Web of Science, Scopus, and Google Scholar citation rates: a case study of medical physics and biomedical engineering: what gets cited and what doesn't?

There are often differences in a publication's citation count, depending on the database accessed. Here, aspects of citation counts for medical physics and biomedical engineering papers are studied using papers published in the journal Australasian physical and engineering sciences in medicine. Comparison is made between the Web of Science, Scopus, and Google Scholar. Papers are categorised into subject matter, and citation trends are examined. It is shown that review papers as a group tend to receive more citations on average; however the highest cited individual papers are more likely to be research papers.

An efficient approach to converting three-dimensional image data into highly accurate computational models.

Image-based meshing is opening up exciting new possibilities for the application of computational continuum mechanics methods (finite-element and computational fluid dynamics) to a wide range of biomechanical and biomedical problems that were previously intractable owing to the difficulty in obtaining suitably realistic models. Innovative surface and volume mesh generation techniques have recently been developed, which convert three-dimensional imaging data, as obtained from magnetic resonance imaging, computed tomography, micro-CT and ultrasound, for example, directly into meshes suitable for use in physics-based simulations. These techniques have several key advantages, including the ability to robustly generate meshes for topologies of arbitrary complexity (such as bioscaffolds or composite micro-architectures) and with any number of constituent materials (multi-part modelling), providing meshes in which the geometric accuracy of mesh domains is only dependent on the image accuracy (image-based accuracy) and the ability for certain problems to model material inhomogeneity by assigning the properties based on image signal strength. Commonly used mesh generation techniques will be compared with the proposed enhanced volumetric marching cubes (EVoMaCs) approach and some issues specific to simulations based on three-dimensional image data will be discussed. A number of case studies will be presented to illustrate how these techniques can be used effectively across a wide range of problems from characterization of micro-scaffolds through to head impact modelling.

The promise of nuclear medicine technology: status and future perspective of high-resolution whole-body PET.

Positron emission tomography has rapidly emerged over the past 50+ years resulting in highly sophisticated tools for medical diagnosis. However, spatial resolution is still one of the drawbacks of PET. Modern whole-body PET devices provide a spatial resolution in the range of 4-6mm FWHM. Physical constraints are equally responsible for limited spatial resolution as factors caused by geometrical effects or by detector crystal properties. This paper focuses on the question why it is still a major challenge--despite the invention of new crystals and readout electronics--to build a high-resolution whole-body PET system for humans. Physical constraints are discussed and possible solutions for high-resolution PET are presented.

The promise of new PET image reconstruction.

Image reconstruction in positron emission tomography (PET) is conventionally regarded as the algorithm applied to the acquired data to produce images used for estimation of physiological parameters, or to determine the presence of disease. There are numerous approaches to image reconstruction, and the method chosen has a significant impact on the utility of PET. The use of iterative image reconstruction algorithms and the use of resolution modelling ("resolution recovery") are two specific advances from recent years which have demonstrated marked improvements in image quality. This paper considers three main aspects of PET image reconstruction in which there are still promising possibilities for further advance: (i) full consideration of the raw acquired PET data (with minimal pre-processing), (ii) careful selection of the parameters to estimate and (iii) accurate definition of the system matrix, which maps the parameters to the measurement space. Specific examples for these three areas include (i) the full use of timing, position and energy information, (ii) selecting physiological parameters as the unknowns to estimate and (iii) using Monte Carlo simulation to model the PET scanner and patient, in conjunction with time-dependent MRI or CT anatomical information to render the model more accurate. Present computational constraints mean that limited but practical methods have to be used, which to some extent compromise the full capabilities of image reconstruction in all of the aforementioned areas of promise. Nonetheless, this paper comments on possible ways forward without being overly concerned about the current limitations.

Technical challenges and opportunities of whole-body magnetic resonance imaging at 3T.

An increasing number of magnetic resonance whole-body units operating at field strengths of 3T and beyond are currently installed in research institutions as well as clinical facilities. This review wants to describe the changes in physical properties at higher field strength and the resulting implications for clinical and experimental examinations of the whole body. An overview is provided on the resulting advantages and disadvantages for anatomical, functional and biochemical MR examinations in different regions of the body (except the brain). It is demonstrated that susceptibility and chemical shift effects increase linearly with field strengths and provide clearly higher sensitivity of most spectroscopic or blood oxygen level dependent (BOLD) techniques. On the other hand, homogeneity of the radiofrequency (RF) field is reduced in the body trunk at higher field strength due to the shorter wavelength. Examinations of the head or extremities provide sufficient homogeneity of the RF field for common examination techniques in most cases, whereas abdominal and pelvic examinations are still sometimes hampered by undesired dielectric effects. Nearly quadratic increase of RF energy deposition with increasing field strengths results in clear limitations for some common sequence types which work without any problems at 1.5 T. New strategies with multi-channel RF excitation have the potential to overcome limitations due to RF inhomogeneities, but a few years of further technological development seem necessary. Many problems have to be solved in the near future regarding the variety of MR techniques and applications in all parts of the human body.

