Gene expression profiling of breast cancer survivability---用21個基因推測乳癌，夠有效率!

文章日期：2013-05-17 12:11

Gene expression profiling of breast cancer survivability by pooled cDNA microarray analysis using logistic regression, artificial neural networks and decision trees

Hsiu-Ling Chou¹, Chung-Tay Yao², Sui-Lun Su³, Chia-Yi Lee³, Kuang-Yu Hu⁴, Harn-Jing Terng⁵, Yun-Wen Shih³, Yu-Tien Chang³, Yu-Fen Lu³, Chi-Wen Chang⁶, Mark L Wahlqvist⁷, Thomas Wetter⁸ and Chi-Ming Chu^3*

BMC Bioinformatics 2013, 14:100 doi:10.1186/1471-2105-14-100

Abstract

Background

Microarray technology can acquire information about thousands of genes simultaneously. We analyzed published breast cancer microarray databases to predict five-year recurrence and compared the performance of three data mining algorithms of artificial neural networks (ANN), decision trees (DT) and logistic regression (LR) and two composite models of DT-ANN and DT-LR. The collection of microarray datasets from the Gene Expression Omnibus, four breast cancer datasets were pooled for predicting five-year breast cancer relapse. After data compilation, 757 subjects, 5 clinical variables and 13,452 genetic variables were aggregated. The bootstrap method, Mann–Whitney U test and 20-fold cross-validation were performed to investigate candidate genes with 100 most-significant p-values. The predictive powers of DT, LR and ANN models were assessed using accuracy and the area under ROC curve. The associated genes were evaluated using Cox regression.

Results

The DT models exhibited the lowest predictive power and the poorest extrapolation when applied to the test samples. The ANN models displayed the best predictive power and showed the best extrapolation. The 21 most-associated genes, as determined by integration of each model, were analyzed using Cox regression with a 3.53-fold (95% CI: 2.24-5.58) increased risk of breast cancer five-year recurrence…

Conclusions

The 21 selected genes can predict breast cancer recurrence. Among these genes, CCNB1, PLK1 and TOP2A are in the cell cycle G2/M DNA damage checkpoint pathway. Oncologists can offer the genetic information for patients when understanding the gene expression profiles on breast cancer recurrence.

Keywords:

Breast cancer; Microarray; Artificial neural network; Logistic regression; Decision tree

使用資料探勘演算法預測非肺小細胞肺癌患者存活情形及其效能比較

使用資料探勘演算法預測非肺小細胞肺癌患者存活情形及其效能比較

文章日期：2013-05-17 12:02

資料越來越多，資料探勘也越來越重要，特別是資訊不足的時候，模式很重要
下面研究三種探勘方法，建議用決策樹決定變項，將變項丟進LOGISTIC MODEL，
不過因為樣本數要夠多，四百多個可能都不太夠，
所以樣本不夠就靠類神經方法可能幫得上忙!

Author: 翁紹宏* 陳麗帆 朱基銘 白璐 楊燦 劉立 孫建安
摘要
本研究使用決策樹、類神經網路和邏輯斯迴歸模型三種資料探勘演算法來探討影響非小細胞肺癌的預後因子及影響模型預測能力的因素（不同資料庫、不同死因、單或複合模型和樣本大小）。本研究的研究對象為美國癌症登記資料檔（the Surveillance, Epidemiology, and End Results, SEER），選取自西元1988年至2004年間診斷為非小細胞肺癌患者，並依據死因的不同將其分為死於肺癌與死於轉移癌;資料經過修整後，共有16個自變項納入分析，並根據其存活情形分為一年、三年和五年存活情形。模型的評估指標為準確率（accuracy, ACC）、ROC曲線下的面積（area under the ROC curve, AUC）和外推力(external generalization)。為避免隨機抽樣造成資料的誤差，本研究將對資料庫進行十折交叉驗證（10-fold cross-validation）。

