Extreme Rank Selections for Linkage Analysis of Quantitative Trait Loci Using Selected Sib-Pairs

It is well known that linkage analysis using simple random sib-pairs has relatively low power for detecting quantitative trait loci with small genetic effects. The power can be substantially increased by using samples selected based on their trait values. Usually, samples that are obtained by truncation selection consist of random samples from a truncated trait distribution. In this article we propose an alternative method using extreme ranks for linkage analysis with selected sib-pairs. This approach approximates the truncation selection. With similar screening sizes and the same sample size of selected sib-pairs, the extreme rank selection and truncation method have similar power performance, both of which are substantially more powerful than when using random sib-pairs. Simulation results on the comparison of powers between the truncation selection and the extreme rank selection and/or random selection for linkage analysis are reported.

Quantitative structure-property relationship studies on electrochemical degradation of substituted phenols using a support vector machine

A quantitative structure-property relationship (QSPR) model has been developed for the electrochemical degradation of substituted phenols using a support vector machine (SVM). Thirty descriptors, including quantum chemical parameters, steric effect descriptors and half wave potential (E1/2), were used for describing twelve substituted phenols, including mono- and multi-substituent phenols. A leave-one-out (LOO) cross validation procedure resulted in the selection of three descriptors, the total of electron and nuclear energies of the two-center terms for the carbon-chlorine or carbon-nitrogen bond (TE2), the net atomic charges on the chlorine or nitrogen (qx), and the largest negative atomic charge on an atom (q-). The model based on SVM yielded a Q2 value of 0.892, indicating a high predictive ability. Compared with models developed with partial least squares (PLS) and multiple linear regression (MLR), where Q2 were 0.804 and 0.799 respectively, SVM showed higher performances.

Navigated open-wedge high tibial osteotomy: advantages and disadvantages compared to the conventional technique in a cadaver study

High tibial osteotomy (HTO) is an established therapy for the treatment of symptomatic varus malaligned knees. A main reason for disappointing clinical results after HTO is the under- and overcorrection of the mechanical axis due to insufficient intraoperative visualisation. Twenty legs of fresh human cadaver were randomly assigned to navigated open-wedge HTO (n=10) or conventional HTO using the cable method (n=10). Regardless of the pre-existing alignment, the aim of all operations was to align the mechanical axis to pass through 80% of the tibial plateau (beginning with 0% at the medial edge of the tibial plateau and ending with 100% at the lateral edge). This overcorrection was chosen to ensure a sufficient amount of correction. Thus, the medial proximal tibia angle (MPTA) increased by 9.1+/-2.9 degrees (range 5.2 degrees -12.3 degrees ) on the average after navigated HTO and by 8.9+/-2.9 degrees (range 4.7 degrees -12.6 degrees ) after conventional HTO. After stabilization with a fixed angle implant, the alignment was measured by CT. After navigated HTO, the mechanical axis passed the tibial plateau through 79.7% (range 75.5-85.8%). In contrast, after conventional HTO, the average intersection of the mechanical axis was at 72.1% (range 60.4-82.4%) (P=0.020). Additionally, the variability of the mean corrections was significantly lower in the navigated group (3.3% vs. 7.2%, P=0.012). Total fluoroscopic radiation time was significantly lower in the navigated group (P=0.038) whereas the mean dose area product was not significantly different (P=0.231). The time of the operative procedure was 23 min shorter after conventional HTO (P<0.001). Navigation systems provide intraoperative 3-dimensional real time control of the frontal, sagittal, and transverse axis and may increase the accuracy of open-wedge HTO. Future studies have to analyse the clinical effects of navigation on corrective osteotomies.

NK cells do not mediate renal injury in murine adriamycin nephropathy

In adriamycin nephropathy (AN), a model of chronic proteinuric renal injury, the absence of functional B and T cells with residual natural killer (NK) cells, and macrophages in severe combined immunodeficient (SCID) mice results in more severe disease than in immunocompetent mice. We have recently shown expression of the stimulatory NK cell molecule NKG2D and its ligand RAE-1 in the adriamycin (ADR) kidney. Therefore, we sought to determine the role of NK cells in AN. We used anti-asialo GM1 NK cell depletion in immunocompetent BALB/c mice with AN, and also compared AN in immunodeficient SCID mice and immunodeficient nonobese diabetic (NOD)-SCID mice (that have impaired NK cell function). The number of NK cells was increased in AN in BALB/c mice compared with normal controls. NK cell depletion or reduction of NK function in NOD-SCID mice did not affect the severity of disease. In both wild type and immunodeficient models, ADR upregulated RAE-1 in the kidney. High levels of Class I major histocompatibility complex molecules were found in both models of AN. In conclusion, NK cells do not play a significant role in AN.

