bluuebunny/crossref_metadata_2025_split huggingface dataset:
A pair‐to‐pair amino acids substitution matrix and its applications for protein structure prediction
Authors: Eyal Eran , Frenkel‐Morgenstern Milana , Sobolev Vladimir , Pietrokovski Shmuel 
Published: January 2007

AbstractWe present a new structurally derived pair‐to‐pair substitution matrix (P2PMAT). This matrix is constructed from a very large amount of integrated high quality multiple sequence alignments (Blocks) and protein structures. It evaluates the likelihoods of all 160,000 pair‐to‐pair substitutions. P2PMAT matrix implicitly accounts for evolutionary conservation, correlated mutations, and residue–residue contact potentials. The usefulness of the matrix for structural predictions is shown in this article. Predicting protein residue–residue contacts from sequence information alone, by our method (P2PConPred) is particularly accurate in the protein cores, where it performs better than other basic contact prediction methods (increasing accuracy by 25–60%). The method mean accuracy for protein cores is 24% for 59 diverse families and 34% for a subset of proteins shorter than 100 residues. This is above the level that was recently shown to be sufficient to significantly improve ab initio protein structure prediction. We also demonstrate the ability of our approach to identify native structures within large sets of (300–2000) protein decoys. On the basis of evolutionary information alone our method ranks the native structure in the top 0.3% of the decoys in 4/10 of the sets, and in 8/10 of sets the native structure is ranked in the top 10% of the decoys. The method can, thus, be used to assist filtering wrong models, complimenting traditional scoring functions. Proteins 2007. © 2007 Wiley‐Liss, Inc.
A novel computer‐assisted technique for pedicle screw insertion
Authors: John P. S. , James C. , Antony J. , Tessamma T. , Ananda R. , Dinesh K. 
Published: January 2007

AbstractBackgroundCommercially available systems for computer‐assisted pedicle screw placement are prohibitively expensive, even in advanced countries. The advantage of the great accuracy of computer‐assisted systems for pedicle screw insertion makes them highly desirable and essential for current spinal surgeries.MethodsWe have tried to develop a new software for pedicle screw placement, based on paired point matching.ResultsThe newly developed software is much less expensive and is an excellent educational tool. Its accuracy has been established by a cadaveric study, described in this paper.ConclusionsThe cadaveric study supports the view that computer‐assisted pedicle screw fixation using the newly developed software is superior to the conventional fluoroscopic method, especially with regard to the thoracic spine, where a higher degree of accuracy is needed. Further clinical studies are planned and the software needs further refinement for complex clinical situations. Copyright © 2007 John Wiley & Sons, Ltd.
Effect of Extraction and Precipitation Conditions During Soybean Protein Isolate Production on the Genistein Series Content
Authors: Speroni Aguirre F. J. , Milesi V. , Añón M. C. 
Published: January 2007

AbstractThe influence of the conditions for isolation of soy protein on the content of genistein and its conjugated forms was studied. The major components of the genistein series isolated from soybean flour were malonyl genistin (54.3%), genistin (36.9%), and equal amounts (4.4%) of genistein and acetyl genistin. A modification in the conjugation profile of genistein between pH 4.5 and 8.0 and above pH 10 was attributed to the action of β‐glucosidase and the saponification reaction, respectively. A decrease in the content of total genistein in the insoluble flour residue and in the soy protein isolate (SPI) with increasing extraction pH was detected, while in the whey, the total genistein content was not affected by pH. The effect of pH variation during acid precipitation on the content of genistein and its conjugated forms, at a constant extraction pH (8.0), was also studied. Under these conditions, the highest absolute content of total genistein in the SPI was obtained at pH 3.5 and the lowest was obtained at pH 5.6. The total genistein content in the whey followed an inverse trend compared with that of the protein yield. A temperature increase did not substantially affect the distribution of the different genistein forms or their total contents. The content of total genistein was higher in the glycinin than in the β‐conglycinin protein fraction. The effect of the pH during the alcohol/water extraction of the isoflavones was also analyzed. The efficiency of the extraction was lower at pH values between 3.25 and 3.5 than at other pH values.
Amoeba proteus displays a walking form of locomotion
Authors: Cameron Ivan , Rinaldi Robert A. , Kirby Gerald , Davidson David 
Published: January 2007