Identification of intratumour low frequency microvascular components via BOLD signal fractal dimension mapping.

Typical clinical evaluation of the tumour microvascular environment is performed by dynamic contrast enhanced MRI (dceMRI). However, this approach has been defined by numerous mathematical models each with their own physiologic assumptions which often leads to inconclusive results in the assessment of microstructure. Alternatively, Blood Oxygen Level Dependent (BOLD) Magnetic Resonance Imaging (MRI) is already known to be sensitive to the microvascular environment through fluctuation in the oxyhemoglobin to deoxyhemoglobin ratio. Consequently, quantification of the BOLD signal's temporal complexity using a fractal dimension index allows maps to be generated that are physiologically distinctive in nature and allow potential insight into tumour microvasculature with no a priori assumptions as in dceMRI. Here, using rectal carcinoma as an example, we present this novel approach to tumour microvascular evaluation using fractal dimension parametric mapping.

Biophysical calculation of cell survival probabilities using amorphous track structure models for heavy-ion irradiation.

Both the microdosimetric kinetic model (MKM) and the local effect model (LEM) can be used to calculate the surviving fraction of cells irradiated by high-energy ion beams. In this study, amorphous track structure models instead of the stochastic energy deposition are used for the MKM calculation, and it is found that the MKM calculation is useful for predicting the survival curves of the mammalian cells in vitro for (3)He-, (12)C- and (20)Ne-ion beams. The survival curves are also calculated by two different implementations of the LEM, which inherently used an amorphous track structure model. The results calculated in this manner show good agreement with the experimental results especially for the modified LEM. These results are compared to those calculated by the MKM. Comparison of the two models reveals that both models require three basic constituents: target geometry, photon survival curve and track structure, although the implementation of each model is significantly different. In the context of the amorphous track structure model, the difference between the MKM and LEM is primarily the result of different approaches calculating the biological effects of the extremely high local dose in the center of the ion track.

Exploring dynamics in living cells by tracking single particles.

In the last years, significant advances in microscopy techniques and the introduction of a novel technology to label living cells with genetically encoded fluorescent proteins revolutionized the field of Cell Biology. Our understanding on cell dynamics built from snapshots on fixed specimens has evolved thanks to our actual capability to monitor in real time the evolution of processes in living cells. Among these new tools, single particle tracking techniques were developed to observe and follow individual particles. Hence, we are starting to unravel the mechanisms driving the motion of a wide variety of cellular components ranging from organelles to protein molecules by following their way through the cell. In this review, we introduce the single particle tracking technology to new users. We briefly describe the instrumentation and explain some of the algorithms commonly used to locate and track particles. Also, we present some common tools used to analyze trajectories and illustrate with some examples the applications of single particle tracking to study dynamics in living cells.

Computational models of molecular self-organization in cellular environments.

The cellular environment creates numerous obstacles to efficient chemistry, as molecular components must navigate through a complex, densely crowded, heterogeneous, and constantly changing landscape in order to function at the appropriate times and places. Such obstacles are especially challenging to self-organizing or self-assembling molecular systems, which often need to build large structures in confined environments and typically have high-order kinetics that should make them exquisitely sensitive to concentration gradients, stochastic noise, and other non-ideal reaction conditions. Yet cells nonetheless manage to maintain a finely tuned network of countless molecular assemblies constantly forming and dissolving with a robustness and efficiency generally beyond what human engineers currently can achieve under even carefully controlled conditions. Significant advances in high-throughput biochemistry and genetics have made it possible to identify many of the components and interactions of this network, but its scale and complexity will likely make it impossible to understand at a global, systems level without predictive computational models. It is thus necessary to develop a clear understanding of how the reality of cellular biochemistry differs from the ideal models classically assumed by simulation approaches and how simulation methods can be adapted to accurately reflect biochemistry in the cell, particularly for the self-organizing systems that are most sensitive to these factors. In this review, we present approaches that have been undertaken from the modeling perspective to address various ways in which self-organization in the cell differs from idealized models.

BPPred: a Web-based computational tool for predicting biophysical parameters of proteins.

