In 2002, cervical cancer was one of the leading causes of death in Mexico. Quantitative techniques allowed for the identification of socioeconomic, behavioral and biological characteristics that are part of its etiology.However such characteristics, are inadequate to explain sufficiently the role that emotions, family networks and socially-constructed categories such as gender play in the demand and utilization of health services for cervical cancer diagnosis and treatment and neither the timely undertaking of preventive actions, such as getting a PAP smear or seeking adequate and continuons treatment.A qualitative study was carried out to analyze the role of different social and cultural factors in the timely detection of cervical cancer. As part of a multi-level, multi-method research effort, this particular study was based on individual interviews with women diagnosed with cervical cancer (identified as the "cases"), their female friends and relatives (identified as the "controls") and the cases' husbands.The results showed that both: denial and fear are two important components that regulate the behavior of both the women and their partners. Women with a small support network may have limited opportunities for taking action in favor of their own health and wellbeing.Women tend not to worry about their health, in general and neither about cervical cancer in particular, as a consequence of their conceptualizations regarding their body and feminine identify – both of which are socially determined. Furthermore, it is necessary to improve the quality of information provided in health services. In 2002, malignant tumors were the first cause of death among the Mexican working-age population and cervical cancer was the most frequent tumor producing a total of 2,958 deaths, with a rate of 4.9 per 100,000 inhabitants aged 15–64 years [In 1995, most new cases of cervical cancer occurred in the State of Veracruz 10.2%), followed by State of Mexico (8.9%) and Mexico City (8.8%), which has a high population density. The states with the highest mortality rates per 100,000 inhabitants were: Nayarit (9.0), Colima (7.6), Zacatecas (7.2) Morelos (6.8) and Veracruz (6.4) [%, followThere are multiple factors involved in cervical cancer etiology, such as: low socioeconomic level, early age at first intercourse, multiple sexual partners, early age at first pregnancy, multiparity, use of hormonal contraceptives and smoking -7. AnothTherefore, cervical cancer has been approached from different study perspectives: at the molecular level, focusing on the search for and the identification of human papillomavirus; at the cellular level, looking for malignant transformation by means of the Papanicolaou test (PAP); and at the individual level, in search of physical, psychological and familial consequences of the disease.Quantitative techniques have traditionally been used to improve our knowledge about the natural history of this disease. However, these techniques do not allow to explore the individual and group contexts which, in theory, determine the demand and successful utilization of preventive measures, such as the PAP test.At the national level, only a few studies provide information about the barriers that limit the effectiveness of programs for the timely detection of cervical cancer. To the best of our knowledge, there is not a single program aimed at increasing male participation in reproductive health matters. The lack of male involvement in early cervical cancer detection programs is a result of the man's position within the couple, and of their ignorance on the consequences of their own attitudes and of their perceptions on this or other diseases -15.The present study attempts to analyze the role of several social and cultural factors in relation to the early detection of cervical cancer, focusing on the influence of the partner and the social networks regarding the utilization of the PAP test ,17.This work is part of a larger multilevel study which collected information from the molecular (HPV), the cellular and the individual levels , and is based on the interpretation of qualitative results from in depth interviews nested within a case-control study.The purpose of the qualitative section was to identify individual and family characteristics that favour the demand and successful utilization of the PAP test, as well as to identify the barriers that work against a its successful use, by comparing cases of cervical cancer and controls . We also compared aspects related to perception and knowledge of the disease, and aspects related to health care access, its effectiveness, and the quality of the program.For the case-control study, all newly dignosed cases of cervical cancer seeking case at the National Institute of Cancer in Mexico City and the dysplasia clinics in the State of Veracruz were enrolled in the study, conditional upon being residents of Mexico city or the states of Mexico and Veracruz.Personal interviews were conducted by trained personnel using a guide of items grouped in four sections: i) subjectivity, ii) family, iii) gender, and iv) health services.At total of 130 cases, 200 controls and 20 husbands of cases were interviewed. For the purpose of this paper, the qualitative analysis was made with a sub-sample of 20 cases (mean age = 45 years), 20 controls (mean age = 42 years) and 11 husbands. A random sample of cases and controls (and husbands) was chosen as soon as we had histological confirmation of the health status. We also verified that the number of subjects was appropriate in view of the theoretical saturation point.Interviews were taped and later transcribed and a discourse analysis was carried out by means of grounded theory techniques . We usedThe analysis was performed with the backing of the Atlas-ti program (v.4.2), independently for each group , and we based it on the following steps:1. Theoretical categories were defined, with conceptual codes for organizing information.2. Interviews were analyzed assigning conceptual codes to data segments that shared the same idea (open coding).3. New categories with analytical capacity were indentified from obtained data.4. Properties of each category were identified .5. Code families were integrated.The following results are organized according to the sections mentioned above for interviews. Results are separated into sections corresponding to cases, controls and husbands.This category included the emotional reactions related to having cervical cancer, including the personal interpretation of signs and symptoms and whatever they elicited inside the woman.A positive diagnosis generated different emotional reactions in women, such as fear, depression, sadness or guilt for letting time pass by while ignoring recommendations to get a PAP smear or not considering the examination important.The depression may be so severe that, at least in one case, professional psychological help was sought. The perception of being at low risk of having cervical cancer was present prior to the women's diagnosis and it was one of the reasons for not having sought a PAP smear.The most frequent perception of cancer was definitely negative, with fatal connotations, which made it very difficult for women to accept this diagnosis.Symptoms interpretation played a very important role here. Symptom severity was related to their frequency and to the woman's lack of control over them, such as continuous vaginal secretions, pain and bleeding. The absence of a preventive attitude towards one's health was noticeable among these women. In fact, they believed that in the absence of symptoms, there is no need for a PAP smear.The strongest contradiction that women express is their tendency to deny the diagnosis while they have high hopes of being cured. This attitude allowed them to face their treatment with courage. Nevertheless, not all these expectations were supported by medical prognoses, but rather by their own will to survive.This category gathered information regarding previous experiences with cancer in the family and the degree of communication and support existing between couples and within families.Most of the women studied women had previous experiences with cervical cancer in their family, either with their mother or a sister.There were few women who requested a PAP smear on their own; generally they followed recommendations from their physicians and sometimes from their daughters, neighbors or friends. When they decided on their own, previous experience with cervical cancer, especially within the family, played an important motivating role.Cancer is an event that nearly always a women experiences in solitude. They seldomly shared their experience with their family, either because they had a poor communication with their partner or because they just wanted to spare their children from suffering. Most women did not know wich other women from their own family had had PAP smears. When they wanted to share their feelings regarding their diagnosis, they usually did so with acquaintances or people of similar religious beliefs. When sharing with acquaintances, the purpose seemed to be to offer advice to other women and motivate them to undergo cancer screening. When sharing feelings with people of similar religious beliefs, women were looking for spiritual support.as much as they could.For these reasons it is quite difficult to identify the kind of family support received by women, even when they declared that their relatives helped them useless as a woman".Facing this experience mostly on their own, women recognized an increased desire for moral support from their partners, but sometimes their reaction was to abandon them. The reason for this rupture was that a woman who was going to lose her womb, also lost the possibility of having children and becames "Women expressed that they needed moral support more than anything else, and to feel protected and not alone. Women who had separated from their partners prior to the diagnosis usually received support from their children.This category took into consideration the perceptions, ideas and actions that reflect the social construction of the sexes as well as current socio-cultural values. Women's partners' reactions and the support they give are discussed as well as the reasons of women for avoiding cervical cancer screening. For most women, the examination itself was regarded as a particularly uncomfortable experience.The notion of submissiveness appeared when women explained that men "must" have intercourse, and if they are not satisfied, they will look for the company of other women. Most women assumed that this behavior is completely natural and legitimate.When faced with a confirmed diagnosis of cervical cancer, women feared abandonment by their partners. The belief standing here is that a woman ought to provide pleasure to her partner even at her own expense, and asking the physician whether it is possible to have intercourse, is a cause for embarrassment. Even among the health care staff, the sexual behavior of woman is questioned before that of her partner, as shown by some testimonies.Another situation that is noticeable in this context is the role of women in the family's health. They look after the different family members, neglecting their own health or placing it in last place, frequently until their own health problems have become unmanageable. The invaluable compensation that these women receive is, undoubtedly, their children's love.Motherhood is a characteristic that defines the condition of being a female. Therefore, the failure to procreate is a cause for abandonment. Aswith pregnancy and child care, health care is another responsibility assumed by women as part of their social role. This assumption is confirmed by the fact that they do not inform their husband about their cervical cancer so as not to worry him – which reflects the woman's belief that she is the only one responsible for her own health. This assumption is also held by the male partner who delegates to the woman the responsibility of following the appropriate treatment. Occasionally, women themselves justify the absence of their partners, saying that they must work in order to pay for food and for their treatment-related expenses.The interviewed women justified their partners' behavior in two ways. Firs, at the time of the PAP smear, because they pointed out that a man does not have to be involved because health maintenance is the woman's exclusive responsibility; and second, when the diagnosis was positive for cervical cancer, women felt thaeir the partner had to become aware of the situation but his support was not an obligation given the severity of the problem.Tolerance towards their partners, despite the lack of affection and communication in the relationship, seems to be accepted as a woman's obligation.Sometimes, the partner's lack of affection is the reason for the woman's poor disposition, yet she does not dare admit it. Faced with the possibility of a diagnosis, women expressed a double social burden: the disclosure of a socially unacceptable behavior in the couple (promiscuity) and the ressponsability of being a women (gender role), which