Number Of Available Methods Research Articles

2°Struc - the Protein Secondary Structure Analysis Server

Protein secondary structure can be defined by the pattern of hydrogen bonding between backbone amide and carboxyl groups, whereby the protein is constrained to adopt repetitive dihedral angle conformations. “Define Secondary Structure of Proteins” (DSSP)(Kabsch and Sander, 1983) is the de facto standard for annotation using rules similar to those described by Pauling and Corey, (1951) to assign eight secondary structure states. However, other methods have been developed to address problems including poor edge residue definition, low-resolution structure elucidation and Cα only structures. These methods define secondary structure in different ways resulting in a wide variation in assignment at the amino acid and segment levels. To enable investigation of this variation we present 2°Struc; a web server that analyses protein secondary structure content derived from a number of available methods. The output is in five sections. Protein structure summary details the ‘whole protein’ percentage structure content and provides a numerical comparison of each method relative to DSSP using several commonly applied metrics including percentage similarity and Matthews correlation coefficient. Structure summary by chain displays percentage content and provides an option to compare each structure assignment method using the Jmol molecular viewer. Multiple structure alignment uses a three-state representation colored to display secondary structure assignments relative to PDB and UniProt sequence records for each method. A majority vote consensus is also provided. Original multiple structure alignment provides a second colored alignment displaying unmodified structure assignments. Sequence structure alignments shows comparative unmodified and modified three-state output relative to UniProt and ATOM record sequences, with an option to download a PDF file containing information about the method run, percentage structure content, chain length and diagram of the three-state structure assignment, also provided. (Supported by a grant from the BBSRC Bioinformatics and Biological Resources Fund, UK).

Model-Free Deconvolution of Femtosecond Kinetic Data

Though shorter laser pulses can also be produced, pulses of the 100 fs range are typically used in femtosecond kinetic measurements, which are comparable to characteristic times of the studied processes, making detection of the kinetic response functions inevitably distorted by convolution with the pulses applied. A description of this convolution in terms of experiments and measurable signals is given, followed by a detailed discussion of a large number of available methods to solve the convolution equation to get the undistorted kinetic signal, without any presupposed kinetic or photophysical model of the underlying processes. A thorough numerical test of several deconvolution methods is described, and two iterative time-domain methods (Bayesian and Jansson deconvolution) along with two inverse filtering frequency-domain methods (adaptive Wiener filtering and regularization) are suggested to use for the deconvolution of experimental femtosecond kinetic data sets. Adaptation of these methods to typical kinetic curve shapes is described in detail. We find that the model-free deconvolution gives satisfactory results compared to the classical "reconvolution" method where the knowledge of the kinetic and photophysical mechanism is necessary to perform the deconvolution. In addition, a model-free deconvolution followed by a statistical inference of the parameters of a model function gives less biased results for the relevant parameters of the model than simple reconvolution. We have also analyzed real-life experimental data and found that the model-free deconvolution methods can be successfully used to get undistorted kinetic curves in that case as well. A graphical computer program to perform deconvolution via inverse filtering and additional noise filters is also provided as Supporting Information. Though deconvolution methods described here were optimized for femtosecond kinetic measurements, they can be used for any kind of convolved data where measured experimental shapes are similar.

Müllerian dysgenesis: A review of recent outcomes at Royal Hospital for Women

Müllerian dysgenesis occurs in approximately 1 in 5000 live-born females. There have been many methods described for creation of a functionally useful vagina in cases of Müllerian dysgenesis. Given the number of available methods and the infrequency of the condition, outcome data can be difficult to obtain. To perform a retrospective review of presentation, treatment and outcomes in cases of Müllerian dysgenesis seen at the adolescent gynaecology unit at the Royal Hospital for Women, Sydney. Thirty women with Müllerian dysgenesis were identified between January 2000 and December 2004. Of these, 23 had Müllerian agenesis and seven had partial vaginal agenesis. As this audit and review conform with the standards established by the National Health and Medical Research Council for ethical quality review, ethics approval was not sought. Dilator therapy under the guidance of a trained clinical nurse educator was successful in creating a functionally useful vagina and was well tolerated in all cases of Müllerian agenesis. Patients suffering from segmental vaginal agenesis all had surgical creation of a neovagina with the aid of an amnion vaginoplasty. All patients who were referred following surgical drainage of their haematocolpos outside the unit became infected and needed to undergo further surgery prior to creation of a neovagina. Fibrotic vaginal bands developed only in these patients. The outcomes reinforce the TASPAG guidelines of management for Müllerian dysgenesis, which suggest that dilators are generally effective in creating a functionally useful vagina, and if surgery is required, the primary operation should be definitive and performed by well-trained experts.

