bluuebunny/crossref_metadata_2025_split huggingface dataset:
Internal motion in protein crystal structures
Authors: Schmidt Andrea , Lamzin Victor S. 
Published: March 2010

AbstractThe binding states of the substrates and the environment have significant influence on protein motion. We present the analysis of such motion derived from anisotropic atomic displacement parameters (ADPs) in a set of atomic resolution protein structures. Local structural motion caused by ligand binding as well as functional loops showing cooperative patterns of motion could be inferred. The results are in line with proposed protonation states, hydrogen bonding patterns and the location of distinctly flexible regions: we could locate the mobile active site loop in a virus integrase, distinguish the subdomains in RNAse A and hydroxynitrile lyase, and reconstruct the molecular architecture in a xylanase. We demonstrate that the ADP‐based motion analysis provides information at high level of detail and that the structural changes needed for substrate attachment or release may be derived from single X‐ray structures.
Gas‐phase reaction mechanism of Pd+ with CH3CHO: A density functional theoretical study
Authors: Ding Ning , Zhang Shi‐Guo 
Published: March 2010

AbstractDetails on the reactions of: (1) Pd+ + CH3CHO → PdCO+ + CH4 and (2) Pd+ + CH3CHO → PdH + CH3CO+ in the gas phase were investigated using density functional theory (B3LYP), in conjunction with the LANL2DZ+6‐311+G(d) basis set. Three encounter complexes were located on the potential energy surfaces and the calculations indicated that both the CC and aldehyde CH bond activation of acetaldehyde could lead to the dominant demethanation reaction. The charge transfer process for PdH abstraction was caused by an intramolecular PdH rearrangement of the newly found η1‐aldehyde attached complex. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011
A model investigation of ab initio geometries for identity and nonidentity substitution with three‐center four‐ and three‐electron transition states
Authors: Buck Henk M. 
Published: March 2010

AbstractWith the van't Hoff model derived from the dynamics of a regular tetrahedron in which the interstitial carbon changes its position from tetrahedral into a trigonal (bi)pyramidal configuration, the introduction of dimensionless ratio numbers (R) can serve to localize significant points on the principal reaction coordinate. These numbers are expressed as R(d) and R(n) based on transition state geometries and the number of electrons involved in the three‐center bonding, respectively. Using this concept, we obtain a model for the evaluation of different ab initio calculations based on identity and nonidentity substitution reactions for three‐center four‐ and three‐electron bonding transition states. Similar ratio numbers have been derived for proton exchange reactions. The reactions under investigation show clearly that in spite of the differences in chemical outcome the transition steps reduced to the first principles of chemical bonding are similar. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011
Development and validation of a NANOGold™ immunoassay for the detection of vascular endothelial growth factor (VEGF) in human serum using inductively coupled plasma mass spectrometry
Authors: Thompson David F. , Eborall William , Dinsmore Andrew , Smith Christopher J. , Duckett Catherine J. 
Published: March 2010

AbstractThis work aimed to develop and validate a NANOGold™ based assay, quantified using inductively coupled plasma mass spectrometry (ICP‐MS), for the detection of human vascular endothelial growth factor (hVEGF) in serum. The initial assay range based on calibration standards was 62.5–2000 pg/mL with a detection limit of approximately 30 pg/mL. After validation using spiked validation controls, a quantification range between 175 and 1928 pg/mL was obtained. The inter‐assay precision was between 2.3 and 18.9% with accuracy between −8.8 and −3.1%. Additional performance parameters, including dilutional linearity, matrix specificity and time‐factored drift, were within ±20%, as defined by the validation acceptance criteria for the validation of macromolecule immunoassays used within our clinical environment. Serum samples from healthy donors were analysed to determine the endogenous levels of VEGF present; these ranged from 164 to 580 pg/mL with a mean of 273 pg/mL. The intra‐ and inter‐assay precision obtained from the healthy donor samples were 1.3–10.7% and 4.2–17.5%, respectively. This demonstration of a validated immunoassay opens further possibilities, utilising the simultaneous detection capabilities of ICP‐MS for the detection of multiple analytes in a single validated immunoassay, for routine use within a clinical environment. Copyright © 2010 John Wiley & Sons, Ltd.
Selective linkage detection of O‐sialoglycan isomers by negative electrospray ionization ion trap tandem mass spectrometry
Authors: Casal Enriqueta , Lebrón‐Aguilar Rosa , Moreno Francisco Javier , Corzo Nieves , Quintanilla‐López Jesús Eduardo 
Published: March 2010

