RNA extraction from ten year old formalin-fixed paraffin-embedded breast cancer samples: a comparison of column purification and magnetic bead-based technologies

Abstract Background The development of protocols for RNA extraction from paraffin-embedded samples facilitates gene expression studies on archival samples with known clinical outcome. Older samples are particularly valuable because they are associated with longer clinical follow up. RNA extracted from formalin-fixed paraffin-embedded (FFPE) tissue is problematic due to chemical modifications and continued degradation over time. We compared quantity and quality of RNA extracted by four different protocols from 14 ten year old and 14 recently archived (three to ten months old) FFPE breast cancer tissues. Using three spin column purification-based protocols and one magnetic bead-based protocol, total RNA was extracted in triplicate, generating 336 RNA extraction experiments. RNA fragment size was assayed by reverse transcription-polymerase chain reaction (RT-PCR) for the housekeeping gene glucose-6-phosphate dehydrogenase (G6PD), testing primer sets designed to target RNA fragment sizes of 67 bp, 151 bp, and 242 bp. Results Biologically useful RNA (minimum RNA integrity number, RIN, 1.4) was extracted in at least one of three attempts of each protocol in 86–100% of older and 100% of recently archived ("months old") samples. Short RNA fragments up to 151 bp were assayable by RT-PCR for G6PD in all ten year old and months old tissues tested, but none of the ten year old and only 43% of months old samples showed amplification if the targeted fragment was 242 bp. Conclusion All protocols extracted RNA from ten year old FFPE samples with a minimum RIN of 1.4. Gene expression of G6PD could be measured in all samples, old and recent, using RT-PCR primers designed for RNA fragments up to 151 bp. RNA quality from ten year old FFPE samples was similar to that extracted from months old samples, but quantity and success rate were generally higher for the months old group. We preferred the magnetic bead-based protocol because of its speed and higher quantity of extracted RNA, although it produced similar quality RNA to other protocols. If a chosen protocol fails to extract biologically useful RNA from a given sample in a first attempt, another attempt and then another protocol should be tried before excluding the case from molecular analysis.

Desafios à organização de programa de rastreamento do câncer do colo do útero em Manaus-AM

Objetivou-se identificar as características sociodemográficas das mulheres que realizam o Papanicolaou em Manaus, Amazonas, e sua associação com os motivos para realização do exame. Pesquisa exploratória incluindo 281 mulheres, que haviam realizado o Papanicolaou nos últimos cinco anos em Manaus. A maioria das entrevistadas tinha entre 18-34 anos (54%), 5-11 anos de estudo (54,4%), renda familiar mensal de até três salários mínimos (84,3%), relação estável (72,2%) e início da vida sexual entre 15-19 anos (69,4%). Os motivos para realização do Papanicolaou foram procura espontânea (66,2%), recomendação médica (23,5%) e sintomas ginecológicos (10,3%). Mulheres que receberam informação dos profissionais de saúde tiveram proporção maior de realização do exame nos últimos três anos (p=0,008). A demanda espontânea é prevalente e o atendimento oportunístico é realizado nas mulheres mais jovens, não alcançando o grupo com maior risco para o câncer. É necessário implantar estratégias de recrutamento ativo alcançando mulheres em desvantagem socioeconômica.

Survey of Bancroftian filariasis infection in humans and Culex mosquitoes in the western Brazilian Amazon region: implications for transmission and control

Introduction: The aim of this work was to identify possible lymphatic filariasis foci in the western Brazilian Amazonian that could be established from the reports of Rachou in the 1950s. The study was conducted in three cities of the western Brazilian Amazon region - Porto Velho and Guajará-Mirim (State of Rondônia) and Humaitá (State of Amazonas). Methods: For human infection evaluation thick blood smear stained with Giemsa was used to analyze samples collected from 10pm to 1am. Polymerase chain reaction (PCR) was used to examine mosquito vectors for the presence of Wuchereria bancrofti DNA. Humans were randomly sampled from night schools students and from inhabitants in neighborhoods lacking sanitation. Mosquitoes were collected from residences only. Results: A total 2,709 night students enrolled in the Program for Education of Young Adults (EJA), and 935 people registered in the residences near the schools were examined, being 641 from Porto Velho, 214 from Guajará-Mirim and 80 from Humaitá. No individual examined was positive for the presence of microfilariae in the blood stream. A total of 7,860 female Culex quinquefasciatus specimens examined were negative by PCR. Conclusions: This survey including human and mosquito examinations indicates that the western Amazon region of Brazil is not a focus of Bancroftian filariasis infection or transmission. Therefore, there is no need to be included in the Brazilian lymphatic filariasis control program.

