De novo Transcriptome Assemblies of Rana (Lithobates) catesbeiana and Xenopus laevis Tadpole Livers for Comparative Genomics without Reference Genomes

In this work we studied the liver transcriptomes of two frog species, the American bullfrog (Rana (Lithobates) catesbeiana) and the African clawed frog (Xenopus laevis). We used high throughput RNA sequencing (RNA-seq) data to assemble and annotate these transcriptomes, and compared how their baseline expression profiles change when tadpoles of the two species are exposed to thyroid hormone. We generated more than 1.5 billion RNA-seq reads in total for the two species under two conditions as treatment/control pairs. We de novo assembled these reads using Trans-ABySS to reconstruct reference transcriptomes, obtaining over 350,000 and 130,000 putative transcripts for R. catesbeiana and X. laevis, respectively. Using available genomics resources for X. laevis, we annotated over 97% of our X. laevis transcriptome contigs, demonstrating the utility and efficacy of our methodology. Leveraging this validated analysis pipeline, we also annotated the assembled R. catesbeiana transcriptome. We used the expression profiles of the annotated genes of the two species to examine the similarities and differences between the tadpole liver transcriptomes. We also compared the gene ontology terms of expressed genes to measure how the animals react to a challenge by thyroid hormone. Our study reports three main conclusions. First, de novo assembly of RNA-seq data is a powerful method for annotating and establishing transcriptomes of non-model organisms. Second, the liver transcriptomes of the two frog species, R. catesbeiana and X. laevis, show many common features, and the distribution of their gene ontology profiles are statistically indistinguishable. Third, although they broadly respond the same way to the presence of thyroid hormone in their environment, their receptor/signal transduction pathways display marked differences

Magnetodielectric coupling and phonon properties of compressively strained EuTiO3 thin films deposited on LSAT

Compressively strained epitaxial (001) EuTiO3 thin films of tetragonal symmetry have been deposited on (001) (LaAlO3)_0.29-(SrAl_{1/2}Ta_{1/2}O3)_0.71 (LSAT) substrates by reactive molecular-beam epitaxy. Enhancement of the Neel temperature by 1 K with 0.9% compressive strain was revealed. The polar phonons ofthe films have been investigated as a function of temperature and magnetic field by means of infrared reflectance spectroscopy. All three infrared active phonons show strongly stiffened frequencies compared to bulk EuTiO3 in accordance with first principles calculations. The phonon frequencies exhibit gradual softening on cooling leading to an increase in static permittivity. A new polar phonon with frequency near the TO1 soft mode was detected below 150 K. The new mode coupled with the TO1 mode was assigned as the optical phonon from the Brillouin zone edge, which is activated in infrared spectra due to an antiferrodistortive phase transition and due to simultaneous presence of polar and/or magnetic nanoclusters. In the antiferromagnetic phase we have observed a remarkable softening of the lowest-frequency polar phonon under an applied magnetic field, which qualitatively agrees with first principles calculations. This demonstrates the strong spin-phonon coupling in EuTiO3, which is responsible for the pronounced dependence of its static permittivity on magnetic field in the antiferromagnetic phase.Comment: Submitted to Phys. Rev.

Coherent Pair Production by Photons in the 20-170 GeV Energy Range Incident on Crystals and Birefringence

The cross section for coherent pair production by linearly polarised photons in the 20-170 GeV energy range was measured for photon aligned incidence on ultra-high quality diamond and germanium crystals. The theoretical description of coherent bremsstrahlung and coherent pair production phenomena is an area of active theoretical debate and development. However, under our experimental conditions, the theory predicted the combined cross section and polarisation experimental observables very well indeed. In macroscopic terms, our experiment measured a birefringence effect in pair production in a crystal. This study of this effect also constituted a measurement of the energy dependent linear polarisation of photons produced by coherent bremsstrahlung in aligned crystals. New technologies for manipulating high energy photon beams can be realised based on an improved understanding of QED phenomena at these energies. In particular, this experiment demonstrates an efficient new polarimetry technique. The pair production measurements were done using two independent methods simultaneously. The more complex method using a magnet spectrometer showed that the simpler method using a multiplicity detector was also viable.Comment: 10 pages, 13 figures, 1 table, REVTeX4 two column, Version for publicatio

Results on the Coherent Interaction of High Energy Electrons and Photons in Oriented Single Crystals

The CERN-NA-59 experiment examined a wide range of electromagnetic processes for multi-GeV electrons and photons interacting with oriented single crystals. The various types of crystals and their orientations were used for producing photon beams and for converting and measuring their polarisation. The radiation emitted by 178 GeV unpolarised electrons incident on a 1.5 cm thick Si crystal oriented in the Coherent Bremsstrahlung (CB) and the String-of-Strings (SOS) modes was used to obtain multi-GeV linearly polarised photon beams. A new crystal polarimetry technique was established for measuring the linear polarisation of the photon beam. The polarimeter is based on the dependence of the Coherent Pair Production (CPP) cross section in oriented single crystals on the direction of the photon polarisation with respect to the crystal plane. Both a 1 mm thick single crystal of Germanium and a 4 mm thick multi-tile set of synthetic Diamond crystals were used as analyzers of the linear polarisation. A birefringence phenomenon, the conversion of the linear polarisation of the photon beam into circular polarisation, was observed. This was achieved by letting the linearly polarised photon beam pass through a 10 cm thick Silicon single crystal that acted as a "quarter wave plate" (QWP) as suggested by N. Cabibbo et al.Comment: Presented at International workshop "Relativistic Channeling and Related Coherent Phenomena", Frascati (Rome) 23-26 March 200

