'''

Created on Oct 8, 2014

@author: agr9

'''

from numpy import zeros

from scipy.linalg import svd

#following needed for TFIDF

from math import log

from numpy import asarray, sum

from sklearn.metrics.pairwise import cosine_similarity

from sklearn.metrics.pairwise import linear_kernel

import math

#===============================================================================

# titles = ["The Neatest Little Guide to Stock Market Investing",

# "Investing For Dummies, 4th Edition",

# "The Little Book of Common Sense Investing: The Only Way to Guarantee Your Fair Share of Stock Market Returns",

# "The Little Book of Value Investing",

# "Value Investing: From Graham to Buffett and Beyond",

# "Rich Dad's Guide to Investing: What the Rich Invest in, That the Poor and the Middle Class Do Not!",

# "Investing in Real Estate, 5th Edition",

# "Stock Investing For Dummies",

# "Rich Dad's Advisors: The ABC's of Real Estate Investing: The Secrets of Finding Hidden Profits Most Investors Miss"

# ]

#===============================================================================

class LSA(object):

print self.Vt

def main(lists):

return return_list

if __name__=="__main__":

from optparse import OptionParser

optparser = OptionParser(description="Get XML from PubMed")

optparser.add_option("-l", "--list", default=["overexpression expression overexpression inhibition overexpression association association interaction binds binds interaction affinity affinity", "expression inducing expression detected lacking expression inducing expression detected lacking expression"], dest="l", help="list")

(options, args) = optparser.parse_args()

