bluuebunny/crossref_metadata_2025_split huggingface dataset:
Development of new methodologies for the mass spectrometry study of bioorganic macromolecules
Authors: Cristoni Simone , Bernardi Luigi Rossi 
Published: September 2003

Abstract

I.
Introduction
370

II.
Techniques That Are Usually Employed in the Study of Bioorganic Macromolecules
371

A. Proteins and Peptides
371

B. Oligonucleotides
374

C. Oligosaccharides and Glycoconjugates
375

D. Various Complexes (DNA–Protein, Antigen–Antibody, Macromolecules–Metals)
377

III.
Common Problems and Developments in the Analysis of Bioorganic Macromolecules by Mass Spectrometry
377

A.  Ionization Source Problems and Developments
377

1.  Sensitivity
377

2.  Problems with Buffers
379

3.  Multicharge Effect
381

B.  Mass Analyzer Problems and Developments
381

1.  Linear Dynamic Range
381

2.  Tandem Mass Spectrometry
382

3.  Sensitivity
382

4.  Resolution
383

5.  Mass Accuracy
383

IV.
New Promising Technologies
384

A.  Interfaces and Ionization Sources
384

1.  Improvements in the Coupling of Liquid‐Phase Separation Systems to Mass Spectrometry
384

2.  AP‐MALDI
384

3.  Deprotonant Agents
385

4.  Sonic Spray Ionization
388

5.  APCI without Corona Discharge
391

B.  Mass Analyzers
393

1.  Linear Quadrupole Ion Trap
394

2.  TOF Analyzers with New Detectors
395

3.  Multiple Mass Analyzers
396

V.
Software for Data Treatment
397

VI.
Conclusions and Future Developments
399

Acknowledgments

400

References

400

In recent years, mass spectrometry has been increasingly used for the analysis of various macromolecules of biological, biomedical, and biochemical interest. This increase has been made possible by two key developments: the advent of electrospray ionization (ESI) and matrix‐assisted laser desorption ionization (MALDI) sources. The two new techniques produce a significant increase in mass range and in sensitivity that led to the development of new applications and of new analyzer designs, software, and robotics. This review, apart from the description of the status of mass spectrometry in the analysis of bioorganic macromolecules, is mainly devoted to the illustration of the more recent promising techniques and on their possible future evolution. © 2003
Wiley Periodicals, Inc., Mass Spec Rev 22:369–406, 2003; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/mas.10062
Non‐specific, on‐probe cleanup methods for MALDI‐MS samples
Authors: Xu Yingda , Bruening Merlin L. , Watson J. Throck 
Published: September 2003

Abstract

I.
Introduction
429

II.
Decontamination with Films of Commercial Polymers
431

A.  Polyvinylidenedifluoride and Nitrocellulose
431

B.  Nylon
431

C.  Nafion
432

D.  Polyethylene (PE) and Polypropylene (PP)
432

E.  Polyurethane
432

F.  Paraffin and Teflon
432

G.  Ion‐Exchange Materials
433

III.
Decontamination with Thin Layers of Matrix Crystals
433

A.  Mechanism of Adsorption to Matrix Crystals
434

B.  Preparation of Desalting Matrix Crystals
434

1.  Thin Layers of Matrix Crystals
434

2.  Hydrophilic Spots of Matrix in Hydrophobic Polymer Layers
435

IV.
Decontamination with SAMs and Ultrathin Polymer Films
435

A.  Decontamination with Hydrophobic Interactions
435

B.  Decontamination with Electrostatic Interactions
436

C.  Patterned SAM/Polymer Films
437

V.
Conclusions
438

Acknowledgments

438

References

438

High concentrations of contaminants such as salts and surfactants are often present in biological samples to solubilize or stabilize analytes such as proteins. Unfortunately, the presence of those contaminants often precludes direct analysis by MALDI‐MS. Selective adsorption of analytes directly on modified MALDI probes, followed by rinsing to remove contaminants, overcomes this problem. This review focuses on various modifications of MALDI probes to allow the adsorption of proteins and DNA, even in a large excess of salt or surfactant. Interfaces deposited on the MALDI probes to adsorb analytes include films of commercial polymers, thin layers of matrix crystals, self‐assembled monolayers, and ultrathin polymer films. Hydrophobic and ionic interactions both effect analyte adsorption on those interfaces, and patterned interfaces allow the concentration and purification of analyte molecules. © 2003 Wiley Periodicals, Inc., Mass Spec Rev 22:429–440, 2003; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/mas.10064
Parallel computational strategies for structural optimization
Authors: Papadrakakis Manolis , Lagaros Nikolaos D. , Fragakis Yannis 
Published: September 2003