results in a sense of duty even if they are reproached by the others.The category included information about the quality of health care services received by women.Women graded the attention received as good and expressed the same opinion about the information received from the physicians and health workers, yet these answers appear to be very limited and women remain with many doubts.Some women stated that the doctor skipped examination (while this is the kind of action expected by them) during the first consultation, and neither told them what they had, but simply prescribed some medication.In spite of not having a positive diagnosis, women in the control group developed a certain fear, which is fostered by the experience of having someone close to them with cervical cancer. Guilt is a feeling the controls share with the cases, generally because, their loved ones have to go through such an unpleasant experience.The controls talked about the need for the cases' husbands to support their wives instead of keeping distant or, even worse to abandon them.The cases close to them, especially when they were relatives, fostered feelings of sadness, pain and depression. This pain turns to fear when accompanied by the frequently mentioned notion of death.Women in the control group often left the issue of survival up to God. Yet along with this idea, there was also the notion that scientific advances can prevent death, even though cervical cancer is seen as an incurable disease. Underlying both notions is the concept of a miracle, mixed with a form of denial.Despite their fear, these women still perceived themselves as being at low risk of cervical cancer, a perception unaffected by living in close contact with cervical cancer cases and expressed as not taking preventive actions. These women used health care services for family consultations, but did not undergo cervical screening on their own.Daughters are the family members that play the most important role in recommending and encouraging their mothers to participate in cervical screening.Women in the control group admitted to have problems and misunderstandings with their husbands, besides the issue of whether or not they should seek a PAP smear. For example, men accepted more openly to have extramarital intercourses that occasionally caused them to feel guilty, and they reckoned on palliatives, such as bringing medication to their wives to cure infections that they believed were caused by their extramarital behavior.In general, women expressed a feeling of abandonement, they perceived they partners as estranged and not at all concerned about them. As in the cases, the controls were also embarrased by the fact that their bodies would be seen during the examination, thus revealing the prejudice that female integrity is closely linked to a sense of shame.In general, women expected a more complete explanation from their doctors; when told that they had a "mild infection", their anxiety lessened but their wish to learn more still remained.The interviewed husbands mentioned that they felt frightened by their wives' symptoms. They found it alarming when symptoms such as bleeding, hemorrhage, intense pain and fainting were present. In view of the severity of the symptoms, surgery was perceived as the only possible treatment.The interviewed men appeared willing to help their wives; some of them accompanied their wives to their examination and remained with them until after diagnosis was confirmed. It is important to point out, however, that the interviewed men were those who accompanied their wives to consultation – implying a potential source of bias. These men also mentioned that the daughters were who generally recommended that their mothers should undergo cervical screening.Among the reactions of the interviewed men, fear of a possible positive diagnosis of cancer was manifest. Concern over the privacy of one's body was not exclusive to women, the men also reported shame for the fact that their wives' bodies were seen.Regarding the possible confirmation of diagnosis, the men expressed fears that had more to do with the children's care and attention than with their wives's health condition.The evaluation of the care received was dependent on the persistence of the symptoms. If symptomps remained after medical care was received, then the service was considered to be deficient. On the other hand, if the symptoms disappeared, health care was graded as being efficient.The subjective way in which the interviewed subjects of the present study expressed their experiences, is nothing more than the collective style constructed in regard to cancer in general. Several authors -22 estabThe lack of attention and concern that women experience in relation to their own health is not coincidental. Within the Mexican culture, women have always been the procurers and not the beneficiaries of health. In this sense, to confront the reality of having cancer requires to repeatedly summon guilt and depression; guilt results from not taking early and preventive actions and depression from a seemingly inevitable and irreversible condition.One of our assumptions was that a close relationship with someone with a confirmed diagnosis would encourage healthy women to undergo cervical screening. However, our results did not confirm this assumption Figure , insteadAs depicted in the experiential map created for women with cervical cancer, . As a result, women tend to blame themselves for the disease. These elements create psychological barriers for early detection and timely treatment.Gender is a category on which ideas regarding masculinity and femininity are constructed. These ideas are the basis upon which women define their lives and their view of themselves, derive their obligations and develop feelings such as guilt.In the Mexican culture, masculinity is built around ideas of toughness and aggression and is associated with work . FemininAnother conspicuous aspect revealed in this study is the concept of the body. The body is considered to be private, yet these women are the last to govern their own body, and this lack of control prevents women from going to the doctor to be examined. In the case et hand, our subjects reported that the daughters were who advised their mothers to seek a PAP smear.Also, the lack of ownership of her own body justifies the woman's submission when faced with the extramarital behavior of her husband or partner. Hence, to confront this behavior bears a pricetag that women are not willing to pay. Such large cultural emphasis on sexuality often forces women to assume responsibility for the couple's failure.These beliefs, which negatively affect women's health, are not easy to overcome or transform. A common effort would be needed involving the society as a whole, given that the social context provides "...the narratives we use to talk and think about ourselves" . NeverthFrom the users' point of view, public health services in Mexico are deficient because of the long waiting periods and brief consultations. This perception was confirmed in the present study. Women delay visits to the doctor because of the long waiting periods, and when they finally decide to go it is may be too late. Hence, the social, psychological and economical costs of disease rise just as Becker refers in the Health Belief Model .These findings should be taken into account when planning the content of health programs which aim to modify behavior significantly.The author(s) declare that they have no competing interests.BEPV participated in the design and data analysis, wrote the first draft of the paper, reviewed different versions of manuscript, including final document; LLTG planned the current study and introduced the methodology, coordinated and helped to draft the manuscript; AMB participated in the development of the study and helped to draft the manuscript; MLC participated in the development of study and helped to draft the manuscript.All authors read and approved the final manuscript.


EHP, In their article published in the February issue of ortho-para directing, leading to non-coplanar halogenated biphenyls. The initial para and/or ortho halogenation makes for an even stronger ortho-para directive. Thus, the major components will be non-coplanar halobiphenyls. Only very small amounts of single ortho halobiphenyls can be found in commercial mixtures, and these mixtures are quite ineffective in eliciting effects associated with binding by the dioxin receptor.Commercial preparations contain few or no strictly coplanar PCB or polybrominated biphenyl congeners. This fact does not seem to be appreciated, and the impression is sometimes given that those very toxic congeners are in the environment. In fact, the coplanar polyhalogenated biphenyls probably receive way too much attention, most likely because they were used rather extensively in research; however, they were used only as model toxic congeners. The synthesis of strictly coplanar halogenated biphenyls  is much different from that of the commercial preparations . Phenyl is strongly


Promoting best gynecologic oncology practice is the subject of a manuscript from the Society of Gynecologic Oncologists of Canada. This manuscript is a descriptive report from a meeting that took place in Montreal involving members of various Canadians societies interested in the management of patients with gynecologic malignancies. Although this manuscript only partly deals with the objectives of the meeting and does not provide a clinical practice guideline report (to be reported later), this important paper may lead and stimulate other oncologic societies to embark on similar exercises.This month’s issue also contains the second part of a manuscript discussing the merits of naturally occurring anti-angiogenetic herbal compounds and their potential relevance to clinical practice. Encouragement is offered to explore the potential (and highly complex) effects in humans through clinical research. These agents have multiple effects and, presumably, a potential for multiple benefits.The Genitourinary Disease Site Group of the Cancer Care Ontario Program in Evidence-based Care undertook a tricky review of the value of maximal androgen blockade in the treatment of meta-static prostate cancer. In this issue, the authors note that many meta-analyses have been published and yet the magnitude of any benefit remains unclear. The reported benefits of these agents  is discussed—together with the their potentially negative impact on quality of life.imrt) treatment of head-and-neck cancers, Ballivy and colleagues address the subject of variation in target volumes and normal tissues during this form of radiation therapy delivery. The issue is not only important and relevant for head-and neck imrt, but also for all of radiotherapy as image guidance becomes the norm.In discussing the impact of the geometric uncertainties associated with intensity modulated radiotherapy (


Vacuum-Assisted Breast Biopsy (VABB) is effective for the preoperative diagnosis of non-palpable mammographic solid lesions. The main disadvantage is underestimation, which might render the management of atypical ductal hyperplasia (ADH), and ductal carcinoma in situ (DCIS) difficult. This study aims to develop and assess a modified way of performing VABB.A total of 107 women with non-palpable mammographic breast solid tumors BI-RADS 3 and 4 underwent VABB with 11G, on the stereotactic Fischer's table. 54 women were allocated to the recommended protocol and 24 cores were obtained according to the consensus meeting in Nordesterdt (1 offset-main target in the middle of the lesion and one offset inside). 53 women were randomly allocated to the extended protocol and 96 cores were excised . A preoperative diagnosis was established. Women with a preoperative diagnosis of precursor/preinvasive/invasive lesion underwent open surgery. A second pathologist, blind to the preoperative results and to the protocol made the postoperative diagnosis. The percentage of the surface excised via VABB was retrospectively calculated on the mammogram. The discrepancy between preoperative and postoperative diagnoses along with the protocol adopted and the volume removed were evaluated by Fisher's exact test and Mann-Whitney-Wilcoxon test, respectively.3, p = 0.037) and higher removed percentage of the lesion Irrespectively of the protocol adopted, 82.2% of the lesions were benign. 14.0% of the lesions were malignancies . 