Reconstruction of heel soft tissue defects using sensate medial plantar flap

Introduction. Reconstruction of heel soft tissue defects represents a true challenge for any surgeon due to the particularities of this anatomical region. The tissue used to reconstruct the heel area must be resistant, innervated, and adapted to take over the body weight. Innervated medial plantar fasciocutaneous flap is one of the best solutions to cover defects at the heel level. Materials and Methods. We studied 5 patients, 4 males and one female, aged 42 to 67 years, who presented heel soft tissue defects of various etiologies. In all cases, the used reconstructive method was an insular innervated medial plantar fasciocutaneous flap. Results. Immediate and late outcomes were good. No immediate complications of necrosis type were recorded in any of the cases, and 2 years postoperatively there was no evidence of ulceration or other type of flap injury. The socio-professional reintegration of the patients was relatively rapid and their satisfaction was high. Donor area morbidity was minimal. Conclusions. Sensate medial plantar fasciocutaneous flap represents the first choice for the reconstruction of the heel soft tissue defects when patients’ local and general status allows it

Between a chicken and a grape: estimating the number of human genes

The number of genes in the human genome is still an estimate

A computational survey of candidate exonic splicing enhancer motifs in the model plant Arabidopsis thaliana

Algorithmic approaches to splice site prediction have relied mainly on the consensus patterns found at the boundaries between protein coding and non-coding regions. However exonic splicing enhancers have been shown to enhance the utilization of nearby splice sites. We have developed a new computational technique to identify significantly conserved motifs involved in splice site regulation. First, 84 putative exonic splicing enhancer hexamers are identified in Arabidopsis thaliana. Then a Gibbs sampling program called ELPH was used to locate conserved motifs represented by these hexamers in exonic regions near splice sites in confirmed genes. Oligomers containing 35 of these motifs have been shown experimentally to induce significant inclusion of A. thaliana exons. Second, integration of our regulatory motifs into two different splice site recognition programs significantly improved the ability of the software to correctly predict splice sites in a large database of confirmed genes. We have released GeneSplicerESE, the improved splice site recognition code, as open source software. Our results show that the use of the ESE motifs consistently improves splice site prediction accuracy.https://doi.org/10.1186/1471-2105-8-15

Efficient decoding algorithms for generalized hidden Markov model gene finders

BACKGROUND: The Generalized Hidden Markov Model (GHMM) has proven a useful framework for the task of computational gene prediction in eukaryotic genomes, due to its flexibility and probabilistic underpinnings. As the focus of the gene finding community shifts toward the use of homology information to improve prediction accuracy, extensions to the basic GHMM model are being explored as possible ways to integrate this homology information into the prediction process. Particularly prominent among these extensions are those techniques which call for the simultaneous prediction of genes in two or more genomes at once, thereby increasing significantly the computational cost of prediction and highlighting the importance of speed and memory efficiency in the implementation of the underlying GHMM algorithms. Unfortunately, the task of implementing an efficient GHMM-based gene finder is already a nontrivial one, and it can be expected that this task will only grow more onerous as our models increase in complexity. RESULTS: As a first step toward addressing the implementation challenges of these next-generation systems, we describe in detail two software architectures for GHMM-based gene finders, one comprising the common array-based approach, and the other a highly optimized algorithm which requires significantly less memory while achieving virtually identical speed. We then show how both of these architectures can be accelerated by a factor of two by optimizing their content sensors. We finish with a brief illustration of the impact these optimizations have had on the feasibility of our new homology-based gene finder, TWAIN. CONCLUSIONS: In describing a number of optimizations for GHMM-based gene finders and making available two complete open-source software systems embodying these methods, it is our hope that others will be more enabled to explore promising extensions to the GHMM framework, thereby improving the state-of-the-art in gene prediction techniques

Global comparative analysis of ESTs from the southern cattle tick, Rhipicephalus (Boophilus) microplus

