Multiple loci in silico mapping in inbred lines

The in silico mapping (ISM) technique and its extension represent major advances for novel gene discovery in germplasm resources of inbred lines. However, the techniques suffer from a relatively high false-positive rate (FPR) and they do not consider the effect of linkage disequilibrium (LD) markers around the identified quantitative trait locus (QTL). In addition, it has not yet been established whether it is optimal to use absolute trait differences as the response variable. To address these problems, this article presents the multiple loci ISM (MLISM) approach, which uses all markers on the entire genome, along with a penalized maximum likelihood. The method proposed here was verified by a series of simulation experiments with a maize pedigree population of inbred lines of known ancestry. Results from the simulated studies show that the best response variable is the trait product. The MLISM FPR is substantially decreased and the proportion of the number of false QTL to the number of LD markers around the identified QTL is adequately reduced. The MLISM method, with the trait product as the response variable, is an improvement on the existing methods for novel QTL mapping in germplasm resources of inbred lines.

Profiling of receptor tyrosine kinases (RTK) activation in circulating tumor cells (CTCs) in metastatic tumors using proximity mediated microarray immunoassay

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Background: The abnormal activation of HER1 and HER2 has been linked to various types of cancer progression, and the changes in their expression status between primary tumor and CTCs have been reported to occur at a significant frequency. Methods for detecting HER1/HER2 phosphorylation in serially collected CTCs may provide valuable insight into the overall disease profile shift, and therefore lead to better selection of therapy combination for individual patient. Methods: A triple-antibody-enzyme-channeling multiplexed protein microarray platform has been developed to detect the phosphorylation on target molecules. It utilizes a unique immuno-complex formation via co-localization of two detector enzyme-conjugated-antibodies once target proteins are captured on the microarray-surface. The channeling events between two detector enzymes in proximity enabled profiling of the RTKs with a single-cell level sensitivity. The simultaneous binding of three different types of target specific antibodies for signal amplification results in extremely high assay specificity. In order to validate the method on clinical samples, CTCs from 75 cancer patients (stage 3/4) on various therapy regimens were analyzed. Results: We identified 6 patients (8%) with activated HER1, 6 patients (8%) with activated HER2 and 14 (18.5%) patients with dual RTK activation in their CTCs from various types of metastatic cancer. 25 samples from normal subjects showed no detectable HER1/HER2 activation. We also observed discrepancies between HER2 activation status in CTCs and their corresponding primary HER2-IHC status among breast cancer patients. CTCs with activated-HER2 were found in 6 out of 16 (38%) patients with HER2-negative primary breast cancer. In addition, 2 out of 5 HER2-positive breast cancer patients had CTCs with no apparent HER2-activation. Conclusions: The multiplexed-proximity mediated immunoassay successfully detected the activation of RTKs in CTCs isolated from various cancer patients. As CTCs found in metastatic stage represent the most aggressive invading cell population, serial CTC-profiling can lead to better therapy selection/adjustment and disease/treatment monitoring as there are available options to choose appropriate kinase inhibitors for RTK-targeted therapies.

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Quantitative trait loci for non-race-specific, high-temperature adult-plant resistance to stripe rust in wheat cultivar Express

