bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effect of clinical audits of radiation use in one hospital district in finland
Authors: Hirvonen-Kari M. , Salo S. , Dean K. , Kivisaari L. 
Published: February 2009

Background: A clinical audit is a systematic, independent, and documented process to improve the quality of radiological processes and radiation safety for patients. Purpose: To evaluate the effect of an audit process by comparing the results of two consecutive audits at the same units. Material and Methods: Audits were carried out twice at each imaging unit in the southwest hospital district of Finland: first, at the end of 2003, and again in November 2007. Both evaluations were carried out in a similar way: by interviewing personnel and examining documents, independent experts from other hospital districts ensured that diagnostic medical imaging processes at each unit were carried out according to generally accepted standards for good medical radiological procedures. The results of the consecutive audits were compared in order to analyze the effects of the clinical audits. Results: The use of radiation was in accordance with the requirements and standards of good medical procedures at every audited unit during both evaluations. The list of audit criteria was fulfilled satisfactorily on both occasions at all of the audited units, and clearly better during the second run. In the first audit, the auditors made 80 recommendations for improving diagnostic procedures and, in the second audit, 53 recommendations. During the first audit, most of the recommendations (22/80) concerned instructions in the fundamental practice of examining a patient. During the second audit, most recommendations were in the category of radiation doses. Conclusion: The clinical audit had a positive impact on the practice of work procedures in radiological departments. Most of the recommendations made after the first audit had been taken into consideration by the time of the second audit.
Colonization Sites of USA300 Methicillin-ResistantStaphylococcus aureusin Residents of Extended Care Facilities
Authors: Shurland Simone M. , Stine O. Colin , Venezia Richard A. , Johnson Jennifer K. , Zhan Min , Furuno Jon P. , Miller Ram R. , Johnson Tamara , Roghmann Mary-Claire 
Published: February 2009

Background.The anterior nares are the most sensitive single site for detecting methicillin-resistantStaphylococcus aureus(MRSA) colonization. Colonization patterns of USA300 MRSA colonization are unknown.Objectives.To assess whether residents of extended care facilities who are colonized with USA300 MRSA have different nares or skin colonization findings, compared with residents who are colonized with non-USA300 MRSA strains.Methods.The study population included residents of 5 extended care units in 3 separate facilities who had a recent history of MRSA colonization. Specimens were obtained weekly for surveillance cultures from the anterior nares, perineum, axilla, and skin breakdown (if present) for 3 weeks. MRSA isolates were categorized as USA300 MRSA or non-USA300 MRSA.Results.Of the 193 residents who tested positive for MRSA, 165 were colonized in the anterior nares, and 119 were colonized on their skin. Eighty-four percent of USA300 MRSA-colonized residents had anterior nares colonization, compared with 86% of residents colonized with non-USA300 MRSA (P= .80). Sixty-six percent of USA300 MRSA–colonized residents were colonized on the skin, compared with 59% of residents colonized with non-USA300 MRSA (P= .30).Conclusions.Colonization patterns of USA300 MRSA and non-USA300 MRSA are similar in residents of extended care facilities. Anterior nares cultures will detect most—but not all—people who are colonized with MRSA, regardless of whether it is USA300 or non-USA300 MRSA.
Biomarker discovery in MALDI-TOF serum protein profiles using discrete wavelet transformation
Authors: Alexandrov Theodore , Decker Jens , Mertens Bart , Deelder Andre M. , Tollenaar Rob A. E. M. , Maass Peter , Thiele Herbert 
Published: February 2009

AbstractMotivation: Automatic classification of high-resolution mass spectrometry proteomic data has increasing potential in the early diagnosis of cancer. We propose a new procedure of biomarker discovery in serum protein profiles based on: (i) discrete wavelet transformation of the spectra; (ii) selection of discriminative wavelet coefficients by a statistical test and (iii) building and evaluating a support vector machine classifier by double cross-validation with attention to the generalizability of the results. In addition to the evaluation results (total recognition rate, sensitivity and specificity), the procedure provides the biomarker patterns, i.e. the parts of spectra which discriminate cancer and control individuals. The evaluation was performed on matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) serum protein profiles of 66 colorectal cancer patients and 50 controls.Results: Our procedure provided a high recognition rate (97.3%), sensitivity (98.4%) and specificity (95.8%). The extracted biomarker patterns mostly represent the peaks expressing mean differences between the cancer and control spectra. However, we showed that the discriminative power of a peak is not simply expressed by its mean height and cannot be derived by comparison of the mean spectra. The obtained classifiers have high generalization power as measured by the number of support vectors. This prevents overfitting and contributes to the reproducibility of the results, which is required to find biomarkers differentiating cancer patients from healthy individuals.Availability: The data and scripts used in this study are available at http://www.math.uni-bremen.de/~theodore/MALDIDWT.Contact: theodore@math.uni-bremen.deSupplementary information: Supplementary data are available at Bioinformatics online.
Barriers to movement: impacts of wind farms on migrating birds
Authors: Masden Elizabeth A. , Haydon Daniel T. , Fox Anthony D. , Furness Robert W. , Bullman Rhys , Desholm Mark 
Published: February 2009

Abstract
Masden, E. A., Haydon, D. T., Fox, A. D., Furness, R. W., Bullman, R., and Desholm, M. 2009. Barriers to movement: impacts of wind farms on migrating birds. – ICES Journal of Marine Science, 66: 746–753. Advances in technology and engineering are enhancing the contribution that wind power makes to renewable energy generation. Wind farms, both operational and in planning, can be expected to impact negatively on wildlife populations, particularly birds. We propose a novel approach to assess the impacts through the energetic costs of avoidance behaviour for a long-distance, migratory seaduck. Flight trajectories were recorded using surveillance radar at a Danish offshore wind farm with emphasis placed on the 200 000+ migrating common eiders that pass through the area annually. Minimum distance to wind farm and curvature of trajectories were compared pre- and post-construction. Additional costs of the avoidance response were estimated using an avian energetic model. The curvature of eider trajectories was greatest post-construction and within 500 m of the wind farm, with a median curvature significantly greater than pre-construction, suggesting that the birds adjusted their flight paths in the presence of the wind farm. Additional distance travelled as a consequence of the wind farm's presence was ca. 500 m and trivial compared with the total costs of a migration episode of 1400 km. However, construction of further wind farms along the migration route could have cumulative effects on the population, especially when considered in combination with other human actions.
Epigenetic Regulation, Somatic Homologous Recombination, and Abscisic Acid Signaling Are Influenced by DNA Polymerase ϵ Mutation inArabidopsis
Authors: Yin Haibo , Zhang Xia , Liu Jun , Wang Youqun , He Junna , Yang Tao , Hong Xuhui , Yang Qing , Gong Zhizhong 
Published: February 2009

AbstractBased on abscisic acid (ABA) inhibition of seed germination and seedling growth assays, we isolated an ABA overly sensitive mutant (abo4-1) caused by a mutation in the Arabidopsis thaliana POL2a/TILTED1(TIL1) gene encoding a catalytic subunit of DNA polymerase ϵ. The dominant, ABA-insensitive abi1-1 or abi2-1 mutations suppressed the ABA hypersensitivity of the abo4-1 mutant. The abo4/til1 mutation reactivated the expression of the silenced Athila retrotransposon transcriptional silent information (TSI) and the silenced 35S-NPTII in the ros1 mutant and increased the frequency of somatic homologous recombination (HR) ∼60-fold. ABA upregulated the expression of TSI and increased HR in both the wild type and abo4-1. MEIOTIC RECOMBINATION11 and GAMMA RESPONSE1, both of which are required for HR and double-strand DNA break repair, are expressed at higher levels in abo4-1 and are enhanced by ABA, while KU70 was suppressed by ABA. abo4-1 mutant plants are sensitive to UV-B and methyl methanesulfonate and show constitutive expression of the G2/M-specific cyclin CycB1;1 in meristems. The abo4-1 plants were early flowering with lower expression of FLOWER LOCUS C and higher expression of FLOWER LOCUS T and changed histone modifications in the two loci. Our results suggest that ABO4/POL2a/TIL1 is involved in maintaining epigenetic states, HR, and ABA signaling in Arabidopsis.
Genome-Wide Analysis of Genes Targeted by PHYTOCHROME INTERACTING FACTOR 3-LIKE5 during Seed Germination inArabidopsis
Authors: Oh Eunkyoo , Kang Hyojin , Yamaguchi Shinjiro , Park Jeongmoo , Lee Doheon , Kamiya Yuji , Choi Giltsu 
Published: February 2009

AbstractPHYTOCHROME INTERACTING FACTOR 3-LIKE5 (PIL5) is a basic helix-loop-helix transcription factor that inhibits seed germination by regulating the expression of gibberellin (GA)- and abscisic acid (ABA)-related genes either directly or indirectly. It is not yet known, however, whether PIL5 regulates seed germination solely through GA and ABA. Here, we used Chromatin immunoprecipitation-chip (ChIP-chip) analysis to identify 748 novel PIL5 binding sites in the Arabidopsis thaliana genome. Consistent with the molecular function of PIL5 as a transcription regulator, most of the identified binding sites are located in gene promoter regions. Binding site analysis shows that PIL5 binds to its target sites mainly through the G-box motif in vivo. Microarray analysis reveals that phytochromes regulate a large number of genes mainly through PIL5 during seed germination. Comparison between the ChIP-chip and microarray data indicates that PIL5 regulates 166 genes by directly binding to their promoters. Many of the identified genes encode transcription regulators involved in hormone signaling, while some encode enzymes involved in cell wall modification. Interestingly, PIL5 directly regulates many transcription regulators of hormone signaling and indirectly regulates many genes involved in hormone metabolism. Taken together, our data indicate that PIL5 inhibits seed germination not just through GA and ABA, but also by coordinating hormone signals and modulating cell wall properties in imbibed seeds.
Epidemiology of immune thrombocytopenic purpura in the General Practice Research Database
Authors: Marieke Schoonen W. , Kucera Gena , Coalson Jenna , Li Lin , Rutstein Mark , Mowat Fionna , Fryzek Jon , Kaye James A. 
Published: February 2009

SummaryThe epidemiology of immune thrombocytopenic purpura (ITP) is not well‐characterised in the general population. This study described the incidence and survival of ITP using the UK population‐based General Practice Research Database (GPRD). ITP patients first diagnosed in 1990–2005 were identified in the GPRD. Overall incidence rates (per 100 000 person‐years) and rates by age, sex, and calendar periods were calculated. Survival analysis was conducted using the Kaplan‐Meier and proportional hazard methods. A total of 1145 incident ITP patients were identified. The crude incidence was 3·9 (95% confidence interval [CI]: 3·7–4·1). Overall average incidence was statistically significantly higher in women (4·4, 95% CI: 4·1–4·7) compared to men (3·4; 95% CI: 3·1–3·7). Among men, incidence was bimodal with peaks among ages under 18 and between 75–84 years. The hazard ratio for death among ITP patients was 1·6 (95% CI: 1·3–1·9) compared to age‐ and sex‐matched comparisons. During follow‐up 139 cases died, of whom 75 had a computerised plausible cause of death. Death was related to bleeding in 13% and infection in 19% of these 75. In conclusion, ITP incidence varies with age and is higher in women than men. This potentially serious medical condition is associated with increased mortality in the UK.
Detection of aberrant transcription of major histocompatibility complex class II antigen presentation genes in chronic lymphocytic leukaemia identifies HLA‐DOA mRNA as a prognostic factor for survival
Authors: Souwer Yuri , Chamuleau Martine E. D. , Van De Loosdrecht Arjan A. , Tolosa Eva , Jorritsma Tineke , Muris Jettie J. F. , Dinnissen‐van Poppel Marion J. , Snel Sander N. , Van De Corput Lisette , Ossenkoppele Gert J. , Meijer Chris J. L. M. , Neefjes Jacques J. , Marieke van Ham S. 
Published: February 2009

SummaryIn human B cells, effective major histocompatibility complex (MHC) class II‐antigen presentation depends not only on MHC class II, but also on the invariant chain (CD74 or Ii), HLA‐DM (DM) and HLA‐DO (DO), the chaperones regulating the antigen loading process of MHC class II molecules. We analysed immediate ex vivo expression of HLA‐DR (DR), CD74, DM and DO in B cell chronic lymphocytic leukaemia (B‐CLL). Real‐time reverse transcription polymerase chain reaction demonstrated a highly significant upregulation of DRA, CD74, DMB, DOA and DOB mRNA in purified malignant cells compared to B cells from healthy donors. The increased mRNA levels were not translated into enhanced protein levels but could reflect aberrant transcriptional regulation. Indeed, upregulation of DRA, DMB, DOA and DOB mRNA correlated with enhanced expression of class II transactivator (CIITA). In‐depth analysis of the various CIITA transcripts demonstrated a significant increased activity of the interferon‐γ‐inducible promoter CIITA‐PIV in B‐CLL. Comparison of the aberrant mRNA levels with clinical outcome identified DOA mRNA as a prognostic indicator for survival. Multivariate analysis revealed that the prognostic value of DOA mRNA was independent of the mutational status of the IGHV genes. Thus, aberrant transcription of DOA forms a novel and additional prognostic indicator for survival in B‐CLL.
TheAnisakis simplexAni s 7 major allergen as an indicator of trueAnisakisinfections
Authors: Anadón A M , Romarís F , Escalante M , Rodríguez E , Gárate T , Cuéllar C , Ubeira F M 
Published: February 2009

SummaryAni s 7 is currently the most important excretory/secretory (ES) Anisakis simplex allergen, as it is the only one recognized by 100% of infected patients. The allergenicity of this molecule is due mainly to the presence of a novel CX17–25CX9–22CX8CX6 tandem repeat motif not seen in any previously reported protein. In this study we used this allergen as a model to investigate how ES allergens are recognized during Anisakis infections, and the usefulness of a recombinant fragment of Ani s 7 allergen (t-Ani s 7) as a marker of true Anisakis infections. The possible antigenic relationship between native Ani s 7 (nAni s 7) from Anisakis and Pseudoterranova decipens antigens was also investigated. Our results demonstrate that nAni s 7 is secreted and recognized by the immune system of rats only when the larvae are alive (i.e. during the acute phase of infection), and that this molecule is not present in, or is antigenically different from, Pseudoterranova allergens. The t-Ani s 7 polypeptide is a useful target for differentiating immunoglobulin E antibodies induced by true Anisakis infections from those induced by other antigens that may cross-react with Anisakis allergens, including P. decipiens. The results also support the hypothesis that the Ani s 7 major allergen does not participate in maintaining the antigenic stimulus during chronic infections.
Differential expression of immunoregulatory genes in monocytes in response toPorphyromonas gingivalisandEscherichia colilipopolysaccharide
Authors: Barksby H E , Nile C J , Jaedicke K M , Taylor J J , Preshaw P M 
Published: February 2009

SummaryPorphyromonas gingivalis lipopolysaccharide (LPS) (strain W50) interacts with Toll-like receptor 2 (TLR-2) leading to cytokine expression and inflammation, and thereby plays a key role in the pathogenesis of periodontal disease. The aims of this study were to investigate gene expression of key regulatory mediators of innate immune responses in a human monocytic cell line (THP-1) to P. gingivalis LPS and to compare these results with those obtained using the TLR-4 ligand, Escherichia coli LPS. Custom-made Taqman low-density arrays were used for expression profiling of 45 different cytokine-related genes. Both types of LPS highly up-regulated interleukin (IL)-1α and IL-1β, IL-18 receptor (IL-18R), IL-18R accessory protein and IL-1 family (IL-1F)9. Expression levels of IL-1F6, IL-1F7 and caspase-1 were unaltered by either LPS. Genes for tumour necrosis factor-α, IL-6, leukaemia inhibitory factor and IL-32 were also highly induced by both LPS. For a subset of genes, including CXC chemokine ligand 5 (CXCL5), expression was induced only by E. coli LPS or was up-regulated more highly by E. coli compared with P. gingivalis LPS in THP-1 monocytes. A similar expression pattern was also observed in dendritic cells. Analysis of signalling pathways which lead to CXCL5 expression indicated that the mechanisms underpinning the differential responses did not involve the recruitment of different adaptor proteins by TLR-2 and TLR-4, and therefore occur downstream of the receptor–adaptor complex. We conclude that differences in signalling pathways activated by TLR-2 and TLR-4 ligands lead to differential innate immune responses which may be important in polymicrobial diseases such as periodontal disease.
Decreased numbers of circulating plasmablasts and differences in IgA1-plasmablast homing to skin in coeliac disease and dermatitis herpetiformis
Authors: Kantele J M , Savilahti E , Westerholm-Ormio M , Pakkanen S , Arvilommi H S , Reunala T , Kantele A M 
Published: February 2009

SummaryThe two clinical phenotypes of gluten enteropathy, coeliac disease (CD) and dermatitis herpetiformis (DH), were characterized for numbers and homing profiles of circulating final effector B cells, plasmablasts, identified as immunoglobulin (Ig)-secreting cells (ISC). In CD, the numbers of ISC were ∼50% lower than in DH or controls. ISC expressed peripheral lymph node homing receptor (HR), L-selectin, less frequently in CD (54%) and DH (52%) patients than in controls (70%). The expression of gut mucosal HR, α4β7, was less frequent in CD (42%) than in DH (65%) or controls (60%). In DH, but not in CD or controls, a higher proportion of IgA1-ISC (40%) than IgA2-ISC (25%) expressed the skin HR, cutaneous lymphocyte-associated antigen. In gluten enteropathy circulating plasmablasts are more mature, but decreased in number, and have distorted homing profiles. Differential IgA1-plasmablast homing could be associated with the development of skin rash with IgA1-deposits in DH but not in CD.
Correlation between plasma calcium, parathyroid hormone (PTH) and the metabolic syndrome (MetS) in a community‐based cohort of men and women
Authors: Ahlström Tommy , Hagström Emil , Larsson Anders , Rudberg Claes , Lind Lars , Hellman Per 
Published: February 2009

SummaryContext  In recent years, an association has been noted between several abnormalities that characterize the metabolic syndrome (MetS) and primary hyperparathyroidism (pHPT). These abnormalities include dyslipidaemia, obesity, insulin resistance and hypertension. The correlations between plasma calcium, parathyroid hormone (PTH) and the variables in the MetS in a normal population are still unclear.Objective  To describe correlations between plasma calcium and PTH and the various abnormalities present in the MetS in a healthy population.Design  We studied 1016 healthy individuals from the Prospective Investigation of the Vasculature in Uppsala Seniors (PIVUS) population of 70 years old, by means of plasma analyses of calcium, PTH, creatinine, lipids, insulin and glucose, as well as by standardized blood pressure measurements. Further, body mass index (BMI) and waist circumference were determined.Results  The more National Cholesterol Education Program (NCEP) criteria for the MetS that were met, the higher the s‐PTH and albumin‐corrected s‐calcium. Further, positive correlations between plasma calcium and BMI (P = 0·0003), waist circumference (P = 0·0009) and insulin resistance (P = 0·079) were found. PTH and BMI (P < 0·0001), waist circumference (P < 0·0001), systolic blood pressure (P = 0·0034), diastolic blood pressure (P = 0·0008), serum triglycerides (P = 0·0003) and insulin resistance (P = 0·0003) were positively correlated, whereas serum high density lipoproteins (HDL) (P = 0·036) and PTH were negatively correlated.Conclusions  We conclude that PTH correlates with several of the metabolic factors included in the MetS within a normocalcaemic population. In addition, individuals with mild pHPT present significantly more NCEP criteria for MetS. We postulate that increased levels of PTH in pHPT may be associated with the increased cardiovascular morbidity and mortality seen in pHPT.
Reduced cardiac functional reserve and quality of life in adults with GH deficiency
Authors: Moisey Robert , Barker Diane , Lewis Nigel , Sharp Lisa , Clements Richard E. , Goldspink David F. , Tan Lip‐Bun , Orme Steve 
Published: February 2009

SummaryIntroduction  Patients with severe GH deficiency (GHD) suffer with a reduced quality of life in addition to diverse changes in cardiac size and performance. So far, the cardiac reserve ability to maintain the circulation during peak exercise has not been measured. We tested the hypothesis that patients with severe GHD have reduced cardiac reserve function compared with healthy controls and that this could explain, in part, their reduced quality of life.Aims  Eighteen patients with severe GHD and an assessment of GHD in adults (AGHDA) score ≥11 (mean 20·0, range 12–25) were studied and compared with 18 age‐, sex‐ and body mass index‐matched healthy controls. Peak cardiac power and cardiorespiratory fitness were investigated using noninvasive haemodynamic measurements during maximal cardiopulmonary exercise testing.Results  Compared with matched controls, the cardiac power of GHD patients during exercise to volitional exhaustion was significantly reduced by 15% (mean ± SD 4·4 ± 1·0 W vs. 5·2 ± 1·0 W, P = 0·02). Patients with GHD also had lower cardiac chronotropic reserve (peak heart rate 154 ± 21/min vs. 174 ± 11/min, P = 0·001) and a lower cardiac pressure‐generating capacity (systolic blood pressure 160 ± 25 mmHg vs. 200 ± 15 mmHg, P < 0·0001). We found no correlation between any measure of peak cardiac power or function and the AGHDA score.Conclusion  Using this robust noninvasive method of assessing functional cardiac pumping capacity, we have for the first time shown that, while patients with severe GHD have a significantly impaired cardiac functional reserve associated with chronotropic incompetence and impaired pressure‐generating capacity, this does not correlate with their reduced quality of life assessed using the current standard AGHDA score.