AbstractSialylated O‐linked oligosaccharides are involved in many biological processes, such as cell‐cell interactions, cell‐substance adhesion, and virus‐host interactions. These activities depend on their structure, which is frequently determined by tandem mass spectrometry. However, these spectra are frequently analyzer‐dependent, which makes it difficult to develop widely applicable analytical methods. In order to deepen the origin of this behavior, two couples of isomers of sialylated O‐linked oligosaccharides, NeuAcα2‐3Galβ1‐3GalNAc‐ol/Galβ1‐3(NeuAcα2‐6)GalNAc‐ol and NeuGcα2‐3Galβ1‐3GalNAc‐ol/Galβ1‐3(NeuGcα2‐6)GalNAc‐ol, were analyzed by liquid chromatography/negative electrospray ionization ion trap tandem mass spectrometry (LC/ESI(−)‐MSn) using both an ion trap and a triple quadrupole mass spectrometer. Results clearly showed that while ions obtained in the triple quadrupole instrument fitted very well with the standard fragmentation routes, in the ion trap several intense ions could not be explained by these rules, specially a fragment at m/z 597. Furthermore, this ion was observed in the mass spectrum of those isomers that sialic acid binds to GalNAc by an α2‐6 linkage. From the MS3 spectrum of this ion an unexpected structure was deduced, and it led to propose alternative fragmentation pathways. Molecular mechanics calculations suggested that the found atypical route could be promoted by a hydrogen bond located only in α2‐6‐linked oligosaccharides. It has also been demonstrated that this process follows a slow kinetic, explaining why it cannot be observed using an ion beam‐type mass analyzer. In conclusion, ion traps seem to be more appropriate than triple quadrupoles to develop a reliable analytical method to distinguish between isomeric O‐linked glycans. Copyright © 2010 John Wiley & Sons, Ltd.
Optimization of electrospray interface and quadrupole ion trap mass spectrometer parameters in pesticide liquid chromatography/electrospray ionization mass spectrometry analysis
Authors: Kruve Anneli , Herodes Koit , Leito Ivo 
Published: March 2010

AbstractOptimization of both the ionization process and ion transportation in the mass spectrometer is of crucial importance in order to achieve high sensitivity and low detection limits and acceptable accuracy in liquid chromatography/electrospray ionization mass spectrometry (LC/ESI‐MS) analysis. In this paper four optimization procedures of electrospray interface and quadrupole ion‐trap mass spectrometer parameters (ESI‐MS) (nebulizer gas and drying gas flow rate, end plate voltage, capillary voltage, skimmer voltage, octopoles direct current and radio frequency, trap drive and lens voltages) were studied on three pesticides – thiabendazole, aldicarb and imazalil. The results demonstrate that the methodology of optimization strongly influences the effectiveness of finding true optima of the operating parameters. Both eluent flow rate and composition during optimization have to mimic the situation during real analysis as closely as possible in order to achieve parameters giving the highest sensitivity. Therefore, post‐column addition of analyte to the mobile phase identical in composition to the one in which analyte elutes during real analysis combined with software‐based optimization was found to be the most effective and fastest method for achieving intensity maxima. The parameters most strongly affecting ion formation and transportation, hence sensitivity, were capillary voltage, direct current of the first octopole, trap drive and the second lens for all pesticides under study. In addition to sensitivity and detection limit matrix effect was considered in the optimization process. It was found that the matrix effect can be reduced but not eliminated by adjusting the ESI and MS parameters. The optimal parameters from the point of view of the matrix effect can only be found with factorial design. Parameters giving higher sensitivity tended to be more affected by matrix effect causing higher ionization suppression by co‐eluting compounds. Copyright © 2010 John Wiley & Sons, Ltd.
Theoretical and computational studies of organometallic reactions: successful or not?
Authors: Sakaki Shigeyoshi , Ohnishi Yu‐Ya , Sato Hirofumi 
Published: March 2010

