Massively parallel analysis of single-molecule dynamics on next-generation sequencing chips.

Single-molecule techniques are ideally poised to characterize complex dynamics but are typically limited to investigating a small number of different samples. However, a large sequence or chemical space often needs to be explored to derive a comprehensive understanding of complex biological processes. Here we describe multiplexed single-molecule characterization at the library scale (MUSCLE), a method that combines single-molecule fluorescence microscopy with next-generation sequencing to enable highly multiplexed observations of complex dynamics. We comprehensively profiled the sequence dependence of DNA hairpin properties and Cas9-induced target DNA unwinding-rewinding dynamics. The ability to explore a large sequence space for Cas9 allowed us to identify a number of target sequences with unexpected behaviors. We envision that MUSCLE will enable the mechanistic exploration of many fundamental biological processes.

Self-sampling of vaginal fluid and high-risk human papillomavirus testing in women aged 50 years or older not attending Papanicolaou smear screening.

OBJECTIVES: To study the value of self-sampling of vaginal fluid at home in combination with high-risk human papillomavirus (HPV) testing in a cohort of older women not attending Papanicolaou (Pap) smear screening. DESIGN: Women (n = 3618), aged 50-65 years, who had not attended screening for at least 6 years were offered self-sampling of vaginal fluid at home (study cohort). The collected material was analysed for the presence of high-risk HPV (using Hybrid capture 2; Hc2). Women with a positive HPV test were referred for colposcopy. These results were compared with the results of Pap smear screening in a corresponding age group of women (controls). The end point of the study was identification of a histological cervical intraepithelial neoplasia stage 2 (CIN2) and above (CIN2+). RESULTS: In all, 39.4% (n = 1426) women participated and 4.6% (n = 66) were high-risk HPV positive. Of the HPV-positive women 56 chose to attend a surgery (84.8%) after a mean time of 2.1 months and ten of these women (17.9%) showed CIN2+, corresponding to 0.70% of all participating women. In the controls, who participated in organised Pap smear screening, the prevalence of CIN2+ was 0.25% (15/6048). The odds ratio for identification of CIN2+ in women aged 50 years or older performing self-sampling and HPV test in comparison with Pap smear was: 2.84 (95% CI 1.14-6.77, P = 0.0174). In older women primary high-risk HPV testing (Hc2) and Pap smear screening showed equal specificity of around 96%. CONCLUSIONS: Self-sampling of vaginal fluid in combination with high-risk HPV testing appears to be an attractive method to improve screening coverage and decrease the prevalence of cervical cancer in women aged 50 years or older.

Short-time repeat high-risk HPV testing by self-sampling for screening of cervical cancer.

BACKGROUND: Testing for high-risk human papillomavirus (HPV) in primary screening for cervical cancer is considered more sensitive, but less specific, in comparison with Pap-smear cytology. Women with persistent HPV infections have a higher risk of developing cervical intraepithelial neoplasia 2+ (CIN2+) lesions. This study was performed to evaluate the gain in specificity for detection of histologically confirmed CIN2+ lesions achieved by short-time repeat testing for high-risk HPV in women aged 30-65 years, with the primary sample for HPV analysis taken by self-sampling. METHODS: A total of 8000 women in Uppsala County, aged 30-65 years, who had not attended organised screening for 6 years or longer, were offered self-sampling of vaginal fluid at home and the samples sent for HPV typing. Of these, 8% (669) were not possible to contact or had performed hysterectomy. Women positive for high-risk HPV in the self-sampling test were invited for a follow-up HPV test and a cervical biopsy on average 3 months after the initial HPV test. RESULTS: In all, 39% (2850/7331) of invited women chose to perform self-sampling of vaginal fluid at home. High-risk HPV infection was found in 6.6% (188) of the women. In all, 89% of the women testing HPV positive performed a follow-up examination, on average 2.7 months, after the first test and 59% of these women were HPV positive in the follow-up test. The prevalence of CIN2+ lesions in women with an initial HPV-positive test was 23% (95% CI 18-30%) and in women with two consecutive HPV-positive tests was 41% (95% CI 31-51%). In women with two positive HPV tests, the prevalence of CIN2+ lesions varied from 49% in women at age 30-39 years to 24% in women at age 50-65 years. Short-time repeat HPV testing increased the specificity for detection of CIN2+ lesions from about 94.2% to 97.8%. The most prevalent HPV types were HPV16 (32%), followed by HPV18/45 (19%) and HPV 33/52/58 (19%). CONCLUSION: The short-time persistence of high-risk HPV infection in this age group was about 60%. Repeat testing for high-risk HPV using self-sampling of vaginal fluid can be used to increase the specificity in the screening for cervical cancer in women aged 30-65 years.

