bluuebunny/crossref_metadata_2025 huggingface dataset:
Reading, Why Not? Literacy Skills in Children With Motor and Speech Impairments
Authors: Ferreira Janna , Rönnberg Jerker , Gustafson Stefan , Wengelin Åsa
Published: March 2008

In this study, 12 participants with various levels of motor and speech deficits were tested to explore their reading skills in relation to letter knowledge, speech level, auditory discrimination, phonological awareness, language skills, digit span, and nonverbal IQ. Two subgroups, based on a median split of reading performance, are described: the low- and high-level readers, where low-level readers perform significantly lower on reading than the other subgroup. The subgroups had a general tendency to perform low versus high on most variables tested, but not on digit span. The study stresses the importance of auditory discrimination skills and general language skills as a fundamental base for literacy. The study also generates new hypotheses that will need to be investigated further. For example, further intervention studies for phonological awareness are proposed, and a hypothesis about the effect of impaired articulation usage during reading is presented.
Phonological Awareness Abilities of 6-Year-Old Children With Mild to Moderate Phonological Impairments
Authors: Gernand Keri Leigh , Moran Michael J.
Published: March 2008

Standardized and nonstandardized assessments of phonological awareness skills were administered to two groups of 6-year-old children. Group 1 passed a language screening but exhibited mild or moderate phonological impairments on the Assessment of Phonological Processes—Revised. Group 2 passed a language screening and exhibited no phonological errors. Results indicated that the children with phonological errors performed significantly more poorly on both the standardized and the nonstandardized tests of phonological awareness. This study provides further evidence that children with relatively mild phonological problems independent of concomitant language disorders should be considered at risk for phonological awareness problems.
Men's Soaps
Authors: Carroll Hamilton
Published: March 2008

In this paper I argue that the Discovery Channel's reality-based automotive show American Chopper produces a recuperative blue-collar masculinity that attenuates the putative losses suffered by working-class men under the postindustrial service economy of the contemporary United States. In its on-screen presentation of blue-collar work, American Chopper valorizes a form of working-class manual labor at precisely the moment when such labor has all but disappeared in the United States. In its presentation of a world of masculine labor and fraternal affect, American Chopper constructs a nostalgic world of blue-collar work in which the skilled manual laborer—always understood to be male—still reigns supreme, untroubled by the supposed defeats suffered by hegemonic masculinity in the post-civil rights era. By celebrating neoliberal consumer capital and the traditional consumption of the American dream as coterminous discourses of celebrity identity, the show elides the still vast gaps in opportunity and remuneration in the contemporary United States.
Prevalence and Significance of G6PD Deficiency in Patients of an Urban HIV Clinic
Authors: Tungsiripat Marisa , Drechsler Henning , Sarlone Christine , Amyot Kathleen , Laffey Elizabeth , Aberg Judith
Published: March 2008

The rationale to screen for glucose-6-phosphate dehydrogenase (G6PD) deficiency in HIV-infected individuals is their increased likelihood to receive oxidant drugs and subsequent potential of hemolytic events. However, current guidelines regarding who should be screened are conflicting. The authors examined the prevalence of G6PD deficiency and the frequency of hemolytic events in an urban HIV clinic. They used data from a military database as a comparison. In both cohorts, a relatively high number of black females were found to be G6PD deficient (10% and 13%), which was similar to the rate in men (15% and 12%). No white females were G6PD deficient. The authors identified 8 drug-related hemolytic events in HIV clinic patients. Two patients necessitated blood transfusions; both were triggered by trimethoprim/sulfamethoxazole (TMP/SMX). Although G6PD screening prior to the use of TMP/SMX is not often considered by clinicians, the authors' finding of 2 hemolytic events requiring transfusion suggests this would be beneficial.
Transcranial Sonogram Through a Sutural Fracture for the Assessment of Posttraumatic Intracranial Mass Lesion in a Child
Authors: Nottidge Tim , Edemekong Inuasit , Emejulu Jude , Shokunbi Tayo
Published: March 2008

The authors present the case of a 7-year-old child with moderate head injury and a closed skull fracture managed nonoperatively. A sonogram through the skull fracture was valuable in determining that there was no significant posttraumatic intracranial mass lesion. The boy was discharged home fully conscious and ambulant and with a mild left hemiparesis.
Anacardic acid (6-nonadecyl salicylic acid), an inhibitor of histone acetyltransferase, suppresses expression of nuclear factor-κB–regulated gene products involved in cell survival, proliferation, invasion, and inflammation through inhibition of the inhibitory subunit of nuclear factor-κBα kinase, leading to potentiation of apoptosis
Authors: Sung Bokyung , Pandey Manoj K. , Ahn Kwang Seok , Yi Tingfang , Chaturvedi Madan M. , Liu Mingyao , Aggarwal Bharat B.
Published: March 2008

