In recent years, much effort has been made in identifying microRNA (miRNA) genes from mammals, insects, worms, plants, and viruses. Continuing the search for more miRNA genes is still important but difficult. This paper presents a computational strategy based on comparative genomics analysis. The algorithm was used to scan four invertebrate genomes, Drosophila melangoster, Bombyx mori, Apis mellifera, and Anopheles gambiae, which are either model organisms or medically/economically important insects. 99 new miRNA genes were predicted from the four insect species which can be grouped into 17 miRNA gene families, of which 10 of the miRNA families are insect-specific. Sequence similarity analysis showed that 16 of the newly predicted insect miRNAs belong to the K-box, GY-box, and Brd-box miRNA families which are important participators in Notch-related pathways. To test the validity of the algorithm, 39 predicted insect miRNA genes from D. melangoster and A. mellifera were selected for further biological validation. 34 (87%) predicted miRNA genes' transcripts were successfully detected by reverse transcription-polymerase chain reaction experiments. Thus, this strategy can be used to efficiently screen for miRNA genes conserved cross species.

A multi-epitope-vaccine MEV^ABC consisting of two linear neutralizing determinants (BC1: aa693–716; A6: aa844–865) located on antigenic unit B/C and unit A of glycoprotein E2 was prepared to evaluate whether a combination strategy is effective in the design of peptide vaccines. After immunization, pig sera collected every one to two weeks were evaluated by enzyme linked immunosorbent assay. C-strain-induced anti-sera and hyper-immune sera cannot recognize overlapping peptides that cover the E2 N-terminus, while MEV^ABC is able to elicit high levels of peptide-specific antibody response. When compared with previously studied peptide vaccines PV-BC1 and PV-A6, the same dose of either component in the MEV^ABC increases the BC1-or A6-specific antibodies (to 1/3–1/2 of the levels of the separate vaccines). However, the synergy between the antibodies may make MEV^ABC much more potent. Moreover, anti-C-strain immunity pre-existing in pigs does not disturb the sequent MEV^ABC vaccination. Thus, MEV^ABC can be administrated to pigs which already possess anti-classical swine fever virus immunity. MEV^ABC is a promising candidate marker vaccine.

Plasma membrane calcium ATPase (PMCA) plays a critical role in transporting Ca²⁺ out of the cytosol across the plasma membrane which is essential both in keeping intracellular Ca²⁺ homeostasis and in biomineralization. In this paper we cloned and localized a gene encoding PMCA from the pearl oyster Pinctada fucata. This PMCA shares similarity with other published PMCAs within the functional domains. Reverse transcription-polymerase chain reaction analysis shows that it is expressed ubiquitously. Furthermore, in situ hybridization reveals that it is expressed in the inner epithelial cells of the outer fold and in the outer epithelial cells of the middle fold, as well as the edge near the shell, which suggests that PMCA may be involved in calcified layer formation. The identification and characterization of oyster PMCA can help to further understand the structural and functional properties of molluscan PMCA, as well as the mechanism of maintaining Ca²⁺ homeostasis and the mechanism of mineralization in pearl oyster.

The cytotoxicity and apoptotic effect of phytoceramide IV (N-palmitoyl-phytospingosine) were investigated by preparaing the ceramide containing liposomes using cholesteryl hemisuccinate (CHEMS) and methoxypolyethylene glycol (2000) cholesteryl succinate (PEGCHS). The ceramide-containing liposomes prepared using ultrasonication contained CHEMS and the phytoceramide IV at a molar ratio of 1:1. Gel chromatography and high performance liquid chromatography equipped with an evaporative light-scattering detection (HPLC-ELSD) were used to analyze the liposomes. The results show that the ceramide entrapment efficiency is over 90% and the molar ratio of phytoceramide IV to CHEMS is 1:1.4. The ratio of ceramide to CHEMS as well as the ultrasonication duration affects the liposome properties. The phytoceramide IV encapsulated in the liposomes reduces the cellular activity of the murine mastocytoma cell line P815 in a dose-dependent manner and the reduction of cellular activity is due to cell apoptosis. 4, 6-diamidino-2-phenylindole dihydrochloride (DAPI) staining further supports this result. The encapsulation of highly hydrophobic ceramides into liposomal formulations could become a potential candidate for enhanced apoptosis.

