bluuebunny/crossref_metadata_2025_split huggingface dataset:
Long-term patency is expected with covered TIPS stents: This effect may not always be desirable!
Authors: Rössle Martin , Mullen Kevin D. , Jaeschke Hartmut , Mullen Kevin , Moradpour Darius 
Published: August 2004

Background & Aims
A 50% dysfunction rate at 1 year is one of the main drawbacks of the transjugular intrahepatic portosystemic shunt procedure. Preliminary experimental and clinical studies suggest that the use of stents covered with polytetrafluorethylene could tremendously decrease this risk.

Methods
Eighty patients with cirrhosis and uncontrolled bleeding (n = 23), recurrent bleeding (n = 25), or refractory ascites (n = 32) were randomized to be treated by transjugular intrahepatic portosystemic shunts with either a polytetrafluorethylene-covered stent (group 1; 39 patients) or a usual uncovered prosthesis (group 2; 41 patients). Follow-up Doppler ultrasound was scheduled at day 7, at 1 month, and then every 3 months for 2 years. Angiography and portosystemic pressure gradient measurements were performed 6,12, and 24 months after the transjugular intrahepatic portosystemic shunt procedure and whenever dysfunction was suspected. Dysfunction was defined as a >50% reduction of the shunt at angiography or a portosystemic pressure gradient >12 mm Hg.

Results
After a median follow-up of 300 days, 5 patients (13%) in group 1 and 18 (44%) in group 2 experienced shunt dysfunction (P < 0.0001). Clinical relapse occurred in 3 patients (8%) in group 1 and 12 (29%) in group 2 (P < 0.05). Actuarial rates of encephalopathy were 21% in group 1 and 41% in group 2 at 1 year (not significant). Estimated probabilities of survival were 71% and 60% at year 1 and 65% and 41% at 2 years in groups 1 and 2, respectively.

Conclusions
The use of polytetrafluorethylene-covered prostheses improves transjugular intrahepatic portosystemic shunt patency and decreases the number of clinical relapses and reinterventions without increasing the risk of encephalopathy.
HEK 293 cell suspension culture using fibronectin‐adsorbed polymer nanospheres in serum‐free medium
Authors: Ryu Ju Hee , Kim Sang‐Soo , Cho Seung‐Woo , Choi Cha Yong , Kim Byung‐Soo 
Published: August 2004

AbstractPreviously, we reported on suspension culture of anchorage‐dependent animal cells using plain polymer nanospheres in serum‐containing medium. For commercial cell culture, it is more advantageous to use serum‐free medium than serum‐containing medium. To culture anchorage‐dependent animal cells using polymer nanospheres in serum‐free medium, the nanospheres need to be coated with cell adhesion proteins. In this study, we utilized fibronectin‐adsorbed polymer nanospheres for suspension culture of anchorage‐dependent animal cells in serum‐free medium. Fibronectin was adsorbed onto poly(lactic‐co‐glycolic acid) nanospheres (433 nm in average diameter) by immersing the nanospheres in fetal bovine serum. The nanospheres were used to culture human embryonic kidney (HEK) 293 cells in serum‐free medium in stirred suspension bioreactors. Nanospheres attached between HEK 293 cells and promoted cell aggregate formation compared with culture without nanospheres. Most cells in the aggregates were viable over a 10‐day culture period. Importantly, the use of poly(lactic‐co‐glycolic acid) nanospheres promoted the cell growth significantly, compared with culture without nanospheres (3.8‐ vs 1.8‐fold growth). The nanosphere culture method developed in this study removes the time‐consuming and costly process of adaptation of anchorage‐dependent animal cells to suspension culture in serum‐free medium. This culture method may be useful for the large‐scale suspension culture of various types of anchorage‐dependent animal cells in serum‐free medium. © 2004 Wiley Periodicals, Inc. J Biomed Mater Res 71A: 128–133, 2004
In vitro study of cell‐promoting multiple‐armed peptides
Authors: Li Cheng , Zheng Yi , Imran Mir 
Published: August 2004

