ssh翻墙方法

中国的“网络长城”把许多境外网站封锁了，比如blogspot，其它众所周知的有facebook, twitter, youtube等。Wikipedia也长期被封，在广大网民压力下最终还是解禁了。
最近需要解决两个网络问题:(1)网络封锁问题；(2)学术期刊网站IP帮定授权问题。发现强大的ssh提供socks5转发功能，可完美地解决这两个问题，当然前提是需要在境外拥有ssh类型账号。具体做法如下：
(1) ssh -D 9000 user@remote_machine
其中9000是端口号，当然可选择其它任意端口。
(2) 在Firefox中设置Manual proxy configuration中SOCKS Host为localhost, port为9000。
(3) 在地址栏中输入about:config,设置network.proxy.socks_remote_dns为true.

如果第3项不设置的话，访问被封锁网站是ssh联接会出现如下类似错误
channel 1: open failed: connect failed: Connection refused。只能通过IP访问。

Biomarkers for Cancer: What have been for biomakers?

1. Jones HB (1848) On a new substance occuring in the urine with mollities ossium. Phil Trans R Soc Lond 138: 55–62
1848, light chain of immunoglobulin in the urine, identified in 75% of patients with myeloma;

1960s
2. Abelev GI et al. (1963) Production of embryonal alpha-globulin by transplantable mouse hepatomas.
Transplantation 1: 174–180
alfa-fetoprotein

3. Gold P and Freedman SO (1965) Specific carcinoembryonic antigens of the human digestive system. J Exp Med 122: 467–481
carcinoembryonic antigen (CEA)

1980s
4. Bast RC Jr et al. (1981) Reactivity of a monoclonal antibody with human ovarian carcinoma. J Clin Invest 68: 1331–1337
carbohydrate antigen (CA) 125 for ovarian epithelial cancer.

5. Papsidero LD et al. (1980) A prostate antigen in sera of prostatic cancer patients. Cancer Res 40: 2428–2432
prostate-specific antigen (PSA [KLK3]) for prostate cancer

6. Diamandis EP et al. (2002) Tumor Markers: Physiology, Pathobiology, Technology, and Clinical Applications. Washington, DC: AACC Press
Alfa-fetoprotein Germ-cell hepatoma 1963
- Diagnosis
- Differential diagnosis of NSGCT (nonseminomatous germ cell tumor)
- Staging
- Detecting recurrence
- Monitoring therapy

7.
Melvin KE et al. (1971) Early diagnosis of medullary carcinoma of the thyroid gland by means of calcitonin assay. N Engl J Med 285: 1115–1120
Sturgeon C (2002) Practice guidelines for tumor marker use in the clinic. Clin Chem 48: 1151–1159

Calcitonin Medullary thyroid carcinoma
- Diagnosis
- Monitoring therapy

8.
Bast RC Jr et al. (1981) Reactivity of a monoclonal antibody with human ovarian carcinoma. J Clin Invest 68: 1331–1337
Diamandis EP et al. (2002) Tumor Markers: Physiology,Pathobiology, Technology, and Clinical Applications. Washington, DC: AACC Press
CA125 Ovarian 1981
- Prognosis
- Detecting recurrence
- Monitoring therapy

9.
Bast RC Jr et al. (2001) 2000 update of recommendations for the use of tumor markers in breast and colorectal cancer: clinical practice guidelines of the American Society of Clinical Oncology. J Clin Oncol 19: 1865–1878
Kufe D et al. (1984) Differential reactivity of a novel monoclonal antibody (DF3) with human malignant versus benign breast tumors. Hybridoma 3: 223–232
Hilkens J et al. (1984) Monoclonal antibodies against human milk-fat globule membranes detecting differentiation antigens of the mammary gland and its tumors. Int J Cancer 34: 197–206
CA 15-3 Breast
1984–5
- Monitoring therapy

