bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Token Economy Package: Social v. Token Reinforcement
Authors: Elliott P. A. , Barwell F. , Hooper A. , Kingerlee P. E. 
Published: June 2009

AbstractThe paper reports a Token Economy project involving 18 long stay male patients (diagnosis chronic schozophrenia), average length of hospitalisation twenty-five years. The project comprised a one month baseline period, a six month Token Economy phase, a two month experimental phase and a second three months Token Economy. Conditions were the same for all patients except during the experimental phase where they were randomly assigned to one of three experimental groups to investigate the relative importance of social reinforcement and other variables involved in token systems. The groups were (1) a social reinforcement only group; (2) a social reinforcement and non-contingent tokens; (3) a social reinforcement and contingent, non-spendable tokens. Each groups' performance was compared both with the other groups and with their own performance over all phases of the study. Assessment measures comprised standardised psychiatric rating scales - the Nurses Observation Scale for In-patient Evaluation (Honigfeld and Klett, 1965; Honigfeld et al 1966), and the Psychotic Reaction Profile (Lorr et al, 1960); other rating checklists, and time-sampling data. Analysis of Variance was carried out on all data over the four phases of the programme. The total token economy package as represented by the first token economy period was shown to be effective in promoting improvements in most areas of patients' functioning as compared to baseline. Results during the experimental phase suggest that contrary to our initial hypothesis social factors involved in exchanging tokens are not demonstrably important sources of reinforcement in Token Economies. There were no inter-group differences during the experimental phase, suggesting that none of the variables studied were critical factors. After the experimental phase the return to the complete token package produced an unclear picture where there were significant improvements on some scales, but significant declines on others.
PROMISE: a tool to identify genomic features with a specific biologically interesting pattern of associations with multiple endpoint variables
Authors: Pounds Stan , Cheng Cheng , Cao Xueyuan , Crews Kristine R. , Plunkett William , Gandhi Varsha , Rubnitz Jeffrey , Ribeiro Raul C. , Downing James R. , Lamba Jatinder 
Published: June 2009

AbstractMotivation: In some applications, prior biological knowledge can be used to define a specific pattern of association of multiple endpoint variables with a genomic variable that is biologically most interesting. However, to our knowledge, there is no statistical procedure designed to detect specific patterns of association with multiple endpoint variables.Results: Projection onto the most interesting statistical evidence (PROMISE) is proposed as a general procedure to identify genomic variables that exhibit a specific biologically interesting pattern of association with multiple endpoint variables. Biological knowledge of the endpoint variables is used to define a vector that represents the biologically most interesting values for statistics that characterize the associations of the endpoint variables with a genomic variable. A test statistic is defined as the dot-product of the vector of the observed association statistics and the vector of the most interesting values of the association statistics. By definition, this test statistic is proportional to the length of the projection of the observed vector of correlations onto the vector of most interesting associations. Statistical significance is determined via permutation. In simulation studies and an example application, PROMISE shows greater statistical power to identify genes with the interesting pattern of associations than classical multivariate procedures, individual endpoint analyses or listing genes that have the pattern of interest and are significant in more than one individual endpoint analysis.Availability: Documented R routines are freely available from www.stjuderesearch.org/depts/biostats and will soon be available as a Bioconductor package from www.bioconductor.org.Contact: stanley.pounds@stjude.orgSupplementary information: Supplementary data are available at Bioinformatics online.
Inferring progression models for CGH data
Authors: Liu Jun , Bandyopadhyay Nirmalya , Ranka Sanjay , Baudis M. , Kahveci Tamer 
Published: June 2009

