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

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

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

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

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

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

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

Clinical and Experimental Biomechanical Studies Regarding Innovative Implants in Traumatology

Fracture treatment has experienced a fascinating evolution in the last years. The aim of this chapter is to reveal some clinical and biomechanical studies regarding innovative implants. After a short introduction (1), we intend to present our results regarding (2) dynamic condylar screw versus condylar blade plate in complex supracondylar femoral fractures; (3) biomechanical analysis of four types of implants in humeral fractures; (4) clinical and experimental studies for optimal stabilization of trochanteric fractures: the gliding nail; (5) intramedullary XS nail for pilon and ankle fractures: design, biomechanics, and clinical results; (6) the XS nail for the treatment of patella and olecranon fractures; and (7) plates with polyaxial stability for fractures of distal radius and proximal humerus. In conclusion, the authors highlight the advantages of these innovative implants in difficult trauma cases

Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments

EVidenceModeler (EVM) is an automated annotation tool that predicts protein-coding regions, alternatively spliced transcripts and untranslated regions of eukaryotic genes

Major data analysis errors invalidate cancer microbiome findings

We re-analyzed the data from a recent large-scale study that reported strong correlations between DNA signatures of microbial organisms and 33 different cancer types and that created machine-learning predictors with near-perfect accuracy at distinguishing among cancers. We found at least two fundamental flaws in the reported data and in the methods: (i) errors in the genome database and the associated computational methods led to millions of false-positive findings of bacterial reads across all samples, largely because most of the sequences identified as bacteria were instead human; and (ii) errors in the transformation of the raw data created an artificial signature, even for microbes with no reads detected, tagging each tumor type with a distinct signal that the machine-learning programs then used to create an apparently accurate classifier. Each of these problems invalidates the results, leading to the conclusion that the microbiome-based classifiers for identifying cancer presented in the study are entirely wrong. These flaws have subsequently affected more than a dozen additional published studies that used the same data and whose results are likely invalid as well