3.7% of the biopsies were precursor lesions. There was no evidence of underestimation in either protocols. In the standard protocol, the preoperative/postoperative diagnoses were identical. In the extended protocol, the postoperative diagnosis was less severe than the preoperative in 55.5% of cases , and preoperative ADH was totally removed. The phenomenon of discrepancy between diagnoses was associated with larger volume removed (8.20 ± 1.10 vs. 3.32 ± 3.50 cmThe extended protocol seems to totally excise precursor lesions, with minimal underestimation. This might possibly point to a modified management of ADH lesions. The increased use of mammograms has led to the frequent detection of breast lesions, which in turn require further evaluation ,2. The mTo establish a preoperative diagnosis, excisional biopsies, core needle biopsies -14 and vNonetheless, VABB has the disadvantage of histological underestimation, which renders the management of atypical ductal hyperplasia (ADH), and ductal carcinoma in situ (DCIS) somewhat difficult . Up to 5This prompts an interesting question: does the removal of larger volumes of breast tissue, obtained contiguously from a single site in the breast at directional vacuum-assisted 11-gauge needle biopsy, result in decreased underestimation?To answer this question, we have developed a modified VABB procedure using a considerably greater number of cores and offsets. The main objective of our study was:(i) to compare the extended way of performing VABB and the recommended way according to the consensus meeting in Norderstedt.3) excised on the management of non-palpable solid lesions without microcalcifications.(ii) to investigate the putative effects of greater volume  years, (mean ± SD: 54.25 ± 9.58) for non-palpable solid lesions of the breast without microcalcifications.Within this period, 355 women with non-palpable mammographic findings successfully underwent VABB; 107 biopsies were performed for mammographic solid tumor without microcalcifications .Before VABB, all patients were evaluated by one of the two radiologists of our Unit and a BI-RADS category was assigned. For lesions categorized as BI-RADS 3, follow-up was generally recommended. However, VABB was performed in the cases where family history was strongly positive or when the patient and referring physician expressed particular concern. In our unit, most of the BI-RADS category 5 cases are directly submitted for surgical biopsy in view of the great likelihood of cancer.During this period of time, VABB was performed by 5 surgeons. In all instances, a radiologist was present to assist in the targeting. All women were informed about the procedure by the surgeon performing the intervention. The Mammotome biopsy was performed on a digital prone table , using 11-gauge Mammotome vacuum probes, under local anesthesia.Women who underwent VABB were randomly allocated to two standard protocols. The first category (recommended protocol) included 54 women. We attempted to obtain 24 cores from these women, according to the consensus meeting in Nordesterdt. For this purpose, we used 1 offset-main target in the middle of the lesion and one offset inside the solid lesion. 12 cores were excised from each offset (12*2 = 24).In the second category (extended protocol), which included 53 women, we used one offset-main target in the middle of the solid lesion and 7 peripheral offsets, each one corresponding to a vertex of the hypothetically inscribed canonical heptagon in the round lesion, i.e. approximately 51 degrees away from each other. 12 cores were excised from each offset [(7+1)*12 = 96] in each patient of this group.In both groups, a clip was placed in the biopsy site. After VABB, a mammogram on the women confirmed the excision of the suspicious non-palpable solid tumor, showing the cavitation in the suspicious area. The cores were examined by a pathologist and a preoperative diagnosis was established.Afterwards, all women  with a preoperative pathological diagnosis of ADH, DCIS, LN, or invasive carcinoma, underwent open surgery under general anesthesia using a hook-wire. A second pathologist, blind to the preoperative results and to the protocol performed on the patient, examined the tissue removed by the surgeon. Thus, a second, postoperative diagnosis was independently and blindly made.2) of the solid tumour. More precisely, we measured the two dimensions of the solid tumour from the face mammogram using a ruler. Using the same method, we estimated the surface of the solid lesion that was left after VABB, using the formula for the area of circle segments. The subtraction of the above surfaces yielded the surface of the lesion excised. Also, the volume of specimens excised by VABB was determined in these patients.The percentage of the surface excised via VABB was retrospectively calculated on the mammogram, in the operated women of both protocols. The remaining surface was measured by calculating firstly the surface  subjected to VABB, the non-palpable solid tumor was characterized as BI-RADS 3 (probably benign). In 68 out of 107 procedures (63.6%) the suspicious lesion was classified as BI-RADS 4. BI-RADS 4A subclassification is presented in Table The specimens obtained by VABB revealed a benign lesion in 88 out of 107 cases (82.2%), irrespective of their BI-RADS classification. The predominant diagnoses were fibrocystic changes, fibroadenoma, and adenosis/sclerosing adenosis; 32 out of 88 cases (36.4%) were fibrocystic changes, 18 lesions out of 88 (20.5%) were fibroadenomas, and 22 out of 88 lesions were adenoses/sclerosing adenoses (25%). Epitheliosis with atypia (5.7%), papillomas (4.5%) and haemangiomas (2.3%) were less common.According to the pathological evaluation of the tissue samples obtained by VABB, in 15 out of 107 cases (14%), a malignancy was found, irrespective of the BI-RADS classification; 3.7% of the cases (4 out of 107) were precursor lesions [two cases of ADH and two cases of lobular neoplasia (LN)] .The random allocation of cases to the two protocols is depicted in detail in Table As described above, for each patient with a precursor or malignant lesion , two pathological diagnosis existed, one preoperative and one postoperative Table . The patThe phenomenon of less severe postoperative diagnosis was more frequent in the extended protocol  Table . As expeClinically significant haematoma developed in 5 out of 107 patients, 2 of them belonging to the standard protocol, and 3 to the extended protocol. None of them required surgical intervention. The rate of clinically important haematoma formation did not differ between the two protocols. Similarly, there was no statistically significant difference in the mean age of women between the two protocols.Finally, in 3 additional procedures (i.e. 3 out of 110), VABB could not be performed, as the solid tumor was too close to the examination plate; these 3 cases have not been included the study.The use of VABB on the Fischer's table has been proven effective for preoperative diagnosis of breast cancer , with veThe main disadvantage of VABB is underestimation -22. The Interestingly, underestimation was not detected in either protocol. In the standard protocol group, the relatively small sample may account for this observation. However, the excision of 96 cores implies a totally different context, i.e. that of a quasi-total excision of the non-palpable solid lesion. The quasi-total excision seems to encompass two constituents: lack of underestimation and frequently no residual precursor/preinvasive/invasive tissue being left after VABB (as documented by the postoperative examination). No residual tissue after VABB has been occasionally reported in the literature -29, but et al., showed that obtaining of more than 10 specimens per lesion leads to reduced underestimation of DCIS [With respect to the first constituent, total elimination of underestimation might seem intriguing, for various reasons. Results with larger (8G) needles have not led to the diminishment of underestimation ,31. Inde of DCIS . Althoug of DCIS , the latIndependently, it has been suggested that the radiological disappearance of the lesion cannot enable the total elimination of underestimation, in the context of 18 cores (range: 5–64 cores) . Howeveret al., (1998) have stated that the complete removal of the mammographic lesion does not ensure the complete excision of carcinomas [With respect to the second constituent, i.e. the lack of residual tissue, Liberman rcinomas . Indeed,On the other hand, a quasi-total excision of ADH might be a different case. When 96 cores were obtained, underestimation was not observed; this implies that a diagnosis of ADH seems accurate, not harboring an underlying carcinoma. Indeed, the percentage of ADH in our series (1.9%) was surprisingly low compared with the international literature on non-palpable solid tumors -20,34,35et al., (2002) have shown that to 'excise' of to 'sample' a lesion does not exert a significant effect on ADH underestimation; however, the distinction between 'excision' and 'sampling' was made within a range of less specimens, i.e. between 4 and 47 (median 15) specimens [In parallel, given the total excision in the case of ADH, interesting implications with respect to ADH management arise. It would be tempting to recommend follow-up for ADH cases after the performance of the extended protocol, as accurate diagnosis plus total excision seem a particularly attractive. At any case, more studies are needed to ascertain whether the current management of ADH might be modified. Liberman pecimens . Nonethepecimens , ADH stiCommenting on the population on which this study was based, most of the Mammotome biopsies were performed on BI-RADS category 4 patients, the most common indicator for the procedure ,39. The In our sample, 86% of the women that underwent VABB did not have breast cancer. All these women could have potentially undergone unnecessary open surgery. The malignancy rates were in accordance with the BI-RADS classification, and exhibited a statistically significant increasing trend along with the BI-RADS subgroups. According to the literature, the frequency of cancer in BI-RADS 3 lesions ranges from 0.5% to 2% ,8; in ouFinally, an important issue which should be addressed is the complication rate. More cores obtained could be associated with a higher degree of complications. However, in this study, VABB was well tolerated by the patients, and there was no significantly higher percentage of haematoma in the extended protocol. Larger studies monitoring the safety of the extended protocol seem though indispensable.This study presents and standardizes a new way of performing VABB which seems capable of reducing underestimation. The use of one main and 7 peripheral offsets, the excision of 96 cores, and the greatest excised volume might also possibly point to a modified management of women with ADH lesions. Further, comparative studies on larger series are needed to evaluate and possibly establish the extended VABB protocol.VABB = Vacuum-assisted breast biopsyADH = atypical ductal hyperplasiaDCIS = ductal carcinoma in situBI-RADS = Breast Imaging Reporting and Data SystemLN = lobular neoplasiaNHL = non-Hodgkin lymphomaIDC = invasive ductal carcinomaThe author(s) declare that they have no competing interests.GCZ: conception of the idea and design of the study, supervisor of VABB procedure, responsible for the critical setting of offsets in all patientsFZ: writing of the manuscript, evaluation of the analyzed findings, critical interpretation of the study results with respect to the international literatureTNS: statistical analysis, writing of the manuscriptDK: evaluation of all mammograms, assignment of BI-RADS categories, assisting at the targeting of the lesionAN: contributing to the design of the study, critical evaluation of pre-operative specimens, establishment of pre-operative diagnosisVO: comparison of pre-operative and post-operative diagnosis, critical evaluation of all discrepanciesPD: VABB performance in both protocolsMK: VABB performance in both protocolsCF: revising the manuscript for important intellectual contentJB: revising the manuscript for important intellectual content, gave the final approval of the version to be published


Background: Although the incidence of toxoplasmosis is low in the United States, up to 6000 congenital casesoccur annually. In September 1998, the Centers for Disease Control and Prevention held a conference abouttoxoplasmosis; participants recommended a survey of the toxoplasmosis-related knowledge and practices ofobstetrician-gynecologists and the development of professional educational materials for them.Methods: In the fall of 1999, surveys were mailed to a 2% random sample of American College of Obstetricians and Gynecologists (ACOG) members and to a demographically representative group of ACOGmembers known as the Collaborative Ambulatory Research Network (CARN). Responses were not significantly different for the randomand CARN groups for most questions .Results: Among 768 US practicing ACOG members surveyed, 364 (47%) responded. Seven per cent  had diagnosed one or more case(s) of acute toxoplasmosis in the past year. Respondents werewell-informed about how to prevent toxoplasmosis. However, only 12%  indicatedthat a positive Toxoplasma IgM test might be a false–positive result, and only 11% were aware that the Food and Drug Administration sent an advisory to all ACOG members in 1997 statingthat some Toxoplasma IgM test kits have high false–positive rates. Most of those surveyed  were opposed to universal screening of pregnant women.Conclusions: Many US obstetrician-gynecologists will encounter acute toxoplasmosis during their careers, butthey are frequently uncertain about interpretation of the laboratory tests for the disease. Most would not recommenduniversal screening of pregnant women.


