SMLSOM: The shrinking maximum likelihood self-organizing map

Determining the number of clusters in a dataset is a fundamental issue in data clustering. Many methods have been proposed to solve the problem of selecting the number of clusters, considering it to be a problem with regard to model selection. This paper proposes an efficient algorithm that automatically selects a suitable number of clusters based on a probability distribution model framework. The algorithm includes the following two components. First, a generalization of Kohonen's self-organizing map (SOM) is introduced. In Kohonen's SOM, clusters are modeled as mean vectors. In the generalized SOM, each cluster is modeled as a probabilistic distribution and constructed by samples classified based on the likelihood. Second, the dynamically updating method of the SOM structure is introduced. In Kohonen's SOM, each cluster is tied to a node of a fixed two-dimensional lattice space and learned using neighborhood relations between nodes based on Euclidean distance. The extended SOM defines a graph with clusters as vertices and neighborhood relations as links and updates the graph structure by cutting weakly-connection and unnecessary vertex deletions. The weakness of a link is measured using the Kullback--Leibler divergence, and the redundancy of a vertex is measured using the minimum description length. Those extensions make it efficient to determine the appropriate number of clusters. Compared with existing methods, the proposed method is computationally efficient and can accurately select the number of clusters

Effects of Water Injection on Generator Output Power Augmentation in a Microturbine

International audienceBoth water atomizing inlet air cooling (WAC) and the evaporative gas turbine cycle are methods to improve gas turbine efficiency and output using water evaporation. Especially, small-amount water injection methods which are used in WAC and the recuperative water injected (RWI) cycle are relatively easy to implement in existing turbines, and they are effective ways to increase output power for microturbines. The purposes of this study are to develop a dynamic simulator which can handle WAC and RWI operations and to clarify the quantitative contribution to power augmentation by the effect of water injection. Heat penetration from the turbine to the compressor which affects the performance of the turbine system is considered in the simulator. Simulation results are compared with measured results which were previously obtained in the operation test of the 150 kW class prototype microturbine. Good agreement is seen between the simulation and measured results for the main output data such as the compressor discharge pressure and the generator output power. In the total output power augmentation of the generator by WAC and RWI operations, about 1/3 is brought about by the reduction of the compressor driving power and about 2/3 is brought about by the increase of the turbine output power. Simulation results also show a big effect from the heat penetration to the compressor on the generator output power

Comparative genomic analysis of 1047 completely sequenced cDNAs from an Arabidopsis-related model halophyte, Thellungiella halophila

<p>Abstract</p> <p>Background</p> <p><it>Thellungiella halophila </it>(also known as <it>T. salsuginea</it>) is a model halophyte with a small size, short life cycle, and small genome. <it>Thellungiella </it>genes exhibit a high degree of sequence identity with Arabidopsis genes (90% at the cDNA level). We previously generated a full-length enriched cDNA library of <it>T. halophila </it>from various tissues and from whole plants treated with salinity, chilling, freezing stress, or ABA. We determined the DNA sequences of 20 000 cDNAs at both the 5'- and 3' ends, and identified 9569 distinct genes.</p> <p>Results</p> <p>Here, we completely sequenced 1047 <it>Thellungiella </it>full-length cDNAs representing abiotic-stress-related genes, transcription factor genes, and protein phosphatase 2C genes. The predicted coding sequences, 5'-UTRs, and 3'-UTRs were compared with those of orthologous genes from Arabidopsis for length, sequence similarity, and structure. The 5'-UTR sequences of <it>Thellungiella </it>and Arabidopsis orthologs shared a significant level of similarity, although the motifs were rearranged. While examining the stress-related <it>Thellungiella </it>coding sequences, we found a short splicing variant of <it>T. halophila </it><it>salt overly sensitive 1 </it>(<it>ThSOS1</it>), designated <it>ThSOS1S</it>. ThSOS1S contains the transmembrane domain of ThSOS1 but lacks the C-terminal hydrophilic region. The expression level of <it>ThSOS1S </it>under normal growth conditions was higher than that of <it>ThSOS1</it>. We also compared the expression levels of Na⁺-transport-system genes between <it>Thellungiella </it>and Arabidopsis by using full-length cDNAs from each species as probes. Several genes that play essential roles in Na⁺excretion, compartmentation, and diffusion (<it>SOS1</it>, <it>SOS2</it>, <it>NHX1</it>, and <it>HKT1</it>) were expressed at higher levels in <it>Thellungiella </it>than in Arabidopsis.</p> <p>Conclusions</p> <p>The full-length cDNA sequences obtained in this study will be essential for the ongoing annotation of the <it>Thellungiella </it>genome, especially for further improvement of gene prediction. Moreover, they will enable us to find splicing variants such as <it>ThSOS1S </it>(AB562331).</p

