bluuebunny/crossref_metadata_2025_split huggingface dataset:
MCCE2: Improving protein pKa calculations with extensive side chain rotamer sampling
Authors: Song Yifan , Mao Junjun , Gunner M. R. 
Published: March 2009

AbstractMulticonformation continuum electrostatics (MCCE) explores different conformational degrees of freedom in Monte Carlo calculations of protein residue and ligand pKas. Explicit changes in side chain conformations throughout a titration create a position dependent, heterogeneous dielectric response giving a more accurate picture of coupled ionization and position changes. The MCCE2 methods for choosing a group of input heavy atom and proton positions are described. The pKas calculated with different isosteric conformers, heavy atom rotamers and proton positions, with different degrees of optimization are tested against a curated group of 305 experimental pKas in 33 proteins. QUICK calculations, with rotation around Asn and Gln termini, sampling His tautomers and torsion minimum hydroxyls yield an RMSD of 1.34 with 84% of the errors being <1.5 pH units. FULL calculations adding heavy atom rotamers and side chain optimization yield an RMSD of 0.90 with 90% of the errors <1.5 pH unit. Good results are also found for pKas in the membrane protein bacteriorhodopsin. The inclusion of extra side chain positions distorts the dielectric boundary and also biases the calculated pKas by creating more neutral than ionized conformers. Methods for correcting these errors are introduced. Calculations are compared with multiple X‐ray and NMR derived structures in 36 soluble proteins. Calculations with X‐ray structures give significantly better pKas. Results with the default protein dielectric constant of 4 are as good as those using a value of 8. The MCCE2 program can be downloaded from http://www.sci.ccny.cuny.edu/∼mcce. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2009
Multiple classifier integration for the prediction of protein structural classes
Authors: Chen Lei , Lu Lin , Feng Kairui , Li Wenjin , Song Jie , Zheng Lulu , Yuan Youlang , Zeng Zhenbin , Feng Kaiyan , Lu Wencong , Cai Yudong 
Published: March 2009

AbstractSupervised classifiers, such as artificial neural network, partition trees, and support vector machines, are often used for the prediction and analysis of biological data. However, choosing an appropriate classifier is not straightforward because each classifier has its own strengths and weaknesses, and each biological dataset has its own characteristics. By integrating many classifiers together, people can avoid the dilemma of choosing an individual classifier out of many to achieve an optimized classification results (Rahman et al., Multiple Classifier Combination for Character Recognition: Revisiting the Majority Voting System and Its Variation, Springer, Berlin, 2002, 167–178). The classification algorithms come from Weka (Witten and Frank, Data Mining: Practical Machine Learning Tools and Techniques, Morgan Kaufmann, San Francisco, 2005) (a collection of software tools for machine learning algorithms). By integrating many predictors (classifiers) together through simple voting, the correct prediction (classification) rates are 65.21% and 65.63% for a basic training dataset and an independent test set, respectively. These results are better than any single machine learning algorithm collected in Weka when exactly the same data are used. Furthermore, we introduce an integration strategy which takes care of both classifier weightings and classifier redundancy. A feature selection strategy, called minimum redundancy maximum relevance (mRMR), is transferred into algorithm selection to deal with classifier redundancy in this research, and the weightings are based on the performance of each classifier. The best classification results are obtained when 11 algorithms are selected by mRMR method, and integrated together through majority votes with weightings. As a result, the prediction correct rates are 68.56% and 69.29% for the basic training dataset and the independent test dataset, respectively. The web‐server is available at http://chemdata.shu.edu.cn/protein_st/. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2009
Retroviral vector‐producing mesenchymal stem cells for targeted suicide cancer gene therapy
Authors: Uchibori Ryosuke , Okada Takashi , Ito Takayuki , Urabe Masashi , Mizukami Hiroaki , Kume Akihiro , Ozawa Keiya 
Published: March 2009