AbstractThis report deals with observations on the directional locomotion of amoeba before and after fixation and scanning electron microscopy. The study was aimed at visualization of the stepwise events of directional movements. After the analysis of the data it is proposed that the amoeba undergoes a sequence of movement events that can be defined as a walking form of locomotion.
Synthesis of β‐alanine C60 derivative and its protective effect on hydrogen peroxide‐induced apoptosis in rat pheochromocytoma cells
Authors: Hu Zhen , Guan Wenchao , Wang Wei , Huang Lizhen , Xing Haiping , Zhu Zhou 
Published: January 2007

AbstractOxidative stress has been considered as a major cause of cellular injuries in a variety of clinical abnormalities, especially prominent in neural diseases. One of the effective ways to prevent the reactive oxygen species (ROS) mediated cellular injury is dietary or pharmaceutical augmentation of some free radical scavenger. Water‐soluble amino‐fullerene derivative is a novel compound that behaves as a free radical scavenger with excellent biocompatibility. In the present study, we synthesized a novel β‐alanine C60 derivative. The product was characterized by FT‐IR, 1H NMR, 13C NMR, LC‐MS and elemental analysis. We investigated the protective effect on hydrogen peroxide‐induced oxidative stress and apoptotic death in cultured rat pheochromocytoma (PC12) cells. PC12 cells treated with hydrogen peroxide underwent apoptotic death determined by MTT, flow cytometry analysis and PI/Hoechst 33342 staining. Moreover, the scavenging ability of β‐alanine C60 derivative to reactive oxygen species both in vivo and in vitro of PC12 cells was measured. The results suggest that β‐alanine C60 derivative has the potential to prevent oxidative stress‐induced cell death without evident toxicity. Hence, on the basis of the above‐mentioned studies, we can hypothesize that the protective effect of β‐alanine C60 derivative on H2O2 induced apoptosis is related to their known scavenger activity toward ROS.
Dynamics of satellite binding protein CENP‐B and telomere binding protein TRF2/MTBP in the nuclei of mouse spermatogenic line
Authors: Dolnik A.V. , Pochukalina G.N. , Parfenov V.N. , Karpushev A.V. , Podgornaya O.I. , Voronin A.P. 
Published: January 2007

AbstractThe location of centromeric protein CENP‐B and telomeric protein TRF2/MTBP in the mouse spermatogenic line has been studied using indirect immunofluorescent and immunoelectron microscopy. CENP‐B localized to the heterochromatic parts of the nuclei at meiotic stages. A clearly distinct chromocenter forms in the nucleus at stages 3–4 of spermatid maturation; CENP‐B localizes in it and in the area adjacent to the future acrosome. CENP‐B localization in the subacrosomal area and in the chromocenters’ periphery demonstrates that centromeres are organized in two groups in mouse spermatozoa, unlike human centromeres. TRF2/MTBP concentrates around the forming chromocenter at spermiogenesis early stages. The TRF2/MTBP main signal migrates into the area of acrosomal membrane at the course of spermatozoon maturation. TRF2/MTBP never localizes inside the synaptonemal complex but can be found in the areas where the synaptonemal complex attaches to the nuclear envelope. At the pachytene and diplotene stages when chromosomes separate from the nuclear envelope, some amount of the protein remains bound to the nuclear membrane while the other part reveals itself in chromosomes. TRF2/MTBP accumulates in the future acrosome from the very beginning of its formation. In the mature spermatozoon TRF2/MTBP decorates the acrosomal membrane as well as spreads in condensed chromatin.
Hsp70 in the atrial neuroendocrine units of the snail, Achatina fulica
Authors: Martynova M.G. , Bystrova O.A. , Shabelnikov S.V. , Margulis B.A. , Prokofjeva D.S. 
Published: January 2007

AbstractHeat shock proteins (Hsps) are evolutionary conserved peptides well known as molecular chaperones and stress proteins. Elevated levels of extracellular Hsps in blood plasma have been observed during the stress responses and some diseases. Information on the cellular sources of extracellular Hsps and mechanisms regulating their release is still scanty. Here we showed the presence and localization of Hsp70 in the neuroendocrine system in the atrium of the snail, Achatina fulica. The occurrence of the peptide in snail atrium lysate was detected by Western blot analysis. Immunoperoxidase and immunogold staining demonstrated that Hsp70‐immunoreactivity is mainly confined to the peculiar atrial neuroendocrine units which are formed by nerve fibers tightly contacted with large granular cells. Immunolabelling intensity differed in morphologically distinct types of secretory granules in the granular cells. The pictures of exocytosis of Hsp70‐immunolabeled granules from the granular cells were observed. In nerve bundles, axon profiles with Hsp70‐immunoreactive and those with non‐immunoreactive neurosecretory granules were found. In addition, Hsp70‐like material was also revealed in the granules of glia‐interstitial cells that accompanied nerve fibers. Our findings provide an immuno‐morphological basis for a role of Hsp70 in the functioning of the neuroendocrine system in the snail heart, and show that the atrial granular cells are a probable source of extracellular Hsp70 in the snail hemolymph.
Scotland in the seventies—Adolescents in care and custody. A survey of adolescent murder in Scotland*
Authors: Fiddes Dorothy O. 
Published: January 2007