New orthopaedic implant management tool for computer-assisted planning, navigation, and simulation: from implant CAD files to a standardized XML-based implant database

Computer-Assisted Orthopaedic Surgery (CAOS) has made much progress over the last 10 years. Navigation systems have been recognized as important tools that help surgeons, and various such systems have been developed. A disadvantage of these systems is that they use non-standard formalisms and techniques. As a result, there are no standard concepts for implant and tool management or data formats to store information for use in 3D planning and navigation. We addressed these limitations and developed a practical and generic solution that offers benefits for surgeons, implant manufacturers, and CAS application developers. We developed a virtual implant database containing geometrical as well as calibration information for orthopedic implants and instruments, with a focus on trauma. This database has been successfully tested for various applications in the client/server mode. The implant information is not static, however, because manufacturers periodically revise their implants, resulting in the deletion of some implants and the introduction of new ones. Tracking these continuous changes and keeping CAS systems up to date is a tedious task if done manually. This leads to additional costs for system development, and some errors are inevitably generated due to the huge amount of information that has to be processed. To ease management with respect to implant life cycle, we developed a tool to assist end-users (surgeons, hospitals, CAS system providers, and implant manufacturers) in managing their implants. Our system can be used for pre-operative planning and intra-operative navigation, and also for any surgical simulation involving orthopedic implants. Currently, this tool allows addition of new implants, modification of existing ones, deletion of obsolete implants, export of a given implant, and also creation of backups. Our implant management system has been successfully tested in the laboratory with very promising results. It makes it possible to fill the current gap that exists between the CAS system and implant manufacturers, hospitals, and surgeons.

Statistical Analysis for Haplotype-Based Matched Case-Control Studies

Using unphased genotype data, we studied statistical inference for association between a disease and a haplotype in matched case-control studies. Statistical inference for haplotype data is complicated due to ambiguity of genotype phases. An estimating equation-based method is developed for estimating odds ratios and testing disease-haplotype association. The method potentially can also be applied to testing haplotype-environment interaction. Simulation studies show that the proposed method has good performance. The performance of the method in the presence of departures from Hardy-Weinberg equilibrium is also studied.

Exploratory study on psychosocial impact of the severe acute respiratory syndrome (SARS) outbreak on Chinese students living in Japan

The aim of this study is to explore the impact of the 2003 SARS outbreak on Chinese students living in Japan. A cross-sectional study was conducted using a semi-structured questionnaire. The participants were recruited at multiple locations at the University of Tokyo, Japan. The results showed approximately 60% (96/161) of the respondents felt an impact of SARS on college life; they had experienced SARS-related fear, worry, depression as well as social discrimination and had taken SARS prevention measures for daily protection in Japan during the epidemic. The magnitude of the impact was associated with socio-demographic factors, including their age, specialty, area of previous residence in China and length of stay in Japan. The findings suggest that the SARS outbreak had a psychosocial impact on the Chinese students living in Japan, even though none of them had SARS. Social support tailored for these foreign students should be provided during such a disease outbreak.

Computer-assisted, fluoroscopy-based ventral spondylodesis of thoracolumbar fractures

OBJECTIVE

To design and evaluate a novel computer-assisted, fluoroscopy-based planning and navigation system for minimally invasive ventral spondylodesis of thoracolumbar fractures.

MATERIALS AND METHODS

Instruments and an image intensifier are tracked with the SurgiGATE navigation system (Praxim-Medivision). Two fluoroscopic images, one acquired from anterior-posterior (AP) direction and the other from lateral-medial (LM) direction, are used for the complete procedure of planning and navigation. Both of them are calibrated with a custom-made software to recover their projection geometry and to co-register them to a common patient reference coordinate system, which is established by attaching an opto-electronically trackable dynamic reference base (DRB) on the operated vertebra. A bi-planar landmark reconstruction method is used to acquire deep-seated anatomical landmarks such that an intraoperative planning of graft bed can be interactively done. Finally, surgical actions such as the placement of the stabilization devices and the formation of the graft bed using a custom-made chisel are visualized to the surgeon by superimposing virtual instrument representations onto the acquired images. The distance between the instrument tip and each wall of the planned graft bed are calculated on the fly and presented to the surgeon so that the surgeon could formalize the graft bed exactly according to his/her plan.

