Recursive regularization for inferring gene networks from time-course gene expression profiles

Background  

Inferring gene networks from time-course microarray experiments with vector autoregressive (VAR) model is the process of identifying functional associations between genes through multivariate time series. This problem can be cast as a variable selection problem in Statistics. One of the promising methods for variable selection is the elastic net proposed by Zou and Hastie (2005). However, VAR modeling with the elastic net succeeds in increasing the number of true positives while it also results in increasing the number of false positives.     

Insect antifeedant secoaromadendrane-type sesquiterpenes from Plagiochila species

The characteristic pungency of the liverworts Plagiochila species P. fruticosa, P. hattoriana, P. ovalifolia and P. yokogurensis is due to a new ent-secoaromadendrane-type sesquiterpene hemiacetal, plagiochiline A, which exhibits very strong antifeedant activity against the African army worm, Spodoptera exempta at 1–10ng/cm². Two new secoaromadendranes, plagiochilide and furanoplagiochilal A, together with the previously known plagiochiline C were isolated from P. yokogurensis. Plagiochilal A, which may be a precursor of plagiochilide and its related hemiacetals, and a bitter principle, plagiochiline B were also isolated from P. hattoriana. P. ovalifolia contained plagiochilines A, B and C. From P. fruticosa, plagiochilide and plagiochilines A, B and C were isolated. The structures of the new secoaromadendrane-type sesquiterpenes were elucidated by extensive ¹H NMR and ¹³CNMR studies.     

Mono- and triglycosylsterols from the leafy stem of rice

Two sterylglycosides have been isolated from rice plants and identified as β-d-glucopyranosyl (1 → 3)-sitosterol and β-d-glucopyranosyl(1     

Frequency,Risk Factors and Survival Associated with an Intrasubsegmental Recurrence after Radiofrequency Ablation for Hepatocellular Carcinoma

Background

In the treatment of hepatocellular carcinoma (HCC), hepatic resection has the advantage over radiofrequency ablation (RFA) in terms of systematic removal of a hepatic segment.

Methods

We enrolled 303 consecutive patients of a single naïve HCC that had been treated by RFA at The University of Tokyo Hospital from 1999 to 2004. Recurrence was categorized as either intra- or extra-subsegmental as according to the Couinaud''s segment of the original nodule. To assess the relationship between the subsegments of the original and recurrent nodules, we calculated the kappa coefficient. We assessed the risk factors for intra- and extra-subsegmental recurrence independently using univariate and multivariate Cox proportional hazard regression. We also assessed the impact of the mode of recurrence on the survival outcome.

Results

During the follow-up period, 201 patients in our cohort showed tumor recurrence distributed in a total of 340 subsegments. Recurrence was categorized as exclusively intra-subsegmental, exclusively extra-subsegmental, and simultaneously intra- and extra-subsegmental in 40 (20%), 110 (55%), and 51 (25%) patients, respectively. The kappa coefficient was measured at 0.135 (95% CI, 0.079–0.190; P<0.001). Multivariate analysis revealed that of the tumor size, AFP value and platelet count were all risk factors for both intra- and extra-subsegmental recurrence. Of the patients in whom recurrent HCC was found to be exclusively intra-subsegmental, extra-subsegmental, and simultaneously intra- and extra-subsegmental, 37 (92.5%), 99 (90.8%) and 42 (82.3%), respectively, were treated using RFA. The survival outcomes after recurrence were similar between patients with an exclusively intra- or extra-subsegmental recurrence.

Conclusions

The effectiveness of systematic subsegmentectomy may be limited in the patients with both HCC and chronic liver disease who frequently undergo multi-focal tumor recurrence.     

Glutamyl Oligopeptides as Factors Responsible for Tastes of a Proteinase-modified Soybean Protein

AK-toxin I, a host-specific toxin to Japanese pear (Pyrus serotina), was synthesized as its methyl ester from three precursor fragments: conjugated diene-carboxylic acid, chiral epoxyalcohol and β-methylphenylalanine. The epoxyalcohol fragment was derived from D-fructose, in which effective homologation of the hemiacetal carbon to alkyne by using dimethyl 1-diazo-2-oxopropylphosphonate was the key reaction. The diene-carboxylic acid fragment was prepared by repeated Wittig reactions, and was combined with the epoxyalcohol fragment by the Stille reaction. Esterification of the combined product with the stereochemically-pure β-methylphenylalanine fragment afforded the target compound. This method was used to prepare the methyl ester of tritium-labeled AK-toxin I with a specific radioactivity of 213 GBq/mmol.     

Flavonoids in Citrus and Related Genera

The occurence and distribution of flavonoid glycosides in young leaves and young and mature fruits of many citrus species and trifoliate orange were investigated. The occurence of neohesperidin in both young leaves and young fruits is fairly common to a number of species in subgenus Archicitrus. Ripe fruits of citrus could be classified into (a) the hesperidin group (b) the neohesperidin group (c) the naringin group and (d) the isonaringin group. A new flavanone glycoside, isonaringin, isolated from young fruits of Jagatarayu and Teng mikan is slightly bitter and has been determined by chemical and spectral evidences to have the structure of naringenin-7-rhamnoglucoside. Data showing the occurence of flavanone glycosides in some artificial citrus hybrids were also given.     

Antimicrobial Activity of Kumazasa (Sasa albo-marginata)

The organic solvent extract of Kumazasa leaves (Sasa albo-marginata) showed antimicrobial activity against bacteria, fungi and yeast. Kumazasa at a concentration of 0.2-1.0% showed stronger antimicrobial activity than potassium sorbate or sodium benzoate at the same concentration. Both acidic and phenolic fractions of the extract showed strong antimicrobial activity. Thirty acidic and phenolic compounds were identified by GC and GC-MS analysis. Acetic, propionic, benzoic, phenylacetic, salicylic, 3-hydroxybenzoic and o-anisic acids, and guaiacol, phenol, 4-ethylphenol, xylenol and 4-vinylphenol were the main components. It was estimated that these components play an important role in the formation of the antimicrobial activity of Kumazasa extract.     

Effect of Cathepsin D Treatment on ATPase Activity of Rabbit Myofibril

The effect of cathepsin D and pepsin treatment on rabbit myofibril was studied by measuring the amount of proteolytic products and Mg-enhanced ATPase activity.

When myofibril was treated with cathepsin D at 3°C and pH 5.0 or 5.5, a little but detectable amount of nonprotein nitrogenous compounds was released. However, there was no change in ATPase activity of myofibril, though treated with cathepsin D of higher units than assumed to be in muscle.

When myofibril was treated with pepsin under the same condition as used above, there was an increase in KCl-concentration dependence of ATPase activity followed by a decrease in the maximal value of ATPase activity.

From the present results, it was concluded that cathepsin D might not take a main role on the post-mortem degradation of myofibril.