Multicentre validation study of nucleic acids extraction from FFPE tissues

In most pathology laboratories worldwide, formalin-fixed paraffin embedded (FFPE) samples are the only tissue specimens available for routine diagnostics. Although commercial kits for diagnostic molecular pathology testing are becoming available, most of the current diagnostic tests are laboratory-based assays. Thus, there is a need for standardized procedures in molecular pathology, starting from the extraction of nucleic acids. To evaluate the current methods for extracting nucleic acids from FFPE tissues, 13 European laboratories, participating to the European FP6 program IMPACTS (www.impactsnetwork.eu), isolated nucleic acids from four diagnostic FFPE tissues using their routine methods, followed by quality assessment. The DNA-extraction protocols ranged from homemade protocols to commercial kits. Except for one homemade protocol, the majority gave comparable results in terms of the quality of the extracted DNA measured by the ability to amplify differently sized control gene fragments by PCR. For array-applications or tests that require an accurately determined DNA-input, we recommend using silica based adsorption columns for DNA recovery. For RNA extractions, the best results were obtained using chromatography column based commercial kits, which resulted in the highest quantity and best assayable RNA. Quality testing using RT-PCR gave successful amplification of 200 bp-250 bp PCR products from most tested tissues. Modifications of the proteinase-K digestion time led to better results, even when commercial kits were applied. The results of the study emphasize the need for quality control of the nucleic acid extracts with standardised methods to prevent false negative results and to allow data comparison among different diagnostic laboratories.

Extremely Violent Societies: Mass Violence in the Twentieth Century World

In this groundbreaking book Christian Gerlach traces the social roots of the extraordinary processes of human destruction involved in mass violence throughout the twentieth century. He argues that terms such as 'genocide' and 'ethnic cleansing' are too narrow to explain the diverse motives and interests that cause violence to spread in varying forms and intensities. From killings and expulsions to enforced hunger, collective rape, strategic bombing, forced labour and imprisonment he explores what happened before, during, and after periods of widespread bloodshed in countries such as Armenia, Indonesia, Bangladesh, Nazi-occupied Greece and in anti-guerilla wars worldwide in order to highlight the crucial role of socio-economic pressures in the generation of group conflicts. By focussing on why so many different people participated in or supported mass violence, and why different groups were victimized, he offers us a new way of understanding one of the most disturbing phenomena of our times.

Study Abroad Increases Risk for Sexual Assault in Female Undergraduates: A Preliminary Report

Since 2007, more than 250,000 American students have studied abroad annually for a semester or more. While there are obvious benefits associated with study abroad programs, personal risks (including interpersonal victimization such as sexual and physical assault) occurring during the experience have been anecdotally reported but not systematically assessed. This study is the first to investigate the possibility of increased risk for sexual assault in female undergraduates while abroad. Two hundred eighteen female undergraduates completed a modified version of the Sexual Experiences Survey (SES: Koss et al., 2007) about their sexual experiences abroad and on campus. Findings indicate increased risk for sexual assault while abroad relative to on-campus rates, particularly in non-English speaking countries. Study abroad programs should consider educating students about increased risk and develop response protocols when sexual assaults happen while abroad.

Predictors of Attitudes toward Lesbians and Transgender Women in Relationships on a College Campus

The purpose of this study was to gain a better understanding of the attitudes which perpetuate intolerance toward LGBT individuals, and to recognize, in particular, the unique attitudes transpeople face as a minority in the nation and even in the LGBT community. This research contributes to the bodies of research concerning the interrelatedness of intrinsic religiosity, political conservatism, sexism, the rape myth, lack of effective legal protection, and the intolerance of gender non-conformists. I have identified distinctions between attitudes on the part of both women and men, as well as toward different gender non-conformists. I have also taken research as a whole further by assessing the predictors of attitudes toward specific members of the LGBT community in public relationships. The implications of these findings are potentially as far reaching as to have an impact on policies effecting healthcare, education, anti-discrimination and employer rights legislation, on both local and national levels.