# main(options.l)

d1 = 'like many women anne berkovitz had decided against taking hormones after menopause but she often wondered whether shed made the right decision among her friends the topic was always a source of debate you hear one persons doctor say you must take it and another persons doctor says you shouldnt take it if you can get by without it says berkovitz 64 of westwood i was feeling ok not taking hormones but i had sort of wondered about it hormone replacement therapy is a drug treatment commonly prescribed to women after menopause to replace natural hormones the body has stopped manufacturing the therapy is popular because it diminishes some uncomfortable side effects of menopause such as hot flashes and can reduce a womans risk of osteoporosis and possibly heart disease but the treatment has drawbacks including a possible increased risk of breast cancer the disparity led berkovitz to enroll as a participant in one of the largest clinical studies on hormone replacement therapy and the first drug trial to study its effects on heart disease the study will begin soon at ucla and six other research institutions ucla researchers hope to enroll another 75 women the postmenopausal estrogenprogestin interventions pepi study should help define the dosage and combination of hormones that best reduce the risk of heart disease in women the leading cause of death in women as well as men says dr howard judd executive director of the division of reproductive endocrinology at ucla and cedarssinai medical centers pepi is sponsored by the national institutes of health estrogen is such a powerful chemical it impacts on so many systems in the body says judd who is directing uclas part of the study our hope is that well be able to say based on cardiovasculardisease risk factors this is the best way to take hormones while men and women share some risk factors for heart disease such as a highfat diet or family history female hormones produced by the body apparently help protect women against heart disease before age 50 when men are at their peak risk but after menopause when hormone production ceases the rate of heart disease in women quickly climbs and eventually equals the rate in men there is a lot of evidence now accumulating that estrogen plays a role in heart disease how it does that is not clear judd says we would suggest that an agent that may reduce the incidence of heart disease by 50 maybe 60 in more than half the population is worth studying this is a very important question that needs to be answered and i believe it will be estrogen appears to lower the bad cholesterol lowdensity lipoproteins in the body and raise the good cholesterol highdensity lipoproteins to reduce the chance of heart disease but those possible benefits while exciting further complicate a therapy that is already enormously complex and the source of much consternation among postmenopausal women and their physicians estrogen and progesterone are hormones produced by the ovaries they regulate the menstrual cycle and fertility at menopause about age 45 to 50 the ovaries stop producing the hormones while the absence of a menstrual period is a welcomed event for many women menopause can trigger uncomfortable symptoms such as hot flashes and thinning of the vaginal and urinary tissues the drop in hormones also causes bone thinning and increases a womans risk of developing osteoporosis a condition in which bones easily break or fracture hormone replacement therapy resolves many of these problems and with the addition of possible cardiovascular benefits its easy to see why hormone therapy which usually consists of a mixture of estrogen and a progesteronelike chemical called progestin is prescribed for 5 to 9 million women but despite its popularity the debate over hormone replacement continues there are combinations of reasons and advantages for using estrogen says dr ezra davidson president of the american college of obstetricians and gynecologists and chairman of obstetrics and gynecology at drew medical school in many instances physicians are totaling those combined advantages and advising women of the benefits but there is insufficient data about the risks besides minor side effects such as menstrual bleeding estrogen replacement is known to promote the growth of uterine tissue called the endometrium which can lead to cancer studies show that adding progestin to the regimen removes the risk of endometrial cancer so physicians usually prescribe progestin for part of the month but progestin therapy opens the door to a whole new set of complex side effects says barbara hulka an epidemiologist at the university of north carolina and chairwoman of a government advisory committee on womens health issues for example progestin appears to erase the cardiovascular protection of estrogen and some studies show progestin increases a womans risk of breast cancer the quandary is basically the issue of taking estrogen alone versus estrogen plus progestin hulka says estrogen alone does cause a growth of the endometrial lining and does cause endometrial cancer in a significant number of women thats why its been recommended to add progestin for half the month fears that estrogenprogestin therapy will increase the risk of breast cancer were elevated last summer when a swedish study revealed that women who took a combination of estrogen and progestin for more than six years were more than four times as likely as other women to develop breast cancer other studies have not shown as great a risk and the significance of the swedish study is debated judd says that data shows more risk than us data judd says whether or not that will be substantiated or not i dont know many of us felt like the swedish data were overinterpreted but the study did underscore the need for a better understanding of the risks and benefits of hormone therapy earlier this year the food and drug administration approved new warnings regarding breast cancer risk on the labels of estrogen therapy drugs and in a more controversial move an fda advisory panel concluded in july that estrogen taken alone without progestin helps prevent heart disease in women who have had hysterectomies because women who have had their uteruses removed do not run the risk of endometrial cancer the committee deemed that estrogen alone would be beneficial in this group says davidson who was a member of the panel the committee made a prudent judgment based on the information on benefits with the understanding that the information was limited about the longterm risks says davidson who added that some committee members had reservations about making any recommendations on estrogen therapy and heart disease the recommendation by the committee which might persuade the fda to allow a change in the labeling of estrogen to include protection against heart disease for women who have had hysterectomies was criticized by some physicians and consumer health groups the national womens health network said in a statement that studies have not been done to verify that the potential protective effects of estrogen replacement therapy outweigh the risks it is alarming to think that millions of women may be given this drug before either its dangers or benefits are understood says davi birnbaum a representative of the washingtonbased womens health organization the panels recommendation which is only for women who have had hysterectomies leaves postmenopausal women who have not had hysterectomies in limbo says dr diana petitti of the university of california san francisco the data on estrogen use alone in postmenopausal women are fairly consistent in showing a lower risk of coronary heart disease she says but most women are not put on estrogen alone and the data to show whether or not the combination of estrogen and progestin also decrease the risk of coronary heart disease is essentially nonexistent the fda advisory panel based its recommendations on a series of small observational studies called epidemiological studies not the expensive clinical trials that are usually more conclusive judd says i think the advisory panel recommendation is premature because its based exclusively on epidemiological studies he says youve got to do drug trials for something this important that impacts on every woman in the country weve got to spend money the pepi study was designed to fill this void judd says in the study 840 women will be randomly assigned to one of five drug regimens a placebo estrogen alone the standard combination of estrogen and progestin widely prescribed in the united states estrogen and a smaller daily dose of progestin and estrogen with a new formulation of progestin created in europe women will be followed for three years while their risk factors for heart disease such as high blood pressure and cholesterol levels are measured the study also will incorporate measurements of bone density to learn more about the prevention of osteoporosis the pepi study will not attempt to resolve the issue of breast cancer risks the results of the study are expected in 1994 it remains a question of what do you do in the interim between now and the time when well have an answer petitti says do you want to take the risk of taking the drug and being wrong or do your take the risk of not taking the drug and being wrong i consider it to be an incredibly hard choice with so many questions remaining physicians need to review each womans circumstances and fears before prescribing hormone replacement therapy says petitti i think the clinicians who are trying to handle their patients on an individual basis are doing the best job she says someone terrified of breast cancer may not want to take the potential risk of breast cancer but someone has a mother or aunt who had a osteoporotic bone fracture may say i dont want that to happen to me and i dont care as much about the risk of breast cancer experts caution that it will take a longterm study perhaps several decades looking at causes of death among women to resolve whether hormone replacement therapy actually prolongs life or merely swaps one risk for another i think the pepi study will be useful petitti says but the bottom line will not be addressed by the pepi study the bottom line is will it save our lives i dont think any single study will answer that question candidates are still needed for ucla intervention study individuals interested in volunteering for the postmenopausal estrogenprogestin interventions study must be healthy women age 4564 who have had a natural or surgical menopause and are willing to take hormones the participants will receive periodic free medical examinations over a threeyear period for more information call the ucla medical center division of reproductive endocrinology 213 8259502'