Effects of mild calorie restriction and high-intensity interval walking in middle-aged and older overweight Japanese

We investigated whether a combination of mild calorie restriction (MCR) and high-intensity interval walking (HIW) improved physical fitness more than HIW alone in middle-aged and older overweight Japanese (40-69 years old, BMI >= 23.6 kg/m(2)). Forty-seven women and 16 men were divided into MCR + HIW and HIW groups. All subjects performed HIW: >= 5 sets of 3-min low-intensity walking (40% peak aerobic capacity for walking, VO2peak) and 3-min high-intensity walking (>= 70% VO2peak) per day, >= 4 days per week, for 16 weeks while energy expenditure was monitored with a tri-axial accelerometer. The MCR + HIW group consumed meal replacement formula (240 kcal): a mixture of low-carbohydrates and -fat and high-protein, for either lunch or dinner everyday and therefore, had similar to 87% of the energy intake of the HIW group during the intervention period. Although the HIW group showed improvements in BMI, blood pressure, and several blood chemicals, the MCR + HIW group had greater improvement. Moreover, the medical expenditure for the 6 months including the intervention period was 59% lower in the MCR + HIW group than in the HIW group. Our strategy of a short-term combination of MCR and HIW may thus prevent lifestyle-associated diseases and improve health in middle-aged and older overweight Japanese.ArticleEXPERIMENTAL GERONTOLOGY. 44(10):666-675 (2009)journal articl

Identification of the ultrahigh-risk subgroup in neuroblastoma cases through DNA methylation analysis and its treatment exploiting cancer metabolism

神経芽腫の新たな診断法と治療戦略を創出 --がん細胞の生存戦略「がん代謝」を逆用する--. 京都大学プレスリリース. 2022-11-02.Neuroblastomas require novel therapies that are based on the exploitation of their biological mechanism. To address this need, we analyzed the DNA methylation and expression datasets of neuroblastomas, extracted a candidate gene characterizing the aggressive features, and conducted functional studies. Based on the DNA methylation data, we identified a subgroup of neuroblastoma cases with 11q loss of heterozygosity with extremely poor prognosis. PHGDH, a serine metabolism-related gene, was extracted as a candidate with strong expression and characteristic methylation in this subgroup as well as in cases with MYCN amplification. PHGDH inhibition suppressed neuroblastoma cell proliferation in vitro and in vivo, indicating that the inhibition of serine metabolism by PHGDH inhibitors is a therapeutic alternative for neuroblastoma. Inhibiting the arginine metabolism, which is closely related to serine metabolism using arginine deiminase, had a combination effect both in vitro and in vivo, especially on extracellular arginine-dependent neuroblastoma cells with ASS1 deficiency. Expression and metabolome analyses of post-dose cells confirmed the synergistic effects of treatments targeting serine and arginine indicated that xCT inhibitors that inhibit cystine uptake could be candidates for further combinatorial treatment. Our results highlight the rational therapeutic strategy of targeting serine/arginine metabolism for intractable neuroblastoma

The effects of heat stress on morphological properties and intracellular signaling of denervated and intact soleus muscles in rats