The effect of dextran on the conformation (or secondary structure) and thermal stability of creatine kinase (CK) was studied using the far-ultraviolet (UV) circular dichroism (CD) spectra. The results showed that lower concentrations of dextran (less than 60 g/L) induced formation of the secondary CK structures. However, the secondary structure content of CK decreased when the dextran concentrations exceeded 60 g/L. Thermally induced transition curves were measured for CK in the presence of different concentrations of dextran by far-UV CD. The thermal transition curves were fitted to a two-state model by a nonlinear, least-squares method to obtain the transition temperature of the unfolding transition. An increase in the transition temperature was observed with the increase of the dextran concentration. These observations qualitatively accord with predictions of a previously proposed model for the effect of intermolecular excluded volume (macromolecular crowding) on protein stability and conformation. These findings imply that the effects of macromolecular crowding can have an important influence on our understanding of how protein folding occurs in vivo.

Ellagic acid (EA) has aroused great interest worldwide owing to its antioxidant, anti-inflammatory, and anticarcinogenetic properties. The EA content in pomegranate leaf was measured in this study using high performance liquid chromatography to investigate the effects of season, variety, and processing method on the EA level. The results show that the EA content in 11 varieties of pomegranate from the Zaozhuang region in China range from 1.30 mg · g⁻¹ to 6.46 mg · g⁻¹ of dry weight in five consecutive seasons from June to October. An analysis of variance (ANOVA) shows that the EA content is significantly dependent on the season (p<0.05). The EA content increases significantly during the growing season to the highest level in September and October. The effect of the leaf variety on the EA content is less significant than the season. The processing methods have different effects on the EA content. Soaking for 24 hours slightly increases the EA content (p<0.05). Heating at 80°C or 100°C for 1 h after soaking has little influence on the EA content, while slow-fired cooking at high temperature significantly elevates the EA content (p<0.05). To improve quality and stability, several parameters such as leaf collection time, slow-fired cooking, and cooking time should be strictly controlled during the processing of pomegranate leaf tea and its extract.

Calreticulin is a unique calcium-binding protein with multiple functions mostly located in the sarcoplasmic/endoplasmic reticulum. A large amount of calcium is absorbed from the medium and transported to mineralization sites during biomineralization in pearl oyster. This paper describes the cloning of the full-length cDNA of calreticulin from Pinctada fucata, namely PCRT. PCRT encodes a deduced 414-amino acid protein, which includes a predicted 17-amino acid signal peptide and an endoplasmic reticulum retrieval sequence HDEL. The protein shows 63%-76% sequence identity and shares some common characteristics with calreticulins from other species. Semi-quantitative RT-PCR indicates that PCRT is ubiquitously expressed in all tissues tested with the highest expression in the hemolymph and the mantle. In situ hybridization analysis of PCRT in the mantle showed strong signals in the inner fold, the inner side of middle fold, and the inner side of outer fold of the mantle epithelium. All these results suggest PCRT might be involved in Ca²⁺ transport and storage during oyster biomineralization.

Antioxidant activities of the 95% ethanol extract from Caesalpinia sappan heartwood (ECS), protosappanin A, protosappanin B, and brazilein were studied in vitro. The inhibition of the formation of malondialdehyde (MDA) and the scavenging of superoxide anions, hydrogen peroxide, and hydroxyl radicals were assayed. The experimental results show that all four substances had antioxidant activity in vitro but their capabilities differed for the different indicators. ECS, protosappanin A, and protosappanin B show more inhibition of MDA and scavenging of hydrogen peroxide, while brazilein shows more scavenging of hydroxyl radicals. All the samples show little scavenging of superoxide anions.

This study investigated the extraction of 5′-phosphodiesterase from malt root and the degradation of nucleic acids by this enzyme. The extraction used grade precipitation with ammonium sulfate and enzymatic hydrolysis. Samples were assayed using the modified Bradford method and high performance liquid chromatography. The results show that 5′-phosphodiesterase is isolated by grade precipitation with 30% and 80% saturation of ammonium sulfate and can be utilized to degrade deoxyribonucleic acid. The hydrolysate has four kinds of deoxynucleotides: 5′-dCMP, 5′-dTMP, 5′-dAMP, and 5′-dGMP. The optimum reaction temperature is 70°C, and the optimum pH is 5.5–6.0 for the reaction. The percentage of deoxynucleotides indicated by the China Pharmacopoeia (2000 edition) in the product is over 70%. The extraction of 5′-phosphodiesterase from malt root is shown to be possible and economical. Products from the enzymatic hydrolysate of DNA meet the pharmacopoeia.

Previous studies have shown that mice experiencing cerebral ischemia reperfusion (CIR) and stress can serve as a model of post stroke depression (PSD). The present study verified the acute antidepressant effects of radix puerariae extract (PE) on PSD mice through behavior and gene expression experiments. CIR was found to reduce the sucrose consumption and tyrosine hydroxylase (TH) gene expression. PE administration after CIR surgery was observed to significantly enhance the mRNA expression of TH in the hippocampus compared with the PSD group on Day 0 and Day 3 postsurgery. These findings indicate that PE contributes to the amelioration of behavior response in PSD mice, which is closely related with the protective effects of catecholamine synthesize against CIR brain damage.