In the last decade many studies have definitely shown that human papillomaviruses (HPVs) are the major cause of cervical carcinogenesis and, in the last few years, HPV testing has been proposed as a new and more powerful tool for cervical cancer screening. This issue is now receiving considerable attention in scientific and non scientific press and HPV testing could be considered the most important change in this field since the introduction of cervical cytology. This paper reports our prevalence data of HPV infection collected in the '90s, while a follow up of these patients is ongoing.For this study we used polymerase chain reaction (PCR) to search HPV DNA sequences in cervical cell scrapings obtained from 503 asymptomatic women attending regular cervical cancer screening program in the city of Genova, Italy. All patients were also submitted to a self-administered, standardized, questionnaire regarding their life style and sexual activity. On the basis of the presence of HPV DNA sequences women were separated into two groups: "infected" and "non infected" and a statistical analysis of the factors potentially associated with the infection group membership was carried out.The infection rate was 15.9% and the most frequent viral type was HPV 16.Our HPV positivity rate (15.9%) was consistent to that reported by other studies on European populations. Although the Pap-test has given a great contribution to early diagnosis of cervical cancer, this is still a very common, worldwide distributed, female neoplasm and a major cause of death in developing countries. Moreover, in developed countries, the treatment of preneoplastic cervical lesions is a considerable public health problem. There is now strong evidence that infection with carcinogenic types of HPV represents a nearly universal event in cervical carcinoma development and sexual transmission is the predominant mode of HPV infection -3. The rHPV testing for cancer-associated HPV DNA is now accepted as a viable and validated option in the management of women with equivocal cytologic findings -7 and, iNevertheless, the lower specificity and the high cost of HPV testing make its use in primary cervical cancer screening still questionable. At the same time very promising trials are ongoing to evaluate the efficacy of prophylactic HPV 16 vaccines ,12. ThesThis study included 514 women attending the Istituto Nazionale per la Ricerca sul Cancro in Genova  for their routine annual Pap smear from June 1992 to June 1993. At the time of their visit all the participants were informed of the research and its purpose and gave their informed consent. Then, they were invited to fill in a self administered questionnaire including items about lifetime number of male sexual partners, age at first intercourse, history of pregnancy and sexually transmitted diseases, contraceptives methods, smoking, prior abnormal Pap smears and other variables. Pap smears were all reviewed by the same pathologist according to the Bethesda System 1991 , 200 ng of sample DNA, double distilled water. The apmplification was performed in a DNA Thermal Cycler (Perkin Elmer/Cetus Instruments), using the following program set: 95°C for 30 sec., 55°C for 30 sec., 72°C for 1 min. for a total number of 30 cycles plus an additional 9 min. at 72°C. Separate rooms were used for: preparation of DNA template, preparation and storage of reagents, setting up the amplification reaction. All reagents used in PCR were prepared, aliquotted and stored in an area that was free of PCR- amplified products. Amplification of a single copy human gene (β-globin), as control of DNA suitability for amplification, was performed in each reaction tube; we also used He-La cells as positive control and K562 cells as negative control in each reation.+  using the Dot-blot apparatus  under constant vacuum conditions. Replicate membranes were used for Hybridization with each of the type specific probes  and the generic probe mix (GP1 and GP2). For detection we used the ECL chemoilluminescence kit .10 μl of the amplification mixture were analysed by electrophoresis in 1.5 agarose gel and visualized by UV light after ethidium bromide staining. Dot-blot analysis was then performed using 2 and 5 μl of the PCR mixture after alkaline denaturation treatment (NaOH 1.5 M and NaCl 0.5 M). DNA was transferred onto nylon membranes Hybond NThe associations between HPV infection (defined as a positive HPV-PCR) and individual covariates, including age, age at first sexual intercourse, marital status, smoking habits, education, number of lifetime partners and use of oral contraceptives was investigated using univariate and multiple logistic regression (MLR) analyses. The analyses were done with the SPSS Statistical Software (SPSS Inc. Chicago Illinois). Odds ratios point estimates (OR) and their 95% confidence intervals (95% CIs) were computed by MLR procedure for binary data to estimate the association between each covariate levels and HPV infections while adjusting for the effect of other variables retained in the model. Statistical tests were considered to be significant if the p value was 0.05 or less.Amongst 514 women enrolled in this study, 503 samples were adequate for PCR. The most important patient characteristics are shown in table In the nineteenth century some investigators noticed that cervical cancer was almost exclusively detected in married women, being rare in the unmarried ones and exceptional in nuns ,21. SincIn our population the "higher education" was the most represented group (205/436 subjects), and this may have affected the observed association with HPV infection, due to a an easier access to health system services.According to other studies, the most frequent viral type was HPV 16 , an impoThe author(s) declare that they have no competing interests.MGC conceived of the study, carried out part of the molecular analysis and drafted the manuscript, AP helped to draft the manuscript, DFM performed the statistical analysis, GP carried out most of the molecular assays, ERC and RS enrolled the patients, CAG participated in the design and coordination of the study and helped to draft the manuscript.The pre-publication history for this paper can be accessed here:


Consensus techniques have been used previously to create explicit criteria to prioritize cataract extraction; however, the appropriateness of the intervention was not included explicitly in previous studies. We developed a prioritization tool for cataract extraction according to the RAND method.Criteria were developed using a modified Delphi panel judgment process. A panel of 11 ophthalmologists was assembled. Ratings were analyzed regarding the level of agreement among panelists. We studied the effect of all variables on the final panel score using general linear and logistic regression models. Priority scoring systems were developed by means of optimal scaling and general linear models. The explicit criteria developed were summarized by means of regression tree analysis.Eight variables were considered to create the indications. Of the 310 indications that the panel evaluated, 22.6% were considered high priority, 52.3% intermediate priority, and 25.2% low priority. Agreement was reached for 31.9% of the indications and disagreement for 0.3%. Logistic regression and general linear models showed that the preoperative visual acuity of the cataractous eye, visual function, and anticipated visual acuity postoperatively were the most influential variables. Alternative and simple scoring systems were obtained by optimal scaling and general linear models where the previous variables were also the most important. The decision tree also shows the importance of the previous variables and the appropriateness of the intervention.Our results showed acceptable validity as an evaluation and management tool for prioritizing cataract extraction. It also provides easy algorithms for use in clinical practice. Cataract extraction is the most frequently performed surgical intervention in developed countries . BecauseThe RAND-UCLA group in the United States  developeThe purpose of the current study was to develop priority criteria, using the RAND method, for patients undergoing cataract extraction and to consider the appropriateness of the indication.We based our development of priority criteria on a modification of the RAND appropriateness method. We first developed criteria to measure the appropriateness of the use of cataract surgery, according to the following steps.First, an extensive literature search was performed to summarize existing knowledge concerning efficacy, effectiveness, risks, costs, and opinions about the use of phacoemulsification for cataract extraction.Second, from this review, a comprehensive and detailed list of mutually exclusive and clinically specific scenarios (indications) was developed in which cataract surgery might be performed using phacoemulsification. Regarding cataract surgery, these indications included the following variables: presence of ocular comorbidities , visual acuity in the cataractous eye and the contralateral eye, visual function, expected visual acuity after surgery, surgical technical complexity, and type of cataract. A total of 765 indications resulted from all possible combinations of the variables described previously and the respective categories. A description of all variables and their categories was reported previously .Third, we compiled a national panel of expert ophthalmologists who were nationally recognized specialists in the field. Their names were provided by their respective medical societies and members of our research team.The appropriateness ratings were confidential and took place in two rounds, using a modified Delphi process. Cataract surgery for a specific indication was considered appropriate if the panel's median score was between 7 and 9 without disagreement, inappropriate if the value was between 1 and 3 without disagreement, or uncertain if the median rating was between 4 and 6 or if the members of the panel disagreed. Disagreement was defined as occurring when at least one third of the panelists rated an indication from 1 to 3 and at least another third rated it from 7 to 9.In a third round, we selected the scenarios judged in the second round as appropriate or uncertain. We selected the following previous variables for this priority round: appropriateness, presence of ocular comorbidities, visual acuity in the cataractous eye, visual function, visual acuity in the contralateral eye, expected visual acuity after the intervention, the type of cataract , and the new variable social dependence. Selection of the variables was based on the review of the bibliography and the research team best judgment. Figure We requested that the same panelists score the 310 scenarios. Ratings also were scored on a 9-point scale, with 9 indicating the highest priority and 1 the lowest compared to other scenarios. Priority in the context of cataract extraction was defined as the benefit that the patient may obtain from undergoing surgery. The higher the benefit was for the patient, for a similar risk of complications, the higher the priority of the intervention was. Benefit was defined in terms of quality-of-life improvement. Three categories, from higher to lower priority, were established. The priority of cataract surgery was considered high for a specific indication if the panel's median rating was between 7 and 9 without disagreement, low if the value was between 1 and 3 without disagreement, or intermediate if the median rating was between 4 and 6 or if the panel members disagreed. Disagreement was defined as occurring when at least one third of the panelists rated an indication from 1 to 3 and at least another third rated it from 7 to 9. This method did not attempt to force panelists to reach agreement on the priority.To determine the use of all theoretical indications created in clinical practice, data related to the algorithm variables were gathered for 936 patients on a waiting list to undergo cataract extraction exclusively by phacoemulsification from the ophthalmologic services of six hospitals of our area. The number of theoretical indications used in clinical practice was calculated for each of the three main diagnostic groups; simple cataract, cataract with diabetic retinopathy, or cataract with other ocular pathologies that may affect the visual prognosis.We estimated the mean priority rating of all indications for each panellist and the median and the deviation from the panel mean. We created a continuous priority score, which is the sum of the ratings of the 