Amplified Dispersive Fourier-Transform Imaging for Ultrafast Displacement Sensing and Barcode Reading

Dispersive Fourier transformation is a powerful technique in which the spectrum of an optical pulse is mapped into a time-domain waveform using chromatic dispersion. It replaces a diffraction grating and detector array with a dispersive fiber and single photodetector. This simplifies the system and, more importantly, enables fast real-time measurements. Here we describe a novel ultrafast barcode reader and displacement sensor that employs internally-amplified dispersive Fourier transformation. This technique amplifies and simultaneously maps the spectrally encoded barcode into a temporal waveform. It achieves a record acquisition speed of 25 MHz -- four orders of magnitude faster than the current state-of-the-art.Comment: Submitted to a journa

Periodically-Poled Silicon [Updated]

We propose a new class of photonic devices based on periodic stress fields in silicon that enable second-order nonlinearity as well as quasi-phase matching. Periodically-poled silicon (PePSi) adds the periodic poling capability to silicon photonics, and allows the excellent crystal quality and advanced manufacturing capabilities of silicon to be harnessed for devices based on second-order nonlinear effects. As an example of the utility of the PePSi technology, we present simulations showing that mid-wave infrared radiation can be efficiently generated through difference frequency generation from near-infrared with a conversion efficiency of 50%. This technology can also be implemented with piezoelectric material, which offers the capability to dynamically control the X(2) nonlinearity.Comment: 11 pages, 4 figure

Compound serum and hemin free medium for cultivation of Leishmania tarentolae: A recombinant protein expression system

Serum free cultivation of Leishmania is cost-effective and improves large scale production of well defined parasite material. Moreover, the production of recombinant pharmaceutical proteins requires cultivation of the host in a culture medium free of animal materials, so several culture media for Leishmania tarentolae expression system have been introduced. Some investigations have established the development of a serum-free, but hemin containing medium, based on yeast extract and buffer salts. Hemin is a substance of animal origin also interferes with nickel ions on Ni-NTA resin. In this study, L. tarentolae from Iranian lizard, cultivated in a compound serum and hemin free medium (LBR medium) and the growth parameters were determined. Here we report that LBR medium could obtain high maximal cell density of 1.8 × 108 cells ml-1 equivalent to that of hemin containing medium in our conditions. This compound medium was confirmed by successful expression of a 28 kDa his-tagged protein. With knowledge of the results, the easy-preparing culture medium could be used as a new culture medium for the production of recombinant proteins in L. tarentolae.Keywords: Leishmania tarentolae, serum free cultivation of Leishmania, protein expression, Leishmania culture media

Limitations of Radar Coordinates

The construction of a radar coordinate system about the world line of an observer is discussed. Radar coordinates for a hyperbolic observer as well as a uniformly rotating observer are described in detail. The utility of the notion of radar distance and the admissibility of radar coordinates are investigated. Our results provide a critical assessment of the physical significance of radar coordinates.Comment: 12 pages, revtex and pictex macros, 3 pictex figures, 1 eps figure. Expanded versio

The Near-Infrared Number Counts and Luminosity Functions of Local Galaxies

This study presents a wide-field near-infrared (K-band) survey in two fields; SA 68 and Lynx 2. The survey covers an area of 0.6 deg.$^2$, complete to K=16.5. A total of 867 galaxies are detected in this survey of which 175 have available redshifts. The near-infrared number counts to K=16.5 mag. are estimated from the complete photometric survey and are found to be in close agreement with other available studies. The sample is corrected for incompleteness in redshift space, using selection function in the form of a Fermi-Dirac distribution. This is then used to estimate the local near-infrared luminosity function of galaxies. A Schechter fit to the infrared data gives: M$^\ast_K = -25.1 \pm 0.3$, $\alpha = -1.3\pm 0.2$ and $\phi^\ast =(1.5\pm 0.5)\times 10^{-3}$ Mpc$^{-3}$ (for H$_0=50$ Km/sec/Mpc and q$_0=0.5$). When reduced to $\alpha=-1$, this agrees with other available estimates of the local IRLF. We find a steeper slope for the faint-end of the infrared luminosity function when compared to previous studies. This is interpreted as due to the presence of a population of faint but evolved (metal rich) galaxies in the local Universe. However, it is not from the same population as the faint blue galaxies found in the optical surveys. The characteristic magnitude ($M^\ast_K$) of the local IRLF indicates that the bright red galaxies ($M_K\sim -27$ mag.) have a space density of $\le 5\times 10^{-5}$ Mpc$^{-3}$ and hence, are not likely to be local objects.Comment: 24 pages, 8 figures, AASTEX 4.0, published in ApJ 492, 45

