【第一期阅读小分队（已结束）】【每日阅读练习贴——速度+越障】【一楼汇总】（另附CD首发花儿阅读教材PDF）

fox0923 · 发表于 2011-7-8 11:02:20

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谢谢fox贴上明天的速度2-2和越障1-11~<img src="/static/legacy-emoticon/21.gif" emoticon="[em:21]" alt="" /><img src="/static/legacy-emoticon/128.gif" emoticon="[em:128]" alt="" />辛苦啦辛苦啦~~ daisy,这是个好主意哇~ 我可以在一楼贴上参与贴文章的ID和要求,但是没有个平台来协调哪天谁来找文章就不太好schedule.. 大家看要不要建一个群?<div style="text-align:right;">-- by 会员 抓抓sandra (2011/7/8 2:27:55)</div> 
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 客气。。。我在这个网站得到了不少的benefit，何况自己阅读也不行，所以大家一起努力了。。。还有抓抓，你有没有觉得有时候在这里的速度练习和真正所作的阅读理解有些出入？我是说似乎到了真正的题目上面，我阅读的速度由慢下来了，因为一快好像就遗漏了重要的信息和总的框架。。。

ccmoom · 发表于 2011-7-8 11:33:48

我才看到1-7，太慢了。  今天报道~任务完成。  晚上继续追你们进度。

fox0923 · 发表于 2011-7-8 13:48:07

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to fox: 大哥哇你已经很快咯~~学习之~~-- by 会员 抓抓sandra (2011/7/7 18:38:33)
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 之前的帖子没看到，跳过其中一部分阅读都不知道。。还有就是，抓抓，我不是大哥来着，侉妞一个。。

daisyの小夢想 · 发表于 2011-7-8 22:49:09

【速度阅读 2-2】 50s 5 0 0 6 【越障1-11】 6:52 说了一种病毒的传播。首先说了它在非洲怎样发展，它不像其他病毒一样只会局限在非洲。 随着全球化，它慢慢被带到亚洲，在亚洲它产生了变异，有了更大的威力，而且使得tiger mosquito也感染了这种病毒。 文章还分析了这种病毒传播性和影响力的两点原因，忘了。好像说了蚊子繁殖力极强。 这种病毒不但在非洲、亚洲爆发，还传播到了美国。而且最恐怖的是它不怕冷，在低温下依然能传播、衍生。 所以文章最后提出要做出相应应对，改善公共卫生。

抓抓sandra · 发表于 2011-7-9 00:59:03

to fox:  哇原来fox是MM~感觉错误~嘿~抱一个~~昨天daisy建议我们大家轮流贴练习,fox你看呢? to CC:  坚持就会有进步的~我这几天长难句搁浅两天了,心慌慌..>< to daisy: 我们俩的速度好类似~嘿~

抓抓sandra · 发表于 2011-7-9 01:00:30

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【速度2-2】 50s 居然差了5行 58s 58s 差6行 第一篇文章被我读成这样了..T T 第二篇略好一些..但是也有点悲剧..今天战斗力不佳..

lus发现对于陌生题材的文章理解力不行.. 考虑到大家大多都是商科专业底子,接下来找速度和越障都要开始多加入一些理科的文章了~ 【越障1-11】 7min5s 今天这篇讲的是传染病C和N的情况.    1. 介绍了C是如何由蚊子传播的.    2. C的起源在Africa,但是后来欧洲也有了.有研究对比欧洲和非洲的C的携带者蚊子的基因,发现欧洲的有一些小小但是很关键的mutation改变,然后介绍了这种改变的影响.具体不记得了.    3. C的快速传播的原因: mosquitos travel easily~说到雨水是母蚊子产卵的最佳环境,同时蚊子一般通过某个介质传播,名称忘记了.    4. 美国也有这种病,而且很多病例是由于美国人出国感染了C之后带回美国的.    5. 最后警示说N很有可能也会形成C这样的全球性的epidemic,因为N和C的起源都在非洲,传播途径都是蚊子,二者非常相似.还说了现在各国在努力控制C的蔓延和国家之间的传播,但是鉴于蚊子太容易travel, adapt and survive,这些努力的尝试都是easily said than done. 所以现在最好的办法就是慢慢等待有效治愈C的药.<div style="text-align:right;">-- by 会员 抓抓sandra (2011/7/8 10:28:37)</div> 
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 我只是选了一些我不太熟悉的题材，算是锻炼一下吧。。反正范围广泛一点，就算是GMAT的考题里遇不到，到了以后MBA学习中我想也是有帮助的。。现在我所找的都是各个不同的经济历史和科技杂志上看到的，还有一些是harvard magazine, chicago U. magazine, etc....还有，要谢谢抓抓帮忙翻译后面的越障文章，我的网络商务有问题，搞了两个小时才把这几篇文章post上来，所以也手懒了！<div style="text-align:right;">-- by 会员 fox0923 (2011/7/8 10:57:55)</div> 
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 我也只是在读完越障之后马上回忆,借鉴小安法第二轮的做法嘿~觉得这样能帮助自己形成注重逻辑结构的习惯~不一定就准确,只能当做一个参考哈~

