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This dataset contains single-nucleus RNA sequencing data from poplar (Populusspp.) roots under control and methyl jasmonate (MeJA) treatment conditions. It was generated to investigate cell type-specific stress responses and to establish a high-resolution transcriptomic atlas in a perennial woody species.
Probabilistic models and statistical methods in processing telemetry data with sequence of data and sync words
In a spread-spectrum communication system, a data sequence of +1's and -1's is expanded into a sequence of +x's (bottom bar) and -x's (bottom bar) where x (bottom bar) is a length n sequence of +1's and -1's. A sub-baud code is the assignment of a different such baud sequence to each of M users with the objective of reducing interference between users. It is shown that this interference can be described in terms of the even and odd correlation functions between pairs of sequences. A technique for deriving sub-baud codes from cyclic error-correcting codes is given, and a theorem proved which bounds the quality of the resultant code. A specific such cyclic code construction procedure is given which, for any M, yields a sub-baud code for which the mutual interference can be made arbitrarily small by choosing n sufficiently large.
In a frequency-hopped (FH) multiple-frequency-shift-keyed (MFSK) communication system, frequency hopping causes the necessary frequency transitions for time synchronization estimation rather than the data sequence as in the conventional (nonfrequency-hopped) system. Making use of this observation, this paper presents a fine synchronization (i.e., time errors of less than a hop duration) technique for estimation of FH timing. The performance degradation due to imperfect FH time synchronization is found in terms of the effect on bit error probability as a function of full-band or partial-band noise jamming levels and of the number of hops used in the FH timing estimate.
An examination has been conducted of the extensive amino acid sequence data now available for five protein families - the alpha crystallin A chain, myoglobin, alpha and beta hemoglobin, and the cytochromes c - with the goal of estimating the true spatial distribution of base substitutions within genes that code for proteins. In every case the commonly used Poisson density failed to even approximate the experimental pattern of base substitution. For the 87 species of beta hemoglobin examined, for example, the probability that the observed results were from a Poisson process was the minuscule 10 to the -44th. Analogous results were obtained for the other functional families. All the data were reasonably, but not perfectly, described by the negative binomial density. In particular, most of the data were described by one of the very simple limiting forms of this density, the geometric density. The implications of this for evolutionary inference are discussed. It is evident that most estimates of total base substitutions between genes are badly in need of revision.
Uranus and Jupiter HD/H2 spectra determine bulk D/H ratios which are significantly different from theoretical expectations, with the Uranus D/H about half the Jovian value. Feasibility of Mars photochemistry study with a PEPSIOS spectrometer was demonstrated with visible band O2, H2O, and CO2 spectra; and near infrared (1.57 micron) spectra of CO and CO2; and NASA/IRTF observations have been proposed in support of the Mars Observer mission objectives. Analysis of monochromatic images clearly resolve the azimuthal and radial structure in the Jovian nebula (ion partitioning, temperature structure, ion/neutral interactions), adding a unique and important post-Voyager perspective and providing a baseline for forthcoming Galileo experiments. Simultaneous ground based and IUE observations of Jovian nebula are under analysis. Doppler resolved image sequences (data cubes) of Io sodium neutrals clearly isolate the high velocity charge exchange jet, a sensitive ground-based probe of the tenuous neutral atmosphere of Io.
The objectives and the background of the Mars Observer mission are briefly reviewed with emphasis on the remote science operations portion of the mission. In particular, the discussion covers observational planning and instrument sequences, data retrieval, instrument health monitoring, and science analysis. Attention is also given to workstation technology utilization, science team, project data base, common data formats, and security.
An electro-optic resonant cavity is used to achieve phase modulation with lower driving voltages. Laser damage thresholds are inherently higher than with previously used integrated optics due to the utilization of bulk optics. Phase modulation is achieved at higher speeds with lower driving voltages than previously obtained with non-resonant electro-optic phase modulators. The instant scheme uses a data locking dither approach as opposed to the conventional sinusoidal locking schemes. In accordance with a disclosed embodiment, a resonant cavity modulator has been designed to operate at a data rate in excess of 100 megabits per sec. By carefully choosing the cavity finesse and its dimension, it is possible to control the pulse switching time to within 4 nano-sec. and to limit the required switching voltage to within 10 V. This cavity locking scheme can be applied by using only the random data sequence, and without the need of dithering of the cavity. Compared to waveguide modulators, the resonant cavity has a comparable modulating voltage requirement. Because of its bulk geometry, the resonant cavity modulator has the potential of accommodating higher throughput power. Mode matching into the bulk device is easier and typically can be achieved with higher efficiency. An additional control loop is incorporated into the modulator to maintain the cavity on resonance.
