Many arrhythmias are triggered by abnormal electrical activity at the ionic channel and cell level, and then evolve spatio-temporally within the heart. To understand arrhythmias better and to diagnose them more precisely by their ECG waveforms, a whole-heart model is required to explore the association between the massively parallel activities at the channel/cell level and the integrative electrophysiological phenomena at organ level.We have developed a method to build large-scale electrophysiological models by using extended cellular automata, and to run such models on a cluster of shared memory machines. We describe here the method, including the extension of a language-based cellular automaton to implement quantitative computing, the building of a whole-heart model with Visible Human Project data, the parallelization of the model on a cluster of shared memory computers with OpenMP and MPI hybrid programming, and a simulation algorithm that links cellular activity with the ECG.We demonstrate that electrical activities at channel, cell, and organ levels can be traced and captured conveniently in our extended cellular automaton system. Examples of some ECG waveforms simulated with a 2-D slice are given to support the ECG simulation algorithm. A performance evaluation of the 3-D model on a four-node cluster is also given.Quantitative multicellular modeling with extended cellular automata is a highly efficient and widely applicable method to weave experimental data at different levels into computational models. This process can be used to investigate complex and collective biological activities that can be described neither by their governing differentiation equations nor by discrete parallel computation. Transparent cluster computing is a convenient and effective method to make time-consuming simulation feasible. Arrhythmias, as a typical case, can be effectively simulated with the methods described. Arrhythmias, a significant direct cause of death in heart diseases, are emergent and evolvable events that come with little prior warnings and allow limited response time . AlthougTo overcome the inherent limitations of clinical investigation, computational modeling and simulation has been widely recognized as a valuable alternative approach. Traditionally, cardiac modeling has centered on ECG simulation. Using the finite element method (FEM), the virtual heart and whole chest are partitioned into numerous elements representing a group of cells. The ECG is then simulated, based on computing the body surface potential of each cardiac element -5. BasicTo study arrhythmias using a large-scale realistic electrophysiological model, two issues need to be effectively resolved: model building and operation. Though the widespread paradigm of modeling with C or C++ remains a workable choice, the huge number of cardiac cells in a realistic three-dimensional (3-D) whole-heart model and the numerous modifications of the model to simulate various pathological conditions, make more desirable efficient modeling based on transparent parallel computing. To build and run a model with parallel computing technologies, two strategies were separately developed in recent years. To provide transparent and parallel descriptions, cellular automata were used -11,50; fThere is compelling evidence that cardiomyocytes are not arranged in a uniformly connected continuum, as has often been assumed and simulated in the past. Along with nonlinear ionic channel electrical activity, discontinuous electrical propagation is another key feature of cardioelectrical activity . The forCellular automata were first introduced by John von Neumann and Stanislaw Ulam in the 1940s, and gradually used to solve a wide range of problems, including multicellular biological modeling in which a natural correspondence between each automaton cell and each biological cell is assumed -21. SimpCellular is a cellular automata system based on the language Cellang [time synchronizes the running of all cells. By conventions, in cellular automata computation quantitative computing is not fully supported and function call is not allowed. To overcome this inherent inadequacy of Cellang in quantitative computing and enable it to solve HH type membrane equations, we have added new language facilities, including the floating-point data type and the mathematical functions provided in the C libraries. Thus, Cellang is able to encode numerical solutions of the HH equations  can access correct neighbors that are located in the outermost m layers of the two neighboring subsets, respectively. Field values of cells in these extra layers should be swapped between neighboring subsets after each round of computation to ensure that cells access updated data. Such data exchange is the major factor for the excessive time needed by cellular automata models running on distributed memory platforms. If cells have many fields, the time spent on such operations may even offset the benefits of parallelism.Running a model may be no easier than building it. The large number of cells, the small time step Δt and the long running time for arrhythmia simulation make it impractical to run a whole heart model on any low-end computer. Since large-scale SMP machines are extremely expensive, the prevailing parallel computing platforms are clusters of small-scale SMP or DMP, and the protocols of programming in Fortran, C, and C++ on such computers are OpenMP and MPI. First, an endless master-slave program structure is adopted  digital male cadaver , which ctype, indicating cell type, is defined in the cell program, but whose value is initially stipulated in the anatomical model when we process tissue slices, such as:The heterogeneity of a model is described in two ways. First, a specific field [x, y, z] = type, ......if-then statement on the value of type, the cell program is divided into several parts, each being executed by cells of the specific type. Second, type can be modified at runtime to simulate pathological changes. After a cell type is changed, its program and therefore its behavior also change.x, y, and z are the coordinates. Values of other fields can be defined or not in the data file. With a nested In a tissue or organ, aside from heterogeneity, cells often show anisotropy and inhomogeneity that cannot be conveniently described while processing the raw data. To describe these two properties needs a bit of pattern formation programming , an inteLet the layer number of SAN cells (at least one SAN cell is on the epicardium) be 0 and the layer number of AVN cells (at least one AVN cell is on the endocardium) be 50.• If the current cell is neither a ventricular nor an atrial cell, then: if it connects to a cell whose layer is 0, its layer is 0; if it connects to a cell whose layer is 50, its layer is 50.Min. The layer of this cell is Min+1.• If the current cell is a ventricular or an atrial cell, then: visit all its neighboring cells and find out their minimal layer number, A slice of the stratified 3-D model and of the stratified 2-D model is shown in Figure The slices of the digital cadaver do not provide any useful information on the distribution of terminal Purkinje fibers. Even if we know that most of them are located in the subendocardium, it is impractical to make a slice-by-slice manual description. Based on the stratified cardiac walls, this issue can be easily solved by using a lateral inhibition algorithm applied to cells on the ventricle subendocardium to generate a mesh-like Purkinje network. On completion of running the algorithm, some of the cell types are changed from ventricular cell to Purkinje cell.n-by-n cell communication among automaton cells of conduction fibers without physically building the fiber structure; n = 4 gives very satisfactory simulation results. Again, we propose that by using a pattern formation algorithm the physical construction of fiber structures is also feasible. In this scenario, a fiber is assembled by n successive automaton cells sharing the same, unique identity number, among which there is no conduction delay. Currently, with the 2-D model we find that even if letting each automaton cell stand for a discrete ventricular cell, the model works quite well in ECG simulation.The more difficult engineering issue is the fine structure of cardiac cells and conduction fibers. Simulation with the 2-D model demonstrates that, even if the HH action potential model of Purkinje cells produces a very fast upstroke, which means a quick transjunctional conduction, yet a one-cell by one-cell conduction can never give normal propagation profiles as observed in Durrer's experiment, due to a too long transjunctional delay . Neverth+ channels are slightly changed to produce action potential duration of human cardiac cells. Time constraints are the only reason for us to adopt early published, simpler action potential models. In the given simulations, all action potential models are solved using explicit Euler integration with a time step, Δt, of 0.01 ms [Each automaton cell is a computing unit for action potential and ECG simulation. The electrical activity of each automaton cell of a specific cell type is described by the corresponding HH type action potential model. Five action potential models are employed to simulate activities of different cardiac cells  -31. Sinc 0.01 ms . An asyn 0.01 ms . ElectriEach automaton cell in the 3-D model has 26 neighbors, linked by gap junctions. When a cell depolarizes, driven by the potential difference between it and its neighboring cells, transjunctional currents generate and propagate to neighbors through gap junctions. Simulations with the 2-D model show that the simple static gap junction model, in which the resistance of the gap junction is a constant and the transjunctional current follows Ohm's law, works quite well. The dynamic gap junction models, in which the resistance of gap junction changes in a nonlinear manner with membrane potential, will significantly increase computational time ,34 and cIstim, that the cell receives. The direction and speed of electrical propagation within the heart are jointly controlled by: (1) the stratification of the ventricular walls, (2) the speed of end-to-end and side-to-side conduction, (3) the ratio of end-to-end conduction speed to side-to-side conduction speed, and (4) the distribution of the trunk conduction bundle.Values of gap junction resistance between different cells and in different directions are initially set according to available experimental data, and then tuned via simulation according to Durrer's experimental observations . Excitatblood, with normal value 1.0 is defined in the cell program, and introduced as an extra parameter in action potential and in gap junction models. To multiply the conductivity of the gap junction by an abnormal value of blood (e.g., blood 0.7) can simulate a lowered gap junction conduction speed. A small value for blood, when inserted into the equation computing Ca++ current, affects the generation of the action potential. Dynamically modified blood can naturally simulate progressive ischemia  which significantly influences action potential. Abnormality of transjunctional conduction constitutes the third class, and the fourth class is is comprised of anomalous dynamics of cellular electrical activity itself. Changes in the HH equations can simulate these aberrations. In most cases, pathological changes affect more than one aspect. For example, in addition to providing an abnormal cell environment, ischemia also results in changed cellular electrical activity and altered gap junction resistance. To simulate the effect of ischemia, a special field Combining these factors, a variety of arrhythmias can be simulated. For example, by partially or completely blocking the activity of cells, or the conduction of gap junctions at specific locations, various conduction blocks such as AV (atrium-ventricle) block, LBBB (left bundle branch block) and RBBB (right bundle branch block) can be conveniently simulated. Many rapid arrhythmias are triggered by successive ectopic beats. Such abnormal beats can be produced in the model by providing cells at specific locations with extra stimulation or by changing them from atrial/ventricular to SAN cells. For abnormal propagations such as long QT syndrome, caused by the extra long refractory period of M cells, we can adjust, either dynamically or statically, the layer number of cells at the middle layers of the ventricular walls. Complex spatiotemporal patterns of arrhythmias are