86 research outputs found

    Identification of putative cis-regulatory elements in Cryptosporidium parvum by de novo pattern finding

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    BACKGROUND: Cryptosporidium parvum is a unicellular eukaryote in the phylum Apicomplexa. It is an obligate intracellular parasite that causes diarrhea and is a significant AIDS-related pathogen. Cryptosporidium parvum is not amenable to long-term laboratory cultivation or classical molecular genetic analysis. The parasite exhibits a complex life cycle, a broad host range, and fundamental mechanisms of gene regulation remain unknown. We have used data from the recently sequenced genome of this organism to uncover clues about gene regulation in C. parvum. We have applied two pattern finding algorithms MEME and AlignACE to identify conserved, over-represented motifs in the 5' upstream regions of genes in C. parvum. To support our findings, we have established comparative real-time -PCR expression profiles for the groups of genes examined computationally. RESULTS: We find that groups of genes that share a function or belong to a common pathway share upstream motifs. Different motifs are conserved upstream of different groups of genes. Comparative real-time PCR studies show co-expression of genes within each group (in sub-sets) during the life cycle of the parasite, suggesting co-regulation of these genes may be driven by the use of conserved upstream motifs. CONCLUSION: This is one of the first attempts to characterize cis-regulatory elements in the absence of any previously characterized elements and with very limited expression data (seven genes only). Using de novo pattern finding algorithms, we have identified specific DNA motifs that are conserved upstream of genes belonging to the same metabolic pathway or gene family. We have demonstrated the co-expression of these genes (often in subsets) using comparative real-time-PCR experiments thus establishing evidence for these conserved motifs as putative cis-regulatory elements. Given the lack of prior information concerning expression patterns and organization of promoters in C. parvum we present one of the first investigations of gene regulation in this important human pathogen

    Phylogenomic evidence supports past endosymbiosis, intracellular and horizontal gene transfer in Cryptosporidium parvum

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    BACKGROUND: The apicomplexan parasite Cryptosporidium parvum is an emerging pathogen capable of causing illness in humans and other animals and death in immunocompromised individuals. No effective treatment is available and the genome sequence has recently been completed. This parasite differs from other apicomplexans in its lack of a plastid organelle, the apicoplast. Gene transfer, either intracellular from an endosymbiont/donor organelle or horizontal from another organism, can provide evidence of a previous endosymbiotic relationship and/or alter the genetic repertoire of the host organism. Given the importance of gene transfers in eukaryotic evolution and the potential implications for chemotherapy, it is important to identify the complement of transferred genes in Cryptosporidium. RESULTS: We have identified 31 genes of likely plastid/endosymbiont (n = 7) or prokaryotic (n = 24) origin using a phylogenomic approach. The findings support the hypothesis that Cryptosporidium evolved from a plastid-containing lineage and subsequently lost its apicoplast during evolution. Expression analyses of candidate genes of algal and eubacterial origin show that these genes are expressed and developmentally regulated during the life cycle of C. parvum. CONCLUSIONS: Cryptosporidium is the recipient of a large number of transferred genes, many of which are not shared by other apicomplexan parasites. Genes transferred from distant phylogenetic sources, such as eubacteria, may be potential targets for therapeutic drugs owing to their phylogenetic distance or the lack of homologs in the host. The successful integration and expression of the transferred genes in this genome has changed the genetic and metabolic repertoire of the parasite

    ShadowTutor: Distributed Partial Distillation for Mobile Video DNN Inference

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    Following the recent success of deep neural networks (DNN) on video computer vision tasks, performing DNN inferences on videos that originate from mobile devices has gained practical significance. As such, previous approaches developed methods to offload DNN inference computations for images to cloud servers to manage the resource constraints of mobile devices. However, when it comes to video data, communicating information of every frame consumes excessive network bandwidth and renders the entire system susceptible to adverse network conditions such as congestion. Thus, in this work, we seek to exploit the temporal coherence between nearby frames of a video stream to mitigate network pressure. That is, we propose ShadowTutor, a distributed video DNN inference framework that reduces the number of network transmissions through intermittent knowledge distillation to a student model. Moreover, we update only a subset of the student's parameters, which we call partial distillation, to reduce the data size of each network transmission. Specifically, the server runs a large and general teacher model, and the mobile device only runs an extremely small but specialized student model. On sparsely selected key frames, the server partially trains the student model by targeting the teacher's response and sends the updated part to the mobile device. We investigate the effectiveness of ShadowTutor with HD video semantic segmentation. Evaluations show that network data transfer is reduced by 95% on average. Moreover, the throughput of the system is improved by over three times and shows robustness to changes in network bandwidth.Comment: Accepted at ICPP 202

    Odontogenic tumors and giant cell lesions of jaws - a nine year study

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    <p>Abstract</p> <p>Objectives</p> <p>A definite geographic variation has been observed in the frequency of odontogenic tumors and giant cell lesions of the jaws reported from different parts of the world. However, there are a few studies on these lesions, especially giant cell lesions, reported from India. Hence, this study was designed to provide a demographic data on the odontogenic tumors and giant cell lesions reported from our institute located in the city of Hyderabad. Hyderabad is the capital city of the southern state of Andhra Pradesh in India. A retrospective analysis of odontogenic tumors and giant cell lesions of jaws reported in our institute between the years 2000 and 2009 was done and this data was compared with previous reports from different parts of the world and India.</p> <p>Methods</p> <p>Biopsies of the lesions received between the years 2000 and 2009 were reviewed and patient's history, clinical, radiological and histopathological characteristics were analyzed.</p> <p>Results</p> <p>A total of 77 biopsies were received during the nine year study period. These lesions were more frequently seen in the males, in a younger age group and showed a predilection for the mandible. Most of them presented as radiolucent, slow growing and painless lesions. Ameloblastomas (71.4%) constituted the majority of odontogenic tumors while central giant cell granulomas (7.8%) constituted the majority of giant cell lesions.</p> <p>Conclusion</p> <p>These lesions showed a definite geographic variation with ameloblastomas being the most common odontogenic tumors and odontomas being relatively rarer lesions in our region.</p
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