研究結果顯示，影響美國非小細胞肺癌患者死於肺癌的一年、三年和五年存活情形預後因子為手術種類、臨床分組和腫瘤擴散程度;影響非小細胞肺癌患者死於轉移癌的一年、三年和五年存活情形預後因子為手術種類、臨床分期和檢驗淋巴結個數。

三個模型的預測力表現以類神經網路模型的表現較好，外推能力則以邏輯斯廻歸模型表現較好。樣本人數建議為至少為3500人，其中以邏輯氏回歸模型最容易受到小樣本的影響; 決策樹則是會因為資料庫提供的訊息不足而無法成樹。複合模型的部份，其結果顯示，當決策樹的測試組的ACC值較另外兩個模型好時，則複合模型的測試組AUC值就會提高。
關鍵字：lung cancer, decision tree, artificial neural network, logistic regression, SEER

Statin Use and Reduced Cancer-Related Mortality--標題寫得好!

Statin Use and Reduced Cancer-Related Mortality--標題寫得好!

文章日期：2013-05-17 11:57

不是只有台灣有健保資料庫~~~

 

Statin Use and Reduced Cancer-Related Mortality

Sune F. Nielsen, Ph.D., Børge G. Nordestgaard, M.D., D.M.Sc., and Stig E. Bojesen, M.D., Ph.D., D.M.Sc.

N Engl J Med 2012; 367:1792-1802November 8, 2012DOI: 10.1056/NEJMoa1201735

BACKGROUND

A reduction in the availability of cholesterol may limit the cellular proliferation required for cancer growth and metastasis. We tested the hypothesis that statin use begun before a cancer diagnosis is associated with reduced cancer-related mortality.

METHODS

We assessed mortality among patients from the entire Danish population who had received a diagnosis of cancer between 1995 and 2007, with follow-up until December 31, 2009. Among patients 40 years of age or older, 18,721 had used statins regularly before the cancer diagnosis and 277,204 had never used statins.

RESULTS

Multivariable-adjusted hazard ratios for statin users, as compared with patients who had never used statins, were 0.85 (95% confidence interval [CI], 0.83 to 0.87) for death from any cause and 0.85 (95% CI, 0.82 to 0.87) for death from cancer. Adjusted hazard ratios for death from any cause according to the defined daily statin dose (the assumed average maintenance dose per day) were 0.82 (95% CI, 0.81 to 0.85) for a dose of 0.01 to 0.75 defined daily dose per day, 0.87 (95% CI, 0.83 to 0.89) for 0.76 to 1.50 defined daily dose per day, and 0.87 (95% CI, 0.81 to 0.91) for higher than 1.50 defined daily dose per day; the corresponding hazard ratios for death from cancer were 0.83 (95% CI, 0.81 to 0.86), 0.87 (95% CI, 0.83 to 0.91), and 0.87 (95% CI, 0.81 to 0.92). The reduced cancer-related mortality among statin users as compared with those who had never used statins was observed for each of 13 cancer types.

CONCLUSIONS

Statin use in patients with cancer is associated with reduced cancer-related mortality. This suggests a need for trials of statins in patients with cancer.

A Conference Just in Time

文章日期：2013-05-16 20:29

A conference just in time
多年前當大學生，喜歡在實驗課之後晃到思亮館去聽研討會
我們總是開玩笑說，最少有機會去吃吃COFFEE BREAK的高級餐點
多年過去，對於COFFEE BREAK越來越挑，卻還是喜歡參加研討會
聽來自不同領域的聲音與想法，
算一天下來只聽到幾句令人心動的話
或者比比人家的簡報技巧，都是收穫，
就像今天這場2013 ILA-ASOL ASIA-PACIFIC RESEARCH FORUM
International law and dispute resolution: challenges in the Asia Pacific
[2013年國際法學會亞洲研究論壇- 亞太地區挑戰: 國際法與爭端解決]
來自日本美國越南台灣中國的國際法學者熱烈討論東海南海的問題
大概在其他地方很難有這麼多國家專家能平和的坐在一起討論這些問題
雖然偶爾聞到些許煙硝味

