bluuebunny/crossref_metadata_2025_split huggingface dataset:
MSMSpdbb: providing protein databases of closely related organisms to improve proteomic characterization of prokaryotic microbes
Authors: de Souza Gustavo A. , Arntzen Magnus Ø. , Wiker Harald G. 
Published: January 2010

Abstract
Summary: The Microbial Proteomic Resource (MPR) is a repository service that contains non-redundant protein databases of related bacterial strains, which were generated through an in-house developed software called Multi-Strain Mass Spectrometry Prokaryotic DataBase Builder (MSMSpdbb). MSMSpdbb merges and clusters protein sequences inferred from genomic sequences, and provide a protein list in FASTA format that covers for divergence in gene annotation, translational start site choice and presence of single nucleotide polymorphisms and other mutations.
Availability: MSMSpdbb was developed in C++ using the Qt libraries (Nokia) and licensed under the GNU General Public License version 2. MSMSpdbb is freely available, and its installation files, instructions for use and additional documentation can be found at the MPR web site http://org.uib.no/prokaryotedb/ can also be found at Proteomecommons.org (see Supplementary Methods for Hash number).
Contact: Gustavo.Souza@biomed.uib.no
Supplementary information: Supplementary data are available at Bioinformatics online.
Bayesian rule learning for biomedical data mining
Authors: Gopalakrishnan Vanathi , Lustgarten Jonathan L. , Visweswaran Shyam , Cooper Gregory F. 
Published: January 2010

Abstract
Motivation: Disease state prediction from biomarker profiling studies is an important problem because more accurate classification models will potentially lead to the discovery of better, more discriminative markers. Data mining methods are routinely applied to such analyses of biomedical datasets generated from high-throughput ‘omic’ technologies applied to clinical samples from tissues or bodily fluids. Past work has demonstrated that rule models can be successfully applied to this problem, since they can produce understandable models that facilitate review of discriminative biomarkers by biomedical scientists. While many rule-based methods produce rules that make predictions under uncertainty, they typically do not quantify the uncertainty in the validity of the rule itself. This article describes an approach that uses a Bayesian score to evaluate rule models.
Results: We have combined the expressiveness of rules with the mathematical rigor of Bayesian networks (BNs) to develop and evaluate a Bayesian rule learning (BRL) system. This system utilizes a novel variant of the K2 algorithm for building BNs from the training data to provide probabilistic scores for IF-antecedent-THEN-consequent rules using heuristic best-first search. We then apply rule-based inference to evaluate the learned models during 10-fold cross-validation performed two times. The BRL system is evaluated on 24 published ‘omic’ datasets, and on average it performs on par or better than other readily available rule learning methods. Moreover, BRL produces models that contain on average 70% fewer variables, which means that the biomarker panels for disease prediction contain fewer markers for further verification and validation by bench scientists.
Contact: vanathi@pitt.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
PSiFR: an integrated resource for prediction of protein structure and function
Authors: Pandit Shashi B. , Brylinski Michal , Zhou Hongyi , Gao Mu , Arakaki Adrian K. , Skolnick Jeffrey 
Published: January 2010

Abstract
Summary: In the post-genomic era, the annotation of protein function facilitates the understanding of various biological processes. To extend the range of function annotation methods to the twilight zone of sequence identity, we have developed approaches that exploit both protein tertiary structure and/or protein sequence evolutionary relationships. To serve the scientific community, we have integrated the structure prediction tools, TASSER, TASSER-Lite and METATASSER, and the functional inference tools, FINDSITE, a structure-based algorithm for binding site prediction, Gene Ontology molecular function inference and ligand screening, EFICAz2, a sequence-based approach to enzyme function inference and DBD-hunter, an algorithm for predicting DNA-binding proteins and associated DNA-binding residues, into a unified web resource, Protein Structure and Function prediction Resource (PSiFR).
Availability and implementation: PSiFR is freely available for use on the web at http://psifr.cssb.biology.gatech.edu/
Contact: skolnick@gatech.edu
Active site prediction using evolutionary and structural information
Authors: Sankararaman Sriram , Sha Fei , Kirsch Jack F. , Jordan Michael I. , Sjölander Kimmen 
Published: January 2010