Abstract
Motivation: One of the mutational processes that has been monitored genome-wide is the occurrence of regional DNA copy number alterations (CNAs), which may lead to deletion or over-expression of tumor suppressors or oncogenes, respectively. Understanding the relationship between CNAs and different cancer types is a fundamental problem in cancer studies.
Results: This article develops an efficient method that can accurately model the progression of the cancer markers and reconstruct evolutionary relationship between multiple types of cancers using comparative genomic hybridization (CGH) data. Such modeling can lead to better understanding of the commonalities and differences between multiple cancer types and potential therapies. We have developed an automatic method to infer a graph model for the markers of multiple cancers from a large population of CGH data. Our method identifies highly related markers across different cancer types. It then builds a directed acyclic graph that shows the evolutionary history of these markers based on how common each marker is in different cancer types. We demonstrated the use of this model in determining the importance of markers in cancer evolution. We have also developed a new method to measure the evolutionary distance between different cancers based on their markers. This method employs the graph model we developed for the individual markers to measure the distance between pairs of cancers. We used this measure to create an evolutionary tree for multiple cancers. Our experiments on Progenetix database show that our markers are largely consistent to the reported hot-spot imbalances and most frequent imbalances. The results show that our distance measure can accurately reconstruct the evolutionary relationship between multiple cancer types.
Availability: All the code developed in this article are available at http://bioinformatics.cise.ufl.edu/phylogeny.html.
Contact: nirmalya@cise.ufl.edu; tamer@cise.ufl.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
A CitationRank algorithm inheriting Google technology designed to highlight genes responsible for serious adverse drug reaction
Authors: Yang Lun , Xu Langlai , He Lin 
Published: June 2009

Abstract
Motivation: Serious adverse drug reaction (SADR) is an urgent, world-wide problem. In the absence of any well-organized gene-oriented SADR information pool, a database should be constructed. Since the importance of a gene to a particular SADR cannot simply be defined in terms of how frequently the two are cited together in the literature, an algorithm should be devised to sort genes according to their relevance to the SADR topics.
Results: The SADR-Gengle database, which is made up of gene–SADR relationships extracted from Pubmed, has been constructed, covering six major SADRs, namely cholestasis, deafness, muscle toxicity, QT prolongation, Stevens–Johnson syndrome and torsades de points. The CitationRank algorithm, which inherits the principle of the Google PageRank algorithm that a gene should be highly ranked when biologically related to other highly ranked genes, is devised. The algorithm performs robustly in recovering SADR-related genes in the presence of extraneous noise, and the use of the algorithm has been extended to sorting genes in our database. Users can browse genes in a Google-type system where genes are ordered according to their descending relevance to the SADR topic selected by the user. The database also provides users with visualized gene–gene knowledge chain networks, helping them to systematize their gene-oriented knowledge chain whilst navigating these networks.
Availability: The SADR-Gengle is freely available at http://Gengle.Bio-X.cn/SADR/.
Contact: helinhelin@gmail.com
Supplementary information: Supplementary data are available at Bioinformatics online.
Modelling the direct impact of bottom trawling on the North Sea fish community to derive estimates of fishing mortality for non-target fish species
Authors: Piet G. J. , van Hal R. , Greenstreet S. P. R. 
Published: June 2009

Abstract
Piet, G. J., van Hal, R., and Greenstreet, S. P. R. 2009. Modelling the direct impact of bottom trawling on the North Sea fish community to derive estimates of fishing mortality for non-target fish species. – ICES Journal of Marine Science, 66: 1985–1998. This study introduces a spatially explicit model that combines abundance data for all the main fish species in the demersal North Sea fish community with international effort data and estimates of gear-, species-, and size-dependent catch efficiency to determine the mortality of non-target fish species caused by bottom trawl fisheries and its spatial variation. Where necessary information was lacking, assumptions were made, and a sensitivity analysis performed to examine the impact of these issues on model results. Model outcomes were validated using international landings and discard data for five target species: cod, haddock, whiting, sole, and plaice. This showed that depending on its configuration, the model could reproduce recorded landings and discards of these species reasonably well. This suggests that the model could be used to simulate rates of fishing mortality for non-target fish species, for which few data are currently available. Sensitivity analyses revealed that model outcomes were most strongly influenced by the estimates of gear catch efficiency and the extent to which the distributions of fishing effort and each species overlapped. Better data for these processes would enhance the contribution that this type of model could make in supporting an ecosystem approach to fisheries management.
Evolution of HIV‐1 in a patient population failing multiple‐drug therapy
Authors: Hong Shaolin , Cao Jingjiang , Tu Ya‐ting 
Published: June 2009

