The Likelihood Ratio as a tool for Radio Continuum Surveys with SKA precursor telescopes

In this paper we investigate the performance of the likelihood ratio method as a tool for identifying optical and infrared counterparts to proposed radio continuum surveys with SKA precursor and pathfinder telescopes. We present a comparison of the infrared counterparts identified by the likelihood ratio in the VISTA Deep Extragalactic Observations (VIDEO) survey to radio observations with 6, 10 and 15 arcsec resolution. We cross-match a deep radio catalogue consisting of radio sources with peak flux density $>$ 60 $\mu$Jy with deep near-infrared data limited to $K_{\mathrm{s}}\lesssim$ 22.6. Comparing the infrared counterparts from this procedure to those obtained when cross-matching a set of simulated lower resolution radio catalogues indicates that degrading the resolution from 6 arcsec to 10 and 15 arcsec decreases the completeness of the cross-matched catalogue by approximately 3 and 7 percent respectively. When matching against shallower infrared data, comparable to that achieved by the VISTA Hemisphere Survey, the fraction of radio sources with reliably identified counterparts drops from $\sim$89%, at $K_{\mathrm{s}}\lesssim$22.6, to 47% with $K_{\mathrm{s}}\lesssim$20.0. Decreasing the resolution at this shallower infrared limit does not result in any further decrease in the completeness produced by the likelihood ratio matching procedure. However, we note that radio continuum surveys with the MeerKAT and eventually the SKA, will require long baselines in order to ensure that the resulting maps are not limited by instrumental confusion noise.Comment: 10 pages, 7 figures, accepted for publication in mnra

A 10 GHz Quasi-Optical Grid Amplifier Using Integrated HBT Differential Pairs

We report the fabrication and testing of a 10 GHz grid amplifier utilizing sixteen GaAs chips each containing an HBT differential pair plus integral bias/feedback resistors. The overall amplifier consists of a 4x4 array of unit cells on an RT Duroid™ board having a relative permittivity of 2.2. Each unit cell consists of an emitter-coupled differential pair at the center, an input antenna which extends horizontally in both directions from the two base leads, an output antenna which extends vertically in both directions from the two collector leads, and high inductance bias lines. In operation, the active grid array is placed between a pair of crossed polarizers. The horizontally polarized input wave passes through the input polarizer and couples to the input leads. An amplified current then flows on the vertical leads, which radiate a vertically polarized amplified signal through the output polarizer. The polarizers serve dual functions, providing both input-output isolation as well as independent impedance matching for the input and output ports. The grid thus functions essentially as a free-space beam amplifier. Calculations indicate that output powers of several watts per square centimeter of grid area should be attainable with optimized structures

Array concepts for solid-state and vacuum microelectronics millimeter-wave generation

The authors have proposed that the increasing demand for contact watt-level coherent sources in the millimeter- and submillimeter-wave region can be satisfied by fabricating two-dimensional grids loaded with oscillators and multipliers for quasi-optical coherent spatial combining of the outputs of large numbers of low-power devices. This was first demonstrated through the successful fabrication of monolithic arrays with 2000 Schottky diodes. Watt-level power outputs were obtained in doubling to 66 GHz. In addition, a simple transmission-line model was verified with a quasi-optical reflectometer that measured the array impedance. This multiplier array work is being extended to novel tripler configurations using blocking barrier devices. The technique has also been extended to oscillator configurations where the grid structure is loaded with negative-resistance devices. This was first demonstrated using Gunn devices. More recently, a 25-element MESFET grid oscillating at 10 GHz exhibited power combining and self-locking. Currently, this approach is being extended to a 100-element monolithic array of Gunn diodes. This same approach should be applicable to planar vacuum electron devices such as the submillimeter-wave BWO (backward wave oscillator) and vacuum FET

A 6.5 GHz-11.5 GHz source using a grid amplifier with a twist reflector

The authors have constructed and tested an oscillator using a grid amplifier with external feedback from a twist reflector. The twist reflector serves two functions; it changes the output polarization to match the input, and its position sets the feedback phase. This permits a wider tuning range than has been possible with previous grid oscillators. The source could be continuously tuned from 8.2 GHz to 11.0 GHz by moving the twist reflector. By moving the polarizer and mirror in the twist reflector independently, a 1.8-to-1 frequency range from 6.5 GHz to 11.5 GHz was achieved. The peak effective radiated power was 6.3 W at 9.9 GHz

Dynamics of Individual Molecules of Linear Polyethylene Liquids under Shear: Atomistic Simulation and Comparison with a Free-draining Bead-rod Chain

Nonequilibrium molecular dynamics (NEMD) simulations of a dense liquid composed of linear polyethylene chains were performed to investigate the chain dynamics under shear. Brownian dynamics (BD) simulations of a freely jointed chain with equivalent contour length were also performed in the case of a dilute solution. This allowed for a close comparison of the chain dynamics of similar molecules for two very different types of liquids. Both simulations exhibited a distribution of the end-to-end vector, |Rete|, with Gaussian behavior at low Weissenberg number (Wi). At high Wi, the NEMD distribution was bimodal, with two peaks associated with rotation and stretching of the individual molecules. BD simulations of a dilute solution did not display a bimodal character; distributions of |Rete| ranged from tightly coiled to fully stretched configurations. The simulations revealed a tumbling behavior of the chains and correlations between the components of Rete exhibited characteristic frequencies of tumbling, which scaled as Wi−0.75. Furthermore, after a critical Wi of approximately 2, another characteristic time scale appeared which scaled as Wi−0.63. Although the free-draining solution is very different than the dense liquid, the BD simulations revealed a similar behavior, with the characteristic time scales mentioned above scaling as Wi−0.68 and Wi−0.66

Proteomic analysis of Bifidobacterium longum subsp. infantis reveals the metabolic insight on consumption of prebiotics and host glycans.

