Shh Plays an Inhibitory Role in Cusp Patterning by Regulation of Sostdc1.

Crown shapes in mammalian teeth vary considerably from species to species, and morphological characters in crown shape have been used to identify species. Cusp pattern is one of the characters in crown shape. In the processes governing the formation of cusp pattern, the Shh pathway has been implicated as an important player. Suppression of Shh signaling activity in vitro in explant assays appears to induce supernumerary cusp formation in wild-type tooth germs. However, the in vivo role of Shh signaling in cusp pattern formation and the molecular mechanisms by which Shh regulates cusp patterning are not clear. Here, through in vivo phenotypic analyses of mice in which Shh activity was suppressed and compared with wild-type mice, we characterized differences in the location, number, incidence, and shape of supernumerary cusps in molars at embryonic day 15.5. We found that the distances between cusps were reduced in molars of Shh activity-suppressed mice in vivo. These findings confirm and extend the previous idea that Shh acts as an inhibitor in the reaction-diffusion model for cusp pattern formation by negatively regulating the intercuspal distance. We uncovered a significant reduction of expression level of Sostdc1, which encodes a secreted modulator of Wnt signaling, after suppression of Shh activity. The supernumerary cusp formation in Sostdc1-/- mice and compound Sostdc1 and Lrp mutant mice indicates a strong association between Wnt and Shh signaling pathways in cusp patterning. In further support of this idea, there is a high degree of similarity in the supernumerary cusp patterns of mice lacking Sostdc1 or Shh at embryonic day 15.5. These results suggest that Shh plays an inhibitory role in cusp pattern formation by modulating Wnt signaling through the positive regulation of Sostdc1.

Integration of piezo-capacitive and piezo-electric nanoweb based pressure sensors for imaging of static and dynamic pressure distribution.

Recently, highly flexible and soft pressure distribution imaging sensor is in great demand for tactile sensing, gait analysis, ubiquitous life-care based on activity recognition, and therapeutics. In this study, we integrate the piezo-capacitive and piezo-electric nanowebs with the conductive fabric sheets for detecting static and dynamic pressure distributions on a large sensing area. Electrical impedance tomography (EIT) and electric source imaging are applied for reconstructing pressure distribution images from measured current-voltage data on the boundary of the hybrid fabric sensor. We evaluated the piezo-capacitive nanoweb sensor, piezo-electric nanoweb sensor, and hybrid fabric sensor. The results show the feasibility of static and dynamic pressure distribution imaging from the boundary measurements of the fabric sensors.

Imaging of regional air distributions in porcine lungs using high-performance electrical impedance tomography system.

Electrical impedance tomography (EIT) allows functional imaging of regional lung ventilation for real-time bedside monitoring of mechanically ventilated patients. Images showing time-changes of regional air distributions in the lungs can provide valuable diagnostic information for lung protective mechanical ventilation. This paper reports in vivo porcine imaging experiments of regional lung ventilation using a 16-channel parallel EIT system. Real-time time-difference chest images of 10 animals were reconstructed during mechanical ventilations with a temporal resolution of 50 frame/s. Analyzing the images together with the airway volume-pressure information from the mechanical ventilator, we could successfully produce regional compliance images at PEEP (positive end expiratory pressure) titration. From in vivo animal experiments, we propose the method as a continuous monitoring means for LPV (lung protective ventilation).

Data of self-made Taq DNA polymerase prepared for screening purposes.

DNA analysis is a key procedure in genetic engineering. Nowadays the analysis is often done by PCR with Taq DNA polymerase. Although the last enzyme price is quite low, demand for numerous analyses results in much money expenditure which are not affordable for many laboratories. In a meanwhile, many screening tasks do not require the highly purified enzyme. Taking into account the enzyme unique properties it makes possible to marginally simplify its production without resorting to costly or lengthy techniques such as column chromatography and/or dialysis. Here the data of routine usage of Taq DNA polymerase prepared according to the protocol developed in our laboratory is presented. The protocol takes only several hours to realize and does not need qualified personnel or expensive equipment. Yet it gives the enzyme preparation suitable for most screening purposes. The isolated Taq DNA polymerase stock can be stored as ammonium sulfate suspension in a refrigerator for prolonged period, not less than 6 months. The working enzyme solution is prepared from the stock suspension on demand, not more than once in a month and can be stored also in a refrigerator.

Can Natural Language Processing Improve the Efficiency of Vaccine Adverse Event Report Review?

