bluuebunny/crossref_metadata_2025 huggingface dataset:
Comparative transcriptome analysis to unveil genes affecting recombinant protein productivity in mammalian cells
Authors: Yee Joon Chong , Gerdtzen Ziomara P. , Hu Wei‐Shou
Published: July 2008

Low temperature culture (33°C) has been shown to enhance the specific productivity of recombinant antibodies in Chinese hamster ovary (CHO) cells but did not affect antibody productivity in hybridoma (MAK) cells. We probed the transcriptional response of both cells undergoing temperature shift using cDNA microarrays. Among the orthologous gene probes, common trends in the expression changes between CHO and MAK are not prominent. Instead, many transcriptional changes were specific to only one cell line. Notably, oxidative phosphorylation and ribosomal genes were downregulated in MAK but not in CHO. Conversely, several protein trafficking genes and cytoskeleton elements were upregulated in CHO but remained unchanged in MAK. Interestingly, at 33°C, immunoglobulin heavy and light chain showed no significant changes in CHO, but the immunoglobulin light chain was downregulated in MAK. Overall, a clear distinction in the transcriptional response to low temperature was seen in the two cell lines. To further elucidate the set of genes responsible for increased antibody productivity, the expression data of low temperature cultures was compared to that of butyrate treatment which increased specific antibody productivity in both cell lines. Genes which are commonly differentially expressed under conditions that increased productivity are likely to reflect functional classes that are important in the productivity changes. This comparative transcriptome analysis suggests that vesicle trafficking, endocytosis and cytoskeletal elements are involved in increased specific antibody productivity. Biotechnol. Bioeng. 2009;102: 246–263. © 2008 Wiley Periodicals, Inc.
Bioreactor strategies for improving production yield and functionality of a recombinant human protein in transgenic tobacco cell cultures
Authors: Huang Ting‐Kuo , Plesha Michael A. , Falk Bryce W. , Dandekar Abhaya M. , McDonald Karen A.
Published: July 2008

Plant cell culture production of recombinant products offers a number of advantages over traditional eukaryotic expression systems, particularly if the product can be targeted to and purified from the cell culture broth. However, one of the main obstacles is product degradation by proteases that are produced during cell culture, and/or the loss of biological activity of secreted (extracellular) products as a result of alteration in the protein conformation. Because proteolysis activity and target protein stability can be significantly influenced by culture conditions, it is important to evaluate bioprocess conditions that minimize these effects. In this study, a bioreactor strategy using a protocol involving pH adjustment and medium exchange during plant cell culture is proposed for improving the production of functional recombinant α1‐antitrypsin (rAAT), a human blood protein, produced using several alternative expression systems, including a Cauliflower mosaic virus (CaMV) 35S constitutive promoter expression system, a chemically inducible, estrogen receptor‐based promoter (XVE) expression system, and a novel Cucumber mosaic virus (CMV) inducible viral amplicon (CMViva) expression system developed by our group. We have demonstrated that higher medium pH help reduce protease activity derived from cell cultures and improve the inherent stability of human AAT protein as well. This strategy resulted in a fourfold increase in the productivity of extracellular functional rAAT (100 µg/L) and a twofold increase in the ratio of functional rAAT to total rAAT (48%) in transgenic N. benthamiana cell cultures using a chemically inducible viral amplicon expression system. Biotechnol. Bioeng. 2009;102: 508–520. © 2008 Wiley Periodicals, Inc.
Reduction of a set of elementary modes using yield analysis
Authors: Song Hyun‐Seob , Ramkrishna Doraiswami
Published: July 2008

This article proposes a new concept termed “yield analysis” (YA) as a method of extracting a subset of elementary modes (EMs) essential for describing metabolic behaviors. YA can be defined as the analysis of metabolic pathways in yield space where the solution space is a bounded convex hull. Two important issues arising in the analysis and modeling of a metabolic network are handled. First, from a practical sense, the minimal generating set spanning the yield space is recalculated. This refined generating set excludes all the trivial modes with negligible contribution to convex hull in yield space. Second, we revisit the problem of decomposing the measured fluxes among the EMs. A consistent way of choosing the unique, minimal active modes among a number of possible candidates is discussed and compared with two other existing methods, that is, those of Schwartz and Kanehisa (Schwartz and Kanehisa, 2005. Bioinformatics 21: 204–205) and of Provost et al. (Provost et al., 2007. Proceedings of the 10th IFAC Symposium on Computer Application in Biotechnology, 321–326). The proposed idea is tested in a case study of a metabolic network of recombinant yeasts fermenting both glucose and xylose. Due to the nature of the network with multiple substrates, the flux space is split into three independent yield spaces to each of which the two‐staged reduction procedure is applied. Through a priori reduction without any experimental input, the 369 EMs in total was reduced to 35 modes, which correspond to about 91% reduction. Then, three and four modes were finally chosen among the reduced set as the smallest active sets for the cases with a single substrate of glucose and xylose, respectively. It should be noted that the refined minimal generating set obtained from a priori reduction still provides a practically complete description of all possible states in the subspace of yields, while the active set covers only a specific set of experimental data. Biotechnol. Bioeng. 2009;102: 554–568. © 2008 Wiley Periodicals, Inc.
A comparative study of awareness methods for peer‐to‐peer distributed virtual environments
Authors: Rueda S. , Morillo P. , Orduña J. M.
Published: July 2008

