bluuebunny/crossref_metadata_2025_split huggingface dataset:
Unite and conquer: univariate and multivariate approaches for finding differentially expressed gene sets
Authors: Glazko Galina V. , Emmert-Streib Frank 
Published: July 2009

Abstract
Motivation: Recently, many univariate and several multivariate approaches have been suggested for testing differential expression of gene sets between different phenotypes. However, despite a wealth of literature studying their performance on simulated and real biological data, still there is a need to quantify their relative performance when they are testing different null hypotheses.
Results: In this article, we compare the performance of univariate and multivariate tests on both simulated and biological data. In the simulation study we demonstrate that high correlations equally affect the power of both, univariate as well as multivariate tests. In addition, for most of them the power is similarly affected by the dimensionality of the gene set and by the percentage of genes in the set, for which expression is changing between two phenotypes. The application of different test statistics to biological data reveals that three statistics (sum of squared t-tests, Hotelling's T2, N-statistic), testing different null hypotheses, find some common but also some complementing differentially expressed gene sets under specific settings. This demonstrates that due to complementing null hypotheses each test projects on different aspects of the data and for the analysis of biological data it is beneficial to use all three tests simultaneously instead of focusing exclusively on just one.
Contact: Galina_Glazko@urmc.rochester.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
‘My friends love to tan’: examining sensation seeking and the mediating role of association with friends who use tanning beds on tanning bed use intentions
Authors: Banerjee Smita C. , Greene Kathryn , Bagdasarov Zhanna , Campo Shelly 
Published: July 2009

AbstractThis paper explored how sensation seeking contributes to the likelihood of tanning bed use intentions both directly and indirectly through the way it shapes interaction with peers who use tanning beds and attitudes toward tanning bed. Eight hundred and ninety six (n = 896) male and female college students were recruited for the study. Measured variables included sensation seeking, association with friends who use tanning beds, attitudes toward tanning and tanning bed use intentions. Structural equation modeling was performed to test the hypotheses. In general, results supported the proposed hypotheses and documented that sensation seeking is indirectly associated with tanning bed use intentions through the mediation of association with peers who use tanning beds and attitudes toward tanning. The article discusses theoretical and methodological implications of the findings demonstrating the pathways of influence of sensation seeking on tanning bed use intentions.
Two components of Northeast Atlantic herring within the same school during spawning: support for the existence of a metapopulation?
Authors: Johannessen Arne , Nøttestad Leif , Fernö Anders , Langård Lise , Skaret Georg 
Published: July 2009

AbstractJohannessen, A., Nøttestad, L., Fernö, A., Langård, L., and Skaret, G. 2009. Two components of Northeast Atlantic herring within the same school during spawning: support for the existence of a metapopulation? – ICES Journal of Marine Science, 66: 1740–1748. It has been hypothesized that some stocks of Atlantic herring are subject to genetic exchange and therefore should fit the definition of a metapopulation with subunits. Genetic exchange requires spatial overlap of individuals from different populations during spawning. We investigated a local herring population that is assumed to feed and spawn within the semi-enclosed marine ecosystem of Lindåspollene in west Norway, which is connected with the outer fjord only by a narrow sill. Acoustic recordings and gillnet samples demonstrated the mixed presence of two components within a single school throughout the spawning period 2005–2007. Members of the two components were of about the same size and in a similar stage of gonad development at all times, but the age composition was completely different. These observations represent the first documented case of different components being present in a spawning school and provide strong indications of regular interbreeding. Our data suggest that the two components represent autochthonous Lindås herring and allochthonous herring of coastal/oceanic origin, thereby supporting the metapopulation concept. Two alternative explanations, based on one migratory and one resident component of a single Lindås stock, are also discussed.
Mechanism of REP27 Protein Action in the D1 Protein Turnover and Photosystem II Repair from Photodamage
Authors: Dewez David , Park Sungsoon , García-Cerdán Jose Gines , Lindberg Pia , Melis Anastasios 
Published: July 2009

