Neural network approaches to dynamic collision-free trajectory generation

In this paper, dynamic collision-free trajectory generation in a nonstationary environment is studied using biologically inspired neural network approaches. The proposed neural network is topologically organized, where the dynamics of each neuron is characterized by a shunting equation or an additive equation. The state space of the neural network can be either the Cartesian workspace or the joint space of multi-joint robot manipulators. There are only local lateral connections among neurons. The real-time optimal trajectory is generated through the dynamic activity landscape of the neural network without explicitly searching over the free space nor the collision paths, without explicitly optimizing any global cost functions, without any prior knowledge of the dynamic environment, and without any learning procedures. Therefore the model algorithm is computationally efficient. The stability of the neural network system is guaranteed by the existence of a Lyapunov function candidate. In addition, this model is not very sensitive to the model parameters. Several model variations are presented and the differences are discussed. As examples, the proposed models are applied to generate collision-free trajectories for a mobile robot to solve a maze-type of problem, to avoid concave U-shaped obstacles, to track a moving target and at the same to avoid varying obstacles, and to generate a trajectory for a two-link planar robot with two targets. The effectiveness and efficiency of the proposed approaches are demonstrated through simulation and comparison studies.

A solid phase extraction-liquid chromatographic-tandem mass spectrometry method for determination of concentrations of GDC-0941, a small molecule class I phosphatidylinositide 3-kinase inhibitor, to support clinical development

A solid phase extraction (SPE) liquid chromatographic-tandem mass spectrometry (LC-MS/MS) method for the determination of GDC-0941 concentrations in human plasma has been developed and validated to support clinical development. An Oasis MCX 10mg 96-well SPE plate was used to extract plasma samples (50 μL) and the resulting extracts were analyzed using reverse-phase chromatography and mass spectrometer coupled with a turbo-ionspray interface. The method was validated over the calibration curve range 0.500-500 ng/mL with linear regression and 1/x(2) weighting. Within-run relative standard deviation (%RSD) ranged from 1.5 to 11.5%, while the between-run %RSD varied from 0.0 to 4.4%. The accuracy ranged from 96.0% to 110.0% of nominal for within-run and 98.0% to 108.0% of nominal for between-run at all concentrations including the LLOQ quality control at 0.500 ng/mL. Extraction recovery of GDC-0941 was between 79.0% and 86.2%. Stability of GDC-0941 was established in human plasma for 602 days at -70 °C and 598 days at -20°C, respectively, and established in reconstituted sample extracts for 167 h when stored at room temperature. Internal standard normalized matrix factor was 1.1, demonstrating that the use of the stable-labeled internal standard GDC-0941-d(8) effectively compensated observed matrix effect and resulting in no adverse impact on the quality of the data produced. This assay was used for the determination of GDC-0941 human plasma concentrations over a sufficient time period to determine pharmacokinetic parameters at relevant clinical doses.

Location and type of mutation in the LIS1 gene do not predict phenotypic severity

BACKGROUND

Lissencephaly is a neuronal migration disorder leading to absent or reduced gyration and a broadened but poorly organized cortex. The most common form of lissencephaly is isolated, referred as classic or type 1 lissencephaly. Type 1 lissencephaly is mostly associated with a heterozygous deletion of the entire LIS1 gene, whereas intragenic heterozygous LIS1 mutations or hemizygous DCX mutations in males are less common.

METHODS

Eighteen unrelated patients with type 1 lissencephaly were clinically and genetically assessed. In addition, patients with subcortical band heterotopia (n = 1) or lissencephaly with cerebellar hypoplasia (n = 2) were included.

RESULTS

Fourteen new and seven previously described LIS1 mutations were identified. We observed nine truncating mutations (nonsense, n = 2; frameshift, n = 7), six splice site mutations, five missense mutations, and one in-frame deletion. Somatic mosaicism was assumed in three patients with partial subcortical band heterotopia in the occipital-parietal lobes or mild pachygyria. We report three mutations in exon 11, including a frameshift which extends the LIS1 protein, leading to type 1 lissencephaly and illustrating the functional importance of the WD domains at the C terminus. Furthermore, we present two patients with novel LIS1 mutations in exon 10 associated with lissencephaly with cerebellar hypoplasia type a.

CONCLUSION

In contrast to previous reports, our data suggest that neither type nor position of intragenic mutations in the LIS1 gene allows an unambiguous prediction of the phenotypic severity. Furthermore, patients presenting with mild cerebral malformations such as subcortical band heterotopia or cerebellar hypoplasia should be considered for genetic analysis of the LIS1 gene.