ABSTRACTTo understand the evolutionary pathway of the multi‐drug‐resistant virus HIV‐1 under drug‐induced selection pressure, plasma from seven patients from baseline to different intervals post‐treatment failure were used in RT‐PCR protocols. Multiple clones were sequenced for each time point. Drug‐resistant mutations were detected in five patients. Phylogenetic analysis showed that at different time points, viral sequences clustered separately and formed independent lineages. Genetic diversity decreased from 1.59 to 0.55, whereas non‐synonymous/synonymous mutation ratios increased from 0.067 to 0.118, respectively. These data suggest that the virus population changed dynamically and clustered in a time point‐specific manner whereas genetic diversity decreased consistently.
Effect of Lactobacillus rhamnosus GR‐1 and Lactobacillus reuteri RC‐14 on the ability of Candida albicans to infect cells and induce inflammation
Authors: Martinez Rafael C.R. , Seney Shannon L. , Summers Kelly L. , Nomizo Auro , De Martinis Elaine C.P. , Reid Gregor 
Published: June 2009

ABSTRACTVulvovaginal candidiasis, a high prevailing infection worldwide, is mainly caused by Candida albicans. Probiotic Lactobacillus reuteri RC‐14 and Lactobacillus rhamnosus GR‐1 have been previously shown to be useful as adjuvants in the treatment of women with VVC. In order to demonstrate and better understand the anti‐Candida activity of the probiotic microorganisms in an in vitro model simulating vaginal candidiasis, a human vaginal epithelial cell line (VK2/E6E7) was infected with C.albicans 3153a and then challenged with probiotic L. rhamnosus GR‐1 and/or L. reuteri RC‐14 or their respective CFS (alone or in combination). At each time point (0, 6, 12 and 24 hr), numbers of yeast, lactobacilli and viable VK2/E6E7 cells were determined and, at 0, 6 and 12 hr, the supernatants were measured for cytokine levels. We found that C. albicans induced a significant increase in IL‐1α and IL‐8 production by VK2/E6E7 cells. After lactobacilli challenge, epithelial cells did not alter IL‐6, IL‐1α, RANTES and VEGF levels. However, CFS from the probiotic microorganisms up‐regulated IL‐8 and IP‐10 levels secreted by VK2/E6E7 cells infected with C. albicans. At 24 hr of co‐incubation, L. reuteri RC‐14 alone and in combination with L. rhamnosus GR‐1 decreased the yeast population recoverable from the cells. In conclusion, L. reuteri RC‐14 alone and together with L. rhamnosus GR‐1 have the potential to inhibit the yeast growth and their CFS may up‐regulate IL‐8 and IP‐10 secretion by VK2/E6E7 cells, which could possibly have played an important role in helping to clear VVC in vivo.
Inhibitory effect of serotonin antagonists on JC virus propagation in a carrier culture of human neuroblastoma cells
Authors: Nukuzuma Souichi , Nakamichi Kazuo , Nukuzuma Chiyoko , Takegami Tsutomu 
Published: June 2009

ABSTRACTHuman polyomavirus, JCV, causes fatal demyelinating disease, progressive multifocal leukoencephalopathy (PML). It has been shown that 5HT2AR acts as a cellular receptor for JCV on human glial cells. In the current study, we examined the inhibitory effects of 5HT2AR antagonists, ketanserin and ritanserin, both on JCV infection and on propagation by using human neuroblastoma cells IMR‐32 and JCI, which continuously produce JCV. Transcriptional analysis revealed that 5HT2AR was constitutively expressed in JCI cells. Treatments with 5HT2AR antagonists led to a significant reduction in the titers of progeny viruses and the population of infected JCI cells. In addition, the amount of JCV genomic DNA was decreased in JCI cells in the presence of 5HT2AR antagonists. These results indicate that 5HT2AR antagonists have an inhibitory effect on JCV infection and reproduction, and JCI cells are applicable to an experimental model for pharmacological evaluation of antiviral agents against JCV.
The use of Bayesian networks to guide investments in flow and catchment restoration for impaired river ecosystems
Authors: STEWART‐KOSTER B. , BUNN S. E. , MACKAY S. J. , POFF N. L. , NAIMAN R. J. , LAKE P. S. 
Published: June 2009

