Tuesday, 25 July 2017

Conformity index (CI)

It is defined as the ratio of the treated volume to the PTV (planning target volume) [1]. It is a tool for treatment plan analysis in conformal radiotherapy [2].
Bibliographic references:
[1] International Commission on Radiation Units and Measurements. ICRU Report 62. Prescribing, Recording and Reporting Photon Beam Therapy. Supplement to ICRU Report 50. Bethesda, MD: ICRU; 1999.
[2] Kataria T, Sharma K, Subramani V, et al. Homogeneity Index: An objective tool for assessment of conformal radiation treatments. J Med Phys. 2012 Oct;37(4):207-13. Available at https://doi.org/10.4103/0971-6203.103606.

Sunday, 18 June 2017

PARP (poly-[adenosine diphosphate-ribose] polymerase)

Poly-(ADP)-ribose polymerase is «a family of proteins involved in a number of cellular processes involving mainly DNA [deoxyribonucleic acid] repair and programmed cell death. The PARP family comprises 17 members (10 putative). They have all very different structures and functions in the cell. One important function of PARP is assisting in the repair of single-strand DNA breaks [1]». It is «a SSB [single-strand break] detector protein» [2].
«Drugs which inhibit (...) PARP (...) are particularly effective in tumors with HR [homologous recombination] deficiencies, such as breast tumors with BCRA1 or BCRA2 [breast cancer 1 or 2] deficiencies. (...) probably (...) PARP inhibitors suppress SSB repair, resulting in greater numbers of unrepaired SSBs, which therefore have a greater chance of hitting a replication fork. Under normal circumstances, the resulting DSB [double-strand break] would be repaired by HR, so the absence or reduction of this backup pathway leads to a substantial increase in DSBs and thus cellular lethality [2].»
Bibliographic references:
[1] Tortora, G., Bergmann, L., Lindh, M., Cervantes-Ruiperez, A., Dziadziuszko, R., Eckhardt, S., Lenz, H., Normanno, N., Perez, D., Scarpa, A., Syrigos, K., Tabernero, J. and Troiani, T. (2014). ESMO glossary in molecular biology of cancer. Viganello-Lugano, Switzerland: European Society for Medical Oncology, p.127.
[2] Joiner, M. and Kogel, A. (2009). Basic clinical radiobiology. 1st ed. Boca Raton, Florida: CRC Press, p.24.

Monday, 15 May 2017


It is the debulking, or reduction «(...) of the size of, a cancerous tumor. Surgery and radiation therapy are two common cytoreductive treatments used to debulk tumors. Debulking means to remove as much of the cancer as possible [1].» «(...) "cytoreduction" refers to reducing the number of tumor cells [2].» «Tumor debulking may increase the chance that chemotherapy or radiation therapy will kill all the tumor cells. It may also be done to relieve symptoms or help the patient live longer [3].» 
Bibliographic references:
[1] CancerCenter.com. (2017). Cytoreductive Therapy : Cancer Glossary | CTCA. [online] Available at: http://www.cancercenter.com/terms/cytoreductive-therapy/ [Accessed 15 May 2017].
[2] En.wikipedia.org. (2017). Debulking. [online] Available at: https://en.wikipedia.org/wiki/Debulking [Accessed 15 May 2017].
[3] National Cancer Institute. (n.d.). NCI Dictionary of Cancer Terms. [online] Available at: https://www.cancer.gov/publications/dictionaries/cancer-terms?cdrid=46635 [Accessed 15 May 2017].

Wednesday, 10 May 2017

Adjuvant therapy

It is an «additional cancer treatment given after the primary treatment to lower the risk that (...) cancer will come back. Adjuvant therapy may include chemotherapy, radiation therapy, hormone therapy, targeted therapy, or biological therapy.»
Bibliographic reference: National Cancer Institute. (n.d.). NCI Dictionary of Cancer Terms. [online] Available at: https://www.cancer.gov/publications/dictionaries/cancer-terms?CdrID=45587 [Accessed 10 May 2017].

Monday, 8 May 2017


It «(...) is one of the most commonly mutated tumor suppressors whose function is to regulate genes that control both cell cycle checkpoints and (...) apoptosis. Consequently, activation of p53 after irradiation can lead either to a block in proliferation or directly to cell death. (...) in unstressed normal cells, p53 is made continuously but is degraded and thus non-functional. Following DNA [deoxyribonucleic acid] damage, ATM [ataxia telangiectasia mutated] phosphorylates both p53 and MDM2 [murine double minute 2]. These events destabilize the p53-MDM2 interaction, and (...) p53 protein is no longer degraded. In addition to this stabilization, direct phosphorylation of p53 by ATM leads to its activation as a transcription factor and thus the upregulation of its many target genes [1].»
«Cells irradiated in the G1 phase are influenced by the action of p53. ATM protein is activated by double-strand DNA breaks and phosphorylates both MDM2 and p53. This leads to stabilization and activation of p53, which induces genes that can promote apoptosis (Bax [Bcl-2-associated X], Puma [p53 upregulated modulator of apoptosis]) and induces checkpoints. (...) cells are blocked at the G1/S border [1].»
Is has «(...) a mass of 53 kDa (hence its name); p53 protein is normally induced in cells having undergone DNA damage, (...); its principal effects are to stop the cell cycle and prevent the cell from undergoing mitosis; thus, DNA mutations/damage can either be repaired or a damaged cell can be eliminated from the organism, for example via apoptosis. p53 is also known as the guardian of the genome [2].»
Bibliographic references:
[1] Joiner, M. and Kogel, A. (2009). Basic clinical radiobiology. 1st ed. Boca Raton, Florida: CRC Press, p.17.
[2] Tortora, G., Bergmann, L., Lindh, M., Cervantes-Ruiperez, A., Dziadziuszko, R., Eckhardt, S., Lenz, H., Normanno, N., Perez, D., Scarpa, A., Syrigos, K., Tabernero, J. and Troiani, T. (2014). ESMO glossary in molecular biology of cancer. Viganello-Lugano, Switzerland: European Society for Medical Oncology, p.117.