11 panelists, standardised to a 0 to 100-point scale.Determinants of priority scores and their contribution to the model explanation were assessed with the general linear model , with thWe used two methods to determine priority coefficients for the categories of each variable that should permit rapid estimation of a priority score in practice. In the first model, the optimal scaling method ,14 consiIn the second model, we performed the same estimation using a general linear model in which we created dummy variables from the categories of the independent variables, with the priority score the dependent variable. Weights for categories within each variable were based on beta values from the general linear model, with weights transformed to a 0 to 100 point scale distributed across variables as the corresponding proportion.Therefore, in both cases weights are apportioned among variables so that the scores range from 0 to 100. The scores obtained with both methods for all scenarios were compared with the original panel priority scores using Pearson and Spearman correlation coefficients.Algorithms in decision-tree form were compiled by means of classification and regression trees (CART) analysis . CART waAll statistical analyses were performed using the SAS for Windows, version 8, except for CART analysis in which we used S-Plus 2000 software , and the optimal scaling analysis in which we used SPSS v.12 statistical software.A panel of 11 experts scored 310 scenarios. Figure Table We evaluated the contribution of each variable included in the algorithm by means of general linear and logistic regression models Table . GloballThe logistic regression model indicated that the same three variables were the most important but in a different order, i.e., the visual function, the visual acuity in the cataractous eye, and the anticipated postoperative visual acuity. The other variables were not statistically significant in this model. Appropriateness of the intervention, despite being forced to enter in the model after the rest of the variables to avoid collinearity, remained highly significant and fourth in the order of importance in both models.We present two alternative methods of obtaining a simpler way to obtain the priority score: optimal scaling and general linear models Table . The antWe studied the correlation of the scores obtained between the two scoring methods with the priority scores of the original panel. The Pearson correlation coefficient was 0.95 for the optimal scaling model and 0.97 for the general linear model. Using the Spearman correlation coefficient, the results were 0.94 and 0.97, respectively.Finally, the criteria developed by the panel of experts were summarized by CART analysis on a decision regression tree Figure , which sWe collected information on 936 patients to identify which of the theoretical indications were used in clinical practice. Globally, 102 of 310 theoretical (33%) indications were assigned to 936 patients. By diagnostic group, for simple cataract, 53 of 86 theoretical (62%) indications were assigned to 761 patients with that diagnosis. Of those with diabetic retinopathy, 11 of 118 theoretical (9%) indications were assigned to 19 patients. Of those with other ocular pathologies, 38 of 106 theoretical (35.8%) indications were assigned to 156 patients with that diagnosis.Cataract extraction has been chosen by different researchers to develop priority scoring systems of ,5,16. ThTo develop our system of prioritization, we used the RAND methodology. Although the RAND methodology was developed primarily to create appropriateness explicit criteria, it also can be used for other purposes . To the best of our knowledge, this is the first time the RAND methodology has been used to develop priority criteria linked with previous appropriateness criteria.We first determined the appropriateness of the indication criteria in two panel rounds. We then selected those indications ultimately classified as appropriate or uncertain. The fact that the appropriate indications were entered in the prioritization algorithm seems logical; however, why should uncertain surgical indications be included? First, because as in some studies in which appropriateness had been related to outcomes, the outcomes of the appropriate and uncertain cases seemed similar ,20. UnceWe initially spent considerable effort defining what we consider priority. Priority differs depending on the health problem and its probability of leading to death or important permanent handicaps if untreated. That introduces the concept of urgency, i.e., if not treated promptly death will result , as withAs we pointed out previously, most priority criteria developed thus far did not consider the appropriateness of the intervention. Some may assume that all patients on the waiting list are appropriate candidates, which it is not necessarily true. Our results from both the general linear model and the CART analysis indicated that appropriateness was an important variable for the panelists when scoring the priority of each scenario. As reported previously, the rate of inappropriate interventions ranges from 1.3%  to 7.7% To the best of our knowledge, one recent study attempted to match appropriateness and priority . HoweverWe presented the results of the panel scoring as a categorical variable or continuous variable. To construct the categorical variable, with three categories of priority (from high to low), we used the same algorithm to develop the three RAND categories of appropriateness . An advantage is that this system may match current priority setting norms in some places such as ours. A disadvantage is that it can seem artificial, or with no conceptual base, to have those categories. On the other hand, the continuous variable provides a priority order for all scenarios, but it can seem less practical. Daily use will determine which one is more useful.On the other hand, to have an easily usable algorithm, we presented our results simply. We presented two alternative priority scoring systems, one developed by optimal scaling and the other by a classical general linear model. The importance of the variables and the weights assigned to the different categories of variables were similar. In addition, both had very high Pearson and Spearman correlations with the original panel scores. An alternative way to use the real panel scores can be provided by simple software that allows the final score to be obtained by clicking on the categories of each variable. We are working on this alternative method.Finally, we presented a decision tree that provides a global idea of which clinical situations should be treated first and indicates the importance of assessing the appropriateness of the intervention for prioritization.In conclusion, this is the first study to combine the appropriateness of an indication with priority criteria following the same methodology. Our results show that appropriateness plays an important role in priority decision making process. The variables included also were identified by other authors, which adds validity to our criteria. We also provide alternative scoring algorithms that allow ease of use of our criteria in clinical practice. Use of them will let us know which one is more useful. Nevertheless, more sophisticated future proposals should include the algorithm in flow models [28] that allows management of patients placed on a waiting list.Variables included in the prioritization algorithm.1. Presence of ocular comorbidities.a. No presence or simple cataract. Patients who do not present with any other ocular pathology in the operated eye that may affect the visual prognosis. This includes glaucoma controlled by medication or surgery without deteriorating central vision, myopia without retinopathy, and vascular occlusion not affecting central vision.b. Cataract with diabetic retinopathy, according to the Early Treatment Diabetic Retinopathy Study classification. This includes nonproliferative diabetic retinopathy, proliferative diabetic retinopathy without high-risk characteristics, cases in which only phacoemulsification will be performed, and the absence of macular edema.c. Cataract with other ocular pathologies that may affect visual prognosis. This includes retinopathies: retinal detachments that have been treated surgically, retinitis from any cause; maculopathies: macular degeneration due to toxicity , medications, hereditary factors, extreme myopia, age-related macular degeneration; vasculopathies: branch retinal vein occlusion, venous thrombosis; neuropathies: optical neuritis and glaucomatous neuropathy; amblyopia; corneal opacity or corneal dystrophies (except Fuchs' dystrophy): leukoma without keratoplasty indication.2. Preoperative visual acuity in the cataractous eye. Best-corrected visual acuity measured by Snellen optotypes. Three visual acuity categories :≥ 0.5; 0.2–0.4; = 0.13. Visual acuity preoperatively in the contralateral eye. Similar to the previous category.4. Visual function. Effect of cataract on the quality of life of the patient. Four categories:a. Unimpaired. The patient reports no impairment in visual function.b. Glare . Visual perception diminished depending on light intensity (outside or inside).c. Recreational difficulties. Visual difficulties with activities that do not affect patient autonomy, e.g., watching TV or reading.d. Difficulties with activities of daily living. Activities that affect patient autonomy, including glare when driving if this affects the patient's work.5. Expected visual acuity postoperatively. A subjective judgment of the ophthalmologist before the intervention. This is the visual acuity that the patient is expected to reach after surgical intervention based on the preoperative ophthalmologic examination. Three visual acuity categories: ≥ 0.5; 0.2–0.4; = 0.1.6. Social dependence. Situation in which the patient is dependent on a relative, friend, or other care giver for help with the activities of daily living.7. Laterality of cataract. Unilateral or bilateral cataract.8. Appropriateness. Appropriate or uncertain indication based on previously developed explicit criteria.The author(s) declare that they have no competing interests'JMQ conceived of the study, coordinated and participated in the design of the study, and drafted the manuscript. AE participated in the design and helped to draft the manuscript. AB performed the statistical analyses and drafted the manuscript. The IRYSS-Appropriateness Cataract Group participated in the design of the study and helped to draft the manuscript. All authors read and approved the final manuscript. The IRYSS-Appropriateness Cataract group included the following co-investigators: Dr. Jesús Martínez-Tapias, Dr. Eduardo Aguayo ; Dr. Emilio Perea-Milla ; Dr. Juan Ramón Lacalle (Universidad de Sevilla); Dra. Marisa Baré, Dra. Gemma Navarro ; Dra. Elena Andradas, Dr. Juan Antonio Blasco ; Inmaculada Arostegui ; Berta Ibáñez (Fundación Vasca de Innovación e Investigación Sanitarias); Dr. Txomin Alberdi ; Dra. Sandra de Fernando ; Dra. Fabiola Eder ; Dr. Jose Ma Beguiristain, Dra. Belén Elizalde ; Dra. Idoia Garai ; Dr. Joseba Pérez de Arriba ; Dr. Jose Ignacio Pijoan ; Dr. Felipe Aizpuru ; Nerea González, Iratxe Lafuente, Urko Aguirre .The pre-publication history for this paper can be accessed here:


Data on 2,754 cases and 18,565 controls from a multinational hospital-based, case-control study were analysed to determine whether observed associations between combined oral contraceptives and breast cancer are similar for oral contraceptives with varying types and doses of oestrogens and progestins. After stratifying on duration of use, risk was found to be increased in current and recent users, and to decline with time since last use. These associations, of similar strength, were observed for users of products that contain mestranol and ethinyl estradiol, for women who used preparations with progestins derived from 19-nortestosterone and 17-alpha-hydroxyprogesterone, and for those who took preparations with relatively higher and lower doses of oestrogen. When products with equal doses of the same oestrogen or progestin and varying doses of the other hormonal constituent were considered, slightly higher relative risks per year of use were estimated for users of products with relatively higher than lower doses of either the constituent oestrogen or progestin, but the differences in relative risk could readily have occurred by chance. This study provides no evidence that risk of breast cancer in users of oral contraceptives varies by the type of oestrogen or progestin consumed.


