Three octave visible to mid-infrared supercontinuum generation seeded by multimode silica fiber pumped at 1064†nm.

Hyperspectral spectroscopy requires light sources with wide spectral ranges from the visible to the mid-infrared. Here, we demonstrate the first fiber-based mid-infrared supercontinuum covering three octaves of frequency by leveraging 1-µm laser technology. The process consists in spectral broadening of a 1064-nm pump toward 0.48-2.5 µm in a graded-index multimode fiber, followed by a fluoro-indate fiber used to reach deeper into the near infrared (4.3 µm). Finally, an arsenic selenide chalcogenide fiber allows us to reach the 6-µm wavelength region, providing a 0.75-6-µm supercontinuum. We illustrate the potential of this light source by recording mid-infrared absorption spectra of organic compounds.

Fiber-based source of 500 kW mid-infrared solitons.

Fiber-based sources delivering high-energy few-cycle pulses at high repetition rates are currently being developed in the near-infrared spectral range, thanks to the wide availability of telecommunication-grade optical fibers and components. Similar sources in the middle-wave infrared (mid-IR) spectral domain, however, are scarce, although such sources are of high interest for applications such as high-precision frequency metrology and molecular spectroscopy or as a seed source to reach further into the mid-IR via coherent nonlinear processes. Here we report on the design of a fiber-based source of 50-nJ energy 90 fs duration pulses up to 2950 nm, corresponding to 500 kW peak power. To obtain this level of peak power we exploit multi-solitonic fission and soliton self-frequency shift in large mode area fibers excited by picosecond pulses emitted at 2 µm from a megahertz repetition rate fiber laser. We leverage mature silica-based fiber technology up to 2.4 µm and restrict the use of fluoride fiber to the very last frequency-shifting stage. The level of instantaneous power and ultra-short duration achieved in this Letter pave the way to all-fiber format generation of an ultra-broadband coherent continuum in the mid-IR with profound implications for applications such as high-resolution molecular spectroscopy and imaging.

3D time-domain beam mapping for studying nonlinear dynamics in multimode optical fibers.

Characterization of the complex spatiotemporal dynamics of optical beam propagation in nonlinear multimode fibers requires the development of advanced measurement methods, capable of capturing the real-time evolution of beam images. We present a new space-time mapping technique, permitting the direct detection, with picosecond temporal resolution, of the intensity from repetitive laser pulses over a grid of spatial samples from a magnified image of the output beam. By using this time-resolved mapping, we provide, to the best of our knowledge, the first unambiguous experimental observation of instantaneous intrapulse nonlinear coupling processes among the modes of a graded index fiber.

Frequency-resolved spatial beam mapping in multimode fibers: application to mid-infrared supercontinuum generation.

We present a new, to the best of our knowledge, spatial-spectral mapping technique permitting measurement of the beam intensity at the output of a graded-index multimode fiber (GIMF) with sub-nanometric spectral resolution. We apply this method to visualize the fine structure of the beam shape of a sideband generated at 1870 nm by geometric parametric instability (GPI) in a GIMF. After spatial-spectral characterization, we amplify the GPI sideband with a thulium-doped fiber amplifier to obtain a microjoule-scale picosecond pump whose spectrum is finally broadened in a segment of InF3 optical fiber to achieve a supercontinuum ranging from 1.7 up to 3.4 µm.

Effects of transdermal mirtazapine on hyporexic rhesus and cynomolgus macaques (Macaca mulatta and Macaca fascicularis).

BACKGROUND: Hyporexia and weight loss are important indicators of physical and psychological well-being in macaque colonies. An FDA-approved transdermal formulated Mirtazapine (MTZ) shows effectiveness in managing feline hyporexia. This study sought to determine its effectiveness as an appetite stimulant in macaques. METHODS: Fourteen macaques with idiopathic hyporexia, intractable to conventional management were treated with transdermal MTZ (0.5 mg/kg) topically administered to aural pinnae once daily for 14 days. Qualitative food consumption was monitored daily for 6 months. Body weights were collected prior to treatment, every 2 weeks for the first 6 weeks, 10 weeks, and 6 months post-treatment. RESULTS: Transdermal MTZ significantly reduced the frequency of hyporexia during treatment and monthly for 6 months. No significant increase in weight noted until approximately 6 months post-treatment. CONCLUSIONS: Results from this study indicate that a short course of transdermal MTZ is an effective way to increase food consumption in macaques chronically.

Optimization of capsaicin-induced dermal blood flow measurement by laser Doppler imaging in cynomolgus macaque.