The increasing popularity of multi‐player online games is leading to the widespread use of large‐scale Distributed Virtual Environments (DVEs) nowadays. In these systems, peer‐to‐peer (P2P) architectures have been proposed as an efficient and scalable solution for supporting massively multi‐player applications. However, the main challenge for P2P architectures consists of providing each avatar with updated information about which other avatars are its neighbors. This problem is known as the awareness problem. In this paper, we propose a comparative study of the performance provided by those awareness methods that are supposed to fully solve the awareness problem. This study is performed using well‐known performance metrics in distributed systems. Moreover, while the evaluations shown in the literature are performed by executing P2P simulations on a single (sequential) computer, this paper evaluates the performance of the considered methods on actually distributed systems. The evaluation results show that only a single method actually provides full awareness to avatars. This method also provides the best performance results. Copyright © 2008 John Wiley & Sons, Ltd.
Exact solution of vibration problems of frame structures
Authors: Ma Haitao
Published: July 2008

Although exact solutions for linear static analysis of most frame structures can be obtained by the finite element method, it is very difficult to get exact solutions for free vibration and harmonic analyses for non‐trivial cases. This paper extends an earlier study on exact solutions of axial vibration problems of elastic bars to dynamic analyses of elastic frame structures. New shape functions for the transverse displacement field are constructed by using the homogeneous governing equations and then a novel beam element is formulated. Combining the new (bending) beam element and the one developed earlier for elastic bars yields a new element for general frame structures. The new frame element can be used to get exact solutions for both natural frequency and undamped harmonic analyses of frame structures. Illustrative examples are presented to demonstrate the effectiveness of the new element and the algorithm. Copyright © 2008 John Wiley & Sons, Ltd.
Improving performance of optimized kernels through fast instantiations of templates
Authors: Khan Minhaj Ahmad , Charles H.‐P. , Barthou D.
Published: July 2008

To fully exploit the instruction‐level parallelism offered by modern processors, compilers need the necessary information available during the execution of the program. This advocates for iterative or dynamic compilation. Unfortunately, dynamic compilation is suitable only for applications where the cost of compilation may be amortized by multiple invocations of the same code. Similarly, the cost of iterative compilation makes it impractical to be widely used for performance improvement. In this article, we suggest a novel approach for improving the performance of mathematical kernels through fast instantiations of templates. Optimized templates are generated at static compile time with a limited number of compilations. The initial instantiations of these templates are performed at static compile time, and the runtime instantiations are performed with a very small overhead through specialized data, requiring no computations at runtime. It represents an effective solution in terms of reduced overhead incurring at static compile time and dynamic compile time. The experiments have been performed on an Itanium‐II architecture using highly optimized kernels ofATLASandFFTWwithiccandgcccompilers. Copyright © 2008 John Wiley & Sons, Ltd.
Writing productive stencil codes with overlapped tiling
Authors: Guo Jia , Bikshandi Ganesh , Fraguela Basilio B. , Padua David
Published: July 2008

Stencil computations constitute the kernel of many scientific applications. Tiling is often used to improve the performance of stencil codes for data locality and parallelism. However, tiled stencil codes typically require shadow regions, whose management becomes a burden to programmers. In fact, it is often the case that the code required to manage these regions, and in particular their updates, is much longer than the computational kernel of the stencil. As a result, shadow regions usually impact programmers' productivity negatively. In this paper, we describeoverlapped tiling, a construct that supports shadow regions in a convenient, flexible and efficient manner in the context of the hierarchically tiled array (HTA) data type. The HTA is a class designed to express algorithms with a high degree of parallelism and/or locality as naturally as possible in terms of tiles. We discuss the syntax and implementation of overlapped HTAs as well as our experience in rewriting parallel and sequential codes using them. The results have been satisfactory in terms of both productivity and performance. For example, overlapped HTAs reduced the number of communication statements in non‐trivial codes by 78% on average while speeding them up. We also examine different implementation options and compare overlapped HTAs with previous approaches. Copyright © 2008 John Wiley & Sons, Ltd.
Service selection and workflow mapping for Grids: an approach exploiting quality‐of‐service information
Authors: Kyriazis Dimosthenis , Tserpes Konstantinos , Menychtas Andreas , Sarantidis Ioannis , Varvarigou Theodora
Published: July 2008

The advent of heterogeneous and distributed environments, such as Grid environments, made feasible the solution to computational‐intensive problems in a reliable and cost‐effective manner. In parallel, workflows with increased complexity that require specialized systems to deal with them are emerging, so as to carry out more composite and mission‐critical applications. In that rationale, quality‐of‐service (QoS) issues need to be tackled in order to ensure that each application satisfies the corresponding user requirements. Therefore, considering the quality provision aspect as fundamental for enabling Grid applications to become QoS compliant, we present an approach for service selection using QoS criteria. The latter is achieved with a suite of components that allow the different mappings of application workflow processes to Grid services that not only meet the user goals and requirements but also maximize his/her benefit in terms of the offered QoS level. We also demonstrate the operation of the aforementioned suite of components and evaluate its performance and effectiveness using a Grid scenario, based on a 3D image rendering application. Copyright © 2008 John Wiley & Sons, Ltd.
Faster, cheaper, and unused: The paradox of grievance mediation in unionized environments
Authors: Monahan Camille
Published: July 2008