Lymphadenectomy for bladder cancer: indications and controversies

Pelvic lymph node dissection (PLND) at the time of cystectomy remains the most accurate method of staging and can have a positive impact on cancer control, and there is general agreement as to its necessity at the time of surgery. There is, however, a lack of consensus regarding the terminology of PLND and controversy concerning the optimal extent of lymph node dissection, especially because recent investigations have suggested a survival benefit with extended PLND.

Comprehensive rehabilitation in chronic heart failure - better psycho-emotional status related to quality of life, brain natriuretic peptide concentrations, and clinical severity of disease

To evaluate the effects of a comprehensive outpatient rehabilitation program in chronic heart failure (CHF) on quality of life (QoL) in relation to emotional status and clinical severity of disease.

A STUDY ON THE FEASIBILITY OF UNIVERSAL CHIP CONTROL IN MACHINING

A novel solution to the long standing issue of chip entanglement and breakage in metal cutting is presented in this dissertation. Through this work, an attempt is made to achieve universal chip control in machining by using chip guidance and subsequent breakage by backward bending (tensile loading of the chip's rough top surface) to effectively control long continuous chips into small segments. One big limitation of using chip breaker geometries in disposable carbide inserts is that the application range is limited to a narrow band depending on cutting conditions. Even within a recommended operating range, chip breakers do not function effectively as designed due to the inherent variations of the cutting process. Moreover, for a particular process, matching the chip breaker geometry with the right cutting conditions to achieve effective chip control is a very iterative process. The existence of a large variety of proprietary chip breaker designs further exacerbates the problem of easily implementing a robust and comprehensive chip control technique. To address the need for a robust and universal chip control technique, a new method is proposed in this work. By using a single tool top form geometry coupled with a tooling system for inducing chip breaking by backward bending, the proposed method achieves comprehensive chip control over a wide range of cutting conditions. A geometry based model is developed to predict a variable edge inclination angle that guides the chip flow to a predetermined target location. Chip kinematics for the new tool geometry is examined via photographic evidence from experimental cutting trials. Both qualitative and quantitative methods are used to characterize the chip kinematics. Results from the chip characterization studies indicate that the chip flow and final form show a remarkable consistency across multiple levels of workpiece and tool configurations as well as cutting conditions. A new tooling system is then designed to comprehensively break the chip by backward bending. Test results with the new tooling system prove that by utilizing the chip guidance and backward bending mechanism, long continuous chips can be more consistently broken into smaller segments that are generally deemed acceptable or good chips. It is found that the proposed tool can be applied effectively over a wider range of cutting conditions than present chip breakers thus taking possibly the first step towards achieving universal chip control in machining.

MODIFICATION AND IMPLEMENTATION OF THE RPC HETEROGENEOUS THORAX PHANTOM FOR VERIFICATION OF PROTON THERAPY TREATMENT PROCEDURES

The Radiological Physics Center (RPC) provides heterogeneous phantoms that are used to evaluate radiation treatment procedures as part of a comprehensive quality assurance program for institutions participating in clinical trials. It was hypothesized that the existing RPC heterogeneous thorax phantom can be modified to assess lung tumor proton beam therapy procedures involving patient simulation, treatment planning, and treatment delivery, and could confirm agreement between the measured dose and calculated dose within 5%/3mm with a reproducibility of 5%. The Hounsfield Units (HU) for lung equivalent materials (balsa wood and cork) was measured using a CT scanner. The relative linear stopping power (RLSP) of these materials was measured. The linear energy transfer (LET) of Gafchromic EBT2 film was analyzed utilizing parallel and perpendicular orientations in a water tank and compared to ion chamber readings. Both parallel and perpendicular orientations displayed a quenching effect underperforming the ion chamber, with the parallel orientation showing an average 31 % difference and the perpendicular showing an average of 15% difference. Two treatment plans were created that delivered the prescribed dose to the target volume, while achieving low entrance doses. Both treatment plans were designed using smeared compensators and expanded apertures, as would be utilized for a patient in the clinic. Plan 1a contained two beams that were set to orthogonal angles and a zero degree couch kick. Plan 1b utilized two beams set to 10 and 80 degrees with a 15 degree couch kick. EBT2 film and TLD were inserted and the phantom was irradiated 3 times for each plan. Both plans passed the criteria for the TLD measurements where the TLD values were within 7% of the dose calculated by Eclipse. Utilizing the 5%/3mm criteria, the 3 trial average of overall pass rate was 71% for Plan 1a. The 3 trial average for the overall pass rate was 76% for Plan 1b. The trials were then analyzed using RPC conventional lung treatment guidelines set forth by the RTOG: 5%/5mm, and an overall pass rate of 85%. Utilizing these criteria, only Plan 1b passed for all 3 trials, with an average overall pass rate of 89%.

