Terahertz nano-spectroscopy with resonant scattering probes

We propose and demonstrate tunable resonant scattering probes for terahertz (THz) near-field microscopy, using sharp indium tips fabricated to the tine of a quartz tuning fork. We find the antenna resonance of the indium tips can be tuned by altering the tip length, which we support with numerical models. We also demonstrate the indium tips can provide nanoscale field confinement at the tip apex, with spatial resolution better than 100 nm

Ultra-high-resolution software-defined photonic terahertz spectroscopy

A novel technique for high-resolution 1.5 µm photonics-enabled terahertz (THz) spectroscopy using software control of the illumination spectral line shape (SLS) is presented. The technique enhances the performance of a continuous-wave THz spectrometer to reveal previously inaccessible details of closely spaced spectral peaks. We demonstrate the technique by performing spectroscopy on LiYF4:Ho3+, a material of interest for quantum science and technology, where we discriminate between inhomogeneous Gaussian and homogeneous Lorentzian contributions to absorption lines near 0.2 THz. Ultra-high-resolution (<100 Hz full-width at half maximum) frequency-domain spectroscopy with quality factor Q > 2 × 109 is achieved using an exact frequency spacing comb source in the optical communications band, with a custom uni-traveling-carrier photodiode mixer and coherent down-conversion detection. Software-defined time-domain modulation of one of the comb lines is demonstrated and used to resolve the sample SLS and to obtain a magnetic field-free readout of the electronuclear spectrum for the Ho3+ ions in LiYF4:Ho3+. In particular, homogeneous and inhomogeneous contributions to the spectrum are readily separated. The experiment reveals previously unmeasured information regarding the hyperfine structure of the first excited state in the 5 I8 manifold complementing the results reported in Phys. Rev. B 94, 205132 (2016)

Probe-sample interaction in aperture-type THz near-field microscopy of complementary resonators

Subwavelength complementary metallic resonators operating in the terahertz (THz) regime are investigated with aperture near-field microscopy and spectroscopy. In contrast to far-field methods, the spectra of individual isolated resonators can be retrieved. We find that we can experimentally gain spectral information without modifying the spectral properties of the resonator with the aperture-type near-field probe by operating it at a separation distance greater than 10 μ {m}

Precise determination of the low-energy electronuclear Hamiltonian of LiY1−x HoxF4

The insulating rare-earth magnet LiY1−xHoxF4 has received great attention because a laboratory field applied perpendicular to its crystallographic c axis converts the low-energy electronic spin Hamiltonian into the (dilute) transverse field Ising model. The mapping between the real magnet and the transverse field Ising model is strongly dependent on the exact nature of the low-energy Hamiltonian for the material, which can be determined by spectroscopy in the dilute limit. The energies of the eigenstates are in the difficult terahertz (THz) regime, and here we use THz time domain and Fourier transform spectroscopy to directly measure the lowest crystal-field levels of LiY1−xHoxF4 in the dilute limit, including nuclear hyperfine substructure. The high resolution of our measurements allows us to observe the nonequidistantly spaced Ho (I = 72 ) hyperfine transitions originating from dipolar and quadrupolar hyperfine interactions. We provide refined crystal-field parameters and extract the dipolar and quadrupolar hyperfine constants AJ = 0.027 03 ± 0.000 03 cm−1 (810.3 ± 0.9 MHz) and B = 0.04 ± 0.01 cm−1(1.2 ± 0.3 GHz), respectively. Thereupon we determine all crystal-field energy levels and magnetic moments of the 5/8 ground-state manifold, including the (nonlinear) hyperfine corrections. The latter improve the prediction precision by a factor of 60 compared to previous crystal-field parameters. Additionally,we establish the far-infrared, low-temperature refractive index of LiY1−xHoxF4

Intestinal Microbiota Shifts towards Elevated Commensal Escherichia coli Loads Abrogate Colonization Resistance against Campylobacter jejuni in Mice