Wheat cultivar Express has durable, high-temperature adult-plant (HTAP) resistance to stripe rust (Puccinia striiformis f. sp. tritici). To elucidate the genetic basis of the resistance, Express was crossed with 'Avocet Susceptible' (AVS). A mapping population of 146 F(5) recombinant inbred lines (RILs) was developed using single-seed descent. The RILs were evaluated at two sites near Pullman in eastern Washington and one site near Mount Vernon in western Washington in 2005, and were evaluated near Pullman in 2006 under natural stripe rust infection of predominant races virulent on seedlings of Express. Infection type (IT) and disease severity (DS) were recorded three times for each line during each growing season. The DS data were used to calculate relative area under the disease progress curve (rAUDPC) values. Both IT and rAUDPC data showed continuous distributions, indicating that the Express HTAP resistance was controlled by quantitative trait loci (QTL). Resistance gene analog polymorphism (RGAP) and simple sequence repeat (SSR) techniques were used to map the HTAP resistance QTL. Three QTL were detected with significant additive effects, explaining 49.5-69.6% of the phenotypic variation for rAUDPC. Two of the QTL explained 30.8-42.7% of the phenotypic variation for IT. The three QTL were mapped to wheat chromosomes 6AS, 3BL and 1BL, and were designated as QYrex.wgp-6AS, QYrex.wgp-3BL and QYrex.wgp-1BL, respectively. QYrex.wgp-6AS and QYrex.wgp-3BL, which had higher effects than QYrex.wgp-1BL, were different from previously reported QTL/genes for adult-plant resistance. Markers Xgwm334-Xwgp56 and Xgwm299-Xwgp66 flanking the two major QTL were highly polymorphic in various wheat genotypes, suggesting that these markers are useful in marker-assisted selection.

Statin use is associated with lower risk of atrial fibrillation in women with coronary disease: the HERS trial

OBJECTIVE

To determine the efficacy of statin treatment in atrial fibrillation (AF) prevention in women.

DESIGN

Cohort study using data obtained in the Heart and Estrogen/Progestin Replacement Study (HERS).

SETTING

Secondary analysis of a multicentre, randomised controlled clinical trial.

PATIENTS

2673 Postmenopausal women with coronary disease.

MAIN OUTCOME MEASURES

AF prevalence at baseline and incident AF over a mean follow-up of 4.1 years.

RESULTS

88 Women with AF were identified: 29 at baseline and 59 during follow-up. Women with AF were significantly less likely to be taking a statin at study enrollment than those without AF (22% vs 37%, p = 0.003). Baseline statin use was associated with a 65% lower odds of having AF at baseline after controlling for age, race, history of myocardial infarction or revascularisation and history of heart failure (odds ratio 0.35, 95% confidence interval (CI) 0.13 to 0.93, p = 0.04). The risk of developing AF during the study among those free from AF at baseline, adjusted for the same covariates, was 55% less for those receiving statin treatment (hazard ratio 0.45, 95% CI 0.26 to 0.78, p = 0.004).

CONCLUSIONS

Statin treatment is associated with a lower prevalence and incidence of AF after adjustment for potential confounders in postmenopausal women with coronary disease.

Quantitative trait loci for non-race-specific, high-temperature adult-plant resistance to stripe rust in wheat cultivar Express

Wheat cultivar Express has durable, high-temperature adult-plant (HTAP) resistance to stripe rust (Puccinia striiformis f. sp. tritici). To elucidate the genetic basis of the resistance, Express was crossed with 'Avocet Susceptible' (AVS). A mapping population of 146 F(5) recombinant inbred lines (RILs) was developed using single-seed descent. The RILs were evaluated at two sites near Pullman in eastern Washington and one site near Mount Vernon in western Washington in 2005, and were evaluated near Pullman in 2006 under natural stripe rust infection of predominant races virulent on seedlings of Express. Infection type (IT) and disease severity (DS) were recorded three times for each line during each growing season. The DS data were used to calculate relative area under the disease progress curve (rAUDPC) values. Both IT and rAUDPC data showed continuous distributions, indicating that the Express HTAP resistance was controlled by quantitative trait loci (QTL). Resistance gene analog polymorphism (RGAP) and simple sequence repeat (SSR) techniques were used to map the HTAP resistance QTL. Three QTL were detected with significant additive effects, explaining 49.5-69.6% of the phenotypic variation for rAUDPC. Two of the QTL explained 30.8-42.7% of the phenotypic variation for IT. The three QTL were mapped to wheat chromosomes 6AS, 3BL and 1BL, and were designated as QYrex.wgp-6AS, QYrex.wgp-3BL and QYrex.wgp-1BL, respectively. QYrex.wgp-6AS and QYrex.wgp-3BL, which had higher effects than QYrex.wgp-1BL, were different from previously reported QTL/genes for adult-plant resistance. Markers Xgwm334-Xwgp56 and Xgwm299-Xwgp66 flanking the two major QTL were highly polymorphic in various wheat genotypes, suggesting that these markers are useful in marker-assisted selection.