The effects of heat stress on the morphological properties and intracellular signaling of innervated and denervated soleus muscles were investigated. Heat stress was applied to rats by immersing their hindlimbs in a warm water bath (42°C, 30 min/day, every other day following unilateral denervation) under anesthesia. During 14 days of experimental period, heat stress for a total of seven times promoted growth‐related hypertrophy in sham‐operated muscles and attenuated atrophy in denervated muscles. In denervated muscles, the transcription of ubiquitin ligase, atrogin‐1/muscle atrophy F‐box (Atrogin‐1), and muscle RING‐finger protein‐1 (MuRF‐1), genes was upregulated and ubiquitination of proteins was also increased. Intermittent heat stress inhibited the upregulation of Atrogin‐1, but not MuRF‐1 transcription. And the denervation‐caused reduction in phosphorylated protein kinase B (Akt), 70‐kDa heat‐shock protein (HSP70), and peroxisome proliferator‐activated receptor γ coactivator‐1α (PGC‐1α), which are negative regulators of Atrogin‐1 and MuRF‐1 transcription, was mitigated. In sham‐operated muscles, repeated application of heat stress did not affect Atrogin‐1 and MuRF‐1 transcription, but increased the level of phosphorylated Akt and HSP70, but not PGC‐1α. Furthermore, the phosphorylation of Akt and ribosomal protein S6, which is known to stimulate protein synthesis, was increased immediately after a single heat stress particularly in the sham‐operated muscles. The effect of a heat stress was suppressed in denervated muscles. These results indicated that the beneficial effects of heat stress on the morphological properties of muscles were brought regardless of innervation. However, the responses of intracellular signaling to heat stress were distinct between the innervated and denervated muscles

Dissecting the genetic control of natural variation in salt tolerance of Arabidopsis thaliana accessions

Many accessions (ecotypes) of Arabidopsis have been collected. Although few differences exist among their nucleotide sequences, these subtle differences induce large genetic variation in phenotypic traits such as stress tolerance and flowering time. To understand the natural variability in salt tolerance, large-scale soil pot experiments were performed to evaluate salt tolerance among 350 Arabidopsis thaliana accessions. The evaluation revealed a wide variation in the salt tolerance among accessions. Several accessions, including Bu-5, Bur-0, Ll-1, Wl-0, and Zu-0, exhibited marked stress tolerance compared with a salt-sensitive experimental accession, Col-0. The salt-tolerant accessions were also evaluated by agar plate assays. The data obtained by the large-scale assay correlated well with the results of a salt acclimation (SA) assay, in which plants were transferred to high-salinity medium following placement on moderate-salinity medium for 7 d. Genetic analyses indicated that the salt tolerance without SA is a quantitative trait under polygenic control, whereas salt tolerance with SA is regulated by a single gene located on chromosome 5 that is common among the markedly salt-tolerant accessions. These results provide important information for understanding the mechanisms underlying natural variation of salt tolerance in Arabidopsis

Complications Associated With Spine Surgery in Patients Aged 80 Years or Older: Japan Association of Spine Surgeons with Ambition (JASA) Multicenter Study

Study Design:Retrospective study of registry data.Objectives:Aging of society and recent advances in surgical techniques and general anesthesia have increased the demand for spinal surgery in elderly patients. Many complications have been described in elderly patients, but a multicenter study of perioperative complications in spinal surgery in patients aged 80 years or older has not been reported. Therefore, the goal of the study was to analyze complications associated with spine surgery in patients aged 80 years or older with cervical, thoracic, or lumbar lesions.Methods:A multicenter study was performed in patients aged 80 years or older who underwent 262 spinal surgeries at 35 facilities. The frequency and severity of complications were examined for perioperative complications, including intraoperative and postoperative complications, and for major postoperative complications that were potentially life threatening, required reoperation in the perioperative period, or left a permanent injury.Results:Perioperative complications occurred in 75 of the 262 surgeries (29%) and 33 were major complications (13%). In multivariate logistic regression, age over 85 years (hazard ratio [HR] = 1.007, P = 0.025) and estimated blood loss ≥500 g (HR = 3.076, P = .004) were significantly associated with perioperative complications, and an operative time ≥180 min (HR = 2.78, P = .007) was significantly associated with major complications.Conclusions:Elderly patients aged 80 years or older with comorbidities are at higher risk for complications. Increased surgical invasion, and particularly a long operative time, can cause serious complications that may be life threatening. Therefore, careful decisions are required with regard to the surgical indication and procedure in elderly patients