Pairwise local structural alignment of RNA sequences with sequence similarity less than 40%

Searching for non-coding RNA (ncRNA) genes and structural RNA elements (eleRNA) are major challenges in gene finding today as these often are conserved in structure rather than in sequence. Even though the number of available methods is growing, it is still of interest to pairwise detect two genes with low sequence similarity, where the genes are part of a larger genomic region. Here we present such an approach for pairwise local alignment which is based on foldalign and the Sankoff algorithm for simultaneous structural alignment of multiple sequences. We include the ability to conduct mutual scans of two sequences of arbitrary length while searching for common local structural motifs of some maximum length. This drastically reduces the complexity of the algorithm. The scoring scheme includes structural parameters corresponding to those available for free energy as well as for substitution matrices similar to RIBOSUM. The new foldalign implementation is tested on a dataset where the ncRNAs and eleRNAs have sequence similarity <40% and where the ncRNAs and eleRNAs are energetically indistinguishable from the surrounding genomic sequence context. The method is tested in two ways: (1) its ability to find the common structure between the genes only and (2) its ability to locate ncRNAs and eleRNAs in a genomic context. In case (1), it makes sense to compare with methods like Dynalign, and the performances are very similar, but foldalign is substantially faster. The structure prediction performance for a family is typically around 0.7 using Matthews correlation coefficient. In case (2), the algorithm is successful at locating RNA families with an average sensitivity of 0.8 and a positive predictive value of 0.9 using a BLAST-like hit selection scheme. The program is available online at http://foldalign.kvl.dk/

26S rRNA-based internal control gene primer pair for reverse transcription-polymerase chain reaction-based quantitative expression studies in diverse plant species

Gene expression analysis is important to understand complex regulatory mechanism and identiWcation of genes relevant to biological processes. Quantitative expression data provide insight into the switched-on and switched-oV genes as well as into the up-regulated and down-regulated genes. This is achieved by a number of available methods, among which reverse transcriptionpolymerase chain reaction (RT-PCR)1-based analysis and real-time RT-PCR-based analysis have the advantage of automation, high speed, high sensitivity, high throughput, and lower requirement of RNA quantity. For relative quantitation, RNA levels of the gene under investigation are compared from sample to sample using an internal control to normalize for diVerences in sample concentration and loading. The use of such genes as internal controls relies on the premise that they exhibit a constant basal level of expression that is consistent, nonregulated, independent of the cell cycle, and nonresponsive to external treatments or developing stage. Housekeeping genes such as �-actin, rRNAs, glyceraldehydes- 3-phosphate dehydrogenase (GAPDH), tubulins, hypoxanthine phosphoribosyl transferase, L32, albumins, and cyclophilins are widely used as internal controls but need to be standardized for the target species [1–3]. Among the reported genes, those for rRNA are less likely to Xuctuate under the conditions that aVect the expression of mRNAs, probably due to much greater abundance of these genes (>80%) and the involvement of diVerent polymerases for transcription of mRNAs and rRNAs [4,5]. We developed primers from the conserved region of the 26S rRNA gene and evaluated them in seven diVerent plant species: Arabidopsis thaliana (arabidopsis), a model system in plant biology; Camellia sinensis (tea), a commercially important crop that possesses medicinal properties primarily attributed to polyphenols [6]; Arnebia euchroma (arnebia), whose roots are the source of alkanins/shikonins that are used as coloring agents and also exhibit antibacterial, antifungal, wound-healing, and antiinXammatory properties [7]; Caragana jubata (caragana), a leguminous high-altitude plant that tolerates extreme environmental conditions [8]; Rheum emodi (rheum), another higher altitude plant that contains a medicinal compound, anthraquinones [9]; Picrorhiza kurroa (picrorhiza), an alpine herb that is known for hepatoprotective and immunomodulatory activities [10]; and Stevia rebaudiana (stevia), which contains stevioside, a noncaloric sweetener that is more than 100 times sweeter than table sugar [11]. Because no internal control gene primers have been reported for these plants (except arabidopsis, which have tremendous scope of metabolic engineering), proactive action has been taken to develop an internal control for gene expression studies. Experiments were conducted on diVerent plant parts, and various treatments were provided to all seven plants (as described in the Wgure legends). RNA was isolated