抓抓sandra · 发表于 2011-7-9 01:02:45

D: k5 K* Q6 [* m* f  S+ F% c <div style="text-align:center;">Abstract</div> * L  J( W% W" e6 Q Background: To identify differentially expressed genes (DEGs) from microarray data, users of the Affymetrix Gene Chip system need to select both a preprocessing algorithm to obtain expression level measurements and a way of ranking genes to obtain the most plausible candidates. We recently recommended suitable combinations of a preprocessing algorithm and gene ranking method that can be used to identify DEGs with a higher level of sensitivity and specificity. However, in addition to these recommendations, researchers also want to know which combinations enhance reproducibility. , |% d' C+ ^) V3 B Results: We compared eight conventional methods for ranking genes: weighted average difference (WAD),average difference (AD), fold change (FC), rank products (RP), moderated tstatistic(modT), significance analysis of microarrays (samT), shrinkage t statistic(shrinkT), and intensity based moderated t statistic (ibmT) with six preprocessing algorithms (PLIER, VSN, FARMS, multimgMOS (mmgMOS), MBEI, and GCRMA). A total of 36 real experimental data sets was evaluated on the basis of the area under the receiver operating characteristic curve (AUC) as a measure for both sensitivity and specificity. We found that the RP method performed well for VSN-, FARMS-, MBEI-, and GCRMA-preprocessed data, and the WAD method performed well for mmgMOS preprocessed data. Our analysis of the MicroArray Quality Control (MAQC) project's data sets showed that the FC-based gene ranking methods (WAD, AD, FC, and RP) had a higher level of reproducibility: The percentages of overlapping genes (POGs) across different sites for the FC-based methods were higher overall than those for the t-statistic-based methods (modT,samT, shrinkT, and ibmT). In particular, POG values for WAD were the highest overall among the FC based methods irrespective of the choice of preprocessing algorithm.2 o' v0 ~; `6 v  g Conclusion: Our results demonstrate that to increase sensitivity, specificity, and reproducibility in microarray analyses, we need to select suitable combinations of preprocessing algorithms and gene ranking methods. We recommend the use of FC-based methods,in particular RP or WAD.: Y- `6 h$ l. G5 u  m, J ! m2 U6 X, L  K. X" n& b <div style="text-align:center;">Background</div> ' m4 ^2 R/ e1 V- N9 U% P Microarray analysis is often used to detect differentially expressed genes (DEGs) under different conditions. As there are considerable differences [1,2] in how well it performs, choosing the best method of ranking these genes is important.Furthermore, Affymetrix GeneChip users need to choose a preprocessing algorithm from a number of competitors in order to obtain expression-level measurements [3]. We recently reported with another group that there are suitable combinations of preprocessing algorithms and gene ranking methods [1,2]. We evaluated three preprocessing algorithms, MAS [4], RMA [5], and DFW [6], and eight gene ranking methods, WAD [1], AD, FC, RP [7], modT [8], samT [9], shrinkT [10], and ibmT[11], by using a total of 38 data sets (including 36 real experimental datasets)[1]. Meanwhile, Pearson [2] evaluated nine preprocessing algorithms, MAS [4],RMA [5], DFW [6], MBEI [12], CP [13], PLIER[14], GCRMA [15], mmgMOS [16], and FARMS[17], and five gene ranking methods, modT [8], FC, a standard t-test,cyberT [18], and PPLR [19], by using only one artificial 'spike-in' dataset,the Golden Spike dataset [13]. 9 ^9 }1 k* w+ ?% A5 D: m' r When were-evaluated the two reports using the common algorithms and methods we found that suitable gene ranking methods for each of the three preprocessing algorithms, i.e., MAS, RMA, and DFW, converge to the same: Combinations of MAS and modT (MAS/modT), RMA/FC, and DFW/FC can thus be recommended. However, the final conclusions for the original reports are understandably different: Our recommendations [1] are MAS/WAD, RMA/FC, and DFW/RP, while Pearson [2] recommends mmgMOS/PPLR, GCRMA/FC, and so on. This difference is mainly because fewer preprocessing algorithms were evaluated in our previous study [1]. 