Alpine ibex (Capra i. ibex) is not a reservoir for chlamydial infections of domestic ruminants and humans

Chlamydophila (C.) abortus is the most common infectious abortigenic agent in small domestic ruminants in Switzerland. In contrast, the knowledge about chlamydiae in wild ruminants is scarce. As interactions between livestock and Alpine ibex (Capra i. ibex) occur on alpine pastures, the question raises if wild ruminants could play a role as carriers of chlamydiae. Thus, we investigated the prevalence of chlamydiae in Alpine ibex in Switzerland. In total, 624 sera, 676 eye swabs, 84 organ samples and 51 faecal samples from 664 ibex were investigated. Serum samples were tested by two commercial ELISA kits specific for C. abortus. Eye swabs, organs and faecal samples were examined by a Chlamydiaceae-specific real-time polymerase chain reaction (PCR). Positive cases were further investigated by the ArrayTube (AT) microarray method for chlamydial species determination. Of 624 serum samples investigated, 612 animals were negative, whereas nine sera (1.5%) reacted positively in one of the two tests and three sera showed an inconclusive result. Eye swabs of seven out of 412 ibex (1.7%) were tested positive for Chlamydiaceae by real-time PCR. By AT microarray, Chlamydophila (C.) pecorum was identified in two animals, Chlamydophila (C.) pneumoniae was detected in one animal and a mixed infection with C. abortus and C. pecorum was found in four animals. Organs and faecal samples were all negative by real-time PCR analysis. In summary, we conclude that C. abortus is not a common infectious agent in the Swiss ibex population. To our knowledge, this is the first description of C. pneumoniae in ibex. Further studies are necessary to elucidate the situation in other species of wild ruminants as chamois (Rupicapra r. rupicapra), red deer (Cervus elaphus) and roe deer (Capreolus c. capreolus) in Switzerland.

Occurrence of Chlamydiaceae, Mycoplasma conjunctivae, and pestiviruses in Alpine chamois (Rupicapra r. rupicapra) of Grisons, Switzerland

Because interactions between livestock and chamois occur on Alpine pastures, transmission of infectious diseases is considered possible. Thus, the occurrence of Chlamydiaceae, Mycoplasma conjunctivae, and pestiviruses in Alpine chamois (Rupicapra r. rupicapra) of the Surselva region (eastern Swiss Alps) was investigated. In total, 71 sera, 158 eye swabs, 135 tissue samples, and 23 fecal samples from 85 chamois were analyzed. The sera were tested by 2 enzyme-linked immunosorbent assay (ELISA) kits specific for Chlamydophila abortus. Eye swabs, tissue, and fecal samples were examined by a Chlamydiaceae-specific real-time polymerase chain reaction (PCR). Positive cases were further investigated by microarray method. One serum sample (1.4%) was positive in 1 of the ELISAs. Eye swabs of 3 chamois (3.8%) were positive for Chlamydiaceae. The microarray method revealed the presence of Chlamydophila abortus, C pecorum, and C pneumoniae. All tissue and fecal samples were negative. With real-time PCR, 3.9% of the chamois tested positive for Mycoplasma conjunctivae. One chamois had a simultaneous infection with Al. conjunctivae and 2 chlamydial species (C abortus, C. pecorum). Skin and tongue tissue samples of 35 chamois were negative for pestivirus antigen by immunohistochemistry. It was concluded that in contrast to the findings in Pyrenean chamois (Capra p. pyrenaica) of Spain, the occurrence of Chlamydiaceae in Alpine chamois of the Surselva region is low, and the transmission between domestic and wild Caprinae seems not to be frequent. Comparably, persistent pestiviral infections do not seem to be common in chamois of the Surselva region.

Attitudes and Social Factors as Predictors of Male Perpetration of Sexual Assault

