Reciprocity breaking during nonlinear propagation of adapted beams through random media

Adaptive optics (AO) systems rely on the principle of reciprocity, or symmetry with respect to the interchange of point sources and receivers. These systems use the light received from a low power emitter on or near a target to compensate phase aberrations acquired by a laser beam during linear propagation through random media. If, however, the laser beam propagates nonlinearly, reciprocity is broken, potentially undermining AO correction. Here we examine the consequences of this breakdown, providing the first analysis of AO applied to high peak power laser beams. While discussed for general random and nonlinear media, we consider specific examples of Kerr-nonlinear, turbulent atmosphere.

Acculturation of Second- and Third-Generation Mexican American Children

Measures of field independence, locus of control, self-esteem, and school achievement were obtained for 144 Anglo American and Mexican American fourth, fifth, and sixth grade children from a "traditional" Mexican American community. From second to third generation, Mexican American children increasingly approach Anglo American norms with respect to field independence, reading achievement, and math achievement. Opposite trends were obtained with regard to self-esteem; no significant effects of generational level were found with regard to locus of control. Several possible explanations of the apparent paradox of decreasing self-esteem alongside increasing achievement levels with generation are suggested.

Locus of Control, Self-Esteem, and Field Independence as Predictors of School Achievement Among Anglo American and Mexican American Children

The relation of measures of locus of control, self-esteem, and field independence to the reading and math achievement of 170 Mexican American and Anglo American children is explored. The Anglo American-Mexican American school achievement gap was confirmed, but no significant cultural difference on any personality variable was observed. The intercorrelations among the personality variables and between the personality variables and school achievement were greater among Mexican American children compared to Anglo American children, and the per sonality variables were also more highly related to school achievement for Mexican American children. This pattern of results is discussed as possibly due to (a) a greater impact of school achievement on personality for Mexican Americans; (b) personality differences as more important precursors of school achievement among Mexican Americans; (c) lack of cultural equivalence of meaning of the personality variables; and (d) grade as a mediating variable. Implications of the findings are discussed.

Using an incoherent target return to adaptively focus through atmospheric turbulence

A laser beam propagating to a remote target through atmospheric turbulence acquires intensity fluctuations. If the target is cooperative and provides a coherent return beam, the phase measured near the beam transmitter and adaptive optics, in principle, can correct these fluctuations. Generally, however, the target is uncooperative. In this case, we show that an incoherent return from the target can be used instead. Using the principle of reciprocity, we derive a novel relation between the field at the target and the returned field at a detector. We simulate an adaptive optics system that utilizes this relation to focus a beam through atmospheric turbulence onto a rough surface.

Atmospheric propagation and combining of high-power lasers

In this paper, we analyze beam combining and atmospheric propagation of high-power lasers for directed-energy (DE) applications. The large linewidths inherent in high-power fiber and slab lasers cause random phase and intensity fluctuations that occur on subnanosecond time scales. Coherently combining these high-power lasers would involve instruments capable of precise phase control and operation at rates greater than ∼10  GHz. To the best of our knowledge, this technology does not currently exist. This presents a challenging problem when attempting to phase lock high-power lasers that is not encountered when phase locking low-power lasers, for example, at milliwatt power levels. Regardless, we demonstrate that even if instruments are developed that can precisely control the phase of high-power lasers, coherent combining is problematic for DE applications. The dephasing effects of atmospheric turbulence typically encountered in DE applications will degrade the coherent properties of the beam before it reaches the target. Through simulations, we find that coherent beam combining in moderate turbulence and over multikilometer propagation distances has little advantage over incoherent combining. Additionally, in cases of strong turbulence and multikilometer propagation ranges, we find nearly indistinguishable intensity profiles and virtually no difference in the energy on the target between coherently and incoherently combined laser beams. Consequently, we find that coherent beam combining at the transmitter plane is ineffective under typical atmospheric conditions.