BACKGROUND: Individual case review of spontaneous adverse event (AE) reports remains a cornerstone of medical product safety surveillance for industry and regulators. Previously we developed the Vaccine Adverse Event Text Miner (VaeTM) to offer automated information extraction and potentially accelerate the evaluation of large volumes of unstructured data and facilitate signal detection. OBJECTIVE: To assess how the information extraction performed by VaeTM impacts the accuracy of a medical expert's review of the vaccine adverse event report. METHODS: The "outcome of interest" (diagnosis, cause of death, second level diagnosis), "onset time," and "alternative explanations" (drug, medical and family history) for the adverse event were extracted from 1000 reports from the Vaccine Adverse Event Reporting System (VAERS) using the VaeTM system. We compared the human interpretation, by medical experts, of the VaeTM extracted data with their interpretation of the traditional full text reports for these three variables. Two experienced clinicians alternately reviewed text miner output and full text. A third clinician scored the match rate using a predefined algorithm; the proportion of matches and 95% confidence intervals (CI) were calculated. Review time per report was analyzed. RESULTS: Proportion of matches between the interpretation of the VaeTM extracted data, compared to the interpretation of the full text: 93% for outcome of interest (95% CI: 91-94%) and 78% for alternative explanation (95% CI: 75-81%). Extracted data on the time to onset was used in 14% of cases and was a match in 54% (95% CI: 46-63%) of those cases. When supported by structured time data from reports, the match for time to onset was 79% (95% CI: 76-81%). The extracted text averaged 136 (74%) fewer words, resulting in a mean reduction in review time of 50 (58%) seconds per report. CONCLUSION: Despite a 74% reduction in words, the clinical conclusion from VaeTM extracted data agreed with the full text in 93% and 78% of reports for the outcome of interest and alternative explanation, respectively. The limited amount of extracted time interval data indicates the need for further development of this feature. VaeTM may improve review efficiency, but further study is needed to determine if this level of agreement is sufficient for routine use.

The contribution of the vaccine adverse event text mining system to the classification of possible Guillain-Barré syndrome reports.

BACKGROUND: We previously demonstrated that a general purpose text mining system, the Vaccine adverse event Text Mining (VaeTM) system, could be used to automatically classify reports of an-aphylaxis for post-marketing safety surveillance of vaccines. OBJECTIVE: To evaluate the ability of VaeTM to classify reports to the Vaccine Adverse Event Reporting System (VAERS) of possible Guillain-Barré Syndrome (GBS). METHODS: We used VaeTM to extract the key diagnostic features from the text of reports in VAERS. Then, we applied the Brighton Collaboration (BC) case definition for GBS, and an information retrieval strategy (i.e. the vector space model) to quantify the specific information that is included in the key features extracted by VaeTM and compared it with the encoded information that is already stored in VAERS as Medical Dictionary for Regulatory Activities (MedDRA) Preferred Terms (PTs). We also evaluated the contribution of the primary (diagnosis and cause of death) and secondary (second level diagnosis and symptoms) diagnostic VaeTM-based features to the total VaeTM-based information. RESULTS: MedDRA captured more information and better supported the classification of reports for GBS than VaeTM (AUC: 0.904 vs. 0.777); the lower performance of VaeTM is likely due to the lack of extraction by VaeTM of specific laboratory results that are included in the BC criteria for GBS. On the other hand, the VaeTM-based classification exhibited greater specificity than the MedDRA-based approach (94.96% vs. 87.65%). Most of the VaeTM-based information was contained in the secondary diagnostic features. CONCLUSION: For GBS, clinical signs and symptoms alone are not sufficient to match MedDRA coding for purposes of case classification, but are preferred if specificity is the priority.

Can high-field MREIT be used to directly detect neural activity? Theoretical considerations.

We sought to determine the feasibility of directly studying neural tissue activity by analysis of differential phase shifts in MRI signals that occurred when trickle currents were applied to a bath containing active or resting neural tissue. We developed a finite element bidomain model of an aplysia abdominal ganglion in order to estimate the sensitivity of this contrast mechanism to changes in cell membrane conductance occurring during a gill-withdrawal reflex. We used our model to determine both current density and magnetic potential distributions within a sample chamber containing an isolated ganglion when it was illuminated with current injected synchronously with the MR imaging sequence and predicted the resulting changes in MRI phase images. This study provides the groundwork for attempts to image neural function using Magnetic Resonance Electrical Impedance Tomography (MREIT). We found that phase noise in a candidate 17.6 T MRI system should be sufficiently low to detect phase signal differences between active and resting membrane states at resolutions around 1 mm(3). We further delineate the broad dependencies of signal-to-noise ratio on activity frequency, current application time and active tissue fractions and outline strategies that can be used to lower phase noise below that presently observed in conventional MREIT techniques. We also propose the idea of using MREIT as an alternative means of studying neuromodulation.