AbstractTheoretical and computational methods are powerful in studying transition metal complexes. Our theoretical studies of C–H σ‐bond activation of benzene by Pd(II)–formate complex and that of methane by Ti(IV)‐imido complex successfully disclosed that these reactions are understood to undergo heterolytic σ‐bond activation and the driving force is the formation of strong O–H and N–H bonds in the former and the latter, respectively. Orbital interactions are considerably different from those of σ‐bond activation by oxidative addition. The transmetallation, which is a key process in the cross‐coupling reaction, is understood to be heterolytic σ‐bond activation. Our theoretical study clarified how to accelerate this transmetallation. Also, we wish to discuss weak points in theoretical and computational studies of large systems including transition metal elements, such as the necessity to incorporate solvation effect and to present quantitatively correct numerical results. The importance of solvation effects is discussed in the oxidative addition of methyliodide to Pt(II) complex which occurs in a way similar to an SN2 substitution. To apply the CCSD(T) (coupled cluster singles and doubles with perturbative triples correction) method, which is the gold standard of electronic structure theory, to large system, we need to reduce the size of the system by employing a small model. But, such modeling induces neglects of electronic and steric effects of substitutents which are replaced in the small model. Frontier‐orbital‐consistent quantum‐capping potential (FOC‐QCP) was recently proposed by our group to incorporate the electronic effects of the substituents neglected in the modeling. The CCSD(T) calculation with the FOC‐QCP was successfully applied to large systems including transition metal elements. © 2010 The Japan Chemical Journal Forum and Wiley Periodicals, Inc. Chem Rec 10: 000–000; 2010: Published online in Wiley InterScience (www.interscience.wiley.com) DOI 10.1002/tcr.200900019
Identification of Mxr1p‐binding sites in the promoters of genes encoding dihydroxyacetone synthase and peroxin 8 of the methylotrophic yeast Pichia pastoris
Authors: Kranthi Balla Venkata , Vinod Kumar Hunsur Rajendra , Rangarajan Pundi N. 
Published: March 2010

AbstractExpression of genes involved in methanol metabolism of Pichia pastoris is regulated by Mxr1p, a zinc finger transcription factor. In this study, we studied the target gene specificity of Mxr1p by examining its ability to bind to promoters of genes encoding dihydroxyacetone synthase (DHAS) and peroxin 8 (PEX8), since methanol‐inducible expression of these genes is abrogated in mxr1‐null mutant strains of P. pastoris. Different regions of DHAS and PEX8 promoter were isolated from P. pastoris genomic DNA and their ability to bind to a recombinant Mxr1p protein containing the N‐terminal 150 amino acids, including the zinc finger DNA‐binding domain, was examined. These studies reveal that Mxr1p specifically binds to promoter regions containing multiple 5′‐CYCC‐3′ sequences, although all DNA sequences containing the 5′‐CYCC‐3′ motif do not qualify as Mxr1p‐binding sites. Key DNA‐binding determinants are present outside 5′‐CYCC‐3′ motif and Mxr1p preferably binds to DNA sequences containing 5′‐CYCCNY‐3′ than those containing 5′‐CYCCNR‐3′ sequences. This study provides new insights into the molecular determinants of target gene specificity of Mxr1p, and the methodology described here can be used for mapping Mxr1p‐binding sites in other methanol‐inducible promoters of P. pastoris. Copyright © 2010 John Wiley & Sons, Ltd.
No differences in outcomes between cemented and uncemented acetabular components after 12–14 years: results from a randomized controlled trial comparing Duraloc with Charnley cups
Authors: Bjørgul Kristian , Novicoff Wendy M. , Andersen S. T. , Brevig K. , Thu F. , Wiig M. , Åhlund O. 
Published: March 2010