Background: The zoonotic pathogen Campylobacter jejuni is a leading cause of bacterial foodborne enterocolitis in humans worldwide. The understanding of immunopathology underlying human campylobacteriosis is hampered by the fact that mice display strong colonization resistance against the pathogen due to their host specific gut microbiota composition. Methodology/Principal Findings: Since the microbiota composition changes significantly during intestinal inflammation we dissected factors contributing to colonization resistance against C. jejuni in murine ileitis, colitis and in infant mice. In contrast to healthy animals C. jejuni could stably colonize mice suffering from intestinal inflammation. Strikingly, in mice with Toxoplasma gondii-induced acute ileitis, C. jejuni disseminated to mesenteric lymphnodes, spleen, liver, kidney, and blood. In infant mice C. jejuni infection induced enterocolitis. Mice suffering from intestinal inflammation and C. jejuni susceptible infant mice displayed characteristical microbiota shifts dominated by increased numbers of commensal Escherichia coli. To further dissect the pivotal role of those distinct microbiota shifts in abrogating colonization resistance, we investigated C. jejuni infection in healthy adult mice in which the microbiota was artificially modified by feeding live commensal E. coli. Strikingly, in animals harboring supra-physiological intestinal E. coli loads, colonization resistance was significantly diminished and C. jejuni infection induced enterocolitis mimicking key features of human campylobacteriosis. Conclusion/Significance: Murine colonization resistance against C. jejuni is abrogated by changes in the microbiot

The importance of parameter choice in modelling dynamics of the eye lens

The lens provides refractive power to the eye and is capable of altering ocular focus in response to visual demand. This capacity diminishes with age. Current biomedical technologies, which seek to design an implant lens capable of replicating the function of the biological lens, are unable as yet to provide such an implant with the requisite optical quality or ability to change the focussing power of the eye. This is because the mechanism of altering focus, termed accommodation, is not fully understood and seemingly conflicting theories require experimental support which is difficult to obtain from the living eye. This investigation presents finite element models of the eye lens based on data from human lenses aged 16 and 35 years that consider the influence of various modelling parameters, including material properties, a wide range of angles of force application and capsular thickness. Results from axisymmetric models show that the anterior and posterior zonules may have a greater impact on shape change than the equatorial zonule and that choice of capsular thickness values can influence the results from modelled simulations

Deep RNA sequencing analysis of readthrough gene fusions in human prostate adenocarcinoma and reference samples

<p>Abstract</p> <p>Background</p> <p>Readthrough fusions across adjacent genes in the genome, or transcription-induced chimeras (TICs), have been estimated using expressed sequence tag (EST) libraries to involve 4-6% of all genes. Deep transcriptional sequencing (RNA-Seq) now makes it possible to study the occurrence and expression levels of TICs in individual samples across the genome.</p> <p>Methods</p> <p>We performed single-end RNA-Seq on three human prostate adenocarcinoma samples and their corresponding normal tissues, as well as brain and universal reference samples. We developed two bioinformatics methods to specifically identify TIC events: a targeted alignment method using artificial exon-exon junctions within 200,000 bp from adjacent genes, and genomic alignment allowing splicing within individual reads. We performed further experimental verification and characterization of selected TIC and fusion events using quantitative RT-PCR and comparative genomic hybridization microarrays.</p> <p>Results</p> <p>Targeted alignment against artificial exon-exon junctions yielded 339 distinct TIC events, including 32 gene pairs with multiple isoforms. The false discovery rate was estimated to be 1.5%. Spliced alignment to the genome was less sensitive, finding only 18% of those found by targeted alignment in 33-nt reads and 59% of those in 50-nt reads. However, spliced alignment revealed 30 cases of TICs with intervening exons, in addition to distant inversions, scrambled genes, and translocations. Our findings increase the catalog of observed TIC gene pairs by 66%.</p> <p>We verified 6 of 6 predicted TICs in all prostate samples, and 2 of 5 predicted novel distant gene fusions, both private events among 54 prostate tumor samples tested. Expression of TICs correlates with that of the upstream gene, which can explain the prostate-specific pattern of some TIC events and the restriction of the <it>SLC45A3-ELK4 </it>e4-e2 TIC to <it>ERG</it>-negative prostate samples, as confirmed in 20 matched prostate tumor and normal samples and 9 lung cancer cell lines.</p> <p>Conclusions</p> <p>Deep transcriptional sequencing and analysis with targeted and spliced alignment methods can effectively identify TIC events across the genome in individual tissues. Prostate and reference samples exhibit a wide range of TIC events, involving more genes than estimated previously using ESTs. Tissue specificity of TIC events is correlated with expression patterns of the upstream gene. Some TIC events, such as <it>MSMB-NCOA4</it>, may play functional roles in cancer.</p