Greater Dynamic Range Research Articles

Seasonal variations in phenology and productivity of a tropical dry deciduous forest from MODIS and Hyperion

Tropical dry deciduous forests exhibit diverse phenological behaviour that has significant impact on Gross Primary Productivity (GPP). However, satellite remote sensing of GPP may be impacted by spectral and spatial resolution of sensor. The Vegetation Photosynthesis Model (VPM) was applied to time-series of Hyperion and MODIS (MOD09A1_500m) reflectance values to evaluate spatial and spectral resolution impacts on inference of seasonal variation in phenology and GPP for Teak, Bamboo and Mixed tropical deciduous vegetation ecosystems of Shoolpaneshwar Wildlife Sanctuary (SWS), Gujarat, India. Seasonal dynamics coinciding with the phenological cycle were seen in Enhanced Vegetation Index (EVI) and Land Surface Water Index (LSWI), though with greater dynamic range in Hyperion than MODIS MOD09A1_500m, as a result primarily of spectral properties. In contrast, GPP values from MOD17A2_1000m did not similarly track observed phenological changes. Hyperion EVI resampled at multiple resolutions (30m; 60m; 120m; 250m; 500m) maintained synchrony with variations in the phenological events of canopy. All three covers showed lower GPP estimates in dry season despite higher Photosynthetically Active Radiation (PAR) values suggesting that water availability rather than PAR is the critical factor governing GPP of tropical dry deciduous forests. Given the patchy landscape and moisture-driven seasonal cycle of phenology and GPP, spatial resolutions of better than 250m and narrowband spectral features like Hyperion are necessary for monitoring phenology and GPP of tropical dry deciduous forests, providing a basis for improving methodologies of photosynthesis products from upcoming EnMAP and HyspIRI programs.

THE ROLE OF STELLAR FEEDBACK IN THE DYNAMICS OF H II REGIONS

Stellar feedback is often cited as the biggest uncertainty in galaxy formation models today. This uncertainty stems from a dearth of observational constraints as well as the great dynamic range between the small scales (<1 pc) where the feedback occurs and the large scales of galaxies (>1 kpc) that are shaped by this feedback. To bridge this divide, in this paper we aim to assess observationally the role of stellar feedback at the intermediate scales of HII regions. In particular, we employ multiwavelength data to examine several stellar feedback mechanisms in a sample of 32 HII regions in the Large and Small Magellanic Clouds (LMC and SMC, respectively). Using optical, infrared, radio, and X-ray images, we measure the pressures exerted on the shells from the direct stellar radiation, the dust-processed radiation, the warm ionized gas, and the hot X-ray emitting gas. We find that the warm ionized gas dominates over the other terms in all of the sources, although two have comparable dust-processed radiation pressures to their warm gas pressures. The hot gas pressures are comparatively weak, while the direct radiation pressures are 1-2 orders of magnitude below the other terms. We discuss the implications of these results, particularly highlighting evidence for hot gas leakage from the HII shells and regarding the momentum deposition from the dust-processed radiation to the warm gas. Furthermore, we emphasize that similar observational work should be done on very young HII regions to test whether direct radiation pressure and hot gas can drive the dynamics at early times.

Front-End Board with Cyclone V as a Test High-Resolution Platform for the Auger_Beyond_2015 Front End Electronics

The surface detector (SD) array of the Pierre Auger Observatory needs an upgrade which allows space for more complex triggers with higher bandwidth and greater dynamic range. To this end this paper presents a front-end board (FEB) with the largest Cyclone V E FPGA 5CEFA9F31I7N. It supports eight channels sampled with max. 250 MSps@14-bit resolution. Considered sampling for the SD is 120 MSps; however, the FEB has been developed with external anti-aliasing filters to retain maximal flexibility. Six channels are targeted at the SD, two are reserved for other experiments like: Auger Engineering Radio Array and additional muon counters. The FEB is an intermediate design plugged into a unified board communicating with a micro-controller at 40 MHz; however, it provides 250 MSPs sampling with an 18-bit dynamic range, is equipped with a virtual NIOS processor and supports 256 MB of SDRAM as well as an implemented spectral trigger based on the discrete cosine transform for detection of very inclined “old” showers. The FEB can also support neural network development for detection of “young” showers, potentially generated by neutrinos. A single FEB was already tested in the Auger surface detector in Malargue (Argentina) for 120 and 160 MSps. Preliminary tests showed perfect stability of data acquisition for sampling frequency three or four times greater. They allowed optimization of the design before deployment of seven or eight FEBs for several months of continuous tests in the engineering array.