AbstractMotivation: The identification of catalytic residues is a key step in understanding the function of enzymes. While a variety of computational methods have been developed for this task, accuracies have remained fairly low. The best existing method exploits information from sequence and structure to achieve a precision (the fraction of predicted catalytic residues that are catalytic) of 18.5% at a corresponding recall (the fraction of catalytic residues identified) of 57% on a standard benchmark. Here we present a new method, Discern, which provides a significant improvement over the state-of-the-art through the use of statistical techniques to derive a model with a small set of features that are jointly predictive of enzyme active sites.Results: In cross-validation experiments on two benchmark datasets from the Catalytic Site Atlas and CATRES resources containing a total of 437 manually curated enzymes spanning 487 SCOP families, Discern increases catalytic site recall between 12% and 20% over methods that combine information from both sequence and structure, and by ≥50% over methods that make use of sequence conservation signal only. Controlled experiments show that Discern's improvement in catalytic residue prediction is derived from the combination of three ingredients: the use of the INTREPID phylogenomic method to extract conservation information; the use of 3D structure data, including features computed for residues that are proximal in the structure; and a statistical regularization procedure to prevent overfitting.Contact: kimmen@berkeley.eduSupplementary information: Supplementary data are available at Bioinformatics online.
Faster computation of exact RNA shape probabilities
Authors: Janssen Stefan , Giegerich Robert 
Published: January 2010

Abstract
Motivation: Abstract shape analysis allows efficient computation of a representative sample of low-energy foldings of an RNA molecule. More comprehensive information is obtained by computing shape probabilities, accumulating the Boltzmann probabilities of all structures within each abstract shape. Such information is superior to free energies because it is independent of sequence length and base composition. However, up to this point, computation of shape probabilities evaluates all shapes simultaneously and comes with a computation cost which is exponential in the length of the sequence.
Results: We device an approach called RapidShapes that computes the shapes above a specified probability threshold T by generating a list of promising shapes and constructing specialized folding programs for each shape to compute its share of Boltzmann probability. This aims at a heuristic improvement of runtime, while still computing exact probability values.
Conclusion: Evaluating this approach and several substrategies, we find that only a small proportion of shapes have to be actually computed. For an RNA sequence of length 400, this leads, depending on the threshold, to a 10–138 fold speed-up compared with the previous complete method. Thus, probabilistic shape analysis has become feasible in medium-scale applications, such as the screening of RNA transcripts in a bacterial genome.
Availability: RapidShapes is available via http://bibiserv.cebitec.uni-bielefeld.de/rnashapes
Contact: robert@techfak.uni-bielefeld.de
Supplementary information: Supplementary data are available at Bioinformatics online.
The dynamic assessment of right‐ventricular function and its relation to exercise capacity in heart failure
Authors: Rubiś Paweł , Podolec Piotr , Kopeć Grzegorz , Olszowska Maria , Tracz Wiesława 
Published: January 2010

AimsTo evaluate right‐ventricular (RV) function during stress echocardiography (SE) and to assess its relationship with exercise capacity in heart failure (HF) patients.Methods and resultsWe included 88 patients aged 60.9 ± 11.2 years with a mean LVEF of 27.2 ± 9.5%. The following RV parameters were measured at baseline and peak exercise during semi‐supine SE: velocity (IVV) and acceleration during isovolumic contraction (IVA), S′, E′, A′, and ratio of early diastolic tricuspid velocity to E′ (E/E′) and longitudinal strain and strain rate. Patients were stratified into two groups according to their VO2peak values: group 1 (n = 35) with VO2peak <14 mL/kg/min and group 2 (n = 53) with VO2peak ≥14 mL/kg/min. At rest, all analysed variables were similar in the two groups, but during stress IVV, S′, and E′ were significantly higher and the E/E′ ratio significantly lower in group 2. In broad terms, parameters measured at stress correlated much better with VO2peak than parameters assessed at baseline. However, results of multivariable analysis determined that the independent predictors of VO2peak were solely the left‐ventricular (LV) parameters: E/E′ and S′.ConclusionsRight‐ventricular function (whether at rest or during stress tests) was not significantly associated with exercise capacity in our patients with HF. In contrast, systolic and, to a greater extent, diastolic LV parameters during the stress tests emerged as the most important indicators linked to exercise capacity in HF.
Redox Balance and Cellular Inflammation in the Diaphragm, Limb Muscles, and Lungs of Mechanically Ventilated Rats
Authors: Marín-Corral Judith , Martínez-Caro Leticia , Lorente José A. , de Paula Marta , Pijuan Lara , Nin Nicolas , Gea Joaquim , Esteban Andrés , Barreiro Esther 
Published: January 2010

Background
High tidal volume (VT) mechanical ventilation was shown to induce organ injury other than lung injury and systemic inflammation in animal models of ventilator-induced lung injury. The authors aimed to explore whether high VT mechanical ventilation per se induces early oxidative stress and inflammation in the diaphragm, limb muscles, and lungs of healthy rats exposed to ventilator-induced lung injury.