Summary1. The provision of environmental flows and the removal of barriers to water flow are high priorities for restoration where changes to flow regimes have caused degradation of riverine ecosystems. Nevertheless, flow regulation is often accompanied by changes in catchment and riparian land‐use, which also can have major impacts on river health via local habitat degradation or modification of stream energy regimes.2. The challenges are determining the relative importance of flow, land‐use and other impacts as well as deciding where to focus restoration effort. As a consequence, flow, catchment and riparian restoration efforts are often addressed in isolation. River managers need decision support tools to assess which flow and catchment interventions are most likely to succeed and, importantly, which are cost‐effective.3. Bayesian networks (BNs) can be used as a decision support tool for considering the influence of multiple stressors on aquatic ecosystems and the relative benefits of various restoration options. We provide simple illustrative examples of how BNs can address specific river restoration goals and assist with the prioritisation of flow and catchment restoration options. This includes the use of cost and utility functions to assist decision makers in their choice of potential management interventions.4. A BN approach facilitates the development of conceptual models of likely cause and effect relationships between flow regime, land‐use and river conditions and provides an interactive tool to explore the relative benefits of various restoration options. When combined with information on the costs and expected benefits of intervention, one can derive recommendations about the best restoration option to adopt given the network structure and the associated cost and utility functions.
Seasonal and inter‐stream variations in the population dynamics, growth and secondary production of an algivorous fish (Pseudogastromyzon myersi: Balitoridae) in monsoonal Hong Kong
Authors: YANG GRACE Y. , DUDGEON DAVID 
Published: June 2009

Summary1. Balitorid loaches are widespread and highly diverse in Asian streams, yet their life history and ecology have received little attention. We investigated seasonal (wet versus dry season) and spatial variation in populations of algivorous Pseudogastromyzon myersi in Hong Kong, and estimated the magnitude of secondary production by this fish in pools in four streams (two shaded and two unshaded) over a 15‐month period.2. Mean population densities of P. myersi ranged from 6.0 to 23.2 individuals m−2, constituting more than half (and typically >70%) of benthic fishes censused. Abundance was c. 25% greater in the wet season, when recruitment occurred. Significant density differences among streams were not related to shading conditions and were evident despite small‐scale variations in P. myersi abundance among pools. Mean biomass varied among streams from 0.85 to 3.87 g ash‐free dry weight (AFDW) m−2. Spatial and seasonal patterns in biomass and density were similar, apart from some minor disparities attributable to differences in mean body size among populations.3. All four P. myersi populations bred once a year in June and July, and life spans varied from 24 to 26 months. Populations consisted of three cohorts immediately after recruitment but, for most of the study period, only two cohorts were evident. Cohort‐specific growth rates did not differ significantly among streams but, in all streams, younger cohorts had higher cohort‐specific growth rates.4. Secondary production of P. myersi estimated by the size‐frequency (SF) method was 2.7–11.5 g AFDW m−2 year−1 and almost twice that calculated by the increment‐summation (IS) method (1.2–6.6 g AFDW m−2 year−1). Annual P/B ratios were 1.17–2.16 year−1 (IS) and 2.73–3.22 year−1 (SF). Highest production was recorded in an unshaded stream and the lowest in a shaded stream, but site rankings by production did not otherwise match shading conditions. Wet‐season production was six times greater than dry‐season production, and daily production fell to almost zero during January and February. Cool temperatures (<17 °C) may have limited fish activity and influenced detectability during some dry‐season censuses. Estimates of abundance and annual production by P. myersi are therefore conservative.5. Comparisons with the literature indicate that the abundance and production of P. myersi in Hong Kong was high relative to other benthic fishes in tropical Asia, or their temperate counterparts in small streams. Manipulative experiments are needed to determine the influence of P. myersi, and algivorous balitorids in general, on periphyton dynamics and energy flow in Asian streams.
Following the common association between testosterone deficiency and diabetes mellitus, can testosterone be regarded as a new therapy for diabetes?
Authors: Corona G. , Mannucci E. , Forti G. , Maggi M. 
Published: June 2009