Vitamin A for treating measles in children

BACKGROUND

Measles is a major cause of childhood morbidity and mortality. Vitamin A deficiency is a recognized risk factor for severe measles infections. The World Health Organization (WHO) recommends administration of an oral dose of vitamin A (200,000 international units (IU), or 100,000 IU in infants) each day for two days to children with measles when they live in areas where vitamin A deficiency may be present.

OBJECTIVES

To determine whether vitamin A therapy, commenced after measles has been diagnosed, is beneficial in preventing mortality, pneumonia and other secondary complications in children.

SEARCH STRATEGY

We searched the Cochrane Central Register of Controlled Trials (CENTRAL) (The Cochrane Library Issue 1, 2005), MEDLINE (1966 to March 2005), EMBASE (1980 to December 2004) and looked for unpublished studies.

SELECTION CRITERIA

Only randomized controlled trials in which children with measles were given vitamin A or placebo along with standard treatment were considered.

DATA COLLECTION AND ANALYSIS

Studies were assessed independently by two authors. The analysis of dichotomous outcomes was done using the StatXact software and results expressed as relative risk (RR) with 95% confidence interval (CI). Subgroup analyses were carried out for dose, formulation, age, hospitalization and pneumonia-specific mortality. Weighted mean differences (WMD) with 95% CI were calculated for continuous outcomes.

MAIN RESULTS

There was no significant reduction in the risk of mortality in the vitamin A group when all the studies were pooled using the random-effects model (RR 0.70; 95% CI 0.42 to 1.15). Using two doses of vitamin A (200,000 IU) on consecutive days was associated with a reduction in the risk of mortality in children under the age of two years (RR 0.18; 95% CI 0.03 to 0.61) and a reduction in the risk of pneumonia-specific mortality (RR 0.33; 95% CI 0.08 to 0.92). There was no evidence that vitamin A in a single dose was associated with a reduced risk of mortality among children with measles. There was a reduction in the incidence of croup (RR 0.53; 95% CI 0.29 to 0.89) but no significant reduction in the incidence of pneumonia (RR 0.92; 95% CI 0.69 to 1.22) or diarrhoea (RR 0.80; 95% CI 0.27 to 2.34) with two doses.

AUTHORS' CONCLUSIONS

Although we found no overall significant reduction in mortality with vitamin A therapy for children with measles there was evidence that two doses were associated with a reduced risk of mortality and pneumonia-specific mortality in children under the age of two years. There were no trials that directly compared a single dose with two doses.

Method development and validation for quantitative determination of methadone enantiomers in human plasma by liquid chromatography/tandem mass spectrometry1

A high-throughput method for quantitative determination of methadone enantiomers in human plasma was developed and validated by liquid chromatography/tandem mass spectrometry. The effects of pH and of types and concentrations of mobile-phase modifiers on the enantioselectivity of (R)- and (S)-methadone were investigated on a Chiral-AGP column. A baseline separation of the enantiomers was achieved with a retention time of less than 5 min. Ionization suppression and other matrix effects were evaluated. Morphine, cocaine, 6-monoacetylmorphine, benzoylecgonine and ecgonine methyl ester did not interfere with the performance of the assay. The specificity, linearity, intra- and inter-assay precision and accuracy, and extraction recovery were fully evaluated. The method showed excellent reproducibility (overall coefficient of variance < 8%) and accuracy (overall bias < 2.7%) with a broad linear range. The enantiomers were stable in human plasma after five freeze-thaw cycles, under bench-top storage at room temperature (RT) for 6h, in the extract reconstitution solution at RT for 17 h, and in processed-extracts stored at RT for 142 h. This validated LC/MS/MS assay offers high-throughput and improved specificity, sensitivity, linear range and ruggedness over previously published methods and has been successfully applied to the analysis of clinical samples.

Biochemical characterization and antifungal activity of an endo-1,3-beta-glucanase of Paenibacillus sp. isolated from garden soil

A 44-kDa 1,3-beta-glucanase was purified from the culture medium of a Paenibacillus strain with a 28-fold increase in specific activity with 31% recovery. The purified enzyme preferentially catalyzes the hydrolysis of glucans with 1,3-beta-linkage and has an endolytic mode of action. The enzyme also showed binding activity to various insoluble polysaccharides including unhydrolyzable substrates such as xylan and cellulose. The antifungal activity of this Paenibacillus enzyme and a previously purified 1,3-beta-glucanase from Streptomyces sioyaensis were examined in this study. Both enzymes had the ability to damage the cell-wall structures of the growing mycelia of phytopathogenic fungi Pythium aphanidermatum and Rhizoctonic solani AG-4. Nonetheless, the Paenibacillus enzyme had a much stronger effect on inhibiting the growth of fungi tested.