This article investigates the paradox that grievance mediation pilot programs, despite their overwhelming successes, have failed to be adopted on a widespread basis in unionized settings. By focusing largely on the labor union perspective, this article suggests that some elements of union organizational identity act as barriers to the mediation of contract‐based labor disputes. Also, a model and a case study are presented to shed light on the factors that create contract‐based, unmediated grievances.
A narrative approach to bioethical decision making: The missing link between bioethics and conflict management?
Authors: Barton Ansley
Published: July 2008

Beginning in the 1990s and continuing today with increasing velocity, advances in science and medicine have profoundly affected not only health and health care, but also ethical thinking as well. Physicians, researchers, patients, and families are increasingly called on to make difficult decisions between competing values, which provides fodder for serious conflict. This article discusses a narrative approach to bioethical decision making and suggests that lessons from the field of conflict management could enhance its promise.
Assessment of pediatric dysphagia and feeding disorders: Clinical and instrumental approaches
Authors: Arvedson Joan C.
Published: July 2008

Assessment of infants and children with dysphagia (swallowing problems) and feeding disorders involves significantly more considerations than a clinical observation of a feeding. In addition to the status of feeding in the child, considerations include health status, broad environment, parent–child interactions, and parental concerns. Interdisciplinary team approaches allow for coordinated global assessment and management decisions. Underlying etiologies or diagnoses must be delineated to every extent possible because treatment will vary according to history and current status in light of all factors that are often interrelated in complex ways. A holistic approach to evaluation is stressed with a primary goal for every child to receive adequate nutrition and hydration without health complications and with no stress to child or to caregiver. Instrumental swallow examinations that aid in defining physiological swallowing status are needed for some children. Successful oral feeding must be measured in quality of meal time experiences with best possible oral sensorimotor skills and safe swallowing while not jeopardizing a child's functional health status or the parent–child relationship. © 2008 Wiley‐Liss, Inc. Dev Disabil Res Rev 2008;14:118–127.
Neuropharmacology of human appetite expression
Authors: Halford Jason C.G. , Harrold Joanne A.
Published: July 2008

The regulation of appetite relies on the integration of numerous episodic (meal) and tonic (energy storage) generated signals in energy regulatory centres within the central nervous system (CNS). These centers provide the pharmacological potential to modify human appetite (hunger and satiety) to increase or decrease caloric intake, or to normalize aberrant eating behavior. With regard to obesity, the satiety enhancing anti‐obesity drug sibutramine has proved effective at reducing body weight. Additionally, the endocannabinoid CB1 antagonist rimonabant has recently been approved for use in Europe (but not in the US). A 5‐HT2C agonist lorcaserin is also currently undergoing large‐scale clinical trials, but the effect of the drug on human appetite is unknown as yet. Appetite enhancing drugs such as magestrol acetate and dronabiol are currently used to promote weight gain. Finally, sibutramine, selective serotonergic reuptake inhibitors such as fluoxetine and some anti‐epileptic drugs have all been used to normalise aberrant eating behaviour. All these drugs act by modifying the expression of human appetite. An assessment of a drug's effectson caloric intake and feelings of hunger and satiety is necessary before they can be considered for clinical use. © 2008 Wiley‐Liss, Inc. Dev Disabil Res Rev 2008;14:158–164.
Grasping force control in consideration of translational and rotational slippage of an object by a flexible contact sensor
Authors: Saito Naoki , Satoh Toshiyuki , Okano Hideharu
Published: July 2008

This paper addresses the issue of translational and rotational slippage that occurs when a robot hand grasps an object. To grasp an object against each directional slippage is an important task. In this study, to deal with rotational slippage, a contact area between a flexible contact sensor which is mounted on the robot hand and the object is considered. A sufficient condition for grasping an object against translational/rotational slippage is derived on the condition that no additional sensors, such as tactile sensors, are required.

Effectiveness of the condition is confirmed by a grasping experiment with the use of a translational gripper where the flexible contact sensor is mounted. © 2008 Wiley Periodicals, Inc. Electr Eng Jpn, 165(3): 51–57, 2008; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/eej.20579
A magnetic yoke probe for in situ magnetic measurements
Authors: Kikuchi Hiroaki , Liu Tong , Ara Katsuyuki , Kamada Yasuhiro , Kobayashi Satoru , Takahashi Seiki
Published: July 2008