<p>Abstract</p> <p>Background</p> <p>The southern cattle tick, <it>Rhipicephalus (Boophilus) microplus</it>, is an economically important parasite of cattle and can transmit several pathogenic microorganisms to its cattle host during the feeding process. Understanding the biology and genomics of <it>R. microplus </it>is critical to developing novel methods for controlling these ticks.</p> <p>Results</p> <p>We present a global comparative genomic analysis of a gene index of <it>R. microplus </it>comprised of 13,643 unique transcripts assembled from 42,512 expressed sequence tags (ESTs), a significant fraction of the complement of <it>R. microplus </it>genes. The source material for these ESTs consisted of polyA RNA from various tissues, lifestages, and strains of <it>R. microplus</it>, including larvae exposed to heat, cold, host odor, and acaricide. Functional annotation using RPS-Blast analysis identified conserved protein domains in the conceptually translated gene index and assigned GO terms to those database transcripts which had informative BlastX hits. Blast Score Ratio and SimiTri analysis compared the conceptual transcriptome of the <it>R. microplus </it>database to other eukaryotic proteomes and EST databases, including those from 3 ticks. The most abundant protein domains in BmiGI were also analyzed by SimiTri methodology.</p> <p>Conclusion</p> <p>These results indicate that a large fraction of BmiGI entries have no homologs in other sequenced genomes. Analysis with the PartiGene annotation pipeline showed 64% of the members of BmiGI could not be assigned GO annotation, thus minimal information is available about a significant fraction of the tick genome. This highlights the important insights in tick biology which are likely to result from a tick genome sequencing project. Global comparative analysis identified some tick genes with unexpected phylogenetic relationships which detailed analysis attributed to gene losses in some members of the animal kingdom. Some tick genes were identified which had close orthologues to mammalian genes. Members of this group would likely be poor choices as targets for development of novel tick control technology.</p

JIGSAW, GeneZilla, and GlimmerHMM: puzzling out the features of human genes in the ENCODE regions

BACKGROUND: Predicting complete protein-coding genes in human DNA remains a significant challenge. Though a number of promising approaches have been investigated, an ideal suite of tools has yet to emerge that can provide near perfect levels of sensitivity and specificity at the level of whole genes. As an incremental step in this direction, it is hoped that controlled gene finding experiments in the ENCODE regions will provide a more accurate view of the relative benefits of different strategies for modeling and predicting gene structures. RESULTS: Here we describe our general-purpose eukaryotic gene finding pipeline and its major components, as well as the methodological adaptations that we found necessary in accommodating human DNA in our pipeline, noting that a similar level of effort may be necessary by ourselves and others with similar pipelines whenever a new class of genomes is presented to the community for analysis. We also describe a number of controlled experiments involving the differential inclusion of various types of evidence and feature states into our models and the resulting impact these variations have had on predictive accuracy. CONCLUSION: While in the case of the non-comparative gene finders we found that adding model states to represent specific biological features did little to enhance predictive accuracy, for our evidence-based 'combiner' program the incorporation of additional evidence tracks tended to produce significant gains in accuracy for most evidence types, suggesting that improved modeling efforts at the hidden Markov model level are of relatively little value. We relate these findings to our current plans for future research

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

TopHat is a popular spliced aligner for RNA-sequence (RNA-seq) experiments. In this paper, we describe TopHat2, which incorporates many significant enhancements to TopHat. TopHat2 can align reads of various lengths produced by the latest sequencing technologies, while allowing for variable-length indels with respect to the reference genome. In addition to de novo spliced alignment, TopHat2 can align reads across fusion breaks, which can occur after genomic translocations. TopHat2 combines the ability to identify novel splice sites with direct mapping to known transcripts, producing sensitive and accurate alignments, even for highly repetitive genomes or in the presence of pseudogenes. TopHat2 is available at http://ccb.jhu.edu/software/tophat

Reconstruction of heel soft tissue defects using sensate medial plantar flap

Introduction. Reconstruction of heel soft tissue defects represents a true challenge for any surgeon due to the particularities of this anatomical region. The tissue used to reconstruct the heel area must be resistant, innervated, and adapted to take over the body weight. Innervated medial plantar fasciocutaneous flap is one of the best solutions to cover defects at the heel level. Materials and Methods. We studied 5 patients, 4 males and one female, aged 42 to 67 years, who presented heel soft tissue defects of various etiologies. In all cases, the used reconstructive method was an insular innervated medial plantar fasciocutaneous flap. Results. Immediate and late outcomes were good. No immediate complications of necrosis type were recorded in any of the cases, and 2 years postoperatively there was no evidence of ulceration or other type of flap injury. The socio-professional reintegration of the patients was relatively rapid and their satisfaction was high. Donor area morbidity was minimal. Conclusions. Sensate medial plantar fasciocutaneous flap represents the first choice for the reconstruction of the heel soft tissue defects when patients’ local and general status allows it

Digging into acceptor splice site prediction : an iterative feature selection approach

Feature selection techniques are often used to reduce data dimensionality, increase classification performance, and gain insight into the processes that generated the data. In this paper, we describe an iterative procedure of feature selection and feature construction steps, improving the classification of acceptor splice sites, an important subtask of gene prediction. We show that acceptor prediction can benefit from feature selection, and describe how feature selection techniques can be used to gain new insights in the classification of acceptor sites. This is illustrated by the identification of a new, biologically motivated feature: the AG-scanning feature. The results described in this paper contribute both to the domain of gene prediction, and to research in feature selection techniques, describing a new wrapper based feature weighting method that aids in knowledge discovery when dealing with complex datasets