AbstractThe objective of this paper is to investigate the efficiency of various computational algorithms implemented in the framework of structural optimization methods based on evolutionary algorithms. In particular, the efficiency of parallel computational strategies is examined with reference to evolution strategies (ES) and genetic algorithms (GA). Parallel strategies are implemented both at the level of the optimization algorithm, by exploiting the natural parallelization features of the evolutionary algorithms, as well as at the level of the repeated structural analysis problems that are required by ES and GA. In the latter case the finite element solutions are performed by the FETI domain decomposition method specially tailored to the particular type of problems at hand. The proposed methodology is generic and can be applied to all types of optimization problems as long as they involve large‐scale finite element simulations. The numerical tests of the present study are performed on sizing optimization of skeletal structures. The numerical tests demonstrate the computational advantages of the proposed parallel strategies, which become more pronounced in large‐scale optimization problems. Copyright © 2003 John Wiley & Sons, Ltd.
Dispersion analysis of a non‐conforming finite element method for the Helmholtz and elastodynamic equations
Authors: Zyserman Fabio I. , Gauzellino Patricia M. , Santos Juan E. 
Published: September 2003

AbstractWe investigate the dispersive properties of a non‐conforming finite element method to solve the two‐dimensional Helmholtz and elastodynamics equations. The study is performed by deriving and analysing the dispersion relations and by evaluating the derived quantities, such as the dimensionless phase and group velocities. Also the phase difference between exact and numerical solutions is investigated. The studied method, which yields a linear spatial approximation, is shown to be less dispersive than a conforming bilinear finite element method in the two cases shown herein. Moreover, it almost halves the number of points per wavelength necessary to reach a given accuracy when calculating the mentioned velocities in both cases here presented. Copyright © 2003 John Wiley & Sons, Ltd.
Time‐decomposed parallel time‐integrators: theory and feasibility studies for fluid, structure, and fluid–structure applications
Authors: Farhat Charbel , Chandesris Marion 
Published: September 2003

AbstractA methodology for squeezing the most out of massively parallel processors when solving partial differential evolution equations by implicit schemes is presented. Its key components include a preferred implicit time‐integrator, a decomposition of the time‐domain into time‐slices, independent time‐integrations in each time‐slice of the semi‐discrete equations, and Newton‐type iterations on a coarse time‐grid. Hence, this methodology parallelizes the time‐loop of a time‐dependent partial differential equation solver without interfering with its sequential or parallel space‐computations. It is particularly interesting for time‐dependent problems with a few degrees of freedom such as those arising in robotics and protein folding applications, where the opportunities for parallelization over the degrees of freedom are limited. Error and stability analyses of the proposed parallel methodology are performed for first‐ and second‐order hyperbolic problems. Its feasibility and impact on reducing the solution time below what is attainable by methods which address only parallelism in the space‐domain are highlighted for fluid, structure, and coupled fluid–structure model problems. Copyright © 2003 John Wiley & Sons, Ltd.
Fetal loss following ultrasound diagnosis of a live fetus at 6–10 weeks of gestation
Authors: Makrydimas G. , Sebire N. J. , Lolis D. , Vlassis N. , Nicolaides K. H. 
Published: September 2003

AbstractObjectiveTo examine prospectively the value of demographic characteristics and ultrasound findings in the prediction of subsequent fetal loss in pregnancies with live fetuses at 6–10 weeks of gestation.MethodsTransvaginal ultrasound examination was performed in 866 pregnancies at 6–10 weeks of gestation. The relation of demographic data and ultrasound findings at the time of the initial assessment to subsequent fetal loss was examined.ResultsIn the 668 singleton pregnancies with live fetuses and complete follow‐up there were 50 (7.5%) fetal losses. The incidence of fetal loss increased significantly with maternal age and decreased with gestation. In the pregnancies resulting in fetal loss, compared to those with live births, the incidence of vaginal bleeding and cigarette smoking was higher, the fetal heart rate was significantly lower and the gestation sac diameter was smaller but the yolk sac diameter was not significantly different.ConclusionIn pregnancies with a live fetus at 6–10 weeks' gestation the rate of subsequent fetal loss is related to maternal age, gestation, cigarette smoking, history of vaginal bleeding and the ultrasound findings of small gestation sac diameter and fetal bradycardia, relative to crown–rump length. Copyright © 2003 ISUOG. Published by John Wiley & Sons, Ltd.
Spatio‐temporal image correlation (STIC): new technology for evaluation of the fetal heart
Authors: DeVore G. R. , Falkensammer P. , Sklansky M. S. , Platt L. D. 
Published: September 2003