Molecular mapping of genes for race-specific overall resistance to stripe rust in wheat cultivar Express

'Express', a hard red spring wheat cultivar that has been widely grown in the western United States, is used to differentiate races of Puccinia striiformis f. sp. tritici, the causal fungal pathogen of wheat stripe rust. To identify genes conferring race-specific, overall resistance to stripe rust, Express was crossed with 'Avocet S'. The parents and F(1), F(2), F(3) and F(5) populations were tested with races PST-1, PST-21, PST-43, and PST-45 of P. striiformis f. sp. tritici in the seedling stage under controlled greenhouse conditions. Two dominant genes for resistance to stripe rust were identified, one conferring resistance to PST-1 and PST-21, and the other conferring resistance to all four races. Linkage groups were constructed for the resistance genes using 146 F(5) lines to establish resistance gene analog and chromosome-specific simple sequence repeat marker polymorphisms. The gene for resistance to races PST-1 and PST-21 was mapped on the long arm of chromosome 1B, and that conferring resistance to all four races was mapped on the long arm of chromosome 5B. We temporarily designate the gene on 1BL as YrExp1 and the gene on 5BL as YrExp2. Polymorphism of at least one of the two markers flanking YrExp2 was detected in 91% of the 44 tested wheat genotypes, suggesting that they would be useful in marker-assisted selection for combining the gene with other resistance genes into many other wheat cultivars. Knowledge of these genes will be useful to understand recent virulence changes in the pathogen populations.

Silencing Livin gene expression to inhibit proliferation and enhance chemosensitivity in tumor cells

Livin, a novel member of the human inhibitors of apoptosis protein (IAP) family, plays an important role in tumor progression and occurrence by inhibiting cell apoptosis. It is selectively expressed in the most common human neoplasms and appears to be involved in tumor cell resistance to chemotherapeutic agents. To investigate its possibility as a therapeutic target for human malignancies, we established two genetically different stable tumor cell lines (LoVo and SPCA-1) and RNA interference (RNAi) technique was employed to downregulate Livin expression in two human tumor cell lines. The specific downregulation of Livin expression in tumor cell lines significantly inhibited in vitro cell proliferation and in vivo tumorigenicity. Furthermore, Livin knockdown led to cell arrest in the G(1)/G(0) phase of cell cycle, eventual apoptosis and chemosensitivity enhancement in tumor cells. All these results indicate that RNAi-mediated downregulation of Livin expression can lead to potent antitumor activity and chemosensitizing effects in human cancers.

Laparoscopically assisted versus open surgery for endometrial cancer--a meta-analysis of randomized controlled trials

There is no clear consensus on the advantages of laparoscopically assisted surgery (LAS) versus open surgery (OS) for endometrial cancer. The present study compared LAS versus OS for patients with endometrial cancer with regard to operative parameters and outcomes. A search of the PubMed, EMBASE, the China Biological Medicine Datadase (CBMdisc), Ovid, and the Cochrane Library identified four studies that met the inclusion criteria for data extraction. Estimates of effectiveness were performed using fixed- and random effects models. The effect was calculated as an odds ratio (OR) or weighted mean difference (WMD) with 95% confidence intervals (CIs). Level of significance was set at P < 0.05. Outcomes of 331 patients were studied. When randomized controlled trials were analyzed, OR for LAS was 0.34 (95% CI: 0.13, 0.89; P = 0.03) for postoperative complications and 0.14 (95% CI: 0.05, 0.39; P = 0.0002) for incidence of transfusion; and WMD for LAS was 263.58 mL (95% CI: 467.71, 59.45 mL; P = 0.01) for blood loss, 38.09 min (95% CI: 10.50, 65.68 min; P = 0.007) for operation time, and 3.35 days (95% CI: 3.84, 2.86 days; P < 0.00001) for hospital stay. There was no difference in patients in terms of recurrence and survival. The present study has shown that LAS was associated with fewer postoperative complications, lower incidence of transfusion, less blood loss, longer operation time, and shorter hospital stay. What's more, no significant difference was found in terms of recurrence and survival. When performed by suitably specialized surgeons in selected patients, it appears to be a better choice than OS.