d2 = 'nancy brinker was remembering susan the older sister who lost a threeyear battle with breast cancer my sister who taught me how to put on makeup also taught me how to die she says when suzie was dying we made a commitment to one another shed never say when i die shed always say when i get well but we both knew what that meant she said i dont want other women to go through what i went through susan goodman komen fashion model and mother of two died in 1980 she was 36 two years later nancy goodman brinker founded the susan g komen foundation for the advancement of breast cancer research there were just the two of us siblings brinker explains and she also happened to be my best friend nancy brinker was remembering susan the older sister who lost a threeyear battle with breast cancer my sister who taught me how to put on makeup also taught me how to die she says when suzie was dying we made a commitment to one another shed never say when i die shed always say when i get well but we both knew what that meant she said i dont want other women to go through what i went through susan goodman komen fashion model and mother of two died in 1980 she was 36 two years later nancy goodman brinker founded the susan g komen foundation for the advancement of breast cancer research there were just the two of us siblings brinker explains and she also happened to be my best friend a difficult time the final months of her sisters illness and the months that followed were rough for brinker there were the pressures of launching the foundation job worries a divorce and custody battle over her only child but her marriage in 1981 to dallas businessman norman brinker after a whirlwind threeweek courtship was a good one and as time passed she was feeling settled and happy then in 1984 she recalls i was getting in bed one night and i put my hands under the sheets and ran over this hard little lump in her left breast i jumped a mile nancy brinker had had three benign breast lumps and she tried to reassure herself this was just another but her doctors diagnosis confirmed her worst fears cancer she was 37 i sobbed she says its like someone stabbed you with a knife then came all those flashback scenes every vivid detail of her sisters very long and painful struggle with breast cancer i thought that i was going to die for norman brinker it also was the rerun of a nightmare his first wife tennis great maureen little mo connolly died of ovarian cancer in 1969 three years after the disease had been diagnosed she was 34 and left two young daughters today five years since her diagnosis nancy brinkers doctors tell her she has no signs of the disease but with cancer she says you just pray you never know she still suffers from attacks of the checkup crazies brinker underwent a modified radical mastectomy followed by chemotherapy that made her fatigued occasionally nauseated and she says matteroffactly i was bald as a bowling ball no piece of cake still she can laugh and say people always say wasnt chemotherapy terrible it wasnt a piece of cake but divorce was worse and she had an immediate goal to play in a polo match that summer both brinkers are avid polo players he was a member of the 1952 us olympic equestrian team and founded the willow bend polo and hunt club in dallas in august 1985 one month after completing chemotherapy she did play and recalls we won the game to my embarrassment my mother showed up on the field with a little oxygen tank nancy brinker since has undergone reconstructive breast surgery as well as a preventive hysterectomy a stunningly good looking woman she has black hair now grown back thick pulled back in a chignon eschewing vanity she wears bold red hornrimmed glasses she is 5feet10 and slender with a chic honed in four years as an executive trainee and assistant buyer with neiman marcus she has no patience with women who whine and besides she has no time for that sort of selfindulgence last saturday in los angeles after speaking at a conference on diet and breast cancer sponsored by the nathan pritikin research foundation she did an interview while packing for a weekend in santa barbara with her husband the first day ive had off in three years she says she routinely logs 120000 air miles a year later this week shell be off to new york to do a segment for phil donahue on women and crisis brinker is perennially named to bestdressed lists in dallas and to committees for the right blacktie events norman brinker a selfmade millionaire who stables strings of polo ponies in dallas and palm beach is chairman of chilis a dallasbased chain with 200 restaurants nationwide and former president of pillsburys restaurant group which includes burger king not a socialite wonderful norman she calls him shaking her head as she thinks about that terrible thing that happened to maureen she does not identify with being a socialite she would rather tell about being appointed in 1986 to the presidents national cancer advisory board one of only six lay persons on the 18member panel at home she typically puts in an eighthour day as founderchairwoman of the foundation which has a paid staff of only two at national headquarters in dallas but a group of 1700 women volunteers who know whom to ask for money the ultimate power lunch may be the annual fall fundraiser at which the foundation presents its betty ford award to an individual who has increased public awareness and understanding of breast cancer last years