Anacardic acid (6-pentadecylsalicylic acid) is derived from traditional medicinal plants, such as cashew nuts, and has been linked to anticancer, anti-inflammatory, and radiosensitization activities through a mechanism that is not yet fully understood. Because of the role of nuclear factor-κB (NF-κB) activation in these cellular responses, we postulated that anacardic acid might interfere with this pathway. We found that this salicylic acid potentiated the apoptosis induced by cytokine and chemotherapeutic agents, which correlated with the down-regulation of various gene products that mediate proliferation (cyclin D1 and cyclooxygenase-2), survival (Bcl-2, Bcl-xL, cFLIP, cIAP-1, and survivin), invasion (matrix metalloproteinase-9 and intercellular adhesion molecule-1), and angiogenesis (vascular endothelial growth factor), all known to be regulated by the NF-κB. We found that anacardic acid inhibited both inducible and constitutive NF-κB activation; suppressed the activation of IκBα kinase that led to abrogation of phosphorylation and degradation of IκBα; inhibited acetylation and nuclear translocation of p65; and suppressed NF-κB–dependent reporter gene expression. Down-regulation of the p300 histone acetyltransferase gene by RNA interference abrogated the effect of anacardic acid on NF-κB suppression, suggesting the critical role of this enzyme. Overall, our results demonstrate a novel role for anacardic acid in potentially preventing or treating cancer through modulation of NF-κB signaling pathway.
EPO receptor circuits for primary erythroblast survival
Authors: Sathyanarayana Pradeep , Dev Arvind , Fang Jing , Houde Estelle , Bogacheva Olga , Bogachev Oleg , Menon Madhu , Browne Sarah , Pradeep Anamika , Emerson Christine , Wojchowski Don M.
Published: March 2008

EPO functions primarily as an erythroblast survival factor, and its antiapoptotic actions have been proposed to involve predominantly PI3-kinase and BCL-X pathways. Presently, the nature of EPO-regulated survival genes has been investigated through transcriptome analyses of highly responsive, primary bone marrow erythroblasts. Two proapoptotic factors, Bim and FoxO3a, were rapidly repressed not only via the wild-type EPOR, but also by PY-deficient knocked-in EPOR alleles. In parallel, Pim1 and Pim3 kinases and Irs2 were induced. For this survival gene set, induction failed via a PY-null EPOR-HM allele, but was restored upon reconstitution of a PY343 STAT5–binding site within a related EPOR-H allele. Notably, EPOR-HM supports erythropoiesis at steady state but not during anemia, while EPOR-H exhibits near wild-type EPOR activities. EPOR-H and the wild-type EPOR (but not EPOR-HM) also markedly stimulated the expression of Trb3 pseudokinase, and intracellular serpin, Serpina-3G. For SERPINA-3G and TRB3, ectopic expression in EPO-dependent progenitors furthermore significantly inhibited apoptosis due to cytokine withdrawal. BCL-XL and BCL2 also were studied, but in highly responsive KitposCD71highTer119neg erythroblasts, neither was EPO modulated. EPOR survival circuits therefore include the repression of Bim plus FoxO3a, and EPOR/PY343/STAT5-dependent stimulation of Pim1, Pim3, Irs2 plus Serpina-3G, and Trb3 as new antiapoptotic effectors.
Epigenetic control of MHC class II expression in tumor-associated macrophages by decoy receptor 3
Authors: Chang Yung-Chi , Chen Tse-Ching , Lee Chun-Ting , Yang Chih-Ya , Wang Hsei-Wei , Wang Chao-Ching , Hsieh Shie-Liang
Published: March 2008

Decoy receptor 3 (DcR3) is a member of the TNF receptor superfamily and is up-regulated in tumors originating from a diversity of lineages. DcR3 is capable of promoting angiogenesis, inducing dendritic cell apoptosis, and modulating macrophage differentiation. Since tumor-associated macrophages (TAMs) are the major infiltrating leukocytes in most malignant tumors, we used microarray technology to investigate whether DcR3 contributes to the development of TAMs. Among the DcR3-modulated genes expressed by TAMs, those that encode proteins involved in MHC class II (MHC-II)–dependent antigen presentation were down-regulated substantially, together with the master regulator of MHC-II expression (the class II transactivator, CIITA). The ERK- and JNK-induced deacetylation of histones associated with the CIITA promoters was responsible for DcR3-mediated down-regulation of MHC-II expression. Furthermore, the expression level of DcR3 in cancer cells correlated inversely with HLA-DR levels on TAMs and with the overall survival time of pancreatic cancer patients. The role of DcR3 in the development of TAMs was further confirmed using transgenic mice overexpressing DcR3. This elucidates the molecular mechanism of impaired MHC-II–mediated antigen presentation by TAMs, and raises the possibility that subversion of TAM-induced immunosuppression via inhibition of DcR3 expression might represent a target for the design of new therapeutics.
Exploration and visualization of gene expression with neuroanatomy in the adult mouse brain
Authors: Lau Christopher , Ng Lydia , Thompson Carol , Pathak Sayan , Kuan Leonard , Jones Allan , Hawrylycz Mike
Published: March 2008

Background

Spatially mapped large scale gene expression databases enable quantitative comparison of data measurements across genes, anatomy, and phenotype. In most ongoing efforts to study gene expression in the mammalian brain, significant resources are applied to the mapping and visualization of data. This paper describes the implementation and utility of Brain Explorer, a 3D visualization tool for studying in situ hybridization-based (ISH) expression patterns in the Allen Brain Atlas, a genome-wide survey of 21,000 expression patterns in the C57BL\6J adult mouse brain.

