Scanning Electron Microscopy and Energy Dispersive Spectroscopy Analysis of Calciotraumatic Lines in Rat Labial Dentin After Acute Exposure to Strontium Chloride

Rats were given strontium chloride (SrCli) intraperitoneally at a dose of 500 mg/kg. The upper incisors were removed after injection of strontium. These incisors were studied by scanning electron microscopy - energy dispersive spectroscopy analysis (SEM-EDS) and light microscopy to examine the calciotraumatic lines of strontium in the rat incisor labial dentin. At 24 hours after injection of strontium, the calciotraumatic response was observed in the predentin using hematoxylin and eosin (H-E) staining. At 5 days, three layers of calciotraurnatic lines were present in the labial dentin using an H-E staining and backscattered electron imaging in the SEM. The external layer consisted of unmineralized dentin, the intermediate layer of relatively unmineralized dentin, and the internal layer of unmineralized dentin. By SEM-EDS analysis, strontium was detected in these layers. The elemental dot map showed that the external and internal unmineralized layers had a low calcium content. The magnesium concentration was higher in the internal unmineralized layer than the external unmineralized layer

Application of the Linux cluster for exhaustive window haplotype analysis using the FBAT and Unphased programs

Background: Genetic association studies have been used to map disease-causing genes. A newly introduced statistical method, called exhaustive haplotype association study, analyzes genetic information consisting of different numbers and combinations of DNA sequence variations along a chromosome. Such studies involve a large number of statistical calculations and subsequently high computing power. It is possible to develop parallel algorithms and codes to perform the calculations on a high performance computing (HPC) system. However, most existing commonly-used statistic packages for genetic studies are non-parallel versions. Alternatively, one may use the cutting-edge technology of grid computing and its packages to conduct non-parallel genetic statistical packages on a centralized HPC system or distributed computing systems. In this paper, we report the utilization of a queuing scheduler built on the Grid Engine and run on a Rocks Linux cluster for our genetic statistical studies. Results: Analysis of both consecutive and combinational window haplotypes was conducted by the FBAT (Laird et al., 2000) and Unphased (Dudbridge, 2003) programs. The dataset consisted of 26 loci from 277 extended families (1484 persons). Using the Rocks Linux cluster with 22 compute-nodes, FBAT jobs performed about 14.4–15.9 times faster, while Unphased jobs performed 1.1–18.6 times faster compared to the accumulated computation duration. Conclusion: Execution of exhaustive haplotype analysis using non-parallel software packages on a Linux-based system is an effective and efficient approach in terms of cost and performance

Calcium Phosphate in Aspergillosis of the Maxillary Sinus

The unique appearance of apatite in fungus balls of aspergillosis in the maxillary sinus was investigated using scanning electron microscopy (SEM), energy-dispersive spectroscopy (EDS), X-ray microdiffraction and Fourier transform infrared spectroscopy (FT-IR). Rod-shaped fragments with tubular structures, and globular vesicles covered with conidia were observed in the fungus balls. Massive fragments of a solid substance were demonstrated inside the fungus balls. Calcium and phosphate were detected in necrotic areas of the fungus balls by EDS. X-ray microdiffraction and FT-IR showed the presence of an apatite-like substance, but failed to demonstrate the presence of calcium oxalate crystals usually found in such fungus balls

Morphology and Chemical Composition of Dental Calculi Mainly Composed of Whitlockite

The morphology and chemical composition of two subgingival calculus samples, which were composed of magnesium-whitlockite with a Mg/Ca molar ratio of approximately 0.1 as shown by X-ray powder diffraction, were analyzed semiquantitatively using energy-dispersive spectroscopy (EDS) combined with scanning electron microscopy (SEM). The Ca/P molar ratio values for 33 EDS-analyzed materials ranged from 1.24 to 2.03 with an average of 1.49, and the (Mg+Ca)/P molar ratio values ranged from 1.43 to 2.28 with an average of 1.63. The average Mg/Ca molar ratio was 0.10, a value very close to that obtained by X-ray diffraction analysis. The EDS-analyzed materials were grouped morphologically into three types; Type A materials were typical rhombohedral crystals, Type B were crystals of ill-defined form or small crystallite aggregations and Type C materials had a small granular structure or were amorphous. The values of (Mg+Ca)/P molar ratio for Type A ranged from 1.57 to 2.28 and averaged 1.81, those for Type B ranged from 1.43 to 1.56 and averaged 1.48, and those for Type C ranged from 1.46 to 2.06 and averaged 1.62. Type A crystals had higher molar ratios while Type B crystallites had values similar to that of whitlockite. Type C materials covered the ranges of both Type A and Type B. These results show that the materials resembling whitlockite morphologically did not have the (Mg+Ca)/P ratio of whitlockite and vice versa. This suggests that whitlockite crystals may substitute some ions for PO4 as well as Mg for Ca to a larger extent than thought previously, and that care is needed in the identification of these materials