A probe with a magnetic yoke for nondestructive evaluation of mechanical properties was developed. This probe can evaluate the magnetic properties of ferromagnetic materials without machining them to a ring core or frame core shape, that is, it can perform in situ measurements. In this paper, the magnetic properties measured by the magnetic yoke probe are compared with the mechanical properties and a good correlation is found, suggesting a potential use of the probe for nondestructive evaluation of mechanical properties in ferromagnetic materials. The effect of an air gap between the probe and the specimen was also investigated in order to address possible contact problems in industrial applications. © 2008 Wiley Periodicals, Inc. Electr Eng Jpn, 165(3): 1– 7, 2008; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/eej.20588
Performance analysis of PSO‐based parallel interference canceller for MC‐CDMA communication systems
Authors: Lee Shu‐Hong , Hung Ho‐Lung , Huang Yung‐Fa , Wen Jyh‐Horng
Published: July 2008

This work analyses the performance of particle swarm optimisation (PSO) algorithm‐based parallel interference cancellation (PIC) multiuser detectors exploited in multicarrier direct‐sequence code‐division multiple‐access (MC‐DS‐CDMA) communication systems over frequency‐selective fading channels. The PSO, which attempts to reduce the complexity in optimal detection caused by the greedy exhausted searching, achieves adequate sub‐optimal multiuser detection in CDMA systems. Simulation results reveal that with a lower generation ofGn = 5, 10, the constant weight PIC (CWPIC) scheme outperform the conventional PIC (CPIC) particularly at heavy load. However, with higher generationGn = 20 in PSO, the CPIC schemes contrarily outperform the CWPIC for all system loads. Copyright © 2008 John Wiley & Sons, Ltd.
Minocycline reduces engraftment and activation of bone marrow‐derived cells but sustains their phagocytic activity in a mouse model of Alzheimer's disease
Authors: Malm Tarja M. , Magga Johanna , Kuh Georges Ful , Vatanen Tero , Koistinaho Milla , Koistinaho Jari
Published: July 2008

Bone marrow (BM)‐derived monocytes contribute to the development of microglial reaction around β‐amyloid (Aβ) plaques in Alzheimer's disease (AD) and possibly clear Aβ. Therefore, it is of great importance to separate the proinflammatory actions of monocytic cells from Aβ phagocytic effects. We used minocycline (mino) to systemically downregulate microglial activation and studied proliferation, expression of markers for activated microglia, and Aβ removal in vitro and in vivo. Mino did not affect proliferation or phagocytic activity of BM‐derived cells toward Aβ in vitro. Intrahippocampal LPS injection used to induce inflammation and increase recruitment of BM cells from periphery, reduced Aβ burden in BM‐transplanted AD transgenic mice. All engrafted cells expressed CD45, ∼50% expressed Iba‐1, and <0.5% of these cells expressed CD3e. About 40% of the engrafted cells were mitotically active. LPS increased immunoreactivity for Iba‐1, MHC II, a marker of antigen presenting cells, and CD68, a marker of lysosomal activity. The endogenous microglia largely contributed to these LPS‐induced immunoreactivities. Mino reduced the engraftment of BM‐derived cells and blocked the LPS‐induced MHC II and Iba‐1 immunoreactivities, but did not prevent the increased CD68‐immunoreactivity or the reduced Aβ burden. Importantly, mino did not block the association of eGFP‐positive cells with Aβ deposits and the percentage of mitotically active BM‐derived cells. In conclusion, mino reduces overall inflammatory potential of BM‐derived monocytic cells without preventing their phagocytic activity. The separation of harmful activation of microglia/monocytic cells from their Aβ clearing mechanism may hold important therapeutic potential. © 2008 Wiley‐Liss, Inc.
Vitamin E increases S100B‐mediated microglial activation in an S100B‐overexpressing mouse model of pathological aging
Authors: Bialowas‐McGoey Lynn A. , Lesicka Agnieszka , Whitaker‐Azmitia Patricia M.
Published: July 2008

S100B is a calcium‐binding protein released by astroglial cells of the brain capable of producing numerous extracellular effects. Although the direct molecular mechanism remains unknown, these effects can be trophic including differentiation, growth, recovery, and survival of neurons when the S100B protein is mainly oxidized and neurotoxic including apoptosis and neuroinflammatory processes marked by microglial activation when in a reduced state. S100B and its receptor RAGE (receptor for advanced glycation end products) have been found to be increased in Alzheimer's disease, Down syndrome, with tissue trauma and ischemia. In the current study, we examined the binding of the S100B receptor (RAGE) on microglial cells and the developmental effects of the antioxidant vitamin E on microglial activation and the upregulation of RAGE in an S100B over‐expressing mouse model of pathological aging. We report that RAGE is co‐localized on activated microglial cells and vitamin E induced dramatic increases in microglial activation as well as total microglial relative optical density that was accompanied by upregulation of the RAGE receptor, particularly in the CA1 region of the hippocampus. Our findings suggest further investigation into the potential role of vitamin E in reducing the oxidation state of the S100B protein and its influence on neuroinflammatory processes marked by microglial activation in vivo. © 2008 Wiley‐Liss, Inc.
Adhesive properties of connexin hemichannels
Authors: Cotrina M. L. , Lin J. H.‐C. , Nedergaard M.
Published: July 2008