Results

Brain Explorer enables users to visualize gene expression data from the C57Bl/6J mouse brain in 3D at a resolution of 100 μm3, allowing co-display of several experiments as well as 179 reference neuro-anatomical structures. Brain Explorer also allows viewing of the original ISH images referenced from any point in a 3D data set. Anatomic and spatial homology searches can be performed from the application to find data sets with expression in specific structures and with similar expression patterns. This latter feature allows for anatomy independent queries and genome wide expression correlation studies.

Conclusion

These tools offer convenient access to detailed expression information in the adult mouse brain and the ability to perform data mining and visualization of gene expression and neuroanatomy in an integrated manner.
Development of a novel data mining tool to find cis-elements in rice gene promoter regions
Authors: Doi Koji , Hosaka Aeni , Nagata Toshifumi , Satoh Kouji , Suzuki Kohji , Mauleon Ramil , Mendoza Michael J , Bruskiewich Richard , Kikuchi Shoshi
Published: March 2008

Background

Information on more than 35 000 full-length Oryza sativa cDNAs, together with associated microarray gene expression data collected under various treatment conditions, has made it feasible to identify motifs that are conserved in gene promoters and may act as cis-regulatory elements with key roles under the various conditions.

Results

We have developed a novel tool that searches for cis-element candidates in the upstream, downstream, or coding regions of differentially regulated genes. The tool first lists cis-element candidates by motif searching based on the supposition that if there are cis-elements playing important roles in the regulation of a given set of genes, they will be statistically overrepresented and will be conserved. Then it evaluates the likelihood scores of the listed candidate motifs by association rule analysis. This strategy depends on the idea that motifs overrepresented in the promoter region could play specific roles in the regulation of expression of these genes. The tool is designed so that any biological researchers can use it easily at the publicly accessible Internet site http://hpc.irri.cgiar.org/tool/nias/ces. We evaluated the accuracy and utility of the tool by using a dataset of auxin-inducible genes that have well-studied cis-elements. The test showed the effectiveness of the tool in identifying significant relationships between cis-element candidates and related sets of genes.

Conclusion

The tool lists possible cis-element motifs corresponding to genes of interest, and it will contribute to the deeper understanding of gene regulatory mechanisms in plants.
Aminopeptidase N (APN)/CD13 inhibitor, Ubenimex, enhances radiation sensitivity in human cervical cancer
Authors: Tsukamoto Hirohisa , Shibata Kiyosumi , Kajiyama Hiroaki , Terauchi Mikio , Nawa Akihiro , Kikkawa Fumitaka
Published: March 2008

Background

Radiotherapy can be used to treat all stages of cervical cancer. For improving local control via radiotherapy, it is important to use additional antitumor agents. Aminopeptidase N (APN)/CD13, a 150-kDa metalloproteinase, is a multifunctional cell surface aminopeptidase with ubiquitous expression. Recent studies have suggested that APN/CD13 plays an important role in tumor progression in several human malignancies.

Methods

We investigated whether the suppression of APN/CD13 using Ubenimex, an inhibitor of APN/CD13 activity, may affect tumor radiosensitivity in cervical cancer cells both in vitro and in vivo. Cell surface APN/CD13 activity in HeLa cells was calculated using alanine-p-nitroanilido as a substrate. For colony formation assays, single-dose radiation and/or Ubenimex were administered to each dish of HeLa cells, and these dishes were cultured for 14 days. Molecular changes of apoptosis were determined by Western blot. Apoptosis was evaluated by Annexin-V PI staining (flow cytometry analysis) and the Tunel method. Moreover, we investigated the effect of combining Ubenimex and low-dose radiation on tumor growth using nude mice.

Results

We demonstrated that Ubenimex enhanced the effectiveness of radiotherapy, acting as a radiosensitizer both in vitro and in vivo. In colony formation assays, a significant decline in clonogenic survival was observed in Ubenimex-treated cells. Mice treated with a combination of radiation and Ubenimex showed a significant prolongation of the tumor-doubling time compared with the control, Ubenimex, or radiation-alone groups. We also showed that ubenimex enhanced radiation-induced apoptosis in vitro and in vivo.

Conclusion

Although further studies are needed, this report suggests that Ubeniemx acts as a radiosensitizer in cervical cancer treatment, and that the inhibition of APN/CD13 activity may represent a new approach for improving the therapeutic efficacy of radiotherapy for uterine cervical cancer.
Transient expression of homologous hairpin RNA interferes with PVY transmission by aphids
Authors: Vargas Marisol , Martínez-García Belén , Díaz-Ruíz José Ramón , Tenllado Francisco
Published: March 2008

Hairpin RNAs have been used to confer resistance to viruses in plants through RNA silencing. However, it has not been demonstrated that RNA silencing was effective against inoculation by aphids of non-persistently transmitted viruses, the major route of plant virus spread in nature. As a proof-of-principle strategy, we made use of Agrobacterium tumefaciens to transiently express a hairpin RNA homologous to Potato virus Y (PVY) in plant tissues. A complete and specific interference with aphid transmission of PVY was achieved by inducers of RNA silencing, as demonstrated by specific siRNAs accumulation in agroinfiltrated tissues. To our knowledge, this is the first report of successful interference with non-persistent transmission of a plant virus using RNA interference.
Immediate gain is long-term loss: Are there foresighted decision makers in the Iowa Gambling Task?
Authors: Chiu Yao-Chu , Lin Ching-Hung , Huang Jong-Tsun , Lin Shuyeu , Lee Po-Lei , Hsieh Jen-Chuen
Published: March 2008

