bluuebunny/crossref_metadata_2025_split huggingface dataset:
PHYLOGENYOF THE VLE‐14 CHLAMYOMONAS (CHLOROPHYCEAE) GROUP: A STUDY OF 18S rRNA GENE SEQUENCES1
Authors: Buchheim Mark A. , Buchheim Julie A. , Chapman Russell L. 
Published: October 2004

ABSTRACTComparative specificity of sporangial wall autolysins (i.e. vegetative lytic enzymes [VLE]) derived from sporulating cultures has been used to group Chlamydomonas taxa into 15 different VLE types. The VLE‐14 group, including isolates of C. geitleri, C. noctigama, C. monoica, C. pinicola, C. terricoia, and C. hindakii, is one of the largest of these VLE groups. Genetic studies have shown that a number of the VLE‐14 taxa are interfertile, albeit with little or reduced viability of progeny. A reevaluation of the VLE‐14 group suggested that all members should be regarded as distinct isolates of C. noctigama. The present investigation tests the phylogenetic implications of the VLE evidence and examines the validity of the taxonomic reevaluation in a phylogenetic context by analysis of 18S rRNA gene sequence data. Results from analyses of the sequence data are consistent with an interpretation of the VLE evidence as indicative of monophyletic taxa. Phylogenetic analyses of the sequence data are also consistent with the taxonomic reevaluation and reidentification of the group. However, at least some of the VLE‐14 isolates studied in this investigation fit criteria for distinct biologic or phylogenetic species. It is concluded that the VLE‐14 taxa represent a very closely allied group that includes some isolates that are in the early stages of speciation ly reproductive isolation.
A MOLECULAR PHYLOGENY OF THE HETEROKONT ALGAE BASED ON ANALYSES OF CHLOROPLAST‐ENCODED rbcL SEQUENCE DATA1
Authors: Daugbjerg Niels , Andersen Robert A. 
Published: October 2004

ABSTRACTNearly complete ribulose‐1,5‐bisphosphate carboxylase/ oxygenase (rbcL)sequences from 27 taxa of heterokont algae were determined and combined with rbcL sequences obtained from GenBank for four other heterokont algae and three red algae. The phylogeny of the morphologically diverse haterokont algae was inferred from an unambiguously aligned data matrix using the red algae as the root, Significantly higher levels of mutational saturation in third codon positions were found when plotting the pair‐wise substitutions with and without corrections for multiple substitutions at the same site for first and second codon positions only and for third positions only. In light of this observation, third codon positions were excluded from phylogenetic analyses. Both weighted‐parsimony and maximum‐likelihood analyses supported with high bootstrap values the monophyly of the nine currently recognized classes of heterokont algae. The Eustigmatophyceae were the most basal group, and the Dictyochophyceae branched off as the second most basal group. The branching pattern for the other classes was well supported in terms of bootstrap values in the weightedparsimony analysis but was weakly supported in the maximum‐likelihood analysis (<50%). In the parsimony analysis, the diatoms formed a sister group to the branch containing the Chrysophyceae and Synurophyceae. This clade, charactetized by siliceous structures (frustules, cysts, scales), was the sister group to the Pelagophyceae/Sarcinochrysidales and Phaeo‐/Xantho‐/ Raphidophyceae clades. In the latter clade, the raphido‐phytes were sister to the Phaeophyceae and Xanthophyceae. A relative rate test revealed that the rbcL gene in the Chrysophyceae and Synurophyceae has experienced a significantly different rate of substitutions compared to other classes of heterokont algae. The branch lengths in the maximum‐likelihood reconstruction suggest that these two classes have evolved at an accelerated rate. Six major carotenoids were analyzed cladistically to study the usefulness of carotenoid pigmentation as a class‐level character in the heterokont algae. In addition, each carotenoid was mapped onto both the rbcL tree and a consensus tree derived from nuclear‐encoded small‐subunit ribosomal DNA (SSU rDNA) sequences. Carotenoid pigmentation does not provide unambiguous phylogenetic information, whether analyzed cladistically by itself or when mapped onto phylogenetic trees based upon molecular sequence data.
RECOGNITION OF TAXONOMICALLY SIGNIFICANT CLUSTERS NEAR THE SPECIES LEVEL, USING COMPUTATIONALLY INTENSE METHODS, WITH EXAMPLES FROM THE STEPHANODISCUS NIAGARAE COMPLEX (BACILLARIOPHYCEAE)1
Authors: Julius Matthew L. , Estabrook George F. , Edlund Mark B. , Stoermer Eugene F. 
Published: October 2004

