A classification system and algorithm for reconstruction of maxillectomy and midfacial defects

Maxillectomy defects become more complex when critical structures such as the orbit, globe, and cranial base are resected, and reconstruction with distant tissues becomes essential. This study reviews all maxillectomy defects reconstructed immediately using pedicled and free flaps to establish (1) a classification system and (2) an algorithm for reconstruction of these complex problems. Over a 5-year period, 60 flaps were used to reconstruct defects classified as the following: type I, limited maxillectomy (n = 7); type II, subtotal maxillectomy (n = 10); type IIIa, total maxillectomy with preservation of the orbital contents (n = 13); type IIIb, total maxillectomy with orbital exenteration (n = 18); and type IV, orbitomaxillectomy (n = 10). Free flaps (45 rectus abdominis and 10 radial forearm) were used in 55 patients (91.7 percent), and the temporalis muscle was transposed in five elderly patients who were not free-flap candidates. Vascularized (radial forearm osteocutaneous) bone flaps were used in four of the 60 patients (6.7 percent) and nonvascularized bone grafts in 17 (28.3 percent). Simultaneous reconstruction of the oral commissure using an Estandler procedure was performed in 10 patients with maxillectomy and through-and-through soft-tissue defects. Free-flap survival was 100 percent, with reexploration in five of 55 patients (9.1 percent) and partial-flap necrosis in one patient. Seven of the 60 patients (11.7 percent) had systemic complications, and four died within 30 days of hospitalization. Fifty patients had more than 6 months of follow-up with a mean time of 27.7 (+/- 15.6) months. Postoperative radiotherapy was administered in 32 of these patients (64.0 percent). Chewing and speech functions were assessed in 36 patients with type II, IIIa, and IIIb defects. A prosthetic denture was fixed in 15 of 36 patients (41.7 percent). Return to an unrestricted diet was seen in 16 patients (44.4 percent), a soft diet in 17 (47.2 percent), and a liquid diet in three (8.3 percent). Speech was assessed as normal in 14 of 36 patients (38.9 percent), near normal in 15 (41.7 percent), intelligible in six (16.7 percent), and unintelligible in one patient (2.8 percent). Globe and periorbital soft-tissue position was assessed in 14 patients with type I and IIIa defects. There were no cases of enophthalmos, and one patient had a mild vertical dystopia. Ectropion was observed in 10 of 14 patients (71.4 percent). Oral competence was considered good in all 10 patients with excision/reconstruction of the oral commissure; however, two patients (20 percent) developed microstomia after receiving radiotherapy. Aesthetic results were evaluated at least 6 months after reconstruction in 50 patients. They were good to excellent in 29 patients (58 percent) for whom cheek skin and lip were not resected, and poor to fair (42 percent) when the external skin or orbital contents were excised. Secondary procedures were required in 16 of 50 patients (32.0 percent). Free-tissue transfer provides the most effective and reliable form of immediate reconstruction for complex maxillectomy defects. The rectus abdominis and radial forearm flaps in combination with immediate bone grafting or as osteocutaneous flaps reliably provide the best aesthetic and functional results. An algorithm based on the type of maxillary resection can be followed to determine the best approach to reconstruction.     

A fast SCOP fold classification system using content-based E-Predict algorithm

Background  

Domain experts manually construct the Structural Classification of Protein (SCOP) database to categorize and compare protein structures. Even though using the SCOP database is believed to be more reliable than classification results from other methods, it is labor intensive. To mimic human classification processes, we develop an automatic SCOP fold classification system to assign possible known SCOP folds and recognize novel folds for newly-discovered proteins.     

A comprehensive classification system for lipids

Lipids are produced, transported, and recognized by the concerted actions of numerous enzymes, binding proteins, and receptors. A comprehensive analysis of lipid molecules, "lipidomics," in the context of genomics and proteomics is crucial to understanding cellular physiology and pathology; consequently, lipid biology has become a major research target of the postgenomic revolution and systems biology. To facilitate international communication about lipids, a comprehensive classification of lipids with a common platform that is compatible with informatics requirements has been developed to deal with the massive amounts of data that will be generated by our lipid community. As an initial step in this development, we divide lipids into eight categories (fatty acyls, glycerolipids, glycerophospholipids, sphingolipids, sterol lipids, prenol lipids, saccharolipids, and polyketides) containing distinct classes and subclasses of molecules, devise a common manner of representing the chemical structures of individual lipids and their derivatives, and provide a 12 digit identifier for each unique lipid molecule. The lipid classification scheme is chemically based and driven by the distinct hydrophobic and hydrophilic elements that compose the lipid. This structured vocabulary will facilitate the systematization of lipid biology and enable the cataloging of lipids and their properties in a way that is compatible with other macromolecular databases.     