AbstractThe purpose of this study was to compare the effectiveness of several linear and branch cell‐binding peptides to promote cell growth in prosthetic vascular grafts. In this in vitro study, the peptides were covalently immobilized onto expanded polytetrafluoroethylene (ePTFE) vascular grafts. Cell‐growth properties were studied using primary human umbilical vein endothelial cells (HUVECs) and primary human umbilical artery smooth muscle cells (HUASMCs). Linear peptides (P15 and P15′) and multiple‐armed peptides (MAP4‐I and MAP4‐II) were covalently bonded onto ePTFE grafts by an atmospheric plasma coating method. X‐ray photoelectron spectroscopy and amino acid analysis were used to analyze the surface characteristics of the peptide‐coated samples. Cell adhesion, proliferation, and morphology were evaluated by culturing HUVECs and HUASMCs onto the surfaces of different samples: ePTFE control, chemically activated ePTFE, P15‐coated ePTFE, and MAP4‐coated ePTFE. The cell culture experiments were repeated several times to obtain statistically reliable cell‐growth data. Cell‐growth data were statistically analyzed by the two‐way statistical analysis of variance. The study showed that multiple‐armed MAP4 peptides were significantly more effective in promoting endothelial cells than the structurally similar linear P15 peptides. There were 800% more HUVECs proliferated on the MAP4‐coated ePTFE samples compared with the ePTFE control. MAP4 peptides were 80% more effective for promoting HUVECs than P15 peptides. In contrast, MAP4 peptides were significantly less effective for promoting HUASMCs than HUVECs. There were only about 100% more HUASMCs proliferated on the MAP4‐coated ePTFE samples compared with the ePTFE control. MAP4 and P15 peptides had similar cell‐promoting characteristics for SMCs. © 2004 Wiley Periodicals, Inc. J Biomed Mater Res 71A: 134–142, 2004
Three‐dimensional gait biomechanics in Parkinson's disease: Evidence for a centrally mediated amplitude regulation disorder
Authors: Morris Meg , Iansek Robert , McGinley Jennifer , Matyas Thomas , Huxham Frances 
Published: August 2004

AbstractWe examined whether people with Parkinson's disease (PD) have a central amplitude regulation disorder using three‐dimensional (3‐D) gait analyses to compare the effects of medication and attentional strategies on gait in 12 PD subjects and 12 matched comparison subjects. Subjects with PD first performed several 10‐m gait trials at preferred speed whileofflevodopa. They then walked at preferred speed on levodopa;offlevodopa with cues; andonlevodopa with cues. Control subjects walked at preferred speed and then with visual cues to match their stride length to PD values. As well as spatiotemporal footstep data, pelvic and lower limb kinematic profiles and angle–angle diagrams were produced for sagittal, coronal, and transverse plane movements using a 3‐D motion analysis system. In people with PD, decreased step length was accompanied by reduced movement amplitude across all lower limb joints, in all movement planes. When control subjects were required to walk with short steps matched to the size of PD comparisons, they displayed a similar multijoint reduction in amplitude. For PD subjects, both levodopa and visual cues increased movement amplitude across all lower limb joints. Amplitude increased further when levodopa and visual cues were combined, resulting in normalization of step length. This finding suggested that reduced step length is due to a mismatch between cortically selected movement amplitude and basal ganglia maintenance mechanisms. Levodopa and cues normalized amplitude across all joints by altering motor set and bypassing defective basal ganglia mechanisms. © 2004 Movement Disorder Society
Melting behavior of polyethylene/α‐olefin copolymers: Narrow composition distribution copolymers and fractions from Ziegler–Natta and single‐site catalyst products
Authors: Mirabella Francis M. , Crist Buckley 
Published: August 2004

AbstractThe melting temperature and heat of fusion were measured for an extensive series of compositionally uniform copolymers of ethylene with butene‐1, hexene‐1, and octene‐1. Fractions and whole polymers that exhibited minimal interchain compositional heterogeneity were from commercial copolymers made with either Ziegler–Natta (ZN) or single‐site metallocene catalysts. The present results do not support recent claims that ZN and corresponding metallocene catalyst copolymers melt at significantly different temperatures, nor the implication that comonomer incorporation is “blocky” in ZN copolymers. In five of the six comonomer/catalyst systems the dependencies of the melting temperature on comonomer type and amount were scarcely distinguishable. This common behavior is the same as that for a model random copolymer, so we conclude that most ethylene/α‐olefin copolymers have random distributions of ethylene sequences. The exception in the present study is a metallocene ethylene/butene‐1 copolymer that melts at lower temperatures and apparently has perceptibly alternating sequence distributions. © 2004 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 42: 3416–3427, 2004
Children with smoking parents have a higher airway resistance measured by the interruption technique
Authors: Kooi Elisabeth M.W. , Vrijlandt Elianne J.L.E. , Boezen H. Marike , Duiverman Eric J. 
Published: August 2004