Saturday, 18 March 2017


It's the relationship between two sets with different characteristics. The numerator is not included in the denominator. It is different from proportion.


It's the relationship between the number of individuals who have a characteristic and the total population. The numerator is included in the denominator. It is different from ratio.

Saturday, 25 February 2017

Symbols with short codes

In: Awesome Daily Staff. StumbleUpon. Stumbleuponcom. 2014. Available at: http://www.stumbleupon.com/su/2XigqH. Accessed February 25, 2017.

Monday, 20 February 2017

Lower urothelium (or lower transitional cell epithelium)

It coats the interior walls of the «urinary bladder, the ureters, the superior urethra, and the prostatic and ejaculatory ducts of the prostate
Bibliographic reference: Transitional epithelium. Enwikipediaorg. 2017. Available at: https://en.wikipedia.org/wiki/Transitional_epithelium. Accessed February 20, 2017.

Upper urothelium (or upper transitional cell epithelium)

It coats the interior walls of the pyelocaliceal cavities and ureter.
Bibliographic references: Rouprêt M, Babjuk M, Böhle A, et al. Upper Urinary Tract Urothelial Cell Carcinoma. EAU - European Association of Urology. 2017. Available at: https://uroweb.org/guideline/upper-urinary-tract-urothelial-cell-carcinoma/#3. Accessed February 20, 2017.

Urological organs

«The organs under the domain of urology include the kidneysadrenal glandsuretersurinary bladderurethra, and the male reproductive organs (testesepididymisvas deferensseminal vesiclesprostate, and penis).»
Bibliographic reference: Urology. Enwikipediaorg. 2016. Available at: https://en.wikipedia.org/wiki/Urology. Accessed February 20, 2017.


«Reassortment. The radiosensitivities of cells vary according to phases of the cell cycle.» «The duration of the cell cycle phases are: G1 = 1.5–14 h, S = 6–9 h, G2 = 1–5 h, and M = 0.5–1 h. The most sensitive are M and G2. The most resistant is S.» «Cells in the resistant phases of the cell cycle may progress into the sensitive phases in the next fraction, when radiation is given in fractions. Therefore, the probability of tumor cells to be exposed to radiation at sensitive phases increases. This probability will continue for the whole treatment, and the benefit from radiation will
Bibliographic reference: Beyzadeoglu M, Ozyigit G, Selek U. Radiation Oncology. 1st ed. Berlin: Springer; 2012:112-114.

Saturday, 7 January 2017

Radiodermatitis or radiation dermatitis

It «is a cutaneous inflammatory reaction to exposure to biologically effective levels of ionizing radiation» [1]. It «can range from erythema to wet desquamation of the skin (tissue sloughing) in acute form; tissue atrophy, fibrosis, and permanent scarring in chronic form. Permanent changes in skin pigmentation can also occur» [2].
Bibliographic references:
[1] Radiodermatitis. (n.d.) Miller-Keane Encyclopedia and Dictionary of Medicine, Nursing, and Allied Health, Seventh Edition. (2003). Retrieved January 7 2017 from http://medical-dictionary.thefreedictionary.com/radiodermatitis.
[2] Radiation dermatitis. (n.d.) Medical Dictionary for the Health Professions and Nursing. (2012). Retrieved January 7 2017 from http://medical-dictionary.thefreedictionary.com/radiation+dermatitis.

Saturday, 26 November 2016

Missing data or missing values

In statistics, they «occur when no data value is stored for the variable in an observation [1].» They are «values of variables within data sets which are not known [2].»
Bibliographic references:
[1] Missing data [Internet]. En.wikipedia.org. 2016 [cited 19 November 2016]. Available from: https://en.wikipedia.org/wiki/Missing_data.
[2] Statistics Glossary: M [Internet]. Statsoft.com. 2016 [cited 19 November 2016]. Available from: http://www.statsoft.com/textbook/statistics-glossary/m#Missing values.

