bluuebunny/crossref_metadata_2025_split huggingface dataset:
Interpreting catch per unit effort data to assess the status of individual stocks and communities
Authors: Maunder Mark N. , Sibert John R. , Fonteneau Alain , Hampton John , Kleiber Pierre , Harley Shelton J. 
Published: August 2006

AbstractDespite being one of the most common pieces of information used in assessing the status of fish stocks, relative abundance indices based on catch per unit effort (cpue) data are notoriously problematic. Raw cpue is seldom proportional to abundance over a whole exploitation history and an entire geographic range, because numerous factors affect catch rates. One of the most commonly applied fisheries analyses is standardization of cpue data to remove the effect of factors that bias cpue as an index of abundance. Even if cpue is standardized appropriately, the resulting index of relative abundance, in isolation, provides limited information for management advice or about the effect of fishing. In addition, cpue data generally cannot provide information needed to assess and manage communities or ecosystems. We discuss some of the problems associated with the use of cpue data and some methods to assess and provide management advice about fish populations that can help overcome these problems, including integrated stock assessment models, management strategy evaluation, and adaptive management. We also discuss the inappropriateness of using cpue data to evaluate the status of communities. We use tuna stocks in the Pacific Ocean as examples.
‘It has to go away, but at the same time it has to be kept’: the Berlin Wall and the making of an urban icon
Authors: SCHLÖR JOACHIM 
Published: August 2006

For 28 years, from 13 August 1961 through 9 November 1989, the city of Berlin was divided by a wall. The borderline was the symbol for the Cold War and the political partition between East and West – but it was also an element of the urban structure: Berliners in the two parts of the city had to live with it and to define themselves in relation to it. After the fall of the wall and its destruction in the euphoric mood of re-unification, a huge inner-urban wasteland became the symbol for the need of a new politics of memory: the missing Berlin Wall became an urban icon.What business do we have in Berlin? Memories.Uwe Johnson
The ATTEMPT cohort: a multi‐national longitudinal study of predictors, patterns and consequences of smoking cessation; introduction and evaluation of internet recruitment and data collection methods
Authors: West Robert , Gilsenan Alicia , Coste Florence , Zhou Xiaolei , Brouard Remi , Nonnemaker James , Curry Susan J. , Sullivan Sean D. 
Published: August 2006

ABSTRACTAims  The ATTEMPT study was designed to chart the natural history of smoking cessation and associated short‐term health outcomes and effects on medical resource utilization among a cohort recruited across multiple countries. This paper describes the methods for recruitment and follow‐up, the baseline population characteristics of the enrolled population and 1‐year response rates.Design  ATTEMPT is a multi‐national prospective cohort study that used the internet for subject recruitment and online assessments every 3 months for 2.5 years.Setting  Subjects were recruited via e‐mail from existing internet panels [Canada (n = 208), France (n = 201), the United Kingdom (n = 200) and the United States (n = 1400].Subjects  Panel members who were aged 35–65 years, smoked at least five cigarettes per day and at initiation stated an intention to quit smoking within the next 3 months were eligible for this study.Measurements  Measures included: attempts to quit, smoking status, smoking history, nicotine dependence and craving, methods used to quit smoking, reasons for quitting or failing to quit smoking, short‐term health effects, health resource utilization, wellbeing, concern over weight gain, confidence in preventing weight gain, body weight and demographics. In addition, in‐home assessments of weight were undertaken by field staff for a random sample of US participants.Findings  Country‐specific recruitment was completed within 17 days. The recruitment method produced a sample with characteristics broadly similar to those found in national surveys of smokers except for higher prevalence of obesity in the US and Canadian samples and higher educational level. At the end of 1 year the response rate was 52%, and there was little evidence of differential loss to follow‐up by key subject characteristics. Weight reported in the survey was found to correlate highly with weight measured during in‐home visits.Conclusion  This paper demonstrates the feasibility of enrolling and following a diverse cohort of smokers for self‐reported health and behaviour measures via the internet.
Reducing substance use improves adolescents’ school attendance
Authors: Engberg John , Morral Andrew R. 
Published: August 2006