Analysis of genomes evolving via block-interchange events leads to a combinatorial problem of sorting by block-interchanges, which has been studied recently to evaluate the evolutionary relationship in distance between two biological species since block-interchange can be considered as a generalization of transposition. However, for genomes consisting of multiple chromosomes, their evolutionary history should also include events of chromosome fusions and fissions, where fusion merges two chromosomes into one and fission splits a chromosome into two.n2) time algorithm to efficiently compute and obtain a minimum series of fusions, fissions and block-interchanges required to transform one circular multi-chromosomal genome into another, where n is the number of genes shared by the two studied genomes. In addition, we have implemented this algorithm as a web server, called FFBI, and have also applied it to analyzing by gene orders the whole genomes of three human Vibrio pathogens, each with multiple and circular chromosomes, to infer their evolutionary relationships. Consequently, our experimental results coincide well with our previous results obtained using the chromosome-by-chromosome comparisons by landmark orders between any two Vibrio chromosomal sequences as well as using the traditional comparative analysis of 16S rRNA sequences.In this paper, we study the problem of genome rearrangement between two genomes of circular and multiple chromosomes by considering fusion, fission and block-interchange events altogether. By use of permutation groups in algebra, we propose an FFBI is a useful tool for the bioinformatics analysis of circular and multiple genome rearrangement by fusions, fissions and block-interchanges. For the past two decades, genome rearrangements have been studied and can be modelled to learn more about the evolution of mitochondrial, chloroplast, viral, bacterial and mammalian genomes . To evaln2) time algorithm, where n is the number of genes, to solve the so-called block-interchange distance problem that is to find a minimum series of block-interchanges for transforming one linear chromosome into another. Later, we  and  of αp. That is, ρ2ρ1 is a block-interchange event affecting on α by swapping  and , two non-intersecting blocks in α.Recently, Lin et al.  further α into another I can be expressed by a product of 2-cycles, say ρkρk-1...ρ1, such that ρkρk-1...ρ1α = I . This property implies that Iα-1 contains all information that can be utilized to derive ρ1, ρ2,...,ρkfor transforming α into I.As discussed above, any series of fusions, fissions and block-interchanges required to transform one circular multi-chromosomal genome α as a product of 2-cycles [α, let f(α) denote the number of the disjoint cycles in the cycle decomposition of α. Notice that f(α) counts also the non-expressed cycles of length one. For example, if α =   is a permutation of E = {1, 2,..., 5}, then f(α) = 3, instead of f(α) = 2, since α =   (3). Then the following lemma shows the lower bound of the number of 2-cycles in any product of 2-cycles of a permutation.It is well known that every permutation can be written as a product of 2-cycles. For example,  =   . However, there are many ways of expressing a permutation 2-cycles . Given aLemma 1 Let α be an arbitrary permutation of E = {1, 2,..., n}. If α can be expressed as a product of m 2-cycles, say α = α1α2...αm with each αi being 2-cycle, then m ≥ n - f(α).Proof. We prove this lemma by induction on m. The lemma is true if m = 0, since α = 1 then, meaning that f(α) = n, and hence m = n - f(α) = 0. Suppose now that the lemma holds for any permutation that can expressed as a product of less than m 2-cycles, where m > 0. Let α' = α2α3, ...,αm. Then by the induction hypothesis, we have m - 1 ≥ n - f(α'). Since α = α1α' and α1 is a 2-cycle, α1 operates on α' either as a fusion by joining two cycles of α' into one cycle  = f(α') - 1) or as a fission by splitting one cycle of α' into two cycles  = f(α') + 1). Whichever α1 operates on α', we have f(α) ≥ f(α') - 1. As a result, m = (m - 1) + 1 ≥ n - f(α') + 1 = n - (f(α') - 1) ≥ n - f(α).     □n genes can be expressed by a permutation of E = {1, 2,..., n}. Given two such genomes G1 and G2 over the same gene set E, the genome rearrangement distance between G1 and G2, denoted by d, is defined to be the minimum number of events needed to transform G1 into G2, where the events allowed to take place are fusions, fissions and block-interchanges. In this section, we shall show that there is an optimal series of events required to transform G1 into G2 such that all fusions come prior to all block-interchanges, which come before all fissions. Here, such an optimal scenario of genome rearrangements is referred as in canonical order.As mentioned previously, each circular multi-chromosomal genome with Lemma 2 d = d.Proof. Let Φ = <σ1, σ2,...,σδ> be an optimal series of events required to transform G1 into G2. Clearly, Φ' = <σδ, σδ-1,...,σ1> is an optimal series of events for transforming G2 into G1 by reversing the role of every event σi, where 1 ≤ i ≤ δ, such that σi is a fission  in Φ' if σi is a fusion  in Φ.Lemma 3 There is an optimal series of events required to transform G1 into G2 such that every fission occurs after every fusion and block-interchange.Proof. Let Φ = <σ1, σ2,...,σδ> be an optimal series of events needed to transform G1 into G2. Of course, if every fission occurs after every fusion and block-interchange in Φ, then the proof is done. Now, suppose that not every fission occurs after every fusion or block-interchange in Φ. Then let i be the largest index in Φ such that σi is a fission preceding σi+1 that is either a fusion or a block-interchange. We can then obtain a new optimal series Φ' = <σ1,...,σi-1, σi+2,...,σδ> to transform G1 into G2 such that σi splits a chromosome α into α1 and α2. If σi+1 is a fusion, then we assume that it joins two chromosomes β1 and β2into β; otherwise, if σi+1 is a block-interchange, then assume that it affects β1 such that β1 becomes β through a block-interchange. Clearly, if neither β1 nor β2 is created by σi, then the desired series Φ' is obtained by swapping σi and σi+1 in Φ . If both β1 and β2 are created by σi, then the net rearrangement of σi (a split operation) followed by σi+1 (a joint operation) either has no effect on α or becomes a block-interchange affecting α. By removing σi and σi+1 from Φ or replacing them with an extra block-interchange, we thus obtain a new optimal series of the events transforming G1 into G2 with strictly less than δ events, a contradiction. Hence, we assume that only one of β1 and β2 is created by σi and without loss of generality, let β1 = α1. Now, we consider the following two cases.σi+1 is a fusion. For simplicity of discussion, we let α = , β2 = , σi =  and σi+1 = , where 1 <x <y - 1 and y <z. Then the net rearrangement caused by σi and σi+1 is to transform α and β into α2 =  and β = . In fact, this rearrangement can also be done by first joining α and β2 into  via σi+1 and then splitting  into α2 and β via . In other words, we can obtain Φ' by letting σi+1 and x, y).Case 1: σi+1 is a block-interchange. Clearly, the net rearrangement caused by σi and σi+1 is to transform α into β and α2, which is equivalent to the rearrangement by first applying σi+1to α and then further splitting it into β and α2 via σi. Then Φ' is obtained by swapping σi and σi+1 in Φ.Case 2: G1 into G2 such that all fissions come after all fusions and block-interchanges.In other words, we can always obtain Φ' from Φ according to the method described above. Repeating this process on the resulting Φ', we can finally obtain an optimal series of events that are required to transform Lemma 4 There is an optimal series of events required to transform G1 into G2 in a canonical order such that all fusions come before all block-interchanges, which come before all fissions.Proof. Let Φ = <σ1, σ2,..., σδ> be an optimal series of events required to transform G1 into G2. If there are no fusions or block-interchanges, then the proof is completed. If not, according to Lemma 3, we may assume that all fusions and block-interchanges occur earlier than all fissions. Let i be the index of the last non-fission in Φ and also let G' be the resulting genome after all σ1, σ2,...σi have affected G1. Since Φ is optimal, it is straightforward to see that Φi = <σ1, σ2,...,σi> is an optimal series of fusions and block-interchanges needed to transform G1 into G'. As discussed in the proof of Lemma 2, σi, σi-1,...,σ1> is an optimal series of fissions and block-interchanges for transforming G' into G1. Moreover, by Lemma 3, we can obtain G' into G1 such that all block- interchanges in G1 into G', and all its fusions occur before all its block-interchanges. Therefore, there is an optimal series of events needed to transform G1 into G2 such that all fusions come earlier than all block-interchanges, which come before all fissions.     □G1 and G2 are two given linear multi-chromosomal genomes, where G1 =   and G2 =  . Then the optimal scenario between them is a fission, splitting  into (1) , followed by a fusion, joining (1) and  to . However, this optimal scenario can not be transformed into another in the canonical order according to the steps as described in Lemmas 3 and 4. Actually, there is no an optimal scenario between such two linear genomes using any two rearrangement events that begin with a fusion.It is worth mentioning that an optimal scenario in a canonical order does not necessarily exist for linear multi-chromosomal genomes. For example, suppose that α and I be two given circular multi-chromosomal genomes over the same gene set E = {1, 2,...,n}. Here, we assume that the genes in I are sorted in the order of increasing and consecutive numbers, and that gene i + 1 is on the right side of gene i within the same chromosome, where 1 ≤ i ≤ n - 1. For example, I =    if I has three circular chromosomes with two, three and four genes, respectively. In this case, the computation of d and its corresponding optimal scenario can be considered as a problem of sorting α using the minimum set of operations, including fusions, fissions and block-interchanges.Let ρλρλ - 1 ... ρ1 is a product of 2-cycles that corresponds to an optimal series Φ of fusions, fissions and block-interchanges for transforming α into I. Then Φ = ρλρλ - 1...ρ1 = Iα-1 and by Lemma 1, λ ≥ n - f(Iα-1). If Φ' = λ 2-cycles with Φ' = Iα-1, then the number of 2-cycles in Φ' that function as fusions or fissions must be greater than or equal to that in Φ; otherwise, the total number of fusions, fissions and block-interchanges in Φ' for transforming α into I must be less than that in Φ, a contradiction. The reason is that a fusion or fission requires only one 2-cycle for rearrangement, whereas a block-interchange requires two 2-cycles. In other words, the number of 2-cycles serving as the fusions and fissions is minimum in any optimal series of events.Suppose that d and its optimal scenario of rearrangement events in a canonical order. Let χ(α) and χ(I) denote the numbers of chromosomes in α and I, respectively, and let α = α1α2...αχ(α) and I = I1I2...Iχ(I). Then, an undirected graph α,I) = }.• I = {I1, I2,...,Iχ(I)}.• αi, Ij) | 1 ≤ i ≤ χ (α), 1 ≤ j ≤ χ (I), and αi and Ij have at least a common gene}.• α = α1α2...