Ring test evaluation of the detection of influenza A virus in swine oral fluids by real-time reverse-transcription polymerase chain reaction and virus isolation

The probability of detecting influenza A virus (IAV) in oral fluid (OF) specimens was calculated for each of 13 assays based on real-time reverse-transcription polymerase chain reaction (rRT-PCR) and 7 assays based on virus isolation (VI). The OF specimens were inoculated with H1N1 or H3N2 IAV and serially diluted 10-fold (10(-1) to 10(-8)). Eight participating laboratories received 180 randomized OF samples (10 replicates × 8 dilutions × 2 IAV subtypes plus 20 IAV-negative samples) and performed the rRT-PCR and VI procedure(s) of their choice. Analysis of the results with a mixed-effect logistic-regression model identified dilution and assay as variables significant (P < 0.0001) for IAV detection in OF by rRT-PCR or VI. Virus subtype was not significant for IAV detection by either rRT-PCR (P = 0.457) or VI (P = 0.101). For rRT-PCR the cycle threshold (Ct) values increased consistently with dilution but varied widely. Therefore, it was not possible to predict VI success on the basis of Ct values. The success of VI was inversely related to the dilution of the sample; the assay was generally unsuccessful at lower virus concentrations. Successful swine health monitoring and disease surveillance require assays with consistent performance, but significant differences in reproducibility were observed among the assays evaluated.

Enhanced backscatter of optical beams reflected in turbulent air

Optical beams propagating through air acquire phase distortions from turbulent fluctuations in the refractive index. While these distortions are usually deleterious to propagation, beams reflected in a turbulent medium can undergo a local recovery of spatial coherence and intensity enhancement referred to as enhanced backscatter (EBS). Here we validate the commonly used phase screen simulation with experimental results obtained from lab-scale experiments. We also verify theoretical predictions of the dependence of the turbulence strength on EBS. Finally, we present a novel algorithm called the "tilt-shift method" which allows detection of EBS in frozen turbulence, reducing the time required to detect the EBS signal.

Asian Citrus Psyllid Expression Profiles Suggest Candidatus Liberibacter Asiaticus-Mediated Alteration of Adult Nutrition and Metabolism, and of Nymphal Development and Immunity

The Asian citrus psyllid (ACP) Diaphorina citri Kuwayama (Hemiptera: Psyllidae) is the insect vector of the fastidious bacterium Candidatus Liberibacter asiaticus (CLas), the causal agent of citrus greening disease, or Huanglongbing (HLB). The widespread invasiveness of the psyllid vector and HLB in citrus trees worldwide has underscored the need for non-traditional approaches to manage the disease. One tenable solution is through the deployment of RNA interference technology to silence protein-protein interactions essential for ACP-mediated CLas invasion and transmission. To identify psyllid interactor-bacterial effector combinations associated with psyllid-CLas interactions, cDNA libraries were constructed from CLas-infected and CLas-free ACP adults and nymphs, and analyzed for differential expression. Library assemblies comprised 24,039,255 reads and yielded 45,976 consensus contigs. They were annotated (UniProt), classified using Gene Ontology, and subjected to in silico expression analyses using the Transcriptome Computational Workbench (TCW) (http://www.sohomoptera.org/ACPPoP/). Functional-biological pathway interpretations were carried out using the Kyoto Encyclopedia of Genes and Genomes databases. Differentially expressed contigs in adults and/or nymphs represented genes and/or metabolic/pathogenesis pathways involved in adhesion, biofilm formation, development-related, immunity, nutrition, stress, and virulence. Notably, contigs involved in gene silencing and transposon-related responses were documented in a psyllid for the first time. This is the first comparative transcriptomic analysis of ACP adults and nymphs infected and uninfected with CLas. The results provide key initial insights into host-parasite interactions involving CLas effectors that contribute to invasion-virulence, and to host nutritional exploitation and immune-related responses that appear to be essential for successful ACP-mediated circulative, propagative CLas transmission.