Background

The Somatic Marker Hypothesis suggests that normal subjects are "foreseeable" and ventromedial prefrontal patients are "myopic" in making decisions, as the behavior shown in the Iowa Gambling Task. The present study questions previous findings because of the existing confounding between long-term outcome (expected value, EV) and gain-loss frequency variables in the Iowa Gambling Task (IGT). A newly and symmetrically designed gamble, namely the Soochow Gambling Task (SGT), with a high-contrast EV between bad (A, B) and good (C, D) decks, is conducted to clarify the issue about IGT confounding. Based on the prediction of EV (a basic assumption of IGT), participants should prefer to choose good decks C and D rather than bad decks A and B in SGT. In contrast, according to the prediction of gain-loss frequency, subjects should prefer the decks A and B because they possessed relatively the high-frequency gain.

Methods

The present experiment was performed by 48 participants (24 males and 24 females). Most subjects are college students recruited from different schools. Each subject played the computer version SGT first and completed a questionnaire for identifying their final preference. The IGT experimental procedure was mostly followed to assure a similar condition of decision uncertainty.

Results

The SGT experiment demonstrated that the prediction of gain-loss frequency is confirmed. Most subjects preferred to choose the bad decks A and B than good decks C and D. The learning curve and questionnaire data indicate that subjects can not "hunch" the EV throughout the game. Further analysis of the effect of previous choice demonstrated that immediate gain increases the probability to stay at the same deck.

Conclusion

SGT provides a balanced structure to clarify the confounding inside IGT and demonstrates that gain-loss frequency rather than EV guides decision makers in these high-ambiguity gambles. Additionally, the choice behavior is mostly following the "gain-stay, lose-randomize" strategy to cope with the uncertain situation. As demonstrated in SGT, immediate gain can bring about a long-term loss under uncertainty. This empirical result may explain some shortsighted behaviors in real life.
VATS intraoperative tattooing to facilitate solitary pulmonary nodule resection
Authors: Willekes Lourens , Boutros Cherif , Goldfarb Michael A.
Published: March 2008

Introduction

Video-assisted thoracic surgery (VATS) has become routine and widely accepted for the removal of solitary pulmonary nodules of unknown etiology. Thoracosopic techniques continue to evolve with better instruments, robotic applications, and increased patient acceptance and awareness.

Several techniques have been described to localize peripheral pulmonary nodules, including pre-operative CT-guided tattooing with methylene blue, CT scan guided spiral/hook wire placement, and transthoracic ultrasound.

As pulmonary surgeons well know, the lung and visceral pleura may appear featureless on top of a pulmonary nodule.

Case description

This paper presents a rapid, direct and inexpensive approach to peripheral lung lesion resection by marking the lung parenchyma on top of the nodule using direct methylene blue injection.

Methods

In two patients with peripherally located lung nodules (n = 3) scheduled for VATS, we used direct methylene blue injection for intraoperative localization of the pulmonary nodule. Our technique was the following: After finger palpation of the lung, a spinal 25 gauge needle was inserted through an existing port and 0.1 ml of methylene blue was used to tattoo the pleura perpendicular to the localized nodule.

The methylene blue tattoo immediately marks the lung surface over the nodule. The surgeon avoids repeated finger palpation, while lining up stapler, graspers and camera, because of the visible tattoo. Our technique eliminates regrasping and repalpating the lung once again to identify a non marked lesion.

Results

Three lung nodules were resected in two patients. Once each lesion was palpated it was marked, and the area was resected with security of accurate localization. All lung nodules were resected in totality with normal lung parenchymal margins. Our technique added about one minute to the operative time. The two patients were discharged home on the second postoperative day, with no morbidity.

Conclusion

VATS with intraoperative tattooing is a safe, easy, and accurate technique to streamline and efficiently resect solitary pulmonary nodules.
A Perl toolkit for LIMS development
Authors: Morris James A , Gayther Simon A , Jacobs Ian J , Jones Christopher
Published: March 2008

Background

High throughput laboratory techniques generate huge quantities of scientific data. Laboratory Information Management Systems (LIMS) are a necessary requirement, dealing with sample tracking, data storage and data reporting. Commercial LIMS solutions are available, but these can be both costly and overly complex for the task. The development of bespoke LIMS solutions offers a number of advantages, including the flexibility to fulfil all a laboratory's requirements at a fraction of the price of a commercial system. The programming language Perl is a perfect development solution for LIMS applications because of Perl's powerful but simple to use database and web interaction, it is also well known for enabling rapid application development and deployment, and boasts a very active and helpful developer community. The development of an in house LIMS from scratch however can take considerable time and resources, so programming tools that enable the rapid development of LIMS applications are essential but there are currently no LIMS development tools for Perl.

