Summary: Biological sequence diagrams are fundamental for visualizing various functional elements in protein or nucleotide sequences that enable a summarization and presentation of existing information as well as means of intuitive new discoveries. Here, we present a software package called illustrator of biological sequences (IBS) that can be used for representing the organization of either protein or nucleotide sequences in a convenient, efficient and precise manner. Multiple options are provided in IBS, and biological sequences can be manipulated, recolored or rescaled in a user-defined mode. Also, the final representational artwork can be directly exported into a publication-quality figure.Availability and implementation: The standalone package of IBS was implemented in JAVA, while the online service was implemented in HTML5 and JavaScript. Both the standalone package and online service are freely available at http://ibs.biocuckoo.org.Contact: renjian.sysu@gmail.com or xueyu@hust.edu.cnSupplementary information: Supplementary data are available at Bioinformatics online.

Penicillium marneffei is an emerging pathogenic fungus that can cause a life-threatening systemic mycosis in immunocompromised hosts, especially in patients with AIDS. This infection is endemic in Southeast Asia. With the prevalence of AIDS in this area, the number of patients with systemic penicilliosis marneffei is found to be increasing rapidly in mainland China in recent years. We recently reviewed 668 cases of penicilliosis marneffei in mainland China from January 1984 to December 2009 in cnki, cqvip, CBMdisc and PubMed. We analyzed epidemiological and clinical features, laboratory findings, reaction to therapy and prognosis of the disease. We found that 99.4% of the cases were reported in the southern part of China; among these cases, 42.8% were from Guangxi (286 cases) and 40.6% were from Guangdong province (271 cases). Five hundred and eighty-six cases (87.7%) of penicilliosis marneffei were reported with infection by the human immunodeficiency virus, 25 cases (3.8%) with other immunocompromised diseases, and 57 cases (8.5%) without any documented underlying diseases. Fever, weight loss, anemia, lymphadenopathy, hepatosplenomegaly, respiratory signs and skin lesions were the common clinical manifestations of P. marneffei infections. The 569 cases received antifungal therapy with a mortality of 24.3% (138 cases), 99 cases who had not received antifungal therapy had a mortality of 50.6%. P. marneffei was an emerging pathogenic fungus and become a medical and public health importance in mainland China. The immunocompromised patients should pay more attention to P. marneffei infection in the endemic areas.

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In this paper, a system designed for helping the deaf to communicate with others is presented. Some useful new ideas are proposed in design and implementation. An algorithm based on geometrical analysis for the purpose of extracting invariant feature to signer position is presented. An ANN–DP combined approach is employed for segmenting subwords automatically from the data stream of sign signals. To tackle the epenthesis movement problem, a DP-based method has been used to obtain the context-dependent models. Some techniques for system implementation are also given, including fast matching, frame prediction and search algorithms. The implemented system is able to recognize continuous large vocabulary Chinese Sign Language. Experiments show that proposed techniques in this paper are efficient on either recognition speed or recognition performance.

We present a novel approach to synthesizing accurate visible speech based on searching and concatenating optimal variable-length units in a large corpus of motion capture data. Based on a set of visual prototypes selected on a source face and a corresponding set designated for a target face, we propose a machine learning technique to automatically map the facial motions observed on the source face to the target face. In order to model the long distance coarticulation effects in visible speech, a large-scale corpus that covers the most common syllables in English was collected, annotated and analyzed. For any input text, a search algorithm to locate the optimal sequences of concatenated units for synthesis is desrcribed. A new algorithm to adapt lip motions from a generic 3D face model to a specific 3D face model is also proposed. A complete, end-to-end visible speech animation system is implemented based on the approach. This system is currently used in more than 60 kindergarten through third grade classrooms to teach students to read using a lifelike conversational animated agent. To evaluate the quality of the visible speech produced by the animation system, both subjective evaluation and objective evaluation are conducted. The evaluation results show that the proposed approach is accurate and powerful for visible speech synthesis.

Talaromyces marneffei is a dimorphic pathogenic fungus, which is a life-threatening invasive mycosis in the immunocompromised host. Prompt diagnosis of T. marneffei infection remains difficult although there has been progress in attempts to expedite the diagnosis of this infection. We previously demonstrated the value of nested polymerase chain reaction (PCR) to detect T. marneffei in paraffin embedded tissue samples with high sensitivity and specificity. In this study, this assay was used to detect the DNA of T. marneffei in whole blood samples. Real-time PCR assay was also evaluated to identify T. marneffei in the same samples. Twenty out of 30 whole blood samples (67%) collected from 23 patients were found positive by using the nested PCR assay, while 23/30 (77%) samples were found positive by using the real-time PCR assay. In order to express accurately the fungal loads, we used a normalized linearized plasmid as an internal control for real-time PCR. The assay results were correlated as the initial quantity (copies/μl) with fungal burden. These data indicate that combination of nested PCR and real-time PCR assay provides an attractive alternative for identification of T. marneffei DNA in whole blood samples of HIV-infected patients.

We present a technique for accurate automatic visible speech synthesis from textual input. When provided with a speech waveform and the text of a spoken sentence, the system produces accurate visible speech synchronized with the audio signal. To develop the system, we collected motion capture data from a speaker's face during production of a set of words containing all diviseme sequences in English. The motion capture points from the speaker's face are retargeted to the vertices of the polygons of a 3D face model. When synthesizing a new utterance, the system locates the required sequence of divisemes, shrinks or expands each diviseme based on the desired phoneme segment durations in the target utterance, then moves the polygons in the regions of the lips and lower face to correspond to the spatial coordinates of the motion capture data. The motion mapping is realized by a key-shape mapping function learned by a set of viseme examples in the source and target faces. A well-posed numerical algorithm estimates the shape blending coefficients. Time warping and motion vector blending at the juncture of two divisemes and the algorithm to search the optimal concatenated visible speech are also developed to provide the final concatenative motion sequence.

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