formed through discrete cell-cell communication. By these means, arrhythmic electrical activities can be simulated in flexible ways, different from those models created by cable equations or other partial differential equations (PDE).Linking ECG simulation directly with cellular and channel electrical activity is crucial for the understanding and treatment of arrhythmias. Since each automaton cell in our model is a computing unit, a cell level ECG simulation algorithm is developed to compute each cell's field point potential. The algorithm, implemented as a backend function coded in C language, shows strengths, because such cell level simulation builds a link between the action potentials of cells and the ECG waveforms. The limitation here is that this heart model does not include the chest, so that the contribution of thoracic tissues to body surface potential is much simplified. The model reads the membrane potential of every automaton cell and computes its field potentials at the standard lead locations.Vm, is uniform on all parts of the cell membrane, except at gap junctions. (b) Gap junctions occupy the same area and are symmetrically distributed on each cell. (c) The distance from cell to field point is long enough so that the two solid angles subtended by the positive and negative sides of a cell membrane to a field point are equal. (d) Dielectric effects on field potential are neglected. σmedia is the average conductivity of the 1-D tissues between a source cell and a field point; σe the conductivity of the intercellular matrix; and σi the conductivity of the intracellular cytoplasm. (e) For any neighboring cells, j and k, σje = σke, σji = σki and φje = φke, φe is the potential in intercellular space. For convenience, we present the algorithm for the 2-D model here; the 3-D case is similar. The equation computing the field potential of an isolated cell at field point P is [Several assumptions are made in the computations on account of established physical laws. (a) Each (automaton) cell has a spherical shape. Thus, the transmembrane potential, int P is i φi - σe φe is the double layer strength of the cell membrane. When there is no propagation on the cell membrane, the field potential is zero. If the cell connects with eight adjacent cells, equation (1) becomes:σi φi - σji φji is the double layer strength of the gap junction between the cell and its jth neighbor. The transjunctional potential difference between the two cells then becomes:Here, σi - φji = φi - φe + φe - φji = φi - φe + φje - φji = Vm - Vjm     (3)φ1 to Ω8 are solid angles subtended by them; and S0 denotes the remaining part of the cell membrane  SB = SA, (b) the same and even number gap junctions distribute symmetrically on SB and SA, and (c) all gap junctions have an equal area, then it can be proved that:S1 to S8 are areas of the eight gap junctions; ΩA is the sum of areas of gap junctions on SA, and Σ KB is the sum of areas on SB. In this circumstance, the first term in equation (2) is zero, and only the second term makes a contribution to field potential. The equation now becomes:Here, Σ K1 = cos α5 = cos 90° = 0, we have:Considering all Sj (j = 1...8) to be equal, and cos α is a constant that affects only the baseline, but not the shape of the ECG waveform. The field potential at point P, generated by the whole heart, is the superposition of all cells' contributions:Here, n is the number of automaton cells, and φj(P) is computed with equation (5).Here, media R2 has to be much simplified, as described in equation (7), where σmedia_i is the conductivity of tissue i, and Ri is the length of tissue i on the line between the source cell and the field point P.Due to the time needed for the numerical solution of massive HH equations, the computing of σDepo = 0.4 mhos/m in depolarization, σRepo = 0.25 mhos/m in repolarization, σRest = 0.2 mhos/m in resting state, σInfarct = 0.1 mhos/m in acute infarcted area, and σIschemia = 0.16 mhos/m in ischemic area. We let σBlood = 0.6 and σChest = 0.1 be the average conductivity of tissues in chest [As noted above, both the boundary effect and order of dielectric distribution are neglected. The 2-D (3-D) boundary between two tissues is treated as a 1-D boundary, and the ordered dielectric distribution is treated as an unordered distribution. Because of the huge number of cardiac cells and various possible field points on body surface, epicardium, endocardium and cardiac cavities, it is impossible to deal with numerous situations of boundary conditions between cells and field points. The method we adopt here is to make a runtime traverse from the source cell to the field point and meanwhile check the conductivity of each tissue and determine the 1-D space it occupies. The scaled distance is 1.0 between two perpendicular-connected cells, and 1.414 between two oblique-connected cells. Although the electrical property of non-cardiac tissues is much simplified, the electrical property of cardiac cells is intensively considered. Cardiac cells under different conditions have different conductivity . It is σin chest ,41. We fFor the physically parallelized whole-heart electrophysiological model built with the extended cellular automata, several factors impair the simulation efficiency on a cluster of SMP.slaves located on different nodes. The time cost of communication, spent on the exchange of boundary sheets between neighboring slaves in each round, rises with the increase of slave number. An extreme case for a 128 × 128 × 128 model is that there are 128 nodes, and each slave deals with just one sheet, requiring every sheet to be exchanged in each round. The physical link between nodes also significantly affects performance. An additional limitation is that the overhead of fork/join operations in the OpenMP parallelized program degrades performance, although not very significantly. The OpenMP directive parallel can be inserted either before the endless while loop, or more simply, before the three for loops. If it is inserted before the for loops, the fork and join operations, which create and delete threads and allocate and collect memory for temporary variables in each thread, will be repeatedly executed in each round. The preferable way, which eliminates this unnecessary expenditure, is to insert the directive omp parallel before the while loop, and the directive omp for before the for loops. Between the omp parallel and the omp for,omp master is used to limit parallelism to only the cell program part. Finally, load balance becomes a limitation when a model has an irregular and/or heterogeneous structure. The heart, with four chambers and an uneven shape, is a typical case. Usually, on a cluster consisting of m identical nodes each containing n CPUs, a program is evenly dispatched to distribute the cell space across all nodes. We find that using this strategy, the 3-D heart model cannot reach the best load balance and performance because different nodes deal with different numbers of cardiac cells. Furthermore, even if each node contains the same number of cardiac cells, since different cells run different action potential models, the burden of computation remains unequal. Only a solid cubic model with homogeneous cells occupying the full cell space can ensure a best performance. Thus, if a model needs to run many simulations, an important issue is to find the best cell space partition.The first difficulty is the graphic display of the simulation. The main display window, as the critical resource in the parallelized program, can only be sequentially accessed by the cells. Thus, to display the updated state of all cells leads to a significant decrease of running speed. We mitigate this problem by displaying the cell state every 20 or even 50 steps, instead of every single step. The second problem is the overhead of communication among master and 4 slaves, are created at each run. The master and a slave are assigned to the head node, and each remaining slave is assigned to a node. Within each slave, four threads are created using the OpenMP parallel directive. Figure slaves-4 threads does not give the best performance. The 4 slaves-2 threads setting behaves better because the overall cost is lower. . However, when the whole cell space is occupied by ventricular cells, the 4 slaves-4 threads version provides the best performance, as predicted.Pilot runs with the 3-D model have been made on a 4-node SUN computer cluster. The head node has eight UltraSparc CPUs, and the other nodes each have four identical CPUs. Five processes, 1 Arrhythmias are a group of complex syndromes not well understood. Many difficult issues exist when investigating arrhythmias through computational modeling. We cover here only a few relating to model building and running.et al. [We adopt early published action potential models in the current 3-D model because they are simpler and more computationally affordable. In the first version of the Luo-Rudy model , there aet al.  in 1993 et al. . This stet al. . We arguet al. . To doubAlthough experimental evidence show that fiber orientation takes a role in arrhythmia generation ,47, to iAnother issue relates to ECG simulation. Although simulation results of the 3-D model have not been acquired thus far, the simulated ECGs with the 2-D model in different lead locations and under physiological and pathological conditions are impressive and qualitatively agree with recorded ECGs, supporting the validity of the algorithm. Theoretically, the boundary effect of dielectrics is not negligible for field potential computing; yet in practice simplifications are often inevitable. So far we find that our simplified treatment of boundary effect on field potential does not visibly affect ECG simulation. There may be two reasons for this. First, the conductivity of the tissues (not including the heart) in the chest may not be significantly different. Second, the boundaries among different tissues are so irregular that the net boundary effect may be effectively neutralized. On the other hand, we find that to let cardiac cells under different conditions (depolarization, repolarization, resting state, and ischemia) have different conductivity can improve the ECG quality, indicating that the precise description of the source may be more important than the precise description of the dielectric.Finally, we point out that, as in single cell models where adaptive time steps can greatly improve the running performance, this same strategy can produce the same results in multicellular models built with this cellular automaton . SimulatEffective simulation of arrhythmias needs a whole-heart model, differential description of electrical properties of cardiac cells, membrane equation based computation, association between cellular activities and ECG generation, flexible description of pathological conditions, and long running time. To comprehensively address these issues, we develop a method based on cellular automata and parallel computing technologies to build large-scale electrophysiological models with extended cellular automata, and run such models on clusters of shared memory machines. The dynamically traced and captured electrical activities at channel, cell, and organ levels can substantially help us understand abnormal cardioelectrical activities through simulation. Simulation results with the 2-D model support the validity of the ECG simulation algorithm. Transparent cluster computing is a convenient and effective solution to the excessive time consumption of computational intensive simulation.in silico research is to facilitate the discovery and evaluation of drugs. This helps to reduce the risk and cost of clinical trials, shorten the cycle of development, and remove randomness in candidate screening. A whole-heart electrophysiological model that links electrical activities at channel, cell, and organ levels can help achieve this result. The modeling method described in this paper shows the advantages of precisely linking cell and organ activities, exploiting the intrinsic parallelism in tissue/organ level biological activities. Besides modeling electrical activity, the method is also applicable to many other multicellular models in which quantitative description is required.In addition to reaching a mechanistic understanding of arrhythmias, an important goal of HZ develops the methods and built the initial 3-D model. AM provides data of conduction system distribution in ventricles. YS and GR help solve some technical issues. PD is responsible for the project.