α5 =      and I = I1I2 ... I6 =      . Then the induced graph α,I) is shown in Figure α and I are independent sets in α, I) . A connected component of α,I) is defined to be a maximal subgraph of α,I) such that there exists a path between any pair of vertices in this subgraph. For example, the induced α,I) as shown in Figure Ik of I there are two genes that appear in two different chromosomes αi and αj of α, then  ∈ αj, Ik) ∈ αi and αj belong to the same connected component in α,I).For instance, suppose that 1, 2,...,ω} denote the collection of all connected components in α,I). For each 1 ≤ i ≤ ω, let βi and Ji denote the chromosomes in α and I, respectively, whose corresponding vertices belong to i in α,I). Let gene(βi) and gene(Ji) be the collections of the genes in all chromosomes of βi and Ji, respectively. Then gene(βi) = gene(Ji) and gene(βi) ∩ gene(βj) = ∅ for any 1 ≤ j ≠ i ≤ ω. Let ni be the number of genes in gene(βi). Clearly, n = n1 + n2 + ... + nω. In addition, it can be verified that Iα-1 = (J1J2Jωf(Iα-1) = f.According to the properties above, we then find a product Φ of 2-cycles so that Φα, I) of a given instance α and I has exactly one connected component. Let Φ = <σ1, σ2, ...., σδ> be an optimal series of events for transforming α into I in which all fusions precede all block-interchanges that further precede all fissions. Let nfu, nbi and nfi denote the numbers of fusions, block-interchanges and fissions, respectively, in Φ. Then δ = nfu + nbi + nfi. In the following, we shall show that Φ can be expressed by a product of n - f(Iα-1) 2-cycles in which the number of 2-cycles functioning as the fusions and fissions is minimum.To simplify our discussion, throughout the rest of this section we assume that the induced αi and αj in α with (αiIk) ∈ αj, Ik) ∈ αi and αj to one chromosome; otherwise, Ik can not be formed from α by a fission later. Since all needed fusions come together in the beginning of Φ, nfu = χ(α) - 1, which is the lower bound of the number of fusions required in any optimal series of events for transforming α into I. After these nfu fusions, the resulting α becomes only one chromosome. Since the next nbi block-interchanges are intra-chromosomal mutations, we have nfi = χ(I) - 1. Actually, χ(I) - 1 is the minimum number of the required fissions in any optimal series of events for transforming α into I, since it is the minimum number of the fusions used in the corresponding optimal series of events to transform I into α.It should be noticed that the chromosomes considered here are disjoint . Hence, for any two chromosomes ρ, we use x ∈ ρ to denote that x is a number in ρ. For any two x ∈ ρ and y ∈ ρ, they are said to be adjacent in ρ if ρ(x) = y or ρ(y) = x. Next, we show a way to derive nfu 2-cycles from Iα-1 such that these 2-cycles function as the fusions that join all chromosomes of α to a single one, if α has multiple chromosomes, where nfu = χ(α) - 1. For simplicity, later in the text we use "cycle in Iα-1" to represent " cycle in the cycle decomposition of Iα-1" in meaning, unless a possible confusion may arise.Given any cycle Lemma 5 Let αi and αj be any two disjoint cycles in α. Then there must exist a cycle in Iα-1 that contains two numbers x and y such that x ∈ αi and y ∈ αj.Proof. Since we assume that the induced α, I) contains exactly and only one connected component, and αi and αj contain some numbers u and v, respectively, such that both u and v are in a cycle Ik of I. Notice that u ∉ αj and v ∉ αi. Suppose that there is no cycle in Iα-1 that contains two numbers x and y such that they are in these two different cycles of α, say x ∈ αi and y ∈ αj. Then all numbers in any cycle of Iα-1 are contained in some cycle of α. Without loss of generality, let Ik =  and let p <q for simplifying the discussion. For each 1 ≤ x ≤ p, let α(ax) = bx. Then we have Iα-1(bx) = ax+1 (since Iα-1α = I), which means that both bx and ax+1 are in the same cycle of Iα-1 and hence they are also in the same cycle of α. If ax is in αi, then bx is also in αi, which further leads to ax+1 ∈ αi. Since u = a1 is in αi, all a2, a3, ..., ap are in αi. As a result, both of u and v are in αi, a contradiction. Hence, there exists a cycle in Iα-1 that contains x and y such that x ∈ αi and y ∈ αj.The following lemma can be easily verified.Lemma 6  =   , where 1 ≤ i <j.αi and αj of α, we can find two numbers x and y in a cycle of Iα-1, say β, such that x ∈ αi and y ∈ αj. Let β = , where q ≥ 2. Then we consider the following two cases. Case 1: x and y are adjacent in β. For simplicity, let x = aq-1 and y = aq. Then by Lemma 6, β =  (aq) . Case 2: x and y are not adjacent in β. Let x = ap and y = aq, where 1 ≤ p <q - 1. Then β =    according to Lemma 6. In other words, we can derive a 2-cycle  from β such that it can join αi and αj to one cycle. After αi, and αj are joined together via , the number of the cycles (including 1-cycles) in the resulting Iα-1 increases by one. Repeatedly based on the procedure above, we can derive consecutive nfu 2-cycles from Iα-1, say φ1, φ2,...,χ (α) cycles in α to a single one, where nfu = χ(α) - 1. In other words, φ1, φ2,...,χ(α) - 1 fusions that transform genome α with χ(α) chromosomes into a genome, denoted by α', with a single chromosome. Clearly, we have α' = φ1α, Iα'-1 = Iα-1 φ1φ2 ... f(Iα'-1) = f(Iα-1) + nfu. Hence, we can immediately claim the following.According to Lemma 5, for any two cycles Claim 1 α' = φ1α, Iα'-1 = Iα-1 φ1φ2 ... f(Iα'-1) = f(Iα-1) + nfu, where nfu = χ(α) - 1.χ(I) > 1. Similarly as the discussion above, we can derive consecutive nfi 2-cycles from α'I-1, say ψ1, ψ2, ..., I with χ(I) chromosomes into a genome, denoted by I', with only one chromosome, where nfi = χ(I) - 1 and α'I-1 is the inverse of Iα'-1 -1). Then we have I' = ψ1I (hence ψ1ψ2 ... I' = I), α'I'-1 = α'I-1ψ1ψ2 ... f(α'I'-1) = f(α'I-1) + nfi. Conversely, we can use ψ1 as fissions to split I' with one chromosome into I with nfi chromosomes. Since α'I-1 is the inverse of Iα'-1, it can be easily obtained from Iα'-1 by just reversing the order of the numbers in each cycle of Iα'-1 and hence f(α'I-1) = f(Iα'-1), which leads to f(α'I'-1) = f(Iα'-1) + nfi. As a result, we have f(I'α'-1) = f(α'I-1) = f(Iα'-1) + nfi since I'α'-1 = (α'I-1)-1. Therefore, the following claim can be obtained.Without loss of generality, we now suppose that Claim 2 ψ1ψ2 ... I' = I, α'I'-1 = α'I-1ψ1ψ2 ... and f(I'α'-1) = f(Iα'-1) + nfi, where nfi = χ(I) - 1.α' and I' now are the genomes with only one chromosome. Then based on the algorithm proposed by Lin et al. [I'α'-1 to transform α' into I'. Certainly, these nbi block-interchanges can be further expressed by a product of 2nbi 2-cycles, say α' into I', where I'α'-1 = Notice that both n et al. , we can Claim 3 I' = α'.ψ1ψ2...α = I (hence Φ = Iα-1) can be easily verified by Claims 1, 2 and 3 as follows.Now we let Φ = nfu + (n - f(I'α'-1)) + nfi) 2-cycles that can transform α into I. More clearly, Φ first uses φ1, φ2,...,nfu fusions) to transform α into α', then uses nbi block-interchanges) to transform α' into I', and finally uses ψ1 (acting as nfi fissions) to transform I' into I. By Claims 1 and 2, we can show that (nfu + (n - f(I'α'-1)) + nfi = n - f(Iα-1) as follows.In other words, Φ is a product of (nfu + (n - f(I'α'-1)) + nfinfu + (n - f(Iα'-1) + nfi) + nfi     (by Claim 2)= nfu + (n - f(Iα-1) + nfu - nfi) + nfi     (by Claim 1)= n - f(Iα-1)= χ(α) - 1 and χ(I) - 1 are the lower bounds of the numbers of fusions and fissions, respectively, required in any optimal series of rearrangement events for transforming α into I. Hence, the number of 2-cycles in Φ that function as the fusions and fissions is minimum. Along with that Φ = Iα-1 can be expressed as a product of n - f(Iα-1) 2-cycles, we thus conclude that Φ is an optimal series of the events that transform α into I with first nfu fusions, then nbi block-interchanges and finally nfi fissions, where nfu = χ(α) -1, nfi = χ(I) - 1.As mentioned before, Lemma 7 fu fusions come before all nbi block-interchanges that come before all nfi fissions, where There is an optimal series of the events needed to transform α into I in a canonical order such that all nnfu = χ(α) - 1, and nfi = χ(I) - 1.α =    and I =     for an example. It should be straightforward to see that α,I) is a connected bipartite graph with χ(α) = 3 and χ(I) = 4, and Iα-1 =    and hence f(-2Iα) = 5, since two 1-cycles  and (5)) are not explicitly shown. First, we are to find two 2-cycles φ1 and φ2 (since nfu = χ(α) -1 = 2) from Iα-1 to transform genome α with three chromosomes into genome α' with exactly one chromosome. To this purpose, we let φ1 =  and φ2 = , since Iα-1 =    . Then by Claim 1, α' = φ2φ1α =  and Iα'-1 = Iα-1φ1φ2 =  . Next, we need to find three 2-cycles ψ1, ψ2 and ψ3 (since nfi = χ(I) - 1 = 3) from α'I-1, which is equal to (Iα'-1)-1 =   =    , to transform I into I' with only one chromosome. By letting ψ1 = , ψ2 =  and ψ3 = , we have I' = ψ3ψ2ψ1 =  and α'I'-1 = α'I-1ψ1ψ2ψ3 =  according to Claim 2. Finally, we will find two 2-cycles n - f(Iα-1) - nfu - nfi = 12 - 5 - 2 - 3 = 2) from I'α'-1 that act as a block-interchange to transform α' into I', where I'α'-1 = (α'I'-1)-1 =  =  . By letting α' =    = , which indeed equals I'. Consequently, we find an optimal series of events Φ= ψ1ψ2ψ3φ2φ1 that transform α into I .Let us take d between two given circular multi-chromosomal genomes α and I, and also to generate an optimal scenario of the required rearrangement events in a canonical order. In Algorithm Sorting-by-ffbi, the purpose of Step 2.3.3  is to find two numbers x and y that are both in some cycle of γ = Jiγ = βi. By Lemma 5, such x and y exist. In fact, they can be found using the following simple approach. For simplicity, let γk =  to compute the genome rearrangement distance Input: Two circular multi-chromosomal genomes α and I.Output: d and a minimum series Φ of events required to transform α into I.1:   Find all connected components 1, 2,...,ω in graph α,I);ni the number of genes in i. */      /* Denote by 2:   for each i, 1 ≤ i ≤ ω,doβi (resp. Ji) the collection of chromosomes in α (resp. I) whose corresponding vertices are in i. */         /* Denote by 2.1:   Compute Jiγ = Ji2.2:   nfu = χ(βi) - 1, nfi = χ(Ji) -1, δi = nfu + nbi + nfi;2.3:   if χ(βi) > 1 then   /* To compute φ1, φ2,...,2.3.1:      for each cycle of βi do         Create a set to contain all the numbers in this cycle;endfor   2.3.2:   /* Let γ1γ2 ... γp be the cycle decomposition of the current γ andγq =  and union;      endfor   2.3.4:   φ1βi and γ = γφ1φ2...γ is Jiendif   2.4:   if χ(Ji) > 1 then/* To compute ψ1, ψ2,...,2.4.1:      γ = γ-1/* New γ becomes 2.4.2:   for each cycle of Ji do         Create a set to contain all the numbers in this cycle;endfor      2.4.3:   /* Let γ1γ2...γp be the cycle decomposition of the current γ andγq =  and union;      endfor   2.4.5:    = ψ1Ji and γ = γψ1ψ2...γ is endif   2.5:   /* To compute 2.5.1:   γ = γ-1;/* New γ becomes 2.5.2:   2.5.3:   for j = 1 to nbi dox and y in γ;      Arbitrarily choose two adjacent elements a1,a2...,      /* Let a1, a2,...,a1 = x and assume y = ak;      Circularly shift ;      for h = 1 to ni do      ah) = h;         index  such that      Find two adjacent elements u) ≤ k - 1 and index(v) ≥ k;      index;      γ = γ      endfor   3:   Let i ≤ ω;.4:   Output d = 1Φ2...