Gap junctions are intercellular channels formed by hemichannels (or connexons) from two neighboring cells. Hemichannels, which are composed of proteins called connexins, can function as conduits of ATP and glutamate, and interact with adhesion molecules and other signaling elements. As a result, their functional repertoire is expanding into other roles, such as control of cell growth or cell migration. Here we further elucidate the involvement of hemichannels in cell–cell adhesion by analyzing how connexins regulate cell adhesion without the need of gap junction formation. Using a short‐term aggregation assay with C6‐glioma and HeLa cells stably transfected with connexin (Cx) 43 or Cx32, we found that the connexin type dictates the ability of these cells to aggregate, even though these two cell types do not usually adhere to each other. We have also found that high expression of Cx43, but not Cx32 hemichannels, can drive adhesion of cells expressing low levels of Cx43. Aggregation was not dependent on high levels of extracellular Ca2+, as Ca2+ removal did not change the aggregation of Cx43‐expressing cells. Our data confirm that connexin hemichannels can establish adhesive interactions without the need for functional gap junctions, and support the concept that connexins act as adhesion molecules independently of channel formation. © 2008 Wiley‐Liss, Inc.
Clusterin is epigenetically regulated in prostate cancer
Authors: Rauhala Hanna E. , Porkka Kati P. , Saramäki Outi R. , Tammela Teuvo L.J. , Visakorpi Tapio
Published: July 2008

Lack of good models has complicated investigations on the mechanisms of prostate cancer. By far, the most commonly used transgenic mouse model of prostate cancer is TRAMP, which, however, has not been fully characterized for genetic and epigenetic aberrations. Here, we screened TRAMP‐derived C2 cell line for the alterations using different microarray approaches, and compared it to human prostate cancer. TRAMP‐C2 had relatively few genomic copy number alterations according to array comparative genomic hybridization (aCGH). However, the gene copy number and expression were significantly correlated (p < 0.001). Screening genes for promoter hypermethylation using demethylation treatment with 5‐aza‐2′‐deoxycytidine and subsequent expression profiling indicated 43 putatively epigenetically silenced genes. Further studies revealed that clusterin is methylated in the TRAMP‐C2 cell line, as well as in the human prostate cancer cell line LNCaP. Its expression was found to be significantly reduced (p < 0.01) in untreated and hormone‐refractory human prostate carcinomas. Together with known function of clusterin, the data suggest an epigenetic component in the regulation of clusterin in prostate cancer. © 2008 Wiley‐Liss, Inc.
Toward an early diagnosis of lung cancer: An autoantibody signature for squamous cell lung carcinoma
Authors: Leidinger Petra , Keller Andreas , Ludwig Nicole , Rheinheimer Stefanie , Hamacher Jürg , Huwer Hanno , Stehle Ingo , Lenhof Hans‐Peter , Meese Eckart
Published: July 2008

Serum‐based diagnosis offers the prospect of early lung carcinoma detection and of differentiation between benign and malignant nodules identified by CT. One major challenge toward a future blood‐based diagnostic consists in showing that seroreactivity patterns allow for discriminating lung cancer patients not only from normal controls but also from patients with non‐tumor lung pathologies. We addressed this question for squamous cell lung cancer, one of the most common lung tumor types. Using a panel of 82 phage‐peptide clones, which express potential autoantigens, we performed serological spot assay. We screened 108 sera, including 39 sera from squamous cell lung cancer patients, 29 sera from patients with other non‐tumor lung pathologies, and 40 sera from volunteers without known disease. To classify the serum groups, we employed the standard Naïve Bayesian method combined with a subset selection approach. We were able to separate squamous cell lung carcinoma and normal sera with an accuracy of 93%. Low‐grade squamous cell lung carcinoma were separated from normal sera with an accuracy of 92.9%. We were able to distinguish squamous cell lung carcinoma from non‐tumor lung pathologies with an accuracy of 83%. Three phage‐peptide clones with sequence homology to ROCK1, PRKCB1 and KIAA0376 reacted with more than 15% of the cancer sera, but neither with normal nor with non‐tumor lung pathology sera. Our study demonstrates that seroreactivity profiles combined with statistical classification methods have great potential for discriminating patients with squamous cell lung carcinoma not only from normal controls but also from patients with non‐tumor lung pathologies. © 2008 Wiley‐Liss, Inc.
Replication of a genome‐wide case–control study of esophageal squamous cell carcinoma
Authors: Ng David , Hu Nan , Hu Ying , Wang Chaoyu , Giffen Carol , Tang Ze‐Zhong , Han Xiao‐You , Yang Howard H. , Lee Maxwell P. , Goldstein Alisa M. , Taylor Philip R.
Published: July 2008