Abstract
The function of the REP27 protein (GenBank accession no. EF127650) in the photosystem II (PSII) repair process was elucidated. REP27 is a nucleus-encoded and chloroplast-targeted protein containing two tetratricopeptide repeat (TPR) motifs, two putative transmembrane domains, and an extended carboxyl (C)-terminal region. Cell fractionation and western-blot analysis localized the REP27 protein in the Chlamydomonas reinhardtii chloroplast thylakoids. A folding model for REP27 suggested chloroplast stroma localization for amino- and C-terminal regions as well as the two TPRs. A REP27 gene knockout strain of Chlamydomonas, termed the rep27 mutant, was employed for complementation studies. The rep27 mutant was aberrant in the PSII-repair process and had substantially lower than wild-type levels of D1 protein. Truncated REP27 cDNA constructs were made for complementation of rep27, whereby TPR1, TPR2, TPR1+TPR2, or the C-terminal domains were deleted. rep27-complemented strains minus the TPR motifs showed elevated levels of D1 in thylakoids, comparable to those in the wild type, but the PSII photochemical efficiency of these strains was not restored, suggesting that the functionality of the PSII reaction center could not be recovered in the absence of the TPR motifs. It is suggested that TPR motifs play a role in the functional activation of the newly integrated D1 protein in the PSII reaction center. rep27-complemented strains missing the C-terminal domain showed low levels of D1 protein in thylakoids as well as low PSII photochemical efficiency, comparable to those in the rep27 mutant. Therefore, the C-terminal domain is needed for a de novo biosynthesis and/or assembly of D1 in the photodamaged PSII template. We conclude that REP27 plays a dual role in the regulation of D1 protein turnover by facilitating cotranslational biosynthesis insertion (C-terminal domain) and activation (TPR motifs) of the nascent D1 during the PSII repair process.
Posttranslational Elevation of Cell Wall Invertase Activity by Silencing Its Inhibitor in Tomato Delays Leaf Senescence and Increases Seed Weight and Fruit Hexose Level
Authors: Jin Ye , Ni Di-An , Ruan Yong-Ling 
Published: July 2009

Abstract
Invertase plays multiple pivotal roles in plant development. Thus, its activity must be tightly regulated in vivo. Emerging evidence suggests that a group of small proteins that inhibit invertase activity in vitro appears to exist in a wide variety of plants. However, little is known regarding their roles in planta. Here, we examined the function of INVINH1, a putative invertase inhibitor, in tomato (Solanum lycopersicum). Expression of a INVINH1:green fluorescent protein fusion revealed its apoplasmic localization. Ectopic overexpression of INVINH1 in Arabidopsis thaliana specifically reduced cell wall invertase activity. By contrast, silencing its expression in tomato significantly increased the activity of cell wall invertase without altering activities of cytoplasmic and vacuolar invertases. Elevation of cell wall invertase activity in RNA interference transgenic tomato led to (1) a prolonged leaf life span involving in a blockage of abscisic acid–induced senescence and (2) an increase in seed weight and fruit hexose level, which is likely achieved through enhanced sucrose hydrolysis in the apoplasm of the fruit vasculature. This assertion is based on (1) coexpression of INVINH1 and a fruit-specific cell wall invertase Lin5 in phloem parenchyma cells of young fruit, including the placenta regions connecting developing seeds; (2) a physical interaction between INVINH1 and Lin5 in vivo; and (3) a symplasmic discontinuity at the interface between placenta and seeds. Together, the results demonstrate that INVINH1 encodes a protein that specifically inhibits the activity of cell wall invertase and regulates leaf senescence and seed and fruit development in tomato by limiting the invertase activity in planta.
The Maize Transcription Factor Myb-Related Protein-1 Is a Key Regulator of the Differentiation of Transfer Cells
Authors: Gómez Elisa , Royo Joaquín , Muñiz Luis M. , Sellam Olivier , Paul Wyatt , Gerentes Denise , Barrero Cristina , López Maribel , Perez Pascual , Hueros Gregorio 
Published: July 2009