Results

We have developed ArrayPipeline, a Perl toolkit providing object oriented methods that facilitate the rapid development of bespoke LIMS applications. The toolkit includes Perl objects that encapsulate key components of a LIMS, providing methods for creating interactive web pages, interacting with databases, error tracking and reporting, and user and session management. The MT_Plate object provides methods for manipulation and management of microtitre plates, while a given LIMS can be encapsulated by extension of the core modules, providing system specific methods for database interaction and web page management.

Conclusion

This important addition to the Perl developer's library will make the development of in house LIMS applications quicker and easier encouraging laboratories to create bespoke LIMS applications to meet their specific data management requirements.
Takayasu's arteritis associated with Crohn's disease: a case report
Authors: Daryani Nasser E , Habibi Atoosa Nayer , Bashashati Mohammad , Keramati Mohammad Reza , Rafiee Moezedin Javad , Ajdarkosh Hossein , Azmi Mehrdad
Published: March 2008

Introduction

The simultaneous presence of Takayasu's arteritis and Crohn's disease in a patient seems to be rare. To our knowledge, no patient with the combination of Crohn's disease and Takayasu's arteritis has been reported from our region.

Case presentation

Herein we present the case of a 22-year-old Iranian woman previously diagnosed as Crohn's disease and who had subsequently developed Takayasu's arteritis.

Conclusion

Clinical suspicion, proper imaging, and consideration of the differential diagnosis are important for the correct diagnosis and management of patients with this coincidence.
Resting CD4+effector memory T cells are precursors of bystander-activated effectors: a surrogate model of rheumatoid arthritis synovial T-cell function
Authors: Brennan Fionula M , Smith Nicola MG , Owen Sally , Li Ching , Amjadi Parisa , Green Patricia , Andersson Anna , Palfreeman Andrew C , Hillyer Philippa , Foey Andrew , Beech Jonathan T , Feldmann Marc
Published: March 2008

Background

Previously we described a system whereby human peripheral blood T cells stimulated for 8 days in a cytokine cocktail acquired effector function for contact-dependent induction of proinflammatory cytokines from monocytes. We termed these cells cytokine-activated (Tck) cells and found that the signalling pathways elicited in the responding monocytes were identical whether they were placed in contact with Tck cells or with T cells isolated from rheumatoid arthritis (RA) synovial tissue.

Methods

Here, using magnetic beads and fluorescence-activated cell sorting, we extensively phenotype the Tck effector cells and conclude that effector function resides within the CD4+CD45RO+, CCR7-, CD49dhigh population, and that these cells are derived from the effector memory CD4+ T cells in resting blood.

Results

After stimulation in culture, these cells produce a wide range of T-cell cytokines, undergo proliferation and differentiate to acquire an extensively activated phenotype resembling RA synovial T cells. Blocking antibodies against CD69, CD18, or CD49d resulted in a reduction of tumour necrosis factor-α production from monocytes stimulated with CD4+CD45RO+ Tck cells in the co-culture assay. Moreover, blockade of these ligands also resulted in inhibition of spontaneous tumour necrosis factor-α production in RA synovial mononuclear cell cultures.

Conclusion

Taken together, these data strengthen our understanding of T-cell effector function, highlight the multiple involvement of different cell surface ligands in cell-cell contact and, provide novel insights into the pathogenesis of inflammatory RA disease.
Transcriptional analysis of highly syntenic regions between Medicago truncatula and Glycine max using tiling microarrays
Authors: Li Lei , He Hang , Zhang Juan , Wang Xiangfeng , Bai Sulan , Stolc Viktor , Tongprasit Waraporn , Young Nevin D , Yu Oliver , Deng Xing-Wang
Published: March 2008

Background

Legumes are the third largest family of flowering plants and are unique among crop species in their ability to fix atmospheric nitrogen. As a result of recent genome sequencing efforts, legumes are now one of a few plant families with extensive genomic and transcriptomic data available in multiple species. The unprecedented complexity and impending completeness of these data create opportunities for new approaches to discovery.

Results

We report here a transcriptional analysis in six different organ types of syntenic regions totaling approximately 1 Mb between the legume plants barrel medic (Medicago truncatula) and soybean (Glycine max) using oligonucleotide tiling microarrays. This analysis detected transcription of over 80% of the predicted genes in both species. We also identified 499 and 660 transcriptionally active regions from barrel medic and soybean, respectively, over half of which locate outside of the predicted exons. We used the tiling array data to detect differential gene expression in the six examined organ types and found several genes that are preferentially expressed in the nodule. Further investigation revealed that some collinear genes exhibit different expression patterns between the two species.

Conclusion

These results demonstrate the utility of genome tiling microarrays in generating transcriptomic data to complement computational annotation of the newly available legume genome sequences. The tiling microarray data was further used to quantify gene expression levels in multiple organ types of two related legume species. Further development of this method should provide a new approach to comparative genomics aimed at elucidating genome organization and transcriptional regulation.
A highly accurate discontinuous Galerkin method for complex interfaces between solids and moving fluids
Authors: Käser Martin , Dumbser Michael
Published: March 2008

