bluuebunny/crossref_metadata_2025_split huggingface dataset:
WEbcoli: an interactive and asynchronous web application for in silico design and analysis of genome-scale E.coli model
Authors: Jung Tae-Sung , Yeo Hock Chuan , Reddy Satty G. , Cho Wan-Sup , Lee Dong-Yup 
Published: August 2009

Abstract
Summary: WEbcoli is a WEb application for in silico designing, analyzing and engineering Escherichia coli metabolism. It is devised and implemented using advanced web technologies, thereby leading to enhanced usability and dynamic web accessibility. As a main feature, the WEbcoli system provides a user-friendly rich web interface, allowing users to virtually design and synthesize mutant strains derived from the genome-scale wild-type E.coli model and to customize pathways of interest through a graph editor. In addition, constraints-based flux analysis can be conducted for quantifying metabolic fluxes and charactering the physiological and metabolic states under various genetic and/or environmental conditions.
Availability: WEbcoli is freely accessible at http://webcoli.org.
Contact: cheld@nus.edu.sg
Improving peptide identification with single-stage mass spectrum peaks
Authors: He Zengyou , Yu Weichuan 
Published: August 2009

Abstract
Motivation: Database searching is the major peptide identification method in shotgun proteomics. It searches tandem mass spectrometry (MS/MS) spectra against a protein database to identify target peptides. The success of such a database searching method relies on a scoring algorithm that can evaluate the quality of peptide-spectrum matches (PSMs) accurately. However, current scoring algorithms frequently generate inaccurate assignments due to variations and noises in the MS/MS spectra. To address this issue, we like to improve peptide identification by using additional information from other data sources.
Results: Single-stage MS data is complementary to MS/MS data in the sense that it provides broader mass coverage but less sequence information. In this article, we show that single-stage MS data can be used to re-rank PSMs. The proposed method explores a linear combination of scores between MS and MS/MS data to perform re-ranking. Experimental results on real data show that such a re-ranking strategy improves the identification performance significantly.
Availability: http://bioinformatics.ust.hk/ReRankPSMwMS1.rar
Contact: eezyhe@ust.hk
Supplementary information: Supplementary data are available at Bioinformatics online.
Coherent trends in contiguous survey time-series of major ecological and commercial fish species in the Gulf of Maine ecosystem
Authors: Nye Janet A. , Bundy Alida , Shackell Nancy , Friedland Kevin D. , Link Jason S. 
Published: August 2009

AbstractNye, J. A., Bundy, A., Shackell, N., Friedland, K. D., and Link, J. S. 2010. Coherent trends in contiguous survey time-series of major ecological and commercial fish species in the Gulf of Maine ecosystem. – ICES Journal of Marine Science, 67: 26–40. Fish are often delineated into distinct population or stock units that reflect human institutional borders more than ecological factors. In the Northwest Atlantic, there are many species in the broader Gulf of Maine area (GOMA), yet the area is surveyed and managed for the most part in the south by the United States and in the north by Canada. Biomass time-series of 19 representative fish species and total biomass from 7 different surveys conducted by the United States and Canada in the GOMA are compared. All species showed coherent trends in relative biomass across at least two survey time-series, and in many species a single trend could describe all time-series trends accurately. For instance, Canadian and the US time-series of Atlantic cod, Atlantic herring, haddock, thorny skate, and goosefish had comparable trends. Conversely, species such as longhorn sculpin and spiny dogfish showed differing survey time-series trends and asynchronous event timing, suggesting that their population dynamics differ spatially. Collectively, the results demonstrate the value of comparing time-series for common species from contiguous ecosystems and elucidate the relative importance of environmental and fishing factors on each species.
Does Postoperative Delirium Limit the Use of Patient-controlled Analgesia in Older Surgical Patients?
Authors: Leung Jacqueline M. , Sands Laura P. , Paul Sudeshna , Joseph Tim , Kinjo Sakura , Tsai Tiffany 
Published: August 2009

Unlabelled
BACKGROUNDPostoperative pain Is an independent predictor of postoperative delirium. Whether postoperative delirium limits patient-controlled analgesia (PCA) use has not been determined.

Methods
The authors conducted a nested cohort study in older patients undergoing noncardiac surgery and used PCA for postoperative analgesia. Delirium was measured by using the Confusion Assessment Method. The authors computed a structural equation model to determine the effects of pain and opioid consumption on delirium status and the effect of delirium on opioid use.