This survey was undertaken as a pilot within a wider ranging study of the most violent and seriously disturbed adolescents who might be candidates for some form of Youth Treatment Centre or Secure Psychiatric Unit in Scotland.It covers all murderers over 12 and under 18 years of age convicted in Scotland in the six years following the implementation of the Social Work (Scotland) Act in April, 1971. The cohort of 37 male adolescents is described in terms of contributing factors surrounding the crime and the differentiating factors which point to social or psychiatric morbidity in this particular population. The conflict is examined between the demands of the penal system and the needs of still developing adolescents in the abnormal, restrictive environments to which they are confined.
CHARACTERIZING THE FACTORY SYSTEM: FACTORY SUBJECTIVITY IN HOUSEHOLD WORDS
Authors: Farina Jonathan V. 
Published: January 2007

Here, we had better stop, though we have not told half that might be related on the subject of buttons. It is wonderful, is it not? That on that small pivot turns the fortune of such multitudes of men, women, and children, in so many parts of the world; that such industry; and so many fine faculties, should be brought out and exercised by so small a thing as the Button.—“What There Is in a Button,” Harriet Martineau (1852)
A SHOCK TO THE SYSTEM: RICHARD FEVEREL AND THE ACTRESS IN THE HOUSE
Authors: Allen Emily 
Published: January 2007

“One of the very worst books of that abominable class!” exclaimed the old lawyer, opening at the coloured frontispiece, from which brazen Miss Random smiled bewitchingly out, as if she had no doubt of captivating Time and all his veterans on a fair field. “Pah!” he shut her to with the energy he would have given to the office of publicly slapping her face.—George Meredith, The Ordeal of Richard FeverelPromiscuous adj. 1. Consisting of diverse and unrelated parts or individuals; confused. 2. Lacking standards of selection; indiscriminate. 3. Indiscriminate in sexual relations. 4. Casual; random. [Latin promiscuus, mixed: pro (intensifier), thoroughly + miscere, to mix.]—American Heritage Dictionary of the English Language
The Systems Biology Markup Language (SBML) Level 2 Version 2
Authors: Hucka Michael , Keating Sarah 
Published: January 2007

AbstractThe Systems Biology Markup Language (SBML) is a machine-readable model representation language for software tools in computational systems biology. By supporting SBML as an input/output format, different tools can all operate on an identical representation of a model, removing opportunities for translation errors and assuring a common starting point for analyses and simulations. SBML is by no means a perfect format, but it has achieved widespread acceptance as a de facto standard. It is supported worldwide by over 100 software systems (both open-source and commercial). The broad acceptance of a common, open format for exchanging models between software tools is a crucial step towards wider use of quantitative modeling in biology, because it allows researchers to build upon each other's work with greater ease and accuracy.SBML can encode models consisting of biochemical entities (species) linked by reactions to form networks. An important principle is that models are decomposed into explicitly-labeled constituent elements, the set of which resembles a verbose rendition of chemical reaction equations. The representation deliberately does not cast the model directly into a set of differential equations or other specific interpretation of the model. The formalisms in SBML allows a wide range of biological phenomena to be modeled, including metabolism, cell signaling, gene regulation, and more. Significant flexibility and power comes from the ability to define arbitrary formulae for the rates of change of variables as well as the ability to express other constraints mathematically.This tutorial covered the latest edition of SBML, which is Level 2 Version 2, finalized in September 2006. Topics covered include the basic common principles in SBML as well the changes introduced in Level 2 Version 2. We also discussed software tools for programmers, in particular libSBML.
The Systems Biology Markup Language (SBML): Where It's Been and Where It's Going
Authors: Hucka Michael 
Published: January 2007

