bluuebunny/crossref_metadata_2025 huggingface dataset:
Robust design and analysis of 4PUS–1RPU parallel mechanism for a 5-degree-of-freedom hybrid kinematics machine
Authors: Hu Y , Li B
Published: May 2011

Based on a proposed 4 degree-of-freedom (DOF) T2R2 parallel mechanism with the structural configuration of 4PUS–1RPU (4-prismatic–universal–spherical and 1-revolute–prismatic–universal), a 5-axis hybrid kinematics machine (HKM) can be developed with an additional linear motion being combined. The kinematic and dynamic performance indices for the 4-DOF parallel mechanism are developed. A novel improved RSM (response surface methodology)-based LKN (Latin hypercube design, Kriging interpolation, and neural network training) method, which is a generic robust design method for dealing with the computation-intensive engineering optimization problem, is developed in this paper. The robust design for the 4PUS–1RPU parallel mechanism by using both traditional RSM and the presented LKN method is carried out, where the first-order natural frequency is regarded as the single response objective, and the design results show that the LKN method is more effective than the traditional RSM. Based on the proposed LKN method the robust design for the 4PUS–1RPU parallel mechanism with consideration of both kinematic and dynamic performance indices is carried out. The characteristics of the robust optimal scheme are analysed in detail. The prototype of the HKM with the parameters obtained from the robust design scheme is developed, and the machining experiments show that the proposed HKM can implement the 5-axis machining with the structural and cross-sectional parameters that are much more robust and optimal.
Effect of impression pressure and anilox specification on solid and halftone density
Authors: Bould D C , Hamblyn S M , Gethin D T , Claypole T C
Published: May 2011

Controlling the transfer of ink to the substrate is a key requirement of the flexographic printing process. Its ability to transfer ink from the image carrier to the substrate at low pressures enables the process to be used for the production of printed matter using pressure-sensitive materials. These can range from substrates where high pressures can damage surface structure (e.g. corrugated board), to specialist inks, which can be damaged by the high shearing action associated with other volume print processes. This paper evaluates the effect of pressure changes on print quality for different anilox specifications and line rulings on the plate.

Data collected from an experimental print trial were used to quantify the effects of anilox roll specifications, dot pitch, and plate-to-substrate engagement on the reproduction of both a continuous ink film and the formation of discrete halftone dots.

The ink-carrying volume of the cells of the anilox roll was shown to have the greatest influence on solid density (a parameter used as an indirect measure of ink film thickness) and halftone dot formation; however, the geometrical characteristics of the cells were also shown to have an effect. An initial increase in the pressure within the printing nip resulted in a significant rise in both solid density and tone gain (growth of the halftone dots) due to improved ink transfer from the plate to the substrate. Subsequent increases in pressure produced little further increase of solid density, indicating ink transfer had reached a plateau. The rate of increase of halftone density was found to be reduced as pressure increased, which was attributed to the ink approaching its maximum capability for spreading on the substrate.
Optimization of parameters for fibre laser cutting of a 10 mm stainless steel plate
Authors: Wandera C , Kujanpää V
Published: May 2011

Optimization of the fibre laser cutting parameters for attainment of high cut edge quality in 10 mm stainless steel plate was demonstrated in this study. The tested process parameters included cutting speed, focal position, and focal length. Optimization of these process parameters enhances the melt removal from the cut kerf so as to prevent the undesired dross adherence on the lower cut edge or even incomplete penetration of the workpiece when the incident intensity is not sufficient to penetrate the workpiece. Dross-free cut edges with lower surface roughness and lower deviation of cut edge squareness could be achieved by reducing the cutting speed from the maximum achievable value, using the longer focal length lens for focusing the laser beam, and with focal position located on the bottom workpiece surface. These conditions enhance a high melt removal rate resulting in a high cut edge quality.
FLT3 expression initiates in fully multipotent mouse hematopoietic progenitor cells
Authors: Buza-Vidas Natalija , Woll Petter , Hultquist Anne , Duarte Sara , Lutteropp Michael , Bouriez-Jones Tiphaine , Ferry Helen , Luc Sidinh , Jacobsen Sten Eirik Waelgaard
Published: May 2011

Lymphoid-primed multipotent progenitors with down-regulated megakaryocyte-erythroid (MkE) potential are restricted to cells with high levels of cell-surface FLT3 expression, whereas HSCs and MkE progenitors lack detectable cell-surface FLT3. These findings are compatible with FLT3 cell-surface expression not being detectable in the fully multipotent stem/progenitor cell compartment in mice. If so, this process could be distinct from human hematopoiesis, in which FLT3 already is expressed in multipotent stem/progenitor cells. The expression pattern of Flt3 (mRNA) and FLT3 (protein) in multipotent progenitors is of considerable relevance for mouse models in which prognostically important Flt3 mutations are expressed under control of the endogenous mouse Flt3 promoter. Herein, we demonstrate that mouse Flt3 expression initiates in fully multipotent progenitors because in addition to lymphoid and granulocyte-monocyte progenitors, FLT3− Mk- and E-restricted downstream progenitors are also highly labeled when Flt3-Cre fate mapping is applied.
BAD-LAMP is a novel biomarker of nonactivated human plasmacytoid dendritic cells
Authors: Defays Axel , David Alexandre , de Gassart Aude , De Angelis Rigotti Francesca , Wenger Till , Camossetto Voahirana , Brousset Pierre , Petrella Tony , Dalod Marc , Gatti Evelina , Pierre Philippe
Published: June 2011