Ionization enhancement in atmospheric pressure chemical ionization and suppression in electrospray ionization between target drugs and stable-isotope-labeled internal standards in quantitative liquid chromatography/tandem mass spectrometry

The phenomena of ionization suppression in electrospray ionization (ESI) and enhancement in atmospheric pressure chemical ionization (APCI) were investigated in selected-ion monitoring and selected-reaction monitoring modes for nine drugs and their corresponding stable-isotope-labeled internal standards (IS). The results showed that all investigated target drugs and their co-eluting isotope-labeled IS suppress each other's ionization responses in ESI. The factors affecting the extent of suppression in ESI were investigated, including structures and concentrations of drugs, matrix effects, and flow rate. In contrast to the ESI results, APCI caused seven of the nine investigated target drugs and their co-eluting isotope-labeled IS to enhance each other's ionization responses. The mutual ionization suppression or enhancement between drugs and their isotope-labeled IS could possibly influence assay sensitivity, reproducibility, accuracy and linearity in quantitative liquid chromatography/mass spectrometry (LC/MS) and liquid chromatography/tandem mass spectrometry (LC/MS/MS). However, calibration curves were linear if an appropriate IS concentration was selected for a desired calibration range to keep the response factors constant.

The helicase-like domain of plant potexvirus replicase participates in formation of RNA 5' cap structure by exhibiting RNA 5'-triphosphatase activity

Open reading frame 1 (ORF1) of potexviruses encodes a viral replicase comprising three functional domains: a capping enzyme at the N terminus, a putative helicase in the middle, and a polymerase at the C terminus. To verify the enzymatic activities associated with the putative helicase domain, the corresponding cDNA fragment from bamboo mosaic virus (BaMV) was cloned into vector pET32 and the protein was expressed in Escherichia coli and purified by metal affinity chromatography. An activity assay confirmed that the putative helicase domain has nucleoside triphosphatase activity. We found that it also possesses an RNA 5'-triphosphatase activity that specifically removes the gamma phosphate from the 5' end of RNA. Both enzymatic activities were abolished by the mutation of the nucleoside triphosphate-binding motif (GKS), suggesting that they have a common catalytic site. A typical m(7)GpppG cap structure was formed at the 5' end of the RNA substrate when the substrate was treated sequentially with the putative helicase domain and the N-terminal capping enzyme, indicating that the putative helicase domain is truly involved in the process of cap formation by exhibiting its RNA 5'-triphosphatase activity.

Functions of the conserved anionic amino acids and those interacting with the substrate phosphate group of phosphoglucose isomerase

Phosphoglucose isomerase catalyzes the isomerization between glucose 6-phosphate and fructose 6-phosphate in cytoplasm, and functions as autocrine motility factor and neuroleukin outside the cells. A phosphoglucose isomerase from Bacillus stearothermophilus (pgiA) was subjected to mutagenesis study to address the catalytic function of the conserved anionic residues and those probably interacting with the phosphate group of substrates. The results suggest that Glu290 works concertedly with His311 as a general acid-base pair to initiate the isomerization step, and Glu150 assists the base function of His311. The conserved loop structure consisting of Gly205-Gly206-Arg207 plays a critical role for the recognition of substrates.

Sequences at the 3' untranslated region of bamboo mosaic potexvirus RNA interact with the viral RNA-dependent RNA polymerase

The 3' untranslated region (UTR) of bamboo mosaic potexvirus (BaMV) genomic RNA was found to fold into a series of stem-loop structures including a pseudoknot structure. These structures were demonstrated to be important for viral RNA replication and were believed to be recognized by the replicase (C.-P. Cheng and C.-H. Tsai, J. Mol. Biol. 288:555-565, 1999). Electrophoretic mobility shift and competition assays have now been used to demonstrate that the Escherichia coli-expressed RNA-dependent RNA polymerase domain (Delta 893) derived from BaMV open reading frame 1 could specifically bind to the 3' UTR of BaMV RNA. No competition was observed when bovine liver tRNAs or poly(I)(C) double-stranded homopolymers were used as competitors, and the cucumber mosaic virus 3' UTR was a less efficient competitor. Competition analysis with different regions of the BaMV 3' UTR showed that Delta 893 binds to at least two independent RNA binding sites, stem-loop D and the poly(A) tail. Footprinting analysis revealed that Delta 893 could protect the sequences at loop D containing the potexviral conserved hexamer motif and part of the stem of domain D from chemical cleavage.