We have extended a new highly accurate numerical scheme for unstructured 2D and 3D meshes based on the discontinuous Galerkin approach to simulate seismic wave propagation in heterogeneous media containing fluid-solid interfaces. Because of the formulation of the wave equations as a unified first-order hyperbolic system in velocity stress, the fluid can be in movement along the interface. The governing equations within the moving fluid are derived from well-known first principles in fluid mechanics. The discontinuous Galerkin approach allows for jumps of the material parameters and the solution across element interfaces, which are handled by Riemann solvers or numerical fluxes. The use of Riemann solvers at the element interfaces makesthe treatment of the fluid particularly simple bysetting the shearmodulus in the fluid region to zero. No additional compatibility relations, such as vanishing shear stress or continuity of normal stresses, are necessary to couple the solid and fluid along an interface. The Riemann solver automatically recognizes the jump of the material coefficients at the interface and provides the correct numerical fluxes for fluid-solid contacts. Therefore, wave propagation in the entire computational domain containing heterogeneous media, namely moving fluids and elastic solids, can be described by a uniform set of acoustic and elastic wave equations. The accuracy of the proposed scheme is confirmed by comparing numerical results against analytic solutions. The potential of the new method was demonstrated in a 3D model problem typical for marine seismic exploration with a fluid-solid interface determined by a complicated bathymetry.
Insulin-Stimulated Rates of Glucose Uptake in Muscle in Hyperthyroidism: The Importance of Blood Flow
Authors: Dimitriadis George , Mitrou Panayota , Lambadiari Vaia , Boutati Eleni , Maratou Eirini , Koukkou Eftychia , Panagiotakos Demosthenes , Tountas Nikos , Economopoulos Theofanis , Raptis Sotirios A.
Published: March 2008

Background: In hyperthyroidism, although hepatic insulin resistance is well established, information on the effects of insulin on glucose uptake in skeletal muscle is variable.

Methods: To investigate this, a meal was given to nine hyperthyroid (HR) and seven euthyroid (EU) subjects. Blood was withdrawn for 360 min from a forearm deep vein and the radial artery for measurements of insulin and glucose. Forearm blood flow (BF) was measured with strain-gauge plethysmography. Glucose flux was calculated as arteriovenous difference multiplied by BF and fractional glucose extraction as arteriovenous difference divided by arterial glucose concentrations.

Results: Both groups displayed comparable postprandial glucose levels, with the HR having higher insulin levels than the EU. In the forearm of HR vs. EU: 1) glucose flux was similar [area under the curve (AUC)0–360 673 ± 143 vs. 826 ± 157 μmol per 100 ml tissue]; 2) BF was increased (AUC0–360 3076 ± 338 vs. 1745 ± 145 ml per 100 ml tissue, P = 0.005); and 3) fractional glucose extraction was decreased (AUC0–360 14.5 ± 3 vs. 32 ± 5%min, P = 0.03).

Conclusions: These results suggest that, in hyperthyroidism, insulin-stimulated glucose uptake in muscle is impaired; this defect is corrected, at least in part, by the increases in BF.
Akt-mediated phosphorylation of CDK2 regulates its dual role in cell cycle progression and apoptosis
Authors: Maddika Subbareddy , Ande Sudharsana Rao , Wiechec Emilia , Hansen Lise Lotte , Wesselborg Sebastian , Los Marek
Published: March 2008

Here, we show that CDK2, an S-phase cyclin-dependent kinase, is a novel target for Akt during cell cycle progression and apoptosis. Akt phosphorylates CDK2 at threonine 39 residue both in vitro and in vivo. Although CDK2 threonine 39 phosphorylation mediated by Akt enhances cyclin-A binding, it is dispensable for its basal binding and the kinase activity. In addition, for the first time, we report a transient nucleo-cytoplasmic shuttling of Akt during specific stages of the cell cycle, in particular during the late S and G2 phases. The Akt that is re-localized to the nucleus phosphorylates CDK2 and causes the temporary cytoplasmic localization of the CDK2–cyclin-A complex. The CDK2 cytoplasmic redistribution is required for cell progression from S to G2-M phase, because the CDK2 T39A mutant, which lacks the phosphorylation site and is defective in cytoplasmic localization, severely affects cell cycle progression at the transition from S to G2-M. Interestingly, we also show that the Akt/CDK2 pathway is constitutively activated by some anticancer drugs, such as methotrexate and docetaxel, and under these conditions it promotes, rather than represses, cell death. Thus, the constitutive activation of the Akt/CDK2 pathway and changed subcellular localization promotes apoptosis. By contrast, the transient, physiological Akt/CDK2 activation is necessary for cell cycle progression.
Depletion of apical transport proteins perturbs epithelial cyst formation and ciliogenesis
Authors: Torkko Juha M. , Manninen Aki , Schuck Sebastian , Simons Kai
Published: March 2008

Epithelial cells are vital for maintaining the complex architecture and functions of organs in the body. Directed by cues from the extracellular matrix, cells polarize their surface into apical and basolateral domains, and connect by extensive cell-cell junctions to form tightly vowen epithelial layers. In fully polarized cells, primary cilia project from the apical surface. Madin-Darby canine kidney (MDCK) cells provide a model to study organization of cells as monolayers and also in 3D in cysts. In this study retrovirus-mediated RNA interference (RNAi) was used to generate a series of knockdowns (KDs) for proteins implicated in apical transport: annexin-13, caveolin-1, galectin-3, syntaxin-3, syntaxin-2 and VIP17 and/or MAL. Cyst cultures were then employed to study the effects of these KDs on epithelial morphogenesis. Depletion of these proteins by RNAi stalled the development of the apical lumen in cysts and resulted in impaired ciliogenesis. The most severe ciliary defects were observed in annexin-13 and syntaxin-3 KD cysts. Although the phenotypes demonstrate the robustness of the formation of the polarized membrane domains, they indicate the important role of apical membrane biogenesis in epithelial organization.
Growth arrest in human T-cells is controlled by the non-coding RNA growth-arrest-specific transcript 5 (GAS5)
Authors: Mourtada-Maarabouni Mirna , Hedge Vanessa L. , Kirkham Lucy , Farzaneh Farzin , Williams Gwyn T.
Published: March 2008