ABSTRACTAims  Substance use initiation and frequency are associated with reduced educational attainments among adolescents. We examined if decreases in substance use substantially improve youths’ school attendance.Design  A total of 1084 US adolescents followed quarterly for 1 year after entering substance abuse treatment.Methods  Random and fixed effects regression models were used to differentiate the lagged effects of drug use from other time‐varying and time‐invariant covariates. Self‐reports of alcohol, marijuana, stimulants, sedatives, hallucinogens and other drug use were used to predict subsequent school attendance, after controlling for demographic and drug use history characteristics, problem indices and other covariates.Findings  Reductions in the frequency of alcohol, stimulants and other drug use and the elimination of marijuana use were each associated independently with increased likelihoods of school attendance.Conclusions  Because years of completed schooling is highly correlated with long‐term social and economic outcomes, the possibility that reductions in substance use may improve school attendance has significant implications for the cost‐effectiveness of substance abuse treatment and other interventions designed to reduce adolescents’ substance use.
Should substance use disorders be considered as categorical or dimensional?
Authors: Muthén Bengt 
Published: August 2006

ABSTRACTAims  This paper discusses the representation of diagnostic criteria using categorical and dimensional statistical models. Conventional modeling using categorical or continuous latent variables in the form of latent class analysis and factor (IRT) analysis has limitations for the analysis of diagnostic criteria.Methods  New hybrid models are discussed which provide both categorical and dimensional representations in the same model using mixture models. Conventional and new models are applied and compared using recent data for Diagnostic and Statistical Manual of Mental Disorders version IV (DSM‐IV) alcohol dependence and abuse criteria from the National Epidemiologic Survey on Alcohol and Related Conditions. Classification results from hybrid models are compared to the DSM‐IV approach of using the number of diagnostic criteria fulfilled.Results  It is found that new hybrid mixture models are more suitable than latent class and factor (IRT) models.Conclusion  Implications for DSM‐V are discussed in terms of reporting results using both categories and dimensions.
The neurobiology of addiction: a neuroadaptational view relevant for diagnosis
Authors: Koob George F. 
Published: August 2006

ABSTRACTAims  The purpose of this review is to provide a synthesis of our knowledge of the neurobiological bases of addiction relevant for the diagnosis of addiction.Methods  A heuristic framework of neuroadaptive changes within key brain neurocircuitry responsible for different stages of the addiction cycle is outlined and linked to human studies to provide important future translational links for diagnosis. Results  Animal studies have revealed dysregulation of specific neurochemical mechanisms (dopamine, opioid peptides) in the brain reward systems and recruitment of brain stress systems (corticotropin‐releasing factor) during the development of dependence that convey vulnerability to relapse. Animal studies have implicated the prefrontal cortex and basolateral amygdala in drug‐ and cue‐induced relapse, respectively, and the brain stress systems in stress‐induced relapse. Genetic studies suggest roles for the genes encoding the neurochemical elements involved in both the brain reward and stress systems in the vulnerability to addiction, and molecular studies have identified transduction and transcription factors that may mediate dependence‐induced reward dysregulation. Human imaging studies reveal similar neurocircuits involved in acute intoxication, chronic drug dependence and vulnerability to relapse. Conclusions  Major neurobiological changes in substance abuse disorders common to human and animal studies relevant for diagnosis include a compromised reward system, overactivated brain stress systems and compromised orbitofrontal/prefrontal cortex function. No biological markers of substance abuse disorders currently exist, but there are many promising neurobiological features of substance abuse disorders that will eventually aid in the specific diagnoses of substance use, misuse and dependence.
Comorbidity between substance use disorders and psychiatric conditions
Authors: Schuckit Marc A. 
Published: August 2006

ABSTRACTAims  To review information relevant to the question of whether substance‐induced mental disorders exist and their implications.Design and method  This paper utilized a systematic review of manuscripts published in the English language since approximately 1970 dealing with comorbid psychiatric and substance use disorders.Findings  The results of any specific study depended on the definitions of comorbidity, the methods of operationalizing diagnostic criteria, the interview and protocol invoked several additional methodological issues. The results generally support the conclusion that substance use mental disorders exist, especially regarding stimulant or cannabinoid‐induced psychoses, substance‐induced mood disorders, as well as substance‐induced anxiety conditions.Conclusions  The material reviewed indicates that induced disorders are prevalent enough to contribute significantly to rates of comorbidity between substance use disorders and psychiatric conditions, and that their recognition has important treatment implications. The current literature review underscores the heterogeneous nature of comorbidity.
Mitochondrial haplotypes of European wild boars with 2n = 36 are closely related to those of European domestic pigs with 2n = 38
Authors: Fang M. , Berg F. , Ducos A. , Andersson L. 
Published: August 2006

