bluuebunny/crossref_metadata_2025_split huggingface dataset:
PathCluster: a framework for gene set-based hierarchical clustering
Authors: Kim Tae-Min , Yim Seon-Hee , Jeong Yong-Bok , Jung Yu-Chae , Chung Yeun-Jun 
Published: July 2008

Abstract
Motivation: Gene clustering and gene set-based functional analysis are widely used for the analysis of expression profiles. The development of a comprehensive method jointly combining the two methods would allow for greater biological insights.
Results: We developed a software package, PathCluster for gene set-based clustering via an agglomerative hierarchical clustering algorithm. The distances between predefined gene sets are illustrated in a dendrogram in which the relationships between gene sets can be visually assessed. Valuable biological insights can be obtained according to the type of gene sets, e.g. coordinated action of molecular functions (functional gene sets) and putative motif synergy (promoter gene set) in a biological process. The combined use of gene sets further enables the interrogation of different biological themes and their putative relationships, such as function-versus-regulatory motif or drug-versus-function. PathCluster can also be used for knowledge-based sample partitioning or class categorization for clinical purposes. With extended applicability, PathCluster will facilitate the gleaning of meaningful biological insights and testable hypotheses in the contexts of given expression profiles.
Availability: PathCluster executable files can be freely downloaded at http://www.systemsbiology.co.kr/PathCluster/.
Contact: yejun@catholic.ac.kr
Specific ligation to double-stranded RNA for analysis of cellular RNA::RNA interactions
Authors: Faridani Omid R. , McInerney Gerald M. , Gradin Katarina , Good Liam 
Published: July 2008

Abstract
Double-stranded RNA (dsRNA) is formed in cells as intra- and intermolecular RNA interactions and is involved in a range of biological processes including RNA metabolism, RNA interference and translation control mediated by natural antisense RNA and microRNA. Despite this breadth of activities, few molecular tools are available to analyse dsRNA as native hybrids. We describe a two-step ligation method for enzymatic joining of dsRNA adaptors to any dsRNA molecule in its duplex form without a need for prior sequence or termini information. The method is specific for dsRNA and can ligate various adaptors to label, map or amplify dsRNA sequences. When combined with reverse transcription–polymerase chain reaction, the method is sensitive and can detect low nanomolar concentrations of dsRNA in total RNA. As examples, we mapped dsRNA/single-stranded RNA junctions within Escherichia coli hok mRNA and the human immunodeficiency virus TAR element using RNA from bacteria and mammalian cells.
Compressive Creep and Creep Failure of 8Y2O3/3Al2O3‐Doped Hot‐Pressed Silicon Nitride
Authors: Crampon Jacques , Duclos Richard , Peni Fation , Guicciardi Stefano , de Portu Goffredo 
Published: July 2008

The compressive creep properties of hot‐pressed Si3N48Y2O3—3Al2O3 (wt%) have been investigated in the temperature range of 1543–1603	K in air. The stress exponent, n, of the power creep law was determined to be 1.5, and the activation energy was determined to be 650 kJ/mol. Transmission electron microscopy observations showed that grain‐boundary sliding occurred with cavitation formation in the grain‐boundary glassy phase. The quasi‐steady‐state creep results were consistent with that of the diffusion‐controlled solution—diffusion—precipitation creep mechanism, and the distinguished failure mechanism was cavitation creep damage controlled by the viscosity of the boundary glassy phase. The compressive creep failure time, obtained at 1573 K, in the stress range of 175–300 MPa, followed the MonkmanGrant relation, indicating that cavity growth was mainly controlled by the creep response of the material.
Electrochemical Determination of the Gibbs Energy of Formation of Na2Fe2O4 and Na3Fe5O9 Employing Na‐β‐Al2O3 Solid Electrolyte
Authors: Kale Girish Madhav , Srikanth Srinivasan 
Published: July 2008