Self-sampling and HPV testing or ordinary Pap-smear in women not regularly attending screening: a randomised study.

BACKGROUND: Most women with cervical cancer have not participated in Pap-smear screening. Self-sampling of vaginal fluid in combination with high-risk HPV testing may be a method to increase the attendance rate. METHODS: A total of 4060 women, 39-60 years old, who had not attended the organised Pap-smear screening for 6 years or more were randomised into two equal groups. A study group was offered to self-sample vaginal fluid (Qvintip) at home and/or recommended to attend the Pap-smear screening. The collected fluid after self-sampling was examined for the presence of high-risk HPV (Hybrid Capture 2 method). Controls were only recommended to attend the Pap-smear screening. The end point was a histological identification of CIN2-3. RESULTS: The participation rate was 39% (771 out of 2000) in the self-sampling group and 9% (188 out of 2060) in the conventional cytology (P<0.001). The number of histological CIN2-3 alterations detected was 0.4% (8 out of 2000) among women offered self-sampling of vaginal fluid and 0.07% (3 out of 4060) in women offered Pap-smears. The odds ratio (OR) for offering self-sampling and HPV testing instead of Pap-smear screening for detection of CIN2-3 was OR=5.42 (95% CI: 1.30-31.8). CONCLUSION: Offering self-sampling of vaginal fluid followed by a high-risk HPV test was considerably more effective for detection of histological CIN2-3 lesions in comparison with offering Pap-test in a midwife reception in women not regularly attending organised screening.

Self-sampling of the vaginal fluid at home combined with high-risk HPV testing.

BACKGROUND: Around 65% of women with cervical carcinoma in Sweden have not attended an organised screening. We therefore investigated the value of using self-sampling at home in combination with a test for high-risk human papilloma virus (HPV) to increase participation. METHODS: A total of 2829 women 30-58 years old, who had not attended the organised screening for > or = 6 years, were recruited. They were offered self-sampling at home (Qvintip) and recommended to send the collected vaginal fluid to a laboratory for analysis of the presence of high-risk HPV (Hybrid Capture 2 method). RESULTS: A total of 39.1% of the women accepted home sampling. These women disclosed a relatively high prevalence of high-risk HPV, which decreased with age, from 11.1% in women 30-39 years old to 2.9% in women > or =50 years . Follow-up disclosed histological cervical intraepithelial neoplasm (CIN) 2-3 lesions in 43.2% of the women with a persistent HPV infection, corresponding to 2.0% of the total number of participating women. The sensitivity of a single smear to detect the histological CIN 2-3 lesions were only 52.6%, even if all abnormal smears (atypical squamous cells of unknown significance (ASCUS)-CIN 3)) were included. CONCLUSION: The use of self-sampling at home in combination with testing for high-risk HPV increases the participation rate of the organised screening and detects almost twice as many women with pre-malignant cell alterations (CIN 2-3) in comparison those with a single cytological smear.

In vivo and mechanistic evidence of nuclear receptor CAR induction by artemisinin.

Artemisinin (a sesquiterpene lactone endoperoxide) has become important in multi-drug treatment of malaria. There is evidence that artemisinin induces drug metabolism which could result in drug-drug interactions. The objective of this study was to characterize the inductive properties of artemisinin on drug-metabolizing cytochrome P450 (CYP450) enzymes. The possibility of artemisinin to induce CYP450 was studied in artemisinin-treated (orally for four days) and vehicle-treated rats using reverse transcriptase polymerase chain reaction (RT-PCR). The effect on enzymatic activities in mouse microsomes from multiple artemisinin administration (intraperitonally) to mice were also studied as well as the effect on the expression in mouse primary hepatocytes and HEK293 cells. Increased CYP2B1 mRNA levels in rats could be seen after artemisinin treatment as well as a weak but reproducible increase in the intensity of CYP1A2. Administration of artemisinin to mice up-regulated hepatic CYP2B10-dependent, and to a lesser extent, CYP2A5-dependent enzyme activities. In primary hepatocyte culture, artemisinin significantly increased the CYP2B10 mRNA levels whereas the CYP2A5 mRNA levels were increased to a lesser extent. No significant changes were seen in the levels of other CYP enzymes. Artemisinin was an activator of constitutive androstane receptor (CAR) but not pregnane X receptor (PXR) in HEK293 cells. The results demonstrate that the drug exerts its effects on drug metabolism via the CAR receptor that results in up-regulation of genes such as the Cyp2b. The weaker up-regulation of CYP2A5 might also be CAR-dependent or alternatively, a consequence of artemisinin toxicity. The results of this study are of importance when predicting potential drug-drug interactions in multi-drug therapies with artemisinin.