安排豐富的圓桌論壇，還有同步翻譯，口譯者技術高超獨撐全場!
主持人是陳長文律師，果然步調沉穩，有大師風範~
左邊惟一的女性則來自日本，她也說道，日本認為釣魚台是沒有主權爭議的地方

每每覺得，其實政府官員更該靜下心來聽幾場
(或者派人認真聽幾場也可以)，
也許對未來施政能更有願景，更有方向，更說得出所以然

[不管聽眾是小學生還是大專家，大家都喜歡圖片繽紛的簡報檔
只是看到連國際學者都有些採用WIKI的圖片檔時
就開始猶豫到底要不要跟學生說不要隨便引用WIKI的資訊了!]


不過，還是跟往常一樣，
首領帶著大批隨扈，發表完開幕詞就走了~~~~
於是，仍就是言者諄諄，聽者藐藐，實在可惜了~~
再說，在晶華酒店開會很花錢的，結果只喝了一杯咖啡!!!




還有就是，英文再好也請不要賣弄，

美國來的講者溫文的慢慢講，讓與會者能夠清楚了解
反倒是有些臺灣人，不是因為覺得英文不好，就越講越小聲，
就是英文太好，怕人家覺得他英文不夠好，說起話跟連珠炮般不休息，
這樣，對於在場的日本、越南等其他非英語系國的人，其實是不禮貌的。

誰能解讀中國的遠洋漁業?

誰能解讀中國的遠洋漁業?

文章日期：2013-05-15 14:07

    幾年前看過外國人寫有關台灣遠洋漁業的文章，不過就是找年報資料開始拼湊，嘗試了解臺灣，總不免有些誤解或偏見出現。最近幾年，臺灣自己學者寫的文章多了，此類情況就少得多。

      相對的，還是有人對中國有興趣，第一篇文章是2001年代Pauly 等人大膽揭露中國大陸高報沿近海漁業產量。此舉讓中國一度不願意提報漁獲量給FAO、繼而展開漁獲量調查，後來宣稱此虛報狀況已經有效改善。

     第二篇Marine Policy文章在度嘗試用各種資訊了解中國遠洋漁業與非洲的漁業合作關係，當然不免用現有統計資料推測(穿鑿附會)一番。

     第三篇Fish and Fisheries的文章，則是Pauly等人捲土重來，認為中國大陸低報遠洋漁業產量。

     但不知這高報與低報之間，到底中國的總產量、乃至全球的總產量是高是低呢？

     說真的，漁業的不確定性太高，比天氣還難預測的多，這些推估能有多準呢？科學家們心裡也有數，特別是參加過很多科學會議之後，發現許多科學其實也參雜政治色彩，就當是成就一篇篇PAPER吧!

 

Reg Watson & Daniel Pauly, 2001, Systematic distortions in world fisheries catch trends, Nature 414, 534-536 | doi:10.1038/35107050

Over 75% of the world marine fisheries catch (over 80 million tonnes per year) is sold on international markets, in contrast to other food commodities (such as rice). At present, only one institution, the Food and Agriculture Organization of the United Nations (FAO) maintains global fisheries statistics. As an intergovernmental organization, however, FAO must generally rely on the statistics provided by member countries, even if it is doubtful that these correspond to reality. Here we show that misreporting by countries with large fisheries, combined with the large and widely fluctuating catch of species such as the Peruvian anchoveta, can cause globally spurious trends. Such trends influence unwise investment decisions by firms in the fishing sector and by banks, and prevent the effective management of international fisheries.

 

Mallory, T. G. (2013). China's distant water fishing industry: Evolving policies and implications. Marine Policy, 38(0), 99-108. doi: http://dx.doi.org/10.1016/j.marpol.2012.05.024

Abstract

This article examines China's distant water fishing industry, with a focus on China's bilateral fisheries access agreements in Africa. The article argues that China largely conforms to international norms and rules on sustainable fisheries, but that challenges remain in efforts to work with China on the sustainable management of fish stocks. Developed countries contribute to China's policies and behavior in international fisheries in both positive and negative ways.

