bluuebunny/crossref_metadata_2025_split huggingface dataset:
Yield, solubility and conformational quality of soluble proteins are not simultaneously favored in recombinant Escherichia coli
Authors: Martínez‐Alonso Mónica , García‐Fruitós Elena , Villaverde Antonio 
Published: June 2008

AbstractMany enzymes or fluorescent proteins produced in Escherichia coli are enzymatically active or fluorescent respectively when deposited as inclusion bodies. The occurrence of insoluble but functional protein species with native‐like secondary structure indicates that solubility and conformational quality of recombinant proteins are not coincident parameters, and suggests that both properties can be engineered independently. We have here proven this principle by producing elevated yields of a highly fluorescent but insoluble green fluorescent protein (GFP) in a DnaK− background, and further enhancing its solubility through adjusting the growth temperature and GFP gene expression rate. The success of such a two‐step approach confirms the independent control of solubility and conformational quality, advocates for new routes towards high quality protein production and intriguingly, proves that high protein yields dramatically compromise the conformational quality of soluble versions. Biotechnol. Bioeng. 2008;101: 1353–1358. © 2008 Wiley Periodicals, Inc.
The neuronal organization of a unique cerebellar specialization: The valvula cerebelli of a mormyrid fish
Authors: Shi Zhigang , Zhang Yueping , Meek Johannes , Qiao Jiantian , Han Victor Z. 
Published: June 2008

AbstractThe distal valvula cerebelli is the most prominent part of the mormyrid cerebellum. It is organized in ridges of ganglionic and molecular layers, oriented perpendicular to the granular layer. We have combined intracellular recording and labeling techniques to reveal the cellular morphology of the valvula ridges in slice preparations. We have also locally ejected tracer in slices and in intact animals to examine its input fibers. The palisade dendrites and fine axon arbors of Purkinje cells are oriented in the horizontal plane of the ridge. The dendrites of basal efferent cells and large central cells are confined to the molecular layer but are not planar. Basal efferent cell axons are thick and join the basal bundle leaving the cerebellum. Large central cell axons are also thick, and they traverse long distances in the transverse plane, with local collaterals in the ganglionic layer. Vertical cells and small central cells also have thick axons with local collaterals. The dendrites of Golgi cells are confined to the molecular layer, but their axon arbors are either confined to the granular layer or proliferate in both the granular and ganglionic layers. Dendrites of deep stellate cells are distributed in the molecular layer, with fine axon arbors in the ganglionic layer. Granule cell axons enter the molecular layer as parallel fibers without bifurcating. Climbing fibers run in the horizontal plane and terminate exclusively in the ganglionic layer. Our results confirm and extend previous studies and suggest a new concept of the circuitry of the mormyrid valvula cerebelli. J. Comp. Neurol. 509:449–473, 2008. © 2008 Wiley‐Liss, Inc.
Murine intestinal cells expressing Trpm5 are mostly brush cells and express markers of neuronal and inflammatory cells
Authors: Bezençon C. , Fürholz A. , Raymond F. , Mansourian R. , Métairon S. , Le Coutre J. , Damak S. 
Published: June 2008

AbstractTo determine the role in chemosensation of intestinal solitary cells that express taste receptors and Trpm5, we carried out a microarray study of the transcriptome of FACS‐sorted transgenic mouse intestinal cells expressing enhanced green fluorescent protein (eGFP) under the control of the Trpm5 promoter and compared it with that of intestinal cells that do not express eGFP. The findings of the study are: 1) Morphology and expression of markers show that most eGFP+ cells are brush cells. 2) The majority of proteins known to be involved in taste signal transduction are expressed in the eGFP+ cells, although the isoforms are not always the same. 3) eGFP+ cells express pre‐ and postsynaptic markers and nerves are often found in close proximity. 4) Several genes that play a role in inflammation are expressed specifically in eGFP+ cells. Furthermore, these cells express the entire biosynthesis pathway of leucotriene C4, an eicosanoid involved in modulation of intestinal smooth muscle contraction. 5) Angiotensinogen, renin, and succinate receptor genes are expressed in the eGFP+ cells, suggesting a role in the regulation of water and sodium transport, vasomotricity, and blood pressure. These data suggest that the Trpm5‐expressing cells integrate many signals, including chemical signals from ingested food, and that they may regulate several physiological functions of the gastrointestinal tract. J. Comp. Neurol. 509:514–525, 2008. © 2008 Wiley‐Liss, Inc.
Grid computing of spatial statistics: using the TeraGrid forG(d) analysis
Authors: Wang Shaowen , Cowles Mary Kathryn , Armstrong Marc P. 
Published: June 2008

