Multivariate dependence and genetic networks inference.

A critical task in systems biology is the identification of genes that interact to control cellular processes by transcriptional activation of a set of target genes. Many methods have been developed that use statistical correlations in high-throughput data sets to infer such interactions. However, cellular pathways are highly cooperative, often requiring the joint effect of many molecules. Few methods have been proposed to explicitly identify such higher-order interactions, partially due to the fact that the notion of multivariate statistical dependence itself remains imprecisely defined. The authors define the concept of dependence among multiple variables using maximum entropy techniques and introduce computational tests for their identification. Synthetic network results reveal that this procedure uncovers dependencies even in undersampled regimes, when the joint probability distribution cannot be reliably estimated. Analysis of microarray data from human B cells reveals that third-order statistics, but not second-order ones, uncover relationships between genes that interact in a pathway to cooperatively regulate a common set of targets.

Fullerene-like WS(2) nanoparticles and nanotubes by the vapor-phase synthesis of WCl(n) and H(2)S.

Inorganic fullerene-like (IF) nanoparticles and nanotubes of WS(2) were synthesized by a gas phase reaction starting from WCl(n) (n = 4, 5, 6) and H(2)S. The effect of the various metal chloride precursors on the formation of the products was investigated during the course of the study. Various parameters have been studied to understand the growth and formation of the IF-WS(2) nanoparticles and nanotubes. The parameters that have been studied include flow rates of the various carrier gases, heating of the precursor metal chlorides and the temperature at which the reactions were carried out. The best set of conditions wherein maximum yields of the high quality pure-phase IF-WS(2) nanoparticles and nanotubes are obtained have been identified. A detailed growth mechanism has been outlined to understand the course of formation of the various products of WS(2).

Inactivation of hepatitis A HM-175/18f, reovirus T1 Lang and MS2 during alkaline stabilization of human biosolids.

AIM: To compare the inactivation rates of male-specific bacteriophage-2 (MS2), hepatitis A HM-175/18f (HM-175) and reovirus T1 Lang (T1 L) during alkaline stabilization of wastewater residues. METHODS AND RESULTS: A bench scale alkaline stabilization model was used to evaluate the inactivation of MS2 seeded into raw sludge simultaneously with HM-175 or T1 L. Stabilization was performed in triplicate at 28 and 4 degrees C for both viral combinations. During stabilization at 28 and 4 degrees C, MS2 and T1 L concentrations were similar at each time point (t = 0.1, 2, 12 and 24 h). MS2 and HM-175 concentrations were also similar at each time point during stabilization at 28 degrees C. At 4 degrees C, MS2 and HM-175 concentrations were not similar at the first two time points (t = 0.1 and 2 h), but were similar at later time points (t = 12 and 24 h). CONCLUSIONS: The inactivation rates of T1 L at 4 degrees C and both T1 L and HM-175 at 28 degrees C were similar to the inactivation rate of MS2 at all time points. At 4 degrees C, MS2 was inactivated at a faster rate during the first two time points (t = 0.1 and 2 h) than HM-175, but was inactivated similarly at later time points (t = 12 and 24 h). SIGNIFICANCE AND IMPACT OF THE STUDY: Phages, such as MS2, would be ideal indicators for the presence of enteric viruses in wastewater residues because of their ubiquity, nonpathogenic nature, low cost and time associated with their detection. The findings of this study suggest that MS2 could serve as an indicator for monitoring the persistence of enteric viruses, such as HM-175 and T1 L, during alkaline stabilization performed at moderate temperatures (28 degrees C), but may not serve as an indicator for HM-175 at reduced temperature (4 degrees C). The utility of MS2 as an indicator of viral persistence during biosolids treatment should be further evaluated, as the increased efficiency and frequency of pathogen monitoring associated with their use may reduce the potential public health risk associated with biosolids, facilitating a greater acceptance for their land application.

Development and evaluation of methods to detect coliphages in large volumes of water.