The control of growth of lymphocyte populations is crucial to the physiological regulation of the immune system, and to the prevention of both leukaemic and autoimmune disease. This control is mediated through modulation of the cell cycle and regulation of cell death. During log-phase growth the rate of proliferation is high and there is a low rate of cell death. As the population density increases, the cell cycle is extended and apoptosis becomes more frequent as the population enters growth arrest. Here, we show that growth-arrest-specific transcript 5 (GAS5) plays an essential role in normal growth arrest in both T-cell lines and non-transformed lymphocytes. Overexpression of GAS5 causes both an increase in apoptosis and a reduction in the rate of progression through the cell-cycle. Consistent with this, downregulation of endogenous GAS5 inhibits apoptosis and maintains a more rapid cell cycle, indicating that GAS5 expression is both necessary and sufficient for normal growth arrest in T-cell lines as well as human peripheral blood T-cells. Control of apoptosis and the cell cycle by GAS5 has significant consequences for disease pathogenesis, because independent studies have already identified GAS5 as an important candidate gene in the development of autoimmune disease.
A benchmark study on rapid prototyping processes and machines: Quantitative comparisons of mechanical properties, accuracy, roughness, speed, and material cost
Authors: Kim G D , Oh Y T
Published: March 2008

Various kinds of layer manufacturing process are available, such as stereo lithography (SL), fused deposition modelling (FDM), Poly-jet, selective laser sintering (SLS), three-dimensional printing (3DP), laminated object manufacturing (LOM), etc. The object of the current study is the quantifications and comparisons of the processes' characteristics using representative apparatus and various materials. Through the tests, mechanical properties, such as tensile and compressive strengths, hardness, impact strength, and heat resistance, and surface roughness, geometric and dimensional accuracy, manufacturing speed, and material costs were compared for each process and machine. It was verified that the SL process is advantageous in hardness, accuracy, and surface roughness and the Poly-jet process in tensile strength at room temperature. The SLS process was advantageous in compressive strength and manufacturing speed, the 3DP process in speed and material costs, and the LOM process in heat resistance. The FDM and LOM processes were superior in impact strength in the scanning direction, but the change of building direction significantly reduced the tensile and impact strengths.
Development of a knowledge-based engineering system for diagnosis and alleviation of defects in aluminium welding
Authors: Tsoukalas V D
Published: March 2008

Defects in aluminium welding that may contribute to the loss of properties comprise cracks, porosity, inclusions, incomplete fusion and penetration, imperfect shape or unacceptable contour, and miscellaneous other defects. Due to the complicated nature of the aluminium welding process, defect formation could be attributed to an infinite number of causes, ranging from process obscurities, inconsistent production procedures, and defective materials to human errors. Therefore, since high quality in aluminium welding is affected by multiple quantitative and chiefly qualitative parameters, aluminium welding requires a sophisticated defect analysis system. A knowledge-based engineering system named WeldES was developed for this purpose and is described in the present work. The WeldES system aims to be used as an industrial tool for the identification, assessment, and correction of defects in the aluminium welding process. The system consists of two modules: the diagnostic module and the adviser module.
Experimental determination of the limiting bulge height in hydromechanical deep drawing
Authors: Khandeparkar T , Liewald M
Published: March 2008

Owing to fluid pressure, the unsupported blank between the punch and the drawing ring is bulged in the direction opposite to the punch movement. The blank is thus drawn over a fluid cushion and does not contact the drawing ring profile radius. The bulge is hence advantageous for ensuring class A surface quality of the workpiece. The blank is stretched bi-axially in the bulged region owing to the acting fluid pressure. This can result in blank fracture at high-fluid counter pressures. High-fluid counter pressures are, however, necessary to achieve higher geometrical accuracies and lower springback. High pressure can also be used to transfer small contours from the punch to the drawn cup. A high-pressure die set for hydraulic bulging has been designed in order to emulate the bulge formation in hydromechanical deep drawing. A series of experiments have been carried out in order to determine the limiting bulge height for different sheet materials. Different punch diameters have been used to determine the influence of drawing clearance on the limiting bulge height. The effect of fluid pressure on the smallest transferable radius has also been investigated. Results thus obtained can be used in determining the dedicated optimal counter pressure curve for a given workpiece geometry, material, and die set combination in order to design a robust computer-aided engineering (CAE) chain for the hydromechanical deep drawing process. Selected representative experimental results for hydromechanical deep drawing of complex part geometries have been shown. The counter pressure curve for hydromechanical deep drawing of the shown cups was selected in conformance to the allowable bulge height for the considered instantaneous sheet material, part shape, and process parameter combination.
Multi-criteria decision-making determination of material gradient for functionally graded material objects fabrication
Authors: Chiu W K , Yu K M
Published: March 2008