Methods
Protein carbonylation and nitration, antioxidants (immunoblotting), and inflammation (immunohistochemistry) were evaluated in the diaphragm, gastrocnemius, soleus, tibialis anterior, and lungs of mechanically ventilated healthy rats and in nonventilated control animals (n = 8/group) for 1 h, using two different strategies (moderate VT [VT = 9 ml/kg] and high VT [VT = 35 ml/kg]).

Results
The main findings are summarized as follows: compared with controls, (1) the diaphragms and gastrocnemius of high-VT rats exhibited a decrease in reactive carbonyls, (2) the soleus and tibialis of high- and moderate-VT rodents showed a reduction in reactive carbonyls and malondialdehyde-protein adducts, (3) the lungs of high-VT rats exhibited a significant rise in malondialdehyde-protein adducts, (4) the soleus and tibialis of both high- and moderate-VT rats showed a reduction in protein nitration, (5) the lungs of high- and moderate-VT rats showed a reduction in antioxidant enzyme levels, but not in the muscles, and (6) the diaphragms and gastrocnemius of all groups exhibited very low inflammatory cell counts, whereas the lungs of high-VT rats exhibited a significant increase in inflammatory infiltrates.

Conclusions
Although oxidative stress and inflammation increased in the lungs of rats exposed to high VT, the diaphragm and limb muscles exhibited a decline in oxidative stress markers and very low levels of cellular inflammation.
Brainstem Regions Affecting Minimum Alveolar Concentration and Movement Pattern during Isoflurane Anesthesia
Authors: Jinks Steven L. , Bravo Milo , Satter Omar , Chan Yuet-Ming 
Published: January 2010

Background
Spinal transection or selective delivery of volatile anesthetics to the spinal cord reduces minimum alveolar concentration (MAC), whereas precollicular decerebration does not. The authors sought to determine which brainstem regions influence anesthetic requirements and movement responses with isoflurane.

Methods
Movement (biceps femoris electromyogram) and MAC were measured in adult rats before and after decerebration at the precollicular, mid-collicular, pontine or medullary level, or decerebellation. Additional experiments assessed the effects of lidocaine inactivation of the mesencephalic locomotor region on MAC and the effects of isoflurane on nociceptive neuronal responses in this region.

Results
Transections placed at the level of the mid-colliculus, rostral pons, and pontomedullary junction significantly reduced MAC by approximately 10, 40, and 45%, respectively. MAC was decreased 9% after mid-medullary transections that were placed caudal to the nucleus raphe magnus but rostral to the dorsal reticular nucleus; however, only weak, single movements occurred. Caudal medullary transections at the obex decreased MAC by 60%. Bilateral inactivation of the mesencephalic locomotor region with lidocaine caused a reversible, 32% decrease in MAC and reduced the number and amplitude of movements at sub-MAC isoflurane concentrations. Neuronal responses of mesencephalic locomotor region neurons to supramaximal noxious tail clamp were reduced by 87% by 1.2 MAC isoflurane.

Conclusions
The authors conclude that the mesencephalic locomotor region influences anesthetic requirements and promotes repetitive movement with sub-MAC isoflurane by facilitating ventral spinal locomotor circuits, where anesthetics seem to exert their key immobilizing effects. However, net brainstem influences on MAC seem to result from interaction among descending nociceptive and locomotor modulatory pathways.
Perioperative Tobacco Interventions by Chinese Anesthesiologists
Authors: Shi Yu , Yu Chunhua , Luo Ailun , Huang Yuguang , Warner David O. 
Published: January 2010

Background
The prevalence of cigarette smoking in China is high. Surgery provides an excellent opportunity for patients to quit smoking, and anesthesiologists can play an important role in tobacco control. However, little is known about the practices, knowledge, and attitudes of Chinese anesthesiologists regarding perioperative tobacco interventions.