Overcoming depolarizing resonances with dual helical partial Siberian snakes

Acceleration of polarized protons in the energy range of 5 to 25 GeV is challenging. In a medium energy accelerator, the depolarizing spin resonances are strong enough to cause significant polarization loss but full Siberian snakes cause intolerably large orbit excursions and are also not feasible since straight sections usually are too short. Recently, two helical partial Siberian snakes with double pitch design have been installed in the Brookhaven Alternating Gradient Synchrotron (AGS). With a careful setup of optics at injection and along the energy ramp, this combination can eliminate the intrinsic and imperfection depolarizing resonances otherwise encountered during acceleration to maintain a high intensity polarized beam in medium energy synchrotrons. The observation of partial snake resonances of higher than second order will also be described.

Decision Making in Fuzzy Discrete Event Systems1

The primary goal of the study presented in this paper is to develop a novel and comprehensive approach to decision making using fuzzy discrete event systems (FDES) and to apply such an approach to real-world problems. At the theoretical front, we develop a new control architecture of FDES as a way of decision making, which includes a FDES decision model, a fuzzy objective generator for generating optimal control objectives, and a control scheme using both disablement and enforcement. We develop an online approach to dealing with the optimal control problem efficiently. As an application, we apply the approach to HIV/AIDS treatment planning, a technical challenge since AIDS is one of the most complex diseases to treat. We build a FDES decision model for HIV/AIDS treatment based on expert's knowledge, treatment guidelines, clinic trials, patient database statistics, and other available information. Our preliminary retrospective evaluation shows that the approach is capable of generating optimal control objectives for real patients in our AIDS clinic database and is able to apply our online approach to deciding an optimal treatment regimen for each patient. In the process, we have developed methods to resolve the following two new theoretical issues that have not been addressed in the literature: (1) the optimal control problem has state dependent performance index and hence it is not monotonic, (2) the state space of a FDES is infinite.

REW– exit-wave reconstruction and alignments for focus-variation high-resolution transmission electron microscopy images

A Windows-based computer program has been developed for exit-wave reconstruction and experimental high-resolution transmission electron microscopy image alignment. While the exit-wave reconstruction is performed mainly using the maximum-likelihood method, image alignments may be carried out using several algorithms, including the time-consuming but robust genetic algorithm.

Genetics and molecular mapping of genes for race-specific all-stage resistance and non-race-specific high-temperature adult-plant resistance to stripe rust in spring wheat cultivar Alpowa