AbstractBackgroundEven though there are multiple studies documenting the outcome of the Charnley low-friction arthroplasty as well as abundant studies on uncemented arthroplasties, there is a dearth of comparative studies of the uncemented acetabular component and a cemented component. In this study we aimed to document the long-term clinical and radiographic outcome as well as component survival in a randomized controlled trial.Materials and methodsTwo hundred fifteen patients (240 hips) were randomly allocated to receive a cemented Charnley cup or uncemented Duraloc 1200 cup. All patients received cemented Charnley stems and were evaluated clinically and radiographically after 6 months, and 2, 5, and 10 years.ResultsHarris Hip Scores improved from 48.3 [95% confidence interval (CI) 45.0–51.6] to 90.2 [95% CI 87.9–92.6] in the Charnley group and from 49.3 [95% CI 86.9–91.3] in the Duraloc group at 6 months. After 10 years, the Charnley group’s Harris Hip Score was 89.8 [95% confidence interval (CI) 87.0–92.6], and the Duraloc group’s score was 87.3 (95% CI 84.1–90.6). In the radiographic analysis after 10 years, there was no statistical difference in the prevalence of radiographic signs of loosening. Nine cups were revised in the Charnley group, and five cups were removed in the Duraloc group. The difference was not statistically significant. There was no statistical difference between the cups when aseptic loosening was the end-point, nor in survival analyses.ConclusionsThere is no statistically significant difference in clinical or radiological outcome between the Charnley cup and the Duraloc after 10 years, and no difference in implant survival after 12–14 years. The uncemented Duraloc cup is as good as the cemented Charnley cup after 10 years.
Collection of Epithelial Cells from Rodent Mammary Gland Via Laser Capture Microdissection Yielding High-Quality RNA Suitable for Microarray Analysis
Authors: McGinley John N , Zhu Zongjian , Jiang Weiqin , Thompson Henry J 
Published: March 2010

Abstract
Laser capture microdissection (LCM) enables collection of cell populations highly enriched for specific cell types that have the potential of yielding critical information about physiological and pathophysiological processes. One use of cells collected by LCM is for gene expression profiling. Samples intended for transcript analyses should be of the highest quality possible. RNA degradation is an ever-present concern in molecular biological assays, and LCM is no exception. This paper identifies issues related to preparation, collection, and processing in a lipid-rich tissue, rodent mammary gland, in which the epithelial to stromal cell ratio is low and the stromal component is primarily adipocytes, a situation that presents numerous technical challenges for high-quality RNA isolation. Our goal was to improve the procedure so that a greater probe set present call rate would be obtained when isolated RNA was evaluated using Affymetrix microarrays. The results showed that the quality of RNA isolated from epithelial cells of both mammary gland and mammary adenocarcinomas was high with a probe set present call rate of 65% and a high signal-to-noise ratio.
An assessment of medical students’ awareness of radiation exposures associated with diagnostic imaging investigations
Authors: O’Sullivan Jennifer , O’Connor Owen J. , O’Regan Kevin , Clarke Bronagh , Burgoyne Louise N. , Ryan Max F. , Maher Michael M. 
Published: March 2010

Abstract

Objectives
This study assessed students’ awareness of radiation exposures and determined the impact a curriculum in clinical radiology (CICR) had on awareness.

Methods
Six hundred seventy medical students at one medical school were studied. CICR was delivered in yearly modules over the 5-year programme. Five hundred twenty-three students (years 1–5), exposed to increasing numbers of CICR modules and 147 students beginning medical school (year 0), represented the study and control groups, respectively. Students completed a multiple choice questionnaire assessing radiation knowledge and radiology teaching.

Results
Most students in the study population received CICR but 87% considered they had not received radiation protection instruction. The percentage of correctly answered questions was significantly higher in the study population than the control group (59.7% versus 38%, p < 0.001). Students who received CICR achieved higher scores than those who did not (61.3% compared with 42.8%, p < 0.001). Increasing exposure to CICR with each year of medical education was associated with improved performance.