Results
Of 335 patients, 108 (32.2%) developed delirium on postoperative day (POD) 1, and 120 (35.8%) on POD 2. Postoperative delirium did not limit the use of PCA. Patients with postoperative delirium used more PCA in a 24-h period (POD 2) compared to those without delirium (mean dose of hydromorphone +/- SE adjusted for covariates was 2.24 +/- 0.71 mg vs. 1.25 +/- 0.67 mg, P = 0.02). Despite more opioid use, patients with delirium reported higher Visual Analogue Scale scores than those without delirium (POD 1: mean visual analog scale +/- SE at rest 4.2 +/- 0.23 vs. 3.3 +/- 0.22, P = 0.0051; POD 2: 3.3 +/- 0.23 vs. 2.5 +/- 0.19, P = 0.004). Path coefficients from structural equation model revealed that pain and opioid use affect delirium status, but delirium does not affect subsequent opioid dose.

Conclusions
Postoperative delirium did not limit PCA use. Despite more opioid use, visual analog scale scores were higher in patients with delirium. Future studies on delirium should consider the role of pain and pain management as potential etiologic factors.
Dreaming and Electroencephalographic Changes during Anesthesia Maintained with Propofol or Desflurane
Authors: Leslie Kate , Sleigh Jamie , Paech Michael J. , Voss Logan , Lim Chiew Woon , Sleigh Callum 
Published: August 2009

Background
Dream recall is reportedly more common after propofol than after volatile anesthesia, but this may be due to delayed emergence or more amnesia after longer-acting volatiles. The electroencephalographic signs of dreaming during anesthesia and the differences between propofol and desflurane also are unknown. The authors therefore compared dream recall after propofol- or desflurane-maintained anesthesia and analyzed electroencephalographic patterns in dreamers and nondreamers and in propofol and desflurane patients for similarities to rapid eye movement and non-rapid eye movement sleep.

Methods
Three hundred patients presenting for noncardiac surgery were randomized to receive propofol- or desflurane-maintained anesthesia. The raw electroencephalogram was recorded from induction until patients were interviewed about dreaming when they became first oriented postoperatively. Using spectral and ordinal methods, the authors quantified the amount of sleep spindle-like activity and high-frequency power in the electroencephalogram.

Results
The incidence of dream recall was similar for propofol (27%) and desflurane (28%) patients. Times to interview were similar (median 20 [range 4-114] vs. 17 [7-86] min; P = 0.1029), but bispectral index values at interview were lower (85 [69-98] vs. 92 [40-98]; P < 0.0001) in propofol than in desflurane patients. During surgery, the raw electroencephalogram of propofol patients showed more and faster spindle activity than in desflurane patients (P < 0.001). The raw electroencephalogram of dreamers showed fewer spindles and more high-frequency power than in nondreamers in the 5 min before interview (P < 0.05).

Conclusions
Anesthetic-related dreaming seems to occur just before awakening and is associated with a rapid eye movement-like electroencephalographic pattern.
Effects of Remifentanil on the Spectrum and Quantitative Parameters of Electroencephalogram in Propofol Anesthesia
Authors: Kortelainen Jukka , Koskinen Miika , Mustola Seppo , Seppänen Tapio 
Published: August 2009

Background
A high dose of opioids associated with a low dose of propofol has become a popular anesthetic technique. However, the influence of opioids on the electroencephalographic phenomenon related to induction of anesthesia and, thereby, on the quantitative parameters used in the depth-of-anesthesia estimation is not well known.

Methods
Twenty-seven patients were divided into three groups to receive saline, low-dose remifentanil (7.5 microg x kg x h) or high-dose remifentanil (30 microg x kg x h) during induction of anesthesia with propofol (30 mg . kg . h). Electroencephalogram was recorded from Fz electrode, and its time-frequency properties in the patient groups were analyzed from the induction of anesthesia to the occurrence of burst suppression pattern. The group differences in 14 quantitative spectral parameters used in the depth-of-anesthesia estimation were examined as well.

Results
The time-frequency properties of electroencephalogram were different between groups. The high-frequency (greater than 14 Hz) activity during light anesthesia was decreased in remifentanil groups; whereas, increased activity in extended alpha band (7-14 Hz) and decreased activity in delta band (0.5-4 Hz) was observed during deep anesthesia. This resulted in statistically significant changes in all 14 quantitative parameters.