Hospital planning for weapons of mass destruction incidents.

As terrorists attacks increase in frequency, hospital disaster plans need to be scrutinized to ensure that they take into account issues unique to weapons of mass destruction. This paper reports a review of the literature addressing hospital experiences with such incidents and the planning lessons thus learned. Construction of hospital disaster plans is examined as an ongoing process guided by the disaster planning committee. Hospitals are conceived as one of the components of a larger community disaster planning efforts, with specific attention devoted to defining important linkages among response organizations. This includes the public health authorities, political authorities, prehospital care agencies, and emergency management agencies. A review is completed of six special elements of weapons of mass destruction incidents that should be addressed in hospital disaster plans: incident command, hospital security, patient surge, decontamination, mental health consequences, and communications. The paper closes with a discussion of the importance of training and exercises in maintaining and improving the disaster plan.

Variable expression of CYP and Pgp genes in the human small intestine.

BACKGROUND: The small intestine is receiving increased attention for its importance in drug metabolism. However, knowledge of the intervariability and regulation of the enzymes involved, cytochrome p450 and P-Glycoproteins (CYP and Pgp), is poor when compared with the corresponding hepatic enzymes. METHODS: The expression of eight different CYP genes and the Pgp were determined by reverse transcription polymerase chain reaction (RT-PCR) in 51 human duodenum biopsies. And the variability and correlation of expression was analyzed. RESULTS: Extensive interindividual variability was found in the expression of most of the genes. Only CYP2C9, CYP3A4 and Pgp were found in all samples. CYP1A2, CYP2A6 and CYP2E1 exhibited the highest interindividual variability. No strong correlation of expression existed between the genes. But a highly significant correlation was found between CYP2D6/1A2, 2D6/2E1, 1A2/2E1 and 2B6/2C9. Acetylsalicylic acid and omeprazole significantly increased the expression of CYPs 2A6, 2E1 and 3A4, respectively. CONCLUSIONS: Extensive interindividual variability is characteristic for the expression of drug-metabolizing CYP and Pgp genes in human duodenum, and external factors such as drugs may further increase the variability. It is possible that the large interindividual variability may lead to variable bioavailability of orally used drugs and hence complicate optimal drug therapy, especially for drugs with a small therapeutic window. Elucidation of factors contributing to clinically important variances warrants further investigation.

Community innovation in hazardous materials management: progress in implementing SARA Title III in the United States. Superfund Amendments and Reauthorization Act.

Title III of the Superfund Amendments and Reauthorization Act (SARA Title III) established a new federal approach to managing toxic chemical hazards. This legislation required industry to disclose the type and quantity of such chemicals and also required the establishment of state and local government organizations to receive those data, evaluate community vulnerability, develop local emergency response plans, and communicate with the public. This paper reviews the law's historical context and empirical studies of its implementation. The available evidence suggests that significant progress has been made in reducing chemical hazards but there is considerable variation across jurisdictions in the effectiveness of the law's implementation. The research results reviewed here suggest a variety of ways in which SARA Title III implementation can be improved.

Accounting for common method variance in cross-sectional research designs.

Cross-sectional studies of attitude-behavior relationships are vulnerable to the inflation of correlations by common method variance (CMV). Here, a model is presented that allows partial correlation analysis to adjust the observed correlations for CMV contamination and determine if conclusions about the statistical and practical significance of a predictor have been influenced by the presence of CMV. This method also suggests procedures for designing questionnaires to increase the precision of this adjustment.

Introduction of an RNA stability element at the 5'-end of an antisense RNA cassette increases the inhibition of target RNA translation.

