Friday, July 29, 2016

Entropy-based feature extraction and decision tree induction for breast cancer diagnosis with standardized thermograph images

Entropy-based feature extraction and decision tree induction for breast cancer diagnosis with standardized thermograph images

by
Ming-Yih Leea,
Chang Gung University, Graduate Institute of Medical Mechatronics

and

Chi-Shih Yanga,
Lee-Ming Institute of Technology, Department of Mechanical Engineering

a b s t r a c t

In this study, a computer-assisted entropy-based feature extraction and decision tree induction
protocol for breast cancer diagnosis using thermograph images was proposed. First,
Beier–Neely field morphing and linear affine transformationwere applied in geometric standardization
for whole body and partial region respectively. Gray levels of pixel population
at the same anatomical position were statistically analyzed for abnormal region classification.
Morphological closing and opening operations were used to identify unified abnormal
regions. Three types of 25 feature parameters (i.e. 10 geometric, 7 topological and 8 thermal)
were extracted for parametric factor analysis. Positive and negative abnormal regions
were further reclassified by decision trees to induce the case-based diagnostic rules. Finally,
anatomical organ matching was utilized to identify the corresponding organ with the positive
abnormal regions. To verify the validity of the proposed cased-based diagnostic protocol,
71 and 131 female patients with and without breast cancer were analyzed. Experimental
results indicated that 1750 abnormal regions (703 positive and 1047 negative) were detected
and 822 branches were broken down into the decision space. Fourteen branches were found
to have more than 4 positive abnormal regions. These critical diagnostic paths with less
than 10% of positive abnormal regions (61/703 = 8.6%) can effectively classify more than half
of the cancer patients (42/71 = 59.2%) in the abovementioned 14 branches.

1. Introduction

Thermographs were designed to capture the infrared ray from
objects if its temperature were higher than the absolute zero
degree. This special characteristic was utilized to display the
metabolic heat that was dissipated from the skin surface
of human body, especially for the medical thermographs of
breast cancer. The pathological mechanisms of breast cancer
are that cancer cells produce nitric oxide (NO) at proliferative
stage [1]. This chemical material will interfere with the
neuronal control of blood vessel flow and lead up to regional
vasodilatation in the early stage of cancerous cell growth. This
angiogenesis facilitates a local temperature rise about several
years earlier than the tumor forming. And even deep
breast lesions seem to have the ability to induce changes
in skin temperature [2]. The abovementioned characteristics
of breast cancer tissue specifically imply some meaningful
graphic patterns (i.e., geometric size and location, topological
shape or thermal features) in thermograph images. Hence
thermographs are better suited than mammography for early
breast cancer prediction even when the tumor is taking shape.

Medical thermographs become a suitable tool for early warning.
This key point of this paper emphasizes the usage of
thermal image to diagnose breast cancer. The algorithm with
high concentration rate of cancer patients in a few rule paths
was proposed. The effect of early diagnosiswas not in the field
of discussion.

Besides, there exists highly false positive prediction due
to the little difference of thermographs between the normal
subject (negative case) and cancer patient (positive case) as
shown in Fig. 1. Due to the lack of effective image processing
methods to support the use of thermographs, the credibility
and sensitivity of thermographs are still in question in
medical applications. Medical thermograph has been quiescent
for a long time due to the limitation of hardware and
software. The hardware limitation was broken recently by the
advancement of the uncooled focal plane array (UFPA) photo
detector and personal computer, and the software limitation
was also overcame by the progress of analyzing algorithms. All
the signs indicate that the infrared thermal images will be successful
in medical usage [3]. Recently, large scale of case-based
studies showed that thermographs had an average sensitivity
and specificity of 90% as the significant biological risk marker
for the existence of breast tumor [4]. But all these analytical
techniques still come to a standstill with the traditional statistics
and manual evaluation. The parametric analysis on ROI
(region of interest) of hot spots and cold spots in the abnormal
regions still remain unsolved.

Different medical applications with thermographs were
received attention from various research groups. To name a
few, female breast cancer [4,5], pain management [6] or diabetic
foot [7]. Also various digitally analytical methods for
image processing algorithms were proposed, such as abnormal
statistics method [8], the thermal asymmetric method
[9,10] and the image standardization and anatomical matching
methods [11], etc. Although these image processing
techniques are important in medical thermograph analysis,
lots of these methods still lack delicate algorithms or cannot
totally be a part of the computer-assisted diagnosis solution.