The brain and dendritic cell (BAD)–associated lysosome-associated membrane protein (LAMP)–like molecule (BAD-LAMP, c20orf103, UNC-46) is a newly identified member of the family of LAMPs. BAD-LAMP expression in the mouse is confined to neurons. We demonstrate here that in humans, BAD-LAMP can specifically be found in the type I IFN-producing plasmacytoid dendritic cells (pDCs). Human BAD-LAMP is localized in the endoplasmic reticulum-Golgi intermediate compartment (ERGIC) of freshly isolated CD123+ pDCs and is rapidly lost upon activation by unmethylated cytosine-phosphate-guanine (CpG) oligonucleotides. The restricted pattern of BAD-LAMP expression allows for the rapid identification of normal and leukemic human pDCs in tissues and blood.
Megakaryocytes differentially sort mRNAs for matrix metalloproteinases and their inhibitors into platelets: a mechanism for regulating synthetic events
Authors: Cecchetti Luca , Tolley Neal D. , Michetti Noemi , Bury Loredana , Weyrich Andrew S. , Gresele Paolo
Published: May 2011

Megakaryocytes transfer a diverse and functional transcriptome to platelets during the final stages of thrombopoiesis. In platelets, these transcripts reflect the expression of their corresponding proteins and, in some cases, serve as a template for translation. It is not known, however, if megakaryocytes differentially sort mRNAs into platelets. Given their critical role in vascular remodeling and inflammation, we determined whether megakaryocytes selectively dispense transcripts for matrix metalloproteinases (MMPs) and their tissue inhibitors (TIMPs) into platelets. Next-generation sequencing (RNA-Seq) revealed that megakaryocytes express mRNA for 10 of the 24 human MMP family members. mRNA for all of these MMPs are present in platelets with the exception of MMP-2, 14, and 15. Megakaryocytes and platelets also express mRNA for TIMPs 1-3, but not TIMP-4. mRNA expression patterns predicted the presence and, in most cases, the abundance of each corresponding protein. Nonetheless, exceptions were observed: MMP-2 protein is present in platelets but not its transcript. In contrast, quiescent platelets express TIMP-2 mRNA but only traces of TIMP-2 protein. In response to activating signals, however, platelets synthesize significant amounts of TIMP-2 protein. These results demonstrate that megakaryocytes differentially express mRNAs for MMPs and TIMPs and selectively transfer a subset of these into platelets. Among the platelet messages, TIMP-2 serves as a template for signal-dependent translation.
Production of the plasma-cell survival factor a proliferation-inducing ligand (APRIL) peaks in myeloid precursor cells from human bone marrow
Authors: Matthes Thomas , Dunand-Sauthier Isabelle , Santiago-Raber Marie-Laure , Krause Karl-Heinz , Donze Olivier , Passweg Jakob , McKee Tomas , Huard Bertrand
Published: June 2011

The bone marrow (BM) is an organ extremely efficient in mediating long-term survival of plasma cells (PCs), ensuring an immune humoral memory. This implies that the BM must provide continuously key PC survival factors. Our results show that the BM is an organ constitutively rich in a proliferation-inducing ligand (APRIL), a member of the tumor necrosis factor superfamily implicated in PC survival. APRIL production is induced during hematopoiesis in myeloid cells by non–lineage-committing factors such as stem cell factor, thrombopoietin, IL-3, and FMS-like tyrosine kinase 3 ligand. Notably, APRIL production, both in the human and mouse systems, peaks in myeloid precursor cells, before dropping in fully mature granulocytes. Myeloid cells secrete APRIL that circulates freely in BM plasma to act on PCs, usually at distance from APRIL production sites. Selective APRIL in vivo antagonism and in vitro coculture experiments further demonstrated that myeloid precursor cells mediates PC survival in an APRIL-dependent manner Thus, APRIL production by myeloid precursor cells shows that the 2 main BM functions, hematopoiesis and long-term PC survival, are linked. Such constitutive and high APRIL production may explain why BM mediates long-term PC survival.
Chromothripsis identifies a rare and aggressive entity among newly diagnosed multiple myeloma patients
Authors: Magrangeas Florence , Avet-Loiseau Hervé , Munshi Nikhil C. , Minvielle Stéphane
Published: May 2011

Multiple myeloma (MM) develops from a premalignant plasma cell proliferative disorder, and with time can progress to a more aggressive disease in extramedullary locations. The gradually clinical evolution is supported by clonal expansion of cells that acquire genetic lesions over years. This model of cancer evolution based on ongoing genomic instability mechanism may apply to development of most MM cases. However, in a small fraction of newly diagnosed MM who relapse quickly and finally die within 2 years, the gradual model appears to be untenable. Analysis of high resolution copy number profiles obtained using single nucleotide polymorphism array data from 764 newly diagnosed MM identified large numbers of genomic rearrangements with the hallmarks of chromothripsis in 1.3% of samples. Moreover, this catastrophic event confers a poor outcome. Because chromothripsis appears to occur in a single crisis, our results suggest that high-risk MM patients use this novel way of cancer evolution.
The effect of cathepsin K deficiency on airway development and TGF-β1 degradation
Authors: Zhang Dongwei , Leung Nelson , Weber Ekkehard , Saftig Paul , Brömme Dieter
Published: May 2011

Background

Cathepsin K, a cysteine protease predominantly expressed in osteoclasts, is a major drug target for the treatment of osteoporosis. Recent findings, however, indicate that cathepsin K is also involved in non-skeletal metabolism. The development of fibrotic phenotypes in lung and skin is a concern for cathepsin K inhibitors presently evaluated in clinical trials. Cathepsin K is expressed in lung tissue and has been implicated in lung fibrosis. However, little is known about the role of cathepsin K in airway development and its effect on TGF-β1 degradation.