6 y  d- O5 A& I& D - e& k; V$ M" g" t( \. D( A We investigated suitable gene ranking methods for each of six preprocessing algorithms: MBEI,VSN [20], PLIER, GCRMA, FARMS, and mmgMOS. We also investigated the best combination of a preprocessing algorithm and gene ranking method using another evaluation metric, i.e., the percentage of overlapping genes (POG), proposed by the MAQC study [21]. Most authors of methodological papers have made claims that their methods have a greater area under the receiver operating characteristic curve (AUC) values, i.e., both high sensitivity and specificity [1,2]. However, reproducibility is rarely mentioned[21]. A good method should produce high POG values, i.e., those indicating reproducibility as well as high AUC ones, i.e., those for sensitivity and specificity. We will discuss suitable combinations of preprocessing algorithms and gene ranking methods.& y! I: q) A" } 7 g& P& w% C; _7 h <div style="text-align:center;">Conclusion</div> We evaluated the performance of combinations between six preprocessing algorithms and eight gene ranking methods in terms of the AUC value, i.e., both sensitivity and specificity, and the POG one, i.e., reproducibility. Our comprehensive evaluation confirmed the importance of using suitable combinations of preprocessing algorithms and gene ranking methods.5 r) w3 C( G7 b9 N * i2 ~' L. J. [" }9 A4 p$ l Overall, two FC-based gene ranking methods (RP and WAD) can be recommended. Our current and previous results indicate that any of the following combinations, RMA/RP,DFW/RP, PLIER/RP, VSN/RP, FARMS/RP, MBEI/ RP, GCRMA/RP, MAS/WAD, and mmgMOS/WAD, enhances both sensitivity and specificity, and also that using the WAD method enhances reproducibility.4 T8 g  o4 j2 M; _, u: z! E" S  L- d6 P% \, M+ p; [4 \ <div style="text-align:center;">Methods</div> : P3 P# F, b% \ The raw data(Affymetrix CEL files) for Datasets 3–38 were obtained from the Gene ExpressionOmnibus (GEO) website [32]. All analysis was performed using R (ver. 2.7.2)[33] and Bioconductor [34]. The versions of R libraries used in this study areas follows: plier (ver. 1.10.0), vsn (3.2.1), farms (1.3),puma (1.6.0), affy (1.16.0) [35], gcrma (2.10.0),RankProd(2.12.0) [36], st (1.0.3) [10], limma (2.14.7) [8], ROC (1.14.0).The main functions in the R libraries are as follows: justPlier for PLIER,vsnrma for VSN, q.farms for FARMS, mmgmosfor mmgMOS, expresso for MBEI (PM only model), gcrma for GCRMA, mas5 for MAS, rmafor RMA, expresso and the R codes available in [37] for DFW, RP forRP, modt.stat for modT,sam.stat for samT, shrinkt.stat forshrinkT, IBMT for ibmT [38], and pumaComb and pumaDEforPPLR [19]. Since the MBEIand MAS expression measures do not output logged values, signal intensities under 1 in those preprocessed data were set to 1 so that the logarithm of the data could be found. Logged values smaller than 0 in PLIER-, VSN-, FARMS-, mmgMOS-,and GCRMA-preprocessed data were set to 0. For reproducible research, we made the R code for analyzing Dataset 4 (GEO ID: GSM189708–189713) available as the additional file [see Additional file 3]. The R codes for the other datasets are available upon request.9 c0 g0 G) S* j8 s+ V  B  S4 v The raw data forthe MAQC datasets were obtained from the MAQC website [39]. The evaluationbased on POG was done with 12 datasets produced by the MAQC project [21] inwhich two RNA sample types and two mixtures of the original samples were used:Sample A, a universal human reference RNA; Sample B, a human brain reference RNA;Sample C, which consisted of 75 and 25% of Sample A and B respectively; andSample D, which consisted of 25 and 75% of Sample A and B respectively. Fivereplicate experiments for each of the four sample types at six independent testsites (Sites 1–6) were conducted, and, thus there are 20 files at each site.The data preprocessing was performed at each site. The application of the gene rankingmethods was independently performed for comparisons of "Sample A versusB" and "Sample C versus D". 来源：<a href="http://bbs.gter.net/bbs/viewthread.php?tid=994272&highlight=" target="_blank">http://bbs.gter.net/bbs/viewthread.php?tid=994272&highlight=</a>