Conclusions
The effect of remifentanil on the spectrum and quantitative parameters of electroencephalogram is significant and strongly dependent on the level of anesthesia. Coadministration of opioids therefore challenges the reliability of the spectral properties of electroencephalogram in the depth-of-anesthesia estimation by using a frontal montage. Furthermore, the finding has implications for design of opioid coadministration studies.
Analgesic Efficacy of Peripheral κ-Opioid Receptor Agonist CR665 Compared to Oxycodone in a Multi-modal, Multi-tissue Experimental Human Pain Model
Authors: Arendt-Nielsen Lars , Olesen Anne E. , Staahl Camilla , Menzaghi Frédérique , Kell Sherron , Wong Gilbert Y. , Drewes Asbjørn M. 
Published: August 2009

Background
Peripherally selective opioids may be beneficial in visceral pain management due to absence of centrally mediated side effects. The objectives of this study were: (1) to assess the effects of a peripherally selective tetrapeptide kappa-opioid receptor agonist, CR665, on experimental pain from multi-modal stimulation of skin, muscle, and viscera, and (2) contrast these effects with those of oxycodone (centrally acting opioid).

Methods
The study was designed as a single-center, single-dose, randomized, double-blind, placebo and active-controlled, double-dummy, three-way, crossover study in healthy males. Subjects received the following treatments in randomized order: (1) CR665 (0.36 mg/kg) administered intravenously over 1 h, (2) oxycodone (15 mg) administered orally, and (3) placebo administered intravenously and orally. The following pain tests were used: (1) cutaneous pinch pain tolerance threshold, (2) pressure pain detection and tolerance thresholds, (3) cuff pressure pain tolerance threshold, and (4) pain rating thresholds to distension and thermal stimulation of the esophagus. Measurements were performed before dosing and at 30, 60, and 90 min after dosing.

Results
Compared to placebo, oxycodone elevated cutaneous pinch pain tolerance (P < 0.001) and cuff pressure pain tolerance threshold (P < 0.001), as well as pain rating thresholds (visual analogue scale = 7) to esophageal distension (P < 0.001) and thermal stimulation (P < 0.002). Compared to placebo, CR665 significantly increased the pain rating threshold to esophageal distension (P < 0.005) but reduced the pain tolerance threshold to skin pinching (P = 0.007).

Conclusion
CR665 had a selective effect on visceral pain. Oxycodone exhibited a generalized effect, elevating thresholds for cutaneous, deep somatic, and visceral pain stimulation.
Bedside Prediction of Airway Length in Adults and Children
Authors: Lee Bong-Jae , Yi Jae-Woo , Chung Jun Young , Kim Dong-Ok , Kang Jong-Man 
Published: August 2009

Background
Malpositioning of the endotracheal tube within the airway leads to serious complications such as endobronchial intubation. Prediction of the correct depth of an endotracheal tube is important and should be individualized. The manubriosternal joint (MSJ) is on the same horizontal plane with the tracheal carina. We compared the straight length from the upper incisor to the MSJ in the fully extended position (incisor-MSJ extension length) with the length from the upper incisor to the carina after intubation with a flexible fiberoptic bronchoscope through the endotracheal tube in the neutral position (incisor-carina neutral length).

Methods
One hundred adults and 50 children were studied. Induction of anesthesia was achieved with 1.5 mg/kg propofol and 0.6 mg/kg rocuronium IV. The incisor-MSJ extension length was measured after adequate mask ventilation. After intubation, the endotracheal tube was positioned properly at the upper incisor teeth, and the incisor-carina neutral length was measured with the fiberoptic bronchoscope at the carina.

Results
The correlation between the incisor-MSJ extension length and the incisor-carina neutral length is significant (P < 0.001) in both adults and children. A formula for the regression line in adults (children) can be obtained as the incisor-carina neutral length (cm) = 0.868 (1.009) x the incisor-MSJ extension length (cm) + 4.260 (0.468) with a high coefficient of determination; r(2) = 0.88 (0.98).

Conclusions
The airway length from the upper incisor to the carina in the neutral position can be predicted by the straight length from the upper incisor to the MSJ in the fully extended position.
Precision of Traditional Approaches for Lumbar Plexus Block
Authors: Heller Axel R. , Fuchs Alexander , Rössel Thomas , Vicent Oliver , Wiessner Diana , Funk Richard H. W. , Koch Thea , Litz Rainer J. 
Published: August 2009

Background
Traditional methods for approaching the lumbar plexus from the posterior rely on finding the intersection of lines that are drawn based on surface landmarks. These methods may be inaccurate in many cases. The aim of this study was to determine the accuracy of these traditional approaches and determine if modifications could increase their accuracy.

Methods
The lumbar plexus region of 48 cadavers (78 +/- 7 yr; 167 +/- 6 cm; 60 +/- 13 kg; men/women: 29/19) was dissected, and relevant anatomic structures were marked. Needle proximity curves were obtained by triangulation for the five traditional approaches and for vectors from the posterior superior iliac spine directed towards the lumbar spinous processes of L3 and towards L4.