A THIRD-GENERATION OPTICAL FIBRE TRANSDUCER FOR LANDSLIDE MONITORING

Monitoring an unstable slope is quite important for environmental safety. Based on our previous studies, this paper presents a third-generation distributed optical fibre transducer. The operating mechanism of this novel transducer was analysed for its response to a single concentrated and uniform load, and a theoretical study was conducted on the elongation of the bottom-surface fibres of a bending resistance model at the phases of linear elasticity and total cross-section cut-off stage. A bending resistance test was conducted when this transducer was grouted with concrete C40 and two types of base materials - expanded polystyrene (EPS) and polyvinyl chloride (PVC). Experimental and theoretical studies results indicate that the minimum diameter of the second coiling of a single mode fibre is more than 20 cm at wavelength 1310 nm. The ratio of the measured value to theoretical value for elongation of optical fibres on the bottom surface is greater than 0.9, indicating significant correlation. The transducer with EPS as its base material provides a better response than the one with PVC, because of its higher initial measurement precision, larger sliding distance, and greater dynamic range. However, sliding is bound to produce shear force; therefore, further research on the performance of the transducer and its grout under shearing loads should be conducted.

Chapter One - Introduction to Sequencing the Brain Transcriptome

High-throughput next-generation sequencing is now entering its second decade. However, it was not until 2008 that the first report of sequencing the brain transcriptome appeared (Mortazavi, Williams, Mccue, Schaeffer, & Wold, 2008). These authors compared short-read RNA-Seq data for mouse whole brain with microarray results for the same sample and noted both the advantages and disadvantages of the RNA-Seq approach. While RNA-Seq provided exon level resolution, the majority of the reads were provided by a small proportion of highly expressed genes and the data analysis was exceedingly complex. Over the past 6 years, there have been substantial improvements in both RNA-Seq technology and data analysis. This volume contains 11 chapters that detail various aspects of sequencing the brain transcriptome. Some of the chapters are very methods driven, while others focus on the use of RNA-Seq to study such diverse areas as development, schizophrenia, and drug abuse. This chapter briefly reviews the transition from microarrays to RNA-Seq as the preferred method for analyzing the brain transcriptome. Compared with microarrays, RNA-Seq has a greater dynamic range, detects both coding and noncoding RNAs, is superior for gene network construction, detects alternative spliced transcripts, and can be used to extract genotype information, e.g., nonsynonymous coding single nucleotide polymorphisms. RNA-Seq embraces the complexity of the brain transcriptome and provides a mechanism to understand the underlying regulatory code; the potential to inform the brain-behavior-disease relationships is substantial.

Mechanical Stress in Actinin and Actin in Stem Cells

cpstFRET is a FRET based force sensor designed to be modulated primarily by the angle between the donor and acceptor. It is physically smaller, less invasive, and has greater dynamic range and better signal-to-noise behavior than the linear probes. Using this sensor with FRET polarization imaging we measured the gradients of constitutional stresses in time and space for actinin and actin in HEK and MDCK cells. We created eight stable cell lines with these probes. Then we derived stem cells from the cell lines and measured stress changes during differentiation and dedifferentiation. We calculated FRET with the parallel/perpendicular polarization images of FRET. Because the FRET signal is always more depolarized, high ratios represent low FRET and high stress, while low ratios represent high FRET and low stress. We induced HEK and MDCK cells into embryoid bodies (EB) which is the characteristic morphology of induced pluripotent stem cells and cancer stem cells. We verified the stem cell in the EBs with alkaline phosphatase (AP) staining. Stem cells in EBs derived from HEKs showed higher AP activities than those derived from MDCK cells. All stem cells showed escalated stress in both actinin and actin relative to the parent. Stress was higher in stem cells of HEK origination. After we removed the EB-induction factors, these stresses declined as the stem cells differentiated into HEK or epithelial cells. We also induced the stem cells differentiate into neurons. The cell body showed low stress while axon extrusions showed increased stress in actin and actinin. The significant stress changes in stem cells and differentiated descendants hint at the potential of inducing pluripotent stem cells through changing cell mechanics. The data also shows that stem cell differentiation involves changes in internal stresses as well as changes in biochemistry.