A microarray technology suitable for analyzing the expression of microRNAs and of other small RNAs was used to determine the microRNA expression profile during mouse-brain development and observed a temporal wave of gene expression of sequential classes of microRNAs. MicroRNAs are a large new class of tiny regulatory RNAs found in nematodes, plants, insects and mammals. MicroRNAs are thought to act as post-transcriptional modulators of gene expression. In invertebrates microRNAs have been implicated as regulators of developmental timing, neuronal differentiation, cell proliferation, programmed cell death and fat metabolism. Little is known about the roles of microRNAs in mammals.We isolated 18-26 nucleotide RNAs from developing rat and monkey brains. From the sequences of these RNAs and the sequences of the rat and human genomes we determined which of these small RNAs are likely to have derived from stem-loop precursors typical of microRNAs. Next, we developed a microarray technology suitable for detecting microRNAs and printed a microRNA microarray representing 138 mammalian microRNAs corresponding to the sequences of the microRNAs we cloned as well as to other known microRNAs. We used this microarray to determine the profile of microRNAs expressed in the developing mouse brain. We observed a temporal wave of expression of microRNAs, suggesting that microRNAs play important roles in the development of the mammalian brain.We describe a microarray technology that can be used to analyze the expression of microRNAs and of other small RNAs. MicroRNA microarrays offer a new tool that should facilitate studies of the biological roles of microRNAs. We used this method to determine the microRNA expression profile during mouse brain development and observed a temporal wave of gene expression of sequential classes of microRNAs. Caenorhabditis elegans [lin-4 led to the surprising discovery that this gene encodes a 21-nucleotide non-coding RNA that regulates the translation of lin-14 mRNA through base-pairing with the lin-14 3' UTR [let-7, encodes another small non-coding RNA that is conserved in flies and mammals [MicroRNAs constitute a large class of small regulatory RNAs . Their m elegans . In hete mammals .C. elegans, plants, Drosophila melanogaster and mammals [lin-4 and let-7 genes, other microRNAs encode 21-25-nucleotide RNAs derived from longer transcripts that are predicted to form stem-loop structures. More than 200 microRNAs are encoded by the human genome [Biochemical and bioinformatic approaches have identified many genes that encode microRNAs in  mammals -18. Liken genome .C. elegans, lin-4 and let-7 act in developmental timing, and the microRNA lsy-6 controls neuronal asymmetry [Drosophila, the microRNAs bantam and mir-14 act in the regulation of cell growth and cell death [The biological roles of microRNAs are poorly understood. In symmetry . In Drosll death ,21. The ll death ,23.Mature microRNAs are excised from a stem-loop precursor that itself can be transcribed as part of a longer primary RNA (pri-miRNA) . The priThe animal microRNAs studied so far act by reducing the levels of proteins from genes that encode mRNAs with sites partially complementary to microRNAs in their 3' UTRs ,31. The Determining spatial and temporal patterns of microRNA expression should yield insight into the biological functions of microRNAs. As the number of microRNAs identified has increased rapidly, the need for a method that allows for the parallel detection of microRNA expression has become apparent. Recent studies used a dot-blot technique to study 44 mouse microRNAs and northern blotting analysis to study 119 microRNAs from mouse and human organs ,40.In this study we cloned microRNAs from rat and monkey brains, developed a microRNA labeling method and used a microarray to monitor expression of microRNAs during mouse brain development. We determined the temporal expression pattern of 138 microRNAs in the mouse brain and found that the levels of 66 microRNAs changed significantly during development. We identified sets of genes with similar expression patterns, including genes that peaked in expression at different stages of development. More generally, the microRNA microarray we have developed can be used to determine the expression of all known microRNAs simultaneously under any set of experimental conditions or constraints.Rattus norvegicus) and from the cerebral wall of a 114-day-old fetal rhesus monkey (Macaca mulatta)  corresponding to the 68 mammalian microRNAs we isolated from rat and monkey brains, to 70 mammalian microRNAs isolated by others from a variety of mouse tissues and mammalian cell lines, and to predicted microRNAs. In addition, we included a set of control probes as well as 19 probes corresponding to presumptive small RNAs that we and others identified but that do not satisfy all the criteria for a microRNA . Probes had a free amine group at the 5' terminus and were printed onto amine-binding glass slides and covalently linked to the glass surface. All probes were printed in quadruplicate .We developed a method for preparing microRNA samples for microarray analysis. Several methods for mRNA sample labeling for microarray analysis have been described -47, but We optimized the conditions for hybridization to our microarray. The small sizes of microRNAs leave little opportunity for oligonucleotide (array probe) design to achieve homogeneous probe-target melting temperatures. Differences in melting temperatures are expected to result in greater nonspecific binding if hybridizations are performed at low temperatures  and in less specific binding if hybridizations are performed at high temperatures . To assess this issue we included control probes with two internal mismatches on the microarray for a subset of the microRNA probes . We tested a range of hybridization temperatures, and, on the basis of the signal of microRNA probes versus control probes, we determined that a hybridization temperature of 50°C was a reasonable compromise between sensitivity and specificity (data not shown).Even at 50°C, specificity as assayed by comparing microarray spot signal intensities from matched and mismatched probes varied among the microRNAs assayed. As expected, specificity at 50°C was negatively correlated with calculated melting temperatures Figure . In all To determine the detection range of the microarray, we synthesized three artificial RNAs with the characteristics of microRNAs. These RNAs were phosphorylated RNA oligonucleotides of 20-23 bases; their sequences were chosen at random and were without any significant sequence similarity to known mammalian microRNAs . We titrated these RNAs into total mouse RNA samples, labeled them and hybridized them to a microarray that in addition to microRNA probes included probes corresponding to these three RNAs, called syn1, syn2 and syn3. Figure We isolated small RNAs from mice at five developmental stages: embryonic days 12.5 and 17.5 (E12.5 and E17.5), postnatal days 4 and 18 (P4 and P18) and 4-month-old adults. E12.5-E17.5 spans a period of major neuronal proliferation and migration in the mouse brain, in particular the birth and subsequent migration of most neurons in the ventricular zone epithelium . Betweenp < 0.001) and 66 (57%) changed more than twofold. Of the microRNAs we cloned from rat and monkey and for which probes against the corresponding mouse homologs were present on the microarray, we detected 97% robustly.We purified and size-selected RNA from whole mouse brains. For each sample, the products of four independent RNA amplifications based on two independent RNA ligations were hybridized to the array. A detailed description of our analysis of the microarray data is presented in Additional data file 5. Of the 138 microRNAs and 19 small RNAs represented by the probe set, 116 (74%) were expressed robustly (more than 75-fold over the level of background controls) at least at one time point. Of these, 83 (71%) changed significantly during the period surveyed  with sequences complementary to microRNAs. Each probe was modified with a free amino group linked to its 5' terminus through a 6-carbon spacer (IDT) and was printed onto amine-binding slides (CodeLink, Amersham Biosciences). Control probes contained two internal mismatches resulting in either C-to-G or T-to-A changes . Printing and hybridization were done using the protocols from the slide manufacturer with the following modifications: the oligonucleotide concentration for printing was 20 μM in 150 mM sodium phosphate pH 8.5, and hybridization was at 50°C for 6 h. Printing was done using a MicroGrid TAS II arrayer (BioRobotics) at 50% humidity.Whole brains from three to eight C57BL/6 mice were pooled. Starting with 250 μg of total RNA for each time point, 18-26-nucleotide RNA was purified on denaturing PAGE gels. The samples were divided, and the following cloning steps were done independently twice for each time point. 3' and 5' adaptor oligonucleotides were ligated to 18-26-nucleotide RNA followed by reverse transcription, essentially as described for microRNA cloning . BrieflyMicroarray slides were scanned using an arrayWoRx biochip reader (Applied Precision), and primary data were analyzed using the Digital Genome System suite (MolecularWare) and Spotfire DecisionSite (Spotfire). Cluster analysis was performed using the CLUSTER/TreeView software . For detNorthern blots were performed as described . Twenty The probes used were: EAM119 (miR-29b), EAM125 (miR-138), EAM224 (miR-17-5p), EAM234 (miR-199a), EAM131 (miR-92), EAM109 (miR-7), EAM150 (miR-9) and EAM103 (miR-124a).The following additional data files are available with the online version of this article. A file (Additional data file A file (Additional data file A file (Additional data file A file (Additional data file A file (Additional data file % are not in the current release of the miRNA registry but are deposited in NCBI and described elsewhere [And a file (Additional data file lsewhere ,15,18.An Excel file (Additional data file A file with details of rat microRNA precursorsClick here for additional data fileA file containing precursor sequences and secondary structure predictions for the novel microRNA miR-421Click here for additional data fileA file with details of other small RNAs cloned from rat and monkey brainsClick here for additional data fileA file showing rno-miR-138 brain specific expressionClick here for additional data fileA file with details of microarray design and data analysisClick here for additional data fileA file with a summary of the microRNA microarray dataClick here for additional data fileAn Excel file with the primary microarray data corresponding to the E12.5 time pointClick here for additional data fileAn Excel file with the primary microarray data corresponding to the E17.5 time pointClick here for additional data filean Excel file with the primary microarray data corresponding to the P4 time pointClick here for additional data fileAn Excel file with the primary microarray data corresponding to the P18 time pointClick here for additional data fileAn Excel file with the primary microarray data corresponding to the Adult time pointClick here for additional data file