Methods

We investigated the effects of cathepsin K-deficiency on alterations in airway integrity, extracellular matrix composition, and TGF-β1 expression and degradation. Lung homogenates of wild-type and cathepsin K-deficient mice were used to evaluate their contents of collagen, glycosaminoglycans, and TGF-β1. The accessibility of TGF-β1 to cathepsin K-mediated degradation was determinedin vitroand lung fibroblast proliferations in wild-type and cathepsin K-deficient cells were evaluated.

Results

Lung airway cathepsin K expression in wild-type mice remained constant between 1 and 6 months of age and the airway integrity was maintained. In contrast, after 2 months of age, allCtsk-/-mice demonstrated increased airway epithelium thickness by 16-28%, a lower structural airway integrity (1-2 score units lower), elevated cytokeratin expression of 12%, increased α-actin and vimentin expression by 50% and 70%, increased area of smooth muscle cells by 15%, elevated hydroxyproline and GAGs content by 20% and 25%, and increased TGF-β1 expression by 25%. TGF-β1 proved an efficient substrate of cathepsin K and TGF-β1 protein content in lung was increased by a potent cathepsin inhibitor. Lung fibroblasts fromCtsk-/-mice after TGF-β1 treatment showed increased proliferation rates, increased levels of TGF-β1 by 30%, and increased ECM secretion.

Conclusion

This study suggests that airway development is partly regulated by cathepsin K and that its expression contributes to the maintenance of the airway structural integrity. The anticipated use of therapeutic cathepsin K inhibitors needs to take potential changes in human lungs into consideration.
Dermatan sulfate in tunicate phylogeny: Order-specific sulfation pattern and the effect of [→4IdoA(2-Sulfate)β-1→3GalNAc(4-Sulfate)β-1→] motifs in dermatan sulfate on heparin cofactor II activity
Authors: Kozlowski Eliene O , Lima Paula C , Vicente Cristina P , Lotufo Tito , Bao Xingfeng , Sugahara Kazuyuki , Pavão Mauro SG
Published: May 2011

Background

Previously, we have reported the presence of highly sulfated dermatans in solitary ascidians from the orders Phlebobranchia (Phallusia nigra) and Stolidobranchia (Halocynthia pyriformis and Styela plicata). Despite the identical disaccharide backbone, consisting of [→4IdoA(2S)β-1→3GalNAcβ-1→], those polymers differ in the position of sulfation on the N-Acetyl galactosamine, which can occur at carbon 4 or 6. We have shown that position rather than degree of sulfation is important for heparin cofactor II activity. As a consequence, 2,4- and 2,6-sulfated dermatans have high and low heparin cofactor II activities, respectively. In the present study we extended the disaccharide analysis of ascidian dermatan sulfates to additional species of the orders Stolidobranchia (Herdmania pallida, Halocynthia roretzi) and Phlebobranchia (Ciona intestinalis), aiming to investigate how sulfation evolved within Tunicata. In addition, we analysed how heparin cofactor II activity responds to dermatan sulfates containing different proportions of 2,6- or 2,4-disulfated units.

Results

Disaccharide analyses indicated a high content of disulfated disaccharide units in the dermatan sulfates from both orders. However, the degree of sulfation decreased from Stolidobranchia to Phlebobranchia. While 76% of the disaccharide units in dermatan sulfates from stolidobranch ascidians are disulfated, 53% of disulfated disaccharides are found in dermatan sulfates from phlebobranch ascidians. Besides this notable difference in the sulfation degree, dermatan sulfates from phlebobranch ascidians contain mainly 2,6-sulfated disaccharides whereas dermatan sulfate from the stolidobranch ascidians contain mostly 2,4-sulfated disaccharides, suggesting that the biosynthesis of dermatan sulfates might be differently regulated during tunicates evolution. Changes in the position of sulfation on N-acetylgalactosamine in the disaccharide [→4IdoA(2-Sulfate)β-1→3GalNAcβ-1→] modulate heparin cofactor II activity of dermatan sulfate polymers. Thus, high and low heparin cofactor II stimulating activity is observed in 2,4-sulfated dermatan sulfates and 2,6-sulfated dermatan sulfates, respectively, confirming the clear correlation between the anticoagulant activities of dermatan sulfates and the presence of 2,4-sulfated units.