We exploit the availability of recent experimental data on a variety of proteins to develop a Web-based prediction algorithm (BPPred) to calculate several biophysical parameters commonly used to describe the folding process. These parameters include the equilibrium m-values, the length of proteins, and the changes upon unfolding in the solvent-accessible surface area, in the heat capacity, and in the radius of gyration. We also show that the knowledge of any one of these quantities allows an estimate of the others to be obtained, and describe the confidence limits with which these estimations can be made. Furthermore, we discuss how the kinetic m-values, or the Beta Tanford values, may provide an estimate of the solvent-accessible surface area and the radius of gyration of the transition state for protein folding. Taken together, these results suggest that BPPred should represent a valuable tool for interpreting experimental measurements, as well as the results of molecular dynamics simulations.

[Urodynamic paradigms: from renaissance fibrilar theory to current Doppler-flowmetry]. / Paradigmas urodinamicos. Desde la teoria fibrilar renacentista, hasta la flujometría-Doppler actual.

UNLABELLED: To perform a historical introduction and a review of the mathematical model, emphasizing that our mathematical model may be the solution to the viscoelastic model. It is evident that the same experiment has been repeated over half a century, with similar results in all cases. We also show one of the projects we are working on: the electro-vesicogram for the evaluation of the filling phase, and Doppler uroflowmetry for the study of the voiding phase. METHODS: We have chosen and studied in depth the results Dr. Virseda presents in his thesis of one of the experiments performed in relation to the viscoelastic model. After applying analytical methods we reach a differential equation we suppose defines detrusor behaviour, as it has been explained by the viscoelastic model. The solution of this equation by means of the Laplace's transform enables to obtain the values of the incognitas set by urodynamics. Besides, we analyzed the behaviour of solutions' stability using a matricial method following the Lyapunov theory. The former may solve the incognitas for the voiding phase. We used urethral Doppler with simultaneous uroflowmetry to obtain the data equations demanded; this is what we named "Doppler uroflowmetry". The filling phase was studied by superficial electromiography. We named it "electrovesicogram". We attach images for both Doppler wave and electrovesicogram. They both are the projects we are working on. RESULTS: Currently we can only explain the methodology we are following. Indeed, this article is the first of a series in which we aim to explain the methodology we are following in detail: Doppler wave capture; mounting process photogram by photogram, and vectorization and cleaning of the wave, either Doppler or flow waves; treatment in autocad to obtain the vector; and management of the vector with the matalab software, which gives us the results we are looking for. CONCLUSIONS: It is intuitive to deduct the usefulness of these methods as not invasive techniques in the urodynamic diagnosis. We have our illusions in these projects which open a window to the future.

Paradigmas urodinámicos. Desde la teoría fibrilar renacentista hasta la flujometría-Doppler actual / Urodynamic paradigms: from renaissance fibrilar theory to current Doppler-flowmetry

OBJETIVO: Hacer una introducción histórica y una revisión del modelo matemático en la que se destaca fundamentalmente que nuestro modelo matemático puede ser la solución del modelo viscoelástico. Es evidente que durante medio siglo se ha estado repitiendo el mismo experimento, y en todas las ocasiones con resultados similares. También exponemos uno de los proyectos en los trabajamos: el electrovesicograma, para la exploración de la fase de llenado y la uroflujometría doppler para el estudio de la fase miccional. MÉTODOS: Basándonos en los resultados de uno de los experimentos realizados en relación con el modelo viscoelástico hemos elegido y estudiado en profundidad los resultados que el Dr. Virseda, presenta en su tesis. Y tras aplicar métodos analíticos, llegamos a una ecuación diferencial que suponemos define el comportamiento del detrusor según nos ha estado diciendo que lo hace el modelo viscoelástico. La solución de esta ecuación mediante la transformada de Laplace, nos permite obtener los valores de las incógnitas que la urodinámica plantea. Por otra parte, mediante el método matricial, analizamos el comportamiento de la estabilidad de las soluciones, según la teoria de Lyapunov. Lo anterior puede resolver las incógnitas de la fase miccional. Para obtener los datos que las ecuaciones nos demandan, utilizamos el doppler uretral, simultaneandolo con la flujometría, en lo que hemos dado en llamar la "Flujometría doppler". La fase de llenado la estudiamos mediante métodos de electromiografía superficial. El "Electrovesicograma", como lo llamamos nosotros. Adjuntamos imágenes tanto de la onda doppler como de la del electrovesicograma. Ambos son proyectos en los que estamos trabajando en la actualidad. RESULTADOS: De momento sólo podemos explicar la metodología que estamos siguiendo. De hecho este es el primero de una serie de artículos en los que nos proponemos detallar la metodología que seguimos: la captura de la onda doppler, su montaje fotograma a fotograma y la vectorización y limpieza de la onda, doppler y de flujo. Su tratamiento en autocad, para obtener el vector y el manejo del vector con el programa matalab, que nos da los resultados buscados. CONCLUSIONES: Es intuitivo deducir la utilidad de estos métodos, como técnicas no invasivas en el diagnóstico urodinámico. Tenemos puestas nuestras ilusiones en estos proyectos que no son otra cosa que abrir una puerta al futuro (AU)