Conclusions
Assessment of students’ awareness of radiation exposures in diagnostic imaging demonstrates improved performance with increasing years in medical school and/or increasing exposure to CICR. Findings support the Euroatom 97 directive position, advocating implementation of radiation protection instruction into the undergraduate medical curriculum.
Implementation of Peer Review into a Physical Medicine and Rehabilitation Program and its Effect on Professionalism
Authors: Bonder Jaclyn , Elwood Douglas , Heckman Jeffrey , Pantel Austin , Moroz Alex 
Published: March 2010

ObjectiveTo examine the effects of implementing a peer review evaluation system on residents' attitudes and perceptions of professionalism, a core competency of the Accreditation Council for Graduate Medical Education (ACGME), in a Physical Medicine and Rehabilitation (PM&R) program.DesignFour classes of residents were divided prospectively into a control and an intervention group. All residents were asked to complete a survey regarding their attitudes and perceptions on both peer review and professionalism. Only 2 of these classes participated in a newly adopted peer review evaluation system, after which time all participants were again asked to fill out the surveys.SettingResidents were from a PM&R residency program at an urban tertiary care medical center.ParticipantsAll residents who completed the entire survey preintervention and postintervention were included.MethodsThe intervention was the introduction of peer review into residents' evaluation assessments. All residents filled out a survey with questions relating to peer review and professionalism before and after this intervention.Main Outcome MeasurementsOutcomes include understanding how residents perceive various attributes of professionalism, peer review, and the interconnection of the 2.ResultsData analysis using SPSS was performed using survey scores for 46 residents preintrodution and postintroduction of a peer review evaluation system. Analysis revealed that residents who participated in the peer review process were more likely to agree that certain aspects of daily patient care, behaviors, and concepts were components of professionalism. However, they continued to believe that residents are ultimately not responsible for their colleagues' professionalism and that peer review might be harmful to a residency program.ConclusionThis study introduces an interesting dichotomy. Peer review clearly influences resident outlook on professionalism and yet there is a high suspicion regarding its implementation. If appropriately implemented, peer review may be a potent method of enhancing the education of this ACGME requirement.
Use of N-butyl cyanoacrylate in nasal septoplasty: histopathological evaluation using rabbit nasal septum model
Authors: Aksoy F , Yılmaz F , Yıldırım Y S , Gideroglu K , Tatar Z 
Published: March 2010

AbstractObjectives:This study was designed to investigate the effects of the tissue adhesive N-butyl cyanoacrylate on nasal septal tissues after septal surgery in a rabbit model.Methods:Forty-two adult New Zealand rabbits were randomly divided into three groups (14 in each group): septoplasty alone, septoplasty plus N-butyl cyanoacrylate, and controls. The open approach was used to explore the nasal septum. After raising mucoperichondrial and mucoperiosteal flaps on both sides of the septum, the septum was detached from the nasal floor in the septoplasty alone and septoplasty plus N-butyl cyanoacrylate groups. In the septoplasty plus N-butyl cyanoacrylate group, the mucoperichondrial and mucoperiosteal flaps were fixed to the septum and the septum was fixed lateral to the nasal spine using N-butyl cyanoacrylate; in the septoplasty alone group, the septum was packed with Merocel. In the control group, no further septal surgery was performed after flap elevation. Animals were observed for bleeding and haematoma formation over the first 24 hours. Seven animals in each group were used to evaluate early histopathological effects on the septal tissues, at four weeks post-operatively; the other seven in each group were used to evaluate late effects, at 12 weeks.Results:Haematoma formation was observed in 10 animals in the septoplasty alone group, in four animals in the control group, and in only one animal in the septoplasty plus N-butyl cyanoacrylate group. The difference in haematoma incidence between the septoplasty alone and the septoplasty plus N-butyl cyanoacrylate groups was significant (p = 0.000). Histopathological evaluation revealed no significant difference between the groups as regards granulation tissue formation at week four versus week 12; however, there was a significant difference between the septoplasty plus N-butyl cyanoacrylate group and the control groups as regards inflammation at week 12 (p = 0.038). There was a significant difference between the septoplasty plus N-butyl cyanoacrylate group and the septoplasty alone group as regards the composition of the bone–cartilage junction zone at week four (p = 0.001). There was also a significant difference between the septoplasty plus N-butyl cyanoacrylate group and the control group as regards the cellular structure of new cartilage formation at week 12 (p = 0.004).Conclusions:In this rabbit septoplasty model, N-butyl cyanoacrylate appeared to be an effective nasal tissue adhesive, with a low complication rate.