Previous research has demonstrated a significant association between sexual assault perpetration and hooking up, male peer support for woman abuse, alcohol consumption, and rape myth acceptance (Burt, 1980; Flack, Daubman, Caron, Asadorian, D’Aureli, Gigliotti & Stine, 2007; Schwartz & DeKeseredy, 1997). In the present study, we tested these relationships on the collegiate level by asking male students to indicate levels of male peer support for woman abuse (MPS), acceptance of rape myths (RMA), alcohol consumption, and history of hooking up and sexual assault perpetration during their undergraduate experience. Participants in this study were 200 male Bucknell students (sophomores - seniors) who completed an online survey concerning these issues. The overall prevalence rate for some type of sexual assault perpetration was 10.5%. Specific prevalence rates for non-invasive contact, completed rape, and attempted rape were 5.5%, 2.0%, and 5.0%, respectively. Sexual assault perpetration was positively correlated with MPS and alcohol consumption but not with RMA. Sexual assault was perpetrated most frequently during acquaintance hook ups. These findings demonstrate direct, significant relationships between sexual assault perpetration, alcohol abuse, different types of hooking up, and rape-supportive attitudes, and an association between perpetration and MPS that requires further elaboration.

Hooking Up, Alcohol Consumption, and Sexual Assault: Differentially Risky Behaviors

Previous research has demonstrated a significant association between sexual assault and alcohol consumption and between unwanted sexual experiences and hooking up (Flack, Daubman, et. al., 2007). In the present study, we tested these relationships more directly by asking sexual assault victims to indicate the primary reason(s) that their assault took place and the type of hook-up, if any, in which they occurred. Participants were 373 female undergraduate students who completed an online survey that included measures of sexual assault, alcohol intoxication, and hooking up. The overall prevalence rate for any type of sexual assault was 44.24% (Koss et al., 2007). Specific prevalence rates for noninvasive contact, rape, and attempted rape were 39.68%, 22.25%, and 22.52%, respectively. Within all types of sexual assault, the most prevalent type of hook-up was with acquaintances, and the most common reason given across all seven types of assault was incapacitation due to intoxication. These findings replicate previous research on assault and alcohol consumption, and demonstrate for the first time direct relationshipsbetween assault victimization and hooking up. The results underscore the need to investigate further the construct of hooking up, especially as a context for sexual assault.

Locational and Temporal Risk Associated With Campus Sexual Assault

The present study investigates the rates of victimization of sexual assault reported by undergraduates at Bucknell University. Specifically, the study aimed to determine where and when sexual assault took place, in order to pinpoint both temporal risks and locational risks associated with certain events on campus. Results of the survey were analyzed for victimization rates across class year, time of year, where victimization took place, as well as where victims and perpetrators met. Data for the study was gathered by means of anonymous survey, sent out to 1752 randomly selected undergraduates via email. Participants filled out the survey which asked if they had ever been sexually assaulted or committed a sexual assault during their past year studying at Bucknell. The results of the survey indicated that dormitories, fraternity houses, and off-campus student houses displayed significantly higher rates of victimization than other locations. In addition, increased risk of unwanted sexual contact in the fall semester was shown to be statistically significant. Moreover, results of the current study support that parties were statistically significant locations for meeting perpetrators of sexual assault. The results suggest that it may be beneficial to direct special attention towards campus sexual assault, specifically to certain locations, times of the year, and campus activities.

Aspiration toxicology of hydrocarbons and lamp oils studied by in vitro technology

Medical literature regularly reports on accidental poisoning in children after aspiration of combustibles such as lamp oils which usually contain hydrocarbons or rape methyl esters (RMEs). We aimed to analyze the toxic potential of alkanes and different combustible classes in vitro with regard to biologic responses and mechanisms mediating toxicity. Two different in vitro models were used, i.e. (i) a captive bubble surfactometer (CBS) to assess direct influence of combustibles on biophysical properties of surfactant film and (ii) cell cultures (BEAS-2B and R3/1 cells, primary macrophages, re-differentiated epithelia) closely mimicking the inner lung surface. Biological endpoints included cell viability, cytotoxicity and inflammatory mediator release. CBS measurements demonstrate that combustibles affect film dynamics, i.e. the surface tension/area characteristics during compression and expansion, in a dose and molecular chain length dependent manner. Cell culture results confirm the dose dependent toxicity. Generally, cytotoxicity and cytokine release are higher in short-chained alkanes and hydrocarbon-based combustibles than in long-chained substances, e.g. highest inducible cytotoxicity in BEAS-2B was for hexane 84.6%, decane 74% and hexadecane 30.8%. Effects of RME-based combustibles differed between the cell models. Our results confirm data from animal experiments and give new insights into the mechanisms underlying the adverse health effects observed.