AbstractChildren exposed to environmental tobacco smoke, during or after pregnancy, are known to have decreased lung function. So far this has been measured using spirometry in schoolchildren and invasive techniques in newborns. The interruption technique (Rint) is a noninvasive technique to measure airway resistance in preschool children. Our aim in this study was to investigate the effect of passive smoke exposure on Rint values in preschool and school‐aged children. Rint values were obtained from 557 children in two nursery and two primary schools in the north of the Netherlands. Besides information on parental smoking habits, we collected data on characteristics that might affect airway resistance (respiratory symptoms, atopy, and family history for asthma), using a short questionnaire. Multiple linear regression was used to estimate the associations of these characteristics with Rint, for the whole group as well as for the preschool group separately. Atopy or a positive family history for asthma did not affect Rint values in the total group of 4–12‐year‐olds. However, as may be expected, height, age, weight, and having respiratory symptoms were associated with Rint. Moreover, Rint was significantly increased if parents smoked three or more cigarettes a day in the presence of their child. This result remained after subgroup analysis in the preschool children (4–6 years old). We conclude that passive smoke exposure is associated with a significantly higher airway resistance in preschool and school‐aged children measured by Rint. © 2004 Wiley‐Liss, Inc.
Opioids in neuropathic pain: clues from animal studies
Authors: Dickenson Anthony H. , Suzuki Rie 
Published: August 2004

AbstractFor many years the clinical consensus was that opioids were ineffective in neuropathic pain. However this view is changing and here we discuss the mechanisms of opioid analgesia in terms of the changes that can occur in preclinical models of nerve injury. We argue that opioid mechanisms can be perturbed by neuropathy but in most cases these negative influences can be overcome by dose‐escalation.
The role of AMPA and metabotropic glutamate receptors on morphine withdrawal in infant rats
Authors: Zhu Hongbo , Barr Gordon A. 
Published: August 2004

AbstractGlutamate receptors, especially N‐methyl‐d‐aspartate (NMDA) receptors, are hypothesized to play key roles in opiate tolerance and withdrawal. There is also accumulating evidence that α‐amino‐3‐hydroxy‐5‐methyl‐4‐isoxazolepropionic acid (AMPA) receptor antagonists and group II metabotropic glutamate receptor (mGluR) agonists attenuate opiate withdrawal. However, most existing data are derived from adult animal models. Glutamate receptor types undergo dramatic developmental changes during early life. Thus, the pharmacological effects on opiate withdrawal of NMDA receptor, AMPA receptor, and mGluR antagonists in the developing organism may not be comparable to those in the adult. Indeed, NMDA receptor antagonists do not block morphine tolerance or withdrawal in the 7‐day‐old rat, but are partially effective in the 14‐day‐old, and fully effective in the 21‐day‐old. Thus, there is a transition period around the second post‐natal week for NMDA receptor antagonists to suppress opiate tolerance and withdrawal. A combination of in vivo and in vitro assays was used in the present studies to test the effect of drugs acting on AMPA and group II mGlu receptors on morphine withdrawal in rats at 7, 14, and 21 days of age. These ages represent the critical periods when various glutamate receptor subunits undergo differential change. In contrast to NMDA receptor antagonists’ early ineffectivness in suppressing morphine withdrawal, the AMPA receptor antagonist and the group II mGluR agonists were effective at all ages tested. Thus, for the human infant patient, pharmacotherapies to reduce opiate tolerance and withdrawal should focus on non‐NMDA ionotropic and metabotropic receptors.
Tumour necrosis factor α, lipid peroxidation and NOº are increased and associated with decreased free‐radical scavenging enzymes in patients with Weill‐Marchesani syndrome
Authors: Evereklioglu Cem , Turkoz Yusuf , Calis Mustafa , Duygulu Fuat , Karabulut Aysun B. 
Published: August 2004

