PASSPORT-seq: A Novel High-Throughput Bioassay to Functionally Test Polymorphisms in Micro-RNA Target Sites

Next-generation sequencing (NGS) studies have identified large numbers of genetic variants that are predicted to alter miRNA-mRNA interactions. We developed a novel high-throughput bioassay, PASSPORT-seq, that can functionally test in parallel 100s of these variants in miRNA binding sites (mirSNPs). The results are highly reproducible across both technical and biological replicates. The utility of the bioassay was demonstrated by testing 100 mirSNPs in HEK293, HepG2, and HeLa cells. The results of several of the variants were validated in all three cell lines using traditional individual luciferase assays. Fifty-five mirSNPs were functional in at least one of three cell lines (FDR ≤ 0.05); 11, 36, and 27 of them were functional in HEK293, HepG2, and HeLa cells, respectively. Only four of the variants were functional in all three cell lines, which demonstrates the cell-type specific effects of mirSNPs and the importance of testing the mirSNPs in multiple cell lines. Using PASSPORT-seq, we functionally tested 111 variants in the 3' UTR of 17 pharmacogenes that are predicted to alter miRNA regulation. Thirty-three of the variants tested were functional in at least one cell line

Mobile camera-space manipulation

The invention is a method of using computer vision to control systems consisting of a combination of holonomic and nonholonomic degrees of freedom such as a wheeled rover equipped with a robotic arm, a forklift, and earth-moving equipment such as a backhoe or a front-loader. Using vision sensors mounted on the mobile system and the manipulator, the system establishes a relationship between the internal joint configuration of the holonomic degrees of freedom of the manipulator and the appearance of features on the manipulator in the reference frames of the vision sensors. Then, the system, perhaps with the assistance of an operator, identifies the locations of the target object in the reference frames of the vision sensors. Using this target information, along with the relationship described above, the system determines a suitable trajectory for the nonholonomic degrees of freedom of the base to follow towards the target object. The system also determines a suitable pose or series of poses for the holonomic degrees of freedom of the manipulator. With additional visual samples, the system automatically updates the trajectory and final pose of the manipulator so as to allow for greater precision in the overall final position of the system

Assessing the Contribution of Heme-Iron Acquisition to Staphylococcus aureus Pneumonia Using Computed Tomography

S. aureus acquires heme-iron using the iron regulated surface determinant (Isd) system and the heme transport system (Hts) with both systems showing critical importance in systemic models of infection. The contribution of heme-iron acquisition to staphylococcal pneumonia has not yet been elucidated. In addition, the use of computed tomography (CT) for the evaluation of staphylococcal pneumonia and its correlation to pathologic examination of infected lung tissue has not been performed to date. We have applied CT-based imaging to a murine model of staphylococcal pneumonia to determine the virulence contribution of heme-iron acquisition through the Hts and Isd systems.Mice were intranasally inoculated with approximately 1.0 x 10(8) colony forming units (CFU) of S. aureus. Lungs from mice infected with wild type S. aureus or strains deficient in isdB and isdH (DeltaisdBH) or htsA and isdE (DeltahtsADeltaisdE) were harvested at 24 hours. Histology, radiographic appearance by computed tomography (CT), percent mortality and bacterial burden were evaluated. Infection with S. aureus DeltaisdBH and DeltahtsADeltaisdE did not result in a statistically significant difference in mortality or bacterial burden as compared to controls. CT imaging of infected mice also did not reveal an appreciable difference between the various strains when compared to wild type, but did correlate with pathologic findings of pneumonia. However, a systemic model of infection using the DeltahtsADeltaisdE strain revealed a statistically significant decrease in bacterial burden in the lung, heart and kidneys.The development of staphylococcal pneumonia in this murine model is not dependent on hemoglobin binding or heme-iron uptake into S. aureus. However, this model does reveal that heme-iron acquisition contributes to the pathogenesis of systemic staphylococcal infections. In addition, CT imaging of murine lungs is an attractive adjunct to histologic analysis for the confirmation and staging of pneumonia

Autonomous Robust Skill Generation Using Reinforcement Learning with Plant Variation

This paper discusses an autonomous space robot for a truss structure assembly using some reinforcement learning. It is difficult for a space robot to complete contact tasks within a real environment, for example, a peg-in-hole task, because of error between the real environment and the controller model. In order to solve problems, we propose an autonomous space robot able to obtain proficient and robust skills by overcoming error to complete a task. The proposed approach develops skills by reinforcement learning that considers plant variation, that is, modeling error. Numerical simulations and experiments show the proposed method is useful in real environments

Dispersive properties of quasi-phase-matched optical parametric amplifiers

The dispersive properties of non-degenerate optical parametric amplification in quasi-phase-matched (QPM) nonlinear quadratic crystals with an arbitrary grating profile are theoretically investigated in the no-pump-depletion limit. The spectral group delay curve of the amplifier is shown to be univocally determined by its spectral power gain curve through a Hilbert transform. Such a constraint has important implications on the propagation of spectrally-narrow optical pulses through the amplifier. In particular, it is shown that anomalous transit times, corresponding to superluminal or even negative group velocities, are possible near local minima of the spectral gain curve. A possible experimental observation of such effects using a QPM Lithium-Niobate crystal is suggested.Comment: submitted for publicatio

Medication Exposure Patterns in Primary Care Patients Prescribed Pharmacogenetically Actionable Opioids