Defining Protein Complexes that Mediate Bacterial Chemotaxis by Pulsed Dipolar ESR Spectroscopy

Bacterial chemotaxis is the process whereby cells modulate their flagella-driven motility in response to environmental cues. This widespread behavior relies upon a complex sensory apparatus composed of transmembrane receptors, histidine kinases and coupling proteins to achieve great sensitivity, gain and dynamic range in signal processing. We have applied pulsed-dipolar ESR spectroscopy (PDS) combined with site-directed spin labeling to probe the structures and mechanisms of proteins that compose these regulatory circuits. Inherent symmetries within the protein complexes require interpretation of signals from systems that contain more than two spins. Tikhonov regularization and maximum entropy refinement when combined with model simulation reproduce accurate inter-spin distance distributions from such multiply labeled species. Disulfide crosslinking and disruptive mutagenesis verify component interfaces predicted by PDS. Weak but specific interactions that produce low population aggregates relevant to complex assembly are detected by an approach that relies on magnetic dilution and baseline analysis of dipolar spectra. The resulting PDS-based models capture key architectural features of the receptor kinase arrays and the flagellar motor. Moreover, distance distributions derived from the multi- spin sites reveal changes in conformation and dynamics that accompany kinase activation and motor switching. Application to the chemotaxis system demonstrates how PDS effectively reports on key structural features of transient protein complexes and in doing so fills the resolution gap between other well-established biophysical techniques such as electron microscopy and x-ray crystallography.

Recent Advances in High Dynamic Range Imaging

This paper aims to present a review of recent techniques in high dynamic range imaging (HDRI), which was the topic in research areas including image processing, computer graphics, and photography. HDRI or just HDR is a set of techniques that allows a greater dynamic range between the lightest and darkest areas of an image than current standard digital imaging techniques or photographic methods. HDR imaging technologies will spread its sphere of influence in imaging industry for its high quality and its powerful expression ability, including digital cinema, digital photography and next generation broadcast. This paper discusses recent advances, future direction in HDRI. The major goal of the paper is to provide a reference source for the researchers involved in HDRI, regardless of particular application areas.

Comparison of Microarrays and RNA-Seq for Gene Expression Analyses of Dose-Response Experiments

Relative to microarrays, RNA-seq has been reported to offer higher precision estimates of transcript abundance, a greater dynamic range, and detection of novel transcripts. However, previous comparisons of the 2 technologies have not covered dose-response experiments that are relevant to toxicology. Male F344 rats were exposed for 13 weeks to 5 doses of bromobenzene, and liver gene expression was measured using both microarrays and RNA-seq. Multiple normalization methods were evaluated for each technology, and gene expression changes were statistically analyzed using both analysis of variance and benchmark dose (BMD). Fold-change values were highly correlated between the 2 technologies, whereas the -log p values showed lower correlation. RNA-seq detected fewer statistically significant genes at lower doses, but more significant genes based on fold change except when a negative binomial transformation was applied. Overlap in genes significant by both p value and fold change was approximately 30%-40%. Random sampling of the RNA-seq data showed an equivalent number of differentially expressed genes compared with microarrays at ~5 million reads. Quantitative RT-PCR of differentially expressed genes uniquely identified by each technology showed a high degree of confirmation when both fold change and p value were considered. The mean dose-response expression of each gene was highly correlated between technologies, whereas estimates of sample variability and gene-based BMD values showed lower correlation. Differences in BMD estimates and statistical significance may be due, in part, to differences in the dynamic range of each technology and the degree to which normalization corrects genes at either end of the scale.