AIM: Weill‐Marchesani syndrome (WMS) is a rare systemic disorder with both autosomal recessive and dominant inheritances. Accumulation of reactive oxygen species such as , H2O2 and OH• causes lipid peroxidation (LPO), whereas antioxidant enzymes (superoxide dismutase (SOD), glutathione peroxidase (GSHPx)) mediate defence against oxidative stress. Excess tumour necrosis factor (TNF)‐α and NO• react with and cause further antioxidant depletion with an increase in mutation frequency by H2O2. This study investigated the levels of SOD, GSHPx, catalase (CAT), TNF‐α, NO• and LPO in patients with WMS.Methods: A group of 10 WMS patients (four males, six females; age, 26.5±19.0 years) and 10 age‐matched and sex‐matched controls (five males, five females; age, 27.3±18.2 years) were included. Serum TNF‐α levels were determined by a spectrophotometer technique using immulite chemiluminescent immunometric assay. Malondialdehyde (MDA) was determined in plasma; CAT in red blood cells (RBCs), and SOD and GSHPx in both plasma and RBCs. Total serum NO• levels were evaluated by Griess reaction.Results: Mean levels of TNF‐α (8.3±0.6 pg/ml) in WMS patients were significantly (p < 0.001) higher than controls (4.3±0.2 pg/ml). Plasma MDA levels in patients and controls were 5.4±0.8 and 1.8±0.6 μmol/l, respectively, and the difference was significant (p = 0.0002). SOD and GSHPx activities were significantly lower in both RBCs and plasma of WMS than in controls (RBC‐SOD, 3981.9±626.6 versus 5261.6±523.0 U/g haemoglobin (Hb), p = 0.0005; plasma‐SOD, 529.4±49.3 versus 713.4±55.7 U/g protein, p = 0.0002; RBC‐GSHPx, 682.7±42.0 versus 756.5±47.6 U/g Hb, p = 0.0011; plasma‐GSHPx, 107.3±15.0 versus 131.4±19.7 U/g protein, p = 0.0113). In addition, serum NO• () levels were also significantly (p = 0.0002) increased in WMS patients (54.4±5.7 versus 26.9±6.7 μmol/l). RBC‐CAT levels were similar between groups (125.6±21.3 versus 131.0±21.5 k/g Hb, p = 0.8798).Conclusions: The elevated LPO, TNF‐α and NO• with decreased antioxidant enzyme activities indicated impaired antioxidative defence mechanisms with an oxidative injury and cell toxicity in WMS patients. The use of multiple antioxidants and free radical scavengers might be helpful in this genetic disorder.
Predicting GPCR–G-protein coupling using hidden Markov models
Authors: Sreekumar Kodangattil R. , Huang Youping , Pausch Mark H. , Gulukota Kamalakar 
Published: August 2004

Abstract
Motivation: Determining the coupling specificity of G-protein coupled receptors (GPCRs) is important for understanding the biology of this class of pharmacologically important proteins. Currently available in silico methods for predicting GPCR–G-protein coupling specificity have high error rate.
Method: We introduce a new approach for creating hidden Markov models (HMMs) based on a first guess about the importance of various residues. We call these knowledge restricted HMMs to emphasize the fact that the state space of the HMM is restricted by the application of a priori knowledge. Specifically, we use only those amino acid residues of GPCRs which are likely to interact with G-proteins, namely those that are predicted to be in the intra-cellular loops. Furthermore, we concatenate these predicted loops into one sequence rather than considering them as four disparate units. This reduces the HMM state space by drastically decreasing the sequence length.
Results: Our knowledge restricted HMM based method to predict GPCR–G-protein coupling specificity has an error rate of &lt;1%, when applied to a test set of GPCRs with known G-protein coupling specificity.
Availability: Academic users can get the data set mentioned herein and HMMs from the authors.
Training HMM structure with genetic algorithm for biological sequence analysis
Authors: Won Kyoung-Jae , Prügel-Bennett Adam , Krogh Anders 
Published: August 2004

Abstract
Summary: Hidden Markov models (HMMs) are widely used for biological sequence analysis because of their ability to incorporate biological information in their structure. An automatic means of optimizing the structure of HMMs would be highly desirable. However, this raises two important issues; first, the new HMMs should be biologically interpretable, and second, we need to control the complexity of the HMM so that it has good generalization performance on unseen sequences. In this paper, we explore the possibility of using a genetic algorithm (GA) for optimizing the HMM structure. GAs are sufficiently flexible to allow incorporation of other techniques such as Baum–Welch training within their evolutionary cycle. Furthermore, operators that alter the structure of HMMs can be designed to favour interpretable and simple structures.
In this paper, a training strategy using GAs is proposed, and it is tested on finding HMM structures for the promoter and coding region of the bacterium Campylobacter jejuni. The proposed GA for hidden Markov models (GA-HMM) allows, HMMs with different numbers of states to evolve. To prevent over-fitting, a separate dataset is used for comparing the performance of the HMMs to that used for the Baum–Welch training. The GA-HMM was capable of finding an HMM comparable to a hand-coded HMM designed for the same task, which has been published previously.
Network structures and algorithms in Bioconductor
Authors: Carey Vincent J. , Gentry Jeff , Whalen Elizabeth , Gentleman Robert 
Published: August 2004