AbstractThe massive quantities of geographic information that are collected by modern sensing technologies are difficult to use and understand without data reduction methods that summarize distributions and report salient trends. Statistical analyses, therefore, are increasingly being used to analyze large geographic data sets over a broad spectrum of spatial and temporal scales. Computational Grids coordinate the use of distributed computational resources to form a large virtual supercomputer that can be applied to solve computationally intensive problems in science, engineering, and commerce. This paper presents a solution to computing a spatial statistic,G(d) using Grids. Our approach is based on a quadtree‐based domain decomposition that uses task‐scheduling algorithms based on GridShell and Condor. Computational experiments carried out on the TeraGrid were designed to evaluate the performance of solution processes. The Grid‐based approach to computing values forG(d) shows improved performance over the sequential algorithm while also solving larger problem sizes. The solution demonstrated not only advances knowledge about the application of the Grid in spatial statistics applications but also provides insights into the design of Grid middleware for other computationally intensive applications. Copyright © 2008 John Wiley & Sons, Ltd.
A Grid‐enabled problem‐solving environment for advanced reservoir uncertainty analysis
Authors: Lei Zhou , Allen Gabrielle , Chakraborty Promita , Huang Dayong , Lewis John , Li Xin , White Christopher D. 
Published: June 2008

AbstractUncertainty analysis is critical for conducting reservoir performance prediction. However, it is challenging because it relies on (1) massive modeling‐related, geographically distributed, terabyte, or even petabyte scale data sets (geoscience and engineering data), (2) needs to rapidly perform hundreds or thousands of flow simulations, being identical runs with different models calculating the impacts of various uncertainty factors, (3) an integrated, secure, and easy‐to‐use problem‐solving toolkit to assist uncertainty analysis. We leverage Grid computing technologies to address these challenges. We design and implement an integrated problem‐solving environmentResGridto effectively improve reservoir uncertainty analysis. The ResGrid consists of data management, execution management, and a Grid portal. Data Grid tools, such as metadata, replica, and transfer services, are used to meet massive size and geographically distributed characteristics of data sets. Workflow, task farming, and resource allocation are used to support large‐scale computation. A Grid portal integrates the data management and the computation solution into a unified easy‐to‐use interface, enabling reservoir engineers to specify uncertainty factors of interest and perform large‐scale reservoir studies through a web browser. The ResGrid has been used in petroleum engineering. Copyright © 2008 John Wiley & Sons, Ltd.
Compositional approach applied to loop specialization
Authors: Djoudi L. , Acquaviva J.‐T. , Barthou D. 
Published: June 2008

AbstractAn optimizing compiler cannot generate one best code pattern for all input data. There is no ‘one optimization fits all’ inputs. To attain high performance for a large range of inputs, it is therefore desirable to resort to some kind of specialization. Data specialization significantly improves the performance delivered by the compiler‐generated codes. Specialization is, however, limited by code expansion and introduces a time overhead for the selection of the appropriate version. We propose a new method to specialize the code at the assembly level for loop structures. Our specialization scheme focuses on different ranges of loop trip count and combines all these versions into a code that switches smoothly from one to the other while the iteration count increases. Hence, the resulting code achieves the same level of performance than each version on its specific iteration interval. We illustrate the benefit of our method on the SPEC benchmarks with detailed experimental results. Copyright © 2008 John Wiley & Sons, Ltd.
A novel reduction approach to analyzing QoS of workflow processes
Authors: Xia Yunni , Zhu Qingsheng , Huang Yu , Wang Zizhen 
Published: June 2008