Effect of remifentanil on mitochondrial oxygen consumption of cultured human hepatocytes

During sepsis, liver dysfunction is common, and failure of mitochondria to effectively couple oxygen consumption with energy production has been described. In addition to sepsis, pharmacological agents used to treat septic patients may contribute to mitochondrial dysfunction. This study addressed the hypothesis that remifentanil interacts with hepatic mitochondrial oxygen consumption. The human hepatoma cell line HepG2 and their isolated mitochondria were exposed to remifentanil, with or without further exposure to tumor necrosis factor-α (TNF-α). Mitochondrial oxygen consumption was measured by high-resolution respirometry, Caspase-3 protein levels by Western blotting, and cytokine levels by ELISA. Inhibitory κBα (IκBα) phosphorylation, measurement of the cellular ATP content and mitochondrial membrane potential in intact cells were analysed using commercial ELISA kits. Maximal cellular respiration increased after one hour of incubation with remifentanil, and phosphorylation of IκBα occurred, denoting stimulation of nuclear factor κB (NF-κB). The effect on cellular respiration was not present at 2, 4, 8 or 16 hours of incubation. Remifentanil increased the isolated mitochondrial respiratory control ratio of complex-I-dependent respiration without interfering with maximal respiration. Preincubation with the opioid receptor antagonist naloxone prevented a remifentanil-induced increase in cellular respiration. Remifentanil at 10× higher concentrations than therapeutic reduced mitochondrial membrane potential and ATP content without uncoupling oxygen consumption and basal respiration levels. TNF-α exposure reduced respiration of complex-I, -II and -IV, an effect which was prevented by prior remifentanil incubation. Furthermore, prior remifentanil incubation prevented TNF-α-induced IL-6 release of HepG2 cells, and attenuated fragmentation of pro-caspase-3 into cleaved active caspase 3 (an early marker of apoptosis). Our data suggest that remifentanil increases cellular respiration of human hepatocytes and prevents TNF-α-induced mitochondrial dysfunction. The results were not explained by uncoupling of mitochondrial respiration.

Improved effectiveness of partner notification for patients with sexually transmitted infections: systematic review

OBJECTIVE: To examine the effectiveness of methods to improve partner notification by patient referral (index patient has responsibility for informing sex partners of their exposure to a sexually transmitted infection). DESIGN: Systematic review of randomised trials of any intervention to supplement simple patient referral. DATA SOURCES: Seven electronic databases searched (January 1990 to December 2005) without language restriction, and reference lists of retrieved articles. REVIEW METHODS: Selection of trials, data extraction, and quality assessment were done by two independent reviewers. The primary outcome was a reduction of incidence or prevalence of sexually transmitted infections in index patients. If this was not reported data were extracted according to a hierarchy of secondary outcomes: number of partners treated; number of partners tested or testing positive; and number of partners notified, located, or elicited. Random effects meta-analysis was carried out when appropriate. RESULTS: 14 trials were included with 12 389 women and men diagnosed as having gonorrhoea, chlamydia, non-gonococcal urethritis, trichomoniasis, or a sexually transmitted infection syndrome. All studies had methodological weaknesses that could have biased their results. Three strategies were used. Six trials examined patient delivered partner therapy. Meta-analysis of five of these showed a reduced risk of persistent or recurrent infection in patients with chlamydia or gonorrhoea (summary risk ratio 0.73, 95% confidence interval 0.57 to 0.93). Supplementing patient referral with information for partners was as effective as patient delivered partner therapy. Neither strategy was effective in women with trichomoniasis. Two trials found that providing index patients with chlamydia with sampling kits for their partners increased the number of partners who got treated. CONCLUSIONS: Involving index patients in shared responsibility for the management of sexual partners improves outcomes. Health professionals should consider the following strategies for the management of individual patients: patient delivered partner therapy, home sampling for partners, and providing additional information for partners.