An arranged marriage for precision medicine: hypoxia and genomic assays in localized prostate cancer radiotherapy

Prostate cancer (CaP) is the most commonly diagnosed malignancy in males in the Western world with one in six males diagnosed in their lifetime. Current clinical prognostication groupings use pathologic Gleason score, pre-treatment prostatic-specific antigen and Union for International Cancer Control-TNM staging to place patients with localized CaP into low-, intermediate- and high-risk categories. These categories represent an increasing risk of biochemical failure and CaP-specific mortality rates, they also reflect the need for increasing treatment intensity and justification for increased side effects. In this article, we point out that 30-50% of patients will still fail image-guided radiotherapy or surgery despite the judicious use of clinical risk categories owing to interpatient heterogeneity in treatment response. To improve treatment individualization, better predictors of prognosis and radiotherapy treatment response are needed to triage patients to bespoke and intensified CaP treatment protocols. These should include the use of pre-treatment genomic tests based on DNA or RNA indices and/or assays that reflect cancer metabolism, such as hypoxia assays, to define patient-specific CaP progression and aggression. More importantly, it is argued that these novel prognostic assays could be even more useful if combined together to drive forward precision cancer medicine for localized CaP.

Very long-term survival patterns of young patients treated with radical prostatectomy for high-risk prostate cancer

OBJECTIVE In patients with a long life expectancy with high-risk (HR) prostate cancer (PCa), the chance to die from PCa is not negligible and may change significantly according to the time elapsed from surgery. The aim of this study was to evaluate long-term survival patterns in young patients treated with radical prostatectomy (RP) for HRPCa. MATERIALS AND METHODS Within a multiinstitutional cohort, 600 young patients (≤59 years) treated with RP between 1987 and 2012 for HRPCa (defined as at least one of the following adverse characteristics: prostate specific antigen>20, cT3 or higher, biopsy Gleason sum 8-10) were identified. Smoothed cumulative incidence plot was performed to assess cancer-specific mortality (CSM) and other cause mortality (OCM) rates at 10, 15, and 20 years after RP. The same analyses were performed to assess the 5-year probability of CSM and OCM in patients who survived 5, 10, and 15 years after RP. A multivariable competing risk regression model was fitted to identify predictors of CSM and OCM. RESULTS The 10-, 15- and 20-year CSM and OCM rates were 11.6% and 5.5% vs. 15.5% and 13.5% vs. 18.4% and 19.3%, respectively. The 5-year probability of CSM and OCM rates among patients who survived at 5, 10, and 15 years after RP, were 6.4% and 2.7% vs. 4.6% and 9.6% vs. 4.2% and 8.2%, respectively. Year of surgery, pathological stage and Gleason score, surgical margin status and lymph node invasion were the major determinants of CSM (all P≤0.03). Conversely, none of the covariates was significantly associated with OCM (all P≥ 0.09). CONCLUSIONS Very long-term cancer control in young high-risk patients after RP is highly satisfactory. The probability of dying from PCa in young patients is the leading cause of death during the first 10 years of survivorship after RP. Thereafter, mortality not related to PCa became the main cause of death. Consequently, surgery should be consider among young patients with high-risk disease and strict PCa follow-up should enforce during the first 10 years of survivorship after RP.