BACKGROUND: Capsaicin is used in several areas of non-human primate research including allodynia and dermal blood flow (DBF). The capsaicin-induced DBF increase was measured using laser Doppler imaging (LDI), but this response is known to diminish upon repeated topical applications. Refinement of the experimental procedures could improve the rigor and reproducibility of the DBF migraine model. METHODS: Optimal anatomical site in cynomolgus was determined, and conditions and experimental settings for DBF measurement using LDI were established. Then, two study design trial structures were compared. RESULTS: Medial thigh was the preferrable site, and an ethanol-Tween 20 formulation of capsaicin was desirable. A 1-week washout for contralateral side or 2-week washout for ipsilateral side was necessary to eradicate capsaicin desensitization. CONCLUSIONS: With the established technicality in DBF measurements in cynomolgus macaques, the capsaicin-induced DBF model may be utilized in translational medical research in developing migraine therapeutics.

Genome properties in 2019: a new companion database to InterPro for the inference of complete functional attributes.

Automatic annotation of protein function is routinely applied to newly sequenced genomes. While this provides a fine-grained view of an organism's functional protein repertoire, proteins, more commonly function in a coordinated manner, such as in pathways or multimeric complexes. Genome Properties (GPs) define such functional entities as a series of steps, originally described by either TIGRFAMs or Pfam entries. To increase the scope of coverage, we have migrated GPs to function as a companion resource utilizing InterPro entries. Having introduced GPs-specific versioned releases, we provide software and data via a GitHub repository, and have developed a new web interface to GPs (available at https://www.ebi.ac.uk/interpro/genomeproperties). In addition to exploring each of the 1286 GPs, the website contains GPs pre-calculated for a representative set of proteomes; these results can be used to profile GPs phylogenetically via an interactive viewer. Users can upload novel data to the viewer for comparison with the pre-calculated results. Over the last year, we have added ∼700 new GPs, increasing the coverage of eukaryotic systems, as well as increasing general coverage through automatic generation of GPs from related resources. All data are freely available via the website and the GitHub repository.

InterPro in 2019: improving coverage, classification and access to protein sequence annotations.

The InterPro database (http://www.ebi.ac.uk/interpro/) classifies protein sequences into families and predicts the presence of functionally important domains and sites. Here, we report recent developments with InterPro (version 70.0) and its associated software, including an 18% growth in the size of the database in terms on new InterPro entries, updates to content, the inclusion of an additional entry type, refined modelling of discontinuous domains, and the development of a new programmatic interface and website. These developments extend and enrich the information provided by InterPro, and provide greater flexibility in terms of data access. We also show that InterPro's sequence coverage has kept pace with the growth of UniProtKB, and discuss how our evaluation of residue coverage may help guide future curation activities.

Large-scale comparative analysis of microbial pan-genomes using PanOCT.

SUMMARY: The JCVI pan-genome pipeline is a collection of programs to run PanOCT and tools that support and extend the capabilities of PanOCT. PanOCT (pan-genome ortholog clustering tool) is a tool for pan-genome analysis of closely related prokaryotic species or strains. The JCVI Pan-Genome Pipeline wrapper invokes command-line utilities that prepare input genomes, invoke third-party tools such as NCBI Blast+, run PanOCT, generate a consensus pan-genome, annotate features of the pan-genome, detect sets of genes of interest such as antimicrobial resistance (AMR) genes and generate figures, tables and html pages to visualize the results. The pipeline can run in a hierarchical mode, lowering the RAM and compute resources used. AVAILABILITY AND IMPLEMENTATION: Source code, demo data, and detailed documentation are freely available at https://github.com/JCVenterInstitute/PanGenomePipeline.

Highly efficient few-mode spatial beam self-cleaning at 1.5µm.

We experimentally demonstrate that spatial beam self-cleaning can be highly efficient when obtained with a few-mode excitation in graded-index multimode optical fibers. By using 160 ps long, highly chirped (6 nm bandwidth at -3dB) optical pulses at 1562 nm, we demonstrate a one-decade reduction of the power threshold for spatial beam self-cleaning, with respect to previous experiments using pulses with laser wavelengths at 1030-1064 nm. Self-cleaned beams remain spatio-temporally stable for more than a decade of their peak power variation. The impact of input pulse temporal duration is also studied.

Generation of 35 kW peak power 80 fs pulses at 2.9 µm from a fully fusion-spliced fiber laser.

Tunable femtosecond light sources in the short wave and middle wave infrared regions are of utmost importance for various applications ranging from multiphoton microscopy, mid-infrared supercontinuum generation to high-harmonic generation. We report on an all-fusion-spliced fiber laser emitting 80 fs pulses up to 2.9 µm with 35 kW peak power. The laser is based on Raman self-frequency shift effect from 1560 nm up to 3000 nm in germanium-doped fibers fabricated by the widespread modified chemical vapor deposition process.