AbstractQuality of service (QoS) of workflows and workflow‐based applications is given increasing attention by both industry and academic. In this paper, we propose a novel analytical framework to analyze QoS (metrics include make‐span, cost, and reliability) of workflow systems based on GWF‐net, which extends traditional workflow net by associating tasks with generally distributed firing delay and time‐to‐failure. The GFW‐net model is used to model process structure and task organization of workflows at the process level. In contrast with prevailing QoS models based on Markovian process, we introduce a reduction technique to evaluate QoS of GWF‐net process avoiding the state‐explosion problem and tedious mathematical derivation of state‐transition probabilities. Through a case study, we show that our framework is capable of modeling real‐world workflow‐based application effectively. Also, experiments and confidence‐interval analysis in the case study indicate that the reduction methods are verified by real results. We also compare our approach with related research in the text. Copyright © 2008 John Wiley & Sons, Ltd.
The Cochrane Library and Procedural Pain in Children: An Overview of Reviews
Authors: Buscemi Nina , Vandermeer Ben , Curtis Sarah 
Published: June 2008

AbstractBackgroundProcedural pain in children is highly prevalent, is a major source of pain, stress and anxiety for children and can have negative long‐lasting effects. Research into effective pain prevention strategies is voluminous and complex, presenting challenges for clinically relevant synthesis.ObjectiveTo summarize Cochrane reviews assessing the effects of various interventions for pain in children undergoing painful medical procedures.MethodsThe Cochrane Database of Systematic Reviews was systematically searched for reviews on interventions for pain in children undergoing painful medical procedures. The type of data to be extracted was determined a priori, and data extraction was carried out by one author.Main ResultsFour systematic reviews were included in the overview. Two reviews assessed the effects of interventions on neonates, and two reviews assessed the effects of interventions on older children. Overall, the quality of the reviews was good.Authors' ConclusionsMany convenient, safe and efficacious modalities for alleviation of paediatric procedural pain exist. Use of sucrose, breastfeeding or breast milk is effective and should always be offered for heel lance pain in neonates. These modalities are likely efficacious for other short painful procedures and may also be useful for older infants. Topical anaesthesia reduces needle pain. Amethocaine was found to be more effective with quicker onset of effect than EMLA, although new topical anaesthetics warrant attention. Behavioural therapies such as distraction are effective, inexpensive and can be used in conjunction with pharmacological analgesics without onerous resource use. Pain research is complex, and achieving consensus on the best methodological approaches will make imminent advances in this field more readily attainable.
Frequency‐domain equalisation for block CDMA transmission
Authors: Adachi F. , Nakajima A. , Takeda K. , Liu L. , Tomeba H. , Yui T. , Fukuda K. 
Published: June 2008

AbstractIn next generation wireless network, significantly higher rate data services of close to 1 Gpbs are expected. The wireless channels for such a broadband data transmission become severe frequency‐selective. Frequency‐domain equalisation (FDE) technique may play an important role for broadband data transmission using multi‐carrier (MC)‐ and direct‐sequence code division multiple access (DS‐CDMA). The performance can be further improved by the use of multi‐input/multi‐output (MIMO) antenna diversity technique. The downlink performance is significantly improved with FDE. However, the uplink performance is limited by the multiple access interference (MAI). To remove the MAI while gaining the frequency diversity effect through the use of FDE, two‐dimensional (2D) block spread CDMA can be used. Recently, particular attention has been paid to MIMO space division multiplexing (SDM) to significantly increase the throughput without expanding the signal bandwidth. In this paper, we present a comprehensive performance comparison of MC‐ and DS‐CDMA using FDE. Copyright © 2008 John Wiley & Sons, Ltd.
Range improvement of UWB systems using adaptive multicarrier spread‐spectrum and MIMO techniques
Authors: Stephan Antoine , Baudais Jean‐Yves , Hélard Jean‐François 
Published: June 2008