Conclusions

Our results indicate that in ascidian dermatan sulfates the position of sulfation on the GalNAc in the disaccharide [→4IdoA(2S)β-1→3GalNAcβ-1→] is directly related to the taxon and that the 6-O sulfation is a novelty apparently restricted to the Phlebobranchia. We also show that the increased content of [→4IdoA(2S)β-1→3GalNAc(4S)β-1→] disaccharide units in dermatan sulfates from Stolidobranchia accounts for the increased heparin cofactor II stimulating activity.
Evidence of association between Nucleosome Occupancy and the Evolution of Transcription Factor Binding Sites in Yeast
Authors: Swamy Krishna BS , Chu Wen-Yi , Wang Chun-Yi , Tsai Huai-Kuang , Wang Daryi
Published: May 2011

Background

Divergence of transcription factor binding sites is considered to be an important source of regulatory evolution. The associations between transcription factor binding sites and phenotypic diversity have been investigated in many model organisms. However, the understanding of other factors that contribute to it is still limited. Recent studies have elucidated the effect of chromatin structure on molecular evolution of genomic DNA. Though the profound impact of nucleosome positions on gene regulation has been reported, their influence on transcriptional evolution is still less explored. With the availability of genome-wide nucleosome map in yeast species, it is thus desirable to investigate their impact on transcription factor binding site evolution. Here, we present a comprehensive analysis of the role of nucleosome positioning in the evolution of transcription factor binding sites.

Results

We compared the transcription factor binding site frequency in nucleosome occupied regions and nucleosome depleted regions in promoters of old (orthologs among Saccharomycetaceae) and young (Saccharomyces specific) genes; and in duplicate gene pairs. We demonstrated that nucleosome occupied regions accommodate greater binding site variations than nucleosome depleted regions in young genes and in duplicate genes. This finding was confirmed by measuring the difference in evolutionary rates of binding sites in sensu stricto yeasts at nucleosome occupied regions and nucleosome depleted regions. The binding sites at nucleosome occupied regions exhibited a consistently higher evolution rate than those at nucleosome depleted regions, corroborating the difference in the selection constraints at the two regions. Finally, through site-directed mutagenesis experiment, we found that binding site gain or loss events at nucleosome depleted regions may cause more expression differences than those in nucleosome occupied regions.

Conclusions

Our study indicates the existence of different selection constraint on binding sites at nucleosome occupied regions than at the nucleosome depleted regions. We found that the binding sites have a different rate of evolution at nucleosome occupied and depleted regions. Finally, using transcription factor binding site-directed mutagenesis experiment, we confirmed the difference in the impact of binding site changes on expression at these regions. Thus, our work demonstrates the importance of composite analysis of chromatin and transcriptional evolution.
The mitochondrial genome sequence of the ciliate Paramecium caudatum reveals a shift in nucleotide composition and codon usage within the genus Paramecium
Authors: Barth Dana , Berendonk Thomas U
Published: May 2011

Background

Despite the fact that the organization of the ciliate mitochondrial genome is exceptional, only few ciliate mitochondrial genomes have been sequenced until today. All ciliate mitochondrial genomes are linear. They are 40 kb to 47 kb long and contain some 50 tightly packed genes without introns. Earlier studies documented that the mitochondrial guanine + cytosine contents are very different between Paramecium tetraurelia and all studied Tetrahymena species. This raises the question of whether the high mitochondrial G+C content observed in P. tetraurelia is a characteristic property of Paramecium mtDNA, or whether it is an exception of the ciliate mitochondrial genomes known so far. To test this question, we determined the mitochondrial genome sequence of Paramecium caudatum and compared the gene content and sequence properties to the closely related P. tetraurelia.

Results

The guanine + cytosine content of the P. caudatum mitochondrial genome was significantly lower than that of P. tetraurelia (22.4% vs. 41.2%). This difference in the mitochondrial nucleotide composition was accompanied by significantly different codon usage patterns in both species, i.e. within P. caudatum clearly A/T ending codons dominated, whereas for P. tetraurelia the synonymous codons were more balanced with a higher number of G/C ending codons. Further analyses indicated that the nucleotide composition of most members of the genus Paramecium resembles that of P. caudatum and that the shift observed in P. tetraurelia is restricted to the P. aurelia species complex.

Conclusions

Surprisingly, the codon usage bias in the P. caudatum mitochondrial genome, exemplified by the effective number of codons, is more similar to the distantly related T. pyriformis and other single-celled eukaryotes such as Chlamydomonas, than to the closely related P. tetraurelia. These differences in base composition and codon usage bias were, however, not reflected in the amino acid composition. Most probably, the observed picture is best explained by a hitherto unknown (neutral or adaptive) mechanism that increased the guanine + cytosine content in P. tetraurelia mtDNA on the one hand, and strong purifying selection on the ancestral amino acid composition on the other hand. These contradicting forces are counterbalanced by a considerably altered codon usage pattern.
In vitro interactions of Candida parapsilosis wild type and lipase deficient mutants with human monocyte derived dendritic cells
Authors: Nagy István , Filkor Kata , Németh Tibor , Hamari Zsuzsanna , Vágvölgyi Csaba , Gácser Attila
Published: May 2011

Background

Candida parapsilosis typically is a commensal of human skin. However, when host immune defense is compromised or the normal microflora balance is disrupted, C. parapsilosis transforms itself into an opportunistic pathogen. Candida-derived lipase has been identified as potential virulence factor. Even though cellular components of the innate immune response, such as dendritic cells, represent the first line of defense against invading pathogens, little is known about the interaction of these cells with invading C. parapsilosis. Thus, the aim of our study was to assess the function of dendritic cells in fighting C. parapsilosis and to determine the role that C. parapsilosis-derived lipase plays in the interaction with dendritic cells.

