Frontal positions and mixed layer evolution in the Seasonal Ice Zone along 140°E in 2001/02

We describe the circulation and seasonal development of the upper ocean in the Seasonal Ice Zone (SIZ) of the Southern Ocean along 140°E. The 140°E section was repeated four times between November 2001 and March 2002, spanning the period from early spring to autumn. The sea ice edge was located at 62°-63°S in November, and retreated to 65°S in January. The circulation in the region is dominated by several fronts: the southern branch of Polar Front (PF-S) was located between 60° and 61.5°S; the northern branch of Southern ACC front (sACCf-N) was located at 61.5°-63°S, and roughly corresponds with the winter sea ice edge; and the southern branch of sACCf, the southern boundary of the ACC, and the Antarctic Slope Front (ASF) were closely spaced and found between 64°S and 65°S. Vigorous cyclonic (clockwise) eddies were identified in the region between the sACCf-N and sACCf-S throughout the period. Changes in salinity made the dominant contribution to changes in density in the SIZ, while changes in temperature made the largest contribution to density changes in the AZ, north of the sACCf. The depth of the mixed layer generally shoaled to the south, in all seasons. The decrease in mixed layer depth occurred in a series of steps. Seasonal variability in the depth of the mixed layer was strongest in the AZ, where summer warming formed a strong seasonal thermocline above the relatively deep (100 m) Winter Water layer. In the SIZ, the mixed layer became warmer, fresher and lighter in summer but the depth of the mixed layer remained at about 50 m throughout the year. The freshest surface waters were observed in the SIZ in January, immediately following the melt and retreat of the sea ice pack. An increase in mixed layer salinity from January to March likely reflects the effect of mixing with saltier waters below the mixed layer. Mixed layer depths south of the ASF were highly variable, both within and between seasons, varying from a minimum of ～20 m in January to over 500 m in March

Extracting glycan motifs using a biochemicallyweighted kernel

Carbohydrates, or glycans, are one of the most abundant and structurally diverse biopolymers constitute the third major class of biomolecules, following DNA and proteins. However, the study of carbohydrate sugar chains has lagged behind compared to that of DNA and proteins, mainly due to their inherent structural complexity. However, their analysis is important because they serve various important roles in biological processes, including signaling transduction and cellular recognition. In order to glean some light into glycan function based on carbohydrate structure, kernel methods have been developed in the past, in particular to extract potential glycan biomarkers by classifying glycan structures found in different tissue samples. The recently developed weighted qgram method (LK-method) exhibits good performance on glycan structure classification while having limitations in feature selection. That is, it was unable to extract biologically meaningful features from the data. Therefore, we propose a biochemicallyweighted tree kernel (BioLK-method) which is based on a glycan similarity matrix and also incorporates biochemical information of individual q-grams in constructing the kernel matrix. We further applied our new method for the classification and recognition of motifs on publicly available glycan data. Our novel tree kernel (BioLK-method) using a Support Vector Machine (SVM) is capable of detecting biologically important motifs accurately while LK-method failed to do so. It was tested on three glycan data sets from the Consortium for Functional Glycomics (CFG) and Kyoto Encyclopedia of Genes and Genomes (KEGG) GLYCAN and showed that the results are consistent with the literature. The newly developed BioLK-method also maintains comparable classification performance with the LK-method. Our results obtained here indicate that the incorporation of biochemical information of q-grams further shows the flexibility and capability of the novel kernel in feature extraction, which may aid in the prediction of glycan biomarkers

Pathway databases and tools for their exploitation: benefits, current limitations and challenges

In past years, comprehensive representations of cell signalling pathways have been developed by manual curation from literature, which requires huge effort and would benefit from information stored in databases and from automatic retrieval and integration methods. Once a reconstruction of the network of interactions is achieved, analysis of its structural features and its dynamic behaviour can take place. Mathematical modelling techniques are used to simulate the complex behaviour of cell signalling networks, which ultimately sheds light on the mechanisms leading to complex diseases or helps in the identification of drug targets. A variety of databases containing information on cell signalling pathways have been developed in conjunction with methodologies to access and analyse the data. In principle, the scenario is prepared to make the most of this information for the analysis of the dynamics of signalling pathways. However, are the knowledge repositories of signalling pathways ready to realize the systems biology promise? In this article we aim to initiate this discussion and to provide some insights on this issue