In a previous pilot case–control study of individuals diagnosed with esophageal squamous cell carcinoma (ESCC) and matched controls from a high‐risk area in China, we identified 38 single nucleotide polymorphisms (SNPs) associated with ESCC located in or near one of 33 genes. In our study, we attempted to replicate the results of these 38 gene‐related SNPs in a new sample of 300 ESCC cases and 300 matched controls from the same study conducted in Shanxi Province, China. Among 36 evaluable SNPs, 4 were significant in one or more analyses, including SNPs located in EPHB1, PGLYRP2, PIK3C3 and SLC9A9, although the odds ratios (ORs) for these genotypes were modest. Associations were found with EPHB1/rs1515366 (OR 0.92, 95% CI 0.86–0.99; p = 0.019), PIK3C3/rs52911 (OR 0.93, 95% CI 0.88–0.99; p = 0.02) and PGLYRP2/rs959117 (OR 0.93, 95% CI, 0.86–1.01; p = 0.061) in general linear models (additive mode); and the genotype distribution differed between cases and controls for SLC9A9/rs956062 (p = 0.024). To examine these 4 genes in more detail, 40 HapMap‐based tag SNPs from these 4 genes were evaluated in the same subjects and 7 additional SNPs associated with ESCC were identified. Further confirmation of these findings in other populations and other studies are needed to determine if the signals from these SNPs are indirectly associated due to linkage disequilibrium, or are directly related to biologic function and the development of ESCC. Published 2008 Wiley‐Liss, Inc.
The human Y‐encoded testis‐specific protein interacts functionally with eukaryotic translation elongation factor eEF1A, a putative oncoprotein
Authors: Kido Tatsuo , Lau Yun‐Fai Chris
Published: July 2008

Testis‐specific protein Y‐encoded (TSPY) is the putative gene for the gonadoblastoma locus on the Y chromosome. TSPY is expressed in normal germ cells of fetal and adult testis and ectopically in tumor germ cells, including gonadoblastoma in intersex patients, testicular germ cell tumors, prostate cancer and other somatic cancers. It is a member of the TSPY/SET/NAP1 superfamily and harbors a highly conserved domain, termed SET/NAP domain. To explore its possible role(s) in tumorigenesis, we had performed a yeast two‐hybrid screen of a fetal gonadal cDNA library and identified the translation elongation factor eEF1A as a binding partner for TSPY at the SET/NAP domain. TSPY and eEF1A were highly expressed and colocalized in tumor germ cells of human seminoma specimens, suggesting their possible interaction in germ cell tumors. They were colocalized in the cytoplasm and could be co‐immunoprecipitated from transfected COS7 cells. Significantly, both eEF1A1 and eEF1A2 have postulated to be involved in various types of human cancer, including breast and prostate cancers. TSPY enhanced protein synthesis of a reporter gene, which was augmented by an overexpression of eEF1A. TSPY also increased the nuclear redistribution of eEF1A, resulting in a parallel increase in reporter gene transcripts. Our results suggest that TSPY could exert its oncogenic function(s) by interacting with eEF1As and stimulating gene expression via its enhancements in protein synthesis and gene transcription. Published 2008 Wiley‐Liss, Inc.
Application of local and global particle swarm optimization algorithms to optimal design and operation of irrigation pumping systems
Authors: Afshar M. H. , Rajabpour R.
Published: July 2008

A particle swarm optimization (PSO) algorithm is used in this paper for optimal design and operation of irrigation pumping systems. An irrigation pumping systems design and management model is first introduced and subsequently solved with the newly introduced PSO algorithm. The solution of the model is carried out in two steps. In the first step an exhaustive enumeration is carried out to find all feasible sets of pump combinations able to cope with a given demand curve over the required period. The PSO algorithm is then called in to search for optimal operation of each set. Having solved the operation problem of all feasible sets, the total cost of operation and depreciation of initial investment is calculated for all the sets and the optimal set and the corresponding optimal operating policy is determined. The proposed model is applied to the design and operation of a real‐world irrigation pumping system and the results are presented and compared with those of a genetic algorithm. Two global and local versions of the PSO algorithm are used and their efficiencies are compared to each other and that of a genetic algorithm (GA) model. The results indicate that the proposed model in conjunction with the PSO algorithm is a versatile management model for the design and operation of real‐world irrigation pumping systems. Copyright © 2008 John Wiley & Sons, Ltd.
Performance assessment of irrigation management transfer from government‐managed to farmer‐managed irrigation system: a case study
Authors: Latif Muhammad , Tariq Javaid A.
Published: July 2008

The government of NWFP, Pakistan, established an autonomous body, the Frontier Irrigation and Drainage Authority (FIDA), in 1997 to effectively cope with the emerging challenges in irrigation management. Six distributaries were recently transferred to farmers' organizations under the irrigation management transfer (IMT) for their operation and management. Results of the study revealed that the irrigation supplies are adequate to meet the crop water requirements. The relative water supply (RWS) index varies from 1.66 to 2.02 during summer, whereas in winter it varies from 2.22 to 2.55. The delivery performance ratio (DPR) during summer varies from 0.78 to 0.83 and in winter from 0.73 to 0.63. Irrigation supplies were reliable during both summer and winter seasons. Due to improved irrigation supply, annual irrigation intensity has increased by 25%. There is a prominent increase in yield of maize (40%), sugarcane (55%) and wheat (43%). The irrigation service fee collected was approximately 60% of the fee assessed. Hydraulic committees at each distributary should be established to operate the distributary according to crop demand. Awareness of the farmers should be created regarding the farm irrigation application methods to avoid over‐irrigation and wastage of water. Copyright © 2008 John Wiley & Sons, Ltd.
Unexpected complexity of the budding yeast transcriptome
Authors: Ito Takashi , Miura Fumihito , Onda Miyuki
Published: July 2008