The results of isothermal equilibration and X‐ray diffraction studies in Fe2O3‐rich compositions of the Na2Fe2O4–Fe2O3 pseudo‐binary system suggests the coexistence of an equilibrium between α‐Na2Fe2O4 and Fe2O3 at low temperatures (923–1023 K) and Na3Fe5O9 and α‐Fe2O3 at higher temperatures (>1023 K). The Gibbs energy of formation for the interoxide compounds Na2Fe2O4 and Na3Fe5O9 has been measured using solid‐state electrochemical cells that use Na‐β‐Al2O3 as the solid electrolyte. The electromotive force (emf) measurements are performed on cell I, which can be described as
image

and cell II, which can be described as
image
The temperature dependence of the steady‐state emf of cells I and II can be represented as
image

with a standard error of ±5 mV for each emf measurement. By combining the measured emf values of cells I and II with the activity of Na 2 O in α‐Al 2 O 3+ Na‐β‐Al 2 O 3 from the literature, the computed Gibbs energy of formation of Na 2 Fe 2 O 4 and Na 3 Fe 5 O 9 from solid Na 2 O and α‐Fe 2 O 3 can be expressed as
image
where the standard error is ±5500 J/mol for each ΔG° measurement. These uncertainty limits are due to the combined errors in the emf measurement and the thermodynamic data of the reference electrode material that have been used in the present study.
Nasal administration of Lactococcus lactis improves local and systemic immune responses against Streptococcus pneumoniae
Authors: Medina Marcela , Villena Julio , Salva Susana , Vintiñi Elisa , Langella Philippe , Alvarez Susana 
Published: July 2008

ABSTRACT Lactococcus lactis NZ9000 is a non‐pathogenic non‐invasive bacterium extensively used for the delivery of antigens and cytokines at the mucosal level. However, there are no reports concerning the per se immunomodulatory capacity of this strain. The aim of the present study was to investigate the intrinsic immunostimulating properties of the nasal administration of L. lactis NZ9000 in a pneumococcal infection model. Mice were preventively treated with L. lactis (2, 5 or 7 days with 108 cells/day per mouse) and then challenged with Streptococcus pneumoniae. The local and the systemic immune responses were evaluated. Our results showed that nasal administration of L. lactis for 5 days (LLN5d) increased the clearance rate of S. pneumoniae from lung and prevented the dissemination of pneumococci into blood. This effect coincided with an upregulation of the innate and specific immune responses in both local and systemic compartments. LLN5d increased phagocyte activation in lung, blood and bone marrow, determined by NBT and peroxidase tests. Anti‐pneumococcal immunoglobulin (Ig)A in bronchoalveolar lavages (BAL) and IgG in BAL and serum were increased in the LLN5d group. Lung tissue injury was reduced by LLN5d treatment as revealed by histopathological examination and albumin concentration and lactate dehydrogenase activity in BAL. The adjuvant effect of L. lactis in our infection model would be an important advantage for its use as a delivery vehicle of pneumococcal proteins and nasal immunization with recombinant L. lactis emerges as an effective route of vaccination for both systemic and mucosal immunity against pneumococcal infection.
Methamphetamine‐related fatalities in Australia: demographics, circumstances, toxicology and major organ pathology
Authors: Kaye Sharlene , Darke Shane , Duflou Johan , McKetin Rebecca 
Published: July 2008

ABSTRACTAim  To examine the demographic characteristics, circumstances of death, toxicological results and major organ pathology of methamphetamine‐related deaths in Australia.Design  Retrospective review of coronial files.Setting  Australia.Methods  Cases in which methamphetamine was listed as a cause of death were identified from the National Coronial Information System (NCIS).Findings  A total of 371 cases were identified. The mean age of decedents was 32.7 years; 77% were male and 35% were employed. Route of administration was predominantly by injection (89%). Drugs other than methamphetamine were detected in 89% of cases, most commonly benzodiazepines (41%) and morphine (36%). The median blood methamphetamine concentration was 0.2 mg/l (range 0.02–15.0 mg/l). Deaths were overwhelmingly accidental, with 14% determined to be suicides, and occurred in a private home (71%). Cardiovascular pathology, typically coronary artery atherosclerosis, was detected in 54% of decedents. Cerebrovascular pathology, most commonly cerebral haemorrhage and hypoxia, was present in 20% of cases.Conclusions  Methamphetamine has contributed to a substantial number of deaths in Australia. Users need to be informed of the potential harms of methamphetamine use, particularly those associated with the cardiotoxicity of methamphetamine and the use of methamphetamine in conjunction with other drugs.
Sleep architecture, cocaine and visual learning
Authors: Morgan Peter T. , Pace‐Schott Edward F. , Sahul Zakir H. , Coric Vladimir , Stickgold Robert , Malison Robert T. 
Published: July 2008