Typing fungal isolates: molecular methods and computerized analysis.

Infections caused by fungi (mycoses) are increasingly reported in many countries owing to greater life expectancy associated with an increase in quality of medical and surgical procedures, as well as the emergence of diseases or infections that affect the immune system such as AIDS. Nosocomial outbreaks of fungal infections are sometimes reported, and typing is then necessary to find the reservoirs, analyze the modes of transmission, study the antifungal susceptibility patterns, and investigate the susceptibility of the host. In addition, the food industry is increasingly demanding typing methods that could help in selection of the best fungal strains, in order to incorporate them in the productive chains and augment the quality and security of food. This is the case for Saccharomyces cerevisiae in the wine industry: the selection and characterization of indigenous or autochthonous strains is an important objective for the production of high-quality certified wines.Several genotyping methods are now widely used for strain delineation of medically or economically important microorganisms belonging to the kingdom Fungi. Most molecular typing methods are comparable to those already described for bacteria, although the peculiarities of their nucleic acids increase the number of available methods. Although typing procedures based on the analysis of nucleic acid sequences have been developed, most genotyping methods currently in use are electrophoretically based, and the procedures include the visual comparison of nucleic acid band profiles or their reading with the help of computerized software. Here we describe some of the most frequently used genotyping methods for fungi, based on polymerase chain reactions (PCR), the isolation of chromosomal or mitochondrial DNA, and their restriction using endonuclease enzymes. The latter methods are exclusive for typing eukaryotic organisms and are based on the expected polymorphism obtained from the separation of large chromosomes using pulsed-field gel electrophoresis (PFGE) and the restriction of mitochondrial or chromosomal DNA. More sophisticated methods, such as those that combine endonuclease restriction with hybridization, are also available, although their use is less extensive and is limited mostly to research laboratories.

Surgical Management of Facial Nerve Injuries

The comprehensive management of facial nerve injuries requires a surgeon with a number of available methods of reconstruction at his or her disposal. Comprehensive evaluation or documentation of injury is required to determine the most appropriate timing and method of surgical intervention. The majority of nerve injuries are limited, and direct repair or simple nerve grafting are the indicated treatment modalities. These procedures are easily applied to the management of the facial nerve by any well-trained microsurgeon. Accurate diagnosis and timely intervention are critical in achieving acceptable outcomes. Multidisciplinary collaboration is occasionally necessary for extremely proximal injuries wherein the skills of a lateral skull base surgeon are critical. Delayed facial reconstruction by facial reanimation requires subspecialty skills and necessitates referrals to centers experienced in such procedures.

Combined Validation of Noise Signals Measured in NPPs

This paper describes and characterizes the noise measurements of a typical nuclear power reactor. Special emphasis is placed on the methods and priactices of signal validation procedures that can be carried out during reactor operation. Taking into account the great number of available methods, a general scheme has been elaborated that can be adapted to a wide range of different requirements. Individual evaluation procedures are constructed as simply as possible even if the reliability of individual judgements is low. These processes supply source values and source uncertainties about the investigated parameter or a decision. An additional pooling method integrates the judgements of individual procedures. This combination method is able to lead to conclusions even if some of the sources are missing. The method of combined individual judgements is equivalent to a human expert judgement making a decision on the quality of a measurement.