The quality of psychosocial assessment of children in consultations varies widely. One reason for this difference is the variability in effective mental health and communication training at undergraduate and post-qualification levels. In recognition of this problem, the Royal College of Paediatrics and Child Health in the United Kingdom have developed the Child in Mind Project that aims to meet this deficit in medical training. This paper describes the evaluation of a workshop that explored the experiences and expectations of health care professionals in the development of a training programme for doctors.The one-day inter-professional workshop was attended by 63 participants who were invited to complete evaluation forms before and immediately after the workshop.The results showed that the workshop was partially successful in providing an opportunity for an inter-professional group to exchange ideas and influence the development of a significant project. Exploring the content and process of the proposed training programme and the opportunity for participants to share experiences of effective practice were valued. Participants identified that the current culture within many health care settings would be an obstacle to successful implementation of a training programme. Working within existing training structures will be essential. Areas for improvement in the workshop included clearer statement of goals at the outset and a more suitable environment for the numbers of participants.The participants made a valuable contribution to the development of the training programme identifying specific challenges. Inter-professional collaborations are likely to result in more deliverable and relevant training programmes. Continued consultation with potential users of the programme – both trainers and trainees will be essential. Childhood mental health disorders are common. A Department of Health survey of 5 to 15 year-olds in England and Wales, 5% had conduct disorder, 4% had emotional disorders and 1% rated as hyperactive -7. FurthKnowledge of psychosocial and mental health problems is only part of the patient assessment process. The ability to communicate effectively with the patient is pivotal for accurate assessment -13. A unNew graduates in the United Kingdom are expected to be able to "communicate clearly, sensitively and effectively with patients and their relatives" . Teachin(RCPCH) aims to develop psychosocial awareness and interviewing skills of paediatricians (in training). This will improve the assessment and management of psychosocial issues that effect children. To achieve this goal, a modular training programme in child and adolescent mental health is proposed. The programme will be piloted with senior house officers (SHOs) on paediatric rotations. Building additional modules into existing SHO training programmes is problematic since clinical and other commitments already consume a shrinking working week. Therefore, a key consideration in developing the training modules is to work within existing SHO training by maximising both planned and opportunistic teaching and learning in psychosocial care and interviewing skills appropriate for working with children, adolescents and their families.In order to address these two issues, the Child in Mind Project at the Royal College of Paediatrics and Child Health At an early stage in the project, the team thought it appropriate to elicit ideas and experiences of interested professionals as well as recruit individuals to help with developing the project. An open invitation to attend a one-day workshop held at the RCPCH was advertised in relevant professional newsletters for paediatricians, child psychiatrists, and child psychologists and by word of mouth in other disciplines. The invitation stated that the workshop would elicit the views of an inter-professional group interested in developing a training programme to improve psychosocial assessment and child-centred communication skills of doctors. Participants were chosen from twice the number of applicants to represent a balance of disciplines and geographical spread. Selection within these criteria was made on the order of receipt of applications. Numbers were limited by the capacity of the College facilities.This paper describes the evaluation of the inter-professional workshop in the development of the training programme.The opening plenary session introduced the Child in Mind Project together with the aims of the workshop Table . These aImmediately after lunch, a plenary session was held in which the key issues from the morning sessions were shared with the entire group. The four parallel sessions that followed focused on core process issues in training: promoting role-play, introducing technology, integrating new with existing programmes, and assessment. The final plenary session provided an opportunity for groups to share their experiences and then a wider discussion considered key issues from both morning and afternoon sessions. An action plan was devised based on this discussion and was shared with participants providing an opportunity for participants to continue to be involved in the project.All participants were invited to complete evaluation forms immediately before and after the workshop. The pre workshop form explored participants' reasons for attending, their expectations, their most important issue in relation to the workshop, their experiences in learning about communication and education, their current role, age and sex Figure . The posSixty-three participants attended the workshop of whom 23 were clinical psychologists (36.5%), 18 paediatricians (28.6%), 9 psychiatrists (14.3%), 9 nurses (14.3%) and one representative from each of the following professions: social work, education, play therapy and occupational therapy (6.4%). Forty-one participants were female (65.1%) and 22 were male (34.9%). Approximately twenty participants (31.8%) left the workshop immediately prior to the closing plenary session. This was unexpected and apparently not triggered by anything more than a need to catch commuter and intercity trains. That is, the exodus seemed unrelated to the quality of the meeting. Twenty-two participants (34.9%) completed the pre workshop form and 28 completed the post workshop form (44.4%).Of the 22 respondents completing the pre workshop form, 17 were female (77.3%) and 5 were male (22.7%) with an age range of 34 to 58 years and mean age of 45. Although the group were inter-professional, the respondents were predominantly medical with 10 paediatricians (45.5%), 5 child and adolescent psychiatrists (22.7%), 4 clinical psychologists (18.2%), one occupational therapist (4.5%) and one educator (4.5%).Nineteen (86.4%) participants reported previous formal training in communication as part of undergraduate, post-graduate and continuing professional development. Training included theoretical and skills practice within and outside of paediatrics at fundamental (e.g. presentation skills, psychology training) and advanced levels . Eighteen participants (81.1%) reported at least some previous formal training in education.Participants' reasons for attending the workshop were diverse and included a strong interest and or experience in the major themes of the workshop – assessment and management of psychosocial issues in paediatrics, paediatric interviewing and training.To enhance the "voice of the child" in paediatrics. (4)I have a long standing interest and involvement in the teaching of junior paediatricians the skills of communication, family therapy and management of behavioural and emotional issues. I have been trying to find ways of formalizing mental health training for paediatricians. (1)Because I have a very real interest in improving the awareness and training of paediatricians in the psychosocial aspects of paediatrics. (7)To participate in the development of paediatric psychological training. (17)To help develop teaching of mental health issues in childhood. (18)Having worked in the area of paediatric psychology for some years, I am particularly interested in developing the awareness of paediatricians re psychological issues. (19)To contribute to the planning of teaching paediatricians how to tackle social and emotional issues. (20)To better understand needs of paediatricians for training in psychological needs of children and families. (11)Some participants wanted to develop existing local programmes.To feedback ideas to our paediatric College/Clinical Tutor who did not get a place at the course. (12)To try and improve our in-house teaching of psychological factors in paediatrics. (13)One participant acknowledged a deficit in current training.I realize we are generally very poor at integrating psychological aspects of child and family health into the busy acute training programme. (2)The second question asked participants what they were expecting from the workshop. Various themes emerged and included the generation of ideas for the Child in Mind project generally and specifically in the development of training materials. Participants expected to be able to exchange ideas on what and how to change existing training and there was an expressed desire not only to influence these developments but to ensure they are deliverable.To meet, share and hopefully influence colleagues. (17)To participate in putting together relevant training modules and to have a voice in the future training of paediatricians. (19)To ensure that programmes will be acceptable. To broaden ideas around what to include in communication programme. (5)To offer my experience in direct work with children, adolescents and families. (9)An understanding of where the project is so far – aims, methods, plans. A chance to contribute. (14)A second theme related to expectations of inter-professional collaboration both in the development and delivery of the training module and the third and overlapping theme focussed on the opportunity for networking.Decrease inter-professional tension and enhance collaboration. (4)Participants' perceptions of the most important issue to be addressed in the workshop reflected their different expectations. Training issues were dominant and focused on both the content and process. Content issues included thinking about ways of raising the significance of the assessment and management of psychological problems in children and adolescents together with the need to identify the child and adolescent's perspective separately to their family's and health care professionals.Developing a culture of respect for child and family. Accessing children's thoughts and feelings independently of their parents or other professionals. (4)Process issues included identifying ways to maximise existing expertise, to use limited resources efficiently, to encourage participation from paediatric trainers and trainees and to consider assessment and evaluation as integral to the training programme.Twenty-eight (44.4%) participants completed the post workshop form. Demographic data was not collected. The "did not attend" option on the evaluation form is not included in Table Using a 3-point scale from not at all, partially to completely, participants rated the helpfulness of the sessions in meeting the objectives of the workshop Table . The majRespondents were asked to identify the most important issues that they thought had been addressed in the workshop. Several participants wrote of the need to change the existing culture to one in which psychosocial assessment and communication skills are valued. There was also acceptance of diversity in workplaces and the training offered therein. To ensure that the new training programme is deliverable