ABSTRACTBackground  Disturbances in sleep associated with chronic cocaine use may underlie abstinence‐related cognitive dysfunction. We hypothesized that sleep‐related cognitive function would be impaired in chronic cocaine users, and that this impairment would be associated with abstinence‐related changes in sleep architecture.Methods  Twelve chronic cocaine users completed a 23‐day in‐patient study that included randomized, placebo‐controlled, cocaine self‐administration sessions. We report polysomnographic measurement of rapid eye‐movement (REM) sleep and slow‐wave activity, and performance on a visual texture discrimination task.Findings  Progressive abstinence from cocaine was associated with characteristic changes in REM sleep. REM sleep was shortest on nights following cocaine use and rebounded in the first week of abstinence before diminishing with progressive abstinence, following a pattern opposite that of slow‐wave activity. Overnight visual learning was observed over the first night following 3 consecutive days of laboratory cocaine use; however, learning was not observed at 3 days or 17 days of abstinence. Across all points of abstinence, early‐night slow‐wave activity was associated strongly with non‐deterioration of visual performance overnight. Furthermore, overnight enhancement of visual performance was predicted by the co‐occurrence of sufficient early‐night slow‐wave activity and late night REM sleep, similar to results from studies in healthy subjects.Conclusions  These results suggest that abstinence‐associated sleep‐dependent learning deficits are related to characteristic changes in sleep architecture, and promote the idea that treatments directed at sleep (‘somno‐tropic’ treatments) could be helpful in offsetting physiological consequences of cocaine abstinence.
Stress, social support and problem drinking among women in poverty
Authors: Mulia Nina , Schmidt Laura , Bond Jason , Jacobs Laurie , Korcha Rachael 
Published: July 2008

ABSTRACTAims Previous studies have found that stress contributes to problem drinking, while social support can buffer its effects. However, these studies are confined largely to middle‐class and general populations. We extend what is known by examining how the unique stressors and forms of social support experienced by women in poverty impact alcohol problems over a 4‐year time‐period.Design, setting and participants This prospective study used generalized estimating equations (GEE) transition modeling and four annual waves of survey data from 392 American mothers receiving Temporary Assistance for Needy Families (TANF) in a large Northern California county.Measurements We examined the effects of neighborhood disorder, stressful life events and economic hardship on psychological distress and problem drinking over time, and whether social support moderated these relationships for women in poverty.Findings Neighborhood disorder and stressful life events increased significantly the risk for problem drinking, largely through their effect on psychological distress. We found little evidence, however, that social support buffers poor women from the effects of these stressors.Conclusions Women in poverty are exposed to severe, chronic stressors within their communities and immediate social networks which increase vulnerability to psychological distress and problem drinking. The finding that social support does not buffer stress among these women may reflect their high level of exposure to stressors, as well as the hardships and scarce resources within their networks. If the ‘private safety net’ of the social network fails to provide a strong buffer, more effective environmental interventions that reduce exposure to stressors may be needed to prevent alcohol problems in poor women's lives.
Genetic and environmental contributions to nicotine, alcohol and cannabis dependence in male twins
Authors: Xian Hong , Scherrer Jeffrey F. , Grant Julia D. , Eisen Seth A. , True William R. , Jacob Theodore , Bucholz Kathleen K. 
Published: July 2008

ABSTRACTAims  To compute the common and specific genetic and environmental contributions to nicotine dependence (ND) alcohol dependence (AD) and cannabis dependence (CD).Design  Twin model.Participants  Data from 1874 monozygotic and 1498 dizygotic twin pair members of the Vietnam Era Twin Registry were obtained via telephone administration of a structured psychiatric interview in 1992.Measurements  Data to derive life‐time diagnoses of DSM‐III‐R ND, AD and CD were obtained via telephone administration of the Diagnostic Interview Schedule.Findings  The best‐fitting model allowed for additive genetic contributions and unique environmental influences that were common to all three phenotypes. Risks for ND and AD were also due to genetic and unique environmental influences specific to each drug. A specific shared environmental factor contributed to CD.Conclusions  These results suggest that the life‐time co‐occurrence of ND, AD and CD is due to common and specific genetic factors as well as unique environmental influences, and vulnerability for CD is also due to shared environmental factors that do not contribute to ND and AD. The majority of genetic variance is shared across drugs and the majority of unique environmental influences are drug‐specific in these middle‐aged men. Because differences between models allowing for specific genetic versus shared environment were small, we are most confident in concluding that there are specific familial contributions—either additive genetic or shared environment—to CD.
Precipitated withdrawal during maintenance opioid blockade with extended release naltrexone
Authors: Fishman Marc 
Published: July 2008