AbstractA cornerstone of systems biology is the use of computational modeling, by which hypotheses can be cast into a quantitative form that can be tested systematically. The use of computational modeling by biologists promises to pave the way for more rigorous analyses of biological functions, and ultimately will lead to new and better treatments for disease.A crucial enabler for more widespread use of computational modeling in biology is reaching agreement on how to represent, store, and communicate models between software tools. The Systems Biology Markup Language (SBML) project is an effort to create a machine-readable format for representing computational models in biology. By supporting SBML as an input and output format, different software tools can operate on the same representation of a model, removing chances for errors in translation and assuring a common starting point for analyses and simulations. SBML has become the most successful effort in this direction so far, with over 100 software systems supporting it today.In this presentation, I will discuss the current state of SBML, including recent developments such as this year's finalization of Version 2 of SBML Level 2. I will also survey some of the software tools that support SBML, and related projects that have arisen to support more effective use of computational models. Lastly, I will discuss expected future developments in SBML.
Alveolar Recruitment in Pulmonary and Extrapulmonary Acute Respiratory Distress Syndrome
Authors: Thille Arnaud W. , Richard Jean-Christophe M. , Maggiore Salvatore M. , Ranieri V Marco , Brochard Laurent 
Published: January 2007

Background
Alveolar recruitment in response to positive end-expiratory pressure (PEEP) may differ between pulmonary and extrapulmonary acute respiratory distress syndrome (ARDS), and alveolar recruitment values may differ when measured by pressure-volume curve compared with static compliance.

Methods
The authors compared PEEP-induced alveolar recruitment in 71 consecutive patients identified in a database. Patients were classified as having pulmonary, extrapulmonary, or mixed/uncertain ARDS. Pressure-volume curves with and without PEEP were available for all patients, and pressure-volume curves with two PEEP levels were available for 44 patients. Static compliance was calculated as tidal volume divided by pressure change for tidal volumes of 400 and 700 ml. Recruited volume was measured at an elastic pressure of 15 cm H2O.

Results
Volume recruited by PEEP (10 +/- 3 cm H2O) was 223 +/- 111 ml in the pulmonary ARDS group (29 patients), 206 +/- 164 ml in the extrapulmonary group (16 patients), and 242 +/- 176 ml in the mixed/uncertain group (26 patients) (P = 0.75). At high PEEP (14 +/- 2 cmH2O, 44 patients), recruited volumes were also similar (P = 0.60). With static compliance, recruitment was markedly underestimated and was dependent on tidal volume (226 +/- 148 ml using pressure-volume curve, 95 +/- 185 ml for a tidal volume of 400 ml, and 23 +/- 169 ml for 700 ml; P < 0.001).

Conclusion
In a large sample of patients, classification of ARDS was uncertain in more than one third of patients, and alveolar recruitment was similar in pulmonary and extrapulmonary ARDS. PEEP levels should not be determined based on cause of ARDS.
Increased Plasminogen Activator Inhibitor-1 Concentrations in Bronchoalveolar Lavage Fluids Are Associated with Increased Mortality in a Cohort of Patients with Pseudomonas aeruginosa
Authors: Song Yuanlin , Lynch Susan V. , Flanagan Judith , Zhuo Hanjing , Tom Wynnson , Dotson Rachel H. , Baek Marshall S. , Rubio-Mills Amua , Singh Gaurav , Kipnis Eric , Glidden David , Brown Ron , Garcia Oscar , Wiener-Kronish Jeanine P. 
Published: January 2007

Background
Increased plasminogen activator inhibitor-1 (PAI-1) concentrations are found in bronchoalveolar lavage (BAL) fluids from patients with ventilator-associated pneumonia or acute respiratory distress syndrome. The authors hypothesized that PAI-1 concentrations were associated with increased mortality in patients with either Pseudomonas aeruginosa-induced ventilator-associated pneumonia or tracheobronchial colonization.

Methods
In a prospective cohort study, daily aspirates from intubated patients were cultured for P. aeruginosa. Positive patients had blind BAL (bBAL) that was processed for biomarker concentrations. Secretion of type III secretion cytotoxins were also analyzed from the P. aeruginosa strains.