Bifidobacterium longum subsp. infantis is a common member of the intestinal microbiota in breast-fed infants and capable of metabolizing human milk oligosaccharides (HMO). To investigate the bacterial response to different prebiotics, we analyzed both cell wall associated and whole cell proteins in B. infantis. Proteins were identified by LC-MS/MS followed by comparative proteomics to deduce the protein localization within the cell. Enzymes involved in the metabolism of lactose, glucose, galactooligosaccharides, fructooligosaccharides and HMO were constitutively expressed exhibiting less than two-fold change regardless of the sugar used. In contrast, enzymes in N-Acetylglucosamine and sucrose catabolism were induced by HMO and fructans, respectively. Galactose-metabolizing enzymes phosphoglucomutase, UDP-glucose 4-epimerase and UTP glucose-1-P uridylytransferase were expressed constitutively, while galactokinase and galactose-1-phosphate uridylyltransferase, increased their expression three fold when HMO and lactose were used as substrates for cell growth. Cell wall-associated proteomics also revealed ATP-dependent sugar transport systems associated with consumption of different prebiotics. In addition, the expression of 16 glycosyl hydrolases revealed the complete metabolic route for each substrate. Mucin, which possesses O-glycans that are structurally similar to HMO did not induced the expression of transport proteins, hydrolysis or sugar metabolic pathway indicating B. infantis do not utilize these glycoconjugates

A 100-element HBT grid amplifier

A 100-element 10-GHz grid amplifier has been developed. The active devices in the grid are chips with heterojunction-bipolar-transistor (HBT) differential pairs. The metal grid pattern was empirically designed to provide effective coupling between the HBTs and free space. Two independent measurements, one with focusing lenses and the other without, were used to characterize the grid. In each case, the peak gain was 10 dB at 10 GHz with a 3-dB bandwidth of 1 GHz. The input and output return losses were better than 15 dB at 10 GHz. The maximum output power was 450 mW, and the minimum noise figure was 7 dB. By varying the bias, a signal could be amplitude modulated with a modulation index as large as 0.65. Tests show that the grid was quite tolerant of failures-the output power dropped by only 1 dB when 10% of the inputs were detuned. The grid amplifier is a multimode device that amplifies beams of different shapes and angles. Beams with incidence angles up to 30° were amplified with less than a 3-dB drop in gain

Transcription activator like effector (TALE)-directed piggyBac transposition in human cells.

Insertional therapies have shown great potential for combating genetic disease and safer methods would undoubtedly broaden the variety of possible illness that can be treated. A major challenge that remains is reducing the risk of insertional mutagenesis due to random insertion by both viral and non-viral vectors. Targetable nucleases are capable of inducing double-stranded breaks to enhance homologous recombination for the introduction of transgenes at specific sequences. However, off-target DNA cleavages at unknown sites can lead to mutations that are difficult to detect. Alternatively, the piggyBac transposase is able perform all of the steps required for integration; therefore, cells confirmed to contain a single copy of a targeted transposon, for which its location is known, are likely to be devoid of aberrant genomic modifications. We aimed to retarget transposon insertions by comparing a series of novel hyperactive piggyBac constructs tethered to a custom transcription activator like effector DNA-binding domain designed to bind the first intron of the human CCR5 gene. Multiple targeting strategies were evaluated using combinations of both plasmid-DNA and transposase-protein relocalization to the target sequence. We demonstrated user-defined directed transposition to the CCR5 genomic safe harbor and isolated single-copy clones harboring targeted integrations

Next generation sequencing of exceptional responders with BRAF-mutant melanoma: implications for sensitivity and resistance.

BackgroundPatients with BRAF mutation-positive advanced melanoma respond well to matched therapy with BRAF or MEK inhibitors, but often quickly develop resistance.MethodsTumor tissue from ten patients with advanced BRAF mutation-positive melanoma who achieved partial response (PR) or complete response (CR) on BRAF and/or MEK inhibitors was analyzed using next generation sequencing (NGS) assay. Genomic libraries were captured for 3230 exons in 182 cancer-related genes plus 37 introns from 14 genes often rearranged in cancer and sequenced to average median depth of 734X with 99% of bases covered >100X.ResultsThree of the ten patients (median number of prior therapies = 2) attained prolonged CR (duration = 23.6+ to 28.7+ months); seven patients achieved either a PR or a short-lived CR. One patient who achieved CR ongoing at 28.7+ months and had tissue available close to the time of initiating BRAF inhibitor therapy had only a BRAF mutation. Abnormalities in addition to BRAF mutation found in other patients included: mutations in NRAS, APC and NF1; amplifications in BRAF, aurora kinase A, MYC, MITF and MET; deletions in CDKN2A/B and PAX5; and, alterations in RB1 and ATM. Heterogeneity between patients and molecular evolution within patients was noted.ConclusionNGS identified potentially actionable DNA alterations that could account for resistance in patients with BRAF mutation-positive advanced melanoma who achieved a PR or CR but whose tumors later progressed. A subset of patients with advanced melanoma may harbor only a BRAF mutation and achieve a durable CR on BRAF pathway inhibitors

Theory and Applications of Robust Optimization

In this paper we survey the primary research, both theoretical and applied, in the area of Robust Optimization (RO). Our focus is on the computational attractiveness of RO approaches, as well as the modeling power and broad applicability of the methodology. In addition to surveying prominent theoretical results of RO, we also present some recent results linking RO to adaptable models for multi-stage decision-making problems. Finally, we highlight applications of RO across a wide spectrum of domains, including finance, statistics, learning, and various areas of engineering.Comment: 50 page