ABSTRACTBackground There has been increasing interest in the use of extended release injectable naltrexone for the treatment of opioid dependence.Case description We report a case of precipitated withdrawal in a 17‐year‐old adolescent female receiving extended release naltrexone (Vivitrol) for opioid dependence, following her third serial monthly dose of the medication, several days after using oxycodone with mild intoxication.Conclusions This case suggests that, in some circumstances, the opioid blockade may be overcome when naltrexone levels drop towards the end of the dosing interval, producing vulnerability to subsequent naltrexone‐induced withdrawal. This may provide cautionary guidance for clinical management and dosing strategies.
Guidelines for research on drugged driving
Authors: Walsh J. Michael , Verstraete Alain G. , Huestis Marilyn A. , Mørland Jørg 
Published: July 2008

ABSTRACTAim  A major problem in assessing the true public health impact of drug‐use on driving and overall traffic safety is that the variables being measured across studies vary significantly. In studies reported in a growing global literature, basic parameters assessed, analytical techniques and drugs tested are simply not comparable due to lack of standardization in the field. These shortcomings severely limit the value of this research to add knowledge to the field. A set of standards to harmonize research findings is sorely needed. This project was initiated by several international organizations to develop guidelines for research on drugged driving.Methods  A September 2006 meeting of international experts discussed the harmonization of protocols for future research on drugged driving. The principal objective of the meeting was to develop a consensus report setting guidelines, standards, core data variables and other controls that would form the basis for future international research. A modified Delphi method was utilized to develop draft guidelines. Subsequently, these draft guidelines were posted on the internet for global review, and comments received were integrated into the final document.Results  The Guidelines Document is divided into three major sections, each focusing upon different aspects of drugged driving research (e.g. roadside surveys, prevalence studies, hospital studies, fatality and crash investigations, etc.) within the critical issue areas of ‘behavior’, ‘epidemiology’ and ‘toxicology’. The behavioral section contains 32 specific recommendations; (2) epidemiology 40 recommendations; and (3) toxicology 64 recommendations.Conclusions  It is anticipated that these guidelines will improve significantly the overall quality of drugged driving research and facilitate future cross‐study comparisons nationally and globally.
Population pharmacokinetics of proguanil in patients with acute P. falciparum malaria after combined therapy with atovaquone
Authors: HUSSEIN Z. , EAVES C. J. , & D. B. HUTCHINSON , CANFIELD C. J. 
Published: July 2008

1 The pharmacokinetics of proguanil were evaluated in patients with acute P. falciparum malaria receiving concomitantly proguanil hydrochloride and atovaquone. The population consisted of 203 Blacks, 112 Orientals and 55 Malays; 274 males and 96 females. Of the 370 patients, 114 and 256 patients were classified as‘poor’and‘extensive’metabolizers of proguanil, respectively. Body weight and age ranged between 11‐110 kg and 3‐65 years, respectively.2 A one compartment model with first‐order absorption and elimination was fitted to proguanil plasma concentration‐time profiles, using non‐linear mixed effect modelling (NONMEM).3 Oral clearance (CLo) showed a 0.785 power relationship with body weight and was 13% higher in Orientals than Blacks and Malays and 17% lower in‘poor’than‘extensive’metabolizers. According to the mean weight of each population, the final population estimates of CLo in Blacks, Orientals and Malays who are‘extensive’metabolizers were 54.0, 61.5 and 64.31 h‐1, respectively. Age, gender and dose had no significant effects on CLo.4 Apparent volume of distribution (V/F) showed a 0.88 power relationship with body weight. The final population estimates were 562 and 16291 in children (± 15 years) and patients aged > 15 years, respectively, who had a mean body weight of 22.6 and 54.8 kg, respectively. The effect of other covariates on V/F was not examined.5 The final magnitudes of interpatient variability in CLo and V/F were relatively low at 22.5 and 17.0%, respectively.6 Population pharmacokinetic parameter estimates in Black, Oriental and Malay patients with acute P. falcipraum malaria are in good agreement with results of pharmacokinetic studies in healthy Caucasian volunteers. In view of the 30‐50% residual variability in proguanil plasma concentrations, the slight effects of Orientals and‘poor’metabolizers on CLo are unlikely to be clinically significant. Hence, dose recommendation will be solely based on body weight.
Comparative bioavailability of oral, rectal, and intramuscular artemether in healthy subjects: use of simultaneous measurement by high performance liquid chromatography and bioassay
Authors: TEJA‐ISAVADHARM P. , NOSTEN F. , KYLE D. E. , LUXEMBURGER C. , TER KUILE F. , PEGGINS J. O. , BREWER T. G. , WHITE N. J. 
Published: July 2008