AN OCCUPATIONAL INJURY MANAGEMENT INFORMATION SYSTEM FOR THE UNIVERSITY OF TEXAS HEALTH SCIENCE CENTER AT HOUSTON

The purpose of this research and development project was to develop a method, a design, and a prototype for gathering, managing, and presenting data about occupational injuries.^ State-of-the-art systems analysis and design methodologies were applied to the long standing problem in the field of occupational safety and health of processing workplace injuries data into information for safety and health program management as well as preliminary research about accident etiologies. The top-down planning and bottom-up implementation approach was utilized to design an occupational injury management information system. A description of a managerial control system and a comprehensive system to integrate safety and health program management was provided.^ The project showed that current management information systems (MIS) theory and methods could be applied successfully to the problems of employee injury surveillance and control program performance evaluation. The model developed in the first section was applied at The University of Texas Health Science Center at Houston (UTHSCH).^ The system in current use at the UTHSCH was described and evaluated, and a prototype was developed for the UTHSCH. The prototype incorporated procedures for collecting, storing, and retrieving records of injuries and the procedures necessary to prepare reports, analyses, and graphics for management in the Health Science Center. Examples of reports, analyses, and graphics presenting UTHSCH and computer generated data were included.^ It was concluded that a pilot test of this MIS should be implemented and evaluated at the UTHSCH and other settings. Further research and development efforts for the total safety and health management information systems, control systems, component systems, and variable selection should be pursued. Finally, integration of the safety and health program MIS into the comprehensive or executive MIS was recommended. ^

Hypogonadism in male cancer patients: A cross-sectional study

Introduction. Cancer is the second most common cause of death in the USA (2). Studies have shown a coexistence of cancer and hypogonadism (9,31,13). The majority of patients with cancer develop cachexia, which cannot be solely explained by anorexia seen in these patients. Testosterone is a male sex hormone which is known to increase muscle mass and strength, maintain cancellous bone mass, and increase cortical bone mass, in addition to improving libido, sexual desire, and fantasy (14). If a high prevalence of hypogonadism is detected in male cancer patients, and a significant difference exists in testosterone levels in cancer patients with cachexia versus those without cachexia, testosterone may be administered in future randomized trials to help alleviate cachexia. Study group and design The study group consisted of male cancer patients and non-cancer controls aged between 40 and 70 years. The primary study design was cross-sectional with a sample size of 135. The present data analysis is done on a subset convenience sample of 72 patients recruited between November 2006 and January 2010. ^ Methods. Patients aged 40-70 years with or without a diagnosis of cancer were recruited into the study. All patients with a BMI over 35, significant edema, non-melanomatous skin cancer, current alcohol or illicit drug abuse, concomitant usage of medications interfering with gonadal axis, and anabolic agents, patients on tube feeds or parenteral nutrition within 3 months prior to enrollment were excluded from the study. The study was approved by the Institutional Review Board of Baylor College of Medicine and is being conducted at the Michael E. DeBakey Veterans Affairs Medical Center at Houston. My thesis is a pilot data analysis that employs a smaller subset convenience sample of 72 patients determined by using the data available for the 72 patients (of the intended sample of 135 patients) recruited between November 2006 and January 2010. The primary aim of this analysis is to compare the proportion of patients with hypogonadism in the male cancer and non-cancer control groups, and to evaluate if a significant difference exists with respect to testosterone levels in male cancer patients with cachexia versus those without cachexia. The procedures of the study relevant to the current data analysis included blood collection to measure levels of testosterone and measurement of body weight to categorize cancer patients into cancer cachexia and cancer non-cachexia sub-groups. ^ Results. After logarithmic transformation of data of cancer and control groups, the unpaired t test with unequal variances was done. The proportion of patients with hypogonadism in the male cancer and non-cancer control groups was 47.5% and 22.7% with a Pearson chi2 statistic of 1.6036 and a p value of 0.205. Comparing the mean calculated Bioavailable testosterone in male cancer patients and non-cancer controls resulted in a t statistic of 21.83 and a p value less than 0.001. When the cancer group alone was taken, the mean free testosterone, calculated bioavailable testosterone and total testosterone levels in the cancer non-cachexia sub-group were 3.93, 5.09, 103.51 respectively and in the cancer cachexia sub-group were 3.58, 4.17, 84.08 respectively. The unpaired t test with equal variances showed that the two sub-groups had p values of 0.2015, 0.1842, and 0.4894 with respect to calculated bioavailable testosterone, free testosterone, and total testosterone respectively. ^ Conclusions. The small sample size of this exploratory study, resulting in a small power, does not allow us to draw definitive conclusions. For the given sub-sample, the proportion of patients with hypogonadism in the cancer group was not significantly different from that of patients with hypogonadism in the control group. Inferences on prevalence of hypogonadism in male cancer patients could not be made in this paper as the sub-sample is small and therefore not representative of the general population. However, there was a statistically significant difference in calculated Bioavailable testosterone levels in male cancer patients versus non-cancer controls. Analysis of cachectic and non-cachectic patients within the male cancer group showed no significant difference in testosterone levels (total, free, and calculated bioavailable testosterone) between both sub-groups. However, to re-iterate, this study is exploratory and the results may change once the complete dataset is obtained and analyzed. It however serves as a good template to guide further research and analysis.^