The aim of this paper is to establish a computer-aided
cased-based diagnostic tool to automatically interpret the
thermal pattern by a bio-statistical technique [4] for investigating
the parametric connection between female breast
cancer and thermal physiology quantitatively. The proposed
algorithm consists of five steps, i.e. geometric lofting
standardization, abnormal region statistics, parametric factors
analysis, decision tree induction and anatomical organ
matching. This methodology is not intended to replace the
traditionally golden method on mammography and also not
to compare the minimal tumor diameter missed by these two
instruments. This paper is intended to explore the potential
benefits of thermograph for early detection of breast
cancer without comparing its sensitivities or specificities
with that of mammography. In addition, a parametric analytical
algorithm was proposed to extract the governing
rules from large scale dataset by decision tree induction
for breast cancer. Finally, the clinical applicability of
the proposed computer-assisted diagnosis tools was analyzed
by 71 and 131 cases with and without breast cancer
respectively.

Wednesday, July 27, 2016

Cancer Glossary 2

Cancer Glossary 2

What is ?

acute lymphoblastic leukemia (ALL): The most common cancer in children, in whom it is highly curable with chemotherapy. Adult ALL is less common and requires an allogeneic stem cell transplant to achieve cure.

acute myelogenous leukemia (AML): The most common acute leukemia in adults, mainly affecting those sixty years of age and older. Treatment often involves intensive chemotherapy and a stem cell transplant to achieve cure.

adjuvant therapy: Cancer treatments administered after surgery in order to prevent a cancer recurrence.

allogeneic stem cell transplant: The transfer of blood stem cells from one individual (donor) to another (recipient), after treatment of the donor with specific medications; used in the treatment of blood and lymph cancers affecting the bone marrow, such as leukemia.

anemia: Condition when the amount of red blood is lower than the normal range; may contribute to fatigue. Anemia has numerous possible causes, one of which is the administration of chemotherapy.

angiogenesis inhibitors: Cancer-fighting medicines that block the blood supply to a cancer.

apoptosis: The biologic term for the organized process of death experienced by cancer cells in response to cancer-fighting treatments.

autologous stem cell transplant: The removal and return of one’s own blood stem cells, separated by the administration of intensive (“high dose”) chemotherapy to treat blood and lymph cancers, testicular cancer, and some sarcomas.

blood stem cells: The population of cells derived from bone marrow that can reconstitute a person’s bone marrow, blood-forming capacity, and immune system when their own bone marrow has been intentionally destroyed or suppressed as part of the transplant process. Blood stem cells can be driven into the bloodstream and harvested through a catheter in a vein.

bone scan: A radiology test that detects cancer deposits in the bone through the intravenous injection of a radioactive bone-seeking compound.

cancer clinical trial: A research study that enrolls people on a voluntary basis to test the effectiveness of a new way to prevent, diagnose, or treat cancer.

cell: The basic structural building block of all living things.

chromosomes: Rodlike structures found in most living cells that are composed of DNA and proteins required to maintain the DNA. Most human cells have forty-six chromosomes; alterations of normal chromosome structure are commonly found in cancer cells.

chronic lymphocytic leukemia (CLL): The most common type of leukemia, mainly affecting those sixty years of age and older.

chronic myelogenous leukemia (CML): A type of leukemia characterized by an initial chronic phase followed, if not successfully treated, by a more aggressive phase. CML is highly treatable with targeted medicines such as Gleevec.

CT (computerized tomography) scan: Detailed pictures of the inside of the body taken using a sophisticated X-ray machine linked to a computer.

cure: When no evidence of a cancer can be found after treatment for the life of the patient. A cancer is commonly described as cured after a period of time after which the chance of a recurrence is extremely low, such as five or ten years.

EGFR (epidermal growth factor receptor): A molecule on the surface of many cancers that stimulates the cancer to grow; it is the target of a class of cancerfighting drugs, called “EGFR inhibitors,” that include such medicines as Tarceva and Erbitux.

genetic testing for cancer: The analysis of a person’s DNA, derived from a simple blood test, to determine their predisposition to develop specific cancers. The results may enable the person tested and/or his or her family members to prevent cancer if recommended precautions are taken.

genomics: The study of a cancer’s DNA through sophisticated scientific techniques.

informed consent: The process by which a person is fully informed and educated about the risks and benefits of a procedure they may undergo; usually relates to participation in a clinical trial or when considering genetic testing for a family cancer gene.