1 The pharmacokinetic and effect kinetic properties of oral (p.o.), intramuscular (i.m.), and intrarectal (i.r.) artemether (5 mg kg‐1) were compared in a crossover study in eight healthy adult volunteers. Plasma concentrations of artemether (AM) and its active metabolite dihydroartemisinin (DHA) were measured by high performance liquid chromatography with reductive mode electrochemical detection (h.p.l.c.‐ECD), and plasma antimalarial activity in vitro (effect) was assessed on the same samples by a sensitive bioassay (BA).2 Artemether was absorbed rapidly after oral administration with a mean (95% CI) Cmax for the parent compound of 406 (249 to 561) nmol l‐1 and for DHA of 1009 (639 to 1379) nmol l‐1 with tmax values of 1.7 (1.2 to 2.2) and 1.8 (1.4 to 2.2) h respectively. The mean (95% CI) elimination half‐life of AM was 2.6 (1.8 to 3.4) h and for DHA was 1.9 (1.4 to 2.4) h. Plasma concentration and effect profiles with h.p.l.c.‐ECD and BA were similar suggesting that other unidentified bioactive metabolites contributed little to antimalarial activity in vivo.3 Absorption was slower, more variable, and DHA concentrations were lower following the i.m. and i.r. routes of administration. The mean (95% CI) relative bioavailability compared with oral artemether in the 6 h following administration AUC(0,6h) was 25 (9 to 41)% following i.m. and 35 (10 to 60)% following i.r. artemether.4 These data demonstrate that oral artemether undergoes extensive first pass metabolism to the more active metabolite DHA. Plasma antimalarial activity following oral administration is significantly greater than following i.m. administration. The i.r. route of administration provided similar bioavailability to i.m. injection but there was considerable variability in absorption following both routes. Further studies are needed to determine whether i.r. artemether would be an effective treatment of severe malaria in the rural tropics in situations where oral or parenteral administration is not possible.
Pharmacokinetics and haemodynamic effects of the angiotensin converting enzyme inhibitor cilazapril in hypertensive patients with normal and impaired renal function
Authors: KLOKE H. J. , AMBROS R. J. , VAN HAMERSVELT H. W. , WETZELS J. F. M. , & R. A. P. KOENE , HUYSMANS F. T. M. 
Published: July 2008

1 The pharmacokinetic and pharmacodynamic properties of the angiotensin converting enzyme (ACE) inhibitor cilazapril were studied in 30 hypertensive patients with various degrees of renal function.2 After a single oral dose, apparent cilazaprilat clearance was dependent on renal function being 16.0±3.0, 11.1 ± 3.0, 8.7 ± 3.7 and 6.7 ± 2.1 l h‐1 (means ± s.d.) in patients with creatinine clearances (CLcr) of > 100, 41‐100, 21‐40, and 8‐20 ml min‐1, respectively.3 During 11 weeks of treatment with cilazapril, doses were adjusted to the CLcr and varied from 0.5 to 5.0 mg once daily. At 24 h after drug administration a clear antihypertensive response was seen only in the low clearance groups (CLcr < 40ml min‐1). In contrast, and despite higher once daily dosages, the decline of mean arterial pressure was small and cilazaprilat concentrations after 24 h were lower in the high clearance groups.4 This study demonstrates that chronic once daily treatment with cilazapril is effective in patients with impaired renal function at dosages adjusted to creatinine clearance. No accumulation was seen. Since cilazaprilat clearance was high in the high creatinine clearance groups, a clear antihypertensive response in these groups was only seen at 3 h after drug administration.