To perform a historical introduction and a review of the mathematical model, emphasizing that our mathematical model may be the solution to the viscoelastic model. It is evident that the same experiment has been repeated over half a century, with similar results in all cases. We also show one of the projects we are working on: the electro-vesicogram for the evaluation of the filling phase, and Doppler uroflowmetry for the study of the voiding phase. METHODS: We have chosen and studied in depth the results Dr. Virseda presents in his thesis of one of the experiments performed in relation to the viscoelastic model. After applying analytical methods we reach a differential equation we suppose defines detrusor behaviour, as it has been explained by the viscoelastic model. The solution of this equation by means of the Laplace'S transform enables to obtain the values of the incognitas set by urodynamics. Besides, we analyzed the behaviour of solutions' stability using a matricial method following the Lyapunov theory. The former may solve the incognitas for the voiding phase. We used urethral Doppler with simultaneous uroflowmetry to obtain the data equations demanded; this is what we named "Doppler uroflowmetry". The filling phase was studied by superficial electromiography. We named it "electrovesicogram". We attach images for both doppler wave and electrovesicogram. They both are the projects we are working on. RESULTS: Currently we can only explain the methodology we are following. Indeed, this article is the first of a series in which we aim to explain the methodology we are following in detail: Doppler wave capture; mounting process photogram by photogram, and vectorization and cleaning of the wave, either Doppler or flow waves; treatment in autocad to obtain the vector; and management of the vector with the matalab software, which gives us the results we are looking for. CONCLUSIONS: It is intuitive to deduct the usefulness of these methods as not invasive techniques in the urodynamic diagnosis. We have our illusions in these projects which open a window to the future (AU)

Modeling the spontaneous activity of the auditory cortex.

We present a rate model of the spontaneous activity in the auditory cortex, based on synaptic depression. A Stochastic integro-differential system of equations is derived and the analysis reveals two main regimes. The first regime corresponds to a normal activity. The second regime corresponds to epileptic spiking. A detailed analysis of each regime is presented and we prove in particular that synaptic depression stabilizes the global cortical dynamics. The transition between the two regimes is induced by a change in synaptic connectivity: when the overall connectivity is strong enough, an epileptic activity is spontaneously generated. Numerical simulations confirm the predictions of the theoretical analysis. In particular, our results explain the transition from normal to epileptic regime which can be induced in rats auditory cortex, following a specific pairing protocol. A change in the cortical maps reorganizes the synaptic connectivity and this transition between regimes is accounted for by our model. We have used data from recording experiments to fit synaptic weight distributions. Simulations with the fitted distributions are qualitatively similar to the real EEG recorded in vivo during the experiments. We conclude that changes in the synaptic weight function in our model, which affects excitatory synapses organization and reproduces the changes in cortical map connectivity can be understood as the main mechanism to explain the transitions of the EEG from the normal to the epileptic regime in the auditory cortex.

Hyperpolarization-activated, cyclic AMP-gated, HCN1-like cation channel: the primary, full-length HCN isoform expressed in a saccular hair-cell layer.

The expression of transcript for hyperpolarization-activated, cyclic nucleotide-sensitive cation channel (HCN) isoforms underlying hyperpolarization-activated, inward current (I(h)) has been determined for a model hair-cell preparation from the saccule of the rainbow trout, Oncorhynchus mykiss. Based upon identification from homology to known vertebrate HCN cDNA sequence, cloning of PCR products amplified with degenerate primers indicated an expression frequency of 7:2:1 (HCN1:HCN2:HCN4) for the hair-cell sheet compared with 1:1:7 for brain. Full-length sequence has been obtained for the HCN1-like isoform representing the primary HCN transcript expressed in the hair-cell preparation. The channel protein is 938 amino acids in length with 93% amino acid identity for the region extending from the S1-S6 membrane spanning domains through the voltage-pore and cyclic nucleotide-binding domains, compared with HCN1 for rabbit, rat, mouse and human. The N- and C-terminal regions are less homologous, with 39-51% and 43-44% amino acid identities, respectively. Compared with other vertebrate HCN1, the hair-cell HCN1 contains additional consensus phosphorylation sites associated with unique repeats in the carboxy terminus. The HCN1-like transcript has been localized to hair cells of the saccular sensory epithelia by in situ hybridization. Previous electrophysiological studies have identified I(h) as the sole inwardly rectifying ion channel in a specific population of hair cells of the saccule of frogs [J Neurophysiol (1995) 73:1484] and fish [J Physiol (1996) 495:665]. I(h) is an important determinant of the resting membrane potential, and for this population of hair cells, is predicted to maintain the membrane potential within a voltage range allowing the voltage-gated calcium channels to open, permitting "spontaneous" release of transmitter. The molecular properties of the HCN1-like isoform underlying I(h) expressed in the saccular hair cells of the teleost, trout, may consequently impact spontaneous release of transmitter from hair cells of the saccule.