An electrode addressing protocol for imaging brain function with electrical impedance tomography using a 16-channel semi-parallel system.

Electrical impedance tomography of brain function poses special problems because applied current is diverted by the resistive skull. In the past, image resolution was maximized with the use of an electrode addressing protocol with widely spaced drive electrode pairs and use of a multiplexer so that many electrode pairs could be flexibly addressed. The purpose of this study was to develop and test an electrode protocol for a 16-channel semi-parallel system which uses parallel recording channels with fixed wiring, the Kyung Hee University (KHU) Mk1. Ten protocols were tested, all addressing pairs of electrodes for recording or current drive, based on recording with a spiral, spiral with suboccipital electrodes (spiral s-o) and zig-zag configurations, and combinations of current injection from electrode pairs at 180 degrees , 120 degrees and 60 degrees . These were compared by assessing the image reconstruction quality of five simulated perturbations in a homogenous model of the human head and of four epileptic foci in an anatomically realistic model in the presence of realistic noise, in terms of localization error, resolution, image distortion and sensitivity in the region of interest. The spiral s-o with current injection at 180 degrees + 120 degrees + 60 degrees gave the best image quality and permitted reconstruction with a localization error of less than 10% of the head diameter. This encourages the view that it might be possible to obtain satisfactory images of focal abnormalities in the human brain with 16 scalp electrodes and improved instrumentation avoiding multiplexers on recording circuits.

A comparison of two EIT systems suitable for imaging impedance changes in epilepsy.

Electrical impedance tomography (EIT) has the potential to produce functional images of the conductivity changes associated with epilepsy to help localization of epileptic foci. Scalp voltage changes associated with internal conductivity changes due to focal seizures have been shown at the limit of detectability for present EIT systems. The performances of two EIT systems, which may be employed in clinical recordings during presurgical assessment of intractable epilepsy, were compared. Those were the 32-channel serial UCH Mk2.5 and the 16-channel semi-parallel KHU Mk1. Images of three conductivity perturbations, simulating epileptic foci, in a head-shaped saline tank without and with a real human skull were recorded using 31-channel and 16-channel protocols with the UCH Mk2.5, while only 16-channel protocols with the KHU Mk1. The UCH Mk2.5 employing the 31-channel protocol had better overall performance with a localization error of 12.7% of the tank diameter, which would be sufficient for lateralization of the epileptic activity. More blurred images, but with similar localization, were obtained using 16 electrodes.

Diffusion PDE-based denoising technique for magnetic resonance electrical impedance tomography.

Recent progress in magnetic resonance electrical impedance tomography (MREIT) research has shown that conductivity images with higher spatial resolution and accuracy are achievable. One of the most important remaining problems to be solved in MREIT before we can apply the technique to human subjects is how to reduce the amount of injection current. Since we use an MRI scanner to measure the induced magnetic flux density data subject to an injection current, the data is contaminated with random noise. In order to obtain enough signal-to-noise ratio (SNR), we need to inject a large amount of current into the subject. However, it is obvious that we must comply with the electrical safety regulations and this means that we should deal with noisy data having a low SNR due to the limited amount of injection current. Furthermore, in the developed reconstruction algorithms, the required numerical differentiations of the noisy data may result in deterioration of the reconstructed conductivity image leading to a loss of important information. We propose a PDE-based denoising technique that diminishes the degradation of reconstructed conductivity images due to the noise in measured data. The proposed PDE-based technique is advantageous in reducing the random noise while preserving useful features in MREIT.

Conductivity images of biological tissue phantoms using a 3.0 tesla MREIT system.

We present cross-sectional conductivity images of a biological tissue phantom obtained by using a 3.0 Tesla magnetic resonance electrical impedance tomography (MREIT) system. Inside the cylindrical phantom with 140 mm diameter and 140 mm height, biological tissues such as bovine tongue and liver, porcine muscle, and chicken breast were placed within an agar gelatin. Injecting current of 480 mA.ms into the tissue phantom, we measured the z-component B/sub z/ of the induced magnetic flux density B=(B/sub x/, B/sub y/, B/sub z/). Using the harmonic B/sub z/ algorithm, we reconstructed cross-sectional conductivity images from the measured B/sub z/ data. Reconstructed images clearly distinguish different tissues in terms of both their shapes and conductivity values.

Phenol block of peripheral nerve conduction: Titrating for optimum effect.