抓抓sandra · 发表于 2011-7-9 01:13:41

Fourteen Scientists and Activists Who areChanging the World计时1 STEVE EMBER: I'm Steve Ember. SHIRLEY GRIFFITH: And I'mShirley Griffith with EXPLORATIONS in VOA Special English. Every year, theNational Geographic Society honors scientists, wildlife experts and others fortheir work. Each honoree receives a ten thousand dollar award to help them withtheir research and future projects. This week we learn about the latestNational Geographic Emerging Explorers. (MUSIC) STEVE EMBER: One of thehonorees is searching for life in faraway places. KEVIN HAND: "The bigpicture for me and many of my colleagues is the search for life beyond Earth.So if we've learned anything about life here on Earth, it's that in generalwhere you find the liquid water, you find life." STEVE EMBER: That is KevinHand, a planetary scientist and astrobiologist who works at the Jet PropulsionLaboratory in California. This lab works with the American space agency onprojects including looking for life in outer space. Kevin Hand is assiting withplans to send an orbital device to Europa, a moon of the planet Jupiter. Spaceagency officials hope to launch the device in about twenty-twenty. SHIRLEY GRIFFITH: Europa iscovered in ice. Under the ice are deep oceans, which could be home to livingorganisms. However, this moon is not easy to explore. Depending on its orbit,Europa can be over nine hundred million kilometers from Earth. Its environmentis freezing, with intense radiation and no atmosphere. KEVIN HAND: "And when itcomes to actually searching for this life, that's a great challenge. We sendthese robots off as our little planetary emissaries to go and do the science.These robots basically have to take the scientific laboratory with them so theycan do the experiments and chemical analysis on the planets." (290 words) 计时2 SHIRLEY GRIFFITH: Kevin Handand coworker Robert Carlson have recreated an environment like Europa in alaboratory to study its conditions. Mister Hand also has visited extreme placeson Earth to see how organisms survive in cold climates. This could help expertsknow what to look for when looking for possible life forms on Europa. (MUSIC) STEVE EMBER: The work ofseveral Emerging Explorers aims to improve the lives of people in differentways. Juan Martinez grew up in poverty in the city of Los Angeles. In highschool, he won a trip to learn about nature in the Teton Science Schoolsprogram in Wyoming. He says experiencing the wilderness and mountains changedhis life. Today, Mister Martinezcampaigns to get young people, especially at-risk youth, interested in natureand the outdoors. He works with groups like the Sierra Club to get young peopleinterested in the environment. And, he heads the Natural Leaders Network of theChildren and Nature Network. The group creates links between environmentalorganizations, businesses, government and individuals to connect children withnature. SHIRLEY GRIFFITH: JenniferBurney is an environmental scientist. She has studied links between climatechange, food production and food security. She is especially interested in howpeople can use new technologies to create a better, more sustainable foodsystem. One of her projects is innorthern Benin. She has worked with the Solar Electric Light Fund to build awater supply system for farming. Energy from the sun provides power for theproject. (250 words) 计时3 JENNIFER BURNEY: "Thissystem enables farmers to cultivate vegetables year around and to cultivate newtypes of crops and to generally increase the area that they cultivate so theyhave much more food for their home consumption but are also able to sell alarge majority of it and earn income that way. SHIRLEY GRIFFITH: JenniferBurney also works with a group in India. They are studying the effects ofreplacing traditional cook stoves with safer, more environmentally-friendlycooking technologies. Traditional cook stoves produce a harmful black smoke. JENNIFER BURNEY: "Weknow that it is a component of particulate matter which makes people sick, butit's also a very potent climate warming agent." SHIRLEY GRIFFITH: Miz Burneysays replacing old stoves with safer ones could have a huge effect on improvinghuman health and slowing climate change. STEVE EMBER: Palestinian AzizAbu Sarah is a cultural educator who grew up in Jerusalem. After his brotherwas jailed and killed, Mister Abu Sarah was filled with hatred and publiclyacted out his anger. He refused to learn Hebrew, which he considered thelanguage of his enemy. But he knew he would have to learn the language to go tocollege and get a good job in Jerusalem. In Hebrew class, he met Jewish men andwomen who were not soldiers with guns. He learned they were human beings, justlike he is. Aziz Abu Sarah has spent hiscareer working to break down emotional barriers between Arabs and Jews. In theUnited States, he helps lead the Center for World Religions, Diplomacy andConflict Resolution at George Mason University. He also created a travelcompany that helps bring