Agile parallel bioinformatics workflow management using Pwrake

<p>Abstract</p> <p>Background</p> <p>In bioinformatics projects, scientific workflow systems are widely used to manage computational procedures. Full-featured workflow systems have been proposed to fulfil the demand for workflow management. However, such systems tend to be over-weighted for actual bioinformatics practices. We realize that quick deployment of cutting-edge software implementing advanced algorithms and data formats, and continuous adaptation to changes in computational resources and the environment are often prioritized in scientific workflow management. These features have a greater affinity with the agile software development method through iterative development phases after trial and error.</p> <p>Here, we show the application of a scientific workflow system Pwrake to bioinformatics workflows. Pwrake is a parallel workflow extension of Ruby's standard build tool Rake, the flexibility of which has been demonstrated in the astronomy domain. Therefore, we hypothesize that Pwrake also has advantages in actual bioinformatics workflows.</p> <p>Findings</p> <p>We implemented the Pwrake workflows to process next generation sequencing data using the Genomic Analysis Toolkit (GATK) and Dindel. GATK and Dindel workflows are typical examples of sequential and parallel workflows, respectively. We found that in practice, actual scientific workflow development iterates over two phases, the workflow definition phase and the parameter adjustment phase. We introduced separate workflow definitions to help focus on each of the two developmental phases, as well as helper methods to simplify the descriptions. This approach increased iterative development efficiency. Moreover, we implemented combined workflows to demonstrate modularity of the GATK and Dindel workflows.</p> <p>Conclusions</p> <p>Pwrake enables agile management of scientific workflows in the bioinformatics domain. The internal domain specific language design built on Ruby gives the flexibility of rakefiles for writing scientific workflows. Furthermore, readability and maintainability of rakefiles may facilitate sharing workflows among the scientific community. Workflows for GATK and Dindel are available at <url>http://github.com/misshie/Workflows</url>.</p

Nonlinear Dynamic Analysis of Vowels in Cleft Palate Children with or without Hypernasality

Objectives. To clarify the difference between Lyapunov exponents (LEs) for cleft palate (CP) patients with hypernasality versus without hypernasality and to investigate the relationship between their LEs and nasalance scores (NSs). Material and Methods. Six CP patients with severe hypernasality (mean age 9.2 years) and six CP patients without hypernasality (mean age 8.0 years) were enrolled. Five Japanese vowels were recorded at 44.1 KHz, and the NSs were measured simultaneously. The mean first LE (mLE1) from all one-second intervals was computed. Results. The mLE1 for /o/ in patients with hypernasality was significantly higher than that in patients without hypernasality. The correlation coefficients between the mLE1 and NS for all vowels were not statistically different. Conclusion. The voice signal of /o/ for the patients with hypernasality was more instable than in those without hypernasality. The chaotic phenomenon was independent of nasal resonance in CP voice

研究室だより : 人間情報科学科生態心理学研究室

departmental bulletin pape

Evaluation of the effect of oral appliance treatment on upper-airway ventilation conditions in obstructive sleep apnea using computational fluid dynamics

Objective: To evaluate the effect of oral appliance (OA) treatment on upper-airway ventilation conditions in patients with obstructive sleep apnea (OSA) using computational fluid dynamics (CFD). Methods: Fifteen patients received OA treatment and underwent polysomnography (PSG) and computed tomography (CT). CT data were used to reconstruct three-dimensional models of nasal and pharyngeal airways. Airflow velocity and airway pressure measurements at inspiration were simulated using CFD. Results: The apnea–hypopnea index (AHI) improved from 23.1 to 10.1 events/h after OA treatment. On CFD analysis, airflow velocity decreased at the retropalatal and epiglottis-tip levels, while airway pressure decreased at the retropalatal, uvular- and epiglottis-tip levels. The AHI of patients with OSA before OA treatment was correlated with airway pressure at the epiglottis-tip level. Discussion: Treatment with OA improved the ventilation conditions of the pharyngeal airway and AHI. Results of CFD analysis of airway pressure and airflow velocity helped determine the severity and ventilatory impairment site of OSA, respectively