AbstractBackgroundMesenchymal stem cells (MSCs) are a promising vehicle for targeted cancer gene therapy because of their potential of tumor tropism. For efficient therapeutic application, we developed retroviral vector‐producing MSCs that enhance tumor transduction via progeny vector production.MethodsRat bone marrow‐derived MSCs were nucleofected with the proviral plasmids (vesicular stomatitis virus‐G protein‐pseudotyped retroviral vector components) (VP‐MSCs) or pLTR plasmid alone (non‐VP‐MSCs). The luciferase‐based in vivo imaging system was used to assess gene expression periodically. To evaluate the anticancer effects, we administered MSCs expressing herpes simplex virus‐thymidine kinase (HSV‐tk) into the left ventricular cavity of nude mice engrafted with 9L glioma cells subcutaneously.ResultsIn vivo imaging revealed that administration of luciferase‐expressing non‐VP‐MSCs enhanced the bioluminescence signal at the inoculation sites of 9L cells, whereas no accumulation was observed in mice at the site of the control Rat‐1 fibroblasts. Compared to non‐VP‐MSCs, the administration of VP‐MSCs resulted in significant augmentation of the signal with an increase in transgene copy number. Immunohistochemical analysis showed marked luciferase expression at the tumor periphery in mice injected with VP‐MSCs, whereas little expression was detected in those injected with non‐VP‐MSCs. Under the continuous infusion of ganciclovir, systemic administration of VP‐MSCs expressing HSV‐tk suppressed tumor growth more effectively than non‐VP‐MSC administration, whereas no anticancer effect was observed without ganciclovir treatment. Furthermore, VP‐MSC administration caused no transgene transduction in the normal tissues and organs.ConclusionsVP‐MSCs accumulated at the site of tumors after intravascular injection in tumor‐bearing mice, followed by in situ gene transfer to tumors without transduction of normal organs. When applied to the HSV‐tk/ganciclovir suicide gene therapy, more efficient tumor growth suppression was observed using VP‐MSCs compared to non‐VP‐MSCs. This VP‐MSC‐based system has great potential for improved cancer gene therapy. Copyright © 2009 John Wiley & Sons, Ltd.
Jaw lever analysis of Hawaiian gobioid stream fishes: A simulation study of morphological diversity and functional performance
Authors: Maie Takashi , Schoenfuss Heiko L. , Blob Richard W. 
Published: March 2009

AbstractDifferences in feeding behavior and performance among the five native Hawaiian gobioid stream fishes (Sicyopterus stimpsoni, Lentipes concolor, Awaous guamensis, Stenogobius hawaiiensis, and Eleotris sandwicensis) have been proposed based on the skeletal anatomy of their jaws and dietary specialization. However, performance of the feeding apparatus likely depends on the proportions and configurations of the jaw muscles and the arrangement of the jaw skeleton. We used a published mathematical model of muscle function to evaluate potential differences in jaw closing performance and their correlations with morphology among these species. For example, high output force calculated for the adductor mandibulae muscles (A2 and A3) of both A. guamensis and E. sandwicensis matched expectations based on the morphology of these species because these muscles are larger than in the other species. In contrast, Stenogobius hawaiiensis exhibited an alternative morphological strategy for achieving high relative output forces of both A2 and A3, in which the placement and configuration of the muscles conveyed high mechanical advantage despite only moderate cross‐sectional areas. These differing anatomical pathways to similar functional performance suggest a pattern of many‐to‐one mapping of morphology to performance. In addition, a functional differentiation between A2 and A3 was evident for all species, in which A2 was better suited for producing forceful jaw closing and A3 for rapid jaw closing. Thus, the diversity of feeding performance of Hawaiian stream gobies seems to reflect a maintenance of functional breadth through the retention of some primitive traits in combination with novel functional capacities in several species. J. Morphol. 2009. © 2009 Wiley‐Liss, Inc.
High‐resolution computed tomography of lobster (Panulirus interruptus) stomach
Authors: Hobbs Kevin H. , Hooper Scott L. 
Published: March 2009