The genome of the budding yeast Saccharomyces cerevisiae was sequenced over a decade ago and has been annotated to encode ∼6,000 genes. However, recent high throughput studies using tiling array hybridization and cDNA sequencing have revealed an unexpectedly large number of previously undescribed transcripts. They largely lack protein‐coding capacity and are transcribed from both strands of intragenic and intergenic regions in the genome. Accordingly, pervasive transcription leading to a plethora of noncoding RNAs, which was first revealed for mammalian genomes to attract intense attentions, is likely an intrinsic feature of eukaryotic genomes. Although it is not clear what fraction of these transcription events are functional, some were shown to induce transcriptional interference or histone modifications to regulate gene expression. The budding yeast may serve as an excellent model to study pervasive transcription and noncoding RNAs. © 2008 IUBMB IUBMB Life, 60(12): 775–781, 2008
Laboratory simulations of astrophysical blast waves with high energy lasers
Authors: Ditmire T. , Edens A.D.
Published: July 2008

We review recent efforts to simulate aspects of supernova remnants in laboratory experiments by creating energetic explosions with high energy lasers. High energy pulsed lasers are uniquely suited for these kinds of studies. By focusing a laser with pulse energy of a few joules to many hundreds of joules onto a solid target or into a dense gas target, explosive shock waves of very high Mach number can be created. With a well chosen set of laser and target parameters it has been shown by a number of groups that radiative blast waves can be produced. Such blast waves have dynamics dominated by radiation transport and exhibit unusual characteristics, the most important of which include hydrodynamic instabilities which may play an important role in the structure of the interstellar medium. As a result there are now prospects for gaining new insights into astronomical observations of supernova remnants by studying laboratory laser driven plasma systems.
Helicobacter pylori infection and motor fluctuations in patients with Parkinson's disease
Authors: Lee Won Yong , Yoon Won Tae , Shin Hee Young , Jeon Seong Hee , Rhee Poong‐Lyul
Published: July 2008

To investigate whether Helicobacter pylori (HP) infection affects the clinical response to levodopa and whether its eradication could improve motor fluctuation in patients with Parkinson's disease (PD). Using the [13C] urea breath test, we monitored HP infection in 65 patients with PD and motor fluctuations of the “wearing‐off” or delayed “on” types, with or without dyskinesia. We compared the clinical features and response to L‐dopa between HP noninfected (n = 30) and HP infected patients (n = 35) by reviewing home diaries kept for 72 hours. Among HP infected patients, we compared the differences in L‐dopa “onset” time, “on‐time” duration, and scores on the motor examination section of the Unified PD Rating Scale (UPDRS‐III) during the medication “on” phase before and after HP eradication. There were no differences in the age, disease duration, Hoehn and Yahr stage, UPDRS‐III score, L‐dopa daily dose, and frequency of dyskinesia between HP noninfected and HP infected groups. However, L‐dopa “onset” time was longer and “on‐time” duration was shorter in HP infected patients than in HP noninfected patients (78.4 ± 28.2 vs. 56.7 ± 25.1 and 210.0 ± 75.7 vs. 257.7 ± 68.9 min, respectively, P < 0.05). HP eradication improved the delay L‐dopa “onset” time and short “on‐time” duration (to 58.1 ± 25.6 and to 234.4 ± 66.5 min, respectively, P < 0.05). These data demonstrated that HP infection could interfere with the absorption of L‐dopa and provoke motor fluctuations. HP eradication can improve the motor fluctuations of HP infected patients with PD. © 2008 Movement Disorder Society
A‐WING: an ad hoc wireless inter‐network gateway
Authors: Brogan D. , Ganchev I. , O'Droma M.
Published: July 2008

This paper presents a design and implementation of a novel ad hoc wireless inter‐network gateway and research platform (A‐WING) which supports heterogeneous wireless and wired networking infrastructures and ad hoc wireless protocols. The driving goal is to explore and realize ways of increasing the ‘always best connected’ options for mobile wireless devices. The platform currently supports IEEE 802.11 (Wi‐Fi), IEEE 802.3 (Ethernet), Bluetooth, IPv4, IPv6, broadcasting and multicasting, stream and datagram transport protocols. The gateway can be readily expanded by the addition of new functionality or support for other networking hardware. This functional variety and inbuilt extensibility ensures that A‐WING can facilitate research into multi‐mode multi‐protocol wireless networking. The A‐WING design is based on a new generic description of link layer services called the ‘9Cs’ and includes a new method for the hierarchical description of networks incorporating nodes with multiple interfaces together with the development of a new XML schema for network, node and interface descriptive inter‐nodal messaging. Copyright © 2008 John Wiley & Sons, Ltd.
A smoothing Newton's method for the construction of a damped vibrating system from noisy test eigendata
Authors: Bai Zheng‐Jian , Ching Wai‐Ki
Published: July 2008