A Novel Heterophilic Antibody Interaction Involves IgG4

IgG4 has been implicated in a diverse set of complex pathologies - e.g. autoimmune pancreatitis (AIP), idiopathic membranous nephropathy - and carries unique features including lack of activation of the classical complement pathway and a dynamic Fab-arm exchange. We recently showed that the rheumatoid factor (RF)-like activity of IgG4 is achieved through a hitherto unknown, Fc-Fc (and not Fab-Fc as is the case in classical RF; CRF) interaction; hence the name, novel RF (NRF). Here, we further explore the resemblance/difference between CRF and NRF. As heterophilic interactions of human IgM RF (CRF) are well known, we checked whether this is the case for IgG4. Human IgG4 showed variable reactivity to animal IgGs: reacting intensely with rabbit and mouse IgGs, but weakly with others. The binding to rabbit IgG was not through the Fab (as in CRF) but via the Fc piece, as was recently shown for human IgG (NRF). This binding correlates with the IgG4 concentration per se and could therefore be of diagnostic usage and incidentally explain some observed interferences in biological assays. In conclusion, here is defined a novel heterophilic antibody interaction and is established the universality of the unique Fc-Fc binding, both involving IgG4.ArticleSCANDINAVIAN JOURNAL OF IMMUNOLOGY. 71(2):109-114 (2010)journal articl

Twelve Week Calcium Collagen Chelate or Calcium plus Vitamin D Supplementation Does Not Affect Bone Metabolism in Trained Cyclists

The purpose of the present study was to determine whether 12 weeks of calcium collagen chelate (CCC) supplementation during habitual training would affect body composition, bone mineral density (BMD), and biomarkers of bone metabolism in competitive cyclists. Twenty trained (maximal aerobic capacity \u3e 50 ml/kg/min, mean training volume: 28 h/wk) male cyclists performed maximal exercise testing and 40-km time trials (TT) on an electronically braked cycle ergometer. BMD of the whole body, lumbar spine (L1-L4), and both hips were measured via dual-energy X-ray absorptiometry (DXA). The cyclists were assigned to one of two groups: 1) 6 g/d of CCC with 600 mg calcium and 400 IU vitamin D or 2) a placebo control (CON) composed of an inert compound with equivalent calcium and vitamin D concentrations to CCC. Two-way repeated measures ANOVA and Pearson product-moment correlations were used to determine the effects of CCC or CON supplementation on BMD, bone alkaline phosphatase (BAP), tartrate resistant acid phosphatase 5b (TRAP5b), and sclerostin (SCL); significance was accepted at p \u3c 0.05. No within- or between-group differences in dependent variables were found. Significant correlations were found between weekly training volume and TRAP5b (r = 0.531), BAP and VO2 max (r = -0.561), and BAP/TRAP5b ratio and both right/left hip BMD (r = -0.649 and r = -0.646, respectively). In conclusion, 12 weeks supplementation of CCC does not affect body composition, BMD, or biomarkers of bone metabolism in trained, competitive cyclists in comparison to equivalent amounts of calcium plus vitamin D

LotuS2: an ultrafast and highly accurate tool for amplicon sequencing analysis

Background: Amplicon sequencing is an established and cost-efficient method for profiling microbiomes. However, many available tools to process this data require both bioinformatics skills and high computational power to process big datasets. Furthermore, there are only few tools that allow for long read amplicon data analysis. To bridge this gap, we developed the LotuS2 (less OTU scripts 2) pipeline, enabling user-friendly, resource friendly, and versatile analysis of raw amplicon sequences.Results: In LotuS2, six different sequence clustering algorithms as well as extensive pre- and post-processing options allow for flexible data analysis by both experts, where parameters can be fully adjusted, and novices, where defaults are provided for different scenarios.We benchmarked three independent gut and soil datasets, where LotuS2 was on average 29 times faster compared to other pipelines, yet could better reproduce the alpha- and beta-diversity of technical replicate samples. Further benchmarking a mock community with known taxon composition showed that, compared to the other pipelines, LotuS2 recovered a higher fraction of correctly identified taxa and a higher fraction of reads assigned to true taxa (48% and 57% at species; 83% and 98% at genus level, respectively). At ASV/OTU level, precision and F-score were highest for LotuS2, as was the fraction of correctly reported 16S sequences.Conclusion: LotuS2 is a lightweight and user-friendly pipeline that is fast, precise, and streamlined, using extensive pre- and post-ASV/OTU clustering steps to further increase data quality. High data usage rates and reliability enable high-throughput microbiome analysis in minutes

Deep Learning in Label-free Cell Classification.

Label-free cell analysis is essential to personalized genomics, cancer diagnostics, and drug development as it avoids adverse effects of staining reagents on cellular viability and cell signaling. However, currently available label-free cell assays mostly rely only on a single feature and lack sufficient differentiation. Also, the sample size analyzed by these assays is limited due to their low throughput. Here, we integrate feature extraction and deep learning with high-throughput quantitative imaging enabled by photonic time stretch, achieving record high accuracy in label-free cell classification. Our system captures quantitative optical phase and intensity images and extracts multiple biophysical features of individual cells. These biophysical measurements form a hyperdimensional feature space in which supervised learning is performed for cell classification. We compare various learning algorithms including artificial neural network, support vector machine, logistic regression, and a novel deep learning pipeline, which adopts global optimization of receiver operating characteristics. As a validation of the enhanced sensitivity and specificity of our system, we show classification of white blood T-cells against colon cancer cells, as well as lipid accumulating algal strains for biofuel production. This system opens up a new path to data-driven phenotypic diagnosis and better understanding of the heterogeneous gene expressions in cells