Characterization of the AdoMet-dependent guanylyltransferase activity that is associated with the N terminus of bamboo mosaic virus replicase

Bamboo mosaic virus (BaMV), a member of the potexvirus group, infects primarily members of the Bambusoideae. Open reading frame 1 (ORF1) of BaMV encodes a 155-kDa polypeptide that has long been postulated to be a replicase involved in the replication and formation of the cap structure at the 5' end of the viral genome. To identify and characterize the enzymatic activities associated with the N-terminal domain of the BaMV ORF1 protein, the intact replicase and two C-terminally truncated proteins were expressed in Saccharomyces cerevisiae. All three versions of BaMV ORF1 proteins could be radiolabeled by [alpha-(32)P]GTP, which is a characteristic of guanylyltransferase activity. The presence of S-adenosylmethionine (AdoMet) was essential for this enzymatic activity. Thin-layer chromatography analysis suggests that the radiolabeled moiety linked to the N-terminal domain of the BaMV ORF1 protein is m(7)GMP. The N-terminal domain also exhibited methyltransferase activity that catalyzes the transfer of the [(3)H]methyl group from AdoMet to GTP or guanylylimidodiphosphate. Therefore, during cap structure formation in BaMV, methylation of GTP may occur prior to transguanylation as for alphaviruses and brome mosaic virus. This study establishes the association of RNA capping activity with the N-terminal domain of the replicase of potexviruses and further supports the idea that the reaction sequence of RNA capping is conserved throughout the alphavirus-like superfamily of RNA viruses.

The crystal structure of phosphoglucose isomerase/autocrine motility factor/neuroleukin complexed with its carbohydrate phosphate inhibitors suggests its substrate/receptor recognition

Phosphoglucose isomerase catalyzes the reversible isomerization of glucose 6-phosphate to fructose 6-phosphate. In addition, phosphoglucose isomerase has been shown to have functions equivalent to neuroleukin, autocrine motility factor, and maturation factor. Here we present the crystal structures of phosphoglucose isomerase complexed with 5-phospho-D-arabinonate and N-bromoacetylethanolamine phosphate at 2.5- and 2.3-A resolution, respectively. The inhibitors bind to a region within the domains' interface and interact with a histidine residue (His(306)) from the other subunit. We also demonstrated that the inhibitors not only affect the enzymatic activity of phosphoglucose isomerase, but can also inhibit the autocrine motility factor-induced cell motility of CT-26 mouse colon tumor cells. These results indicate that the substrate and the receptor binding sites of phosphoglucose isomerase and autocrine motility factor are located within close proximity to each other. Based on these two complex structures, together with biological and biochemical results, we propose a possible isomerization mechanism for phosphoglucose isomerase.

Validation of biomarkers in humans exposed to benzene: urine metabolites

BACKGROUND

The present study was conducted among Chinese workers employed in glue- and shoe-making factories who had an average daily personal benzene exposure of 31+/-26 ppm (mean+/-SD). The metabolites monitored were S-phenylmercapturic acid (S-PMA), trans, trans-muconic acid (t,t-MA), hydroquinone (HQ), catechol (CAT), 1,2, 4-trihydroxybenzene (benzene triol, BT), and phenol.

METHODS

S-PMA, t,t-MA, HQ, CAT, and BT were quantified by HPLC-tandem mass spectrometry. Phenol was measured by GC-MS.

RESULTS

Levels of benzene metabolites (except BT) measured in urine samples collected from exposed workers at the end of workshift were significantly higher than those measured in unexposed subjects (P < 0.0001). The large increases in urinary metabolites from before to after work strongly correlated with benzene exposure. Concentrations of these metabolites in urine samples collected from exposed workers before work were also significantly higher than those from unexposed subjects. The half-lives of S-PMA, t,t-MA, HQ, CAT, and phenol were estimated from a time course study to be 12.8, 13.7, 12.7, 15.0, and 16.3 h, respectively.

CONCLUSIONS

All metabolites, except BT, are good markers for benzene exposure at the observed levels; however, due to their high background, HQ, CAT, and phenol may not distinguish unexposed subjects from workers exposed to benzene at low ambient levels. S-PMA and t,t-MA are the most sensitive markers for low level benzene exposure.

An efficient neural network approach to dynamic robot motion planning

In this paper, a biologically inspired neural network approach to real-time collision-free motion planning of mobile robots or robot manipulators in a nonstationary environment is proposed. Each neuron in the topologically organized neural network has only local connections, whose neural dynamics is characterized by a shunting equation. Thus the computational complexity linearly depends on the neural network size. The real-time robot motion is planned through the dynamic activity landscape of the neural network without any prior knowledge of the dynamic environment, without explicitly searching over the free workspace or the collision paths, and without any learning procedures. Therefore it is computationally efficient. The global stability of the neural network is guaranteed by qualitative analysis and the Lyapunov stability theory. The effectiveness and efficiency of the proposed approach are demonstrated through simulation studies.