LDH (lactate dehydrogenase): An easily measurable chemical found in the bloodstream that may be generated in high amounts by rapidly growing cancers, in particular lymphomas.

mediastinum: The area of the human body located in the middle of the chest between the lungs, containing the heart, portions of the aorta and vena cava, main bronchial tubes, thymus gland, lymph nodes, and other structures.

metastasis: The spread of cancer to regions of the body away from the original site of the cancer, for example, when colon cancer spreads to the liver.

MGUS (monoclonal gammopathy of undetermined significance): Condition when an M-spike is detected in the bloodstream but there is no evidence of cancer; patients must be followed for the possible development of multiple myeloma and related disorders.

micrometastases: Cancer deposits that have spread in the body but are too small to be detected by imaging techniques, such as CT scans.

M-protein (also called M-spike): An abnormal protein found in the bloodstream of patients with multiple myeloma, Waldenstrom’s macroglobulinemia, and some other blood/lymph cancers; the protein is made by the cancerous cells and declines in amount with effective treatment. May also be found in MGUS.

MRI (magnetic resonance imaging) scan: Detailed pictures of the inside of the body taken using a sophisticated machine that uses a powerful magnet linked to a computer.

mutation: A change in the DNA sequence that may alter the function of a gene and its corresponding protein. The DNA of a cancer cell is characterized by the presence of numerous mutations.

neoadjuvant therapy: Cancer treatments administered before and in preparation for surgery.

neutropenia: Condition when the bacteria-fighting blood cells called neutrophils are present in levels significantly below the normal range; usually associated with the use of chemotherapy or radiation. Neutropenia places the patient at increased risk for infection.

oncogenes: Normal genes that function abnormally as a result of genetic mutation and that contribute to the development of cancer; many oncogenes are the targets of new cancer-fighting medicines called targeted therapies.

PET (positron emission tomography) scan: A technique to measure the activity level of some cancers through the injection of radioactive glucose (sugar) into the vein.

primary site: The original location where a cancer begins, for example, the breast, prostate, or lung.

prognostic factor: Some aspect of a patient or their cancer used to predict the aggressiveness and survivability of that cancer; for example, being estrogen receptor (ER) positive is a good prognostic factor in breast cancer.

progressive disease: The term used by doctors to convey that a cancer is growing.

PSA (prostate specific antigen): A blood marker of prostate cancer used in screening for the disease and in following the effectiveness of treatment for metastatic prostate cancer.

radiologist: A physician expert at interpreting imaging tests of the human body.
A type of radiologist called an interventional radiologist is expert at performing procedures (such as the placement of a central venous catheter or the instillation of chemotherapy directly into the liver) under the guidance of an imaging machine, such as a CT scan.

recurrence: Regrowth of a cancer after it has been in remission for some time.

remission: The term used to relate that a cancer has stopped growing and has shrunken in size or amount; in a partial remission, the cancer has shrunken by at least 30 percent, whereas in a complete remission, no cancer can be detected.

stable disease: When a cancer has stopped growing but has not significantly shrunken in size or decreased in amount.

staging workup: The battery of tests performed to determine the extent of a particular cancer in the body.

stereotactic radiosurgery: A technique in which high-intensity radiation is focused on a small region of the body in order to eradicate a limited area of cancer.

support group: A meeting of cancer survivors or their loved ones, often led by an experienced professional, to help the participants cope with the many effects of cancer on their lives.

survivor: Anyone who has been diagnosed with cancer.

targeted therapy: A type of cancer-fighting medication designed to bind to one or a few critical targets in a cancer cell.

tumor marker: A chemical measured from the bloodstream and made by a particular cancer that is an indirect measure of the growth of that cancer; for example, many testicular cancers generate a marker called AFP.

tumor suppressor genes: Genes that prevent cancer from developing and are commonly inactivated in many cancers. Mutations in tumor suppressor genes are commonly inherited in families with a predisposition to cancer, such as mutations in the BRCA1 and BRCA2 genes in hereditary breast and
ovarian cancers.

whole brain radiation therapy: Administration of radiation to the entire brain in order to treat the spread of cancer there.