AbstractWe used micro computed tomography to produce a high‐resolution density image of the lobster (Panulirus interruptus) stomach and identified on this image the previously defined stomach ossicles. These data are the first coordinate‐based, three‐dimensional description of the stomach and are a necessary first step for developing biomechanical models of it. They are also interesting for several reasons in their own right. First, the ossicles showed large shape and density variations. These data suggest that different ossicles may serve different functions, with some acting as force‐delivering levers, some as spring‐like elements, and some as wall‐like elements that resist internal stomach pressure or function as two‐dimensional force‐delivering plates. Second, large intra‐ossicle density variations were present in individual ossicles, reminiscent of I‐beams, oval bicycle frames, and similar mass‐minimizing structural elements, suggesting that evolution has minimized ossicle mass and identifying which ossicle regions are most likely important in force delivery. Third, joints appeared to be either continuous density interconnections without distinct separations between the ossicles or ‘floating’ joints in which the ends of the two ossicles were separated by relatively large distances spanned by connective tissue. In these latter joints, although the distance between ossicle ends is likely maintained at a relatively constant value, a wide range of ossicle angles would thus be theoretically possible. Notably absent are close‐apposition, morphologically specialized joints such as hinge or ball‐and‐socket joints. J. Morphol. 2009. © 2009 Wiley‐Liss, Inc.
Modulation of osteogenesis in human mesenchymal stem cells by specific pulsed electromagnetic field stimulation
Authors: Tsai Ming‐Tzu , Li Wan‐Ju , Tuan Rocky S. , Chang Walter H. 
Published: March 2009

AbstractHuman mesenchymal stem cells (hMSCs) are a promising candidate cell type for regenerative medicine and tissue engineering applications by virtue of their capacity for self‐renewal and multipotent differentiation. Our intent was to characterize the effect of pulsed electromagnetic fields (PEMFs) on the proliferation and osteogenic differentiation of hMSCs in vitro. hMSCs isolated from the bone marrow of adult patients were cultured with osteogenic medium for up to 28 days and exposed to daily PEMF stimulation with single, narrow 300 µs quasi‐rectangular pulses with a repetition rate of 7.5 Hz. Relatively greater cell numbers were observed at late stages of osteogenic culture with PEMF exposure. The production of alkaline phosphatase (ALP), an early marker of osteogenesis, was significantly enhanced at day 7 with PEMF treatment in both basal and osteogenic cultures as compared to untreated controls. Furthermore, the expressions of other early osteogenic genes, including Runx2/Cbfa1 and ALP, were also partially modulated by PEMF exposure, indicating that osteogenesis in hMSCs was associated with the specific PEMF stimulation. Based on ALP and alizarin red S staining, the accumulation of ALP protein produced by the hMSCs as well as calcium deposits reached their highest levels at day 28. Our results indicate that extremely low‐frequency PEMF stimulation may play a modulating role in hMSC osteogenesis. Taken together, these findings provide insights on the development of PEMF as an effective technology for regenerative medicine. © 2009 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res
In vivo remodeling of intervertebral discs in response to short‐ and long‐term dynamic compression
Authors: Wuertz Karin , Godburn Karolyn , MacLean Jeffrey J. , Barbir Ana , Stinnett Donnelly Justin , Roughley Peter J. , Alini Mauro , Iatridis James C. 
Published: March 2009

AbstractThis study evaluated how dynamic compression induced changes in gene expression, tissue composition, and structural properties of the intervertebral disc using a rat tail model. We hypothesized that daily exposure to dynamic compression for short durations would result in anabolic remodeling with increased matrix protein expression and proteoglycan content, and that increased daily load exposure time and experiment duration would retain these changes but also accumulate changes representative of mild degeneration. Sprague‐Dawley rats (n = 100) were instrumented with an Ilizarov‐type device and divided into three dynamic compression (2 week–1.5 h/day, 2 week–8 h/day, 8 week–8 h/day at 1 MPa and 1 Hz) and two sham (2 week, 8 week) groups. Dynamic compression resulted in anabolic remodeling with increased matrix mRNA expression, minimal changes in catabolic genes or disc structure and stiffness, and increased glysosaminoglycans (GAG) content in the nucleus pulposus. Some accumulation of mild degeneration with 8 week–8 h included loss of annulus fibrosus GAG and disc height although 8‐week shams also had loss of disc height, water content, and minor structural alterations. We conclude that dynamic compression is consistent with a notion of “healthy” loading that is able to maintain or promote matrix biosynthesis without substantially disrupting disc structural integrity. A slow accumulation of changes similar to human disc degeneration occurred when dynamic compression was applied for excessive durations, but this degenerative shift was mild when compared to static compression, bending, or other interventions that create greater structural disruption. © 2009 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res
Differential regulation of blood vessel formation between standard and delayed bone healing
Authors: Lienau Jasmin , Schmidt‐Bleek Katharina , Peters Anja , Haschke Franek , Duda Georg N. , Perka Carsten , Bail Hermann J. , Schütze Norbert , Jakob Franz , Schell Hanna 
Published: March 2009