event honoring nancy reagan drew 2200 including former first ladies ford and lady bird johnson seven years after its founding the komen foundation has raised 6 million to fight breast cancer operates seven screening centers in four cities has satellite groups in san francisco sioux falls sd peoria ill and new york and supports 22 national research projects in 1987 the foundation was responsible for pushing through the texas legislature a bill requiring thirdparty insurers to pay for breast cancer screening tests for women 35 and over nine other states including california have since followed suit brinker is driven by one goal she says i dont want other women to suffer the way my sister did a brochure introducing the foundation the only national group of its kind focusing on breast cancer offers a startling summary during the 10year vietnam war 57000 men died in combat during the same 10year period 330000 women died of breast cancer brinker knows the statistics well and they are dismaying in 1960 one in 13 american women contracted the disease it is one in 10 today in speeches she tells audiences look to your right look to your left one in 10 each year 40000 women in the united states die of breast cancer one every 13 minutes most victims of a disease that was welladvanced before detection with early detection before the cancer has spread to the lymph nodes a woman has a 93 chance of surviving diseasefree for 20 years komens treatment had been she is convinced a botchup she speaks of the four wrongs of that case the wrong city peoria ill where komen lived the wrong doctor who did not really want her to seek a second opinion inappropriate treatment and on her part wrong attitude she was petrified brinker remembers that when she and komen were children they had visited a great aunt in new york the aunt had had a radical mastectomy and brinker says suzie saw her undressed she always carried that burning image in her mind and she was petrified of having a mastectomy she had the mastectomy but with neither followup radiation nor chemotherapy only 10 days after the surgery she had a breast implant which brinker says was totally inappropriate only after the disease had spread was radiation tried by the time she died komen had endured nine surgeries and three courses of chemotherapy and radiation her mission brinker says is to empower women who develop breast cancer to teach them what questions to ask and how to understand the answers in her view weapons in that fight include diet and life style changes regular exercise fewer fatty foods as well as regular checkups including monthly selfexamination of the breasts and after age 35 screening by mammography in dallas the foundation has made mammography available to indigent women a stress factor she is convinced too that stress plays a role when she was going through her personal crises she says i honestly think my immune system went somewhere on a handcart and she became vulnerable to cancer race for the cure the foundations allwomens 5k run each year in dallas attracts 2500 participants now brinker is writing a book to be published by simon schuster and tentatively titled my race for the cure she says its a story about sisters and daughters and mothers and a very personal story about my struggle with breast cancer beyond that she says she wants the book sales of which will benefit the foundation to teach a woman stricken with breast cancer to be an assertive good consumer one who can assemble a team surgeon oncologist radiologist and have the three of them sit down with her in a room and discuss options theres so much fear out there she says she wants women to be armed with coping strategies among hers get your hair cut very short the day before starting chemotherapy when it starts to fall out pull it out i dont think anybody should wake up and find their hair on the pillow and fight back in every way possible my friends who are fighters do better nancy brinker comes by her activism genetically in peoria where she and her sister grew up in a big frame house with a front porch her grandmother started the red cross chapter and her mother was president of the girl scouts she recalls her mother telling her youll never get anything done sitting on your duff after graduation from the university of illinois in 1968 brinker decided to go west to dallas before her marriage to brinker she was a radio and television reporter and talk show host there today the foundation is her job in 1987 it expanded its scope with creation of the susan g komen alliance for breast cancer research education and treatment a triumvirate that includes the foundation the university of texas southwestern medical center in dallas and baylor university medical center the alliances goal is a national network of researchers specialists and treatment facilities nationally the foundation has funded research at johns hopkins in baltimore the national cancer institute at bethesda md the peralta cancer research institute in oakland and the m d anderson cancer center in houston she does not expect a cure for breast cancer in her lifetime but she thinks that cutting the mortality rate in half by the year 2000 is possible sometimes she admits ive had enough of cancer sometimes she would like turn the work over to others but then she will hear of someone else who has been diagnosed with the disease i just cant tell you how many friends ive lost she says i just cant tell you'