10.
Koprowski H et al. (1979) Colorectal carcinoma antigens detected by hybridoma antibodies. Somatic Cell Genet 5: 957–971
Ludwig JA and Weinstein JN (2005) Biomarkers in cancer staging, prognosis and treatment selection. Nat Rev Cancer 5: 845–856
CA 19-9 Pancreatic 1979
- Monitoring therapy

11.
Ludwig JA and Weinstein JN (2005) Biomarkers in cancer staging, prognosis and treatment selection. Nat Rev Cancer 5: 845–856
Bast RC Jr et al. (2001) 2000 update of recommendations for the use of tumor markers in breast and colorectal cancer: clinical practice guidelines of the American Society of Clinical Oncology. J Clin Oncol 19: 1865–1878
Diamandis EP et al. (2002) Tumor Markers: Physiology, Pathobiology, Technology, and Clinical Applications. Washington, DC: AACC Press
Carcinoembryonic antigen Colon 1965
- Monitoring therapy
- Prognosis
- Detecting recurrence
- Screening for hepatic metastases

12.
Bast RC Jr et al. (2001) 2000 update of recommendations for the use of tumor markers in breast and colorectal cancer: clinical practice guidelines of the American Society of Clinical Oncology. J Clin Oncol 19: 1865–1878
McGuire WL et al. (1977) Current status of estrogen and progesterone receptors in breast cancer. Cancer 39:2934–2947
ER (estrogen receptor) and PgR (progesterone receptor) Breast
1970s
- Select patients for endocrine therapy

13.
Bast RC Jr et al. (2001) 2000 update of recommendations for the use of tumor markers in breast and colorectal
cancer: clinical practice guidelines of the American Society of Clinical Oncology. J Clin Oncol 19: 1865–1878
Coussens L et al. (1985) Tyrosine kinase receptor with extensive homology to EGF receptor shares chromosomal location with neu oncogene. Science 230: 1132–1139
Yamamoto T et al. (1986) Similarity of protein encoded by the human c-erb-B-2 gene to epidermal growth factor receptor. Nature 319: 230–234
HER2 Breast1985–6
- Select patients for trastuzumab therapy

14.
Bagshawe KD et al. (1980) Markers in gynaecological cancer. Arch Gynecol 229: 303–310
Diamandis EP et al. (2002) Tumor Markers: Physiology, Pathobiology, Technology, and Clinical Applications. Washington, DC: AACC Press
Human chorionic gonadotropin-β Testicular 1938
- Diagnosis
- Staging
- Detecting recurrence
- Monitoring therapy

15.
Diamandis EP et al. (2002) Tumor Markers: Physiology, Pathobiology, Technology, and Clinical Applications. Washington, DC: AACC Press
Hill BR and Levi C (1954) Elevation of a serum component in neoplastic disease. Cancer Res 14: 513–515
Lactate dehydrogenase Germ cell 195491
- Diagnosis
- Prognosis
- Detecting recurrence
- Monitoring therapy

16.
Diamandis EP et al. (2002) Tumor Markers: Physiology, Pathobiology, Technology, and Clinical Applications. Washington, DC: AACC Press
Wang MC et al. (1979) Purification of a human prostate specific antigen. Invest Urol 17: 159–163
Prostate-specific antigen Prostate 197992
- Screening (with DRE (digital rectal examination) )
- Diagnosis (with DRE)

17.
Carayanniotis G and Rao VP (1977) Searching for pathogenic epitopes in thyroglobulin: parameters and caveats. Immunol Today 18: 83–88
Sturgeon C (2002) Practice guidelines for tumor marker use in the clinic. Clin Chem 48: 1151–1159
Thyroglobulin Thyroid 195693
- Monitoring

Biomarkers for Cancer: What can be biomarkers?