it must be sufficiently flexible to fit within these diverse settings and that it must be evaluated. The need for training both supervisors and trainers was considered requisite for implementing any programme.Learning about the hospital paediatric culture and previous difficulties of teaching SHOs and getting the culture right. (20)The importance of mental health teaching/learning for all doctors caring for children/families. (2)Delivering training for trainers and that the child mental health programme needs to be integrated into existing paediatric training. (3)Need to address appropriate training and supervision of SHOs and for consultants to be trained first themselves. (5)The importance of introducing a general shift. The extreme inflexibility of the system as a whole. (9)The realities of teaching busy SHOs who are preoccupied with passing exams. (14)Changing culture of consultants to understand importance of training for mental health and communication skills. (24)Some participants valued the opportunity to learn about existing effective practices while others gave consideration to who should teach, how and that whatever is taught must be relevant.The importance of taking a full history and empowering SHOs to ask difficult questions, to reflect on their practice and to have supervision in order to understand what to do with the information they have gathered. (17)Introduction of video review of consultations/interactions with children and parents to paediatrics. (22)Participants used a 3-point scale from not at all, partially to completely to rate the degree to which they met their expectations. Eight participants completely met their expectations (28.6%) while twenty participants (71.4%) partially met their expectations.In response to being asked what worked well in the workshop, participants identified the opportunity to exchange ideas with colleagues with different levels of experience, who work in different settings and have different professional backgrounds.The group sizes for sessions were valued since they were sufficiently small to enable several participants to express their views and large enough for diverse experiences to be shared. The plenary sessions were helpful in summarising group sessions and consolidating broad ranging issues.The enthusiasm of delegates was thought to contribute to the success of the workshop together with the relaxed atmosphere and the genuine desire of participants and organisers to change existing practices.Most participants recorded at least one response to being asked how the workshop could be improved. The single most frequently cited issue related to the venue. Groups were too large for their rooms and for two groups, their presence in the same large room impeded discussion.Other improvements included stronger facilitation in some groups to ensure all views were heard and that the discussion stayed focused. Providing delegates with basic information prior to the workshop on the aims, objectives and content of group sessions could have improved the quality of the discussions. Participants expressed a desire to attend the group sessions of their choice. One participant thought that the workshop was too rigidly organised between content and process and that this limited creativity in thinking about training. Two participants suggested including SHOs for whom the training will initially be delivered.I felt unable to contribute much of my experience and knowledge with the tight preset agenda. I was particularly wanting to discuss raising awareness of child protection issues, and working with children in complex and or chaotic home situations. Also were there many current paediatric SHOs here today. If not, there should have been. If so, could they have contributed more? (17)Sign up for preferred workshops on arrival – I don't remember what preferences I indicated but they certainly weren't the ones I was allocated. More general paediatricians – meeting seemed to be dominated by psychiatrists/psychologists (23)The workshop was planned with definite areas for discussion and a very strong split between content and process. This defined structure led to cramping of ideas (27)Maybe including some real SHOs just for the occasional reality check (14)The workshop was valuable in contributing to the development of the Child in Mind Project training programme. The content and process of the programme were explored and several issues emerged that will need serious consideration by the Child in Mind project team. These include the strongly expressed need for a change in culture within the health care system that will embrace child-centred mental health care. The magnitude of change required is uncertain but may well be extensive given evidence that a study based in general practice in The Netherlands reported that the inclusion of the child in all phases of the consultation was "limited" with parents frequently speaking for the child, the child not questioning the parent, and the GP supporting this behaviour by minimal exploration of meta-communicative behaviours. The authors described this process resulting in a dyadic emphasis as being "institutionally co-constructed" .Ways to change the health care culture in the United Kingdom were not explicitly identified. However, the project teams' desire to implement the training programme in a few centres that were already enthusiastic suggests that creating centres of best practice is inherent in their approach for change. This supports theoretical approaches for effective institutional change ,26. ThatThe inter-professional nature of the workshop was beneficial in exchanging views from different perspectives. This supports the findings of the few studies in medical curriculum development that reports this approach . Most paAlthough consultation with other stakeholders (children, adolescents and their families) was not identified by this group, it is important that they are also included in the development and evaluation of the training programme. Community participation – especially of key stakeholders, is often lacking in all phases of professional education . In order that the training can best meet the needs of its intended targets their voices should be considered. The medical education literature strongly supports inclusion of patient voices in all aspects of curricula development -30.The importance of training the trainers of the programme was identified as key to success of implementation. Although agreement was not sought, there was a powerful sentiment that trainers should be inter-professional. This notion may also address cultural barriers that relate to doctors' lack of understanding of other health care professional roles by exposing them to trainers who have mental health assessment and/or communication skills expertise. The nature of support provided to trainers may vary reflecting the diverse settings in which the training programme will eventually be implemented.There appeared to be agreement that the workshop was not an appropriate forum for identifying the details of content and process of the training programme. Rather core issues were identified in psychosocial assessment, mental health and communication. Effective approaches to learning patient-centred communication skills are labour-intensive (videotaped interviews with feedback) ,32 so maThe purpose of eliciting participants' reasons for attending and their expectations of the workshop is to help make sense of their satisfaction afterwards. Although the invitation outlined the purpose of the workshop, participants came with varied views that to some extent reflected their level of experience, their unique professional perspective and their interpretation of the information provided in the invitation. However, there was an overarching expectation that each would contribute to the development of a training programme. It is important to reflect on the reasons that only 28.6% of the participants reported that their expectations were completely met.The suggestions given for improvements offer insight into why more participants did not meet their expectations. Restating the project team's aims at the commencement of the workshop may have been helpful. Although some participants felt able to express their views others were unable to do so because of the structure of sessions, the way in which they were facilitated and the settings in which the discussions took place. Providing a more open forum for discussion may have generated different ideas. The breadth and depth of the "culture change" some participants consider essential for implementation of the training programme is extensive and is likely to have influenced their judgement as to what could be realistically achieved both in the workshop and the training programme.The physical limitations of the workshop impeded discussion in some groups.Although group sizes were thought appropriate, providing spaces in which they could work will need to be considered in future workshops.There are several limitations with this evaluation project some of which were beyond the control of the evaluator (DN).• Higher response rates may have improved the quality of the evaluation. It is possible that respondents differed to non-respondents which may influence the results in someway although it is difficult speculate how.• Scheduling the evaluation forms as part of the workshop may have increased response rates and may also help participants to focus on their expectations immediately before the meeting and then afterwards in considering what they achieved.• The low response rate in relation to the final plenary session may be explained by the request to complete the forms immediately after the workshop. It is possible that some participants wanted more time to reflect on their experiences. It may have been more helpful to contact participants after the workshop.• Further, the responses may not represent the diversity of opinions expressed during the workshop nor were the professional groups equally represented in the evaluation forms. For example, no nurses completed the pre workshop evaluation form. It is unclear why this was the case as all respondents were equally encouraged to complete the forms.Future evaluations of workshops attended by disparate groups may consider:• Scheduling the completion of evaluation forms into the workshop timetable• Using identifiers to link pre and post workshop evaluation forms• Following-up participants some time after the workshop to elicit their considered viewsDespite these methodological weaknesses, the evaluation offers useful insights to the management of an inter-professional workshop for curricula development.The workshop provided the Child in Mind project team with valuable insight relevant to the development of a deliverable training programme in mental health and communication. This was an adequate forum in which the ideas and experiences of an interested inter-professional group could contribute although there were several ways in which this could have been improved. The diversity of the settings in which the programme will be delivered was highlighted as was the need for cultural change and support not only for trainees but the trainers themselves. Continued consultation with this inter-professional group together with broadening the consultation process to include other stakeholders may lead to the development of an effective training programme. Commencing the programme in sites with clinicians who are receptive to change of this nature is likely to influence its' success. Evaluation will continue to be essential to monitor the process. The enthusiasm of the participants needs to be harnessed to ensure that the long-term goals of the project team will be met.The author(s) declare that they have no competing interests.All authors contributed to each phase of the project although DN took a lead role in writing the paper. DN was responsible for the evaluation while ST and QS were instrumental in the development of the workshop.The pre-publication history for this paper can be accessed here:


Virology Journal is an exclusively on-line, Open Access journal devoted to the presentation of high-quality original research concerning human, animal, plant, insect bacterial, and fungal viruses. Virology Journal will establish a strategic alternative to the traditional virology communication process. Previously unknown viruses, such as the SARS coronavirus, may emerge at anytime, anywhere in the world. Viruses previously thought to be geographically restricted, such as WNV, may appear in new regions and spread rapidly. Poliovirus, once thought to be on the brink of elimination, has surged with a widespread distribution in nearly a dozen African nations that now poses a serious risk to the polio eradication initiative. Governments and individuals are increasingly aware of the threats posed by viruses, including established viruses, emerging viruses and the many viruses that are potential agents of bioterrorism. However, lack of information or misinformation regarding viruses can further exacerbate their impact on public health. There is an urgent need for a rapid forum for communications among virologists. Virology Journal will present high-quality original research concerning human, animal, plant, insect bacterial, and fungal viruses, while establishing a strategic alternative to the traditional virology communication process. Links to an extensive database of virology information on the Internet will be provided through our "All the Virology" (ATV) web site Virology Journal's Open Access policy changes the way in which articles in virology can be published [Virology Journal's articles are archived in PubMed Central [ublished . First,  Central , the US  Central  in Germa Central  in Franc Central , the NatOpen Access has four broad benefits for science and the general public. First, authors are assured that their work is disseminated to the widest possible audience, given that there are no barriers to access their work. This is accentuated by the authors being free to reproduce and distribute their work, for example by placing it on their institution's website. It has been suggested that free online articles are more highly cited because of their easier availability . Second,Virology Journal will consider: research, book reports, case reports, commentaries, debate articles, hypotheses, methodology articles, reviews, short reports and short protocols. An editorial board of 30 members has been established . In addiVirology Journal whose authors and readers will benefit from learning about viruses in regions of the world with limited financial resources. No member of the editorial or advisory boards of Virology Journal or their Institutions will receive any portion of the article-processing charge.Critics of Open Access often suggest that Editors have a financial incentive to accept articles as more articles means more revenue. However, BioMed Central insists that decisions about a manuscript must be based on the quality of the work, not on whether the article-processing charge can be paid. This policy will certainly apply for It is also a BioMed Central policy that Editors should declare their competing interests. Several years ago, I suggested that it would be a useful policy for the Editors of scientific and medical journals to declare their competing interests on a yearly basis . Few edi"I declare that my institution holds or has applied for several United Stated and International patents based on technology developed in my laboratory. These patents or patent applications cover a range of technologies including diagnostic assays, human A-type retroviruses and a B-type retrovirus (betaretrovirus), and peptides that inhibit viral infectivity. Tulane University has licensed some of these technologies to private companies for commercial development (list available on request), and I receive royalties from these licenses. I have also served on several study sections for the National Institutes of Health and currently served as the Chair of a biodefense study section (SSS-Z). I receive a per diem and reimbursement from the NIH for service on the study sections. Except for mutual funds in a retirement account managed through Tulane University, I own no stocks or other commercial instruments."Virology Journal, we hope to catalyse a fuller utilization of the Internet for scientific communication in virology drawing on our long experience with the ATV website. We welcome any advice and input.There are several outstanding virology journals covering all aspects of this dynamic field, but none of the general virology journals are exclusively published on-line or are Open Access. With the launch of


This paper attempts to clarify the usefulness of various simple pre-operative measures in estimating the potential for a visually successful capsulotomy.24 patients attending for capsulotomy had pre-operative measures of glare with BAT tester, visibility of posterior pole and grading of posterior capsular pearls and fibrosis seen at slit lamp. Visual function was measured before and after standardised capsulotomy. Correlations of the various preoperative measures with eventual visual function improvements were calculated.Pearls at slit lamp and poor posterior pole visualisation were all correlated with improvements in visual acuity and contrast sensitivity after capsulotomy. Amount of fibrosis visible at slit lamp and glare assessment were not correlated with vision improvements after laser.Of the various measures that are taken prior to Nd : YAG capsulotomy, some correlate with eventual visual improvement but for others no clinical utility was found. Practitioners should note these findings as they are especially of use in more questionable or high-risk cases to help determine whether referral for PCO treatment by Nd: YAG capsulotomy is likely to benefit the patient. Posterior capsular opacification (PCO) remains one of the most common post operative morbidities in modern day cataract surgery ,2 and NdHowever, the Nd: YAG capsulotomy procedure has been associated with complications such as damage to intraocular lenses , post opUntil recently Nd:YAG laser treatments have cost the U.S healthcare system up to $250 million annually . Apart fPCO is an extremely common development in patients after cataract extraction and in many mild cases it may not be immediately obvious whether it is visually significant. Patients may have reduced vision from other undetermined causes or have some measures of visual function that are not reduced at all.Information is needed that will help the practitioners to decide on the visual significance of a patient's PCO using tools that are easily available.The specific aim of this study was to assess the correlation between preoperative measures that are easily performed  with eventual visual function improvements after Nd: YAG capsulotomy. This information would be of use to practitioners when deciding whether a patient had PCO that was clinically significant. In other words, we aimed to test the clinical utility of these preoperative tests for Nd:YAG laser capsulotomy.Local research ethical committee approval for the study was obtained and the study was performed in accordance with the treaty of Helsinki. 26 consecutive patients who had been referred for Nd: YAG capsulotomies for posterior capsular opacification were recruited and full informed consent was obtained. Patients excluded were those that had media opacities other than PCO or were not suitable for capsulotomy treatment. Patients in whom macular or disc pathologies were present were excluded from posterior pole assessment arm of the study as grading of visualisation would not be valid. Patients were roughly equally divided between silicone and acrylic IOLs.Prior to Nd:YAG capsulotomy, the patients visual function was assessed with their normal physiological pupil state in terms of best corrected distance and near visual acuity using Bailey Lovie logMAR charts and contrast sensitivity with and without glare, using a Pelli-Robson chart under standard illumination levels at 1 meter. Glare was tested using a Mentor brightness acuity tester (BAT) instrument (set at medium illumination levels) and recorded as the level of contrast sensitivity chart read when exposed to the BAT.Pupils were dilated with topical 1% tropicamide. After a minimum of 20 minutes, the size of the pupil was recorded using a millimetre ruler and the PCO was graded according to the slit-lamp appearance (grade 0 to 4). Use of such slit lamp grading has been established in scientific literature for PCO assessment -16 There0 None visible at all1 Visible but none reaching to IOL edge2 At IOL edge3 Well Inside IOL edge but visual axis clear4 Across visual axisVisualisation of the posterior pole was then assessed by examining the optic disc and macula using a Volk 90D lens. Visualisation of the optic disc was subjectively graded according to the following scale (adapted from the Madurai Intraocular lens study IV ):0 Clear view of optic disc margin, blood vessels at the optic disc and nerve fibre layer (NFL examined using the red-free filter)1 Clear view of optic disc margin, but disc blood vessels and/or nerve fibre layer are not clearly seen2 Optic disc margin, as well as disc blood vessels and nerve fibre layer are not clearly seenVisualisation of the macula was subjectively graded according to the following scale:0 Clear view of foveal reflex, peri-foveal blood vessels and nerve fibre layer1 Diminished foveal reflex, but clear view of peri-foveal blood vessels and nerve fibre layer2 Blurred foveal reflex, peri-foveal blood vessels and/or nerve fibre layerPolVS), ranging from 0 to 4 in order of decreasing visualisation.The totals for the visualisations of the optic disc and the macula were combined to produce a total posterior pole visualisation score (All examinations of the posterior pole were carried out by the same examiner (NP). In order to be masked as to whether the patient was pre- or post- Nd:YAG capsulotomy, NP examined the fundus with the lenses already placed in front of the eye, thus obscuring any anterior segment view.The patients then had Nd:YAG capsulotomy by the same surgeon (TA). This involved initial setting of 1 mJ and subsequent rises of 0.5 mJ as necessary to pierce the posterior capsule. The laser treatment was initiated off axis in a horizontal line across centre, followed by a line in the vertical axis to form a cross. Any obvious lines of capsule tear were treated with laser if deemed beneficial and overall energy used was kept to a minimum. Treatments in this manner produced small capsulotomies of size 2–3 mm diameter. Size of capsulotomy was dictated by ease of making openings, and concerns over energy used. In general the aim was to create an opening using minimum energy, which might be small, but which could be enlarged at follow up visits if deemed necessary.Four weeks post Nd: YAG capsulotomy, the patients were reassessed again in terms of visual function as described earlier, by the same practitioner (TA). The pupils were dilated using 1% tropicamide and after a minimum 20-minute interval, the size of the pupil was recorded. The PolVS was again graded according to the same scales as before, by the same examiner (NP), again masked as to the state of the posterior capsule. Four weeks post-capsulotomy was chosen for re-examination, on the basis of evidence suggesting that capsulotomies enlarged progressively up to one month after Nd: YAG laser and then stabilised thereafter On inspection, the data was found to be of skewed distribution. All correlation calculations were therefore performed using the Spearman's rank correlation coefficients. Means were compared using Wilcoxon signed ranks test for non-normally distributed data. Significance was at the p < 0.05 level. Because the visualisation scale was composed of a combination of sub-scales (2 items for PolVS), internal validity was determined by the Cronbach test of reliability19,20. This is a commonly used test statistic to determine the degree with which constituent items within a scale correlate with each other. An alpha coefficient of = 0.7 is considered necessary for a composite of measurements to be considered a scale. Statistical analysis was performed using SPSS for Windows (version 8.0) for all calculations.A total of 26 eyes of 26 patients were recruited into the study. Mean age was 75.2 years (range 52 to 90). There were 14 females and 12 males. 