AbstractBlood vessel formation is a prerequisite for bone healing. In this study, we tested the hypothesis that a delay in bone healing is associated with an altered regulation of blood vessel formation. A tibial osteotomy was performed in two groups of sheep and stabilized with either a rigid external fixator leading to standard healing or with a highly rotationally unstable one leading to delayed healing. At days 4, 7, 9, 11, 14, 21, and 42 after surgery, total RNA was extracted from the callus. Gene expressions of vWF, an endothelial cell marker, and of several molecules related to blood vessel formation were studied by qPCR. Furthermore, histology was performed on fracture hematoma and callus sections. Histologically, the first blood vessels were detected at day 7 in both groups. mRNA expression levels of vWF, Ang1, Ang2, VEGF, CYR61, FGF2, MMP2, and TIMP1 were distinctly lower in the delayed compared to the standard healing group at several time points. Based on differential expression patterns, days 7 and 21 postoperatively were revealed to be essential time points for vascularization of the ovine fracture callus. This work demonstrates for the first time a differential regulation of blood vessel formation between standard and mechanically induced delayed healing in a sheep osteotomy model. © 2009 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res
Testing the precision of a weighable gravitation lysimeter
Authors: Xiao Huijie , Meissner Ralph , Seeger Juliane , Rupp Holger , Borg Heinz 
Published: March 2009

AbstractTests were carried out to determine the weighing precision of a 2 m deep lysimeter with a 1 m² cross‐sectional area and a total mass of 3500 to 3850 kg, depending on the soil water content. The weighing mechanism consists on three shear‐stress cells laid out for a load capacity of 1320 kg each. Mass changes as small as 20 g, which is equivalent here to a water gain or loss of 0.02 mm, can be measured with good accuracy and stability under favorable environmental conditions (low wind speed, relatively constant temperature). This precision does not depend on the position on the lysimeter where the mass change occurs and is as good as the best values reported in the literature for other lysimeters. To prevent water and debris from entering the cleavage between lysimeter vessel and pit casing, a rubber collar can be placed across the cleavage. It is attached to the casing and extends about 1–2 cm into the vessel. Although the collar is not supposed to touch the vessel, it does at a few points. This seriously lowers weighing precision, because this contact exerts forces on the vessel, which distort the true weight. Hence, one should refrain from using this type of collar and develop another one. Weighing precision decreases with increasing wind speed, because wind exerts forces on the lysimeter vessel and can thus alter its apparent weight. It is temperature‐dependent, too.
Mechanical behaviour and quality traits of highbush blueberry during postharvest storage
Authors: Chiabrando Valentina , Giacalone Giovanna , Rolle Luca 
Published: March 2009

AbstractBACKGROUND: Berry firmness is one of the most important characteristics for fresh market consumption. Blueberry firmness is also an important attribute because it is considered to be a measure of its freshness. Berries lose their firmness by loss of water and by changes in their structure.RESULTS: The postharvest life of two highbush blueberry cultivars (Bluecrop and Coville) was investigated. Several parameters related to blueberry quality were evaluated during the postharvest storage period. To assess berry texture characteristics (firmness, hardness, cohesiveness, gumminess, chewiness, springiness, resilience), a rapid non‐destructive penetrometer test by Durofel® and texture profile analysis (TPA) using a texture analyser were carried out. Low temperature inhibited the decrease of total soluble solids, total titratable acidity and increase of flesh pH value, thereby maintaining good taste quality. There was an increase in fruit firmness (Durofel index) and hardness and a decrease in chewiness and springiness during storage.CONCLUSION: There was a significant correlation among the TPA parameters and Durofel index. The Durofel index could therefore be used as a suitable indicator of fruit quality and storability, and low‐temperature storage is beneficial to maintain the taste quality of blueberry fruit after harvest. Copyright © 2009 Society of Chemical Industry
Vocal fold augmentation with calcium hydroxylapatite: Twelve‐month report
Authors: Rosen Clark A. , Gartner‐Schmidt Jackie , Casiano Roy , Anderson Timothy D. , Johnson Felicia , Remacle Marc , Sataloff Robert T. , Abitbol Jean , Shaw Gary , Archer Sanford , Zraick Richard I. 
Published: March 2009