Standard error (SE)

«These are the SEs for the descriptive statistics. The SE gives some idea about the variability possible in the statistic [1].» It «(...) is a measure of the variability of a statistic. It is an estimate of the standard deviation of a sampling distribution [2].» It «(...) is the standard deviation of the sampling distribution of a statistic, (...) (Everitt BS, 2003, cited in [3]). «The SE of the mean [SEM] (...) is the theoretical standard deviation of all sample means of size n drawn from a population and depends on both the population variance (sigma) and the sample size (n) (...) [4].» «The SEM can be seen to depict the relationship between the dispersion of individual observations around the population mean (the standard deviation), and the dispersion of sample means around the population mean (the SE). Different samples drawn from that same population would in general have different values of the sample mean, so there is a distribution of sampled means (with its own mean and variance). (...) As the sample size increases, the dispersion of the sample means clusters more closely around the population mean and the SE decreases [3].» «The SE depends on three factors: the number of observations in the population (N), the number of observations in the sample (n), and the way that the random sample is chosen. If the population size is much larger than the sample size, then the sampling distribution has roughly the same SE, whether we sample with or without replacement . On the other hand, if the sample represents a significant fraction (say, 1/20) of the population size, the SE will be noticeably smaller, when we sample without replacement [2].» «The SE of the proportion (...) is the standard deviation of the distribution of the sample proportion over repeated samples [4].»
Bibliographic references:
[1] Annotated SPSS Output: Descriptive statistics [Internet]. Ats.ucla.edu. 2016 [cited 20 November 2016]. Available from: http://www.ats.ucla.edu/stat/spss/output/descriptives.htm.
[2] Statistics Dictionary [Internet]. Stattrek.com. 2016 [cited 20 November 2016]. Available from: http://stattrek.com/statistics/dictionary.aspx.
[3] Standard error [Internet]. En.wikipedia.org. 2016 [cited 20 November 2016]. Available from: https://en.wikipedia.org/wiki/Standard_error#cite_note-1.
[4] Statistics Glossary: S [Internet]. Statsoft.com. 2016 [cited 20 November 2016]. Available from: http://www.statsoft.com/textbook/statistics-glossary/s#Standard.

Sunday, 13 November 2016

Confidence interval (CI)

It is «a range of values, calculated from the sample observations, that is believed, with a particular probability, to contain the true parameter value» [1]. It is used «to express the degree of uncertainty associated with a sample statistic. A confidence interval is an interval estimate combined with a probability statement.» One «might describe the interval estimate as a "95% confidence interval". This means that if» one «used the same sampling method to select different samples and computed an interval estimate for each sample,» one «would expect the true population parameter to fall within the interval estimates 95% of the time» [2]. «Precision is taken to be the narrowness of the confidence interval. (...) The interval estimate is an expression of the uncertainty surrounding the point estimate and derives mainly from sampling variation as well as measurement variation/error. In general, the degree of uncertainty is inversely related to the size of the study. On one hand, if a study is too small, the uncertainty may increase to a level considered to be undesirable or useless. On the other, as the study size increases, the degree of uncertainty decreases, and the interval estimate becomes narrower» [3]. «Confidence intervals are preferred to point estimates and to interval estimates, because only confidence intervals indicate the precision of the estimate and the uncertainty of the estimate» [2].
Bibliographic references:
[1] Everitt, B. and Skrondal, A. (2010). The Cambridge dictionary of statistics. 4th ed. Cambridge, UK: Cambridge University Press.
[2] Stattrek.com. (2016). Statistics Dictionary. [online] Available at: http://stattrek.com/statistics/dictionary.aspx [Accessed 13 Nov. 2016].
[3] Broeck, J. and Brestoff, J. (2013). Epidemiology: Principles and Practical Guidelines. 1st ed. Dordrecht: Springer.

Saturday, 12 November 2016

Standard deviation (σ or s)

«The standard deviation of a population is denoted by σ and the standard deviation of a sample, by s [1].» It is a measure of dispersion or absolute variability [2,3] in original units (unit of measurement equal to that of the mean). It is the positive square root of the variance (σ2 or s2 or Var[X]). It «is useful as a measure of variation within a given set of data» [4]. «A small value of the standard deviation indicates that most values are close to the sample mean. A large value of the standard deviation indicates many values are far from the sample mean. Other words which are used to convey the concept of the standard deviation are “spread” and “scale.”» It is «the “typical” spread of observations about the sample mean [2].» It «is a numerical value used to indicate how widely individuals in a group vary. If individual observations vary greatly from the group mean, the standard deviation is big; and vice versa [1].»
Bibliographic references:
[1] Stattrek.com. (2016). Statistics Dictionary. [online] Available at: http://stattrek.com/statistics/dictionary.aspx [Accessed 13 Nov. 2016].
[2] Supino, P. and Borer, J. (2012). Principles of research methodology. 1st ed. New York, NY: Springer.
[3] Doi, S. and Williams, G. (2013). Methods of clinical epidemiology. 1st ed. Berlin: Springer.
[4] Daniel, W. and Cross, C. (2013). Biostatistics: a foundation for analysis in the health sciences. 10th ed. Danvers, Massachusetts, USA: John Wiley & Sons, Inc.