2 patients only had one examination pre-Nd:YAG capsulotomy, and declined any further examinations. Therefore, 24 patients were seen pre- and post- Nd:YAG capsulotomy. The PolVS scale was found to be internally reliable and consistent (α coefficient = 0.7824). Mean "pearl" grading score was 3.3 (± 1.3) and mean "fibrosis" grading score was 2.3 (± 1.4).5 patients were omitted from PolVS score as macular or disc pathology prevented objective grading. Mean improvement of PolVS (n = 19) was 1.95 (S.D. ± 1.31) (95% C.I. 1.32 to 2.58) (p < 0.0001, Wilcoxon signed ranks test).Improvements in the PolVS score after Nd: YAG capsulotomies are shown in fig. Mean improvement of distance logMAR visual acuity was 0.32 (± 0.29) (95% CI 0.20 to 0.44) and near logMAR visual acuity was 0.32 (± 0.29) (95% CI 0.20 to 0.44). Mean improvement of log contrast sensitivity was -0.41 (± 0.39) (95% CI 0.25 to 0.57) and glare testing vision was -0.35 (S.D. ± 0.41) (95% CI 0.18 to 0.52).  For all the above analyses, p < 0.0001, except for mean improvement in glare testing (p = 0.001) (Wilcoxon signed ranks test).The main aim of the study was to determine which pre-operative assessments on patients attending for Nd: YAG capsulotomy would correlate with eventual visual function outcome of the patient, and thus be useful clinical measures. The results of the various correlation coefficient analyses are shown in table Measurements of fibrosis at slit lamp and of glare do not correlate with eventual improvements in vision after capsulotomy.If it is decided to offer a patient Nd; YAG capsulotomy treatment they need to be told of the likely benefits of the treatment as well as risks. Information on potential visual function improvements for each specific patient would be especially welcome in decisions in uncertain cases and higher risk patients such as high myopes.Practitioners should have some evidence for the potential benefit to visual function before suggesting treatment. Retroilluminated photograph analysis by computer have been correlated with improvements in vision  but thesAlthough all of the above tests have been used to try to assess how much benefit a particular patient may gain from capsulotomy, there has previously been little empirical evidence supporting their use. This study provides some evidence for the use and avoidance of various preoperative tests in assessing potential benefit from Nd; YAG laser capsulotomy.There has been some controversy as to the relative usefulness of the different measures of visual function for assessing PCO severity -27, withThere were two types of PCO assessed, pearls and fibrosis, both graded 0–4 with identical criteria for severity. The study shows very clearly that the fibrosis score was not significantly correlated to any improvements in visual function. The pearl score however was significant in correlating with the eventual improvement of all visual functions. This agrees with previous work using computerised analysis of retro-illumination photographs, which showed that only very central fibrosis affected vision whereas pearls could be detrimental even in para-axial locations  Other stThe assessment of fibrosis at slit lamp is commonly performed before Nd:YAG capsulotomy, but according to this study does not correlate with eventual visual outcomes. This finding was perhaps the most poignant due to the common clinical use of amount of fibrosis at slit lamp when deciding whether a patient would benefit from capsulotomy. The finding deserves further investigation, but it may be that antero-posterior thickness of the fibrosis as well as density of opacification are important contributory variables to any visual loss. This thickness of PCO would not be easily assessed accurately and routinely at slit lamp, and was not incorporated into the grading scale used for this experiment.In contrast, clinical utility of pearl assessment is demonstrated, by its correlation with eventual improvement of visual function.Visualisation of posterior pole according to the scale above correlated with improvements in visual acuity and contrast sensitivity. Using the specific criteria as described may have increased the objectivity of the test. This confirms expected agreement between the difficulty of visualization of the posterior pole and the patient's own vision of the outside world.An assessment of the posterior pole along the suggested guidelines is shown to have significant clinical utility.It may be that some of the correlations found were due to some criteria measured being closely related, for example, pearls at sit lamp and visualisation of fundus. The numbers in this analysis were unfortunately insufficient for stepwise multiple linear regression analysis, which could be used in future studies to determine the relative importance of the different measures. However the principle aims of the current study were realised with the presented experimental protocol and statistical analysis.This study confirms the clinical value of pre-YAG measurements of pearls graded at slit lamp and posterior pole visualisation.However, other measures were not significantly correlated with improvements in visual function, namely pre-YAG testing of glare with BAT and pre-YAG grading of fibrosis seen at slit lamp.If a practitioner is uncertain as to the potential visual benefit of an Nd:YAG capsulotomy, an assessment of posterior pole visualisation or pearls at slit lamp should be useful. There is little clinical utility shown from this study in attempting glare assessment or assessment of fibrosis at slit lamp and these assessments may lead to erroneous expectations from treatment.This information is of practical value to practitioners faced with the common problem of assessing suitability of patients for Nd: YAG capsulotomy. It should especially be of use in more uncertain or high-risk cases to determine whether referral to PCO treatment by Nd: YAG capsulotomy is clinically appropriate.The author(s) declare that they have no competing interests.Both authors were involved in planning, design, execution and writing of this paper. Both read and approved the final manuscript.The pre-publication history for this paper can be accessed here:


Clinical trials on osteoarthritis (OA) flare-ups treatment usually focus only on objective measures of health status, albeit recent literature suggestions on the importance of patients' subjectivity. Aim of the study was to evaluate the effects of OA and of its different types of medical treatment(s) on Health Related Quality of Life (HRQoL) in terms of both subjective satisfaction and functional status.An observational study on prospective data collected from the Evaluation of Quality of life in OA (EQuO) clinical trial (April 1999-November 2000) was conducted; outpatients from 70 participating centers  with a diagnosis of OA of the hip or knee were consecutively enrolled. Patients were observed at OA flare-ups (baseline) and at follow up 4 weeks after treatment. Patients' objective and subjective HRQoL were assessed by means of the SF-36 and the Satisfaction Profile (SAT-P, which focuses on subjective satisfaction); Present Pain at baseline and Pain Relief at follow up were also evaluated.Among the 1323 patients, 1138 (86%) were prescribed one drug/treatment of osteoarthritis, 169 (13%) 2 drugs/treatments, and 16 (1%) 3 drugs/treatments; most of treatments involved the prescription of NSAIDs; non-coxib, COX2 selective NSAIDs were prescribed in about 50% of patients. Follow-up visits were performed after 29.0 days on average (± 7.69 SD). For all SF-36 domains, all SAT-P items and factors, the differences between baseline and follow up scores resulted statistically significant (p < 0.001), enlighting an improvement both in health status and in subjective HRQoL.Besides the classic health status measures, the assessment of patients' subjective satisfaction provides important clues on treatments efficacy of OA within the patient-centered medicine model. In clinical practice this could lead to a better doctor-patient communication and to higher levels of treatment adherence. The impact of osteoarthritis (OA) on patient's functional levels is well known -3. Pain Usually OA affects elderly people, and is one of the main causes of physical disability. In OA patients, Health Related Quality of Life (HRQoL) and activities of daily living are negatively affected. Significant work disability, reduced ability to deal with household duties and sleep disorders are reported in patients with symptoms of OA flare-ups, together with dysfunctions in the areas of ambulation, body-care and movement , and emotional behaviour  ,2,4-8.As a chronic condition, the impact of OA has been studied mainly focusing on its consequences on health status. Similarly, treatment efficacy is assessed within the context of health status and/or symptomatology in many clinical trials ,7,9-12. In literature, HRQoL refers to patients' appraisals of their current levels of functioning and satisfaction, compared to what they perceive to be ideal . HRQoL aThe aim of the present study is to evaluate the effects of OA and of its different types of medical treatment(s) on HRQoL in terms of both subjective satisfaction and functional status.Data from collaborating, educated outpatients aged 50–80 years with a diagnosis of OA of the hip or knee according to the criteria of the American College of Rheumatology  were colOutpatients (n = 1340) were consecutively enrolled in 70 Italian participating centers  from April 1999 to November 2000. 