Myopic aberrations: Simulation based comparison of curvature and Hartmann Shack wavefront sensors

In comparison with a Hartmann Shack wavefront sensor, the curvature wavefront sensor is known for its higher sensitivity and greater dynamic range. The aim of this study is to numerically investigate the merits of using a curvature wavefront sensor, in comparison with a Hartmann Shack (HS) wavefront sensor, to analyze aberrations of the myopic eye. Aberrations were statistically generated using Zernike coefficient data of 41 myopic subjects obtained from the literature. The curvature sensor is relatively simple to implement, and the processing of extra- and intra-focal images was linearly resolved using the Radon transform to provide Zernike modes corresponding to statistically generated aberrations. Simulations of the HS wavefront sensor involve the evaluation of the focal spot pattern from simulated aberrations. Optical wavefronts were reconstructed using the slope geometry of Southwell. Monte Carlo simulation was used to find critical parameters for accurate wavefront sensing and to investigate the performance of HS and curvature sensors. The performance of the HS sensor is highly dependent on the number of subapertures and the curvature sensor is largely dependent on the number of Zernike modes used to represent the aberration and the effective propagation distance. It is shown that in order to achieve high wavefront sensing accuracy while measuring aberrations of the myopic eye, a simpler and cost effective curvature wavefront sensor is a reliable alternative to a high resolution HS wavefront sensor with a large number of subapertures.

Dynamic Infrared Scene Simulation Study Based on DMD Imaging System

Dynamic infrared scene generator is one of the important means to test the detection,track and anti-interference performance of the infrared seeker. The article to a certain type of air-to-air missile seeker loop simulation application object, based on the micro-mirror array (DMD), Vega Prime software and its infrared module for the development of tools,Real-time infrared images with vary objects and backgrounds in different conditions are generated to simulate the infrared radiation at the pupil of the guide system.The radiation of blackbody is reflected and modulated by digital micro mirror device based on infrared video signal,which is used to test and evaluate the performance of infrared seeker.The results indicate that the system has the advantages of compact structure,high real-time performance,high frame frequency,high resolution,and great dynamic range.

An Electricity Parameter Measurement for Off-Grid PWM Converter

The input voltage of off-grid PWM converters has a great dynamic range in amplitude and frequency. In addition, the frequent changing of these parameters also makes it hard to measure preciously via traditional ways. Details of window function are presented. A modified FFT spectrum analyzing method using interpolation is also given and checked. Finally, a feasible solution which balances both precision and real-time data processing comes up considering the speed of MCUs mainly used in industry. Simulations and experiments show that this solution settles the troubles which cant be cleared up by traditional methods.

A case study in bio-inspired engineering design: defense applications of exoskeletal sensors

As part of a bio-inspired design process, the authors examine exoskeletal sensors found in insects and their potential application to armor and hardened buildings. In this way, the outer hardening of a structure or vehicle would not limit the ability of occupants to arrive at an actionable picture of the outer environment. To this end, various sensor modalities employed by insects are compared and contrasted with their current human-engineered equivalents. In several sensing modalities, biosensors perform better, are smaller, and more energy efficient than human-engineered equivalents. They note that biological designs tend to employ non-linear response to signal amplitude and respond with heightened sensitivity over a greater dynamic range of signals than human-engineered sensors. The insect biological sensors have structural and mechanical innovations that preserve the protective capacity of the exoskeleton.

How Locusts Breathe

Insect tracheal-respiratory systems achieve high fluxes and great dynamic range with low energy requirements and could be important models for bioengineers interested in developing microfluidic systems. Recent advances suggest that insect cardiorespiratory systems have functional valves that permit compartmentalization with segment-specific pressures and flows and that system anatomy allows regional flows. Convection dominates over diffusion as a transport mechanism in the major tracheae, but Reynolds numbers suggest viscous effects remain important.

Novel Bipolar Photonic Digital-to-Analog Conversion Employing Differential Phase Shift Keying Modulation and Balanced Detection

A novel weighed and summing bipolar photonic digital-to-analog converter (BPDAC) scheme employing optical differential phase shift keying modulation and balanced detection is proposed and demonstrated in a proof-of-principle experiment of three-bit resolution and 2.5-GS/s conversion rate. Compared with the existing unipolar PDAC schemes, this BPDAC has a greater dynamic range and a larger noise margin. Compared with our previously proposed BPDAC based on optical differential quadrature phase shift keying modulation, it is much more robust to the phase detuning, and the tolerable range is greatly expanded from ±1° to ±18°.