AbstractTransfer cells are highly modified plant cells specialized in the transport of solutes. They differentiate at many plant exchange surfaces, including phloem loading and unloading zones such as those present in the sink organs and seeds. In maize (Zea mays) seeds, transfer cells are located at the base of the endosperm. It is currently unknown how apical-basal polarity is established or why the peripheral cells at the base of the endosperm differentiate into transfer instead of aleurone cells. Here, we show that in epidermal cells committed to develop into aleurone cells, the ectopic expression of the transfer cell-specific transcriptional activator Myb-Related Protein-1 (MRP-1) is sufficient to temporarily transform them into transfer cells. These transformed cells acquire distinct transfer cell features, such as cell wall ingrowths and an elongated shape. In addition, they express a number of MRP-1 target genes presumably involved in defense. We also show that the expression of MRP-1 is needed to maintain the transfer cell phenotype. Later in development, an observed reduction in the ectopic expression of MRP-1 was followed by the reversion of the transformed cells, which then acquire aleurone cell features.
Review article: cellular and molecular mechanisms of NSAID‐induced peptic ulcers
Authors: MUSUMBA C. , PRITCHARD D. M. , PIRMOHAMED M. 
Published: July 2009

SummaryBackground Nonsteroidal anti‐inflammatory drugs (NSAIDs) are some of the most prescribed drugs worldwide and have now probably overtakenHelicobacter pylorias the most common cause of gastrointestinal injury in Western countries. Further understanding of the pathogenesis of NSAID‐induced ulcers is important to enable the development of novel and effective preventive strategies.Aims To provide an update on recent advances in our understanding of the cellular and molecular mechanisms involved in the development of NSAID‐induced ulcers.Methods A Medline search was performed to identify relevant literature using search terms including ‘nonsteroidal anti‐inflammatory drugs, aspirin, gastric ulcer, duodenal ulcer, pathogenesis, pharmacogenetics’.Results The mechanisms of NSAID‐induced ulcers can be divided into topical and systemic effects and the latter may be prostaglandin‐dependent (through COX inhibition) or prostaglandin‐independent. Genetic factors may play an important role in determining individual predisposition.Conclusions The pathogenesis of NSAID‐induced peptic ulcers is complex and multifactorial. Recent advances in cellular and molecular biology have highlighted the importance of various prostaglandin‐independent mechanisms. Pharmacogenetic studies may provide further insights into the pathogenetic mechanisms of NSAID‐induced ulcers and help identify patients at increased risk.
Systematic review: accuracy of symptom‐based criteria for diagnosis of irritable bowel syndrome in primary care
Authors: JELLEMA P. , VAN DER WINDT D. A. W. M. , SCHELLEVIS F. G. , VAN DER HORST H. E. 
Published: July 2009

SummaryBackground  Despite the trend towards making a positive diagnosis of irritable bowel syndrome (IBS), many health care providers approach IBS as a diagnosis of exclusion.Aim  To summarize available evidence on the diagnostic performance of symptom‐based IBS criteria in excluding organic diseases, and of individual signs and symptoms in diagnosing IBS and to additionally assess the influence of sources of heterogeneity on diagnostic performance.Methods  We searched PubMed and EMBASE and screened references. Studies were selected if the design was a primary diagnostic study; the patients were adults consulting because of non‐acute abdominal symptoms; the diagnostic test included an externally validated set of IBS criteria, signs, or symptoms. Data extraction and quality assessment were performed by two reviewers independently. The review adhered to the most recent guidelines as described in the Cochrane Diagnostic Reviewers’ Handbook.Results  A total of 25 primary diagnostic studies were included in the review. The performance of symptom‐based criteria in the exclusion of organic disease was highly variable. Patients fulfilling IBS criteria had, however, a lower risk of organic diseases than those not fulfilling the criteria.Conclusions  With none of the criteria showing sufficiently homogeneous and favourable results, organic disease cannot be accurately excluded by symptom‐based IBS criteria alone. However, the low pre‐test probability of organic disease especially among patients who meet symptom‐based criteria in primary care argues against exhaustive diagnostic evaluation. We advise validation of the new Rome III criteria in primary care populations.
Prospective assessment of the effect on quality of life of anti‐tumour necrosis factor therapy for perineal Crohn’s fistulas
Authors: NG S. C. , PLAMONDON S. , GUPTA A. , BURLING D. , KAMM M. A. 
Published: July 2009