SummaryWild boars from Western Europe have a 2n = 36 karyotype, in contrast to a karyotype of 2n = 38 in wild boars from Central Europe and Asia and in all domestic pigs. The phylogenetic status of this wild boar population is unclear, and it is not known if it has contributed to pig domestication. We have now sequenced the mtDNA control region from 30 European wild boars (22 with a confirmed 2n = 36 karyotype) and six Asian wild boars (two Hainan and four Dongbei wild boars) to address this question. The results revealed a close genetic relationship between mtDNA haplotypes from wild boars with 2n = 36 to those from domestic pigs with 2n = 38. Thus, we cannot exclude the possibility that wild boars with 2n = 36 may have contributed to pig domestication despite the karyotype difference. One of the European wild boars carried an Asian mtDNA haplotype, and this most likely reflects gene flow from domestic pigs to European wild boars. However, this gene flow does not appear to be extensive because the frequency of Asian haplotypes detected among European wild boars (c. 3%) were 10‐fold lower than among European domestic pigs (c. 30%). Previous studies of mtDNA haplotypes have indicated that pig populations in Europe and Asia have experienced a population expansion, but it is not clear if the expansion occurred before or after domestication. The results of the present study are consistent with an expansion that primarily occurred prior to domestication because the mtDNA haplotypes found in European and Asian wild boars did not form their own clusters but were intermingled with haplotypes found in domestic pigs, indicating that they originated from the same population expansion.
A dominant role for chemoattractant receptor‐homologous molecule expressed on T helper type 2 (Th2) cells (CRTH2) in mediating chemotaxis of CRTH2+ CD4+ Th2 lymphocytes in response to mast cell supernatants
Authors: Gyles Shân L. , Xue Luzheng , Townsend Elizabeth R. , Wettey Frank , Pettipher Roy 
Published: August 2006

SummaryHuman cultured mast cells, immunologically activated with immunoglobuin E (IgE)/anti‐IgE, released a factor(s) that promoted chemotaxis of human CRTH2+ CD4+ T helper type 2 (Th2) lymphocytes. Mast cell supernatants collected at 20 min, 1 hr, 2 hr and 4 hr after activation caused a concentration‐dependent increase in the migration of Th2 cells. The effect of submaximal dilutions of mast‐cell‐conditioned media was inhibited in a dose‐dependent manner by ramatroban (IC50 = 96 nm), a dual antagonist of both the thromboxane‐like prostanoid (TP) receptor and the chemoattractant receptor‐homologous molecule expressed on Th2 cells (CRTH2), but not by the selective TP antagonist SQ29548, implicating CRTH2 in mediating the chemotactic response of these Th2 cells. The effect of mast‐cell‐conditioned media was mimicked by prostaglandin D2 (PGD2) and this eicosanoid was detected in the conditioned media from activated mast cells in concentrations sufficient to account for the activity of the mast cell supernatants. Treatment of the mast cells with the cyclo‐oxygenase inhibitor diclofenac (10 μm) inhibited both the production of PGD2 and the CRTH2+ CD4+ Th2‐stimulatory activity, while addition of exogenous PGD2 to conditioned media from diclofenac‐treated mast cells restored the ability of the supernatants to promote chemotaxis of these Th2 cells. The degree of inhibition caused by diclofenac treatment of the mast cells was concordant with the degree of inhibition of chemotactic responses afforded by CRTH2 blockade. These data suggest that PGD2, or closely related metabolites of arachidonic acid, produced from mast cells may play a central role in the activation of CRTH2+ CD4+ Th2 lymphocytes through a CRTH2‐dependent mechanism.
Endodontics and infective endocarditis – is antimicrobial chemoprophylaxis required?
Authors: Brincat M. , Savarrio L. , Saunders W. 
Published: August 2006