AbstractSpatio‐temporal image correlation (STIC) is a new approach for clinical assessment of the fetal heart. It offers an easy to use technique to acquire data from the fetal heart and to aid in visualization with both two‐dimensional and three‐dimensional (3D) cine sequences. The acquisition is performed in two steps: first, images are acquired by a single, automatic volume sweep. Second, the system analyzes the image data according to their spatial and temporal domain and processes an online dynamic 3D image sequence that is displayed in a multiplanar reformatted cross‐sectional display and/or a surface rendered display. The examiner can navigate within the heart, re‐slice, and produce all of the standard image planes necessary for a comprehensive diagnosis. The advantages of STIC for use in evaluation of the fetal heart are as follows: the technique delivers a temporal resolution which corresponds to a B‐mode frame rate of approximately 80 frames/s; it provides the examiner with an unlimited number of images for review; it allows for correlation between image planes that are perpendicular to the main image acquisition plane; it may shorten the evaluation time when complex heart defects are suspected; it enables the reconstruction of a 3D rendered image that contains depth and volume which may provide additional information that is not available from the thin multiplanar image slices (e.g. for pulmonary veins, septal thickness); it lends itself to storage and review of volume data by the examiner or by experts at a remote site; it provides the examiner with the ability to review all images in a looped cine sequence. Copyright © 2003 ISUOG. Published by John Wiley & Sons, Ltd.
Uterine intramural bone after mid‐trimester termination of pregnancy may not affect fertility: a case report
Authors: Van den Bosch T. , Van Schoubroeck D. , Timmerman D. , Deprest J. 
Published: September 2003

AbstractWe present a case of a 27‐year‐old asymptomatic woman, gravida 2 para 0 abortus 2, diagnosed with uterine intramural fetal bone 30 days after a mid‐trimester termination of pregnancy (TOP) by dilatation and evacuation (D&E). On ultrasound part of a fetal spine was seen within the right lateral isthmocervical area, adjacent to the descending branch of the uterine artery. Within 4 months after TOP the patient conceived again. This case illustrates the risk of myometrial penetration during mid‐trimester TOP by D&E. Removal of intramural bony fragments may not be needed in an asymptomatic patient, as their presence does not seem to compromise fertility. Copyright © 2003 ISUOG. Published by John Wiley & Sons, Ltd.
Acardiac twin: a systematic review of minimally invasive treatment modalities
Authors: Tan T. Y. T. , Sepulveda W. 
Published: September 2003

AbstractThis review of the literature aimed to determine pregnancy outcomes after minimally invasive treatment for occluding vascular supply to acardiac twins. A MEDLINE search was performed until 2002 using the terms ‘acardiac’, ‘acardius’, ‘twin reversed arterial perfusion (TRAP) sequence’ and ‘chorangiopagus parasiticus’ and 207 articles published in the English‐language literature were identified. These articles and the corresponding cited references in English were reviewed. We identified 32 reports involving 74 cases of acardiac twin treated by minimally invasive techniques. Seventy one cases were included for analysis including 40 treated by cord occlusion and 31 by intrafetal ablation. Cord occlusion was first attempted by embolization (n = 5), cord ligation (n = 15), laser coagulation (n = 10), bipolar diathermy (n = 7) and monopolar diathermy (n = 3). Intrafetal ablation was performed by alcohol (n = 5), monopolar diathermy (n = 9), interstitial laser (n = 4) and radiofrequency (n = 13). The overall median gestational ages at treatment and delivery were 21 (range, 14–28) weeks and 36 (range, 19–42) weeks, respectively, with a median treatment–delivery interval of 13 (range, 0–25) weeks. The overall pump twin survival rate was 76% (n = 54). Intrafetal ablation was associated with later median gestational age at delivery (37 vs. 32 weeks, P = 0.04) and higher median treatment–delivery interval (16 vs. 9.5 weeks, P = 0.02) compared with cord occlusion techniques. It was also associated with a lower technical failure rate (13% vs. 35%, P = 0.03), lower rate of premature delivery or rupture of membranes before 32 weeks (23% vs. 58%, P = 0.003) and higher rate of clinical success (77% vs. 50%, P = 0.02) than cord occlusion techniques. There were no statistically significant differences in terms of outcome between the subgroups of fetoscopic‐ or ultrasound‐guided cord occlusion techniques. This review suggests that intrafetal ablation is the treatment of choice for acardiac twins because it is simpler, safer and more effective when compared with the cord occlusion techniques. Copyright © 2003 ISUOG. Published by John Wiley & Sons, Ltd.
First‐trimester uterine artery blood flow and birth weight
Authors: Hollis B. , Prefumo F. , Bhide A. , Rao S. , Thilaganathan B. 
Published: September 2003