SummaryType 2 diabetes mellitus (T2DM) is increasing at epidemic proportions worldwide, representing a risk factor for cardiovascular diseases. Nowadays, hypogonadism and erectile dysfunction (ED) are considered frequent, although often under‐diagnosed, complications of T2DM. Recent evidence suggests that in a diabetic population ED itself is an efficient predictor of silent coronary heart diseases. Patients with T2DM have an impaired sexual life, which is worsened by hypogonadism. Low T in T2DM is in fact associated with more severe ED, hypoactive sexual desire and low intercourse frequency. Testosterone replacement therapy (TRT) has been proven to improve sexual function in hypogonadal men. In addition, TRT improves adiposity, insulin resistance and total cholesterol. Specific studies on the effect of TRT in T2DM are scanty. This review will evaluate the contribution of low testosterone in diabetic subjects with sexual dysfunction. In addition, we have also reviewed available evidence on potential metabolic benefits of testosterone supplementation in T2DM patients.
Plasma ladderlectin concentration following sterile inflammation and Aeromonas salmonicida subsp. salmonicida infection
Authors: Young K M , Czyrny A , Russell S , Huber P , Lumsden J S 
Published: June 2009

AbstractPlasma samples obtained from rainbow trout either experimentally infected with Aeromonas salmonicida or injected with either A. salmonicida lipopolysaccharide (LPS) or a commercial A. salmonicida vaccine (Lipogen) were analysed by enzyme immunoassay to evaluate changes in rainbow trout ladderlectin (RTLL) concentrations during the acute phase response (APR). Plasma RTLL concentrations in fish injected with A. salmonicida LPS, vaccine or live A. salmonicida varied over a 10 day period, but did not significantly increase. In contrast, fish experimentally infected with A. salmonicida exhibited a modest, but statistically significant (P < 0.05), decrease in RTLL concentration. These studies demonstrate that RTLL is not detectably induced during the trout APR to sterile inflammation or A. salmonicida infection, but plasma concentration of this protein may be reduced during bacterial infection.
PIRA‐PCR for detection of Fusarium graminearum genotypes with moderate resistance to carbendazim
Authors: Luo Q. Q. , Xu J. Q. , Hou Y. P. , Chen C. J. , Wang J. X. , Zhou M. G. 
Published: June 2009

PIRA‐PCR (primer‐introduced restriction analysis PCR) was developed to detect isolates of Fusarium graminearum with moderate resistance to carbendazim, a methyl benzimidazole carbamate (MBC)‐group fungicide. Two primer pairs were designed and synthesized according to the nucleotide sequence of the β2‐tubulin gene from F. graminearum. Fragments of 164 bp were amplified by nested PCR from isolates differing in carbendazim sensitivity. A HindIII restriction enzyme recognition site was introduced artificially by inner primers to detect a mutation at codon 167, and TaaI (Tsp4CI) restriction enzyme was used to detect a mutation at codon 200. The sensitivity of isolates to carbendazim was determined by analyzing electrophoresis patterns of the resulting PCR products after simultaneous digestion with both HindIII and TaaI. Results from PIRA‐PCR and a conventional method (mycelial growth on agar) were identical but PIRA‐PCR required only 7–8 h while the conventional method required 5–7 days. This study demonstrates that PIRA‐PCR not only monitors the appearance of moderately resistant isolates, but can be useful for detecting genotypes of F. graminearum with moderate resistance to carbendazim.