This communication describes improvement strategies used on a previously described two-unit antisense RNA cassette system. This cassette system encodes RNA with noncontiguous regions of complementarity to a bacterial target RNA, lacI mRNA. One of the units of complementarity was contained within an RNA stem-loop resembling that of the very efficient, naturally occurring antisense RNA CopA. As relatively low inhibitory activity was obtained previously, we tested variants in which several stem-loops were combined within one RNA, each of them directed against a different stretch of target RNA. One to four stem-loop RNAs were tested and found to be relatively ineffective, likely because of low metabolic stability. To increase the intracellular stability of these and other antisense RNAs, a stabilizer element (stem-loop derived from gene 32 mRNA of phage T4) was inserted at their 5'-ends. The results indicate that addition of this element indeed increased antisense RNA efficiency in vivo. As expected, this effect was primarily due to a longer antisense RNA half-life, as shown by RNA abundance (Northern analysis) and decay rates (rifampicin runout experiments). In summary, the results reported indicate that rational design of antisense RNA is feasible, but that the degree of inhibition (approximately 75% maximum inhibition) accomplished here could still be improved.

Monitoring of persistent organic pollutants (POPs): examples from Lake Vättern, Sweden.

Lake Vättern in southern Sweden is a large oligotrophic lake with high surface to catchment area ratio (ca. 0.4) and a water residence time of 60 years. The lake combines sensitivity to atmospheric POP-pollution with general susceptibility for effects of POPs and slow concentration decline. Time series, from the 1960s until 1996, of PCBs and DDT in fish and data on TCDD in sediment of L. Vättern are presented and compared to other large lakes. The long time dataset of POPs in Arctic char (Salvelinus salvelinus) shows a significant annual decline of about 5% for PCBs and 13% for DDT. These rates are in agreement with other studies. Nutrients as well as biological effects and factors affecting the fate of POPs in oligotrophic lakes with long residence times are discussed. We propose that oligotrophic clear lakes are important ecosystems for monitoring POPs in biota.

Climate quality and climate consensus as mediators of the relationship between organizational antecedents and outcomes.

Research has shown that climate quality (average climate ratings) is related to organizational antecedents and outcomes, but researchers have yet to examine climate consensus (the variance of climate ratings). Similarly, studies have investigated typical behavior (members' average performance), but have neglected behavioral similarity (within-group variance). Data from 1,196 members in 180 organizations were used to test relationships of climate quality and consensus with organizational antecedents and outcomes. Climate quality and consensus both had significant correlations with organizational antecedents and outcomes, but climate consensus did not contribute a significant increment to the prediction of organizational outcomes. Finally, quality mediated many relationships between organizational antecedents and outcomes.

An overview of protective action decision-making for a nuclear power plant emergency.

Protection of the public in a nuclear power plant emergency requires decision-makers to balance the time requirements from two chains of events: the events associated with a radiological release and the events involved with the response to that release. The management of these events is distributed among personnel at the nuclear plant, in the local community, and in state and federal agencies. All of these parties must coordinate their response to the emergency to assure that timely and effective protective response can be made by the risk area population. This article describes the process by which protective action recommendations (PARs) are developed in nuclear power plant emergency exercises and provides recommendations from research on emergency response in other types of natural and technological hazards.

Correlates of household seismic hazard adjustment adoption.

This study examined the relationships of self-reported adoption of 12 seismic hazard adjustments (pre-impact actions to reduce danger to persons and property) with respondents' demographic characteristics, perceived risk, perceived hazard knowledge, perceived protection responsibility, and perceived attributes of the hazard adjustments. Consistent with theoretical predictions, perceived attributes of the hazard adjustments differentiated among the adjustments and had stronger correlations with adoption than any of the other predictors. These results identify the adjustments and attributes that emergency managers should address to have the greatest impact on improving household adjustment to earthquake hazard.

Occupational safety and health inspection scores predict rates of workers' lost-time injuries.

This study examined statistical relationships between safety inspection scores and occupational injury rates among civilian employees in 11 types of United States Navy shore facilities ranging from shipyards to research and development centers. The study's results indicate that workplace inspection scores are significantly predictive of lost-time injury rates, even in the presence of statistical controls for differences in facility characteristics. Further, these results suggest that even a 1% improvement in these facilities' safety inspection scores would yield an expected 1% decrease in the rate of severe injuries. Although this is a very small decrease in the injury rate, the number of civilian workers at these Navy shore facilities is so large, and the average cost of such injuries is so great, that the reduction in total injury costs would be nearly $2 million per year. These data suggest that periodic, comprehensive safety inspections can be rewarded with lower rates of occupational lost-time injuries.

Effects of buried charged groups on cysteine thiol ionization and reactivity in Escherichia coli thioredoxin: structural and functional characterization of mutants of Asp 26 and Lys 57.