Stripe rust, caused by Puccinia striiformis f. sp. tritici, is one of the most widespread and destructive wheat diseases worldwide. Growing resistant cultivars is the preferred control of the disease. The spring wheat cultivar 'Alpowa' has both race-specific, all-stage resistance and non-race-specific, high-temperature adult-plant (HTAP) resistances to stripe rust. To identify genes for the stripe rust resistances, Alpowa was crossed with 'Avocet Susceptible' (AVS). Seedlings of the parents, and F(1), F(2) and F(3) progeny were tested with races PST-1 and PST-21 of P. striiformis f. sp. tritici under controlled greenhouse conditions. Alpowa has a single partially dominant gene, designated as YrAlp, conferring all-stage resistance. Resistance gene analog polymorphism (RGAP) and simple sequence repeat (SSR) techniques were used to identify molecular markers linked to YrAlp. A linkage group of five RGAP markers and two SSR markers was constructed for YrAlp using 136 F(3) lines. Amplification of a set of nulli-tetrasomic Chinese Spring lines with RGAP markers Xwgp47 and Xwgp48 and the two SSR markers indicated that YrAlp is located on the short arm of chromosome 1B. To map quantitative trait loci (QTLs) for the non-race-specific HTAP resistance, the parents and 136 F(3) lines were tested at two sites near Pullman and one site near Mount Vernon, Washington, under naturally infected conditions. A major HTAP QTL was consistently detected across environments and was located on chromosome 7BL. Because of its chromosomal location and the non-race-specific nature of the HTAP resistance, this gene is different from previously described genes for adult-plant resistance, and is therefore designated Yr39. The gene contributed to 64.2% of the total variation of relative area under disease progress curve (AUDPC) data and 59.1% of the total variation of infection type data recorded at the heading-flowering stages. Two RGAP markers, Xwgp36 and Xwgp45 with the highest R (2) values were closely linked to Yr39, should be useful for incorporation of the non-race-specific resistance gene into new cultivars and for combining Yr39 with other genes for durable and high-level resistance.

Discovering Classes of Strongly Equivalent Logic Programs

In this paper we apply computer-aided theorem discovery technique to discover theorems about strongly equivalent logic programs under the answer set semantics. Our discovered theorems capture new classes of strongly equivalent logic programs that can lead to new program simplification rules that preserve strong equivalence. Specifically, with the help of computers, we discovered exact conditions that capture the strong equivalence between a rule and the empty set, between two rules, between two rules and one of the two rules, between two rules and another rule, and between three rules and two of the three rules.

Ammonium exchange in aqueous solution using Chinese natural clinoptilolite and modified zeolite

In this study, the Chinese natural clinoptilolite (sample 1) was fused with sodium hydroxide prior to hydrothermal reaction, and it was transformed to modified zeolite Na-Y (sample 2). The uptake of ammonium ion from aqueous solutions in the concentration range 50-250 mg NH(4)(+)/l on to the two samples was compared and the equilibrium isotherms have been got. The influence of other cations present in water upon the ammonia uptake was also determined. The cations studied were potassium, calcium and magnesium. In all cases the anionic counterion present was chloride. The results showed that sample 2 exhibited much higher uptake capacity compared with sample 1. At the initial concentration of 250 mg NH(4)(+)/l, the ammonium ion uptake value of sample 2 was 19.29 mg NH(4)(+)g(-1) adsorbent, while sample 1 was only 10.49 mg NH(4)(+)g(-1) adsorbent. For the natural clinoptilolite, the effect of the metal ions suggested an order of preference K(+)>Ca(2+)>Mg(2+). These contrasted with the modified zeolite, where the order appeared to be Mg(2+)>Ca(2+)>K(+).

FEM model for evaluating buttock tissue response under sitting load

Development of a model for evaluating tissue compression during sitting has been hampered by limitation of implementing the anatomical and mechanical parameters of the various layers of tissue. This study proposes a new method to setup and validate a finite element model for buttock tissue to evaluate the tissue response under external sitting load. Multi-layer tissue deformation was measured with ultrasound imaging under simulated sitting load, applied and monitored through an indenter which integrates ultrasound probe and force/pressure sensors. Subject-specific FE model can then be setup and validated. Pilot test of this model revealed that the highest peak stress was found in the vicinity of the ischial tuberosity and the greatest deformation seen in the muscle layer. The authors conclude that this new method allows accurate multi-layer tissue deformation be obtained under close to real sitting load, therefore, provides a better way to evaluate tissue response to external sitting load for seated individuals in a true and subject-specific fashion, which may provide helpful information to improve the sitting comfort and prevent pressure ulcers in wheelchair bound individuals.