In this paper we consider an inverse problem for a damped vibration system from the noisy measured eigendata, where the mass, damping, and stiffness matrices are all symmetric positive‐definite matrices with the mass matrix being diagonal and the damping and stiffness matrices being tridiagonal. To take into consideration the noise in the data, the problem is formulated as a convex optimization problem involving quadratic constraints on the unknown mass, damping, and stiffness parameters. Then we propose a smoothing Newton‐type algorithm for the optimization problem, which improves a pre‐existing estimate of a solution to the inverse problem. We show that the proposed method converges both globally and quadratically. Numerical examples are also given to demonstrate the efficiency of our method. Copyright © 2008 John Wiley & Sons, Ltd.
On computing the forces from the noisy displacement data of an elastic body
Authors: Reddy A. Narayana , Ananthasuresh G. K.
Published: July 2008

This study is concerned with the accurate computation of the unknown forces applied on the boundary of an elastic body using its measured displacement data with noise. Vision‐based minimally intrusive force‐sensing using elastically deformable grasping tools is the motivation for undertaking this problem. Since this problem involves incomplete and inconsistent displacement/force of an elastic body, it leads to an ill‐posed problem known as Cauchy's problem in elasticity. Vision‐based displacement measurement necessitates large displacements of the elastic body for reasonable accuracy. Therefore, we use geometrically non‐linear modelling of the elastic body, which was not considered by others who attempted to solve Cauchy's elasticity problem before. We present two methods to solve the problem. The first method uses the pseudo‐inverse of an over‐constrained system of equations. This method is shown to be not effective when the noise in the measured displacement data is high. We attribute this to the appearance of spurious forces at regions where there should not be any forces. The second method focuses on minimizing the spurious forces by varying the measured displacements within the known accuracy of the measurement technique. Both continuum and frame elements are used in the finite element modelling of the elastic bodies considered in the numerical examples. The performance of the two methods is compared using seven numerical examples, all of which show that the second method estimates the forces with an error that is not more than the noise in the measured displacements. An experiment was also conducted to demonstrate the effectiveness of the second method in accurately estimating the applied forces. Copyright © 2008 John Wiley & Sons, Ltd.
Cracking node method for dynamic fracture with finite elements
Authors: Song Jeong‐Hoon , Belytschko Ted
Published: July 2008

A new method for modeling discrete cracks based on the extended finite element method is described. In the method, the growth of the actual crack is tracked and approximated with contiguous discrete crack segments that lie on finite element nodes and span only two adjacent elements. The method can deal with complicated fracture patterns because it needs no explicit representation of the topology of the actual crack path. A set of effective rules for injection of crack segments is presented so that fracture behavior beginning from arbitrary crack nucleations to macroscopic crack propagation is seamlessly modeled. The effectiveness of the method is demonstrated with several dynamic fracture problems that involve complicated crack patterns such as fragmentation and crack branching. Copyright © 2008 John Wiley & Sons, Ltd.
Sensitivity analysis of flexible multibody systems using composite materials components
Authors: Neto Maria Augusta , Ambrósio Jorge A. C. , Leal Rogério Pereira
Published: July 2008

In this paper, a general formulation for the computation of the first‐order analytical sensitivities based on the direct method using automatic differentiation of flexible multibody systems is presented. The direct method for sensitivity calculation is obtained by differentiating the equations that define the response of the flexible multibody systems of composite materials with respect to the design variables, which are the ply orientations of the laminated. In order to appraise the benefits of the approach suggested and to highlight the risks of the procedure, the analytical sensitivities are compared with the numerical results obtained by using the finite difference method. For the beam composite material elements, the section properties and their sensitivities are found using an asymptotic procedure that involves a two‐dimensional (2‐D) finite element analysis of their cross section. The equations of the sensitivities are obtained by automatic differentiation and integrated in time simultaneously with the equations of motion of the multibody systems. The equations of motion and the sensitivities of the flexible multibody system are solved and the accelerations, velocities and the sensitivities of accelerations and velocities are integrated in time using a multi‐step multi‐order integration algorithm. Through the application of the methodology to two simple flexible multibody systems the difficulties and benefits of the procedure, with respect to finite difference approaches or to the direct implementation of the analytic sensitivities, are discussed. Copyright © 2008 John Wiley & Sons, Ltd.
Geographical variation of the conversion efficiency of crystalline silicon photovoltaic modules in Europe
Authors: Huld Thomas , Šúri Marcel , Dunlop Ewan D.
Published: July 2008

We present a geographical assessment of the performance of crystalline silicon photovoltaic (PV) modules over Europe. We have developed a method that is based on a material specific analytical expression of the PV conversion efficiency, relative to nominal efficiency, as a function of module temperature and irradiance. This method is combined with a climate database that includes average daytime temperature and irradiance profiles. It is found that the geographical variation in ambient temperature and yearly irradiation causes a decrease in overall yearly PV performance from 3 to 13% relative to the performance under Standard Test Conditions, with the highest decrease found in the Mediterranean region. Based on the above results we developed a simplified linear expression of the relative PV module efficiency that is a simple function of yearly total irradiation and yearly average daytime temperature. The coefficients to the linear expression are found by fitting to the map resulting from the above‐mentioned analytical approach. The prediction of total yearly PV output from this linear fit deviates less than 0·5% from the more detailed calculation, thus providing a faster and more simplified alternative to the yield estimate, in the case when only limited climate data are available. Copyright © 2008 John Wiley & Sons, Ltd.