AbstractObjectivesTo determine reference values for first‐trimester uterine artery resistance index (RI) in healthy pregnant women with uncomplicated pregnancies and to investigate the relationship between uterine artery Doppler indices and birth weight.MethodsThis was a cross‐sectional study of 265 consecutive pregnant women attending routine ultrasound examination at 11–14 weeks' gestation. Both uterine arteries were identified using color Doppler ultrasound and the RI was measured. The presence or absence of an early diastolic notch was also noted. Pregnancy outcomes were obtained from the delivery suite database and birth weight was expressed as Z‐scores.ResultsThe 5th, 50th and 95th centiles for uterine artery RI between 11 and 14 weeks' gestation were 0.53, 0.71 and 0.85, respectively. Complete pregnancy outcome data were available for 246 fetuses. There was a significant negative correlation between birth‐weight Z‐scores and first‐trimester uterine artery mean RI (r = − 0.219, P = 0.001). The difference in birth weight between fetuses with absent and those with bilateral diastolic notches was also significant (P < 0.001). Multiple regression analysis demonstrated that both mean RI (standardized regression coefficient = − 0.14, P = 0.039) and uterine artery notching (standardized regression coefficient = − 0.17, P = 0.017) contributed independently towards the prediction of birth‐weight Z‐score.ConclusionsA significant negative correlation exists between birth weight and first‐trimester uterine artery Doppler parameters, a reliable and non‐invasive method of examining uteroplacental perfusion. The value of first‐trimester uterine artery Doppler as a prognostic screening tool, either in isolation or in conjunction with maternal biochemistry, remains to be determined. Copyright © 2003 ISUOG. Published by John Wiley & Sons, Ltd.
Retrograde aortic isthmus net blood flow and human fetal cardiac function in placental insufficiency
Authors: Mäkikallio K. , Jouppila P. , Räsänen J. 
Published: September 2003

AbstractObjectiveRetrograde aortic isthmus (AoI) net blood flow has been associated with diminished oxygen delivery to cerebral circulation. This study was designed to characterize the cardiac function in human fetuses with retrograde AoI net blood flow in pregnancies complicated by placental insufficiency.MethodsThe control group comprised 43 fetuses in uncomplicated pregnancies. Study groups consisted of fetuses with placental insufficiency, and either antegrade (Group 1; n = 18) or retrograde (Group 2; n = 11) AoI net blood flow. Volume blood flows (Q) of left (LVCO) and right (RVCO) ventricles, ductus arteriosus (QDA), pulmonary arterial bed (QP) and foramen ovale (QFO) were calculated and their proportions (%) of combined cardiac output (CCO) were determined. Ventricular ejection forces were calculated. Blood velocity waveforms of the mitral (MV) and tricuspid (TV) valves were obtained. The proportion of left ventricular isovolumetric relaxation time (IRT%) of the cardiac cycle, and index of myocardial performance (IMP) were calculated.ResultsIn Group 1, QDA% was increased (P < 0.05) and QP% decreased (P < 0.05) compared with the control group, and QFO% was greater (P < 0.01) compared with the control group and Group 2. In Group 2, the distribution of CCO did not differ from that of the control group. Ventricular ejection forces were similar among the groups. In Group 2, the MV early filling/atrial contraction time‐velocity integral ratio was greater (P < 0.05) compared with those of the control group and Group 1. In Groups 1 and 2, IRT% and IMP were increased (P < 0.001) compared with the control group.ConclusionsIn placental insufficiency, fetuses with antegrade AoI net blood flow show a shift in RVCO from the pulmonary to the systemic circulation, and QFO makes up the majority of LVCO. Fetuses with retrograde AoI net blood flow fail to demonstrate these changes, suggesting a relative drop in the oxygen content of the blood entering the left ventricle. Copyright © 2003 ISUOG. Published by John Wiley & Sons, Ltd.
The role of the three vessels and trachea view (3VT) in the diagnosis of congenital heart defects
Authors: Viñals F. , Heredia F. , Giuliano A. 
Published: September 2003