Cancer General Resources 3

Cancer General Resources 3


National Hospice and Palliative Care Organization (NHPCO)

1731 King Street, Suite 100
Alexandria, VA 22314
(703) 837-1500
(703) 837-1233 (fax)
www.nhpco.org
Provides information on hospice services nationally, including information on communication about hospice, insurance coverage and locating hospice services. Provides explanations of palliative care, Medicare benefits, and other frequently asked questions. Information is also available in Spanish.


NeedyMeds, Inc.

P.O. Box 219
Gloucester, MA 01931
(215) 625-9609
www.needymeds.com
Offers information about programs sponsored by pharmaceutical manufacturers to help people who cannot afford to purchase necessary drugs. You can search their Web site for the name of the drug (name brand and generic) to determine if financial assistance plans are available.


New LifeStyles Online

4144 N. Central Expressway, Suite 1000
Dallas, TX 75204
(800) 869-9549
www.newlifestyles.com
Provides information on independent retirement communities, assisted living, nursing homes, Alzheimer’s care, and home or hospice care. You can order a free guide or search online.


The Partnership for Prescription Assistance

(888) 4PPA-NOW (888-477-2669)
www.pparx.org/Intro.php
Through its Web site, “The Partnership for Prescription Assistance offers a single point of access to more than 475 public and private patient assistance programs, including more than 180 programs offered by pharmaceutical companies.”


Patient Access Network Foundation

P.O. Box 221858
Charlotte, NC 28222
(866) 316-PANF (866-316-7263)
www.panfoundation.org
“Patient Access Network (PAN) Foundation is an independent, not-for-profit established in 2004, dedicated to assisting patients who cannot afford the outof-pocket costs associated with their treatment needs” (Web site). Contact the organization for a list of covered diseases; PAN also provides trained case managers with whom patients or advocates may speak about their care.


The Patient Advocate Foundation/Co-Pay Relief Program

700 Thimble Shoals Boulevard
Newport News, VA 23606
(866) 512-3861
(757) 952-0119 (fax)
www.copays.org
“Patient Advocate Foundation is a national non-profit organization that seeks to safeguard patients through effective mediation, assuring access to care, maintenance of employment and preservation of their financial stability relative to their diagnosis of life threatening or debilitating diseases” (Web site). The Co-Pay Relief Program provides direct co-pay assistance for pharmaceutical products to insured patients who financially and medically qualify, for a restricted number of specific cancers; contact the organization for a list of covered conditions.


Social Security Administration (SSA)

Office of Public Inquiries
Windsor Park Building
6401 Security Boulevard
Baltimore, MD 21235
(800) 772-1213
(800) 325-0778 (TTY)
www.ssa.gov
This Federal program provides extensive information on Social Security benefits, including Social Security Disability (SSD), Medicare, Supplemental Security Income (SSI), contact information to state Medicaid offices, and much more. You may be able to apply online to these programs, and even
check your claim status. Information is available in many languages; call or check the Web site for a complete list.


United Ostomy Associations of America, Inc. (UOAA)

UOAA
P.O. Box 66
Fairview, TN 37062-0066
(800) 826-0826
www.uoaa.org
The UOAA “is an association of affiliated, nonprofit, support groups who are committed to the improvement of the quality of life of people who have, or will have, an intestinal or urinary diversion” (Web site). Coordinates educational and support groups through local chapters, and publishes The Phoenix.
Provides information on practical ostomy care issues, including answers to common insurance coverage questions, and support information.


The United Way

(703) 836-7112
www.liveunited.org
“The United Way is a national network of nearly 1,300 local organizations that work to advance the common good by focusing on education, income and health” (Web site). For information about specific United Way programs in your area or other social services available in your area (including, in some locations, financial assistance programs), contact your local chapter of the United Way.


U.S. Department of Health and Human Services (HHS)

200 Independence Avenue, SW
Washington, DC 20201
(877) 696-6775
www.hhs.gov
The mission of this government organization is to “protect health and give a special helping hand to those who need assistance.” HHS provides information on many topics, including Medicare, Medicaid, childcare and health initiatives, referrals to information on cancer, and much more. HHS publishes the “Guide to Health Insurance for People with Medicare.”