ABSTRACTSince the early 1960s, numerical techniques have produced a wide variety of methods to suggest classifications of organisms based on quantitative measurements. A long‐recognized shortcoming of these methods is that they will suggest classifications for any group of organisms and any set of measurements, whether or not the clusters in the suggested classification have any natural meaning or significance. Some progress has been made in assessing the reality of clusters determined by various methods. Data simulated to reflect known cluster structure have been used to test the accuracy of different methods, Various methods have been applied to the same data sets to compare how well they realize various desirable properties. Here we define a data‐based model of randomness to represent what might be meant by “no natural basis for subdivision into clusters” and use it to compare an observed measure of cluster distinctness to the distribution of this measure predicted by this model of randomness. In this way, unwarranted subdivision can be statistically avoided, and significant subdivisions can be investigated with confidence. Our methods are illustrated with some examples from the Stephanodiscus niagarae Ehrenb. species complex. Significant differences in morphologic expression are identified in S. reimerii Theriot and Stoermer in Theriot, S. superiorensis Theriot and Stoermer and S. yellowstonensis Theriot and Stoermer. In addition, statistically significant clusters are identified in S. niagarae populations from different geographic locations and in members of the same population grown in different environments. These results suggest current criteria for resolving diatom taxa may not be sufficient to discern subtle differences that occur between real species.
CHARACTERIZATION AND MOLECULAR PHYLOGENYOF A PROTEIN KINASE cDNA FROM THE DINOFLAGELLATE GONYAULAX (DINOPHYCEAE)1
Authors: Salois Patrick , Morse David 
Published: October 2004

ABSTRACTDegenerate primers corresponding to conserved protein kinase motifs were used to amplify potential kinase DNA fragments from a Gonyaulax polyedra Stein cDNA library using PCR. One PCR fragment, potentially encoding a CAMP‐dependent protein kinase, was used as a probe to isolate a near full‐length cDNA from the library. The nucleic acid sequence of the entire cDNA clone had a high homology to the catalytic subunit of cAMP‐dependent protein kinase (cAPK subfamily and affiliated members. Northern blot analysis showed that the corresponding mRNA had a size (about 1.4 kb) and a relative high abundance consistent with a cAPK homologue. Southern blot analysis showed that while there are roughly 30 copies of the kinase gene per genome, the pattern of restriction fragments is inconsistent with the hypothesis of a large gene family. Phylogenetic analyses comparing the deduced amino acid sequence from the Gonyaulax cDNA with other cAPK sequences place Gonyaulax close to the slime mold Dictyostelium discoideum. This is the first phylogenetic analysis of dinoflagellates based on protein sequence, and the results are in agreement with similar analyses based on rRNA sequences.
THE USE OF IMMOBILIZATION IN ALGINATE BEADS FOR LONG‐TERM STORAGE OF PSEUDANABAENA GALEATA (CYANOBACTERIA) IN THE LABORATORY1
Authors: Romo Susana , Pérez‐Martínez Carmen 
Published: October 2004