This paper presents a time-domain method to identify a state space model of a linear system and its corresponding observer/Kalman filter from a given set of general input-output data. The identified filter has the properties that its residual is minimized in the least squares sense, orthogonal to the time-shifted versions of itself, and to the given input-output data sequence. The connection between the state space model and a particular auto-regressive moving average description of a linear system is made in terms of the Kalman filter and a deadbeat gain matrix. The procedure first identifies the Markov parameters of an observer system, from which a state space model of the system and the filter gain are computed. The developed procedure is shown to improve results obtained by an existing observer/Kalman filter identification method, which is based on an auto-regressive model without the moving average terms. Numerical and experimental results are presented to illustrate the proposed method.
A new modulation technique called combinatorial pulse position modulation (CPPM) is presented as a power-efficient alternative to quaternary pulse position modulation (QPPM) for direct-detection, free-space laser communications. The special case of 16C4PPM is compared to QPPM in terms of data throughput and bit error rate (BER) performance for similar laser power and pulse duty cycle requirements. The increased throughput from CPPM enables the use of forward error corrective (FEC) encoding for a net decrease in the amount of laser power required for a given data throughput compared to uncoded QPPM. A specific, practical case of coded CPPM is shown to reduce the amount of power required to transmit and receive a given data sequence by at least 4.7 dB. Hardware techniques for maximum likelihood detection and symbol timing recovery are presented.
An electro-optic resonant cavity is used to achieve phase modulation with lower driving voltages. Laser damage thresholds are inherently higher than with previously used integrated optics due to the utilization of bulk optics. Phase modulation is achieved at higher speeds with lower driving voltages than previously obtained with non-resonant electro-optic phase modulators. The instant scheme uses a data locking dither approach as opposed to the conventional sinusoidal locking schemes. In accordance with a disclosed embodiment, a resonant cavity modulator has been designed to operate at a data rate in excess of 100 Mbps. By carefully choosing the cavity finesse and its dimension, it is possible to control the pulse switching time to within 4 ns and to limit the required switching voltage to within 10 V. Experimentally, the resonant cavity can be maintained on resonance with respect to the input laser signal by monitoring the fluctuation of output intensity as the cavity is switched. This cavity locking scheme can be applied by using only the random data sequence, and without the need of additional dithering of the cavity. Compared to waveguide modulators, the resonant cavity has a comparable modulating voltage requirement. Because of its bulk geometry, resonant cavity modulator has the potential of accommodating higher throughput power. Furthermore, mode matching into a bulk device is easier and typically can be achieved with higher efficiency. On the other hand, unlike waveguide modulators which are essentially traveling wave devices, the resonant cavity modulator requires that the cavity be maintained in resonance with respect to the incoming laser signal. An additional control loop is incorporated into the modulator to maintain the cavity on resonance.
Progress in the past three months has occurred in two areas, reconstruction of ancestral proteins and improved understanding of chemical features that are likely to be universal in generic matter regardless of its genesis. Ancestral ribonucleases have been reconstructed, and an example has been developed that shows how physiological function can be assigned to in vitro behaviors observed in biological systems. Sequence data have been collected to permit the reconstruction of src homology 2 domains that underwent radiative divergence at the time of the radiative divergence of chordates. New studies have been completed that show how genetic matter (or its remnants) might be detected on Mars (or other non-terrean locations.) Last, the first in vitro selection experiments have been completed using a nucleoside library carrying positively charged functionality, illustrating the importance of non-standard nucleotides to those attempting to obtain evidence for an "RNA world" as an early episode of life on earth.