To investigate the role of Asp 26 and Lys 57, two conserved, buried residues, in the redox mechanism of Escherichia coli thioredoxin (Trx), three mutant proteins, Asp 26 --> Ala (D26A), Lys 57 --> Met (K57M), and the double mutant D26A/K57M, were prepared, replacing the charged amino acids with hydrophobic residues with similar sizes. Both the oxidized (Trx-S2) and reduced [Trx-(SH)2] forms of the mutant thioredoxins are fully folded and similar in overall structure to the wild-type protein (wt). The structure of the active site hydrophobic surface is unchanged by the mutation of Asp 26 and Lys 57, since DNA polymerase activity in the 1:1 complex of the T7 gene 5 protein and mutant Trx-(SH)2 shows similar Kd values (approximately 5 nM) for both mutants and wt. In contrast, redox reactions involving thioredoxin as a catalyst of the reduction of disulfides or oxidation of dithiols are strongly affected by the mutations. In the reaction of Trx-S2 with thioredoxin reductase at pH 8.0, the kcat/Km value for the D26A mutant is decreased by a factor of 10 from that of wt, while the value for the D26A/K57M mutant is reduced 40-fold. The activity of Trx-(SH)2 as a protein disulfide reductase was measured with insulin, using fluorescence to detect oxidation of thioredoxin. At 15 degrees C and pH 8.0, both the D26A and K57M mutants showed 5--10-fold decreases in rates of reaction compared to those of the wild type, and the pH-rate profiles for the mutants were shifted 1 (K57M) and 2 (D26A) units to higher pH compared with the wt curve. NMR measurements for the three mutant proteins indicate that the proteins have the same global fold as that of the wild type, although changes in the chemical shifts of a number of resonances indicate local structural changes in the active site region. The resonances of oxidized D26A and D26A/K57M are pH-independent between pH 6.0 and 10.0, confirming the identification of the active site group titrating with a pKa of 7.5 in wt Trx-S2 as Asp 26. A profound change in the pKa of Asp 26, from 7.5 in the wild type to 9.4 in the mutant, is observed for K57M Trx-S2. The pH-dependent behavior of the resonances is affected in all mutant Trx-(SH)2 proteins. A single pKa shifted to higher values is observed on both the Cys 32 and Cys 35 Cbeta resonances. Ultraviolet absorbance measurements (A240) as a function of pH for wt Trx-(SH)2 demonstrate that the cysteine thiols titrate with apparent pK(a)s of about 7.1 and 9.9. The mutant proteins each show a single transition in the A240 measurements, with a midpoint at pH 7.8-8.0, consistent with the NMR results. The change in absorbance at 240 nm with increasing pH indicates that the number of thiols titrating in each mutant is greater than one but less than two. It is clear that both thiol pK(a)s have been significantly shifted by the mutations. The Cys 32 pKa is moved from 7.1 in wt to 7.8-8.0 in the mutants. The value of the Cys 35 pKa either is indistinguishable from that of Cys 32, thus accounting for more than one thiol titrating in the UV absorbance measurements or else is shifted to much higher pHs (> 10) where its transition is masked in both UV and NMR measurements by the effects of ionization of the tyrosine residues and unfolding of the protein. Our results strongly suggest that the buried Asp 26 carboxyl and Lys 57 epsilon-amino groups significantly affect the pK(a)s of the active site thiols, particularly that of the exposed low-pKa thiol Cys 32, thereby enhancing the rates of thiol-disulfide reactions at physiological pH.

Aged citizens in the warning phase of disasters: re-examining the evidence.

While there is a strong consistent empirical literature on older citizens in the recovery period of disasters, there is much less research on how the elderly respond to disaster warnings. Furthermore, there are conflicting findings among these studies, some characterizing the elderly as noncompliant and less likely to cooperate with authorities, while others find the elderly no less responsive than other age groups. The current article reviews the literature in this area and tries to sort out conflicting findings in terms of the timing of the research and methodological considerations. Data are analyzed from nine disasters-representing flood events, volcanic eruptions, and hazardous materials emergencies-which show citizens over sixty-five years old no less likely to comply with disaster warnings.

Prevalence of skin and genital mucous membrane irritations in patients confined to bed.

A comparative and prospective study of the skin and genital mucous membrane conditions of 50 intensive care patients, who were entirely confined to bed, was conducted. Skin and/or genital mucous membrane irritations were developed by 31 patients during their stay in the ICU. These patients had a significantly longer stay in bed in the ICU than those who did not develop such changes. Patients with lesions were significantly washed more often using the pH 8.5 soap than those without lesions. Erythematous was the most commonly observed symptom and the area between the buttocks and saccrum was the most affected.