Comparison of amplification methods for transcriptomic analyses of low abundance prokaryotic RNA sources

Microarrays have established as instrumental for bacterial detection, identification, and genotyping as well as for transcriptomic studies. For gene expression analyses using limited numbers of bacteria (derived from in vivo or ex vivo origin, for example), RNA amplification is often required prior to labeling and hybridization onto microarrays. Evaluation of the fidelity of the amplification methods is crucial for the robustness and reproducibility of microarray results. We report here the first utilization of random primers and the highly processive Phi29 phage polymerase to amplify material for transcription profiling analyses. We compared two commercial amplification methods (GenomiPhi and MessageAmp kits) with direct reverse-transcription as the reference method, focusing on the robustness of mRNA quantification using either microarrays or quantitative RT-PCR. Both amplification methods using either poly-A tailing followed by in vitro transcription, or direct strand displacement polymerase, showed appreciable linearity. Strand displacement technique was particularly affordable compared to in vitro transcription-based (IVT) amplification methods and consisted in a single tube reaction leading to high amplification yields. Real-time measurements using low-, medium-, and highly expressed genes revealed that this simple method provided linear amplification with equivalent results in terms of relative messenger abundance as those obtained by conventional direct reverse-transcription.

Drug-specific in vitro release of IL-2, IL-5, IL-13 and IFN-gamma in patients with delayed-type drug hypersensitivity

BACKGROUND: The most prevalent drug hypersensitivity reactions are T-cell mediated. The only established in vitro test for detecting T-cell sensitization to drugs is the lymphocyte transformation test, which is of limited practicability. To find an alternative in vitro method to detect drug-sensitized T cells, we screened the in vitro secretion of 17 cytokines/chemokines by peripheral blood mononuclear cells (PBMC) of patients with well-documented drug allergies, in order to identify the most promising cytokines/chemokines for detection of T-cell sensitization to drugs. METHODS: Peripheral blood mononuclear cell of 10 patients, five allergic to beta-lactams and five to sulfanilamides, and of five healthy controls were incubated for 3 days with the drug antigen. Cytokine concentrations were measured in the supernatants using commercially available 17-plex bead-based immunoassay kits. RESULTS: Among the 17 cytokines/chemokines analysed, interleukin-2 (IL-2), IL-5, IL-13 and interferon-gamma (IFN-gamma) secretion in response to the drugs were significantly increased in patients when compared with healthy controls. No difference in cytokine secretion patterns between sulfonamide- and beta-lactam-reactive PBMC could be observed. The secretion of other cytokines/chemokines showed a high variability among patients. CONCLUSION: The measurement of IL-2, IL-5, IL-13 or IFN-gamma or a combination thereof might be a useful in vitro tool for detection of T-cell sensitization to drugs. Secretion of these cytokines seems independent of the type of drug antigen and the phenotype of the drug reaction. A study including a higher number of patients and controls will be needed to determine the exact sensitivity and specificity of this test.

Methods for identification of Staphylococcus aureus isolates in cases of bovine mastitis

A total of 272 staphylococcal isolates from cases of bovine mastitis (159 Staphylococcus aureus) belonging to 12 different species were identified with ID32 STAPH galleries, and 51 of them were confirmed by 16S rRNA gene (rrs) sequencing. The same isolates were examined for their hemolytic activity on sheep blood agar, DNase activity, and coagulase activity and with two rapid identification kits (Slidex Staph Plus kit and RAPIDEC Staph from Bio-Merieux). The results of this study confirm those obtained by other groups with hemolysis, DNase, and coagulase. Only 50% of S. aureus isolates from mastitis cases show coagulase activity after 4 h of incubation, and a 24-h incubation is necessary for the full sensitivity of this test. In contrast to results from other studies with human isolates, the Slidex Staph Plus kit was not sensitive enough for the identification of S. aureus from bovine mastitis samples. The aurease test of the RAPIDEC Staph kit showed 100% sensitivity and 100% specificity. Used in conjunction with hemolysis patterns, the RAPIDEC Staph kit is therefore very well adapted to rapid, efficient, and cost-effective identification of S. aureus in cultures from bovine mastitis samples. Sequencing of rrs genes also proved very efficient in identifying the Staphylococcus species encountered in these samples and confirming phenotypical identification results with unsatisfactory scores. With continuously improving technologies and decreasing costs, genetic identification methods like rrs gene sequencing will soon find a place in routine veterinary diagnostics.