A review of the Malaria Chemoprophylaxis Compliance Program at ExxonMobil Corporation

ExxonMobil, a Fortune 500 oil and gas corporation, has a global workforce with employees assigned to projects in areas at risk for infectious diseases, particularly malaria. As such, the corporation has put in place a program to protect the health of workers and ensure their safety in malaria endemic zones. This program is called the Malaria Control Program (MCP). One component of this program is the more specific Malaria Chemoprophylaxis Compliance Program (MCCP), in which employees enroll following consent to random drug testing for compliance with the company's chemoprophylaxis requirements. Each year, data is gathered on the number of employees working in these locations and are selected randomly and tested for chemoprophylaxis compliance. The selection strives to test each eligible worker once per year. Test results that come back positive for the chemoprophylaxis drug are considered "detects" and tests that are negative for the drug and therefore show the worker is non-compliant at risk for severe malaria infection are considered "non-detect". ^ The current practice report used aggregate data to calculate statistics on test results to reflect compliance among both employees and contractors in various malaria-endemic areas. This aggregate, non-individualized data has been compiled and reflects the effectiveness and reach of ExxonMobil's Malaria Chemoprophylaxis Compliance Program. In order to assess compliance, information on the number of non-detect test results was compared to the number of tests completed per year. The data shows that over time, non-detect results have declined in both employee and contractor populations, and vary somewhat by location due to size and scope of the MCCP implemented in-country. Although the data indicate a positive trend for the corporation, some recommendations have been made for future implementation of the program.^

Colorectal cancer screening: Participation and determinants in West Texas

Early detection by screening is the key to colorectal cancer control. However, colorectal cancer screening and its determinants in rural areas have not been adequately studied. This goal of this study was to investigate the screening participation and determinants of colonoscopy, sigmoidoscopy, and/or fecal occult blood test (FOBT) in subjects of Project Frontier from the rural counties of Cochran, Bailey and Parmer, Texas. Subjects ( n=820 with 435 Hispanics, 355 Non-Hispanic Whites, 26 African Americans, and 4 unknown ethnicity; 255 males, 565 females, aged from 40 to 92 years) were from Project FRONTIER. Stepwise logistic regression analysis was performed. Explanatory variables included ethnicity (Hispanic, Non-Hispanic white and African American), gender, health insurance, smoking status, household income, education (years), physical activity, overweight, other health screenings, personal physicians, family history (first-degree relatives) of cancers, and preferred language (English vs. Spanish) for interview/testing. The screening percentage for ever having had a colonoscopy/sigmoidoscopy (51.8%) in this cohort aged 50 years or older is well below the percentage of the nation (65.2%) and Texas (64.6%) while the percentage for FOBT (29.2%) is higher than in the nation (17.2%) and Texas (14.9%). However, Hispanics had significantly lower participation than non-Hispanic whites for colonoscopy/sigmoidoscopy (37.0% vs. 66.0%) and FOBT (16.5% vs. 41.7%), respectively. Stepwise logistic regression showed that predictors for colonoscopy, sigmoidoscopy or FOBT included Hispanic race (p = 0.0045), age (p < 0.0001), other screening procedure (p < 0.0001), insurance status (p < 0.0001) and physician status (p = 0.0053). Screening percentage for colonoscopy/sigmoidoscopy in this rural cohort is well below the national and Texas level mainly due to the lower participation of Hispanics vs. Non-Hispanic whites. Health insurance, having had a personal physician, having had screenings for other cancers, race, and older age are among the main predictors.^

High-extraction coal mining in Illinois : effects on crop production, 1985-1987 /

"IMSRP-IV."

Summary of property damage control programs of the United States Department of Energy.

"DOE/EV-0053."