Results
Proximity curves (mean +/- SD) showed that except Pandin's approach (13 +/- 5 mm too medial), all others were too lateral: Winnie (17 +/- 8 mm), Chayen (8 +/- 5 mm), Capdevila (6 +/- 4 mm), and Dekrey (17 +/- 6 mm). Further, the curves had a narrow parabolic shape and thus a narrow margin of error. Both diagonal vectors had a significantly higher proximity to the lumbar plexus as compared with traditional approaches with a wide parabola, indicating more error tolerance. Using the vector posterior superior iliac spine-L3 with a length between 1/6-1/3 (= 16-22 mm) of the distance posterior superior iliac spine-L3, a proximity to the lumbar plexus < 5.0 +/- 0.3 mm was reached.

Conclusion
Improvement of both the proximity and the margin of error is possible by using diagonal landmark vectors. Relying on the position of the posterior superior iliac spine eliminates the sex and sided differences and individual body size, which can be problematic if firm metric distances are used in determining the entry point.
Isoflurane Inhibits the Tetrodotoxin-resistant Voltage-gated Sodium Channel Nav1.8
Authors: Herold Karl F. , Nau Carla , Ouyang Wei , Hemmings Hugh C. 
Published: August 2009

Background
Voltage-gated sodium channels (Nav) mediate neuronal action potentials. Tetrodotoxin inhibits all Nav isoforms, but Nav1.8 and Nav1.9 are relatively tetrodotoxin-resistant (TTX-r) compared to other isoforms. Nav1.8 is highly expressed in dorsal root ganglion neurons and is functionally linked to nociception, but the sensitivity of TTX-r isoforms to inhaled anesthetics is unclear.

Methods
The sensitivities of heterologously expressed rat TTX-r Nav1.8 and endogenous tetrodotoxin-sensitive (TTX-s) Nav to the prototypic inhaled anesthetic isoflurane were tested in mammalian ND7/23 cells using patch-clamp electrophysiology.

Results
From a holding potential of -70 mV, isoflurane (0.53 +/- 0.06 mM, 1.8 minimum alveolar concentration at 24 degrees C) reduced normalized peak Na current (INa) of Nav1.8 to 0.55 +/- 0.03 and of endogenous TTX-s Nav to 0.56 +/- 0.06. Isoflurane minimally inhibited INa from a holding potential of -140 mV. Isoflurane did not affect voltage-dependence of activation, but it significantly shifted voltage-dependence of steady-state inactivation by -6 mV for Nav1.8 and by -7 mV for TTX-s Nav. IC50 values for inhibition of peak INa were 0.67 +/- 0.06 mM for Nav1.8 and 0.66 +/- 0.09 mM for TTX-s Nav; significant inhibition occurred at clinically relevant concentrations as low as 0.58 minimum alveolar concentration. Isoflurane produced use-dependent block of Nav1.8; at a stimulation frequency of 10 Hz, 0.56 +/- 0.08 mM isoflurane reduced INa to 0.64 +/- 0.01 versus 0.78 +/- 0.01 for control.

Conclusion
Isoflurane inhibited the tetrodotoxin-resistant isoform Nav1.8 with potency comparable to that for endogenous tetrodotoxin-sensitive Nav isoforms, indicating that sensitivity to inhaled anesthetics is conserved across diverse Nav family members. Block of Nav1.8 in dorsal root ganglion neurons could contribute to the effects of inhaled anesthetics on peripheral nociceptive mechanisms.
Epinephrine Impairs Lipid Resuscitation from Bupivacaine Overdose
Authors: Hiller David B. , Gregorio Guido Di , Ripper Richard , Kelly Kemba , Massad Malek , Edelman Lucas , Edelman Guy , Feinstein Douglas L. , Weinberg Guy L. 
Published: August 2009

Background
Lipid emulsion infusion reverses local anesthetic-induced cardiac toxicity, but the effect of adding epinephrine has not been studied. We compared escalating doses of epinephrine on recovery with lipid infusion in a rat model of bupivacaine overdose.

Methods
Rats anesthetized with isoflurane received an IV bolus of 20 mg/kg bupivacaine, producing asystole (zero time) in all animals. Ventilation (100% oxygen) and chest compressions were started immediately, and at 3 min the rats received one of six IV treatments (n = 5 for all groups): 5 ml/kg saline followed by infusion for 2 min at 1.0 ml x kg x min, and a second 5 ml/kg bolus at 5 min; or the same bolus and infusion treatment using 30% lipid emulsion plus a single injection of epinephrine at one of five doses: 0 (lipid control), 1, 2.5, 10, or 25 mcg/kg. An electrocardiogram and arterial pressure were monitored continuously, and arterial blood gas was measured at 7.5 and 15 min.