A double classification tree search algorithm for index SNP selection

Background  

In population-based studies, it is generally recognized that single nucleotide polymorphism (SNP) markers are not independent. Rather, they are carried by haplotypes, groups of SNPs that tend to be coinherited. It is thus possible to choose a much smaller number of SNPs to use as indices for identifying haplotypes or haplotype blocks in genetic association studies. We refer to these characteristic SNPs as index SNPs. In order to reduce costs and work, a minimum number of index SNPs that can distinguish all SNP and haplotype patterns should be chosen. Unfortunately, this is an NP-complete problem, requiring brute force algorithms that are not feasible for large data sets.     

A TRIZ-inspired bat algorithm for gene selection in cancer classification

Gene expression data are expected to make a great contribution in the producing of efficient cancer diagnosis and prognosis. Gene expression data are coded by large measured genes, and only of a few number of them carry precious information for different classes of samples. Recently, several researchers proposed gene selection methods based on metaheuristic algorithms for analysing and interpreting gene expression data. However, due to large number of selected genes with limited number of patient's samples and complex interaction between genes, many gene selection methods experienced challenges in order to approach the most relevant and reliable genes. Hence, in this paper, a hybrid filter/wrapper, called rMRMR-MBA is proposed for gene selection problem. In this method, robust Minimum Redundancy Maximum Relevancy (rMRMR) as filter to select the most promising genes and an modified bat algorithm (MBA) as search engine in wrapper approach is proposed to identify a small set of informative genes. The performance of the proposed method has been evaluated using ten gene expression datasets. For performance evaluation, MBA is evaluated by studying the convergence behaviour of MBA with and without TRIZ optimisation operators. For comparative evaluation, the results of the proposed rMRMR-MBA were compared against ten state-of-arts methods using the same datasets. The comparative study demonstrates that the proposed method produced better results in terms of classification accuracy and number of selected genes in two out of ten datasets and competitive results on the remaining datasets. In a nutshell, the proposed method is able to produce very promising results with high classification accuracy which can be considered a promising contribution for gene selection domain.     

A unified classification system for eukaryotic transposable elements

Our knowledge of the structure and composition of genomes is rapidly progressing in pace with their sequencing. The emerging data show that a significant portion of eukaryotic genomes is composed of transposable elements (TEs). Given the abundance and diversity of TEs and the speed at which large quantities of sequence data are emerging, identification and annotation of TEs presents a significant challenge. Here we propose the first unified hierarchical classification system, designed on the basis of the transposition mechanism, sequence similarities and structural relationships, that can be easily applied by non-experts. The system and nomenclature is kept up to date at the WikiPoson web site.     

An algorithm for feature classification and structural memorization

Given a finite set of strings of elements (e.g. words or syllables written in terms of letters, which may be true alphabetic symbols, or markers for features which put together form the word describing an object), the problem is posed of memorizing the strings not in lexicographic order, but by grouping them into classes, each of which can be taken as an entry into a multilayered, fast-access memory; this is equivalent to memorizing, rather than the strings, the structural rules which characterize them. This problem is solved by means of a heuristic algorithm, which gives results that stay invariant under arbitrary permutations of the elements; heuristics may affect optimality, not exactness of the solution, and provides considerable gains in computing costs. The exposition, for convenience of the reader, is self-contained, although this work is part of a more general program on form and language analysis.     

A functional-phylogenetic classification system for transmembrane solute transporters.