OBJECTIVES: To verify the dose-response relationship in phenol nerve block and to determine the concentration and volume of phenol injectate required for effective nerve conduction block. DESIGN: Before-after, experimental study. SETTING: A research institute laboratory. ANIMALS: Seventy-one New Zealand white rabbits. INTERVENTIONS: Group I (n = 48) received tibial nerve block by perineural injection (phenol, n = 40; saline, n = 8), group II (n = 21) by submerging the nerve in phenol solution. The 6 subgroups of group I each received different concentrations (3%, 4%, 5%) and volumes (0.1mL, 0.2mL, 0.3mL). The 2 subgroups of group II received 3% (n = 8) and 5% (n = 13) phenol. MAIN OUTCOME MEASURES: Compound muscle action potential (CMAP) and tension of triceps surae muscles by electric stimulation of the sciatic nerve were measured preintervention and at day 1, and weeks 1, 2, 4, and 8 postblock. Histologic studies were performed on 2 animals from group I. RESULTS: Two rabbits in group I died before results were obtained. In the remaining animals, CMAP amplitude reduced significantly (p <.05) as the volume of 5% phenol solution increased from 0.1mL, 0.2mL, to 0.3mL. A high concentration of phenol produced a more pronounced conduction block; however, no significant (p =.0589) difference existed among the 3 concentrations. Submerged tibial nerve had a greater degree of conduction block than perineurally injected nerve. Depth of the degeneration area in nerve fascicle varied with distance from the injection point. CONCLUSIONS: The nerve block effect of phenol can be titrated by adjusting the concentration and volume of phenol solution if the technique of application and localization of a block site are standardized.

Crystal structure of mannanase 26A from Pseudomonas cellulosa and analysis of residues involved in substrate binding.

The crystal structure of Pseudomonas cellulosa mannanase 26A has been solved by multiple isomorphous replacement and refined at 1.85 A resolution to an R-factor of 0.182 (R-free = 0.211). The enzyme comprises (beta/alpha)(8)-barrel architecture with two catalytic glutamates at the ends of beta-strands 4 and 7 in precisely the same location as the corresponding glutamates in other 4/7-superfamily glycoside hydrolase enzymes (clan GH-A glycoside hydrolases). The family 26 glycoside hydrolases are therefore members of clan GH-A. Functional analyses of mannanase 26A, informed by the crystal structure of the enzyme, provided important insights into the role of residues close to the catalytic glutamates. These data showed that Trp-360 played a critical role in binding substrate at the -1 subsite, whereas Tyr-285 was important to the function of the nucleophile catalyst. His-211 in mannanase 26A does not have the same function as the equivalent asparagine in the other GH-A enzymes. The data also suggest that Trp-217 and Trp-162 are important for the activity of mannanase 26A against mannooligosaccharides but are less important for activity against polysaccharides.

Thermal--electrical finite element modelling for radio frequency cardiac ablation: effects of changes in myocardial properties.

Finite element (FE) analysis has been utilised as a numerical tool to determine the temperature distribution in studies of radio frequency (RF) cardiac ablation. However, none of the previous FE analyses clarified such computational aspects as software requirements, computation time or convergence test. In addition, myocardial properties included in the previous models vary greatly. A process of FE modelling of a system that included blood, myocardium, and an ablation catheter with a thermistor embedded at the tip is described. The bio-heat equation is solved to determine the temperature distribution in myocardium using a commercial software application (ABAQUS). A Cauchy convergence test (epsilon = 0.1 degree C) was performed and it is concluded that the optimal number of elements for the proposed system is 24610. The effects of changes in myocardial properties (+/- 50% electric conductivity, +100%/-50% thermal conductivity, and +100%/-50% specific heat capacity) in both power-controlled (PCRFA) and temperature-controlled RF ablation (TCRFA) were studied. Changes in myocardial properties affect the results of the FE analyses of PCRFA more than those of TCRFA, and the maximum changes in lesion volumes were -58.6% (-50% electric conductivity), -60.7% (+100% thermal conductivity), and +43.2% (-50% specific heat).

Germin is a manganese containing homohexamer with oxalate oxidase and superoxide dismutase activities.

Germin is a hydrogen peroxide generating oxalate oxidase with extreme thermal stability; it is involved in the defense against biotic and abiotic stress in plants. The structure, determined at 1.6 A resolution, comprises beta-jellyroll monomers locked into a homohexamer (a trimer of dimers), with extensive surface burial accounting for its remarkable stability. The germin dimer is structurally equivalent to the monomer of the 7S seed storage proteins (vicilins), indicating evolution from a common ancestral protein. A single manganese ion is bound per germin monomer by ligands similar to those of manganese superoxide dismutase (MnSOD). Germin is also shown to have SOD activity and we propose that the defense against extracellular superoxide radicals is an important additional role for germin and related proteins.