New and improved methods have been developed to detect somatic and male-specific coliphages in large volumes of water by single agar layer (SAL), enrichment and membrane filter methods. Somatic coliphages were detected efficiently on E. coli hosts C and CN13, male-specific coliphages were detected more efficiently on E. coli Famp than on Salmonella typhimurium WG49 and both types of coliphages were detected simultaneously on E. coli C3000. For water volumes of up to 100 ml, the SAL method was efficient and reliable. For water volumes of <1 L and as many as 10 multiple 1 L volumes, the enrichment method was efficient in detecting very low numbers of coliphages. Membrane filter methods, in which coliphages were adsorbed to and eluted from filters, also were relatively efficient, but they were less efficient than SAL and enrichment methods and were considered to be more cumbersome. For filter adsorption-elution methods, coliphage recoveries were most efficient for cellulose ester filters, less efficient for electropositive 1 MDS filters and least efficient for a direct membrane filter method. Overall, the enrichment method was preferred because of its ability to easily and rapidly detect low levels of coliphages in large sample volumes by either presence-absence or most probable number quantification.

How injection drug users coped with testing HIV-seropositive: implications for subsequent health-related behaviors.

At entry into methadone maintenance treatment, 94 HIV-positive injection drug users (IDUs) completed the Coping Reponses Inventory, which asked them to "describe your feelings and experiences when you first learned you were HIV positive." Controlling for time since HIV testing, a reliance on avoidance coping following HIV testing was correlated with high levels of recent HIV risk behavior and poor health at entry into the study. The use of any coping strategy, particularly approach strategies, was related to medication adherence. Hierarchical regression analysis showed that avoidance coping accounted for a significant proportion of the variance in recent HIV risk behavior over and above that accounted for by the other variables. Other independent predictors of continued risk behavior were poor health, lack of social support, and low levels of HIV/AIDS knowledge. The need for interventions to help injection drug users (IDUs) cope subsequent to testing HIV seropositive is discussed.

Spiritual and religious support in recovery from addiction among HIV-positive injection drug users.

The current study examined the association between support and comfort derived from religion or spirituality and abstinence from illicit drugs in a sample of 43 HIV-positive injection drug users entering a methadone maintenance program. Patients with high ratings of perceived spiritual or religious support were abstinent from illicit drugs significantly longer during the first six months of methadone maintenance than were patients with lower ratings. Controlling for the influence of pretreatment variables (addiction and psychiatric severity, CD4 count, social support, and optimism), and during-treatment variables (methadone dose and attendance at counseling sessions), hierarchical regression analysis showed that strength of religious and spiritual support was a significant independent predictor of abstinence. These findings suggest that spirituality may be an important dimension of patient experience to assess in future addiction treatment outcome research.

Stability of crystalline proteins.

By using two model proteins, glucose oxidase and lipase, we demonstrate that dry crystalline formulations are significantly more stable than their amorphous counterparts. The results of Fourier-transform infrared spectroscopy indicate that crystalline proteins better maintain their native conformation in accelerated stability studies. The lower tendency of crystalline proteins to aggregate is confirmed by size-exclusion chromatography. The data suggest that protein crystallization may significantly improve some aspects of protein handling, and change the way biopharmaceuticals are produced, formulated, and delivered.

Predictors of nonadherence to HIV-related medication regimens during methadone stabilization.

Nonadherence to HIV-related medication regimens among drug-abusing patients decreases therapeutic effectiveness and may limit patient access to newer, highly active antiretroviral therapies (HAART). A number of factors have been associated with medication nonadherence; however, few studies have examined predictors of nonadherence specifically in HIV-positive drug abusers. In the current study, a comprehensive assessment battery was administered to 42 HIV-positive, injection drug users beginning methadone maintenance. HIV-related medication adherence was assessed weekly by self-report during the 4-week methadone stabilization phase. Thirty-six percent of patients reported less than 80% adherence to their medication regimen at entry into methadone. Medication adherence increased significantly during the 4-week stabilization phase. Significant zero-order correlations were found between nonadherence during stabilization and viral load, low educational attainment, depression, and neuropsychological tests of problem solving ability and cognitive flexibility. Independent predictors of nonadherence were low levels of education and poor emotional functioning. Implications for early intervention are discussed.