Genes, behavior and next-generation RNA sequencing.

Advances in next-generation sequencing suggest that RNA-Seq is poised to supplant microarray-based approaches for transcriptome analysis. This article briefly reviews the use of microarrays in the brain-behavior context and then illustrates why RNA-Seq is a superior strategy. Compared with microarrays, RNA-Seq has a greater dynamic range, detects both coding and noncoding RNAs, is superior for gene network construction, detects alternative spliced transcripts, detects allele specific expression and can be used to extract genotype information, e.g. nonsynonymous coding single nucleotide polymorphisms. Examples of where RNA-Seq has been used to assess brain gene expression are provided. Despite the advantages of RNA-Seq, some disadvantages remain. These include the high cost of RNA-Seq and the computational complexities associated with data analysis. RNA-Seq embraces the complexity of the transcriptome and provides a mechanism to understand the underlying regulatory code; the potential to inform the brain-behavior relationship is substantial.

Novel 2N bit bipolar photonic digital-to-analog converter based on optical DQPSK modulation coupled with differential detection

A novel 2N bit bipolar photonic digital-to-analog converter (PDAC) scenario based on the optical differential quadrature phase shift keying (ODQPSK) modulation coupled with differential detection is proposed. Compared with other proposed schemes, this bipolar PDAC has a greater dynamic range and a larger noise margin with good scalabilities both in speed and resolution. We demonstrate a 4 bit PDAC in a proof-of-principle experiment at a sampling rate of 2.5 GS/s.

Abstract 1003: A link between lactate dehydrogenase A, lactate and tumor phenotype identified by imaging

Abstract Metabolic changes in primary tumors have a significant impact on tumor progression and on the development of the metastatic phenotype. In cancer patients, serum total lactate dehydrogenase (LDH) levels are often increased, and the gene for LDH-A protein, is frequently upregulated in tumors (Koukourakis, Giatromanolaki et al. 2003). These features have been linked to poor prognosis, and a greater metastatic potential has been reported in patients with high LDH serum levels. Since LDH-A protein is required for the maintenance and progression of many tumors (Fantin, St-Pierre et al. 2006), it is also becoming a potential target for cancer therapy (Le, Cooper et al. 2010; Seth, Grant et al. 2011). We investigated the relationship between LDH-A expression and lactate production in two isogenic breast cancer lines (67NR and 4T1) (Serganova, Rizwan et al. 2011). These two cell lines were derived from a single mammary tumor that developed spontaneously in a BALB/c mouse. Each subclone was shown to have different phenotypic properties (Aslakson and Miller 1992). LDH-A expression, lactate concentration, glucose utilization and oxygen consumption were measured in cells, and the potential relationship between tumor lactate levels (measured by magnetic resonance spectroscopic imaging (MRSI)) and tumor glucose utilization (measured by [18F] 2-deoxy-2-fluoro-D-glucose positron emission tomography ([18F]FDG-PET)) was assessed in orthotopic breast tumors derived from these cell lines. We show a substantial difference in LDH-A expression between 67NR and 4T1 cells under normoxia and hypoxia. We also show that small orthotopic 4T1 tumors generate ten-fold more lactate than corresponding 67NR tumors. The high lactate levels in small primary 4T1 tumors are associated with intense pimonidazole staining (a hypoxia indicator). Less intense hypoxia staining was observed in the larger 67NR tumors, and is consistent with the gradual increase and plateau of lactate concentration in enlarging 67NR tumors. We show that lactate-MRSI has a greater dynamic range than [18F]FDG-PET and may be a more sensitive measure to evaluate the aggressive and metastatic potential of primary breast tumors. We hypothesized that tumor lactate levels monitored by MRSI will reflect LDH-A enzymatic activity and tumor phenotype. We also suggest that lactate-MRSI is a more sensitive measure than [18F]FDG-PET, and could be used in the clinic to evaluate the aggressive potential of primary breast tumors. Aslakson, C. J. and F. R. Miller (1992). Cancer Res 52(6): 1399-1405. Fantin, V. R., J. St-Pierre, et al. (2006). Cancer Cell 9(6): 425-434. Koukourakis, M. I., A. Giatromanolaki, et al. (2003). Br J Cancer 89(5): 877-885.Le, A., C. R. Cooper, et al. (2010). Proc Natl Acad Sci U S A 107(5): 2037-2042. Serganova, I., A. Rizwan, et al. (2011). Clin Cancer Res 17(19): 6250-6261. Seth, P., A. Grant, et al. (2011). Neoplasia 13(1): 60-71. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 1003. doi:1538-7445.AM2012-1003