d3 = 'when a lifesize version of the pink panther cartoon came to hoag hospital ailing children laughed and clasped his fuzzy paws with delight but the panther a gangling but dapper beast with bright pink fur and a spangled black vest got his most enthusiastic response on the oncology ward from adults cancer patients looked startled as the panther danced a jig from room to room but they cheered quickly greeting him with laughs and broad smiles hes all right cried jan hakinson 52 a visit from a cartoon figure may seem childish she said but what else can you do to cheer yourself up if you lose your mood your ability to laugh its an uphill struggle to get well the panthers recent visit was mainly a publicity bid by mgm to celebrate the films 25th anniversary hoag seized the moment to showcase the hospitals new laughter therapy program administrators at hoags cancer center base the program on recent theories that laughter releases tension and grief as well as powerful brain chemicals called endorphins that promote healing a growing number of medical researchers report that laughter interrupts normal breathing rhythms promoting relaxation and lowering blood pressure hohoholistic medicine some proponents have called it and in anatomy of an illness writer norman cousins espouses his conviction that 20 minutes of hearty laughter each day cured him of a crippling spinal disease hoag officials dont agree with cousins that continuous laughter can cure disease to cure it is too strong said oncology nurse sharon macdonald administrative director of hoags cancer center but your outlook will impact your response to the illness just as a chemotherapy agent impacts your whole being anything that increases endorphins will impact your wholeness and there is evidence to suggest that those with a positive outlook have a longer diseasefree period across the nation a handful of hospitals have begun laughter programs in the last five years locally st joseph hospital in orange includes laughter in its support groups humor becomes a way to cope with the disease cancer patients there for example will joke about losing their hair they see the humor in this terrible thing thats happening to them said clinical social worker donna baker but hoag appears to be the only hospital in the county with a fullfledged laughter program macdonald became interested in the idea several years ago as she attended oncology workshops and conferences at one symposium she watched with amazement as the speaker persuaded 350 oncologists to stand on their chairs turn in circles and flap their wings like turkeys afterward as the meeting continued she noted the participants tone was upbeat they seemed to have found new energy macdonald hopes hoags cancer patients will react the same way at the moment the programs offerings are a bit thin the oncology floor has a laughter board a bulletin board of cartoons to which patients and their families are encouraged to add items she is also building a comedy library so far she has several dozen books two portable videotape recorders and 25 video selections a mix of i love lucy and laurel and hardy reruns some eddie murphy movies and a half dozen pink panther shorts macdonald has ambitious plans she has persuaded corona del mar animator chuck jones to lend some of his bugs bunny road runner and wile e coyote cartoons to decorate the cancer ward in december and jones is expected to meet with cancer patients whats more when hoags 65000squarefoot cancer center building opens in may or june one conference room will be dedicated to laughter therapy macdonald is convinced patients and their families need it i just think these people undergo so much aggressive treatment they need to do something to feel better about themselves she said so the visit from the pink panther and the panthers creator producer and animator friz freling is just a beginning hospital officials said the panthers bright mood also befell hospital staff the head nurse prepared for the visit by cutting out large pink panther paw prints and posting them on the walls other nurses selected patients who were well enough to meet with the panther and pose for pictures with him and freling and when the panther danced through the ward cancer patients shook his paw and beamed one 75year old mary forrester effused thank you thank you what a beautiful panther i love it as the panther finished his rounds macdonald proclaimed the visit a success this wasnt a childrens thing she stressed they will feel good up there all day'