Φω;Theorem 1 Given two circular multi-chromosomal genomes α and I over the same gene set E = {1,2,..., n}, the problem of computing the genome rearrangement distance between α and I using fusions, fissions and block-interchanges can be solved and an optimal series of such events in a canonical order can be obtained in n2) time.Proof. As discussed above, Algorithm Sorting-by-ffbi transforms α into I using the minimum number of fusions, fissions and block-interchanges. Next, we follow to analyze its time-complexity. Notice that given an undirected graph with p vertices and q edges, all the connected components in this graph can be found in p + q) time using depth-first search or breadth-first search [n2) time for computing the connected components in the induced bipartite graph α, I), since in the worst case, the number of edges in α,I) is χ(α) × χ(I) and χ(α) = n) and χ(I) = n). In Step 2, there are ω outer iterations, each computing the minimum series of events needed to transform βi into Ji, where 1 ≤ i ≤ ω. Clearly, Steps 2.1 costs ni) time for computing Jinfu inner iterations in Step 2.3, each with the purpose of finding two numbers x and y that are both in the same cycle in γ and, however, in the different cycles in βi. In the worst case, Step 2.3 needs ni find-set operations and nfu union operations to finish its overall process. Note that Step 2.3.1 can be implemented by initially creating a set for each number in gene(βi) and then performing ni - χ(βi) union operations to generate χ(βi) sets with each corresponding to a cycle in βi, where χ(βi) = nfu + 1. Hence, the total number of union operations is ni - 1 in Step 2.3. In fact, these find-set and union operations can be implemented in ni) time using the so-called "static disjoint set union and find" algorithm proposed by Gabow and Tarjan [ni) time. By the same principle, it can be verified that the time cost of Step 2.4 is ni). As for Step 2.5, adopted from our previous work [nbini) time, where  = ni). As a result, the time cost of Step 2 is ζn), where ζ is the maximum nbi among all iterations in Step 2 and ζ <n. Clearly, Steps 3 and 4 cost constant time. Therefore, the total time-complexity of Algorithm Sorting-by-ffbi is n2).t search . As a red Tarjan . In otheous work , it takeVibrio genomes, we identified and constructed a table of orthologous genes that are putatively not involved in horizontal gene transfer (HGT) events by adopting the so-called symmetrical best hits (SymBets for short). In principle, two genes match and give SymBets if they are more similar to each other than they are to any other genes from the compared genomes [Vibrio genomes. First, the GenePlot [Vibrio genomes. Next, after removing all one-to-many or many-to-many SymBets, the three resulting tables of SymBet genes were joined to give a new one of one-to-one orthologous genes for all the three Vibrio genomes by using a rule as follows. If genes a (from genome A) and b (from genome B),b and c (from genome C), and c and a are all one-to-one SymBet pairs, then a, b and c are considered as one-to-one orthologous genes for the genomes A,B and C. In other words, the SymBet relationships among a, b and c result in a triangle. Finally, those genes that were involved in the putative HGT events detected and available in the Horizontal Gene Transfer Database [To analyze the rearrangement of three  genomes ,34. Dete genomes ,34. Part genomes ,34. For GenePlot  program Database  were theCLL and HTC contributed equally to this work. CLL conceived of the study, participated in the design and analysis of algorithm and drafted the manuscript. YLH participated in the algorithm design and software development, and carried out the bioinformatics experiments. TCW participated in the software development. HTC participated in the design and coordination of this study as well as in drafting the manuscript.1The Institute for Genome Research (TIGR) offers a website of Comprehensive Microbial Resource (CMR) that provides information on all of the publicly available and complete bacterial genomes.


The role of exogenous hormone exposures in the development of meningioma is unclear, but these exposures have been proposed as one hypothesis to explain the over-abundance of such tumors in women.The association between oral contraception (OC) or hormone replacement therapy (HRT) and intracranial meningioma in women was investigated using a population-based, matched case-control study. Exposures for 143 cases and 286 controls matched on age within five years were obtained by interview. Diagnoses were confirmed histopathologically and estrogen and progesterone receptor assays conducted.Although risk of meningioma appeared modestly elevated in past OC users , and in current users , the confidence intervals were wide. No significant association between meningioma risk and duration of OC use was found. Likewise, risk of meningioma was only weakly associated with past use of HRT , and not at all with current use of HRT . Of 142 available specimens, 2 (1%) expressed estrogen receptors, whereas 130 (92%) expressed progesterone receptors (PR). OC use was associated with increased risk of a meningioma expressing less rather than more PR . Overall, in post menopausal women, HRT use appeared to confer a non-significant protective effect, and was not associated with low or high PR expressing meningiomas.This study found little evidence of associations between meningioma and exogenous hormone exposures in women but did suggest that some hormonal exposures may influence tumor biology in those women who develop meningioma. Meningiomas occur more frequently in women than men and have the highest incidence in the fifth and sixth decades of life,2. ConsiResearch has focused on the similarities and risk factors common to meningioma and other neoplasms in addition to other mechanisms. In particular, meningioma may be associated with breast carcinoma,5 but thWe conducted a population-based, matched case-control study of risk factors for intracranial meningioma, as detailed previously,19. InstExposure histories were obtained from all enrolled participants through a structured in-person interview and questionnaire that focused on the entire history of exposures before the reference date. Reference date was the date of the case's surgery that yielded histological confirmation and was the same for the case's matched controls. Seven of the 143 female cases identified for this study were unable to complete the interview due to disability or death. Proxy interviews of a spouse or next-of-kin were conducted for these cases, but were not conducted for the matched controls. For reproductive and medical history in women, we specifically asked about factors such as age at menarche, pregnancy, breastfeeding, and menstrual status in addition to other exposures common to both men and women. For use of oral contraceptives and hormone replacement therapy, we inquired about the type of prescription using visual prompts, the calendar time of use, and duration of use for any hormone therapy. Interview responses on the type of oral contraceptive preparation used were often incomplete, and so we were unable to examine the influence of the type of preparation on the risk of meningioma.For all 143 cases, we confirmed the meningioma diagnosis by requesting tumor specimens and pathology reports from the resecting hospital. The study neuropathologist confirmed the diagnosis of meningioma. In addition, specimens were submitted to Phenopath Laboratories, Seattle, Washington, for estrogen and progesterone receptor analysis. New tumor tissue slices were prepared from specimens embedded in paraffin, pretreated in citrate buffer pH 6.0 in a steamer for 30 minutes, and placed on an autostainer. For estrogen receptor analysis, antibody clone 1D4 was used . For progesterone receptor analysis, antibody clone 88 was used . Detection was performed using the labeled streptavidin-biotin system (LSAB+) with horseradish peroxidase followed by 3,3'-diaminobenzidine chromogen (DAB+). Receptor assays were successful in all but one case.We used conditional logistic regression to measure the association between each exposure and intracranial meningioma. For all analyses, we used never-exposed or no exposure as the referent category. Results are reported as odds ratios (OR) with 95% confidence intervals (CI). Where appropriate, tests for linear trend were conducted. Multiplicative interactions were assessed using the likelihood ratio (LR) test. Given their slow growth, most meningiomas have probably been present for a decade or more by the time a diagnosis is made. TherefoAlthough the 143 cases and 286 matched controls were similar on age, race and marital status, controls were more educated than cases  reported they were no longer menstruating on the corresponding reference date for each matched group. Of these women, 63 (62%) cases and 114 (66%) controls reported hormone replacement therapy use on or before the reference date.We found no statistically significant association between hormone replacement therapy and meningioma. With never users of hormone replacement therapy as the referent group, the odds ratio for women reporting past use was lower than 1.0 but not significantly so Table . CurrentWe examined a potential combined effect of hormone replacement therapy and past oral contraceptive use in post menopausal women compared to never exposed women by grouping women into three categories: exposure to both, exposure to one or the other and never exposure, and we also examined duration of exposure as never, up to ten years, and ten or more years. In each analysis, point estimates and associated confidence intervals were not appreciably different than for hormone replacement therapy alone (results not shown).Results for either oral contraception or hormone replacement therapy were unchanged when the seven cases in whom proxies interviews were used and their matched controls were removed from the analyses (results not shown).We evaluated several exposure categories related to reproduction and endogenous hormones, including age at menarche, number of live births, age at first live birth, history of breastfeeding and did not find significant associations with meningioma Table . In addiWe also assessed body mass index (BMI) grouped as under/normal weight (<25), overweight (25–30), and obese (≥30). CompareProgesterone receptor (PR) expression was common with 62 (44%) of tumors having >75% of cells expressing PR, 35 (24%) of tumors having 25–75 percent of cells expressing PR, 33 (23%) of tumors having <25% of cells expressing PR, and 12 (8%) of tumors with no cells expressing PR. In contrast, estrogen receptor (ER) expression was uncommon with only 1 tumor having >75% cells expressing ER and 1 tumor with <25% of cells expressing ER. The remaining 140 tumors (98%) did not express ER. In exploratory analyses we focused on associations between exposure categories and progesterone receptor expression dichotomized as low (<25% of cells expressing PR) or high (25% or more expressing PR). We were unable to compare never, current and past oral contraceptives or hormone replacement therapy use to PR expression due to insufficient numbers, so we compared never and ever oral contraceptive or hormone replacement therapy exposure  declare that they have no competing interests.WL, TK, GvB participated in the design of the study and acquisition of funding.WL, BC participated in data collection.LP, BC participated in data preparation and statistical analysis.BC drafted the manuscript.BC, WL, LP, TK, GvB provided interpretation of the results, critical revision and approval of the final version of the manuscript.The pre-publication history for this paper can be accessed here: