bluuebunny/crossref_metadata_2025_split huggingface dataset:
RBM19 is essential for preimplantation development in the mouse
Authors: Zhang Jian , Tomasini Amber J , Mayer Alan N 
Published: December 2008

Abstract

Background
RNA-binding motif protein 19 (RBM19, NCBI Accession # NP_083038) is a conserved nucleolar protein containing 6 conserved RNA recognition motifs. Its biochemical function is to process rRNA for ribosome biogenesis, and it has been shown to play a role in digestive organ development in zebrafish. Here we analyzed the role of RBM19 during mouse embryonic development by generating mice containing a mutation in the Rbm19 locus via gene-trap insertion.

Results
Homozygous mutant embryos failed to develop beyond the morula stage, showing defective nucleologenesis, activation of apoptosis, and upregulation of P53 target genes. A unique feature of RBM19 is its localization to the cytoplasm in morula stage-embryos, whereas most other nucleolar proteins are localized to the nucleolar precursor body (NPB). The nucleoli in the Rbm19 mutant embryos remain immature, yet they can carry out rRNA synthesis. The timing of developmental arrest occurs after expression of the inner cell mass markers OCT3/4 and NANOG, but prior to the specification of trophectoderm as reflected by CDX2 expression.

Conclusion
The data indicate that RBM19 is essential for preimplantation development, highlighting the importance of de novo nucleologenesis during this critical developmental stage.
Fluorescent-BOX-PCR for resolving bacterial genetic diversity, endemism and biogeography
Authors: Brusetti Lorenzo , Malkhazova Iana , Gtari Maher , Tamagnini Isabella , Borin Sara , Merabishvili Maya , Chanishvili Nina , Mora Diego , Cappitelli Francesca , Daffonchio Daniele 
Published: December 2008

Abstract

Background
BOX-A1R-based repetitive extragenic palindromic-PCR (BOX-PCR) is one of the most used techniques in biogeography studies of microbial isolates. However the traditional separation of BOX-PCR patterns by agarose gel electrophoresis suffers many limitations. The aim of this research was to set up a fluorescent BOX-PCR (F-BOX-PCR) assay in which separation of PCR products is automated in a capillary electrophoresis system. F-BOX-PCR was compared with the traditional BOX-PCR using bacterial strains with different G+C content (Bacillus cereus; Escherichia coli; isolates of the family Geodermatophilaceae). Resolution, discriminatory power and reproducibility were evaluated by assaying different electrophoretic runs, PCR reactions and independent DNA extractions. BOX-PCR and F-BOX-PCR were compared for the analysis of 29 strains of Modestobacter multiseptatus isolated from three different microsites in an altered carbonatic wall from Cagliari, Italy, and 45 strains of Streptococcus thermophilus isolated from 34 samples of the hand-made, yogurt-like product Matsoni, collected in different locations in Georgia.

Results
Fluorophore 6-FAM proved more informative than HEX and BOX-PCR both in agarose gel electrophoresis (p < 0.004 and p < 0.00003) and in capillary electrophoresis (compared only with HEX, p < 2 × 10-7). 6-FAM- and HEX-based F-BOX-PCR respectively detected up to 12.0 and 11.3 times more fragments than BOX-PCR. Replicate separations of F-BOX-PCR showed an accuracy of the size calling of ± 0.5 bp until 500 bp, constantly decreasing to ± 10 bp at 2000 bp. Cluster analysis of F-BOX-PCR profiles grouped M. multiseptatus strains according to the microsite of isolation and S. thermophilus strains according to the geographical origin of Matsoni, but resulted intermixed when a BOX-PCR dataset was used.

Conclusion
F-BOX-PCR represents an improved method for addressing bacterial biogeography studies both in term of sensitivity, reproducibility and data analysis.
Estimating adjusted prevalence ratio in clustered cross-sectional epidemiological data
Authors: Santos Carlos Antônio ST , Fiaccone Rosemeire L , Oliveira Nelson F , Cunha Sérgio , Barreto Maurício L , do Carmo Maria Beatriz B , Moncayo Ana-Lucia , Rodrigues Laura C , Cooper Philip J , Amorim Leila D 
Published: December 2008

Abstract

Background
Many epidemiologic studies report the odds ratio as a measure of association for cross-sectional studies with common outcomes. In such cases, the prevalence ratios may not be inferred from the estimated odds ratios. This paper overviews the most commonly used procedures to obtain adjusted prevalence ratios and extends the discussion to the analysis of clustered cross-sectional studies.

Methods
Prevalence ratios(PR) were estimated using logistic models with random effects. Their 95% confidence intervals were obtained using delta method and clustered bootstrap. The performance of these approaches was evaluated through simulation studies. Using data from two studies with health-related outcomes in children, we discuss the interpretation of the measures of association and their implications.

Results
The results from data analysis highlighted major differences between estimated OR and PR. Results from simulation studies indicate an improved performance of delta method compared to bootstrap when there are small number of clusters.

Conclusion
We recommend the use of logistic model with random effects for analysis of clustered data. The choice of method to estimate confidence intervals for PR (delta or bootstrap method) should be based on study design.
Functional characterization of the vaccinia virus I5 protein
Authors: Unger Bethany , Nichols R Jeremy , Stanitsa Eleni S , Traktman Paula 
Published: December 2008

Abstract
The I5L gene is one of ~90 genes that are conserved throughout the chordopoxvirus family, and hence are presumed to play vital roles in the poxvirus life cycle. Previous work had indicated that the VP13 protein, a component of the virion membrane, was encoded by the I5L gene, but no additional studies had been reported. Using a recombinant virus that encodes an I5 protein fused to a V5 epitope tag at the endogenous locus (vI5V5), we show here that the I5 protein is expressed as a post-replicative gene and that the ~9 kDa protein does not appear to be phosphorylated in vivo. I5 does not appear to traffic to any cellular organelle, but ultrastructural and biochemical analyses indicate that I5 is associated with the membranous components of assembling and mature virions. Intact virions can be labeled with anti-V5 antibody as assessed by immunoelectron microscopy, indicating that the C' terminus of the protein is exposed on the virion surface. Using a recombinant virus which encodes only a TET-regulated copy of the I5V5 gene (vΔind I5V5), or one in which the I5 locus has been deleted (vΔI5), we also show that I5 is dispensable for replication in tissue culture. Neither plaque size nor the viral yield produced in BSC40 cells or primary human fibroblasts are affected by the absence of I5 expression.
Hyperfractionated Accelerated Radiotherapy in the Milan Strategy for Metastatic Medulloblastoma
Authors: Gandola Lorenza , Massimino Maura , Cefalo Graziella , Solero Carlo , Spreafico Filippo , Pecori Emilia , Riva Daria , Collini Paola , Pignoli Emanuele , Giangaspero Felice , Luksch Roberto , Berretta Serena , Poggi Geraldina , Biassoni Veronica , Ferrari Andrea , Pollo Bianca , Favre Claudio , Sardi Iacopo , Terenziani Monica , Fossati-Bellani Franca 
Published: December 2008

PurposeWith a view to improving the prognosis for patients with metastatic medulloblastoma, we tested the efficacy and toxicity of a hyperfractionated accelerated radiotherapy (HART) regimen delivered after intensive sequential chemotherapy.Patients and MethodsBetween 1998 and 2007, 33 consecutive patients received postoperative methotrexate (8 g/m2), etoposide (2.4 g/m2), cyclophosphamide (4 g/m2), and carboplatin (0.8 g/m2) in a 2-month schedule, then HART with a maximal dose to the neuraxis of 39 Gy (1.3 Gy/fraction, 2 fractions/d) and a posterior fossa boost up to 60 Gy (1.5 Gy/fraction,2 fractions/d). Patients with persistent disseminated disease before HART were consolidated with two myeloablative courses and circulating progenitor cell rescue.ResultsPatients were classified as having M1 (n = 9), M2 (n = 6), M3 (n = 17), and M4 (n = 1) disease. Seven patients younger than 10 years old who achieved complete response after chemotherapy received a lower dose to the neuraxis (31.2 Gy). Twenty-two of the 32 assessable patients responded to chemotherapy; disease was stable in five patients and progressed in five patients. One septic death occurred before radiotherapy. Eight patients experienced relapse after a median of 12 months. Fourteen of the 33 patients underwent consolidation therapy after HART. With a median 82-month survivor follow-up, the 5-year event-free, progression-free, and overall survival rates were 70%, 72%, and 73%, respectively. No severe clinical complications of HART have emerged so far.ConclusionHART after intensive postoperative chemotherapy, followed by myeloablative chemotherapy in selected cases, proved feasible in children with metastatic medulloblastoma. The results of our treatment compare favorably with other series treated using conventional therapies.
Phase II Study of Erlotinib Plus Temozolomide During and After Radiation Therapy in Patients With Newly Diagnosed Glioblastoma Multiforme or Gliosarcoma
Authors: Prados Michael D. , Chang Susan M. , Butowski Nicholas , DeBoer Rebecca , Parvataneni Rupa , Carliner Hannah , Kabuubi Paul , Ayers-Ringler Jennifer , Rabbitt Jane , Page Margaretta , Fedoroff Anne , Sneed Penny K. , Berger Mitchel S. , McDermott Michael W. , Parsa Andrew T. , Vandenberg Scott , James C. David , Lamborn Kathleen R. , Stokoe David , Haas-Kogan Daphne A. 
Published: December 2008

Purpose This open-label, prospective, single-arm, phase II study combined erlotinib with radiation therapy (XRT) and temozolomide to treat glioblastoma multiforme (GBM) and gliosarcoma. The objectives were to determine efficacy of this treatment as measured by survival and to explore the relationship between molecular markers and treatment response. Patients and Methods Sixty-five eligible adults with newly diagnosed GBM or gliosarcoma were enrolled. We intended to treat patients not currently treated with enzyme-inducing antiepileptic drugs (EIAEDs) with 100 mg/d of erlotinib during XRT and 150 mg/d after XRT. Patients receiving EIAEDs were to receive 200 mg/d of erlotinib during XRT and 300 mg/d after XRT. After XRT, the erlotinib dose was escalated until patients developed tolerable grade 2 rash or until the maximum allowed dose was reached. All patients received temozolomide during and after XRT. Molecular markers of epidermal growth factor receptor (EGFR), EGFRvIII, phosphatase and tensin homolog (PTEN), and methylation status of the promotor region of the MGMT gene were analyzed from tumor tissue. Survival was compared with outcomes from two historical phase II trials. Results Median survival was 19.3 months in the current study and 14.1 months in the combined historical control studies, with a hazard ratio for survival (treated/control) of 0.64 (95% CI, 0.45 to 0.91). Treatment was well tolerated. There was a strong positive correlation between MGMT promotor methylation and survival, as well as an association between MGMT promotor-methylated tumors and PTEN positivity shown by immunohistochemistry with improved survival. Conclusion Patients treated with the combination of erlotinib and temozolomide during and following radiotherapy had better survival than historical controls. Additional studies are warranted.
Sex-specific effects of prenatal testosterone on nestling plasma antioxidant capacity in the zebra finch
Authors: Tobler Michael , Sandell Maria I. 
Published: December 2008

SUMMARYTrans-generational transfer of non-genetic, maternal resources such as hormones can have a substantial influence on offspring phenotype in many vertebrate species. In birds, maternal androgens enhance both growth and competitive behaviour, but also suppress the immune system. It has been hypothesised that high levels of egg androgens could also influence the prooxidant–antioxidant balance through their positive effect on growth and metabolism. We tested this hypothesis in the zebra finch (Taeniopygia guttata). Eggs were injected with testosterone dissolved in sesame oil or sesame oil only (control). We subsequently assessed the effect of the egg hormone manipulation on nestling growth and nestling plasma total antioxidant capacity (TAC). Growth rates of zebra finch nestlings were not significantly affected by egg hormone treatment. However, male offspring hatched from eggs with experimentally elevated testosterone had reduced plasma TAC at 10 days of age compared with male offspring hatching from control eggs. At the age of 34 days, males had similar plasma TAC irrespective of egg treatment. No effects of egg testosterone manipulation on nestling plasma TAC were found in females. Our results demonstrate that embryonic exposure to elevated levels of testosterone modulates chick antioxidant status, but this seems to be independent of chick growth. Sex-specific effects of prenatal testosterone on plasma TAC of zebra finch nestlings may have important consequences for sex allocation.
Multiplicity of expression of Na+,K+–ATPaseα-subunit isoforms in the gill of Atlantic salmon (Salmo salar): cellular localisation and absolute quantification in response to salinity change
Authors: Madsen Steffen S. , Kiilerich Pia , Tipsmark Christian K. 
Published: December 2008

SUMMARYThe ability to reverse the net direction of gill ion transport in response to a salinity change is critical for euryhaline teleosts and involves a complex cellular and molecular remodelling of the gill epithelium. The present study aimed to clarify the cellular localisation and exact quantitative inter-relationship of Na+,K+–ATPase α- andβ-subunit transcripts in Atlantic salmon gill during salinity change. The combined expression level of all α-isoforms in the gill increased by 100% after freshwater (FW) to seawater (SW) transfer. The α1aand α1b isoforms were both in the range 1–6 amol 20 ng–1 total RNA; α1a decreased andα 1b increased after SW-transfer, their ratio changing from 5:1 in FW to 0.26:1 in SW. The α1c and α3levels were 10- and 100-fold lower, respectively. Theβ 1-subunit mRNA level was 0.1–0.3 amol 20 ng–1 total RNA, thus much lower than the sum ofα-subunits. Even though increasing 3-fold after SW-transfer,β-subunit availability may still limit functional pump synthesis. The mRNAs of the predominant α1a and α1bisoforms were localised by in situ hybridisation in specific gill cells of both FW and SW salmon. Labelling occurred mainly in presumed chloride cells and cells deep in the filament but occasionally also on lamellae. Overall, the salinity-induced variation in labelling pattern and intensity matched the quantification data. In conclusion, the predominant switching of Na+,K+–ATPase α-subunit isoform mRNA during salinity acclimation reflects a marked remodelling of mitochondrion-rich cells(MRCs) in the gill and probably tuning of the pump performance to accomplish a net reversal of gill ion transport in hypo- and hypertonic environments.
An IS Quality Measurement Using Gap and Multicriteria Decision-Making Model: A Case Study for Supply Chain Management System
Authors: Chang Che-Wei , Horng Der-Juinn , Lin Hung-Lung 
Published: December 2008

Abstract
This study proposes a novel method for controlling and measuring supply chain management software quality. The expert decision-making algorithm-based method offers an evaluation method that can provide information system (IS) industry decision makers or administrators with a valuable reference for evaluating the IS quality between the end user and developer. Importantly, the proposed model can provide a reference material for decision makers or administrators, making it highly applicable for academic and management purposes.
Inference of Historical Changes in Migration Rate From the Lengths of Migrant Tracts
Authors: Pool John E , Nielsen Rasmus 
Published: December 2008

AbstractAfter migrant chromosomes enter a population, they are progressively sliced into smaller pieces by recombination. Therefore, the length distribution of “migrant tracts” (chromosome segments with recent migrant ancestry) contains information about historical patterns of migration. Here we introduce a theoretical framework describing the migrant tract length distribution and propose a likelihood inference method to test demographic hypotheses and estimate parameters related to a historical change in migration rate. Applying this method to data from the hybridizing subspecies Mus musculus domesticus and M. m. musculus, we find evidence for an increase in the rate of hybridization. Our findings could indicate an evolutionary trajectory toward fusion rather than speciation in these taxa.
Use of Health Information Technology by Children's Hospitals in the United States
Authors: Menachemi Nir , Brooks Robert G. , Schwalenstocker Ellen , Simpson Lisa 
Published: December 2008

OBJECTIVE. The purpose of this study was to examine the adoption of health information technology by children's hospitals and to document barriers and priorities as they relate to health information technology adoption.
METHODS. Primary data of interest were obtained through the use of a survey instrument distributed to the chief information officers of 199 children's hospitals in the United States. Data were collected on current and future use of a variety of clinical health information technology and telemedicine applications, organizational priorities, barriers to use of health information technology, and hospital and chief information officer characteristics.
RESULTS. Among the 109 responding hospitals (55%), common clinical applications included clinical scheduling (86.2%), transcription (85.3%), and pharmacy (81.9%) and laboratory (80.7%) information. Electronic health records (48.6%), computerized order entry (40.4%), and clinical decision support systems (35.8%) were less common. The most common barriers to health information technology adoption were vendors' inability to deliver products or services to satisfaction (85.4%), lack of staffing resources (82.3%), and difficulty in achieving end-user acceptance (80.2%). The most frequent priority for hospitals was to implement technology to reduce medical errors or to promote safety (72.5%).
CONCLUSION. This first national look at health information technology use by children's hospitals demonstrates the progress in health information technology adoption, current barriers, and priorities for these institutions. In addition, the findings can serve as important benchmarks for future study in this area.
Electronic and optical properties of ZnSxSe1âˆ’x
alloys
Authors: Feng Zhenbao , Hu Haiquan , Cui Shouxin 
Published: December 2008