Results
Epinephrine improved initial return of spontaneous circulation (rate-pressure product > 30% baseline) but only 3 of 5 rats at 10 mcg/kg and 1 of 5 rats at 25 mcg/kg sustained return of spontaneous circulation by 15 min. Lipid alone resulted in slower but more sustained recovery. Epinephrine doses above a threshold near 10 mcg/kg increased lactate, worsened acidosis, and resulted in poor recovery at 15 min, as compared with lipid controls. There was tight correlation of epinephrine dose to serum lactate at 15 min.

Conclusions
Epinephrine over a threshold dose near 10 mcg/kg impairs lipid resuscitation from bupivacaine overdose, possibly by inducing hyperlactatemia.
In Vitro Effects of Propofol and Volatile Agents on Pharmacologically Induced Chloride Channel Myotonia
Authors: Bandschapp Oliver , Ginz Hans F. , Soule Charles L. , Girard Thierry , Urwyler Albert , Iaizzo Paul A. 
Published: August 2009

Background
Anesthetic choice for patients with chloride channel myotonia remains under debate. The authors have, therefore, investigated the in vitro effects of various anesthetic agents on pharmacologically induced chloride channel myotonia.

Methods
Functionally viable (> 10 mN force generation) rectus abdominis muscle preparations obtained from normal swine were investigated using in vitro muscle contracture test baths. During continuous 0.1-Hz supramaximal electrical stimulation, the chloride channel blocker 9-anthracenecarboxylic acid (64 microM) was added before the addition of propofol or one of three volatile anesthetics. The concentration of propofol in either Intralipid (n = 11) or dimethyl sulfoxide (n = 10) was doubled every 10 min (from 4-512 microM). The concentration of halothane (n = 8), isoflurane (n = 8), and sevoflurane (n = 8) was doubled from 0.25 vol% up to the maximum dose according to calibrated vaporizers. Control muscle bundles were either untreated (n = 30) or exposed to 9-anthracenecarboxylic acid (n = 19).

Results
The myotonic reactions induced by 9-anthracenecarboxylic acid were reversed by high-dose (> 64 microM) propofol (P < 0.01). Halothane, isoflurane, or sevoflurane each enhanced the myotonic reactions at 5.4 (P < 0.001), 0.21 (P < 0.01), and 0.5 minimum alveolar concentrations (P < 0.05), respectively.

Conclusions
The authors' in vitro data imply that propofol administration for general anesthesia may be better suited for patients with chloride channel myotonia versus volatile anesthetics. In isolated swine skeletal muscle bundles, propofol elicited a reversal of 9-anthracenecarboxylic acid-induced chloride channel myotonia, whereas volatile anesthetics further increased the associated myotonic reactions.
Spinal Microglial Expression and Mechanical Hypersensitivity in a Postoperative Pain Model: Comparison with a Neuropathic Pain Model
Authors: Ito Naomi , Obata Hideaki , Saito Shigeru 
Published: August 2009

Background
Postoperative pain control contributes to quality of life. Activation of spinal cord microglia after peripheral nerve injury contributes to mechanical hypersensitivity. The contribution of spinal cord microglia to hypersensitivity after surgery, however, is not well understood. Here, the authors evaluated whether inhibition of spinal microglia reduced postoperative mechanical hypersensitivity, and if so, whether the effect differed from that in a rat neuropathic pain model.

Methods
Male Sprague-Dawley rats underwent either unilateral plantar hind paw incision (postoperative pain model) or L5 spinal nerve transection (neuropathic pain model), and the development of mechanical hypersensitivity was assessed using von Frey filaments. The microglial inhibitor minocycline was intraperitoneally administered daily for either 3 or 7 days. Spinal microglial activation was evaluated by OX42 immunohistochemistry. We also tested the effect of intrathecal administration of a p38 mitogen-activated protein kinase inhibitor, SB203580.

Results
In the postoperative pain model, minocycline did not suppress mechanical hypersensitivity, but did inhibit an increase in spinal OX42 expression. In contrast, in the neuropathic pain model, minocycline reduced mechanical hypersensitivity in a dose-related manner and inhibited spinal OX42 expression. SB203580 attenuated hypersensitivity in the neuropathic pain model, but not in the postoperative pain model.

Conclusions
The results of the present study suggest that spinal OX42 expression has a more important role in the development of neuropathic pain than in postoperative pain, and that an increase in spinal OX42 expression does not contribute to postoperative mechanical hypersensitivity.