Techniques for assessing polygonal approximations of curves

Given the enormous number of available methods for finding polygonal approximations to curves techniques are required to assess different algorithms. Some of the standard approaches are shown to be unsuitable if the approximations contain varying numbers of lines. Instead, we suggest assessing an algorithm's results relative to an optimal polygon, and describe a measure which combines the relative fidelity and efficiency of a curve segmentation. We use this measure to compare the application of 23 algorithms to a curve first used by Teh and Chin (1989); their integral square errors (ISEs) are assessed relative to the optimal ISE. In addition, using an example of pose estimation, it is shown how goal-directed evaluation can be used to select an appropriate assessment criterion.

Default reasoning by deductive planning

This paper deals with the automation of reasoning from incomplete information by means of default logics. We provide proof procedures for default logics' major reasoning modes, namely, credulous and skeptical reasoning. We start by reformulating the task of credulous reasoning in default logics as deductive planning problems. This interpretation supplies us with several interesting and valuable insights into the proof theory of default logics. Foremost, it allows us to take advantage of the large number of available methods, algorithms, and implementations for solving deductive planning problems. As an example, we demonstrate how credulous reasoning in certain variants of default logic is implementable by means of a planning method based on equational logic programming. In addition, our interpretation allows us to transfer theoretical results, such as complexity results, from the field of planning to that of default logics. In this way, we have isolated two yet unknown classes of default theories for which deciding credulous entailment is polynomial.

Three-dimensional sonographic reconstruction: techniques and diagnostic applications.

In this review, we summarize the techniques of obtaining and reconstructing three-dimensional (3D) sonograms in a number of anatomic areas, catalog the clinical efforts at 3D sonography so far, and introduce more recent work in this area that takes advantage of the unique features of sonography. Although it is an active area of 3D imaging research, cardiac 3D imaging is not discussed because it has unique requirements stemming from the heart's anatomic inaccessibility and motion. Image analysis and display also are not covered, as no clear consensus has been reached about the usefulness of the large number of available methods.

Models for Sample Selection Bias

When observations in social research are selected so that they are not independent of the outcome variables in a study, sample selection leads to biased inferences about social processes. Nonrandom selection is both a source of bias in empirical research and a fundamental aspect of many social processes. This chapter reviews models that attempt to take account of sample selection and their applications in research on labor markets, schooling, legal processes, social mobility, and social networks. Variants of these models apply to outcome variables that are censored or truncated—whether explicitly or incidentally—and include the tobit model, the standard selection model, models for treatment effects in quasi-experimental designs, and endogenous switching models. Heckman’s two-stage estimator is the most widely used approach to selection bias, but its results may be sensitive to violations of its assumptions about the way that selection occurs. Recent econometric research has developed a wide variety of promising approaches to selection bias that rely on considerably weaker assumptions. These include a number of semiand nonparametric approaches to estimating selection models, the use of panel data, and the analyses of bounds of estimates. The large number of available methods and the difficulty of modelling selection indicate that researchers should be explicit about the assumptions behind their methods and should present results that derive from a variety of methods.

Materials Selection-Chaos or Cooperation

Selection and specification of materials is an important part of the design and development process of the simplest component or the most complex system. It also is one of the most difficult and controversial items. The difficulties confronting the people involved in materials selection and specification are numerous, and can be divided into objective and subjective difficulties. The objective difficulties are the staggering and rapidly increasing number of materials available; the broad range of properties of such materials, depending on processing conditions; the numerous factors to consider in selection such as functional performance, manufacturability, availability, and cost, etc. The subjective difficulties center around the problems of information and communication--or, rather, the lack of these items. To avoid chaos that results in less-than-optimum performance, poor reliability, high cost, and further polarization of the people involved, the magnitude of the problem has to be realized. Furthermore, design engineers and materials specialists must be willing to communicate and to utilize the large number of available methods, devices, and vehicles in order to arrive at proper materials selection. This paper describes available sources of materials information, and surveys the communication vehicles between the designer and the materials specialist. It points out the responsibilities of both parties in providing proper input in the materials selection process. It also suggests some organizational approaches to provide optimum materials support for the design engineer.