Cocaine, HIV, and their cardiovascular effects: is there a role for ACE-inhibitor therapy?

Cocaine abuse and HIV disease each have potentially adverse effects upon the heart and cardiovascular system which may be exacerbated when these risk factors are combined. The development of a safe and effective agent to treat both cocaine addiction and its cardiovascular sequelae, that is well-tolerated by HIV patients, would thus be of considerable clinical utility. In this article we discuss the rationale for the investigation of angiotensin converting enzyme (ACE) inhibitors, commonly used to treat hypertension, for treatment in cocaine-abusing populations, based on their potential to reduce cocaine use by modulating levels of dopamine and corticotropin releasing factor in the brain, and on their ability to reverse cardiovascular and platelet abnormalities. We present preliminary findings from echocardiographic and platelet activation studies in 16 HIV-positive, cocaine abusing patients, as well as tolerability and efficacy studies of the ACE-inhibitor, fosinopril, for the treatment of cocaine abuse in both HIV-positive (n=6) and HIV-negative (n=5) methadone-maintained cocaine abusers. Findings suggest that HIV-positive cocaine-abusing patients possess abnormalities of diastolic heart function and platelet activation that are potentially reversible with ACE-inhibitor therapy. Findings also suggest that fosinopril is well-tolerated regardless of HIV serostatus, does not appear to cause hypotension, and may possess effectiveness for reducing cocaine use. We conclude that ACE-inhibitor therapy may offer a new pharmacologic approach to the treatment of cocaine abuse and its complications, and that controlled research of this class of agents may be promising.

A path analysis of cognitive, affective, and behavioral predictors of treatment response in a methadone maintenance program.

PURPOSE: Continued illicit drug use by opioid-dependent patients maintained on methadone is a serious problem, undermining the goal of methadone maintenance treatment and increasing the risk for HIV. The current study employed structural equation modeling (SEM) to examine cognitive, affective, and behavioral predictors of treatment response during the first 12 weeks of methadone maintenance treatment. METHODS: 302 opioid-dependent individuals (72% male; 28% female) entering a methadone maintenance program (MMP) were provided with a comprehensive intake assessment. Heroin and cocaine use were assessed using twice weekly urine toxicology screens. The model accounted for 37 percent of the variance in abstinence from illicit opiates and 38 percent of the variance in abstinence from cocaine. RESULTS: Continued heroin use while maintained on methadone was predicted by pre-treatment severity of addiction and by strength of self-identity as an "addict." Cocaine use was predicted by pre-treatment severity of addiction, low self-efficacy, lack of negative affect, and strength of self-schema. The strongest predictor of abstinence from both heroin and cocaine was attendance at the adjunctive manual-guided psychosocial group interventions. IMPLICATIONS: Implications for treatment are discussed.

The influence of coping and depression on abstinence from illicit drug use in methadone-maintained patients.

Use of illicit drugs by opioid-dependent patients maintained on methadone undermines the benefits of methadone maintenance treatment. Because supplemental pharmacologic approaches have met with limited success, it is important to identify psychological mechanisms associated with drug use that potentially could contribute to the development of more effective treatments. To investigate this issue, the current study assessed coping and depression in 307 methadone-maintained patients and found a reliance on avoidant coping strategies, most notably by depressed patients. Patients who achieved abstinence following a 12-week coping skills training intervention decreased the use of avoidant coping strategies. Drug use at the 6-month follow-up was related to gains made during treatment, specifically reduced cognitive avoidance, reduced depression, and number of drug-free weeks during treatment.

The detection of astrovirus in sludge biosolids using an integrated cell culture nested PCR technique.

The work presented here demonstrates the utility of the integrated cell culture-reverse transcriptase-polymerase chain reaction (ICC-RT-PCR) coupled with nested PCR to detect human astroviruses and enteroviruses in sludge biosolids. Viruses were concentrated by beef extract elution and organic flocculation prior to analysis by a plaque assay and ICC-RT-PCR. Astroviruses were detected in all but one sample and all of the samples were positive for enteroviruses. We have demonstrated the prevalence and frequency ofastrovirus in sludge and validated the ICC-RT-PCR/nested PCR technique as a useful tool to detect viruses in sludge.