AbstractIn this paper, we investigate the use of multiple‐input multiple‐output (MIMO) techniques with a linear precoded orthogonal frequency division multiplexing (LP‐OFDM) waveform, known as spread‐spectrum multicarrier multiple access (SS‐MC‐MA), for high data rate ultra‐wideband (UWB) systems. This scheme is an evolution of the well‐known multiband OFDM (MB‐OFDM) solution supported by the WiMedia Alliance. The aim of this paper is to improve the UWB system range while not significantly increasing the system complexity compared to the WiMedia solution. Firstly, an analytical study of the single‐input single‐output (SISO) LP‐OFDM waveform allows to find how to efficiently precode an OFDM signal in order to improve the system range. To go further and exploit the available spatial diversity, a MIMO component is added and a new geometric statistic MIMO channel model is considered. Secondly, a global MIMO LP‐OFDM system study is led to highlight the benefits of combining MIMO and LP techniques for UWB applications. The analytical and simulation results show that the joint use of MIMO and LP‐OFDM leads to a significant range improvement compared to the WiMedia solution. Copyright © 2008 John Wiley & Sons, Ltd.
Food group intake and risk of subtypes of esophageal and gastric cancer
Authors: Navarro Silvera Stephanie A. , Mayne Susan T. , Risch Harvey , Gammon Marilee D. , Vaughan Thomas L. , Chow Wong‐Ho , Dubrow Robert , Schoenberg Janet B. , Stanford Janet L. , West A. Brian , Rotterdam Heidrun , Blot William J. , Fraumeni Joseph F. 
Published: June 2008

AbstractIncidence rates for adenocarcinomas of the esophagus and gastric cardia have been increasing rapidly, while rates for non‐cardia gastric adenocarcinoma and esophageal squamous cell carcinoma have declined. We examined food group intake as a risk factor for subtypes of esophageal and gastric cancers in a multicenter, population‐based case–control study in Connecticut, New Jersey and western Washington state. Associations between food groups and risk were estimated using adjusted odds ratios (OR), based on increasing intake of one serving per day. Total vegetable intake was associated with decreased risk of esophageal adenocarcinoma (OR = 0.85, 95% CI = 0.75, 0.96). Conversely, total meat intake was associated with increased risk of esophageal adenocarcinoma (OR = 1.43, 95% CI = 1.11, 1.83), gastric cardia adenocarcinoma (OR = 1.37, 95% CI = 1.08, 1.73) and noncardia gastric adenocarcinoma (OR = 1.39, 95% CI = 1.12, 1.71), with red meat most strongly associated with esophageal adenocarcinoma risk (OR = 2.49, 95% CI = 1.39, 4.46). Poultry was most strongly associated with gastric cardia adenocarcinoma (OR = 1.89, 95% CI = 1.15, 3.11) and noncardia gastric adenocarcinoma (OR = 1.90, 95% CI = 1.19, 3.03). High‐fat dairy was associated with increased risk of both esophageal and gastric cardia adenocarcinoma. Higher intake of meats, particularly red meats, and lower intake of vegetables were associated with an increased risk of esophageal adenocarcinoma, while higher intake of meats, particularly poultry, and high‐fat dairy was associated with increased risk of gastric cardia adenocarcinoma. © 2008 Wiley‐Liss, Inc.
UV irradiation increases ROS production via PKCδ signaling in primary murine fibroblasts
Authors: Bossi Orit , Gartsbein Marina , Leitges Michael , Kuroki Toshio , Grossman Shlomo , Tennenbaum Tamar 
Published: June 2008

AbstractUltraviolet (UV) irradiation is a major environmental factor responsible for a high incidence of premature skin aging, referred to as photoaging, as well as skin cancer and melanoma. UVA irradiation represents 90% of the solar UV light reaching the earth's surface, and yet the mechanisms by which it exerts its biological effects are not clear. UVA penetrates into the skin tissue, reaching the basal layers of the active dividing cells and, therefore, the contribution of UVA to skin damage may be significant. The majority of UVA energy is absorbed by unidentified photosensitizers in the cells which are postulated to generate reactive oxygen species (ROS). It has been believed that both chronological aging and photoaging share the same molecular features and, as such, it is very common to utilize UV irradiation for induction of skin aging. To determine the involvement of protein kinase isoforms in chronological aging and photoaging, we utilized in vitro aging model systems of primary murine fibroblasts and primary fibroblasts isolated from PKC null mice. We show for the first time distinct involvement of PKC isoforms PKCδ and PKCα in photoaging versus cellular senescence. While chronological aging is accompanied by overexpression and activation of PKCα, UV irradiation and ROS production are associated with photoaging accompanied by PKCδ downregulation and nuclear translocation. J. Cell. Biochem. 105: 194–207, 2008. © 2008 Wiley‐Liss, Inc.
Study of a newly isolated thermophilic bacterium capable of Kuhemond heavy crude oil and dibenzothiophene biodesulfurization following 4S pathway at 60 °C
Authors: Torkamani Sarah , Shayegan Jalal , Yaghmaei Soheila , Alemzadeh Iran 
Published: June 2008