Temperature measurement within myocardium during in vitro RF catheter ablation.

While most commercial ablation units and research systems can provide catheter tip temperature during ablation, they do not provide information about the temperature change inside the myocardium, which determines the lesion size. We present the details of a flow simulation and temperature measurement system, which allows the monitoring of the temperature change inside the myocardium during in vitro radio frequency (RF) cardiac catheter ablation at different blood flow rates to which the catheter site may be exposed. We set up a circulation system that simulated different blood flow rates of 0 to 5 L/min at 37 degrees C. We continuously measured the temperature at the catheter tip using the built-in thermistor and inside the myocardium using a three-thermocouple probe. The system provides a means for further study of the temperature inside myocardium during RF catheter ablation under different flow conditions and at different penetration depths.

Functional inactivation of the IGF-I receptor delays differentiation of skeletal muscle cells.

Skeletal myoblasts are inherently programmed to leave the cell cycle and begin the differentiation process following removal of exogenous growth factors. Serum withdrawal results in a marked induction of IGF production which is essential for skeletal muscle differentiation in vitro. However, the potential role of the tyrosine kinase IGF-I receptor (thought to be the principal mediator of both IGF-I and II signaling in skeletal muscle) in the decision of myoblasts to begin differentiation following serum withdrawal is unknown. To explore the role of the IGF-I receptor in this decision by skeletal myoblasts, we functionally inactivated endogenous IGF-I receptors in mouse C2C12 cells using a dominant negative, kinase-inactive IGF-I receptor in which the ATP-binding site lysine (K) at residue 1003 has been mutated to alanine (A). Cell lines with the greatest degree of mutant IGF-I receptor expression (A/K cells) demonstrated functional inactivation of endogenous IGF-I receptors as determined by their impaired ability to phosphorylate the principal substrate of the IGF-I receptor, IRS-1, in response to treatment with IGF-I. In addition, the proliferative response of myoblasts to IGF-I was completely abolished in A/K cells. Following withdrawal of exogenous growth factors, A/K cells demonstrated a marked delay in the induction of the gene expression of myogenin, a skeletal muscle-specific transcription factor essential for differentiation, and a subsequent delay in the induction of muscle creatine kinase activity. Delayed differentiation in A/K cells was associated with prolonged phosphorylation of the cell cycle regulatory retinoblastoma (Rb) protein; it is the un- (or hypo-) phosphorylated form of Rb which is known to promote differentiation in skeletal myoblasts. Thus, the IGF-I receptor regulates the timing of myoblast differentiation induced by serum withdrawal. The delayed differentiation of skeletal myoblasts with functionally inactive IGF-I receptors may result, at least in part, from delayed induction of myogenin gene expression and prolonged phosphorylation of the Rb protein.

Crystallization and preliminary X-ray analysis of the auxin receptor ABP1.

Auxin-binding protein (ABP1) is an important receptor for the plant hormone auxin that is involved with many growth and developmental responses in plants. The maize ABP1 gene has been expressed in insect cells, purified and crystallized. Type II crystals are monoclinic, with two glycosylated homodimers in the asymmetric unit, and diffract to 1.9 A using synchrotron radiation.

A new catheter design using needle electrode for subendocardial RF ablation of ventricular muscles: finite element analysis and in vitro experiments.

Radio-frequency (RF) cardiac ablation has been very successful for treating arrhythmias related with atrioventricular junction and accessory pathways with successful cure rates of more than 90%. Even though ventricular tachycardia (VT) is a more serious problem, it is known to be rather difficult to cure VT using RF ablation. In order to apply RF ablation to VT, we usually need to create a deeper and wider lesion. Conventional RF ablation electrodes often fail to produce such a lesion. We propose a catheter-electrode design including one or more needle electrodes with a diameter of 0.5-1.0 mm and length of 2.0-10 mm to create a lesion large enough to treat VT. One temperature sensor could be placed at the middle of the needle electrode for temperature-controlled RF ablation. From finite element analyses and in vitro experiments, we found that the depth of a lesion is 1-2 mm deeper than the insertion depth of the needle and the width increases as we increase the diameter of the needle and the time duration. We showed that a single needle electrode can produce a lesion with about 10-mm width and any required depth. If a wider lesion is required, more than one needle with suggested structures can be used. Or, repeated RF ablations around a certain area using one needle could produce a cluster of lesions. In some cases, a catheter with both conventional electrode and needle electrode at its tip may be beneficial to take advantage of both types of electrode.