AbstractObjectiveTo analyse the anomalies seen at the three vessels and trachea (3VT) view in fetuses with antenatally diagnosed congenital heart disease (CHD), specifically in defects involving the upper mediastinum, including the outflow tracts and/or arteries.MethodsSeventy‐four consecutive fetuses of singleton pregnancies with antenatally diagnosed structural heart defects were initially included in the study. We selected those in which there was an anomaly seen on the 3VT view and classified them into groups: abnormalities detected on the upper mediastinum (abnormal vessel size, alignment, arrangement and number), abnormal location of the transverse aortic arch in relation to the trachea, and abnormal functional behavior of the arterial vessels (reversed flow and turbulent flow) detected using color Doppler. The abnormalities detected were confirmed postnatally by a pediatric cardiologist, echocardiography and/or autopsy.ResultsThirty‐four of the 74 fetuses showed an abnormal 3VT view that could be classified into one of the groups. We classified the lesions according to the most evident abnormal finding during the examination. Gestational age ranged from 17 to 39 (mean, 30) weeks. Abnormal vessel size was found in 20 of the 74 fetuses, abnormal vessel alignment was found in two fetuses, and abnormal vessel arrangement in three fetuses. Two vessels instead of three were found in five fetuses and four vessels were found in two fetuses. Abnormal visualization of the trachea, between the pulmonary artery and the transverse arch, occurred in one fetus with isolated right aortic arch. We found reversed flow in the transverse aortic arch in three fetuses with aortic atresia and in two fetuses with severe coarctation of the aorta. Reversed flow in the pulmonary trunk was seen in a fetus with pulmonary atresia and double outlet right ventricle. Turbulent flow was found in two fetuses with outflow tract stenosis.ConclusionOur study, descriptive in nature, demonstrates that the 3VT view is a reliable method with which to determine abnormalities in the upper mediastinum. It proved to be efficient in identifying an important group of critical heart defects involving the outflow tracts and the aortic arch. It also provided important clues to the diagnosis of minor anomalies considered as markers of other CHD. We believe that use of the 3VT view should become routine in screening for CHD. Copyright © 2003 ISUOG. Published by John Wiley & Sons, Ltd.
Spatio‐temporal image correlation (STIC): a new tool for the prenatal screening of congenital heart defects
Authors: Viñals F. , Poblete P. , Giuliano A. 
Published: September 2003

AbstractObjectiveTo assess the feasibility and capability of STIC acquisition, performed by a general obstetrician performing antenatal ultrasound, to visualize fetal cardiac structures in women undergoing routine obstetric ultrasound examination, in order to obtain information to confirm normality of the fetal heart during intrauterine life.MethodsThis was a prospective study of one hundred fetuses with echocardiographically confirmed normal hearts and no extracardiac anomalies with gestational ages ranging between 18 and 37 weeks. A general obstetrician was invited to acquire the STIC volumes. The four‐chamber view was obtained as a starting point. A standard 7.5‐s acquisition time and 30° angle of acquisition were used and the resulting STIC was stored for later offline analysis by a fetal echocardiologist. For each patient, the stored STIC data were first evaluated by sweeping from the initial acquisition plane, in the caudal direction and then cranially, zooming, slowing or stopping the cardiac motion to visualize views and structures. If a structure or view was rated as inadequate or not identifiable, a multiplanar three‐dimensional (3D) examination of the STIC volume was taken in order to try to visualize it adequately. The rates obtained using just the STIC sweeps were compared independently, and then the 3D multiplanar study was added.ResultsSTIC acquisition was possible in all cases. The mean time required for STIC acquisition was 7.5 min. A complete cardiac examination according to the set criteria was achieved in 94.2% (95% confidence interval (CI), 90–99) of cases. We obtained a 94.2% success rate of visualizing different structures and views of the fetal heart using the STIC sweep alone (95% CI, 90–99) and 96.2% adding 3D multiplanar examination (95% CI, 92–100).ConclusionSTIC acquisition of the fetal heart is feasible with high success rates in visualization of the principal connections. The STIC data acquired by a general obstetrician can subsequently be used by a fetal echocardiologist for prenatal confirmation of normal cardiac structure or exclusion of major cardiac malformations. Copyright © 2003 ISUOG. Published by John Wiley & Sons, Ltd.