Adiponectin is one of the hormones secreted exclusively by the adipose tissue with anti-diabetic, anti-inflammatory, anti-atherogenic, anti-atherosclerotic, and insulin-sensitizing effects. Adiponectin has structural features including a signal peptide at the N terminus, a short variable region, a collagenous domain, and a C-terminal globular domain homologous to C1q. The family of proteins containing this globular domain is called the C1q/tumor necrosis factor-α-related proteins (CTRP). Among all the CTRPs characterized so far, the CTRP9 protein has the highest homology to adiponectin. However, little is known about the functions of CTRP9. This study examines the tissue expression of CTRP9 as well as the expression of CTRP9 during mouse development and 3T3-L1 preadipocyte differentiation. The effects of LPS, TNFα, and starvation on the expression of CTRP9 were also investigated. CTRP9 mRNA is shown to be expressed in a variety of tissues including the adipose tissues. The expression profile of CTRP9 differs from that of adiponectin, implying that they are functionally diverse although structurally homologous.

This study presents evidence from analyses of the acoustic parameters of fluent continuous speech to show that within-paragraph prosodic phrase boundaries are related more to contrasts of neighborhood prosodic states rather than between-phrase pause durations; prosodic states receive more constraints from higher level discourse information. By revising a modular acoustic model by Tseng's hierarchical prosodic phrase grouping framework and examining the much varied prosodic phrase (PPh) boundary B3 within speech paragraph, we show that statistical accounts of layered contributions reveal distinct contrasts between boundary immediate duration and intensity patterns irrespective of pause duration. Contrasts of F0 contour patterns were also observed in these locations. Evidence was also obtained to illustrate how PPh boundary states are specified more by higher level discourse information than by lower level prosodic word construction. These combined results suggest that contrastive neighboring prosodic states are more significant cues to PPh boundaries than boundary pause duration. The results also help explain why in fluent speech between-phrase pause durations vary greatly, and can be applied to automatic speech segmentation.

This paper proposes a novel voice conversion method by frequency warping. The frequency warping function is generated based on mapping formants of the source speaker and the target speaker. In addition to frequency warping, fundamental frequency adjustment, spectral envelope equalization, breathiness addition, and duration modification are also used to improve the similarity to the target speaker. The proposed voice conversion method needs only a very small amount of training data for generating the warping function, thereby greatly facilitating its application. Systems based on the proposed method were used for the 2007 TC-STAR intra-lingual voice conversion evaluation for English and Spanish and a cross-lingual voice conversion evaluation for Spanish. The evaluation results show that the proposed method can achieve a much better quality of converted speech than other methods as well as a good balance between quality and similarity. The IBM1 system was ranked No. 1 for English evaluation and No. 2 for Spanish evaluation. Evaluation results also show that the proposed method is a convenient and competitive method for cross-lingual voice conversion tasks.

The employment of non-uniform processes assists greatly in the corpus-based text-to-speech (TTS) system to synthesize natural speech. However, tailoring a TTS voice font, or pruning redundant synthesis instances, usually results in loss of non-uniform synthesis instances. In order to solve this problem, we propose the concept of virtual non-uniform instances. According to this concept and the synthesis frequency of each instance, the algorithm named StaRp-VPA is constructed to make up for the loss of non-uniform instances. In experimental testing, the naturalness scored by the mean opinion score (MOS) remains almost unchanged when less than 50% instances are pruned, and the MOS is only slightly degraded for reduction rates above 50%. The test results show that the algorithm StaRp-VPA is effective.

For text-independent speaker verification, the Gaussian mixture model (GMM) using a universal background model strategy and the GMM using support vector machines are the two most commonly used methodologies. Recently, a new SVM-based speaker verification method using GMM super vectors has been proposed. This paper describes the construction of a new speaker verification system and investigates the use of nuisance attribute projection and test normalization to further enhance performance. Experiments were conducted on the core test of the 2006 NIST speaker recognition evaluation corpus. The experimental results indicate that an SVM-based speaker verification system using GMM super vectors can achieve appealing performance. With the use of nuisance attribute projection and test normalization, the system performance can be significantly improved, with improvements in the equal error rate from 7.78% to 4.92% and detection cost function from 0.0376 to 0.0251.