l = [d1,d2,d3]

d1 = 'adam adam adam adam'

d2 = 'adam adam adam adam'

d3 = 'adam adam adam roth'

l = [d1,d2,d3]

main(l)

titles = ['induction localization detected produced accumulation inhibition accumulation translocation downregulated downregulation interacts interacts expression overexpression co-expression inhibition expression knockout down-regulation down-regulation inhibition accumulation target transcription expression transcription induction inhibition accumulation induced binds regulated loss deficiency inactivation interacted downregulated downregulation inhibitor inhibition interactions interactions expressed interacting overexpression co-expression interacted mechanism downregulated expression',

'dysfunction association interaction phosphorylation expressions expression increased expression present expression expression rest-regulated expressed localize upregulation expression expression expression expression increases overexpression increased expression expression',

'abundance effect expression inhibited phosphorylation phosphorylation activation inhibited interacts interacts expression expression expression expressed interacted expression expression transcription interaction inhibited inhibited phosphorylation inhibiting phosphorylation activation phosphorylation expression interaction expression recognized phosphorylation expressed regulation expression expression expression activation interacted region binding loss interaction binds interacts expression phosphorylation phosphorylation increases expression increases regulating activate interacted activation interacted interacted regulates loss required blocking contributes required expression loss promoter expressed abundance effect expression inhibition inhibition activator']

main(titles)

titles= ['overexpression expression over expression inhibition over expression association association interaction binds binds interaction affinity affinity',

'expression induce expression detected lacking expression inducing expression detected lacking expression',

'overexpression induce expression adam went to the store to find some tomatoes ended up buying fish']

# main(titles)

titles = ['activated increase binding expression production screening screening reduces binding binding expression phosphorylation regulation activation activation activation activation activation interacts inhibit activation activation dependent disruption activated phosphorylation mediated activation activators expressed expression reduction structure structure overexpression expression expression expression down-regulation expression levels expression activators binding binding production upregulation binding bound activation activation phosphorylated inhibition inhibition reduced expression downregulation expression increase changes activation reduction targeting levels structure activation reduced suppression suppression regulating activation increase levels inhibition levels levels redefines levels production',

'interacts screening synthesis expression effect effect effect production production effect effect effect levels levels expression associated production control activators production induction bind bind phosphorylation mediated activation activators characterization activation activators expression activators inhibit production interacting effect production effect effect effect expression phosphorylation expression expression interacting phosphorylation production activation bind interacts inhibit expression expression inhibition up-regulation phosphorylation activators activate expressed produce']

main(titles)

titles = ['overexpression expression over expression inhibition over expression association association interaction binds binds interaction affinity affinity', 'expression inducing expression detected lacking expression inducing expression detected lacking expression', 'overexpression adam went to the store to find some tomatoes ended up buying fish']

# main(titles)