Characterization of the AmpC ß-Lactamase from Burkholderia multivorans.

Burkholderia multivorans is a member of the Burkholderia cepacia complex, a group of >20 related species of nosocomial pathogens that commonly infect individuals suffering from cystic fibrosis. ß-Lactam antibiotics are recommended as therapy for infections due to Bmultivorans, which possesses two ß-lactamase genes, blapenA and blaAmpC PenA is a carbapenemase with a substrate profile similar to that of the Klebsiella pneumoniae carbapenemase (KPC); in addition, expression of PenA is inducible by ß-lactams in Bmultivorans Here, we characterize AmpC from Bmultivorans ATCC 17616. AmpC possesses only 38 to 46% protein identity with non-Burkholderia AmpC proteins (e.g., PDC-1 and CMY-2). Among 49 clinical isolates of Bmultivorans, we identified 27 different AmpC variants. Some variants possessed single amino acid substitutions within critical active-site motifs (Ω loop and R2 loop). Purified AmpC1 demonstrated minimal measurable catalytic activity toward ß-lactams (i.e., nitrocefin and cephalothin). Moreover, avibactam was a poor inhibitor of AmpC1 (Kiapp > 600 µM), and acyl-enzyme complex formation with AmpC1 was slow, likely due to lack of productive interactions with active-site residues. Interestingly, immunoblotting using a polyclonal anti-AmpC antibody revealed that protein expression of AmpC1 was inducible in Bmultivorans ATCC 17616 after growth in subinhibitory concentrations of imipenem (1 µg/ml). AmpC is a unique inducible class C cephalosporinase that may play an ancillary role in Bmultivorans compared to PenA, which is the dominant ß-lactamase in Bmultivorans ATCC 17616.

Targeted methylation sequencing of plasma cell-free DNA for cancer detection and classification.

Background: Targeted methylation sequencing of plasma cell-free DNA (cfDNA) has a potential to expand liquid biopsies to patients with tumors without detectable oncogenic alterations, which can be potentially useful in early diagnosis. Patients and methods: We developed a comprehensive methylation sequencing assay targeting 9223 CpG sites consistently hypermethylated according to The Cancer Genome Atlas. Next, we carried out a clinical validation of our method using plasma cfDNA samples from 78 patients with advanced colorectal cancer, non-small-cell lung cancer (NSCLC), breast cancer or melanoma and compared results with patients' outcomes. Results: Median methylation scores in plasma cfDNA samples from patients on therapy were lower than from patients off therapy (4.74 versus 85.29; P = 0.001). Of 68 plasma samples from patients off therapy, methylation scores detected the presence of cancer in 57 (83.8%), and methylation-based signatures accurately classified the underlying cancer type in 45 (78.9%) of these. Methylation scores were most accurate in detecting colorectal cancer (96.3%), followed by breast cancer (91.7%), melanoma (81.8%) and NSCLC (61.1%), and most accurate in classifying the underlying cancer type in colorectal cancer (88.5%), followed by NSCLC (81.8%), breast cancer (72.7%) and melanoma (55.6%). Low methylation scores versus high were associated with longer survival (10.4 versus 4.4 months, P < 0.001) and longer time-to-treatment failure (2.8 versus 1.6 months, P = 0.016). Conclusions: Comprehensive targeted methylation sequencing of 9223 CpG sites in plasma cfDNA from patients with common advanced cancers detects the presence of cancer and underlying cancer type with high accuracy. Methylation scores in plasma cfDNA correspond with treatment outcomes.

Two-photon microscopy with a frequency-doubled fully fusion-spliced fiber laser at 1840 nm.

We introduce a fiber-based laser system providing 130 fs pulses with 3.5 nJ energy at 920 nm at a 43 MHz repetition rate and illustrate the potential of the source for two-photon excited fluorescence microscopy of living mouse brain. The laser source is based on frequency-doubling high-energy solitons generated and frequency-shifted to 1840 nm in large mode area fibers. This simple laser system could unleash the potential of two-photon microscopy techniques in the biology laboratory where green fluorescent proteins with two-photon absorption spectrum peaking around 920 nm are routinely used.

Landau-Zener-Stückelberg Interferometry in Quantum Dots with Fast Rise Times: Evidence for Coherent Phonon Driving.