AbstractThe purpose of this review is to evaluate the evidence implicating nonsurgical endodontic procedures in inducing infective endocarditis (IE). The literature is reviewed and findings about dental procedures that elicit bacteraemia [in particular root canal treatment (RCT)], sequelae of bacteraemia, relationship between IE and RCT and variation between antibiotic prophylaxis (AP) guidelines are highlighted. At present, there is still significant debate as to which dental procedures require chemoprophylaxis and what antibiotic regimen should be prescribed. Currently, there are insufficient primary data to know whether AP is effective or ineffective against IE. Practitioners are bound by current guidelines and medico‐legal considerations. Thus, the profession requires clear, uniform guidelines that are evidence‐based.
Parent and child reports of fruit and vegetable intakes and related family environmental factors show low levels of agreement
Authors: Tak N. I. , Te Velde S. J. , De Vries J. H. M. , Brug J. 
Published: August 2006

AbstractObjective  The purpose of the present study was to determine the level of agreement between child and parent reports of 9‐ to 10‐year‐old children's consumption of fruit and vegetables and potential family–environmental determinants.Methods  Schoolchildren and their parents completed parallel questionnaires at baseline and at follow‐up (1 year later) about usual fruit and vegetable consumption of the child, potential determinants and general demographics. Matched child–parent couples were included in the analyses (baseline = 380; follow‐up = 307). To assess the level of agreement between child and parent reports at both points in time, dependent‐sample t‐test, correlation coefficients, weighted Cohen's kappa coefficients and Bland–Altman plots including limits of agreement were used.Results  Both at baseline and at follow‐up, the mean intake of fruit and vegetable reported by the children were significantly higher than reported by their parents, but differences were smaller at follow‐up. Correlation coefficients between child and parent reports (0.28–0.43) and weighted Cohen's kappa coefficients (0.25–0.28) were weak to moderate. Limits of agreement were wide.Conclusion  The agreement between parent and child reports is weak to moderate and may depend on the age of the child. Fourth graders may overestimate their own intake of fruit and vegetables.
Automatic identification of Mycobacterium tuberculosis by Gaussian mixture models
Authors: FORERO M. G. , CRISTÓBAL G. , DESCO M. 
Published: August 2006

SummaryTuberculosis and other kinds of mycobacteriosis are serious illnesses for which early diagnosis is critical for disease control. Sputum sample analysis is a common manual technique employed for bacillus detection but current sample‐analysis techniques are time‐consuming, very tedious, subject to poor specificity and require highly trained personnel. Image‐processing and pattern‐recognition techniques are appropriate tools for improving the manual screening of samples. Here we present a new technique for sputum image analysis that combines invariant shape features and chromatic channel thresholding. Some feature descriptors were extracted from an edited bacillus data set to characterize their shape. They were statistically represented by using a Gaussian mixture model representation and a minimal error Bayesian classification procedure was employed for the last identification stage. This technique constitutes a step towards automating the process and providing a high specificity.
Structure and reactivity of Trypanosoma brucei pteridine reductase: inhibition by the archetypal antifolate methotrexate
Authors: Dawson Alice , Gibellini Federica , Sienkiewicz Natasha , Tulloch Lindsay B. , Fyfe Paul K. , McLuskey Karen , Fairlamb Alan H. , Hunter William N. 
Published: August 2006

SummaryThe protozoan Trypanosoma brucei has a functional pteridine reductase (TbPTR1), an NADPH‐dependent short‐chain reductase that participates in the salvage of pterins, which are essential for parasite growth. PTR1 displays broad‐spectrum activity with pterins and folates, provides a metabolic bypass for inhibition of the trypanosomatid dihydrofolate reductase and therefore compromises the use of antifolates for treatment of trypanosomiasis. Catalytic properties of recombinant TbPTR1 and inhibition by the archetypal antifolate methotrexate have been characterized and the crystal structure of the ternary complex with cofactor NADP+ and the inhibitor determined at 2.2 Å resolution. This enzyme shares 50% amino acid sequence identity with Leishmania major PTR1 (LmPTR1) and comparisons show that the architecture of the cofactor binding site, and the catalytic centre are highly conserved, as are most interactions with the inhibitor. However, specific amino acid differences, in particular the placement of Trp221 at the side of the active site, and adjustment of the β6‐α6 loop and α6 helix at one side of the substrate‐binding cleft significantly reduce the size of the substrate binding site of TbPTR1 and alter the chemical properties compared with LmPTR1. A reactive Cys168, within the active site cleft, in conjunction with the C‐terminus carboxyl group and His267 of a partner subunit forms a triad similar to the catalytic component of cysteine proteases. TbPTR1 therefore offers novel structural features to exploit in the search for inhibitors of therapeutic value against African trypanosomiasis.
Specialized ‘dauciform’ roots of Cyperaceae are structurally distinct, but functionally analogous with ‘cluster’ roots
Authors: SHANE MICHAEL W. , CAWTHRAY GREGORY R. , CRAMER MICHAEL D. , KUO JOHN , LAMBERS HANS 
Published: August 2006