SummaryBackground  Anti‐tumour necrosis factor (TNF) therapy effectively treats Crohn’s perineal fistulas (CPF); the effect on health‐related quality of life (HRQoL) remains unknown.Aims  To evaluate the effect of anti‐TNF therapy on the HRQoL of patients with CPF in daily clinical practice.Methods  Prospective evaluation of clinical and magnetic resonance imaging (MRI) responses, disease activity (Perianal Disease Activity Index – PDAI), and HRQoL assessment [Inflammatory Bowel Disease Questionnaire (IBDQ)] in patients receiving anti‐TNF therapy for CPF treated up to 12 months.Results  In all, 26 patients with CPF were treated (mean age 39 years; 19 infliximab, 7 adalimumab). At baseline, 85% patients had impaired IBDQ scores (mean 137; ‘normal’ >170). At 12 months, mean increases in IBDQ score for infliximab and adalimumab treated patients were 40 and 41 points respectively (P < 0.05). There were significant improvements in all IBDQ subscores (bowel, emotional, systemic, social) at 12 months (all P ≤ 0.003). Fourteen patients (74%) on infliximab and six on adalimumab (86%) achieved IBDQ score ≥170. Mean increase in IBDQ score was 50, 34 and 16 points in patients with clinical fistula closure (P < 0.001), clinical response (P = 0.002) and no response (n = 1) respectively. IBDQ score increased for patients with MRI healing (P < 0.001) and MRI improvement (P = 0.016), but not for those with no MRI change (n = 2). IBDQ correlated significantly with PDAI at baseline and at 12 months.Conclusion  Anti‐TNF therapy improves HRQoL in patients with CPF at 12 months and this improvement is most pronounced in patients with clinical and MRI healing.
Young people's views of mental health education in secondary schools: a Scottish study
Authors: Woolfson R. , Woolfson L. , Mooney L. , Bryce D. 
Published: July 2009

AbstractBackground  This exploratory study used mixed methods to investigate young people's preferences in the delivery of mental health education and to investigate possible age and gender differences.Method  Information was gathered about the delivery of mental health education in three secondary schools. Nine pupil focus groups were carried out to identify key themes which were then further developed and administered through questionnaires to a larger sample of 773 pupils.Results  Gender and age differences were found in young people's preferences about who should deliver mental health education, and what, when, where and how this should be delivered.Conclusion  Mental health education should reflect the needs of young people. Age and gender preferences should be considered when designing these programmes.
Very high prevalence of thyroid nodules detected by high frequency (13 MHz) ultrasound examination
Authors: Guth S. , Theune U. , Aberle J. , Galach A. , Bamberger C. M. 
Published: July 2009

AbstractBackground  The prevalence of thyroid nodules in a healthy population is high: in the German Papillon study, nationwide ultrasound screening of more than 90 000 people using 7·5 MHz scanners revealed the presence of thyroid nodules in 33% of the normal population. A study employing more sensitive 13 MHz scanners has not been conducted so far.Materials and methods  Six hundred and thirty‐five consecutive patients (33% female, 67% male, mean 56·7 years) presenting for a preventive health check up underwent ultrasound screening of the thyroid gland (Siemens Acuson Antares, 13 MHz‐linear scanner, B‐mode and Power mode) and measurement of the basal TSH (thyroid stimulating hormone) value. Size and degree of vascularization of the thyroid gland and of nodules were determined and analysed retrospectively.Results  In 432 of 635 patients, thyroid nodules could be detected with an increasing incidence with age, in 338 without goiter. Mean thyroid size was 12·3 mL for women and 20·5 mL for men correlating strongly with body weight. Fifty‐three percentage of the nodules were smaller than 5 mm. Incidence of thyroid dysfunction was only 4%. No cancerous lesions could be found.Conclusions  Using the 13 MHz technology, we found a substantially higher prevalence of thyroid nodules (68%) than the Papillon study (33%). Even if our population is older than in Papillon, the difference remains in comparable age groups. This is due to the higher sensitivity of 13 MHz scanning. Our study underlines the clinical significance of iodine deficiency and should renew the discussion on routine iodine supplementation.
Ecological assessment of an intermittent Mediterranean river using community structure and function: evaluating the role of different organism groups
Authors: HUGHES SAMANTHA JANE , SANTOS JOSÉ MARIA , FERREIRA MARIA TERESA , CARAÇA RUTE , MENDES ANA M. 
Published: July 2009