Pauly, D., D. Belhabib, R. Blomeyer, W. W. W. L. Cheung, A. M. Cisneros-Montemayor, D. Copeland, S. Harper, V. W. Y. Lam, Y. Mai, F. Le Manach, H. Österblom, K. M. Mok, L. van der Meer, A. Sanz, S. Shon, U. R. Sumaila, W. Swartz, R. Watson, Y. Zhai, and D. Zeller. 2013. China's distant-water fisheries in the 21st century. Fish and Fisheries: doi: 10.1111/faf.12032.

We conservatively estimate the distant-water fleet catch of the People's Republic of China for 2000–2011, using a newly assembled database of reported occurrence of Chinese fishing vessels in various parts of the world and information on the annual catch by vessel type. Given the unreliability of official statistics, uncertainty of results was estimated through a regionally stratified Monte Carlo approach, which documents the presence and number of Chinese vessels in Exclusive Economic Zones and then multiplies these by the expected annual catch per vessel. We find that China, which over-reports its domestic catch, substantially under-reports the catch of its distant-water fleets. This catch, estimated at 4.6 million t year−1 (95% central distribution, 3.4–6.1 million t year−1) from 2000 to 2011 (compared with an average of 368 000 t·year−1 reported by China to FAO), corresponds to an ex-vessel landed value of 8.93 billion € year−1 (95% central distribution, 6.3–12.3 billion). Chinese distant-water fleets extract the largest catch in African waters (3.1 million t year−1, 95% central distribution, 2.0–4.4 million t), followed by Asia (1.0 million t year−1, 0.56–1.5 million t), Oceania (198 000 t year−1, 144 000–262 000 t), Central and South America (182 000 t year−1, 94 000–299 000 t) and Antarctica (48 000 t year−1, 8 000–129 000 t). The uncertainty of these estimates is relatively high, but several sources of inaccuracy could not be fully resolved given the constraints inherent in the underlying data and method, which also prevented us from distinguishing between legal and illegal catch.

已開發與開發中國家漁業合作的爭論~~

已開發與開發中國家漁業合作的爭論~~

文章日期：2013-05-14 11:48

Gagern, A. and J. van den Bergh (2013). "A critical review of fishing agreements with tropical developing countries." Marine Policy 38(0): 375-386.
心得
-從魚線的盡頭開始，就有不少聲音質疑雙邊漁業合作的模式，美其名能夠充分利用海洋資源、也提供開發中國家經濟資助。
-此篇文章作者(來自歐洲西班牙等國的環保團體)認為許多漁業協定中的遠洋漁業國家已經越來越不負責任(這是在說誰呢)，對於資源傷害日增，而沿岸國受益有限!
-這些文章裡面多少會提到台灣，但因為資訊不充分，往往顯得片段
 ==>我們真的應該好好寫篇有關台灣遠洋漁業雙邊多邊合作的"貢獻"~
Abstract
 Many African, Caribbean and Pacific (ACP) countries sell fishing licenses to distant water fleets. Fishing agreements have the potential to improve the performance of local fishing sectors. They create income that can be reinvested into domestic industries and often go along with partnerships in management and enforcement. However, many fishing agreements run a serious risk of undermining sustainable resource management. The present study critically reviews trends in distant water fishing as well as identifies those tropical host countries most dependent on fishing agreements. It is shown that traditional, more responsible distant water fleets (DWFs) are being displaced by less responsible, low-cost DWFs and that the most vulnerable host countries are small coastal states with large exclusive economic zones that lack the ability to benefit from value adding processes associated with fishing. The results suggest that the once-promising concept of fishing agreements is gradually posing a threat to both economic development and environmental sustainability of ACP countries.