Transcriptome analysis of the model protozoan, Tetrahymena thermophila, using Deep RNA sequencing.

BackgroundThe ciliated protozoan Tetrahymena thermophila is a well-studied single-celled eukaryote model organism for cellular and molecular biology. However, the lack of extensive T. thermophila cDNA libraries or a large expressed sequence tag (EST) database limited the quality of the original genome annotation.Methodology/Principal FindingsThis RNA-seq study describes the first deep sequencing analysis of the T. thermophila transcriptome during the three major stages of the life cycle: growth, starvation and conjugation. Uniquely mapped reads covered more than 96% of the 24,725 predicted gene models in the somatic genome. More than 1,000 new transcribed regions were identified. The great dynamic range of RNA-seq allowed detection of a nearly six order-of-magnitude range of measurable gene expression orchestrated by this cell. RNA-seq also allowed the first prediction of transcript untranslated regions (UTRs) and an updated (larger) size estimate of the T. thermophila transcriptome: 57 Mb, or about 55% of the somatic genome. Our study identified nearly 1,500 alternative splicing (AS) events distributed over 5.2% of T. thermophila genes. This percentage represents a two order-of-magnitude increase over previous EST-based estimates in Tetrahymena. Evidence of stage-specific regulation of alternative splicing was also obtained. Finally, our study allowed us to completely confirm about 26.8% of the genes originally predicted by the gene finder, to correct coding sequence boundaries and intron-exon junctions for about a third, and to reassign microarray probes and correct earlier microarray data.Conclusions/SignificanceRNA-seq data significantly improve the genome annotation and provide a fully comprehensive view of the global transcriptome of T. thermophila. To our knowledge, 5.2% of T. thermophila genes with AS is the highest percentage of genes showing AS reported in a unicellular eukaryote. Tetrahymena thus becomes an excellent unicellular model eukaryote in which to investigate mechanisms of alternative splicing.

A digital microfluidic method for multiplexed cell-based apoptosis assays

Digital microfluidics (DMF), a fluid-handling technique in which picolitre-microlitre droplets are manipulated electrostatically on an array of electrodes, has recently become popular for applications in chemistry and biology. DMF devices are reconfigurable, have no moving parts, and are compatible with conventional high-throughput screening infrastructure (e.g., multiwell plate readers). For these and other reasons, digital microfluidics has been touted as being a potentially useful new tool for applications in multiplexed screening. Here, we introduce the first digital microfluidic platform used to implement parallel-scale cell-based assays. A fluorogenic apoptosis assay for caspase-3 activity was chosen as a model system because of the popularity of apoptosis as a target for anti-cancer drug discovery research. Dose-response profiles of caspase-3 activity as a function of staurosporine concentration were generated using both the digital microfluidic method and conventional techniques (i.e., pipetting, aspiration, and 96-well plates.) As expected, the digital microfluidic method had a 33-fold reduction in reagent consumption relative to the conventional technique. Although both types of methods used the same detector (a benchtop multiwell plate reader), the data generated by the digital microfluidic method had lower detection limits and greater dynamic range because apoptotic cells were much less likely to de-laminate when exposed to droplet manipulation by DMF relative to pipetting/aspiration in multiwell plates. We propose that the techniques described here represent an important milestone in the development of digital microfluidics as a useful tool for parallel cell-based screening and other applications.