Predicting state transitions in the transcriptome and metabolome using a linear dynamical system model

<p>Abstract</p> <p>Background</p> <p>Modelling of time series data should not be an approximation of input data profiles, but rather be able to detect and evaluate dynamical changes in the time series data. Objective criteria that can be used to evaluate dynamical changes in data are therefore important to filter experimental noise and to enable extraction of unexpected, biologically important information.</p> <p>Results</p> <p>Here we demonstrate the effectiveness of a Markov model, named the Linear Dynamical System, to simulate the dynamics of a transcript or metabolite time series, and propose a probabilistic index that enables detection of time-sensitive changes. This method was applied to time series datasets from <it>Bacillus subtilis </it>and <it>Arabidopsis thaliana </it>grown under stress conditions; in the former, only gene expression was studied, whereas in the latter, both gene expression and metabolite accumulation. Our method not only identified well-known changes in gene expression and metabolite accumulation, but also detected novel changes that are likely to be responsible for each stress response condition.</p> <p>Conclusion</p> <p>This general approach can be applied to any time-series data profile from which one wishes to identify elements responsible for state transitions, such as rapid environmental adaptation by an organism.</p

TGF-β type II receptor expression in thymic epithelial cells inhibits the development of Hassall's corpuscles in mice

TGF-βRII signaling prevents the development of Hassall's corpuscle

Effect of Boron Incorporation on Slow Interface Traps in SiO2/4H-SiC Structures

The reason for the effective removal of interface traps in SiO2/4H-SiC (0001) structures by boron (B) incorporation was investigated by employing low-temperature electrical measurements. Low-temperature capacitance–voltage and thermal dielectric relaxation current measurements revealed that the density of electrons captured in slow interface traps in B-incorporated oxide is lower than that in dry and NO-annealed oxides. These results suggest that near-interface traps can be removed by B incorporation, which is considered to be an important reason for the increase in the field-effect mobility of 4H-SiC metal–oxide–semiconductor devices. A model for the passivation mechanism is proposed that takes account of stress relaxation during thermal oxidation

Insight into enhanced field-effect mobility of 4H-SiC MOSFET with Ba incorporation studied by Hall effect measurements

Improved performance in 4H-SiC metal-oxide-semiconductor field-effect transistors (MOSFETs) by incorporating Ba into insulator/SiC interfaces was investigated by using a combination of the Hall effect and split capacitance-voltage measurements. It was found that a moderate annealing temperature causes negligible metal-enhanced oxidation, which is rather beneficial for increments in field-effect mobility (μFE) of the FETs together with suppressed surface roughness of the gate oxides. The combined method revealed that, while severe μFE degradation in SiC-MOSFETs is caused by a reduction of effective mobile carriers due to carrier trapping at the SiO2/SiC interfaces, Ba incorporation into the interface significantly increases mobile carrier density with greater impact than the widely-used nitrided interfaces

女子学生の月経の経験からみた養護教諭が行う健康相談の必要性

This study aimed to investigate experiences and concerns related to symptoms of menstrual discomfort in female students, and obtain basic data for yogo teachers to provide health consultation. A questionnaire survey was conducted involving 334 female students from B College and Junior College located in A Prefecture. Although the students had already reached sexual maturity, 30% of them had an irregular menstrual cycle. Almost all subjects had experienced some kind of discomfort during the premenstrual and menstrual phases, and a majority of the them had experienced severer discomfort during menstruation. Although “taking medicines” was the most common self-care to relieve menstrual cramps, the number of subjects who “endure” menstrual pain was also high. Seventy-percent of the subjects had calculated the first day of their next expected menstrual cycle. Most of such subjects had experienced pain severe enough to affect their daily activities, and a half of them desired to learn about menstrual health.The results suggest the need for yogo teachers to provide education on menstruation according to the stages of development, and instruct students to seek health consultation from them

Biphasic Aire expression in early embryos and in medullary thymic epithelial cells before end-stage terminal differentiation

The roles of autoimmune regulator (Aire)–expressing medullary thymic epithelial cells (mTECs) in the organization of the thymic microenvironment for establishing self-tolerance are enigmatic. We sought to monitor the production and maintenance of Aire-expressing mTECs by a fate-mapping strategy in which bacterial artificial chromosome transgenic (Tg) mice expressing Cre recombinase under the control of the Aire regulatory element were crossed with a GFP reporter strain. We found that, in addition to its well recognized expression within mature mTECs, Aire was expressed in the early embryo before emergence of the three germ cell layers. This observation may help to explain the development of ectodermal dystrophy often seen in patients with AIRE deficiency. With the use of one Tg line in which Cre recombinase expression was confined to mTECs, we found that Aire+CD80high mTECs further progressed to an Aire−CD80intermediate stage, suggesting that Aire expression is not constitutive from after its induction until cell death but instead is down-regulated at the beginning of terminal differentiation. We also demonstrated that many mTECs of Aire-expressing lineage are in close contact with thymic dendritic cells. This close proximity may contribute to transfer of tissue-restricted self-antigens expressed by mTECs to professional antigen-presenting cells

Use of the Hydrogen Breath Test to Determine the Influence of Antibiotic Prophylaxis on Intestinal Flora

Purpose: This experimental study was designed to use the hydrogen (H2) breath test to investigate changes in the intestinal flora of patients that were administered prophylactic antibiotics for 48 hours after surgery. Methods: Altogether, 22 patients were divided into two groups and the antimicrobial prophylactics, cefazolin (3.0 g/day) or sulbactam/ampicillin (4.5 g/day), were administered on induction of anaesthesia for 48 hours after surgery. End expiratory breath samples were collected on the morning of the day of surgery and every morning for 1-6 days after surgery. Results: H2 breath concentration significantly decreased in each group on day 1 (cefazolin: 1.20 ± 0.39 ppm vs. sulbactam/ampicillin: 1.17 ± 0.34 ppm). On day 2, the H2 concentration in the sulbactam/ampicillin group was significantly lower than the cefazolin group (cefazolin: 6.4 ± 2.2 ppm vs. sulbactam/ampicillin: 1.0 ± 0.4 ppm, p < 0.05). H2 concentration was still lower in the sulbactam/ampicillin group (1.3 ± 0.3 ppm vs. 3.3 ± 1.0 ppm, p = 0.10) on day 3. On days 4-6, H2 concentration was essentially the same for both groups. Discussion: Colonic anaerobes are thought to be a reservoir of resistant organisms and prolonged antimicrobial treatment is a major cause for the development of resistance. Surgical prophylaxis is basically recommended for use within 24 hours after surgery. The breath H2 concentration in both groups significantly decreased 24 hours after administration. These results suggest that both antibiotics influence the activity of colonic anaerobes and the duration of surgical antibiotic prophylaxis should be as short as possible