私下就各自生活進行交流。他們的溝通意願增強，溝通能力也獲得開展。第四、劇本寫作計畫的獨特情境，打破制式的課室學習，帶動即興創作，加上同儕之間良好關係的建立，都提升了學習者的學習興趣。

DeepPick: A Deep Learning Approach to Unveil Outstanding Users Ranking with Public Attainable Features

Outstanding users (OUs) denote the influential, 'core' or 'bridge' users in online social networks. How to accurately detect and rank them is an important problem for third-party online service providers and researchers. Conventional efforts, ranging from early graph-based algorithms to recent machine learning-based approaches, typically rely on an entire social network's information. However, for privacy-conscious users or newly-registered users, such information is not easily accessible. To address this issue, we present DeepPick, a novel framework that considers both the generalization and specialization in the detection task of OUs. For generalization, we introduce deep neural networks to capture dynamic features of the users. For specialization, we leverage the traditional descriptive features to make use of public information about users. Extensive experiments based on real-world datasets demonstrate that our approach achieves a high efficacy of detection performance against the state-of-the-art.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.Information and Communication Technolog

Preparation of bio-bitumen by bio-oil based on free radical polymerization and production process optimization

Bio-oil produced during the production of biodiesel is a burden to the environment. Recycling and utilization of bio-oil as a substitute for pavement bitumen can help to build an environmentally-friendly and clean infrastructure. In this study, the bio-bitumen was prepared by bio-oil based on free radical polymerization. Different kinds of bio-bitumen products were produced by reacting bio-oil with an initiator and an accelerator solution at different reaction conditions. The orthogonal experimental method was employed to determine the optimal bio-bitumen production process by evaluating the indices of viscosity, rutting factors and fatigue factors. The test results show that the optimal mass proportions of bio-oil:initiator:accelerator solution is 100:1:2. Materials with these mass proportions should react at 100 °C for 2 h to yield the best bio-bitumen product. This kind of bio-bitumen product can be considered as a promising substitute for traditional petroleum bitumen.Pavement Engineerin

Chemical and rheological properties of polymer modified bitumen incorporating bio-oil derived from waste cooking oil

The chemical and rheological properties of polymer modified bitumen incorporating bio-oil derived from waste cooking oil (WCO) were investigated in this paper. At first, the chemical composition and mixing mechanism of the experimental materials were analysed from the perspective of functional group, and the influence of bio-oil on the activation energy was also researched. Then, the effect of bio-oil on the rotational viscosities of polymer modified bitumen and construction temperatures of corresponding mixtures was studied. Finally, the shear and bending rheological properties of polymer modified bitumen containing bio-oil were investigated. The results show that the bio-oil and styrene–butadiene–styrene (SBS) modified bitumen is mainly physically mixed, the addition of bio-oil decreases the activation energy of SBS modified bitumen. Additionally, the SBS modified bitumen containing bio-oil has lower viscosity values, and corresponding mixtures also have lower construction temperatures. Furthermore, the addition of bio-oil in SBS modified bitumen reduces the shear modulus and increases the bending creep compliance, which means bio-oil has positive effect on the low-temperature thermal cracking resistance performance while sacrificing the high-temperature rutting resistance performance to some extent. Therefore, the incorporation of WCO-based bio-oil in polymer modified bitumen is a promising technique to be used in cold regions where the low-temperature problems are more crucial.Accepted Author ManuscriptPavement Engineerin

A review on the pumping behavior of modern concrete

Pumping is the most common technique used to transport fresh concrete in construction sites. The large-scale use of concrete all over the world makes the pumping increasingly important. A wide variety of additives and admixtures are incorporated into modern concrete in order for sustainable development. The performance of modern concrete is rather complex and its pumping behavior differs significantly from that of conventional concrete, especially in the fresh stage. This paper presents a comprehensive overview on the state of the art of concrete pumping. The models and methods used for characterizing the concrete pumpability and lubrication layer are described. The factors influencing the pumping behavior are discussed. A couple of ultra-high pumping engineering of concrete conducted in China are introduced.Accepted Author ManuscriptMaterials and Environmen