Results

Monocyte-derived immature and mature dendritic cells (iDCs and mDCs, respectively) co-cultured with live wild type or lipase deficient C. parapsilosis strains were studied to determine the phagocytic capacity and killing efficiency of host cells. We determined that both iDCs and mDCs efficiently phagocytosed and killed C. parapsilosis, furthermore our results show that the phagocytic and fungicidal activities of both iDCs and mDCs are more potent for lipase deficient compared to wild type yeast cells. In addition, the lipase deficient C. parapsilosis cells induce higher gene expression and protein secretion of proinflammatory cytokines and chemokines in both DC types relative to the effect of co-culture with wild type yeast cells.

Conclusions

Our results show that DCs are activated by exposure to C. parapsilosis, as shown by increased phagocytosis, killing and proinflammatory protein secretion. Moreover, these data strongly suggest that C. parapsilosis derived lipase has a protective role during yeast:DC interactions, since lipase production in wt yeast cells decreased the phagocytic capacity and killing efficiency of host cells and downregulated the expression of host effector molecules.
Optimizing the diagnostic power with gastric emptying scintigraphy at multiple time points
Authors: Hou Qingjiang , Lin Zhiyue , Dusing Reginald , Gajewski Byron J , McCallum Richard W , Mayo Matthew S
Published: May 2011

Background

Gastric Emptying Scintigraphy (GES) at intervals over 4 hours after a standardized radio-labeled meal is commonly regarded as the gold standard for diagnosing gastroparesis. The objectives of this study were: 1) to investigate the best time point and the best combination of multiple time points for diagnosing gastroparesis with repeated GES measures, and 2) to contrast and cross-validate Fisher's Linear Discriminant Analysis (LDA), a rank based Distribution Free (DF) approach, and the Classification And Regression Tree (CART) model.

Methods

A total of 320 patients with GES measures at 1, 2, 3, and 4 hour (h) after a standard meal using a standardized method were retrospectively collected. Area under the Receiver Operating Characteristic (ROC) curve and the rate of false classification through jackknife cross-validation were used for model comparison.

Results

Due to strong correlation and an abnormality in data distribution, no substantial improvement in diagnostic power was found with the best linear combination by LDA approach even with data transformation. With DF method, the linear combination of 4-h and 3-h increased the Area Under the Curve (AUC) and decreased the number of false classifications (0.87; 15.0%) over individual time points (0.83, 0.82; 15.6%, 25.3%, for 4-h and 3-h, respectively) at a higher sensitivity level (sensitivity = 0.9). The CART model using 4 hourly GES measurements along with patient's age was the most accurate diagnostic tool (AUC = 0.88, false classification = 13.8%). Patients having a 4-h gastric retention value >10% were 5 times more likely to have gastroparesis (179/207 = 86.5%) than those with ≤10% (18/113 = 15.9%).

Conclusions

With a mixed group of patients either referred with suspected gastroparesis or investigated for other reasons, the CART model is more robust than the LDA and DF approaches, capable of accommodating covariate effects and can be generalized for cross institutional applications, but could be unstable if sample size is limited.
Novel variants in the PRDX6 Gene and the risk of Acute Lung Injury following major trauma
Authors: Rushefski Melanie , Aplenc Richard , Meyer Nuala , Li Mingyao , Feng Rui , Lanken Paul N , Gallop Robert , Bellamy Scarlett , Localio A Russell , Feinstein Sheldon I , Fisher Aron B , Albelda Steven M , Christie Jason D
Published: May 2011

Background

Peroxiredoxin 6 (PRDX6) is involved in redox regulation of the cell and is thought to be protective against oxidant injury. Little is known about genetic variation within the PRDX6 gene and its association with acute lung injury (ALI). In this study we sequenced the PRDX6 gene to uncover common variants, and tested association with ALI following major trauma.

Methods

To examine the extent of variation in the PRDX6 gene, we performed direct sequencing of the 5' UTR, exons, introns and the 3' UTR in 25 African American cases and controls and 23 European American cases and controls (selected from a cohort study of major trauma), which uncovered 80 SNPs. In silico modeling was performed using Patrocles and Transcriptional Element Search System (TESS). Thirty seven novel and tagging SNPs were tested for association with ALI compared with ICU at-risk controls who did not develop ALI in a cohort study of 259 African American and 254 European American subjects that had been admitted to the ICU with major trauma.

Results

Resequencing of critically ill subjects demonstrated 43 novel SNPs not previously reported. Coding regions demonstrated no detectable variation, indicating conservation of the protein. Block haplotype analyses reveal that recombination rates within the gene seem low in both Caucasians and African Americans. Several novel SNPs appeared to have the potential for functional consequence using in silico modeling. Chi2 analysis of ALI incidence and genotype showed no significant association between the SNPs in this study and ALI. Haplotype analysis did not reveal any association beyond single SNP analyses.