AbstractObjectives:To evaluate the long‐term effectiveness of calcium hydroxylapatite (CaHA) vocal fold injection for patients with glottal insufficiency.Study Design:Multicenter, open‐label, prospective clinical study of CaHA vocal fold injection.Methods:Each patient served as his/her own control. Voice‐related outcome measures were collected for pre‐injection, 1, 3, 6, and 12 months.Results:Sixty‐three patients were available for evaluation. Fifty‐three percent of the injection procedures were done in the office. Fifty‐seven percent of patients were diagnosed with unilateral paralysis and 43% with glottal incompetence with mobile vocal folds. Patient satisfaction 12 months after injection showed 67% reporting a significant improvement in voice and 81% reporting at least a moderate improvement in voice. Utilizing the Voice Handicap Index–10, visual analog scale (vocal effort), Consensus Assessment Perceptual Evaluation V (judgments of voice severity), and objective voice measures of glottal closure (maximum phonation time and S:Z ratio), paired t tests showed significant improvements after treatment. A 22% further treatment rate was found at the 12‐month time point.Conclusions:One‐year results in this large cohort of patients with glottal incompetence treated with CaHA vocal fold injection demonstrate that excellent clinical results were achieved. Laryngoscope, 2009
Incidence of perioperative airway complications in patients with previous medialization thyroplasty
Authors: Lin Harrison W. , Bhattacharyya Neil 
Published: March 2009

AbstractObjectives/Hypothesis:Determine the incidence and characterize perioperative airway complications in patients who have undergone medialization thyroplasty (MT) and subsequently undergo procedures requiring anesthesia.Study Design:Retrospective review of post‐MT anesthesia encounters in a large academic hospital.Methods:A series of post‐MT patients was reviewed, identifying anesthesia encounters undergoing endotracheal intubation (ETI) or laryngeal mask airway (LMA) placement. Details on the perioperative course of each encounter were extracted and examined for evidence of airway complications. The incidence of airway obstruction and need for airway intervention were determined and compared to those of control patients matched for type of procedure. Relationships between complications and perioperative management were analyzed.Results:A total of 74 anesthesia encounters were identified among 219 post‐MT patients. Perioperative airway complications among post‐MT patients arose in five procedures (6.8%; 95% CI: 1.0–12.4%). Stridor in the operating or recovery room was exhibited three times, with all episodes requiring nebulized racemic epinephrine and intravenous steroids for resolution of symptoms. One patient underwent an urgent tracheotomy for severe stridor leading to airway compromise in the recovery room. Immediately after induction with an LMA, one patient failed to maintain oxygen saturations above 90% and consequently required conversion to ETI. Among 79 matched controls without prior MT, no perioperative complications (0%) occurred (P = .027).Conclusions:The incidence of perioperative airway complications in post‐MT patients is non‐neglible and may be serious. Surgical, anesthesia, and recovery room staff should be made aware of the significantly increased risk of airway complications in post‐MT patients. Laryngoscope, 2009
Effect of Comonomer‐Unit Compositional Distribution on Thermal and Crystallization Behavior of Bacterial Poly[(3‐hydroxybutyrate)‐co‐(3‐mercaptopropionate)]
Authors: Yu Fang , Zhu Bo , Dong Tungalag , Inoue Yoshio 
Published: March 2009

AbstractThe physical properties of novel sulfur‐containing biopolymers, poly[(3‐hydroxybutyrate)‐co‐(3‐mercaptopropionate)]s [P(3HB‐co‐3MP)s], have been investigated in detail by1H and 13C NMR spectroscopy, wide‐angle X‐ray diffraction (WAXD) analysis, DSC, and FT‐IR spectroscopy. Based on a solvent/non‐solvent (chloroform/heptane) fractionation method, an original P(3HB‐co‐3MP) sample with 3MP unit content of 16.3 mol‐% was fractionated into eight fractions with 3MP unit content ranging from 10.3 to 37.2 mol‐% and number‐average molecular weight from 0.4 × 105 to 2.9 × 105. The thermal and crystallization behavior were found to be greatly affected by the comonomer‐unit composition and its distribution. Furthermore, the 3MP comonomer unit was found to be included in the crystalline phase in some fractions.magnified image