Possible improvements on the mass of the tau neutrino using leptonic Ds±D^\pm_s decays

We show how a very accurate measurement of the branching ratios of the leptonic decay modes of the $D^\pm_s$ mesons can lead to a significant improvement in the mass limit for the tau neutrino.Comment: 1 typo in Eq.2 correcte

QED Corrections to the Scattering of Solar Neutrinos and Electrons

We discuss recent calculations of the O(alpha) QED corrections to the recoil electron energy spectrum in neutrino electron scattering, and to the spectrum of the combined energy of the recoil electron and a possible accompanying photon emitted in the scattering process. We then examine the role of these corrections in the interpretation of precise measurements from solar neutrino electron scattering experiments.Comment: (16 Pages, 4 Figures) Presented at the Symposium in Honor of Professor Alberto Sirlin's 70th Birthday: ``50 Years of Precision Electroweak Physics'', New York University, October 27-28, 200

Towards Prediction of Pancreatic Cancer Using SVM Study Model

published_or_final_versio

Tokyo SHIKU-KAISEI Committee’s View of the Values of Landscape Revealed in Debates on the Extension of a Railway Track of KOBU-TETUDO

東京市区改正委員会の甲武鉄道延伸計画審議の議事録から,当時の委員会の景観に対する姿勢を明らかにした。本件は,明治22年委員会に付議されたが,この時は景観には触れることなく決定された。その後,関係筋との協議を経て明治25年再度付議された。今度は,鉄道予定地の外濠の樹木保全,四谷･牛込間の眺望の保全等景観に関する議論がなされ条件を付して承認した。着工後も委員会は数次の現場視察を行い粗雑な工事が景観を害していると知事に改善方指示している。さらに明治33年万世橋への延伸の審議の際にも,お茶の水付近の景観保全等の議論がなされた。こうして完成した甲武鉄道の景観は,当時の「風俗画報」にも掲載され,市民からもかなり高く評価されていたといえる。この10年間の委員会の議論の流れの中には景観というものに関する時代の潮流が感じられる

A weighted q-gram method for glycan structure classification

<p>Abstract</p> <p>Background</p> <p>Glycobiology pertains to the study of carbohydrate sugar chains, or glycans, in a particular cell or organism. Many computational approaches have been proposed for analyzing these complex glycan structures, which are chains of monosaccharides. The monosaccharides are linked to one another by glycosidic bonds, which can take on a variety of comformations, thus forming branches and resulting in complex tree structures. The <it>q</it>-gram method is one of these recent methods used to understand glycan function based on the classification of their tree structures. This <it>q</it>-gram method assumes that for a certain <it>q</it>, different <it>q</it>-grams share no similarity among themselves. That is, that if two structures have completely different components, then they are completely different. However, from a biological standpoint, this is not the case. In this paper, we propose a weighted <it>q</it>-gram method to measure the similarity among glycans by incorporating the similarity of the geometric structures, monosaccharides and glycosidic bonds among <it>q</it>-grams. In contrast to the traditional <it>q</it>-gram method, our weighted <it>q</it>-gram method admits similarity among <it>q</it>-grams for a certain <it>q</it>. Thus our new kernels for glycan structure were developed and then applied in SVMs to classify glycans.</p> <p>Results</p> <p>Two glycan datasets were used to compare the weighted <it>q</it>-gram method and the original <it>q</it>-gram method. The results show that the incorporation of <it>q</it>-gram similarity improves the classification performance for all of the important glycan classes tested.</p> <p>Conclusion</p> <p>The results in this paper indicate that similarity among <it>q</it>-grams obtained from geometric structure, monosaccharides and glycosidic linkage contributes to the glycan function classification. This is a big step towards the understanding of glycan function based on their complex structures.</p