Symbiodinium transcriptome and global responses of cells to immediate changes in light intensity when grown under autotrophic or mixotrophic conditions

Symbiosis between unicellular dinoflagellates (genus Symbiodinium) and their cnidarian hosts (e.g. corals, sea anemones) is the foundation of coral reef ecosystems. Dysfunction of this symbiosis under changing environmental conditions has led to global reef decline. Little information is known about Symbiodinium gene expression and mechanisms by which light impacts host-symbiont associations. To address these issues, we generated a transcriptome from axenic Symbiodinium strain SSB01. Here we report features of the transcriptome, including occurrence and length distribution of spliced leader sequences, the functional landscape of encoded proteins and the impact of light on gene expression. Expression of many Symbiodinium genes appears to be significantly impacted by light. Transcript encoding cryptochrome 2 declined in high light while some transcripts for Regulators of Chromatin Condensation (RCC1) declined in the dark. We also identified a transcript encoding a light harvesting AcpPC protein with homology to Chlamydomonas LHCSR2. The level of this transcript increased in high light autotrophic conditions, suggesting that it is involved in photo-protection and the dissipation of excess absorbed light energy. The most extensive changes in transcript abundances occurred when the algae were transferred from low light to darkness. Interestingly, transcripts encoding several cell adhesion proteins rapidly declined following movement of cultures to the dark, which correlated with a dramatic change in cell surface morphology, likely reflecting the complexity of the extracellular matrix. Thus, light-sensitive cell adhesion proteins may play a role in establishing surface architecture, which may in turn alter interactions between the endosymbiont and its host.

Comparative proteomic analysis of developing rhizomes of the ancient vascular plant Equisetum hyemale and different monocot species

The rhizome is responsible for the invasiveness and competitiveness of many plants with great economic and agricultural impact worldwide. Besides its value as an invasive organ, the rhizome plays a role in the establishment and massive growth of forage, providing biomass for biofuel production. Despite these features, little is known about the molecular mechanisms that contribute to rhizome growth, development, and function in plants. In this work, we characterized the proteome of rhizome apical tips and elongation zones from different species using a GeLC-MS/MS (one-dimensional electrophoresis in combination with liquid chromatography coupled online with tandem mass spectrometry) spectral-counting proteomics strategy. Five rhizomatous grasses and an ancient species were compared to study the protein regulation in rhizomes. An average of 2200 rhizome proteins per species were confidently identified and quantified. Rhizome-characteristic proteins showed similar functional distributions across all species analyzed. The over-representation of proteins associated with central roles in cellular, metabolic, and developmental processes indicated accelerated metabolism in growing rhizomes. Moreover, 61 rhizome-characteristic proteins appeared to be regulated similarly among analyzed plants. In addition, 36 showed conserved regulation between rhizome apical tips and elongation zones across species. These proteins were preferentially expressed in rhizome tissues regardless of the species analyzed, making them interesting candidates for more detailed investigative studies about their roles in rhizome development.

Comparison of potato and asian citrus psyllid adult and nymph transcriptomes identified vector transcripts with potential involvement in circulative, propagative liberibacter transmission

The potato psyllid (PoP) Bactericera cockerelli (Sulc) and Asian citrus psyllid (ACP) Diaphorina citri Kuwayama are the insect vectors of the fastidious plant pathogen, Candidatus Liberibacter solanacearum (CLso) and Ca. L. asiaticus (CLas), respectively. CLso causes Zebra chip disease of potato and vein-greening in solanaceous species, whereas, CLas causes citrus greening disease. The reliance on insecticides for vector management to reduce pathogen transmission has increased interest in alternative approaches, including RNA interference to abate expression of genes essential for psyllid-mediated Ca. Liberibacter transmission. To identify genes with significantly altered expression at different life stages and conditions of CLso/CLas infection, cDNA libraries were constructed for CLso-infected and -uninfected PoP adults and nymphal instars. Illumina sequencing produced 199,081,451 reads that were assembled into 82,224 unique transcripts. PoP and the analogous transcripts from ACP adult and nymphs reported elsewhere were annotated, organized into functional gene groups using the Gene Ontology classification system, and analyzed for differential in silico expression. Expression profiles revealed vector life stage differences and differential gene expression associated with Liberibacter infection of the psyllid host, including invasion, immune system modulation, nutrition, and development.