Results
Thirty-three patients were enrolled. Ten of the 33 patients died. bBAL PAI-1 concentrations were significantly increased in nonsurvivors compared with survivors (31.7 vs. 3.4 ng/ml, P = 0.001 for hospital mortality; 35.9 vs. 4.7 ng/ml, P = 0.02 for 28-day mortality). Even when acute respiratory distress syndrome patients were excluded, there was a significant difference between the survivors and nonsurvivors for bBAL PAI-1 concentrations (P = 0.005). Eighty-three percent of P. aeruginosa strains isolated from patients with high concentrations of bBAL PAI-1 also had strains that secreted cytotoxins.

Conclusions
PAI-1 concentrations in bBALs correlated with mortality in ventilated patients with positive cultures for P. aeruginosa. Elevated bBAL PAI-1 concentrations also correlated with the secretion of type III exotoxins by P. aeruginosa.
Accelerating the Washout of Inhalational Anesthetics from the Dräger Primus Anesthetic Workstation
Authors: Crawford Mark W. , Prinzhausen Heike , Petroz Guy C. 
Published: January 2007

Background
To establish guidelines for the preparation of the Primus anesthetic workstation (Dräger, Lübeck, Germany) for malignant hyperthermia-susceptible patients, the authors evaluated the effect of replacing the workstation's exchangeable internal components on the washout of isoflurane.

Methods
Primus workstations were exposed to isoflurane, and contaminated internal components were replaced as follows: group 1, no replacement; group 2, new ventilator diaphragm; group 3, autoclaved ventilator diaphragm; group 4, autoclaved integrated breathing system; group 5, flushed integrated breathing system; group 6, autoclaved ventilator diaphragm and integrated breathing system. The fresh gas flow was set at 10 l/min, and subsequently reduced to 3 l/min when a concentration of 5 ppm was achieved. Isoflurane concentration was measured in the inspiratory limb of the circle circuit every minute.

Results
Washout times for isoflurane decreased in the following order: group 1 (67 +/- 6.5 min) > groups 2 and 3 (50 +/- 4.1 and 50 +/- 5.7 min, respectively) > group 5 (43 +/- 9.5 min) > group 4 (12 +/- 1.5 min) > group 6 (3.2 +/- 0.4 min). Isoflurane concentration increased approximately threefold when the fresh gas flow was reduced to 3 l/min.

Conclusion
Washout of isoflurane increased 20-fold with the use of an autoclaved ventilator diaphragm and integrated breathing system. To prepare the Primus for malignant hyperthermia-susceptible patients, the authors recommend replacing the ventilator diaphragm and integrated breathing system with autoclaved components, flushing the workstation for 5 min at a fresh gas flow of 10 l/min, and maintaining this flow for the duration of anesthesia.
Comparison of the Particle Sizes of Different Steroids and the Effect of Dilution
Authors: Benzon Honorio T. , Chew Teng-Leong , McCarthy Robert J. , Benzon Hubert A. , Walega David R. 
Published: January 2007

Background
Central nervous system injuries after transforaminal epidural steroid injections have been ascribed to occlusion of the blood vessels supplying the spinal cord and brain by the particulate steroid.

Methods
The authors compared the sizes of the particles of the steroids methylprednisolone acetate, triamcinolone acetonide, dexamethasone sodium phosphate, betamethasone sodium phosphate/betamethasone acetate (both Celestone Soluspan; Schering-Plough, Kenilworth, NJ, the commercial betamethasone; and betamethasone repository, a betamethasone preparation that can be ordered from a compounding company), and betamethasone sodium phosphate. Both undiluted and diluted samples were examined. The samples were examined with a laser scanning confocal microscope, and images were analyzed and measured. The particles were categorized (or tabulated) into groups: 0-20, 21-50, 51-1000, and greater than 1000 mu. Chi-square analyses, with Bonferroni correction, were used to compare the proportion of particles among the undiluted and diluted drug formulations.

Results
Dexamethasone and betamethasone sodium phosphate were pure liquid. The proportion of larger particles was significantly greater in the methylprednisolone and the compounded betamethasone preparations compared with the commercial betamethasone. There was no statistical difference between the commercial betamethasone and triamcinolone, although betamethasone had a smaller percentage of the larger particles. Increased dilution of the compounded betamethasone with lidocaine decreased the percentage of the larger particles, whereas increased dilution of methylprednisolone 80 mg/ml with saline increased the proportion of larger particles.

Conclusion
Commercial betamethasone is the recommended preparation if a nonsoluble steroid is preferred. Dexamethasone is a nonparticulate steroid, but its routine use awaits further studies on its safety and efficacy.