Coherent bremsstrahlung, boherent pair production, birefringence and polarimetry in the 20-170 GeV energy range using aligned crystals

The processes of coherent bremsstrahlung (CB) and coherent pair production (CPP) based on aligned crystal targets have been studied in the energy range 20-170 GeV. The experimental arrangement allowed for measurements of single photon properties of these phenomena including their polarization dependences. This is significant as the theoretical description of CB and CPP is an area of active theoretical debate and development. With the theoretical approach used in this paper both the measured cross sections and polarization observables are predicted very well. This indicates a proper understanding of CB and CPP up to energies of 170 GeV. Birefringence in CPP on aligned crystals is applied to determine the polarization parameters in our measurements. New technologies for high energy photon beam optics including phase plates and polarimeters for linear and circular polarization are demonstrated in this experiment. Coherent bremsstrahlung for the strings-on-strings (SOS) orientation yields a larger enhancement for hard photons than CB for the channeling orientations of the crystal. Our measurements and our calculations indicate low photon polarizations for the high energy SOS photons.Comment: 23 pages, 27 figures, 2 tables, REVTeX4 two column

What Is the Important Point Related to Follow-Up Sonographic Evaluation for the Developmental Dysplasia of the Hip?

Developmental dysplasia of the hip (DDH) is an important cause of childhood disability. Subluxation or dislocation can be diagnosed through pediatric physical examination; nevertheless, the ultrasonographic examination is necessary in diagnosing certain borderline cases. It has been evaluated routine sonographic examination of 2,444 hips of 1,222 babies to determine differences in both, developmental dysplasia and types of hips, and evaluated their development on the 3-month follow-up. Evaluating the pathologic alpha angles under 59, there was no statistically significant differences between girls and boys in both right (55.57 +/- 3.73) (56.20 +/- 4.01), (p = 0.480), and left (55.79 +/- 3.96) (57.00 +/- 3.84), (p = 0.160) hips on the 45th day of life. Routine sonographic examinations on the 45th day of life revealed that 51 of (66.2%) 77 type 2a right hips were girls and 26 (33.8%) were boys. The number of the right hips that develop into type 1 was 38 (74.5%) for girls and 26 (100%) for boys on the 90th day of life (p = 0.005). A total of 87 type 2a left hips included 64 girls (73.6%) and 23 boys (26.4%). In the 90th day control, 49 right hip of girls (76.6%) and 21 right hip of boys (91.3%) developed into type 1 (p = 0.126). In the assessment of both left and right hips, girls showed a significantly higher frequency in latency and boys showed significantly higher development in the control sonography. A total of 31 girls (2.5%) and 11 boys (0.9%) accounted for a total of 42 (3.4%) cases who showed bilateral type 2a hips in 1,222 infants. On the 90th day control, 26 girls (83.9%) and all 11 boys (100%) developed into type 1 (p = 0.156). The study emphasizes the importance of the sonographic examination on the 90th day of life. Results of the investigation include the data of sonographic screening of DDH on the 45th day, and also stress the importance of the 90th-day control sonography after a close follow-up with physical examination between 45th and 90th days of life

First-order phase transition vs. spin-state quantum-critical scenarios in strain-tuned epitaxial cobaltite thin films

Pr-containing perovskite cobaltites exhibit unusual valence transitions, coupled to coincident structural, spin-state, and metal-insulator transitions. Heteroepitaxial strain was recently used to control these phenomena in the model (Pr$_{1-y}$Y$_y$)$_{1-x}$Ca$_x$CoO$_{3-\delta}$ system, stabilizing a nonmagnetic insulating phase under compression (with a room-temperature valence/spin-state/metal-insulator transition) and a ferromagnetic metallic phase under tension, thus exposing a potential spin-state quantum critical point. The latter has been proposed in cobaltites and can be probed in this system as a function of a disorder-free variable (strain). We study this here via thickness-dependent strain relaxation in compressive SrLaAlO$_4$(001)/(Pr$_{0.85}$Y$_{0.15}$)$_{0.70}$Ca$_{0.30}$CoO$_{3-\delta}$ epitaxial thin films to quasi-continuously probe structural, electronic, and magnetic behaviors across the nonmagnetic-insulator/ferromagnetic-metal boundary. High-resolution X-ray diffraction, electronic transport, magnetometry, polarized neutron reflectometry, and temperature-dependent magnetic force microscopy provide a detailed picture, including abundant evidence of temperature- and strain-dependent phase coexistence. This indicates a first-order phase transition as opposed to spin-state quantum-critical behavior, which we discuss theoretically via a phenomenological Landau model for coupled spin-state and magnetic phase transitions.Comment: main text + supplementary materia

Dissect: detection and characterization of novel structural alterations in transcribed sequences

Motivation: Computational identification of genomic structural variants via high-throughput sequencing is an important problem for which a number of highly sophisticated solutions have been recently developed. With the advent of high-throughput transcriptome sequencing (RNA-Seq), the problem of identifying structural alterations in the transcriptome is now attracting significant attention