147 patients withdrawn OA treatment before follow-up visit.All patients signed an informed consent in which the purposes of the study (HRQoL assessment and treatment efficacy, as primary and secondary outcomes respectively) were clearly stated. Approval for this research was obtained by the ethics committee, patients did not receive any remuneration for their participation.Patients with concomitant osteoarticular disorders, impairment of motor function not due to OA of the hip or knee, concomitant systemic disease(s) affecting HRQoL or requiring NSAIDs/steroids use on a regular basis were not included into the study, in order to avoid biases in the results due to treatments other than OA treatments.Patients were observed at OA flare-ups, when attending for a visit (baseline) and at follow up 4 weeks after treatment. According to the observational design of this trial, no "study treatments" were assigned to patients, but any drug(s)/medical treatment(s) considered by the physician as adequate to the patient's clinical condition was freely prescribed; therefore patients were not previously randomized to treatment.During both visits, patients were administered the following: the Visual Analogue Scale (VAS)  on PreseMoreover, at follow up, the global assessments of efficacy and tolerability of the medical treatment(s) prescribed for OA flare ups  were collected. Side effects to this/these treatment(s), if any, were registered as well.The assessment procedure was standardized for all the participating centres. During the visit patients were invited to compile alone all the questionnaires and rating scales, only if required patients were assisted by a trained health professional.Self-reporting bias in HRQoL improvements was kept under control by the assessment procedure and by the adoption of valid and reliable questionnaires.The VAS is perhaps the most widely used instrument for the measurement of pain intensity. The classic version of the VAS was administered: 10 centimeter line, horizontal. "It is a simple, robust, sensitive, and reproducible instrument that enables a patient to express the severity of his pain in such a way that it can be given a numerical value."  Its psycThe SF-36 is a well known self-administered and generic health status measure which encompasses 8 domains related to daily life activities: physical functioning, role limitations due to physical problems, role limitations due to emotional problems, vitality, bodily pain, social functioning, mental health and general health perception -35. EachThe SAT-P is a self-administered, generic questionnaire which provides a satisfaction profile in daily life and can be considered as an indicator of subjective QoL. Satisfaction can be defined as the cognitive product of the comparison between ideal life and reality, and can therefore be quantitatively measured. The subject is asked to evaluate his/her satisfaction about 32 life aspects with reference to the last month  independently of his/her objective health status . It provides 32 individual scores and 5 factor scores, all ranging from 0 (lowest level of satisfaction) to 100 (highest level of satisfaction). Together with its ability to detect patient's subjective satisfaction, the SAT-P addresses some aspects of daily life which are not included in SF-36 items . Its psychometric properties and clinical utility have been confirmed ,36,37.Sociodemographic data and clinical values were analysed by means of descriptive statistics. Since the incidence of withdrawals resulted low, analyses were performed on complete cases and no solutions for handling missing data was adopted.Baseline and follow-up of SF-36 and SAT-P item and factor scores were compared by means of Analusis of Covariance (ANCOVA). Moreover, ANCOVAs were adopted in order to evaluate the impact of clinical variables on SF-36 and SAT-P factor delta scores . The variables included into the models were: age, gender, body weight, OA localization (hip, knee, or both), VAS Present Pain, presence of concomitant disease(s), type of treatment (COX2 selective NSAIDs vs. other treatments). Results were summarized using mean ± SE for continuous variables and frequency (absolute and percent) for categorical variables. All p values are two-tailed and p < .05 was considered statistically significant. All computations were carried-out by resorting to SAS 8.0 procedures.Patients demographic and clinical characteristics , VAS Present Pain, type of medical treatment(s) of OA flare-ups, concomitant diseases and treatments are shown in Table The most frequent concomitant diseases were: hypertension (19.1%), metabolic and nutritional disorders 9.2%), muscoloskeletal, connective tissue and bone disorders (8.2%) and gastrointestinal system disorders (4.3%). The most frequently prescribed concomitant treatments were: cardiologic drugs (9.7%) and antihypertensive (9.4%), antidiabetic drugs (8.4%), antithrombotic agents (4.5%), antiacids (6.7%), sedatives (4.8%). 1138 patients (86%) were prescribed one drug/treatment of OA, 169 patients (13%) 2 drugs/treatments, and 16 patients (1%) received 3 drugs/treatments. Most of treatments involved the prescription of NSAIDs; non-coxib, COX2 selective NSAIDs  were prescribed in about 50% of patients (Table %, muscolFollow-up visits were performed after 29.0 days on average (± 7.69 SD). Only a small number of patients  did not attend follow-up visit.For all SF-36 domains, the difference between baseline and follow up scores resulted statistically significant (p < 0.001)  Table .Baseline pain was significantly associated with all SAT-P factors Table . The preFigure At follow-up, mean VAS Pain Relief was 61.1 mm (± 24.3 SD).In 65% of cases treatment efficacy was evaluated as good or excellent by patients themselves, in 67% of cases it was evaluated as good or excellent by physicians. In 81% of cases treatment tolerability was evaluated as good or excellent by patients themselves, in 84% of cases it was evaluated as good or excellent by physicians. It was evaluated as poor in 7% and 6% of cases respectively  and of a tool addressing subjective satisfaction (SAT-P) allows to wider the focus on patients' life.This methodological approach could help clinicians and researchers in transferring into practice the ICF model issues , with spANCOVA Analysis of CovarianceHRQoL Health Related Quality of LifeNSAID Non Steroid Anti Inflammatory DrugsOA OsteoarthritisSAT -P Satisfaction ProfileSF-36 Medical Outcome Study Short-Form 36 Health Status SurveyVAS Visual Analogue ScaleThe author AS is employee of the company that partially funded the study.GM: responsible for the design of the study, contributed to the statistical evaluation, contributed to the writing of the paper.AG: responsible for the statistical evaluation, contributed to the writing of the paper.AS: contributed to the design of the study and data collection, contributed to the statistical evaluation, contributed to revise the manuscript.Appendix A – Participating CentersClick here for file


At Stanford University, the Virtual Labs project takes full advantage of information technology to provide innovative resources for learning and teaching Because of the explosive growth in our scientific understanding, today's students are required to learn and maintain a rapidly expanding knowledge base. Students are also expected to understand and follow the crossover of information between different disciplines. As a result, they often have to understand the fundamentals of several disciplines, and be able to integrate that knowledge.Students of every discipline are facing these new challenges, and it is clear that today's students are markedly different from those of the past. Influenced by a lifetime surrounded by media, computers, and the Internet, they bring with them different expectations. As educators, we need to meet these expectations in order to motivate students to move forward.And it's not just the student population that is driving change. The National Institutes of Health, which sponsors many biological and medical advances in the United States, has a new initiative called “Digital Biology: The Emerging Paradigm,” whose goal is to merge biomedical computation with biology and medicine over the next ten years. One way to facilitate this movement is to use information technology (IT) as a teaching tool, so that students, in turn, learn how to use IT most effectively.IT presents educators and teachers with a unique opportunity to devise innovative methods of teaching. Students today are more likely than ever to use new tools and technologies to advance their understanding of the sciences. Currently, this usage is mainly limited to searching the Web for information. However, computers and the Web can be used for much more—with computers, you can create learning scenarios like virtual patient simulations, and with the Web, these learning resources can be disseminated to the global community. Educators must harness the power of these enabling technologies, which students have already adopted, to create new and more powerful methods of teaching that will better prepare the students for the next phase of their lives.The Virtual Labs Project at SUMMIT  in the Stanford University School of Medicine has been funded by the Howard Hughes Medical Institute (Chevy Chase, Maryland, United States) since 1998. It is an initiative to augment the Department of Biological Sciences and the Program in Human Biology at Stanford University by developing technology-enhanced materials for these curricula. A major goal of the Virtual Labs Project is to increase scientific literacy by using interactive multimedia to teach the fundamental concepts of biology, and to share those resources via the Internet. The Virtual Labs material is currently hosted on a password-protected site and is freely available to interested parties for educational use.A wise individual once said that a picture is worth a thousand words; with Virtual Labs we use not just pictures, but also animations and interactive simulations. Students are able to visualize and interact with dynamic processes in the body. We have developed learning modules in cardiovascular, gastrointestinal, respiratory, renal , visual Virtual Labs also strives to make learning science fun. The more engaged the user is, the more likely the learning experience is to be positive. For example, after learning about how the kidney filters blood  we are designing content for the education of local schoolchildren. Abroad, we are working with global partners in Sweden via the Wallenberg Global Learning Network (http://www.wgln.org). We have also partnered with the MedFarmDoIT group at Uppsala University in Uppsala, Sweden (http://doit.medfarm.uu.se/multimedia.html) to help them with multimedia development and IT integration in the classroom. The MedFarmDoIT group shares our vision of bringing IT into the classroom, and together, we are designing content for their medicine/pharmacy program.Local schools and other universities are looking for opportunities to bring IT into their classrooms. Access to resources like Virtual Labs, and expertise on how to develop and integrate multimedia content into curricula, are on the rise. In 2003, the Virtual Labs Project began building a network of collaborators in the community and abroad. Together with H.E.L.P for Kids (The Virtual Labs Project is dedicated to supporting its partners by distributing customized Virtual Labs content and offering consultation or workshops to train teachers and developers. As integrated partners, we can bridge the gap between the physical and information sciences, and in doing so, can improve the learning process of students for years to come.