Propagation of Bessel and Airy beams through atmospheric turbulence

We investigate, through simulation, the modifications to Bessel and Airy beams during propagation through atmospheric turbulence. We find that atmospheric turbulence disrupts the quasi-non-diffracting nature of Bessel and Airy beams when the transverse coherence length (Fried parameter) nears the initial aperture diameter or diagonal, respectively. The turbulence-induced transverse phase distortion limits the effectiveness of Bessel and Airy beams for applications requiring propagation over long distances in the turbulent atmosphere.

A systems-wide comparison of red rice (Oryza longistaminata) tissues identifies rhizome specific genes and proteins that are targets for cultivated rice improvement

BACKGROUND

The rhizome, the original stem of land plants, enables species to invade new territory and is a critical component of perenniality, especially in grasses. Red rice (Oryza longistaminata) is a perennial wild rice species with many valuable traits that could be used to improve cultivated rice cultivars, including rhizomatousness, disease resistance and drought tolerance. Despite these features, little is known about the molecular mechanisms that contribute to rhizome growth, development and function in this plant.

RESULTS

We used an integrated approach to compare the transcriptome, proteome and metabolome of the rhizome to other tissues of red rice. 116 Gb of transcriptome sequence was obtained from various tissues and used to identify rhizome-specific and preferentially expressed genes, including transcription factors and hormone metabolism and stress response-related genes. Proteomics and metabolomics approaches identified 41 proteins and more than 100 primary metabolites and plant hormones with rhizome preferential accumulation. Of particular interest was the identification of a large number of gene transcripts from Magnaportha oryzae, the fungus that causes rice blast disease in cultivated rice, even though the red rice plants showed no sign of disease.

CONCLUSIONS

A significant set of genes, proteins and metabolites appear to be specifically or preferentially expressed in the rhizome of O. longistaminata. The presence of M. oryzae gene transcripts at a high level in apparently healthy plants suggests that red rice is resistant to this pathogen, and may be able to provide genes to cultivated rice that will enable resistance to rice blast disease.

TCW: transcriptome computational workbench

BACKGROUND

The analysis of transcriptome data involves many steps and various programs, along with organization of large amounts of data and results. Without a methodical approach for storage, analysis and query, the resulting ad hoc analysis can lead to human error, loss of data and results, inefficient use of time, and lack of verifiability, repeatability, and extensibility.

METHODOLOGY

The Transcriptome Computational Workbench (TCW) provides Java graphical interfaces for methodical analysis for both single and comparative transcriptome data without the use of a reference genome (e.g. for non-model organisms). The singleTCW interface steps the user through importing transcript sequences (e.g. Illumina) or assembling long sequences (e.g. Sanger, 454, transcripts), annotating the sequences, and performing differential expression analysis using published statistical programs in R. The data, metadata, and results are stored in a MySQL database. The multiTCW interface builds a comparison database by importing sequence and annotation from one or more single TCW databases, executes the ESTscan program to translate the sequences into proteins, and then incorporates one or more clusterings, where the clustering options are to execute the orthoMCL program, compute transitive closure, or import clusters. Both singleTCW and multiTCW allow extensive query and display of the results, where singleTCW displays the alignment of annotation hits to transcript sequences, and multiTCW displays multiple transcript alignments with MUSCLE or pairwise alignments. The query programs can be executed on the desktop for fastest analysis, or from the web for sharing the results.

CONCLUSION

It is now affordable to buy a multi-processor machine, and easy to install Java and MySQL. By simply downloading the TCW, the user can interactively analyze, query and view their data. The TCW allows in-depth data mining of the results, which can lead to a better understanding of the transcriptome. TCW is freely available from www.agcol.arizona.edu/software/tcw.