1. Vathany Kulasingam and Eleftherios P Diamandis, Nature Clinical Practice Oncology, 2008, 5(10), 588-599.

- DNA
- mRNA (messenger RNA)
- proteins
- metabolites
- processes
(such as apoptosis, angiogenesis or proliferation)

Biomarkers for Cancer: What is Biomarker?

1. Vathany Kulasingam and Eleftherios P Diamandis, Nature Clinical Practice Oncology, 2008, 5(10), 588-599.

diagnostic (screening) biomarker
A marker that is used to detect and identify a given type of cancer in an individual. These markers are expected to have high specificity and sensitivity; for example, the presence of Bence–Jones protein in urine remains one of the strongest diagnostic indicators of multiple myeloma.

Prognostic biomarker
This type of marker is used once the disease status has been established. These biomarkers are expected to predict the probable course of the disease including its recurrence, and they therefore have an important influence on the
aggressiveness of therapy. For example, in testicular teratoma, human chorionic gonadotropin and alfa-fetoprotein levels can discriminate two groups with different survival rates.

stratification (predictive) biomarker
This type of marker serves to predict the response to a drug before treatment is started. This marker classifies individuals as likely responders or nonresponders to a particular treatment. These biomarkers mainly arise from array-type experiments that make it possible to predict clinical outcome from the molecular characteristics of a patient’s tumor.

Biomarkers for Cancer : Facts on Cancer

In this post and the following ones, I will summary the facts about what I learned about biomarkers, particularly cancer biomarkers.

1.. Jemal A et al. (2007) Cancer statistics, 2007. CA Cancer J Clin 57: 43–66

Cancer continues to be a major cause of morbidity and mortality among men and women. In the US in 2006, over 1.4 million new cases of cancer were diagnosed and over half a million people died from this disease; the disease accounts for approximately 25% of all deaths in the US each year.

Getting Married ~

I am going to get married soon with the girl that I mentioned in a previous post in the past May. We planned to register on Sept. 10th, Chinese Teacher's Day, since both us are teachers. She is in-charge for the begging, primary school education, and I am for the concluding, college education. The wedding ceremony was planned on the 30th this January (Lunar calendar, Layue Shiliu, Dec. 16th).
Thank God for letting us meet, know each other and join together. Although the future life will be definitely not always smooth, we see our lives will be tied forever.

Develop a Cheminformatics Platform with Mathematica

My first encounter with Mathematica happened more than 12 years ago. Since 2001, I have intensively used it as a tool in my research work. Till now, i virtually use it on a daily basis for many different tasks. I don't think I have every aspects of the tool, but I do think my understanding of Mathematica is beneficial to researchers who are interested in learning Mathematica. I feel the necessity to organize my previous codes into a tutorial for two reasons. The first is that there are no good if any books available on market on the application in the cheminformatics or bioinformatics, particularly for those intermediate users who have known the basics of Mathematica but want to sharpen their tools. The other reason is that I have the motive to clean up my codes and thoughts for the development of my research. This tutorial is intended to show the essentials of Mathematica through the anatomy of projects from design to implementation. I see many users (and some tutorials books as well) writing codes in the style of C, Fortran or other programming languages for which they have been familiar with. To me, a good programming style is extremely important to master the language, in terms of development time, efficiency and terseness. A rule of thumb is that the development process helps you to organize your thoughts and to let you understand the problems at a deeper level, instead of making you feel cumbersome and work as a laborer. On the surface, we could think Mathematica as an advanced dialect of Lisp. "Advanced" here means millions of built-in functions and packaged as the extension of the kernel delivered with the language.
My plan is to include the following chapters.
Chapter 1. Introduction
Chapter 2. Compounds collection database
Chapter 3. Graph theory representation of molecules and its applications
Chapter 4. Descriptor development, similarity comparison, and virtual screening
Chapter 5. CIF parser, molecular structural operations and interface to quantum mechanics calculation
Chapter 6. Spectra processing (including both Image and Graph)
Chapter 7. Schroedinger equation solutions
Appendices
Subject Index