U.S. Department of Labor

Frances Perkins Building
200 Constitution Avenue, NW
Washington, DC 20210
(866) 4-USA-DOL (866-487-2365)
www.dol.gov
The U.S. Department of Labor has created an online program to help people understand their eligibility for and rights regarding the Family and Medical Leave Act  (www.dol.gov/elaws/esa/fmla/fmlamenu.asp). Additional information regarding employee rights, including health plans and benefits, is available on the e-laws section of the Web site.


The Wellness Community

National Office
919 18th Street, NW
Suite 54
Washington, DC 20006
(888) 793-WELL (888-793-9355)
(202) 659-9709
www.thewellnesscommunity.org
This organization provides supportive services to people with cancer and their loved ones by offering a variety of services, including online information and support (through the “Virtual Wellness Community”) and on-site locations nationwide. Also includes a list of suggested books addressing common issues people with cancer and their families face. Information is provided in both English and Spanish.

Stress and emotions as CANCER TRIGGERS

Stress and emotions


While diet and exercise may play a big role in health, emotional well-being is just as important. Johannesburg-based psychologist Melissa Card says: ‘Some people believe in a mind-body connection, while others do not. Regardless of whether you believe in this connection or not, research has shown that our bodies react to the way we think and feel about situations.’

Examples of this include high blood pressure and ulcers caused by extremely stressful situations, especially in people with no family history of such conditions. ‘Negative emotions such as anxiety, doubt, fear and frustration can affect our health to a large extent,’ says Card. ‘Most of life’s
uncertainties, like finances, employment, marriage, education, divorce or death, can have a detrimental effect on one’s mental and emotional health, if not dealt with in an appropriate manner, which can in turn affect the body.’

Our bodies send us signals when we are not coping with stress. The most common include chronic fatigue, irritability, stomach problems, significant weight fluctuations (gain/loss), changes in appetite, neck pain and backaches, insomnia, sexual dysfunction, breathing problems and decreased immunity.

If you are aware of some of these symptoms when you are feeling stressed, it could be time to slow down and take stock of where you are in your life.

‘When we feel overwhelmed and bogged down by everything happening around us, we tend to neglect our bodies and health,’ says Card. ‘When one is anxious, fearful, depressed or frustrated, it’s easier to indulge in all the negative “stress relievers” or addictive tendencies, such as alcohol, smoking, bad eating habits (comfort food) and even drug abuse – all of which ultimately have a detrimental effect on our physical and mental well-being.’

Luckily, these symptoms and feelings can easily be reversed, by getting enough sleep, following a balanced diet and engaging in regular exercise, which, Card explains, not only has a beneficial effect physically but also in terms of emotional well-being. Setting realistic goals may also be helpful when
it comes to maintaining emotional health. ‘We’re often left with many negative emotions when we cannot or do not reach the goals we’ve set for ourselves, and thus allow for stress to creep in and overwhelm us,’ Card explains. Adopting coping mechanisms like relaxation techniques, walking,
reading, listening to music, yoga and meditation can play a big role in giving you a break from your stressful lifestyle.

When it comes to life-threatening illnesses like cancer, Card acknowledges that emotions like fear, sadness, anger, disbelief and dismay can be overwhelming. She advises trying not to overthink or overanalyse the situation, as this could lead to unnecessary worry and the secretion of stress chemicals. ‘Regular exercise does help with this by releasing other chemicals to counter the negative emotions. Expressing yourself is always better than bottling everything up. If you are not able to speak to close friends and family, perhaps try a counsellor or therapist, doctor or religious advisor, whomever you feel comfortable with.’

She adds that one of the most important things you can do is ensure that you have social support to help you cope. Journaling, painting or drawing may also serve as forms of expression while dealing with the stress of illness.


CHOCOLATE FUDGE RECIPES by Noel Marten & Natalie Reid

CHOCOLATE FUDGE RECIPES by Noel Marten & Natalie Reid


MAKES ABOUT 40 PIECES


1 cup pitted dates
1⁄2 cup warm water
1 cup coconut oil
1⁄2 cup cocoa powder
1 tsp vanilla powder
pinch of salt


1. Soak the dates in the water until soft.
2. Place all the ingredients in a food processor or blender and process with the S-blade until completely smooth and mixed. This takes up to 20 minutes.
3. Pour the mixture into a shallow dish and refrigerate for 3–4 hours until set.
4. Cut into squares and store in an airtight container in the fridge.


Notes
Add flavours such as mint, sweet orange, rose geranium or lavender. When
using essential oils in food, remember to use food grade only.