Conclusions

This study revealed novel SNPs within the PRDX6 gene and its 5' and 3' flanking regions via direct sequencing. There was no association found between these SNPs and ALI, possibly due to a low sample size, which was limited to detection of relative risks of 1.93 and above. Future studies may focus on the role of PRDX6 genetic variation in other diseases, where oxidative stress is suspected.
Development of an ICF-based eligibility procedure for education in Switzerland
Authors: Hollenweger Judith
Published: May 2011

Starting in January 2011, Switzerland will implement a multidimensional, context-sensitive procedure to establish eligibility in education systems. This paper provides a brief overview of the different eligibility-related practices with a special focus on children with disabilities. The paper then outlines the philosophical and conceptual framework of the eligibility procedure based on the International Classification of Functioning, Disability and Health, and the UN Convention on the Rights of Persons with Disability. The different components and methodology applied to organise information in the process towards establishing eligibility are also presented. Finally, some observations are made regarding transparent and just applications of the eligibility procedure, and the implementation of this new eligibility procedure.
Use of imaging biomarkers to assess perfusion and glucose metabolism in the skeletal muscle of dystrophic mice
Authors: Ahmad Nabeel , Welch Ian , Grange Robert , Hadway Jennifer , Dhanvantari Savita , Hill David , Lee Ting-Yim , Hoffman Lisa M
Published: June 2011

Background

Duchenne muscular dystrophy (DMD) is a severe neuromuscular disease that affects 1 in 3500 boys. The disease is characterized by progressive muscle degeneration that results from mutations in or loss of the cytoskeletal protein, dystrophin, from the glycoprotein membrane complex, thus increasing the susceptibility of contractile muscle to injury. To date, disease progression is typically assessed using invasive techniques such as muscle biopsies, and while there are recent reports of the use of magnetic resonance, ultrasound and optical imaging technologies to address the issue of disease progression and monitoring therapeutic intervention in dystrophic mice, our study aims to validate the use of imaging biomarkers (muscle perfusion and metabolism) in a longitudinal assessment of skeletal muscle degeneration/regeneration in two murine models of muscular dystrophy.

Methods

Wild-type (w.t.) and dystrophic mice (weakly-affected mdx mice that are characterized by a point mutation in dystrophin; severely-affected mdx:utrn-/- (udx) mice that lack functional dystrophin and are null for utrophin) were exercised three times a week for 30 minutes. To follow the progression of DMD, accumulation of18F-FDG, a measure of glucose metabolism, in both wild-type and affected mice was measured with a small animal PET scanner (GE eXplore Vista). To assess changes in blood flow and blood volume in the hind limb skeletal muscle, mice were injected intravenously with a CT contrast agent, and imaged with a small animal CT scanner (GE eXplore Ultra).

Results

In hind limb skeletal muscle of both weakly-affected mdx mice and in severely-affected udx mice, we demonstrate an early, transient increase in both18F-FDG uptake, and in blood flow and blood volume. Histological analysis of H&E-stained tissue collected from parallel littermates demonstrates the presence of both inflammatory infiltrate and centrally-located nuclei, a classic hallmark of myofibrillar regeneration. In both groups of affected mice, the early transient response was succeeded by a progressive decline in muscle perfusion and metabolism; this was also evidenced histologically.

Conclusions

The present study demonstrates the utility of non-invasive imaging biomarkers in characterizing muscle degeneration/regeneration in murine models of DMD. These techniques may now provide a promising alternative for assessing both disease progression and the efficacy of new therapeutic treatments in patients.
Immunocytochemical characterisation of cultures of human bladder mucosal cells
Authors: Woodman Jacqueline R , Mansfield Kylie J , Lazzaro Vittoria A , Lynch William , Burcher Elizabeth , Moore Kate H
Published: May 2011

Background

The functional role of the bladder urothelium has been the focus of much recent research. The bladder mucosa contains two significant cell types: urothelial cells that line the bladder lumen and suburothelial interstitial cells or myofibroblasts. The aims of this study were to culture these cell populations from human bladder biopsies and to perform immunocytochemical characterisation.

Methods

Primary cell cultures were established from human bladder biopsies (n = 10). Individual populations of urothelial and myofibroblast-like cells were isolated using magnetic activated cell separation (MACS). Cells were slow growing, needing 3 to 5 weeks to attain confluence.

Results

Cytokeratin 20 positive cells (umbrella cells) were isolated at primary culture and also from patients' bladder washings but these did not proliferate. In primary culture, proliferating cells demonstrated positive immunocytochemical staining to cytokeratin markers (AE1/AE3 and A0575) as well fibroblasts (5B5) and smooth muscle (αSMA) markers. An unexpected finding was that populations of presumptive urothelial and myofibroblast-like cells, isolated using the MACS beads, stained for similar markers. In contrast, staining for cytokeratins and fibroblast or smooth muscle markers was not co-localised in full thickness bladder sections.

Conclusions

Our results suggest that, in culture, bladder mucosal cells may undergo differentiation into a myoepithelial cell phenotype indicating that urothelial cells have the capacity to respond to environmental changes. This may be important pathologically but also suggests that studies of the physiological function of these cells in culture may not give a reliable indicator of human physiology.
Premenstrual symptoms in young adults born preterm at very low birth weight - from the Helsinki Study of Very Low Birth Weight Adults
Authors: Mustaniemi Sanna , Sipola-Leppänen Marika , Hovi Petteri , Halbreich Uriel , Vääräsmäki Marja , Räikkönen Katri , Pesonen Anu-Katriina , Heinonen Kati , Järvenpää Anna-Liisa , Eriksson Johan G , Andersson Sture , Kajantie Eero
Published: June 2011

Background

Clinically significant premenstrual symptoms are common among young women. Premenstrual syndrome (PMS) is characterized by emotional, behavioural and physical symptoms that consistently occur during the luteal phase of the menstrual cycle. Premenstrual dysphoric disorder (PMDD) is a severe form of PMS. Individual variation in stress responsiveness may be involved in the pathophysiology of premenstrual symptoms. Preterm birth at very low birth weight (VLBW, < 1500g) has a multitude of consequences that extend to adult life, including altered stress responsiveness which could affect the prevalence of premenstrual symptoms.