Untreatable pain resulting from abdominal cancer: new hope from biophysics?

CONTEXT: Visceral pain characterizing pancreatic cancer is the most difficult symptom of the disease to control and can significantly impair the quality of life which remains and increase the demand for euthanasia. AIM: To investigate a possible new method based on biophysical principles (scrambler therapy) to be used in the effective treatment of drug-resistant oncological pain of the visceral/neuropathic type. SETTING: Eleven terminal cancer patients (3 pancreas, 4 colon, 4 gastric) suffering from elevated drug resistant visceral pain. DESIGN: The trial program was related to the first ten treatment sessions. Subsequently, each patient continued to receive treatment until death. MAIN OUTCOME MEASURES: Pain measures were performed using the visual analogue scale before and after each treatment session and accompanied by diary recordings of the duration of analgesia in the hours following each single application. Any variation in pain-killing drug consumption was also recorded. RESULTS: All patients reacted positively to the treatment throughout the whole reference period. Pain intensity showed a significant decrease (P<0.001), accompanied by a gradual rise both in the pain threshold and the duration of analgesia. Nine (81.8%) of the patients suspended pain-killers within the first 5 applications, while the remaining two (18.2%) considerably reduced the dosage taken prior to scrambler therapy. No undesirable side effects were observed. Compliance was found to be optimal. CONCLUSIONS: The preliminary results obtained using scrambler therapy are extremely encouraging, both in terms of enhanced pain control after each treatment session and in view of the possible maintenance of effectiveness over time.

Beyond U(crit): matching swimming performance tests to the physiological ecology of the animal, including a new fish 'drag strip'.

Locomotor performance of animals is of considerable interest from management, physiological, ecological and evolutionary perspectives. Yet, despite the extensive commercial exploitation of fishes and interest in the health of various fish stocks, the relationships between performance capacity, natural selection, ecology and physiology are poorly known for fishes. One reason may be the technical challenges faced when trying to measure various locomotor capacities in aquatic species, but we will argue that the slow pace of developing new species-appropriate swim tests is also hindering progress. A technique developed for anadromous salmonids (the U(crit) procedure) has dominated the fish exercise physiology field and, while accounting for major advances in the field, has often been used arbitrarily. Here we propose criteria swimming tests should adhere to and report on several attempts to match swimming tests to the physiological ecology of the animal. Sprint performance measured with a laser diode/photocell timed 'drag strip' is a new method employing new technology and is reported on in some detail. A second new test involves accelerating water past the fish at a constant rate in a traditional swim tunnel/respirometer. These two performance tests were designed to better understand the biology of a bentho-pelagic marine fish, the Atlantic cod (Gadus morhua). Finally, we report on a modified incremental velocity test that was developed to better understand the biology of the blacknose dace (Rhinichthys atratulus), a Nearctic, lotic cyprinid.

Induced current measurements in whole body exposure condition to radio frequency electric fields.

The current induced in a human exposed to radio frequency electric fields has been studied by the use of a stripline, in which whole body exposure to vertical electric fields (3-27 MHz) can be produced. We have examined two different techniques to measure the induced current; parallel plate meters and current probes. When the subject has good connection to the ground, the choice of measurement technique is not crucial, since there are only minor differences in readings between the instruments. But when the subject is wearing shoes and/or standing on a wooden plate, the difference between the instruments increases considerably. The difference can mainly be explained by the capacitive coupling between the parallel plate meters and the ground; therefore, the current probes are preferred when the subject does not have perfect contact with the ground. Since the International Commission on Non-Ionizing Radiation Protection guidelines demand measurements of induced current in humans exposed to radio frequency fields in the range of 10-110 MHz, the importance of finding an appropriate measurement procedure becomes apparent.