RESULTS

Laboratory studies on phantom and on 27 plastic vertebras demonstrate the high precision of the proposed navigation system. Compared with CT-based measurement, a mean error of 1.0 mm with a standard deviation of 0.1 mm was found.

CONCLUSIONS

The proposed computer assisted, fluoroscopy-based planning and navigation system promises to increase the accuracy and reliability of minimally invasive ventral spondylodesis of thoracolumbar fractures.

QSAR study on the Ah receptor-binding affinities of polyhalogenated dibenzo-p-dioxins using net atomic-charge descriptors and a radial basis neural network

A radial basis function neural network (RBFN) has been used to correlate Ah receptor-binding affinities of polychlorinated, polybrominated, and polychlorinated-brominated dibenzo-p-dioxins with molecular weight and eight net atomic charge descriptors. Support vector machine (SVM) and partial least square (PLS) regression models based on the same data set have also been built. Leave-one-out cross-validation was used to train the RBFN, SVM, and PLS models. For predicting Ah receptor-binding affinities, the RBFN model with a squared cross-validation correlation coefficient (q2) of 0.8818 outperforms the SVM and PLS models and also compares favorably with any other reported quantitative structure-activity relationship model based on the same activity data set. The significance of the RBFN model with net atomic charges as descriptors suggests that electrostatic and dispersion-type interactions play important roles in governing the Ah receptor binding of polychlorinated, polybrominated, and polychlorinated-brominated dibenzo-p-dioxins.

Tilt and rotation correction of acetabular version on pelvic radiographs

Anteroposterior pelvic radiographs are the gold standard of imaging for mechanical hip problems. However, correct interpretation is difficult because the projected morphologic features of the acetabulum and nearly all routinely used hip parameters depend on individual pelvic position, which can vary considerably during acquisition. We developed software that recreates the projected acetabular rim and the measured hip parameters as if obtained in a standardized orientation. The vertical and horizontal distances between two easy identifiable points were used as indicators of tilt and rotation. These points were the middle of the sacrococcygeal joint and the middle of the upper border of the symphyseal gap. Calibration of the indicators was achieved by means of serial pelvic radiographs of 20 cadaver pelves. Validation of tilt indicator in 100 patients and a theoretical error analysis revealed that for accurate tilt prediction an additional one-time lateral radiograph of the pelvis is mandatory. The computer-assisted method allows standardized evaluation of anatomic morphologic differences of femoral coverage (dysplasia, retroversion), making their clinical relevance for development of early osteoarthritis more valuable.

Tests for candidate-gene association using case-parents design

In the case-parents design for testing candidate-gene association, the conditional likelihood method based on genotype relative risks has been developed recently. A specific relation of the genotype relative risks is referred to as a genetic model. The efficient score tests have been used when the genetic model is correctly specified under the alternative hypothesis. In practice, however, it is usually not able to specify the genetic model correctly. In the latter situation, tests such as the likelihood ratio test (LRT) and the MAX3 (the maximum of the three score statistics for dominant, additive, and recessive models) have been used. In this paper, we consider the restricted likelihood ratio test (RLRT). For a specific genetic model, simulation results demonstrate that RLRT is asymptotically equivalent to the score test, and both are more powerful than the LRT. When the genetic model cannot be correctly specified, the simulation results show that RLRT is most robust and powerful in the situations we studied. MAX3 is the next most robust and powerful test. The TDT is the easiest statistic to compute, compared to MAX3 and RLRT. When the recessive model can be eliminated, it is also as robust and powerful as RLRT for other genetic models.

Metabolism-enhanced tumor localization by fluorescence imaging: in vivo animal studies

We present a high-sensitivity near-infrared optical imaging system for noninvasive cancer detection and localization based on molecularly labeled fluorescent contrast agents. This frequency-domain system utilizes the interferencelike pattern of diffuse photon density waves to achieve high detection sensitivity and localization accuracy for the fluorescent heterogeneity embedded inside the scattering media. A two-dimensional localization map is obtained through reflectance probe geometry and goniometric reconstruction. In vivo measurements with a tumor-bearing mouse model by use of the novel Cypate-mono-2-deoxy-glucose fluorescent contrast agent, which targets the enhanced tumor glycolysis, demonstrate the feasibility of detection of a 2-cm-deep subsurface tumor in the tissuelike medium, with a localization accuracy within 2-3 mm.