Methods

In this cohort study, we compared 75 VLBW women with 95 women born at term (mean age 22.5). We used a standardized retrospective questionnaire assessing the presence and severity of a variety of symptoms before and after menses. The symptom scores were used both as continuous and as dichotomized variables, with cutoffs based on DSM-IV criteria for PMDD and ACOG criteria for PMS, except prospective daily ratings could not be used. We used multiple linear and logistic regression to adjust for confounders.

Results

There was no difference in the continuous symptom score before menses (mean difference VLBW-term -18.3%, 95% confidence interval -37.9 to 7.5%) or after menses. The prevalence of premenstrual symptoms causing severe impairment to daily life was 13.3% for VLBW women and 14.7% for control women. For PMDD, it was 8.0% and 4.2%, and for PMS, 12.0% and 11.6%, respectively. These differences were not statistically significant (p > 0.1).

Conclusion

Our findings suggest that the severity of premenstrual symptoms and the prevalence of PMDD and PMS among young women born preterm at VLBW is not higher than among those born at term.
Health service utilization in IBD: comparison of self-report and administrative data
Authors: Longobardi Teresa , Walker John R , Graff Lesley A , Bernstein Charles N
Published: May 2011

Background

The reliability of self-report regarding health care utilization in inflammatory bowel disease (IBD) is unknown. If proven reliable, it could help justify self-report as a means of determining health care utilization and associated costs.

Methods

The Manitoba IBD Cohort Study is a population-based longitudinal study of participants diagnosed within 7 years of enrollment. Health care utilization was assessed through standardized interview. Participants (n = 352) reported the total number of nights hospitalized, frequency of physician contacts in the prior 12 months and whether the medical contacts were for IBD-related reasons or not. Reports of recent antibiotic use were also recorded. Actual utilization was drawn from the administrative database of Manitoba Health, the single comprehensive provincial health insurer.

Results

According to the administrative data, 15% of respondents had an overnight hospitalization, while 10% had an IBD-related hospitalization. Self-report concordance was highly sensitive (92%; 82%) and specific (96%; 97%, respectively). 97% of participants had contact with a physician in the previous year, and 69% had IBD-related visits. Physician visits were significantly under-reported and there was a trend to over-report the number of nights in hospital.

Conclusions

Self-report data can be helpful in evaluating health service utilization, provided that the researcher is aware of the systematic sources of bias. Outpatient visits are well identified by self-report. The discordance for the type of outpatient visit may be either a weakness of self-report or a flaw in diagnosis coding of the administrative data. If administrative data are not available, self-report information may be a cost-effective alternative, particularly for hospitalizations.
A novel family VII esterase with industrial potential from compost metagenomic library
Authors: Kang Chul-Hyung , Oh Ki-Hoon , Lee Mi-Hwa , Oh Tae-Kwang , Kim Bong Hee , Yoon Jung- Hoon
Published: May 2011

Background

Among the vast microbial genomic resources now available, most microbes are unculturable in the laboratory. A culture-independent metagenomic approach is a novel technique that circumvents this culture limitation. For the screening of novel lipolytic enzymes, a metagenomic library was constructed from compost, and the clone of estCS2 was selected for lipolytic properties on a tributyrin-containing medium.

Results

The estCS2 sequence encodes a protein of 570 amino acid residues, with a predicted molecular mass of 63 kDa, and based on amino acid identity it most closely matches (45%) the carboxylesterase from Haliangium ochraceum DSM 14365. EstCS2 belong to family VII, according to the lipolytic enzyme classification proposed by Arpigny and Jaeger, and it retains the catalytic triad Ser245-Glu363-His466 that is typical of an α/β hydrolase. The Ser245 residue in the catalytic triad of EstCS2 is located in the consensus active site motif GXSXG. The EstCS2 exhibits strong activity toward p-nitrophenyl caproate (C6), and it is stable up to 60°C with an optimal enzymatic activity at 55°C. The maximal activity is observed at pH 9, and it remains active between pH 6-10. EstCS2 shows remarkable stability in up to 50% (v/v) dimethyl sulfoxide (DMSO) or dimethylformamide (DMF). The enzyme has the ability to cleave sterically hindered esters of tertiary alcohol, as well as to degrade polyurethanes, which are widely used in various industries.