Manipulating qubits via electrical pulses in a piezoelectric material such as GaAs can be expected to generate incidental acoustic phonons. In this Letter we determine theoretically and experimentally the consequences of these phonons for semiconductor spin qubits using Landau-Zener-Stückelberg interferometry. Theoretical calculations predict that phonons in the presence of the spin-orbit interaction produce both phonon-Rabi fringes and accelerated evolution at the singlet-triplet anticrossing. Observed features confirm the influence of these mechanisms. Additionally, evidence is found that the pulsed gates themselves act as phonon cavities increasing the influence of phonons under specific resonant conditions.

The dynamic genome of Hydra.

The freshwater cnidarian Hydra was first described in 1702 and has been the object of study for 300 years. Experimental studies of Hydra between 1736 and 1744 culminated in the discovery of asexual reproduction of an animal by budding, the first description of regeneration in an animal, and successful transplantation of tissue between animals. Today, Hydra is an important model for studies of axial patterning, stem cell biology and regeneration. Here we report the genome of Hydra magnipapillata and compare it to the genomes of the anthozoan Nematostella vectensis and other animals. The Hydra genome has been shaped by bursts of transposable element expansion, horizontal gene transfer, trans-splicing, and simplification of gene structure and gene content that parallel simplification of the Hydra life cycle. We also report the sequence of the genome of a novel bacterium stably associated with H. magnipapillata. Comparisons of the Hydra genome to the genomes of other animals shed light on the evolution of epithelia, contractile tissues, developmentally regulated transcription factors, the Spemann-Mangold organizer, pluripotency genes and the neuromuscular junction.

Long-range spin transfer in triple quantum dots.

Tunneling in a quantum coherent structure is not restricted to only nearest neighbors. Hopping between distant sites is possible via the virtual occupation of otherwise avoided intermediate states. Here we report the observation of long-range transitions in the transport through three quantum dots coupled in series. A single electron is delocalized between the left and right quantum dots, while the center one remains always empty. Superpositions are formed, and both charge and spin are exchanged between the outermost dots. The delocalized electron acts as a quantum bus transferring the spin state from one end to the other. Spin selection is enabled by spin correlations. The process is detected via the observation of narrow resonances which are insensitive to Pauli spin blockade.

Quantum interference between three two-spin states in a double quantum dot.

Qubits based on the singlet (S) and the triplet (T(0), T(+)) states in double quantum dots have been demonstrated in separate experiments. It has been recently proposed theoretically that under certain conditions a quantum interference could occur from the interplay between these two qubit species. Here we report experiments and modeling that confirm these theoretical predictions and identify the conditions under which this interference occurs. Density matrix calculations show that the interference pattern manifests primarily via the occupation of the common singlet state. The S/T(0) qubit is found to have a much longer coherence time as compared to the S/T(+) qubit.

Feasibility of Targeted Delivery of AAV5-GFP into the Cerebellum of Nonhuman Primates Following a Single Convection-Enhanced Delivery Infusion.

In this study, we built upon our previous work to demonstrate the distribution and transport of AAV5-green fluorescent protein (GFP) following a single convection-enhanced delivery infusion into the nonhuman primate cerebellum, with no untoward side effects noted. Dosing under magnetic resonance imaging guidance revealed a sixfold larger volume of distribution compared with the volume of infusion, with no evidence of reflux underscoring the convective properties of the cerebellum and step design of the cannula. Postmortem tissue analysis, 4 weeks post-adeno-associated viral (AAV) delivery, revealed the robust presence of the transgene in situ, with GFP detection in secondary regions not directly targeted by the infusion, denoting distal transport of the vector. Irrespective of tropism, a twofold larger area of transgene expression was found and was corroborated against the presence of contrast on T1-weighted images. Different levels of transduction were detected between animals, which were negatively correlated with the level of antibody titer against the GFP construct, whereby the higher the antibody titer, the lower the level of transgene expression. These findings support the use of the posterior fossa as a potential target site for direct delivery of gene-based therapeutics for cerebellar diseases.

Non-intrusive and reliable speciation of organically bound tritium in environmental matrices.

Measurements of tritium in its various forms within the environment and especially in organic matter are keys to improving the current understanding of its environmental behavior and distribution. Validated or standardized analytical procedures for tritium determination methods have now been developed for several forms of tritium in environmental samples, yet an analytical lack remains regarding the quantifications of exchangeable and non-exchangeable forms of organically bound tritium (OBT) fractions. The present work therefore aims to provide a means of developing a standardized method for OBT fraction determination by evaluating the robustness and relevance of two methods (intrusive and non-intrusive methods) developed for non-exchangeable OBT quantification on a broad panel of pertinent environmental matrices. The validity and reliability of a non-intrusive method has thus been confirmed through a robust comparative study. Moreover, its relevance for standardization purposes is discussed, while the fundamental weakness of the conventional and most widespread method is highlighted and directly quantified for the first time in relying on many demonstrated biases.