In contemporary discrete product design, to fulfil some of the design requirements (such as mechanical, thermal, etc.), the material properties (such as material composition) of a design should be graded so that a functionally graded material (FGM) object is produced. With the advent of solid freeform fabrication (SFF) or layer manufacturing (LM) technologies, FGM objects are now possible and there different modelling schemes are proposed for modelling and representing an FGM object. However, determining the proper material composition of an object is an issue to be considered and methodology must be investigated. In the current paper, a methodology is proposed and used to determine the material composition of the model based on the computer-aided engineering (CAE) analysis results. The issue of material composition selection is formulated as a multi-criteria decision-making (MCDM) problem and one of the MCDM methods — ELECTRE III — is employed in the proposed methodology for identifying the optimal material composition alternative for different regions of the model. Applying the methodology, an FGM object will be produced and a reinforced FGM prototype can be fabricated by an appropriate LM process. Apart from the FGM object, the application of the proposed methodology in rapid tooling (RT) will also be discussed.
Optimum design of partially tapered rectangular thin-walled tubes in axial crushing
Authors: Shariatpanahi M , Masoumi A , Ataei A
Published: March 2008

Straight and tapered thin-walled tubes of rectangular cross-section have been well established as impact energy absorbers under axial loading. This paper investigates the energy absorption capacity and peak transmitted load of partially tapered rectangular tubes. It is shown that these characteristics are notably affected by such design variables as the taper angle and the length of the tapered section. A simulation-based approach is proposed for the fast determination of the optimum geometry of partially tapered tubes. The approach is based on the numerical prediction of the tube's load—deflection response in dynamic loading for various values of design parameters within their respective ranges, followed by a neural net approximation of the finite element (FE) model. The verified neural model would then be used in a multiobjective optimization algorithm that would find Pareto optimal solutions to the design problem. Each solution would be characterized by a non-dominated compromise between maximizing the energy absorption capacity and minimizing the peak impact load.
Development trends and Review of free-machining steels
Authors: Luiz N E , Machado Á R
Published: March 2008

This work presents the technologies more widely used to improve the machinability of metal materials, mainly focusing on the free-machining steels. A wide literature and patent review are included with the purpose of presenting the state of the art on free-machining steels.
Earliness—tardiness scheduling on uniform parallel machines using simulated annealing and fuzzy logic approach
Authors: Raja K , Selladurai V , Saravanan R , Arumugam C
Published: March 2008

Just-in-time production philosophy has led to the growing interest in scheduling problems considering both earliness and tardiness penalties. This research work considers the uniform parallel machine earliness—tardiness non-common due date sequence-dependent set-up time scheduling problem (UPETNDDSP) for jobs with varying processing times, where the objective is to minimize the sum of the absolute deviations of job completion times from their corresponding due dates. A simulated annealing (SA) —fuzzy logic approach has been proposed to select the optimal weighted earliness—tardiness combinations in a non-identical parallel machine environment. The SA algorithm identifies the best sequences for the different weighted combinations of earliness and tardiness measures for each given set of jobs. Fuzzy logic is then used to select the optimal weighted combination, which satisfies the combined objective function to a larger extent. The performance of the combined objective function and individual objective measure obtained by the proposed SA—fuzzy technique has been compared with the solutions yielded by the genetic algorithm technique known as the genetic algorithm with partially mapped cross-over operator (GA-PMX) and with those of the results reported in literature. The comparison shows that the proposed SA—fuzzy technique outperforms the existing available techniques.
An experimental analysis of the dieless drawing process (Variant B) using ELI grade Ti-6AL-4V wire alloy
Authors: Naughton M D , Tiernan P
Published: March 2008

Dieless drawing is a novel forming process which enables a workpiece to be reduced in a cross-sectional area without using conventional multipass dies. This paper reports on a series of dieless drawing (Variant B) experiments on ELI grade Ti-6AL-4V. A sample of the titanium alloy wire was fixed at one end and loaded in tension by the application of a specific velocity, V1, at the other end. Simultaneously, a heating and cooling device travelled along the longitudinal length of the sample with a velocity V2. The deformation process utilized the mechanics of superplasticity to take advantage of the reduction in flow stress caused by the temperature increase. First, the suitability of ELI Ti-6AL-4V to the process of dieless wire drawing was considered by determining the materials strain rate sensitivity index m, the measure of a material's ability to deform in a superplastic manner. It was determined that this material had an m value of 0.45 within a narrow strain rate band of 10-4—10-2 / s at a temperature of 950 °C. Second, a comprehensive series of experiments was carried out to determine the dieless drawing variables of Variant B. Results indicated that the dieless drawing process is capable of producing up to 40 per cent reductions per pass but the process is dependent upon both the ratio of V1/ V2 and the separation distance between the heating and cooling devices, S. It was also established that there was a direct relationship between the wire diameter variation (maximum—minimum wire-drawn diameter) and the V1/ V2 ratio. The experimentally determined results showed good agreement with a mathematical model proposed by Gliga and Canta. A mathematical analysis was undertaken to determine the temperature distribution within the heated sample.