Summary1. Reliable lotic ecological monitoring requires knowledge of river typology, environmental factors, the effect of stressors known here as ‘pressures’ and appropriate indicators of anthropogenically induced change. We sampled benthic macroinvertebrate, fish, bird and macrophyte communities along an intermittent Mediterranean river and analysed community structure (relative abundance) and function (metrics) relative to environmental and pressure gradients in order to identify suitable indicator group(s) for future monitoring and mitigation programmes.2. Principal components analysis revealed that scale‐dependent longitudinal differences in valley form separated narrower higher lying sites and tributaries with good quality habitats from more open degraded sites lower down the river continuum on a small floodplain and large scale pressures describing changes in land use related to agriculture with associated physical bankside and channel impacts.3. Forward selection of variables in redundancy analysis (RDA) showed that reach scale environmental variables were selected more frequently than pressure variables for each organism group. Altitude and pH were highly redundant within and between groups, indicating essentially longitudinal structural and functional distribution patterns. Redundancy was far lower between selected pressure variables, but single or no pressure variables were retained for some organism groups indicating poor association of functional data, in particular, with the identified pressures. All RDA results indicated a longitudinal pH gradient, highlighting the combined effect of multiple environmental and pressure based mechanisms on organism groups.4. Large, mobile organisms such as fish and birds provided a reliable link between organism structure and function, environmental factors and physical disturbance of the channel, bankside and wider river corridor. Benthic macroinvertebrate and macrophyte structural data revealed distribution patterns in relation to water velocity, a key parameter for developing appropriate compensation measures.5. Results clearly show the importance of assessing patterns of both functional and structural change across multiple organism groups in order to identify typologically appropriate links with complex environmental and pressure gradients and develop and implement appropriate monitoring systems.
Intraspecific variation in the consumption of exotic prey – a mechanism that increases biotic resistance against invasive species?
Authors: CARLSSON NILS O. L. , STRAYER DAVID L. 
Published: July 2009

Summary1. Hyper‐successful exotic species can both displace the native prey that formerly made up a native predator’s diet and represent an abundant potential prey resource for native predators. Little is known about how this drastic change affects native predators, or their short‐ and long term potential to regulate the exotic species.2. We compared zebra mussel consumption by pumpkinseed sunfish (Lepomis gibbosus), redbreast sunfish (Lepomis auritus) and rock bass (Ambloplites rupestris) from populations that were either previously exposed to zebra mussels or naive to them.3. Fish from populations with longer exposure to zebra mussels consumed many more zebra mussels than fish from populations with shorter or no previous exposure to zebra mussels.4. Our experiment does not allow us to identify the mechanisms that underlie the patterns we found, but we discuss several plausible scenarios and their ecological implications.5. Predator adaptation to exotic prey may be an important but overlooked factor in invasion biology. The initial response to exotic prey by a native predator may be a poor estimate of its ability to present biotic resistance to the invasion over the long term.
Low semen volume in 47 adolescents and adults with 47,XXY Klinefelter or 46,XX male syndrome
Authors: Aksglaede L. , Jørgensen N. , Skakkebæk N. E. , Juul A. 
Published: July 2009

SummaryKlinefelter syndrome is characterized by progressive testicular failure causing androgen deficiency and azoospermia in most patients. The aim of this study was to evaluate semen quality in consecutive patients with an additional X chromosome as compared with healthy males. Forty‐seven males with non‐mosaic 47,XXY (n = 40) or SRY‐positive 46,XX male (n = 7) karyotypes aged 26.1 (range: 15.0–51.7) years participated. Semen quality was compared with 2136 (control group I) men from the general population aged 18.9 (17.9–28.6) years and with 349 fertile men (control group II) aged 30.9 (22.0–43.8) years. Semen volume adjusted for duration of abstinence was significantly smaller in the patients [2.0 (0.2–5.7) mL] when compared with control group I [3.1 (0.3–12.5) mL, p < 0.0001] and group II [3.6 (0.6–12.5) mL, p < 0.0001]. There was no difference in semen volume between 47,XXY and 46,XX males. All patients had azoospermia except two 47,XXY males aged 29 years who had sperm concentrations of 0.5 and 1.6 million/mL, respectively. We found significantly smaller semen volume in the patients when compared with controls, and the presence of motile spermatozoa in two out of 47 patients. The small semen volume supports the notion of 47,XXY patients being androgen insufficient despite serum testosterone levels within the normal range.