Current approaches to assessing medication exposure fail to capture the complexity of the phenomenon and the context in which it occurs. This study’s purpose was to develop a typology of subgroups of patients who share common patterns of medication exposure. To create the typology, we used an exemplar sample of 30 patients in a large public healthcare system who had been prescribed the pharmacogenetically actionable opioids codeine or tramadol. Data related to medication exposure were drawn from large data repositories. Using a person-oriented qualitative approach, eight subgroups of patients who shared common patterns of medication exposure were identified. The subgroups had one of five opioid prescription patterns (i.e., singular, episodic, switching, sustained, multiplex), and one of three types of primary foci of medical care (i.e., pain, comorbidities, both). The findings reveal medication exposure patterns that are dynamic, multidimensional, and complex, and the typology offers an innovative approach to assessing medication exposure

CYP2D6 drug-gene and drug-drug-gene interactions among patients prescribed pharmacogenetically actionable opioids

Purpose When codeine and tramadol are used for pain management, it is imperative that nurses are able to assess for potential drug-gene and drug-drug-gene interactions that could adversely impact drug metabolism and ultimately pain relief. Both drugs are metabolized through the CYP2D6 metabolic pathway which can be affected by medications as well the patient's own pharmacogenotype. The purpose of this brief report is to identify drug-gene and drug-drug-gene interactions in 30 adult patients prescribed codeine or tramadol for pain. Methods We used three data sources: (1) six months of electronic health record data on the number and types of medications prescribed to each patient; (2) each patient's CYP2D6 pharmacogenotype, and (3) published data on known CYP2D6 gene-drug and drug-drug-gene interactions. Results Ten patients (33%) had possible drug-gene or drug-drug-gene interactions. Five patients had CYP2D6 drug-gene interactions indicating they were not good candidates for codeine or tramadol. In addition, five patients had potential CYP2D6 drug-drug-gene interactions with either codeine or tramadol. Conclusion Our findings from this exploratory study underscores the importance of assessing and accounting for drug-gene and drug-drug-gene interactions in patients prescribed codeine or tramadol

Hacking commercial quantum cryptography systems by tailored bright illumination

The peculiar properties of quantum mechanics allow two remote parties to communicate a private, secret key, which is protected from eavesdropping by the laws of physics. So-called quantum key distribution (QKD) implementations always rely on detectors to measure the relevant quantum property of single photons. Here we demonstrate experimentally that the detectors in two commercially available QKD systems can be fully remote-controlled using specially tailored bright illumination. This makes it possible to tracelessly acquire the full secret key; we propose an eavesdropping apparatus built of off-the-shelf components. The loophole is likely to be present in most QKD systems using avalanche photodiodes to detect single photons. We believe that our findings are crucial for strengthening the security of practical QKD, by identifying and patching technological deficiencies.Comment: Revised version, rewritten for clarity. 5 pages, 5 figures. To download the Supplementary information (which is in open access), go to the journal web site at http://dx.doi.org/10.1038/nphoton.2010.21

Anxiogenic CO2 Stimulus Elicits Exacerbated Hot Flash-like Responses in a Rat Menopause Model and Hot Flashes in Menopausal Women

Objective Since longitudinal studies determined that anxiety is a strong risk factor for hot flashes, we hypothesized that an anxiogenic stimulus that signals air hunger (hypercapnic, normoxic gas) would trigger an exacerbated hot flash-associated increase in tail skin temperature (TST) in a rat ovariectomy (OVEX) model of surgical menopause and hot flashes in symptomatic menopausal women. We also assessed TST responses in OVEX serotonin transporter (SERT)+/− rats that models a common polymorphism that is associated with increased climacteric symptoms in menopausal women and increases in anxiety traits. Methods OVEX and sham-OVEX rats (initial experiment) and wildtype and SERT+/− OVEX rats (subsequent experiment) were exposed to a 5 min infusion of 20%CO2 normoxic gas while measuring TST. Menopausal women were given brief 20% and 35%CO2 challenges, and hot flashes were self-reported and objectively verified. Results Compared to controls, OVEX rats had exacerbated increases in TST, and SERT+/− OVEX rats had prolonged TST increases following CO2. Most women reported mild/moderate hot flashes after CO2 challenges, and the hot flash severity to CO2 was positively correlated with daily hot flash frequency. Conclusions The studies demonstrate that this anxiogenic stimulus is capable of inducing cutaneous vasomotor responses in OVEX rats, and eliciting hot flashes in menopausal women. In rats, the severity of the response was mediated by loss of ovarian function and increased anxiety traits (SERT+/−), and, in women, by daily hot flash frequency. These findings may provide insights into anxiety related triggers and genetic risk factors for hot flashes in thermoneutral environments

Age-Related Changes in MicroRNA Expression and Pharmacogenes in Human Liver

Developmental changes in the liver can significantly impact drug disposition. Due to the emergence of microRNAs (miRNAs) as important regulators of drug disposition gene expression, we studied age-dependent changes in miRNA expression. Expression of 533 miRNAs was measured in 90 human liver tissues (fetal, pediatric [1-17 years], and adult [28-80 years]; n = 30 each). In all, 114 miRNAs were upregulated and 72 were downregulated from fetal to pediatric, and 2 and 3, respectively, from pediatric to adult. Among the developmentally changing miRNAs, 99 miRNA-mRNA interactions were predicted or experimentally validated (e.g., hsa-miR-125b-5p-CYP1A1; hsa-miR-34a-5p-HNF4A). In human liver samples (n = 10 each), analyzed by RNA-sequencing, significant negative correlations were observed between the expression of >1,000 miRNAs and mRNAs of drug disposition and regulatory genes. Our data suggest a mechanism for the marked changes in hepatic gene expression between the fetal and pediatric developmental periods, and support a role for these age-dependent miRNAs in regulating drug disposition