太平洋島國絕對不是省油的燈

文章日期：2013-05-14 12:11

Havice, E. and K. Reed (2012). "Fishing for Development? Tuna Resource Access and Industrial Change in Papua New Guinea." Journal of Agrarian Change 12(2-3): 413-435.

心得
  PNG(巴布亞紐新幾內亞，業者又稱之巴新，可不是巴西)，是在國內"赫赫有名"的太平洋島國，早期台灣圍網船(還有其他國家)付費入漁，彼此各取所需，相安無事。
 近來，PNG不再只要"魚"，更想擁有釣竿，這下子開始要求投資罐頭廠、使用當地勞工，於是，重新改寫漁業合作的模式，
   未來將如何發展呢？to be continued.
Abstract
 Papua New Guinea (PNG) is an island state with sovereign rights over valuable tuna resources. Historically, PNG captured value from tuna only by charging licensing fees to foreign fishing fleets, which relegated PNG as a source of raw material for the global tuna industry. To capture more value from tuna – including much-needed jobs and infrastructure – the PNG government now offers firms that invest in domestic tuna processing plants strategic, long-term fishing licences. This strategy of ‘obligating embeddedness’ enables PNG to reorder the international division of labour in the canned tuna sector, but socio-economic outcomes are shaped by competition within the global tuna industry, the core business strategies of foreign firms and domestic conditions in PNG. Ultimately, a state's right to control the terms of access to tuna is not synonymous with its ability to shape the local-level consequences that emerge as firms comply. These findings reveal the peculiar nature of state sovereignty over pelagic marine resources and the complications of exploiting them to achieve domestic economic and social objectives.

新北市可以釣魚的漁港不少

新北市可以釣魚的漁港不少! (不能釣的港也大有人去!)

文章日期：2013-05-14 08:26

在新北市非開放港區下竿 最高罰15萬

【聯合報╱記者黃福其／板橋報導】 2013.05.14 03:37 am

新北市海岸有30處漁港，市府僅公告開放10處漁港部分港區供垂釣；但許多釣友任意在非開放港區或其他漁港下竿，不但妨害漁船、港區車輛進出，還曾發生甩鉛垂、丟酒瓶擊傷漁民等糾紛。市府農業局已與海巡署、警方組成聯合稽查小組，本月至10月鎖定13座漁港加強稽查違法下竿，若釣友拒絕配合，依漁港法可開罰3萬至15萬元。 新北市農業局自1996年配合漁港法修法，在全市30處漁港擇定淡水第二、後厝、草里、中角、水尾、野柳、深澳、水湳洞、和美及福隆等10處漁港，公告部分不影響漁船進出的港區可下竿港釣。 但不少釣客卻常在10處漁港的非公告港釣區下竿，甚至其餘20處漁港也常見釣客身影，以富基、磺港、澳底最多。尤其魚況佳時，釣客蜂擁而至，車輛在港區亂停，屢生糾紛，以夏季晚間最常見。 萬里區漁會總幹事許順發舉例說，野柳港曾發生港區停滿釣客的車，釣客多到連攤販都趕來作生意，不但造成髒亂，還導致接運紅蟳的水車受阻，無法進碼頭接運，船上紅蟳死了不少，漁民平白損失。 另曾有漁船進港受阻，與堤岸上釣客喊話爭吵時，釣客群裡突然拋出一只酒瓶砸傷漁民，因查不到丟瓶者而不了了之。 他說，漁民熱情好客，不會排斥守規矩的釣客，但不守規矩的釣客讓人深惡痛絕，除了市府加強稽查，也希望釣客自制。 漁管處長汪昭華說，夏季白帶魚、硬尾仔或鯖魚等洄游性魚類追逐小魚進漁港，釣客就會湧入，造成漁民困擾、作業受阻；去年起首度進行聯合稽查，共開出約500張勸導單，今年自本月起再度聯合稽查，每周至少一次。

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