Reducing whole-body vibration of vehicle drivers with a new sitting concept

A new car seat design, which allows the back part of the seat (BPS) to lower down while a protruded cushion supports the lumbar spine, was quantitatively tested to determine its effectiveness in reducing whole-body vibration (WBV) in automobile drivers. Results on 12 drivers show that, by reducing contact between the seat and the ischial tuberosities (TTs), the new seating design reduced both contact pressure and amplitude of harmful vibrations transmitted through the body. Significant reduction of WBV, in terms of RMS and VDV, was found as large as 30% by this seating design (P < 0.05), especially at lumbar spine region. This reduction in WBV allows more sustained driving than permitted by conventional seating devices, by around 2 hours daily, before reaching harmful WBV levels. The new seating design also promotes improved posture by restoring normal spinal curvature. Such seating devices, implemented in cars, buses, large trucks, and other high-vibration vehicles, may effectively reduce the risk of musculoskeletal disorders among long term drivers.

Diffusion tensor tractography-based group mapping of the pyramidal tract in relapsing-remitting multiple sclerosis patients

BACKGROUND AND PURPOSE

Many studies have reported abnormal changes in relapsing-remitting multiple sclerosis (RRMS) by histogram and region-of-interest-based methods by using diffusion tenor imaging. However, there are few studies on specific white matter fiber tracts of RRMS. Our study sought to use diffusion tensor tractography-based group mapping to investigate the presence of abnormal diffusion in the normal-appearing pyramidal tract (PYT) of RRMS and its possible mechanism.

METHODS

A PYT probability map was first constructed from data on 20 healthy patients based on the deterministic-based tractography method. The PYT probability map was then applied to 29 RRMS patients to calculate diffusion indices of the PYT. In this study, 4 quantitative indices-fractional anisotropy (FA), directionally averaged diffusion coefficient (D(av)), axial diffusion coefficient (lambda(1)), and radial diffusion coefficient (lambda(23))-were used to characterize the abnormal diffusion.

RESULTS

Compared with healthy controls, RRMS patients had a significantly higher D(av) and lambda(23) but a lower FA and a trend toward a lower lambda(1) in the normal-appearing PYT. In RRMS patients, PYT lesions had a significantly higher lambda(23) and a lower FA, but there were no differences for D(av) and lambda(1) when compared with the normal-appearing PYT. Moreover, the diffusion indices derived from the normal-appearing PYT were significantly correlated with PYT lesion volumes by using the Spearman correlation analysis.

CONCLUSION

Our findings confirm the presence of abnormal diffusion in the normal-appearing PYT of RRMS patients and suggest that wallerian degeneration might be its mechanism.

Modulation of the oxidative stress and nuclear factor kappaB activation by theaflavin 3,3'-gallate in the rats exposed to cerebral ischemia-reperfusion

The major pathobiological mechanisms of IR injury include excitotoxicity, oxidative stress, and inflammation. TF3, a major constituent of black tea, possesses biological functions such as anti-oxidative and anti-inflammatory activities. The purpose of this study was to verify the neuronal protective potential of TF3 and its mechanisms against cerebral IR injury in rats. TF3 administration (10 and 20 mg.kg-1) ameliorated the infarct volume. TF3 also decreased the content of MDA and NO. TF3 significantly increased the activity of SOD and GSH-Px, which were reduced by IR injury. Administration of TF3 decreased mRNA and protein expression of COX-2 and iNOS. DNA binding and Western blotting revealed an increase in NF-kappaB activation and IkappaB depletion in IR brain tissue. Pretreatment with TF3 markedly inhibited IRinduced increase in nuclear localization of NF-kappaB, and preserved IkappaB in the cytoplasm. The results show that TF3 exerts protective effects against cerebral IR injury by reducing oxidative stress and modulating the NF-kappaB activation.