A randomized controlled trial of auricular acupuncture for cocaine dependence.

BACKGROUND: Partly because of a lack of a conventional, effective treatment for cocaine addiction, auricular acupuncture is used to treat this disorder in numerous drug treatment facilities across the country for both primary cocaine-dependent and opiate-dependent populations. OBJECTIVE: To evaluate the effectiveness of auricular acupuncture for the treatment of cocaine addiction. METHODS: Eighty-two cocaine-dependent, methadone-maintained patients were randomly assigned to 1 of 3 conditions: auricular acupuncture, a needle-insertion control condition, or a no-needle relaxation control. Treatment sessions were provided 5 times weekly for 8 weeks. The primary outcome was cocaine use assessed by 3-times-weekly urine toxicology screens. RESULTS: Longitudinal analysis of the urine data for the intent-to-treat sample showed that patients assigned to acupuncture were significantly more likely to provide cocaine-negative urine samples relative to both the relaxation control (odds ratio, 3.41; 95% confidence interval, 1.33-8.72; P =. 01) and the needle-insertion control (odds ratio, 2.40; 95% confidence interval, 1.00-5.75; P =.05). CONCLUSIONS: Findings from the current study suggest that acupuncture shows promise for the treatment of cocaine dependence. Further investigation of this treatment modality appears to be warranted.

Continuation of high-risk behavior by HIV-positive drug users. Treatment implications.

Drug users who are positive for the human immunodeficiency virus (HIV) represent a major vector of HIV transmission, yet relatively little is known about their continued drug- and sex-related HIV-risk behavior, which may impede the development of effective risk-reduction interventions. In this study, 50 HIV-seropositive injection drug users entering methadone maintenance treatment completed a comprehensive risk assessment battery, including self-report of HIV-risk behavior since learning HIV serostatus, and measures of risk-reduction information, motivation, and behavioral skills. We found that a disconcertingly high proportion of patients (66%) reported having engaged in HIV-risk behavior since learning their HIV-seropositive status. Level of HIV-related knowledge did not predict high-risk behavior. Drug-related risk behavior was predicted by psychiatric severity and poor behavioral skills. Sex-related risk was predicted by low levels of motivation and poor behavioral skills. Implications of these findings for treatment are discussed.

Detection of astroviruses, enteroviruses, and adenovirus types 40 and 41 in surface waters collected and evaluated by the information collection rule and an integrated cell culture-nested PCR procedure.

We evaluated the use of an integrated cell culture-reverse transcription-PCR (ICC-RT-PCR) procedure coupled with nested PCR to detect human astroviruses, enteroviruses, and adenovirus types 40 and 41 in surface water samples that were collected and evaluated by using the Information Collection Rule (ICR) method. The results obtained with the ICC-RT-PCR-nested PCR method were compared to the results obtained with the total culturable virus assay-most-probable-number (TCVA-MPN) method, the method recommended by the U.S. Environmental Protection Agency for monitoring viruses in surface and finished waters. Twenty-nine ICR surface water samples were analyzed. Viruses were concentrated by using filter adsorption-beef extract elution and organic flocculation techniques, and then the preparations were evaluated for viruses by visualizing cytopathic effects in the Buffalo green monkey kidney (BGMK) cell line. In the ICC-RT-PCR-nested PCR technique we used Caco-2 cells to propagate astroviruses and enteroviruses (ICC step), and we used BGMK cells to propagate adenovirus types 40 and 41, as well as enteroviruses. Fifteen of the 29 samples (51.7%) were positive for astrovirus as determined by the ICC-RT-PCR-nested PCR method, and eight of these samples (27.5%) contained infectious astrovirus. Seventeen of the 29 samples (58.6%) were positive for enteroviruses when the BGMK cell line was used, and six (27.6%) of these samples were determined to be infectious. Fourteen of the 29 samples (48.3%) were positive for adenovirus types 40 and 41, and 11 (37.9%) of these samples were determined to be infectious. Twenty-seven of the 29 samples (93.1%) were positive for a virus, and 19 (68.9%) of the samples were positive for an infectious virus. Only 5 of the 29 samples (17.2%) were positive as determined by the TCVA-MPN method. The ICC-RT-PCR-nested PCR method provided increased sensitivity compared to the TCVA-MPN method.