Conclusions

The high stability of EstCS2 in organic solvents and its activity towards esters of ketoprofen and tertiary alcohols, and in polyurethane suggests that it has potential uses for many applications in biotransformation and bioremediation.
Fabrication of HfO2 patterns by laser interference nanolithography and selective dry etching for III-V CMOS application
Authors: Benedicto Marcos , Galiana Beatriz , Molina-Aldareguia Jon M , Monaghan Scott , Hurley Paul K , Cherkaoui Karim , Vazquez Luis , Tejedor Paloma
Published: May 2011

Nanostructuring of ultrathin HfO2 films deposited on GaAs (001) substrates by high-resolution Lloyd's mirror laser interference nanolithography is described. Pattern transfer to the HfO2 film was carried out by reactive ion beam etching using CF4 and O2 plasmas. A combination of atomic force microscopy, high-resolution scanning electron microscopy, high-resolution transmission electron microscopy, and energy-dispersive X-ray spectroscopy microanalysis was used to characterise the various etching steps of the process and the resulting HfO2/GaAs pattern morphology, structure, and chemical composition. We show that the patterning process can be applied to fabricate uniform arrays of HfO2 mesa stripes with tapered sidewalls and linewidths of 100 nm. The exposed GaAs trenches were found to be residue-free and atomically smooth with a root-mean-square line roughness of 0.18 nm after plasma etching.

PACS: Dielectric oxides 77.84.Bw, Nanoscale pattern formation 81.16.Rf, Plasma etching 52.77.Bn, Fabrication of III-V semiconductors 81.05.Ea
A novel deconvolution method for modeling UDP-N-acetyl-D-glucosamine biosynthetic pathways based on 13C mass isotopologue profiles under non-steady-state conditions
Authors: Moseley Hunter NB , Lane Andrew N , Belshoff Alex C , Higashi Richard M , Fan Teresa WM
Published: May 2011

Background

Stable isotope tracing is a powerful technique for following the fate of individual atoms through metabolic pathways. Measuring isotopic enrichment in metabolites provides quantitative insights into the biosynthetic network and enables flux analysis as a function of external perturbations. NMR and mass spectrometry are the techniques of choice for global profiling of stable isotope labeling patterns in cellular metabolites. However, meaningful biochemical interpretation of the labeling data requires both quantitative analysis and complex modeling. Here, we demonstrate a novel approach that involved acquiring and modeling the timecourses of 13C isotopologue data for UDP-N-acetyl-D-glucosamine (UDP-GlcNAc) synthesized from [U-13C]-glucose in human prostate cancer LnCaP-LN3 cells. UDP-GlcNAc is an activated building block for protein glycosylation, which is an important regulatory mechanism in the development of many prominent human diseases including cancer and diabetes.

Results

We utilized a stable isotope resolved metabolomics (SIRM) approach to determine the timecourse of 13C incorporation from [U-13C]-glucose into UDP-GlcNAc in LnCaP-LN3 cells. 13C Positional isotopomers and isotopologues of UDP-GlcNAc were determined by high resolution NMR and Fourier transform-ion cyclotron resonance-mass spectrometry. A novel simulated annealing/genetic algorithm, called 'Genetic Algorithm for Isotopologues in Metabolic Systems' (GAIMS) was developed to find the optimal solutions to a set of simultaneous equations that represent the isotopologue compositions, which is a mixture of isotopomer species. The best model was selected based on information theory. The output comprises the timecourse of the individual labeled species, which was deconvoluted into labeled metabolic units, namely glucose, ribose, acetyl and uracil. The performance of the algorithm was demonstrated by validating the computed fractional 13C enrichment in these subunits against experimental data. The reproducibility and robustness of the deconvolution were verified by replicate experiments, extensive statistical analyses, and cross-validation against NMR data.

Conclusions

This computational approach revealed the relative fluxes through the different biosynthetic pathways of UDP-GlcNAc, which comprises simultaneous sequential and parallel reactions, providing new insight into the regulation of UDP-GlcNAc levels and O-linked protein glycosylation. This is the first such analysis of UDP-GlcNAc dynamics, and the approach is generally applicable to other complex metabolites comprising distinct metabolic subunits, where sufficient numbers of isotopologues can be unambiguously resolved and accurately measured.
Co-expression of Ubiquitin gene and capsid protein gene enhances the potency of DNA immunization of PCV2 in mice
Authors: Fu Fang , Li Xuesong , Lang Yuekun , Yang Yuju , Tong Guangzhi , Li Guoxin , Zhou Yanjun , Li Xi
Published: May 2011

A recombinant plasmid that co-expressed ubiquitin and porcine circovirus type 2 (PCV2) virus capsid protein (Cap), denoted as pc-Ub-Cap, and a plasmid encoding PCV2 virus Cap alone, denoted as pc-Cap, were transfected into 293T cells. Indirect immunofluorescence (IIF) and confocal microscopy were performed to measure the cellular expression of Cap. Three groups of mice were then vaccinated once every three weeks for a total of three doses with pc-Ub-Cap, pc-Cap or the empty vector pCAGGS, followed by challenging all mice intraperitoneally with 0.5 mL 106.5TCID50/mL PCV2. To characterize the protective immune response against PCV2 infection in mice, assays of antibody titer (including different IgG isotypes), flow cytometric analysis (FCM), lymphocyte proliferation, cytokine production and viremia were evaluated. The results showed that pc-Ub-Cap and pc-Cap were efficiently expressed in 293T cells. However, pc-Ub-Cap-vaccinated animals had a significantly higher level of Cap-specific antibody and induced a stronger Th1 type cellular immune response than did pc-Cap-vaccinated animals, suggesting that ubiquitin conjugation improved both the cellular and humoral immune responses. Additionally, viral replication in blood was lower in the pc-Ub-Cap-vaccinated group than in the pc-Cap and empty vector groups, suggesting that the protective immunity induced by pc-Ub-Cap is superior to that induced by pc-Cap.