ABSTRACTA new method for long‐term storage of algal cultures in the laboratory was tested. The procedure is based on the cell immobilization technique. Cells of the filamentous cyanobacterium Pseudanabaena galeata Bocher were immobilized in sodium‐alginate beads and stored for 14–18 months. The structure and functional features of the organism were maintained in this immobilized state and no ultrastructural biochemical, or growth rate differences were detected between stock and previously immobilized cell cultures after this period. We discuss the advantages of this method compared to other preservation methods and recommend the use of immobilization in alginate beads for long‐term algal storage.
IL‐10 is not required to prevent immune hyperactivity during memory responses to Toxoplasma gondii
Authors: Wille U. , Nishi M. , Lieberman L. , Wilson E. H. , Roos D. S. , Hunter C. A. 
Published: October 2004

SUMMARY Primary infection of IL‐10 knockout (KO) mice with the protozoan parasite Toxoplasma gondii leads to a CD4+‐T‐cell dependent shock‐like reaction with high systemic levels of IL‐12 and IFN‐γ, severe liver pathology and death of mice. In the present study, this immune‐mediated pathology was prevented by treatment of IL‐10 KO mice with the anti‐parasitic drug sulfadiazine, allowing these mice to progress to the chronic phase of infection. To address the role of endogenous IL‐10 in the regulation of secondary immune responses to T. gondii, IL‐10 KO mice were infected with the avirulent Me49 strain of this parasite, treated with sulfadiazine for 2 weeks starting at day 3 p.i., and were rechallenged 6 weeks p.i. with RH, a highly virulent strain of T. gondii. In these studies, chronically infected IL‐10 KO mice survived secondary infection with RH and controlled parasite load. Although serum levels of IL‐12 and IFN‐γ were higher in IL‐10 KO mice than in wild type (WT) mice 8 days after RH rechallenge, these levels were well controlled in the absence of endogenous IL‐10, suggesting that IL‐10 is not required to down‐regulate cytokine production during the memory response. Antigen‐specific ex vivo recall responses further revealed that splenocytes from chronically infected WT and IL‐10 KO mice responded to parasite antigen with similar production of IL‐12 and IFN‐γ, and there was also no significant difference in ex vivo production of these cytokines by splenocytes in response to parasite antigen 7 days after secondary infection with T. gondii. Furthermore, IL‐10 KO mice immunized with the Ts‐4 vaccine‐strain of T. gondii were protected when rechallenged with the virulent RH strain. Together, these studies demonstrate that the inhibitory effect of IL‐10, which is required to prevent immune‐mediated pathology during primary infection, is not required to prevent immune hyperactivity during a secondary response to T. gondii, and a highly effective memory response is generated in the absence of endogenous IL‐10.
Primary sweat gland carcinosarcoma of the scrotal skin
Authors: Lin Tzu‐Ping , Pan Chin‐Chen , Huang William Ji‐Sien , Murphy George F. 
Published: October 2004

Background:  Carcinosarcoma is a biphasic tumor composed of malignant epithelial and mesenchymal elements. Although the tumors have been reported in different locations, they rarely occur in the skin and have not been reported in the skin of external genitalia.Case report:  We present such a case in a 71‐year‐old Taiwanese man. He had had a long‐term indolent nodule on scrotal skin, but it enlarged rapidly in 2 weeks. Wide excision of the tumor was performed.Results and Discussion:  The pathologic examination revealed a sweat gland carcinosarcoma consisting of admixed mucin‐producing adenocarcinoma and solid spindle cell sarcoma. The two components exhibited contrasting immunohistochemical profiles with the epithelial component diffusely positive for epithelial markers and S‐100 protein, while the sarcomatous component positive for vimentin and smooth muscle actin but negative for epithelial markers and S‐100 protein. The immunoreactivity for S‐100 protein in the epithelial component supports sweat gland origin. The tumor behaved aggressively. Local recurrence and distant metastases to lungs and brain occurred 6 months and 18 months later. The patient died of the disease 20 months after the initial diagnosis.
The natural history of adolescent alcohol use disorders
Authors: Clark Duncan B. 
Published: October 2004