Probability of detecting influenza A virus subtypes H1N1 and H3N2 in individual pig nasal swabs and pen-based oral fluid specimens over time

The probability of detecting influenza A virus (IAV) by virus isolation (VI), point-of-care (POC) antigen detection, and real-time reverse-transcription polymerase chain reaction (rRT-PCR) was estimated for pen-based oral fluid (OF) and individual pig nasal swab (NS) specimens. Piglets (n=82) were isolated for 30 days and confirmed negative for porcine reproductive and respiratory syndrome virus, Mycoplasma hyopneumoniae, and IAV infections. A subset (n=28) was vaccinated on day post inoculation (DPI) -42 and -21 with a commercial multivalent vaccine. On DPI 0, pigs were intratracheally inoculated with contemporary isolates of H1N1 (n=35) or H3N2 (n=35) or served as negative controls (n=12). OF (n=370) was collected DPI 0-16 and NS (n=924) DPI 0-6, 8, 10, 12, 14, 16. The association between IAV detection and variables of interest (specimen, virus subtype, assay, vaccination status, and DPI) was analyzed by mixed-effect repeated measures logistic regression and the results used to calculate the probability (pˆ) of detecting IAV in OF and NS over DPI by assay. Vaccination (p-value<0.0001), DPI (p-value<0.0001), and specimen-assay interaction (p-value<0.0001) were significant to IAV detection, but virus subtype was not (p-value=0.89). Vaccination and/or increasing DPI reduced pˆ for all assays. VI was more successful using NS than OF, but both VI and POC were generally unsuccessful after DPI 6. Overall, rRT-PCR on OF specimens provided the highest pˆ for the most DPIs, yet significantly different results were observed between the two laboratories independently performing rRT-PCR testing.

Quantum gravity extension of the inflationary scenario

Since the standard inflationary paradigm is based on quantum field theory on classical space-times, it excludes the Planck era. Using techniques from loop quantum gravity, the paradigm is extended to a self-consistent theory from the Planck scale to the onset of slow roll inflation, covering some 11 orders of magnitude in energy density and curvature. This preinflationary dynamics also opens a small window for novel effects, e.g., a source for non-Gaussianities, which could extend the reach of cosmological observations to the deep Planck regime of the early Universe.

Factors associated with 'caregiver burden' for atrial fibrillation patients

BACKGROUND

The burden on caregivers providing support to atrial fibrillation (AF) patients has not been evaluated.

OBJECTIVE

To examine the interrelationship between unpaid caregiver, patient and thromboprophylaxis characteristics and caregiver burden in AF.

METHODS

We conducted a cross-sectional survey study of AF patient-caregiver dyads recruited from cardiology clinics at an urban teaching hospital. Eligible patients had a diagnosis of AF, received thromboprophylaxis to prevent stroke, lived in the community and had an adult, unpaid, English-speaking caregiver. Hierarchical multivariate regression was used to evaluate the association between caregiver, patient and thromboprophylaxis characteristics and caregiver burden as measured by the 'Caregiver Reaction Assessment' (CRA).

RESULTS

Eighty patient-caregiver dyads were surveyed. The mean ± standard deviation scores for each CRA domain were 'Disrupted schedule' (2.4 ± 1.0), 'Financial problems' (2.1 ± 0.8), 'Lack of family support' (1.9 ± 0.7), 'Health problems' (1.9 ± 0.7) and 'Self-esteem' (0.9 ± 0.5). Significantly greater caregiver burden due to 'Disrupted schedule' was seen in those spending > 4 h/week providing care and when caring for frail, sick or disabled patients, with higher CHADS2 scores and requiring help with their medications. 'Financial problems' burden scores were significantly associated with caring for frail patients and those requiring more frequent office follow-up. 'Lack of family support' scores were inversely associated with having somebody else to help provide care and increased as patients CHADS2 score increased. Lower 'Health problem' burden scores were associated with female gender and higher scores with the need to spend > 4 h/week providing care.

CONCLUSION

The greatest burden to caregivers of AF patients occurs due to schedule disruption.