Methods
Chinese anesthesiologists were surveyed at a national meeting in 2009, with written questionnaires distributed to 800 practicing anesthesiologists.

Results
The survey response rate was 60.3%, and 10% of respondents themselves smoked cigarettes. Most (73%) of them frequently or almost always asked about smoking status; 51% advised about the health risk of tobacco use; and 60% advised patients to quit. Compared with nonsmokers, smokers were significantly less likely to advise about the health risks of smoking and quitting. A high proportion of respondents had accurate perceptions of perioperative and long-term health risks of smoking. Although most respondents agreed that advising patients to quit is the responsibility of anesthesiologists and the perioperative period is a good time to help patients quit smoking, few knew how to counsel about smoking or help patients get the help they needed to quit. Nonetheless, most of the respondents were willing to learn about perioperative interventions and spend an extra 5 min to help patients quit smoking.

Conclusions
Given their adequate knowledge of health risks of smoking, strong perception of responsibilities, and willingness to participate in tobacco control, Chinese anesthesiologists are poised to play a significant role in tobacco control in China that could improve perioperative outcomes and promote long-term health.
Propofol Anesthesia Significantly Alters Plasma Blood Levels of Melatonin in Rats
Authors: Dispersyn Garance , Pain Laure , Touitou Yvan 
Published: January 2010

Background
General anesthesia combined with surgery has been shown to decrease the nocturnal peak of melatonin in patients. However, the role of anesthesia itself on melatonin secretion remains unknown. We previously showed that anesthesia induced by propofol modifies the circadian time structure in both rats and humans and phase advances the circadian rest-activity rhythm in rats. In this study, we examined the secretion of melatonin during 24 h after a 30-min propofol anesthesia in rats.

Methods
Rats were exposed to 12-h light/12-h dark alteration conditions and anesthetized with propofol (120 mg/kg intraperitoneally) around their peak of melatonin secretion (Zeitgeber time 16). Trunk blood samples were collected at seven subsequent Zeitgeber times to assess the effects of propofol on circadian melatonin secretion.

Results
Propofol modifies the peripheral melatonin by significantly decreasing its concentration ( approximately 22-28%) during the immediate 3 h after the wake up from anesthesia and then significantly increasing melatonin secretion 20 h after anesthesia ( approximately 38%). Cosinor analysis suggests that propofol induces a phase advance of the circadian secretion of peripheral melatonin.

Conclusions
The results demonstrate the disturbing effects of propofol anesthesia on the circadian rhythm of plasma melatonin in rats under normal light conditions. These results parallel the desynchronization of the circadian rhythms of locomotor activity and temperature previously observed after propofol anesthesia.
Comparison of Single-use and Reusable Metal Laryngoscope Blades for Orotracheal Intubation during Rapid Sequence Induction of Anesthesia
Authors: Amour Julien , Manach Yannick Le , Borel Marie , Lenfant François , Nicolas-Robin Armelle , Carillion Aude , Ripart Jacques , Riou Bruno , Langeron Olivier 
Published: January 2010

Background
Single-use metal laryngoscope blades are cheaper and carry a lower risk of infection than reusable metal blades. The authors compared single-use and reusable metal blades during rapid sequence induction of anesthesia in a multicenter cluster randomized trial.

Methods
One thousand seventy-two adult patients undergoing general anesthesia under emergency conditions and requiring rapid sequence induction were randomly assigned on a weekly basis to either single-use or reusable metal blades (cluster randomization). After induction, a 60-s period was allowed to complete intubation. In the case of failed intubation, a second attempt was performed using the opposite type of blade. The primary endpoint was the rate of failed intubation, and the secondary endpoints were the incidence of complications (oxygen desaturation, lung aspiration, and/or oropharynx trauma) and the Cormack and Lehane score.

Results
Both groups were similar in their main characteristics, including the risk factors for difficult intubation. The rate of failed intubation was significantly decreased with single-use metal blades at the first attempt compared with reusable blades (2.8 vs. 5.4%, P < 0.05). In addition, the proportion of grades III and IV in Cormack and Lehane score were also significantly decreased with single-use metal blades (6 vs. 10%, P < 0.05). The global complication rate did not reach statistical significance, although the same trend was noted (6.8% vs. 11.5%, P = not significant). An investigator survey and a measure of illumination pointed that illumination might have been responsible for this result.