ABSTRACTAim  To examine clinically relevant research on the development, course and outcomes of adolescence alcohol use disorders (AUDs).Methods  Observational studies with adolescent samples were selected for inclusion based on systematic assessment of AUDs and clinical relevance. The literature was searched using Medline and Psychinfo. Articles on childhood predictors, characteristics, course, complications and adult outcomes of adolescent AUDs were reviewed.Results  The developmental trajectory toward adolescent AUDs begins with the emergence of childhood mental disorders. These problems are transmitted from parent to child in a developmentally specific fashion, reflect psychological dysregulation dimensions and predict adolescent AUDs. While most DSM‐IV AUD diagnostic criterion items are valid for adolescents, tolerance and impaired control items are problematic, and some adolescents with significant alcohol problems are not identified by this diagnostic system. Understanding the psychosocial and biomedical complications that accompany AUDs requires attention to factors other than alcohol involvement itself, including childhood maltreatment and comorbid psychopathology. While some adolescents with AUDs manifest chronic alcohol dependence in adulthood, a substantial proportion overcome alcohol problems and transition to abstinence or normative drinking.Conclusions  Developmentally specific phenotypic characteristics define the natural history of adolescent AUDs, inform clinical assessment and provide the developmental context for treatment research. While alcohol consumption may be the primary treatment focus, other important consequences, comorbidities and complications need to be addressed for successful developmental outcomes to result.
Salient variables for treatment research of adolescent alcohol and other substance use disorders
Authors: Bukstein Oscar G. , Winters Ken 
Published: October 2004

ABSTRACTAims  To seek a level of uniformity and consistency in the type of data or variables collected to allow cross‐study comparison and ease in meta‐analyses of adolescent treatment studies.Design  The rationale for adoption of such a core set of variables for adolescent treatment research, the main categories and specific types of variables, methods for collecting these variables, including the use of specific instruments are reviewed and discussed.Findings  There is a relatively small number of adolescent treatment outcome studies. Between studies, there are highly variable methodologies, including differences in how outcome or treatment success is measured, differences in ascertainment in substance use, differences in the measurement of non‐substance use variables such as social and academic functioning, poor follow‐up rates and a lack of comparison groups in many studies.Conclusions  Differences in the types and collection of baseline and outcome variables and the need to achieve some level of uniformity across adolescent substance use disorders (SUD) treatment studies suggest that investigators interested in adolescent treatment outcome research should develop a set of ‘core variables’ that are relatively consistent, or at least comparable, across studies.
Measuring youth outcomes from alcohol and drug treatment
Authors: Brown Sandra A. 
Published: October 2004

ABSTRACTAims  This report examines adolescent alcohol and drug treatment outcome research from a process‐oriented, developmental perspective. A dynamic developmental model is proposed in which adolescent treatment outcome research incorporate considerations relevant to changes occurring typically during this stage of life as well as developmental distinctions pertinent to the early onset of abuse and dependence.Method  Findings from our developmentally focused longitudinal research of adolescent treatment participants and the extant literature on adolescent treatment outcome are reviewed. Conceptual, research design and measurement recommendations are presented from this double developmental perspective of addiction.Findings  Techniques for engaging youth in the research process, managing confidentiality and facilitating self‐disclosure are described. Developmental considerations in the type and timing of outcome assessments, measurement content, predictor domains and data analytical approaches are discussed. Predictors and process measures for adolescent alcohol treatment outcome study are suggested based on current findings.Conclusions  Inclusion of developmental considerations may enhance the utility of adolescent treatment outcome research.
On the learning curve: the emerging evidence supporting cognitive–behavioral therapies for adolescent substance abuse
Authors: Waldron Holly Barrett , Kaminer Yifrah 
Published: October 2004