Fortified sera and their use in environmental virology.

Four commercially available fortified sera were compared to fetal bovine serum (FBS) with regard to their ability to maintain or increase the sensitivity of the Buffalo green monkey (BGM) kidney cell line to viral infection. Nine virus strains and five wastewater samples were used. Fortified sera were comparable to FBS for the enumeration of some viruses by the plaque method and for the detection of virus in wastewater by the most-probable-number assay.

Preliminary results of a new method for locating auricular acupuncture points.

Auricular acupuncture is widely used for the treatment of cocaine addiction, and there is an urgent need to conduct controlled clinical research of this intervention. One impediment to this endeavor is the lack of an objective and reliable method for identifying the hypothesized active and control points. In order to address this issue, we conducted two studies employing a constant current electrical device and a novel probing technique. In the first study, we assessed the reliability of our technique for measuring electrical skin resistance points (acupuncture or non-acupuncture) on the body and auricles. In the second study, we analyzed and compared the measurements of skin resistance of auricular acupuncture and control zones in a group of cocaine abusing patients. Findings suggest that our measurement method produced reliable measurements, and that active acupuncture zones revealed a significantly different pattern of electrical skin resistance readings compared to control zones. This method may be useful for locating active and control points in controlled clinical trials of auricular acupuncture.

The efficacy of three common hospital liquid germicides to inactivate Cryptosporidium parvum oocysts.

We evaluated three commonly used hospital disinfectants against three concentrations of Cryptosporidium parvum oocysts (1.5 x 10(6), 1.5 x 10(5), 1.5 x 10(4)). A 10% phenol product, a 10% povidone-iodine product and a 2.5% glutaraldehyde product were tested against Cryptosporidium parvum oocysts without organic load. In-vitro excystation was used to determine viability and a cell culture assay was used to determine infectivity of germicide-treated oocysts. A 2.5% glutaraldehyde product was the most effective in halting excystation of sporozoites and infection in cell monolayers. However, this occurred only at the longest exposure time of 10 h and with the lowest concentration of oocysts (1.5 x 10(4)). The 10% phenol product and the 10% povidone-iodine product also decreased excystation, but were unable to halt infection. Although the ability of C. parvum to with-stand chemical treatment is well known, the ability of oocysts to remain viable and infectious after a 10 h treatment in glutaraldehyde is cause for concern. Endoscopic equipment that may come into contact with these organisms cannot be immersed into glutaraldehyde for this length of time due to its corrosive nature. Thus, the results of this research are cause for concern in hospital disinfection units.

Cross-linked protein crystals for vaccine delivery.

The progress toward subunit vaccines has been limited by their poor immunogenicity and limited stability. To enhance the immune response, subunit vaccines universally require improved adjuvants and delivery vehicles. In the present paper, we propose the use of cross-linked protein crystals (CLPCs) as antigens. We compare the immunogenicity of CLPCs of human serum albumin with that of soluble protein and conclude that there are marked differences in the immune response to the different forms of human serum albumin. Relative to the soluble protein, crystalline forms induce and sustain over almost a 6-month study a 6- to 10-fold increase in antibody titer for highly cross-linked crystals and an approximately 30-fold increase for lightly cross-linked crystals. We hypothesize that the depot effect, the particulate structure of CLPCs, and highly repetitive nature of protein crystals may play roles in the enhanced production of circulating antibodies. Several features of CLPCs, such as their remarkable stability, purity, biodegradability, and ease of manufacturing, make them highly attractive for vaccine formulations. This work paves the way for a systematic study of protein crystallinity and cross-linking on enhancement of humoral and T cell responses.