Abstract
A series of calculations from first principles have been carried out to study structural, electronic, and optical properties of ZnSxSe1âˆ’x alloys. Our results show that the lattice constant scales linearly with sulfur composition. The imaginary parts of the dielectric function are calculated, which are in good agreement with the experimental data. We have also interpreted the origin of the spectral peaks on the basis of band structure and density of states. Additionally, we find that no bowing effect in the absorption edge is observed, unlike other II-VI semiconductor alloys.
Diffraction microtomography with sample rotation: influence of a missing apple core in the recorded frequency space
Authors: Vertu Stanislas , Delaunay Jean-Jacques , Yamada Ichiro , Haeberlé Olivier 
Published: December 2008

Abstract
Diffraction microtomography in coherent light is foreseen as a promising technique to image transparent living samples in three dimensions without staining. Contrary to conventional microscopy with incoherent light, which gives morphological information only, diffraction microtomography makes it possible to obtain the complex optical refractive index of the observed sample by mapping a three-dimensional support in the spatial frequency domain. The technique can be implemented in two configurations, namely, by varying the sample illumination with a fixed sample or by rotating the sample using a fixed illumination. In the literature, only the former method was described in detail. In this report, we precisely derive the three-dimensional frequency support that can be mapped by the sample rotation configuration. We found that, within the first-order Born approximation, the volume of the frequency domain that can be mapped exhibits a missing part, the shape of which resembles that of an apple core. The projection of the diffracted waves in the frequency space onto the set of sphere caps covered by the sample rotation does not allow for a complete mapping of the frequency along the axis of rotation due to the finite radius of the sphere caps. We present simulations of the effects of this missing information on the reconstruction of ideal objects.
Fine structure of the dipole excitations of the even-even 160Gd nucleus in the spectroscopic region
Authors: Ertuğral Filiz , Guliyev Ekber , Kuliev Ali , Yildirim Zemine 
Published: December 2008

Abstract
In this study, the result of calculations using rotational, translational and Galilean invariant quasiparticle random-phase approximation is presented for the low-lying dipole excitations in the even-even 160Gd nucleus. Calculations are carried out for both ΔK=1 and ΔK=0 branches. The analysis shows that the main part of spin-1 states, observed at energy 2.4–4 MeV in 160Gd, have M1 character and are interpreted as main fragments of the scissors mode. The calculations indicate the presence of a few prominent negativeparity dipole ΔK=1 states in the investigated energy region, in agreement with experiment.
Perspectives for Medical Informatics
Authors: Ganslandt T. , Prokosch H. U. 
Published: December 2008

Summary
Objectives: Even though today most university hospitals have already implemented commercial hospital information systems and started to build up comprehensive electronic medical records, reuse of such data for data warehousing and research purposes is still very rare. Given this situation, the focus of this paper is to present an overview on exemplary projects, which have already tackled this challenge, reflect on current initiatives within the United States of America and the European Union to establish IT infrastructures for clinical and translational research, and draw attention to new challenges in this area.
Methods: This paper does not intend to provide a fully comprehensive review on all the issues of clinical routine data reuse. It is based, however, on a presentation of a large variety of historical, but also most recent activities in data warehousing, data retrieval and linking medical informatics with translational research.
Results: The article presents an overview of the various international approaches to this issue and illustrates concepts and solutions which have been published, thus giving an impression of activities pursued in this field of medical informatics. Further, problems and open questions, which have also been named in the literature, are presented and three challenges (to establish comprehensive clinical data warehouses, to establish professional IT infrastructure applications supporting clinical trial data capture and to integrate medical record systems and clinical trial databases) related to this area of medical informatics are identified and presented.
Conclusions: Translational biomedical research with the aim “to integrate bedside and biology” and to bridge the gap between clinical care and medical research today and in the years to come, provides a large and interesting field for medical informatics researchers. Especially the need for integrating clinical research projects with data repositories built up during documentation of routine clinical care, today still leaves many open questions and research challenges. Consideration of regulatory requirements, data privacy issues, data standards as well as people/organizational issues are prerequisites in order to vanquish existing obstacles.