ABSTRACTAims  Cognitive–behavioral therapy (CBT) approaches to intervention for adolescent substance use disorders has been limited and formal controlled clinical efficacy trials have been rare. Moreover, the early literature on the efficacy of CBT for adolescent substance abuse has been characterized by significant methodological limitations. Recent innovations in the treatment of adolescent substance abuse and the recent completion of several randomized clinical trials has brightened the picture with respect to establishing the empirical support for CBT. The aim of this review is to integrate the findings from controlled trials of CBT for adolescent substance abuse.Method  Studies representing randomized clinical trials were reviewed using criteria provided by Lonigan et al. and Nathan & Gorman as a guide.Findings and conclusions  Despite some prominent differences in design and methodology, the studies reviewed provide consistent empirical evidence that group and individual CBT are associated with significant and clinically meaningful reductions in adolescent substance use. The evidence for the efficacy of group therapy is particularly important, countering the assertion that aggregating problem youths into group treatment settings is associated with iatrogenic effects. The findings from the randomized trials reviewed represent significant developments in treatment outcome research and lay the foundation for validating CBT for adolescent substance use disorders. Future research directions include improving short‐ and long‐term outcomes, enhancing treatment motivation and engagement, and identifying mechanisms and processes associated with positive change, especially for youths with comorbid conditions.
Implementing school‐based substance abuse interventions: methodological dilemmas and recommended solutions
Authors: Wagner Eric F. , Tubman Jonathan G. , Gil Andrés G. 
Published: October 2004

ABSTRACTAims  To review current knowledge about the most effective school‐based interventions for child and adolescent problems, and to present dilemmas and potential solutions in mounting and evaluating school‐based interventions for adolescent alcohol and other drug (AOD) use problems.Design  Two literature reviews were conducted: (1) a broad and encompassing review of English‐language articles published from 1990 to the present concerning school‐based interventions for child and adolescent problems and (2) an exhaustive review of articles concerning Student Assistance Programs, which are the most popular approach to school‐based AOD intervention in the United States.Findings  Ten key components of effective school‐based interventions were identified. In addition, six pervasive dilemmas in school‐based AOD intervention research were discussed. Examples of potential solutions to these dilemmas were gleaned from an ongoing randomized clinical trial of a Student Assistance Program.Conclusions  School‐based AOD interventions have several potential advantages over more traditional clinic‐based AOD interventions. Nonetheless, there are many challenges and dilemmas to conducting and evaluating interventions in school settings. With patience and guidance, these challenges can be addressed successfully.
Thirty‐month relapse trajectory cluster groups among adolescents discharged from out‐patient treatment
Authors: Godley Susan H. , Dennis Michael L. , Godley Mark D. , Funk Rodney R. 
Published: October 2004

ABSTRACTAims  To identify adolescent relapse trajectory groups following discharge from out‐patient substance abuse treatment.Design, setting and participants  Adolescents aged 12–18, who were assigned randomly to one of five out‐patient interventions (n = 563) in four United States communities and followed‐up 3, 6, 9, 12 and 30 months post‐intake.Outcome measures  Self‐report measures of days using any alcohol or other drugs (AOD), days of alcohol use, days of cannabis use, days of heavy use, days of crack/cocaine use, days of heroin/opiate use, days AOD use interfered with responsibilities and days in a controlled environment.Findings  Adolescents can be grouped empirically into five relapse trajectories over 30 months following out‐patient treatment: (a) low AOD use with limited days in a controlled environment; (b) low AOD use with high days in a controlled environment; (c) moderate/decreasing AOD use; (d) increasing AOD use; and (e) consistently high AOD use.Conclusions  There was considerable heterogeneity in the relapse trajectories, varying by the initial response to treatment, the stability (versus increase/decrease) of the response and an interaction with time in a controlled environment. Cannabis and alcohol were the two main substances involved, although the two groups with the poorest trajectories had increasing levels of cocaine, opiate and other substance use at the 30‐month follow‐up. This study demonstrates the chronicity of substance use even among a subgroup of adolescents and the importance of studying more complex longitudinal patterns of recovery.