ABSTRACTWhen grown in nutrient solutions of extremely low [P] (≤1.0 µm), the sedge Schoenus unispiculatus Benth. (Cyperaceae) develops dauciform roots, which are short and carrot shaped, and produce dense numbers of long root hairs. It has been suggested that dauciform roots of monocotyledonous sedges function to acquire P from nutrient‐poor, P‐fixing soils in a manner similar to that of cluster (proteoid) roots developed by some dicotyledonous species, but without evidence to substantiate this claim. To elucidate the ecophysiological role of dauciform roots, we assessed carboxylate exudation, internal carboxylate and P concentrations and O2 uptake rates during dauciform root development. We showed that O2 consumption was fastest [9 nmol O2 g−1 fresh mass (FM) s−1] and root [P] greatest (0.4 mg P g−1 FM) when dauciform roots were young and rapidly developing. Citrate was the most abundant carboxylate in root tissues at all developmental stages, and was most concentrated (22.2 µmol citrate g−1 FM) in young dauciform roots, decreasing by more than half in mature dauciform roots. Peak citrate‐exudation rates (1.7 nmol citrate g−1 FM s−1) occurred from mature dauciform roots, and were approximately an order of magnitude faster than those from roots of species without root clusters, and similar to those of mature proteoid (cluster) roots of Proteaceae. Both developing and mature dauciform roots had the capacity to acidify (but not alkalinize) the rhizosphere. Anatomical studies showed that epidermal cells in dauciform roots were greatly elongated in the transverse plane; epidermal cells of parent roots were unmodified. Although structurally distinct, the physiology of dauciform roots in sedges appears to be analogous to that of proteoid roots of Proteaceae and Fabaceae, and hence, dauciform roots would facilitate access to sorbed P and micronutrients from soils of low fertility.
Phosphoenolpyruvate carboxylase genes in C3, crassulacean acid metabolism (CAM) and C3/CAM intermediate species of the genus Clusia: rapid reversible C3/CAM switches are based on the C3 housekeeping gene
Authors: VAASEN ANJA , BEGEROW DOMINIK , HAMPP RÜDIGER 
Published: August 2006

ABSTRACTThe genus Clusia includes species that exhibit either the C3 or crassulacean acid metabolism (CAM) mode of photosynthesis, or those that are able to switch between both modes according to water availability. In order to screen for species‐specific genetic variability, we investigated the key carboxylase for CAM, phosphoenolpyruvate carboxylase (PEPC). Sequence analysis of DNA isolated from the obligate CAM species, Clusia hilariana, the obligate C3 species, Clusia multiflora, and an intermediate species that can switch between C3 and CAM photosynthesis, Clusia minor, revealed three different isoforms for C. hilariana and one each for the other two species. Sequence alignments indicated that PEPC from the intermediate species had high homology with the C3 protein and with one of CAM plant proteins. These were assumed to constitute ‘housekeeping’ proteins, which can also support CAM in intermediate species. The other two isoforms of the CAM plant C. hilariana were either CAM‐specific or showed homologies with PEPC from roots. Phylogenetic trees derived from neighbour‐joining analysis of amino acid sequences from 13 different Clusia species resulted in two distinct groups of plants with either ‘housekeeping’ PEPC only, or additionally CAM‐related isoforms. Only C. hilariana showed the third, probably root‐specific isoform. The high homology of the PEPC from the intermediate species with the C3 protein indicates that for the reversible transition from the C3 to CAM mode of photosynthesis, the C3 type of PEPC is sufficient. Its expression, however, is strongly increased under CAM‐inducing conditions. The use of the C3 isoform could have facilitated the evolution of CAM within the genus, which occurred independently for several times.