A comprehensive classification system for transmembrane molecular transporters has been developed and recently approved by the transport panel of the nomenclature committee of the International Union of Biochemistry and Molecular Biology. This system is based on (i) transporter class and subclass (mode of transport and energy coupling mechanism), (ii) protein phylogenetic family and subfamily, and (iii) substrate specificity. Almost all of the more than 250 identified families of transporters include members that function exclusively in transport. Channels (115 families), secondary active transporters (uniporters, symporters, and antiporters) (78 families), primary active transporters (23 families), group translocators (6 families), and transport proteins of ill-defined function or of unknown mechanism (51 families) constitute distinct categories. Transport mode and energy coupling prove to be relatively immutable characteristics and therefore provide primary bases for classification. Phylogenetic grouping reflects structure, function, mechanism, and often substrate specificity and therefore provides a reliable secondary basis for classification. Substrate specificity and polarity of transport prove to be more readily altered during evolutionary history and therefore provide a tertiary basis for classification. With very few exceptions, a phylogenetic family of transporters includes members that function by a single transport mode and energy coupling mechanism, although a variety of substrates may be transported, sometimes with either inwardly or outwardly directed polarity. In this review, I provide cross-referencing of well-characterized constituent transporters according to (i) transport mode, (ii) energy coupling mechanism, (iii) phylogenetic grouping, and (iv) substrates transported. The structural features and distribution of recognized family members throughout the living world are also evaluated. The tabulations should facilitate familial and functional assignments of newly sequenced transport proteins that will result from future genome sequencing projects.     

A hybrid parameter estimation algorithm for beta mixtures and applications to methylation state classification

Background

Mixtures of beta distributions are a flexible tool for modeling data with values on the unit interval, such as methylation levels. However, maximum likelihood parameter estimation with beta distributions suffers from problems because of singularities in the log-likelihood function if some observations take the values 0 or 1.

Methods

While ad-hoc corrections have been proposed to mitigate this problem, we propose a different approach to parameter estimation for beta mixtures where such problems do not arise in the first place. Our algorithm combines latent variables with the method of moments instead of maximum likelihood, which has computational advantages over the popular EM algorithm.

Results

As an application, we demonstrate that methylation state classification is more accurate when using adaptive thresholds from beta mixtures than non-adaptive thresholds on observed methylation levels. We also demonstrate that we can accurately infer the number of mixture components.

Conclusions

The hybrid algorithm between likelihood-based component un-mixing and moment-based parameter estimation is a robust and efficient method for beta mixture estimation. We provide an implementation of the method (“betamix”) as open source software under the MIT license.

     

A robust orthogonal algorithm for system identification and time-series analysis

We describe and illustrate methods for obtaining a parsimonious sinusoidal series representation or model of biological time-series data. The methods are also used to identify nonlinear systems with unknown structure. A key aspect is a rapid search for significant terms to include in the model for the system or the time-series. For example, the methods use fast and robust orthogonal searches for significant frequencies in the time-series, and differ from conventional Fourier series analysis in several important respects. In particular, the frequencies in our resulting sinusoidal series need not be commensurate, nor integral multiples of the fundamental frequency corresponding to the record length. Freed of these restrictions, the methods produce a more economical sinusoidal series representation (than a Fourier series), finding the most significant frequencies first, and automatically determine model order. The methods are also capable of higher resolution than a conventional Fourier series analysis. In addition, the methods can cope with unequally-spaced or missing data, and are applicable to time-series corrupted by noise. Fially, we compare one of our methods with a wellknown technique for resolving sinusoidal signals in noise using published data for the test time-series.     

MOBCENTR: A nonhierarchical classification algorithm for exploratory data analysis (EDA)

MOBCENTR is a classification algorithm combining features of classification about mobile centres, Ward algorithm and of the Hard-Isodata method. The results of this new algorithm and of Ward algorithm are compared by morphological characters of species ofSolidago andPimpinella.     

The radial forearm flap: reconstructive applications and donor-site defects in 35 consecutive patients

Thirty-five consecutive patients treated with the radial forearm flap were reviewed. This flap was used in head and neck reconstruction in 25 patients, soft-tissue cover of an extremity in 9 patients, and as a new technique for penile reconstruction in 1 patient. Osteocutaneous flaps were used for mandibular reconstruction in 13 patients. In 6 patients innervated flaps were used to provide sensation on the dorsum of the hand or on the weight-bearing surface of the foot. There was only one total flap failure and no partial failures. Recipient-site complications were few, with prompt healing and very acceptable appearance. Donor-site complications included partial loss of the skin graft with tendon exposure in 10 patients (33 percent), an unsatisfactory appearance in 5 patients (17 percent), and one case of radial fracture (8 percent). On functional testing, there was no significant loss of strength or joint mobility in the donor extremity in 19/20 patients. The authors recommend measures to reduce donor-site morbidity and conclude that, with an acceptable donor site, this flap is valuable in a variety of reconstructive applications.