Prediction of n-octanol/water partition coefficients for polychlorinated dibenzo-p-dioxins using a general regression neural network

A general regression neural network was used for the first time to study quantitative structure and property relationships of organic pollutants to correlate and predict n-octanol/water partition coefficients of polychlorinated dibenzo- p -dioxins from their topological molecular descriptors. In total, 42 polychlorinated dibenzo- p -dioxins and dibenzo- p -dioxins were available for this study-42 polychlorinated dibenzo- p -dioxins and dibenzo- p -dioxins in the training data set and 41 polychlorinated dibenzo- p -dioxins in the test data set. Partial least squares regression, back propagation network and general regression neural network models were trained using the training data set, and the accuracy of the models obtained were examined by the use of leave-one-out cross-validation. For prediction of the n-octanol/water partition coefficient, the best method is the general regression neural network. With the test data set, the correlation coefficient, root mean square error and mean absolute relative error for the general regression neural network model are 0.9276, 0.22 and 2.79%, respectively. For describing the structure of polychlorinated dibenzo- p -dioxins, the topological molecular descriptors outperform the mobile order and disorder thermodynamic method.

Trend tests for case-control studies of genetic markers: power, sample size and robustness

The Cochran-Armitage trend test is commonly used as a genotype-based test for candidate gene association. Corresponding to each underlying genetic model there is a particular set of scores assigned to the genotypes that maximizes its power. When the variance of the test statistic is known, the formulas for approximate power and associated sample size are readily obtained. In practice, however, the variance of the test statistic needs to be estimated. We present formulas for the required sample size to achieve a prespecified power that account for the need to estimate the variance of the test statistic. When the underlying genetic model is unknown one can incur a substantial loss of power when a test suitable for one mode of inheritance is used where another mode is the true one. Thus, tests having good power properties relative to the optimal tests for each model are useful. These tests are called efficiency robust and we study two of them: the maximin efficiency robust test is a linear combination of the standardized optimal tests that has high efficiency and the MAX test, the maximum of the standardized optimal tests. Simulation results of the robustness of these two tests indicate that the more computationally involved MAX test is preferable.

Robust TDT-type candidate-gene association tests

In studies of association between genetic markers and a disease, the transmission disequilibrium test (TDT) has become a standard procedure. It was introduced originally as a test for linkage in the presence of association and can be used as a test for association under appropriate assumptions. The power of the TDT test for association between a candidate gene and disease depends on the underlying genetic model and the TDT is the optimal test if the additive model holds. Related methods have been obtained for a given mode of inheritance (e.g. dominant or recessive). Quite often, however, the true model is unknown and selection of a single method of analysis is problematic, since use of a test optimal for one genetic model usually leads to a substantial loss of power if another genetic model is the true one. The general approach of efficiency robustness has suggested two types of robust procedures, which we apply to TDT-type association tests. When the plausible range of alternative models is wide (e.g. dominant through recessive) our results indicate that the maximum (MAX) of several test statistics, each of which is optimal for quite different models, has good power under all genetic models. In situations where the set of possible models can be narrowed (e.g. dominant through additive) a simple linear combination also performs well. In general, the MAX has better power properties than the TDT for the study of candidate genes when the mode of inheritance is unknown.

Synthesis of beta-galactose-conjugated chlorins derived by enyne metathesis as galectin-specific photosensitizers for photodynamic therapy

A first report on the synthesis and biological evaluation of the beta-galactose-conjugated purpurinimides (a class of chlorins containing a six-membered fused imide ring system) as Gal-1 (galectin-1) recognized photosensitizers, prepared from purpurin-N-propargylimide via enyne metathesis, is discussed. On the basis of examination of the available crystal structure of the galectin-1 N-acetyllactose amine complex, it was considered that the chlorin-based photosensitizers could be introduced into a carbohydrate skeleton to expand the repertoire of the galectin-1-specific ligands. Preliminary molecular modeling analysis utilizing the modeled photosensitizers and the available crystal structures of galectin-carbohydrate complexes indicated that addition of the photosensitizer to the carbohydrate moiety at an appropriate position does not interfere with the galectin-carbohydrate recognition. Under similar drug and light doses, compared to the free purpurinimide analogue, the purpurinimides conjugated either with galactose or with lactose (Gal(beta1-4)-Glc) produced a considerable increase in photosensitizing efficacy in vitro. This indicates the possibility for development of a new class of specific photosensitizers for photodynamic therapy (PDT) based on recognition of a cellular receptor.