Unseen handset mismatch is the major source of performance degradation in speaker identification in telecommunication environments. To alleviate the problem, a maximum likelihood a priori knowledge interpolation (ML-AKI)-based handset mismatch compensation approach is proposed. It first collects a set of handset characteristics of seen handsets to use as the a priori knowledge for representing the space of handsets. During evaluation the characteristics of an unknown test handset are optimally estimated by interpolation from the set of the a priori knowledge. Experimental results on the HTIMIT database show that the ML-AKI method can improve the average speaker identification rate from 60.0% to 74.6% as compared with conventional maximum a posteriori-adapted Gaussian mixture models. The proposed ML-AKI method is a promising method for robust speaker identification.

To investigate how a low tone (tone-3, T3) syllable in Chinese can be perceived to be focal accented or not, a total of 156 sentences containing tone-3 words were synthesized and used as stimuli in a perceptual study. The sentences differed in the falling value between the two high pitches, and in the duration and phonation types of the T3 syllables. Thirty-nine subjects were asked to judge where the focus or accent was for each sentence. The results show that at least three degrees of pitch drop are involved in the focus recognition: a big sized drop of about 10 semitones; a middle sized drop of about 6 semitones; a small sized drop of about 2 semitones. The results suggest that the three sizes of pitch drop have different indications in Chinese intonation, depending on both the tone and the tone combination. In perception, there are various ways to realize tone-3 focus in the Tx-T3-Ty sentences series, but in production or for text-to-speech synthesis, the rule simply is making a middle sized pitch drop with a long and creaky T3 syllable. Similarly, to focus on the low tone syllable in the T3-Tx-Ty sentences, a creaky T3 syllable is essential. However, a long T3 syllable is a strong determinant for a low tone focus in the Tx-Ty-T3 sentences.

This paper describes the latest version of the Chinese-Japanese-English handheld speech-to-speech translation system developed by NICT/ATR, which is now ready to be deployed for travelers. With the entire speech-to-speech translation function being implemented into one terminal, it realizes real-time, location-free speech-to-speech translation. A new noise-suppression technique notably improves the speech recognition performance. Corpus-based approaches of speech recognition, machine translation, and speech synthesis enable coverage of a wide variety of topics and portability to other languages. Test results show that the character accuracy of speech recognition is 82%-94% for Chinese speech, with a bilingual evaluation understudy score of machine translation is 0.55–0.74 for Chinese-Japanese and Chinese-English.

This paper introduces several important features of the Chinese large vocabulary continuous speech recognition system in the NICT/ATR multi-lingual speech-to-speech translation system. The features include: (1) a flexible way to derive an information rich phoneme set based on mutual information between a text corpus and its phoneme set; (2) a hidden Markov network acoustic model and a successive state splitting algorithm to generate its model topology based on a minimum description length criterion; and (3) advanced language modeling using multi-class composite N-grams. These features allow a recognition performance of 90% character accuracy in tourism related dialogue with a real time response speed.

Most change-point models assume that the response is continuous or cross sectional binary. However, in many public health problems, the data is longitudinal binary. There are few studies of change-point problems for longitudinal outcomes. This paper describes a flexible change-point model which includes random-effects and takes into account the difference between various individuals in longitudinal binary data. A transition function is used to make the linear-linear logistic model differentiable at the change-point. The location of the change-point is estimated using the maximum likelihood method. Adjustment of the transition parameter from zero to one controls the sharpness of the transition. The performance of this estimation procedure is illustrated with simulations using SAS/proc nlmixed and a detailed analysis of data relating hormone levels and ovary functions based on data from the Obstetrics and Gynecology Hospital, Medical Center of Fudan University.

This paper studies the existence, semiclassical limit, and long-time behavior of weak solutions to the unipolar isentropic quantum drift-diffusion model, a fourth order parabolic system. Semi-discretization in time and entropy estimates give the global existence and semiclassical limit of nonnegative weak solutions to the one-dimensional model with a nonnegative large initial value and a Dirichlet-Neumann boundary condition. Furthermore, the weak solutions are proven to exponentially approach constant steady state as time increases to infinity.

This research examines how to use an option contract to coordinate a retailer-led supply chain where the market information can be updated. Based on Stackelberg game theory, we build a mode with one supplier and one retailer in which the retailer designs contracts to coordinate the supplier's production in a two-mode production environment. This focuses on an option contract that consists of two option prices and one exercise price. By theoretical analysis and numerical example, we find that such a contract can coordinate the supplier and retailer to act in the best interest of the channel. The optimal pricing conditions are given as follows: First, option prices should be negatively correlated to the exercise price and should be in a relevant range. Second, the first-period option price should be no greater than the second-period price and should be linearly correlated to the second-period option price when the latter is beyond some threshold. The results show that such option contracts can arbitrarily allocate the extra system profit between the two parties so that each party is in a win-win situation.