AbstractBACKGROUND: To meet stringent emission standards stipulated by regulatory agencies, the oil industry is required to bring down the sulfur content in fuels. As some compounds cannot be desulfurized by existing desulfurizing processes (such as hydrodesulfurization, HDS) biodesulfurization has become an interesting topic for researchers. Most of the isolated biodesulfurizing microorganisms are capable of desulfurization of refined products whose predominant sulfur species are dibenzothiophenes so biocatalyst development is still needed to desulfurize the spectrum of sulfur‐bearing compounds present in whole crude.RESULTS: The first desulfurizing bacterium active at 60 °C has been isolated, which reduces DBT concentration from 2 mmol L−1 to 0.1 mmol L−1 after 95 h, following the 4S pathway. Its DBT desulfurization pattern was represented by the Michaelis‐Menten equation. Various parameters such as Vmax, Km, µm, Ks and maximum specific DBT desulfurization rate were calculated which are 0.092 mmol L−1 h−1, 3.554 mmol L−1, 0.157 h−1, 3.722 mmol L−1 and 0.192 mmol L−1 DBT g−1 DCW (dry cell weight) h−1, respectively. It can desulfurize 50% of the sulfur content of Kuhemond heavy crude oil (KHC oil) with an initial sulfur content of 7.6%wt in 6 days. Its maximum specific desulfurization rate for KHC oil is equivalent to 0.005 g sulfur g−1 DCW h−1. The bacterium was isolated during a heavy crude oil biodesulfurization project initiated by PEDEC, a subsidiary of National Iranian Oil Company.CONCLUSION: The KHC oil sulfur removal efficiency of the bacterium is approximately five times that of BBRC‐9016 bacterium. It removes sulfur selectively without using sulfur‐containing compounds as its carbon source. By applying various media during its isolation, the probability of screening the correct microorganism is increased. Copyright © 2008 Society of Chemical Industry
The influence of femoral internal and external rotation on cartilage stresses within the patellofemoral joint
Authors: Besier Thor F. , Gold Garry E. , Delp Scott L. , Fredericson Michael , Beaupré Gary S. 
Published: June 2008

AbstractInternal and external rotation of the femur plays an important role in defining the orientation of the patellofemoral joint, influencing contact areas, pressures, and cartilage stress distributions. The purpose of this study was to determine the influence of femoral internal and external rotation on stresses in the patellofemoral cartilage. We constructed finite element models of the patellofemoral joint using magnetic resonance (MR) images from 16 volunteers (8 male and 8 female). Subjects performed an upright weight‐bearing squat with the knee at 60° of flexion inside an open‐MR scanner and in a gait laboratory. Quadriceps muscle forces were estimated for each subject using an electromyographic‐driven model and input to a finite element analysis. Hydrostatic and octahedral shear stresses within the cartilage were modeled with the tibiofemoral joint in a “neutral” position and also with the femur rotated internally or externally by 5° increments to ±15°. Cartilage stresses were more sensitive to external rotation of the femur, compared with internal rotation, with large variation across subjects. Peak patellar shear stresses increased more than 10% with 15° of external rotation in 75% of the subjects. Shear stresses were higher in the patellar cartilage compared to the femoral cartilage and patellar cartilage stresses were more sensitive to femoral rotation compared with femoral cartilage stress. Large variation in the cartilage stress response between individuals reflects the complex nature of the extensor mechanism and has clinical relevance when considering treatment strategies designed to reduce cartilage stresses by altering femoral internal and external rotation. © 2008 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res