Abstract
Summary: In this paper, we review the central concepts and implementations of tools for working with network structures in Bioconductor. Interfaces to open source resources for visualization (AT&T Graphviz) and network algorithms (Boost) have been developed to support analysis of graphical structures in genomics and computational biology.
Availability: Packages graph, Rgraphviz, RBGL of Bioconductor (www.bioconductor.org).
Contact: stvjc@channing.harvard.edu
PIML: the Pathogen Information Markup Language
Authors: He Yongqun , Vines Richard R. , Wattam Alice R. , Abramochkin Georgiy V. , Dickerman Allan W. , Eckart J. Dana , Sobral Bruno W. S. 
Published: August 2004

AbstractMotivation: A vast amount of information about human, animal and plant pathogens has been acquired, stored and displayed in varied formats through different resources, both electronically and otherwise. However, there is no community standard format for organizing this information or agreement on machine-readable format(s) for data exchange, thereby hampering interoperation efforts across information systems harboring such infectious disease data.Results: The Pathogen Information Markup Language (PIML) is a free, open, XML-based format for representing pathogen information. XSLT-based visual presentations of valid PIML documents were developed and can be accessed through the PathInfo website or as part of the interoperable web services federation known as ToolBus/PathPort. Currently, detailed PIML documents are available for 21 pathogens deemed of high priority with regard to public health and national biological defense. A dynamic query system allows simple queries as well as comparisons among these pathogens. Continuing efforts are being taken to include other groups' supporting PIML and to develop more PIML documents.Availability: All the PIML-related information is accessible from http://www.vbi.vt.edu/pathport/pathinfo/Contact: pathinfo@vbi.vt.edu
Using amphiphilic pseudo amino acid composition to predict enzyme subfamily classes
Authors: Chou Kuo-Chen 
Published: August 2004

Abstract
Motivation: With protein sequences entering into databanks at an explosive pace, the early determination of the family or subfamily class for a newly found enzyme molecule becomes important because this is directly related to the detailed information about which specific target it acts on, as well as to its catalytic process and biological function. Unfortunately, it is both time-consuming and costly to do so by experiments alone. In a previous study, the covariant-discriminant algorithm was introduced to identify the 16 subfamily classes of oxidoreductases. Although the results were quite encouraging, the entire prediction process was based on the amino acid composition alone without including any sequence-order information. Therefore, it is worthy of further investigation.
Results: To incorporate the sequence-order effects into the predictor, the ‘amphiphilic pseudo amino acid composition’ is introduced to represent the statistical sample of a protein. The novel representation contains 20 + 2λ discrete numbers: the first 20 numbers are the components of the conventional amino acid composition; the next 2λ numbers are a set of correlation factors that reflect different hydrophobicity and hydrophilicity distribution patterns along a protein chain. Based on such a concept and formulation scheme, a new predictor is developed. It is shown by the self-consistency test, jackknife test and independent dataset tests that the success rates obtained by the new predictor are all significantly higher than those by the previous predictors. The significant enhancement in success rates also implies that the distribution of hydrophobicity and hydrophilicity of the amino acid residues along a protein chain plays a very important role to its structure and function.
Contact: kchou@san.rr.com
Construction of robust prognostic predictors by using projective adaptive resonance theory as a gene filtering method
Authors: Takahashi Hiro , Kobayashi Takeshi , Honda Hiroyuki 
Published: August 2004

Abstract
Motivation: For establishing prognostic predictors of various diseases using DNA microarray analysis technology, it is desired to find selectively significant genes for constructing the prognostic model and it is also necessary to eliminate non-specific genes or genes with error before constructing the model.
Results: We applied projective adaptive resonance theory (PART) to gene screening for DNA microarray data. Genes selected by PART were subjected to our FNN-SWEEP modeling method for the construction of a cancer class prediction model. The model performance was evaluated through comparison with a conventional screening signal-to-noise (S2N) method or nearest shrunken centroids (NSC) method. The FNN-SWEEP predictor with PART screening could discriminate classes of acute leukemia in blinded data with 97.1% accuracy and classes of lung cancer with 90.0% accuracy, while the predictor with S2N was only 85.3 and 70.0% or the predictor with NSC was 88.2 and 90.0%, respectively. The results have proven that PART was superior for gene screening.
Availability: The software is available upon request from the authors.
Contact: honda@nubio.nagoya-u.ac.jp