people to the Middle East for multicultural visits. (MUSIC) (286 words) 计时4 SHIRLEY GRIFFITH: TwoEmerging Explorers are working to turn waste into a valuable resource.Ecologist Sasha Kramer is helping to fight poverty in Haiti. She also isworking to solve one of the country's environmental problems. Living in Haiti,Sasha Kramer learned that only sixteen percent of Haitians had access totoilets. Many people throw out bodily waste in the ocean, rivers, and emptyareas. She helped create a non-profit organization that helps turn waste intofertilizer. This fertilizer helps improve the quality of Haiti's soil. And ithelps poor farmers increase their harvests. STEVE EMBER: Ashley Murray isa wastewater engineer living in Ghana. She is working to persuade governmentsthat turning wastewater into clean water can be profitable. She says theprofits made from reusing waste could change waste treatment systems and healtharound the world. SHIRLEY GRIFFITH: Several ofthe Emerging Explorers are working to protect and explore undeveloped areas. Ecologist Paula Kahumbu headsan organization called WildlifeDirect, which has offices in Kenya and theUnited States. The organization's website describes over one hundredconservation projects. The goal of WildlifeDirect is to connect scientistsworking to protect the environment with people who want to help. The group alsohelps spread information quickly to raise support during environmental crises. STEVE EMBER: Tuy Sereivathanais working to save endangered elephants in Cambodia. Up until now, manyCambodians have hunted elephants to protect their land and crops. TuySereivathana works with Cambodians to educate rural populations on how to besuccessful farmers without harming the animals and the areas where they live.The National Geographic Society says his program has been very successful. Buthe says there is still much work to be done in getting government anddevelopers to support growth that does not harm the environment. (298 words) 计时5 SHIRLEY GRIFFITH: AdrianSeymour is an ecologist and filmmaker. He studies the Indonesian population ofa small meat-eating creature called the Malay civet. He says studying creaturesat the top of the food chain can help explain what is happening in the wholeecosystem. He also makes movies about human issues linked to environmentalefforts. STEVE EMBER: Four EmergingExplorers study creatures. ?a?an ?ekercio?lu is a biology professor at theUniversity of Utah. The Turkish native has studied the effects of environmentalpressures on decreasing bird populations. He helps to show people how importantbirds are for health, farming, and the environment. Jorn Hurum studies theancient fossil remains of animals in northern Norway. He and his team havefound important fossils of sea reptiles, including several huge creatures thatonce stood over fifteen meters tall. In Germany, he helped unearth a fortyseven million year old fossil of a primate. Jorn Hurum feels strongly aboutmaking his scientific publications available free of cost so that thisknowledge can be seen by everyone. Dino Martins is a scientistwho studies insects. He studies environments in which bees and otherpollinating insects are threatened. He helps educate farmers and others in eastAfrica about the importance of these insects in food production and how theycan be protected. SHIRLEY GRIFFITH: KakaniKatija is a bioengineer who studies the power sources responsible for theocean's movements. Winds and tides drive the oceans, but so do the movements ofswimming animals. Her research shows that the movement of sea creatures has abig effect on climate systems by continuously mixing the seawater. Mixing thewater moves oxygen and nutrients from one layer of water to another. (283 words) 计时结束 今天这篇蛮长的,就没有办法加进Economist上面的文章咯,明天换Economist的试试~ 以下自由阅读. We close this program withHayat Sindi, a Saudi-born health technology expert. She is helping to spreadthe use of a low-cost, paper device that can help people in poor, rural areasto find disease. The device is the size of a postage stamp. It is being used tohelp people learn if they have health problems like liver damage. The devicequickly provides important information to people in areas without medicalworkers or a laboratory. The National Geographic Society says the device sheand her team developed holds promise to be an invention that will save millionsof lives. 来源:  <a href="http://www.51voa.com/VOA_Special_English/Fourteen-Scientists-and-Activists-Who-are-Changing-the-World-41915.html" target="_blank">http://www.51voa.com/VOA_Special_English/Fourteen-Scientists-and-Activists-Who-are-Changing-the-World-41915.html</a>

MarsTOF · 发表于 2011-7-9 10:11:54

1-2 速度 1,2,3 每个差4行。。4 55s 5 60s 越障 7min15s 速度太慢了诶。。

mahaofei001 · 发表于 2011-7-9 19:11:03

矮油~速度太慢了~都是差个四五行的样子~~

【第一期阅读小分队（已结束）】【每日阅读练习贴——速度+越障】【一楼汇总】（另附CD首发花儿阅读教材PDF）

【越障1-12】Ranking differentially expressed genes from Affymetrix gene expression d

【速度2-3】VOA SPECIAL ENGLISH

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