Conclusions
The single-use metal blade was more efficient than a reusable metal blade in rapid sequence induction of anesthesia.
Estrogen Is Renoprotective via a Nonreceptor-dependent Mechanism after Cardiac Arrest In Vivo
Authors: Hutchens Michael P. , Nakano Takaaki , Kosaka Yasuharu , Dunlap Jennifer , Zhang Wenri , Herson Paco S. , Murphy Stephanie J. , Anderson Sharon , Hurn Patricia D. 
Published: January 2010

Background
Severe ischemia induces renal injury less frequently in women than men. In this study, cardiac arrest and cardiopulmonary resuscitation were used to assess whether estradiol is renoprotective via an estrogen receptor (ER)-dependent mechanism.

Materials and Methods
Male and female C57BL/6 and ER gene-deleted mice underwent 10 min of cardiac arrest followed by cardiopulmonary resuscitation. Serum chemistries and renal stereology were measured 24 h after arrest.

Results
Estrogen did not affect mean arterial pressure, regional renal cortical blood flow, and arterial blood gases. Hence, female kidneys were protected (mean +/- SEM: blood urea nitrogen, 65+/- 21 vs.149+/- 27 mg/dl, P = 0.04; creatinine, 0.14 +/- 0.05 vs. 0.73 +/- 0.16 mg/dl, P = 0.01; volume of necrotic tubules, 7 +/- 1% vs. 10 +/- 0%, P = 0.04). Estrogen also reduced renal injury. In intact females (n = 5), ovariectomized/vehicle-treated (n = 8), and ovariectomized/estrogen-treated (n = 8) animals, blood urea nitrogen was 65 +/- 21, 166 +/- 28, and 50 +/- 14 mg/dl (P = 0.002); creatinine was 0.14 +/- 0.05, 0.74 +/- 0.26, and 0.23 +/- 0.27 mg/dl (P = 0.014); necrotic tubules were 2.5 +/- 0.25%, 12.0 +/- 1.9%, and 5.0 +/- 1.6% (P = 0.004), respectively. In ER-[alpha] and ER-[beta] gene-deleted mice and controls estradiol-reduced functional injury (blood urea nitrogen: estradiol 117 +/- 71, vehicle 167 +/- 56, P = 0.007; creatinine: estradiol 0.5 +/- 0.5, vehicle 1.0 +/- 0.4, P = 0.013), but the effect of estradiol was not different between ER-[alpha] or ER-[beta] gene-deleted mice. Adding ICI 182,780 to estradiol did not alter injury.

Conclusions
In women, kidneys were protected from cardiac arrest through estrogen. Estradiol-mediated renoprotection was not affected by ER deletion or blockade. Estradiol is renoprotective after cardiac arrest. The results indicate that estradiol renoprotection is ER-[alpha] and ER-[beta] independent.
Adverse Events with Medical Devices in Anesthesia and Intensive Care Unit Patients Recorded in the French Safety Database in 2005–2006
Authors: Beydon Laurent , Ledenmat Pierre Yves , Soltner Christophe , Lebreton Frédéric , Hardin Vincent , Benhamou Dan , Clergue François , Laguenie Gérard 
Published: January 2010

Background
French regulations require that adverse events involving medical devices be reported to the national healthcare safety agency. The authors evaluated reports made in 2005-2006 for patients in anesthesiology and critical care.

Methods
For each type of device, the authors recorded the severity and cause of the event and the manufacturer's response where relevant. The authors compared the results with those obtained previously from the reports (n = 1,004) sent in 1998 to the same database.

Results
The authors identified 4,188 events, of which 91% were minor, 7% severe, and 2% fatal. The cause was available for 1,935 events (46%). Faulty manufacturing was the main cause of minor events. Inappropriate use was the cause in a significantly larger proportion of severe events than minor events (P < 0.001) and was usually considered preventable via improved knowledge or device verification before use. Compared to with that in 1998, the annual number of reported events doubled and the rate of severe events decreased slightly (12-10%, P = 0.03). The rate of events related to manufacturing problems remained stable (59-60%, P = nonsignificant), and the rate of events caused by human errors was 32-42% (P = 0.01). There were no changes in the mortality rate (2% in both studies).

Conclusions
The number of adverse events related to medical devices indicates a need for greater attention to these complex pieces of equipment that can suffer from faulty design and manufacturing and from inappropriate use. Improvements in clinician knowledge of medical devices, and to a lesser extent improvement in manufacturing practices, should improve safety.