In December 1993, the Environmental Protection Agency (EPA) Emission Standards Division and the National Aeronautics and Space Administration's (NASA's) Marshall Space Flight Center (MSFC) signed an Interagency Agreement (IA) initiating a task force for the technical assessment of alternative technologies for aerospace depainting operations. The United States Air Force (USAF) joined the task force in 1994. The mandates of the task force were: (1) To identify available alternative depainting systems that do not rely on methylene chloride or other ozone-depleting, chlorinated, and volatile organic carbon solvents. (2) To determine the viability, applicability, and pollution prevention potential of each identified alternative. (3) To address issues of safety, environmental impact, reliability, and maintainability. Through a Technical Implementation Committee (TIC), the task force selected and evaluated eight alternative paint stripping technologies: chemical stripping, carbon dioxide (CO2) blasting, xenon flashlamp and CO2 coatings removal (FLASHJET(R)), CO2 laser stripping, plastic media blasting (PMB), sodium bicarbonate wet stripping, high-pressure water blasting (WaterJet), and wheat starch abrasive blasting (Enviro-Strip(R)). (The CO2 blasting study was discontinued after the first depainting sequence.) This final report presents the results of the Joint EPA/NASA/USAF Interagency Depainting Study. Significant topics include: (1) Final depainting sequence data for the chemical stripping, PMB, sodium bicarbonate wet stripping, and WaterJet processes. (2) Strip rates for all eight technologies. (3) Sequential comparisons of surface roughness measurements for the seven viable depainting technologies. (4) Chronological reviews of and lessons learned in the conduct of all eight technologies. (5) An analysis of the surface roughness trends for each of the seven technologies. (6) Metallurgic evaluations of panels Summaries of corrosion and hydrogen embrittlement evaluations of chemical stripping panels, detailed descriptions of which appear in previous reports. Because the requirements for alternative systems are diverse, as are initial setup, training, and on-going operational considerations, this study does not recommend a particular product or process. Users of this study will draw their own conclusions from the data presented herein.
The effect of human induced change in the aerosol concentration and properties, or the aerosol response to climate change (e.g. droughts producing fires or dust) should be measured relative to a "background aerosol". How to define this background aerosol, so that it is both measurable and useful? Here we use 10 stations located in the Pacific, Atlantic and Indian Oceans to answer this question. Using a data set of the spectral optical thickness measured by the Aerosol Robotic network (AERONET), extending 1-3 years, we find the background conditions for these stations. The oceanic background aerosol is the result of ocean emission and spray, and some residual long lived continental aerosol. Its source is very broadly spread and is expected to vary little in time. Pollution or dust sources are from specific locations, emitted and transported to the measuring site in specific combination of meteorological conditions. Therefore they are expected to vary with time. It follows that the background aerosol can be identified as the median for conditions with small variations. To define the background we compute the median of N consequent measurements. We use N=50 that in average cloudy conditions corresponds to 2-3 days of measurements and N=100 (4-5 days). Most high polluted or dusty conditions correspond to data sequences with high standard deviation (greater than 0.02 in optical thickness) and are excluded. From the remaining N point running medians with low standard deviations we derive again the median. This excludes those rare cases of pollution or dust that is stable during the N measurements. The results show that the background aerosol over the Pacific Ocean is characterize by optical thickness of 0.055 at 500 nm and Angstrom exponent of 0.74. Over the Atlantic Ocean the values are 0.070 and 1.1 respectively, with little influence of the assumed value of N (50 or 100). The derivation of the background uses 20,000 and 5000 medians respectively that passed the criteria. The contribution of coarse and fine aerosol to the background aerosol is also calculated.
Despite the importance of plant lignans and isoflavonoids in human health protection (e.g. for both treatment and prevention of onset of various cancers) as well as in plant biology (e.g. in defense functions and in heartwood development), systematic studies on the enzymes involved in their biosynthesis have only recently begun. In this investigation, three NADPH-dependent aromatic alcohol reductases were comprehensively studied, namely pinoresinol-lariciresinol reductase (PLR), phenylcoumaran benzylic ether reductase (PCBER), and isoflavone reductase (IFR), which are involved in central steps to the various important bioactive lignans and isoflavonoids. Of particular interest was in determining how differing regio- and enantiospecificities are achieved with the different enzymes, despite each apparently going through similar enone intermediates. Initially, the three-dimensional x-ray crystal structures of both PLR_Tp1 and PCBER_Pt1 were solved and refined to 2.5 and 2.2 A resolutions, respectively. Not only do they share high gene sequence similarity, but their structures are similar, having a continuous alpha/beta NADPH-binding domain and a smaller substrate-binding domain. IFR (whose crystal structure is not yet obtained) was also compared (modeled) with PLR and PCBER and was deduced to have the same overall basic structure. The basis for the distinct enantio-specific and regio-specific reactions of PCBER, PLR, and IFR, as well as the reaction mechanism and participating residues involved (as identified by site-directed mutagenesis), are discussed.
Potato virus X (PVX) TGBp3 is required for virus cell-to-cell movement. Cell-to-cell movement of TGBp3 was studied using biolistic bombardment of plasmids expressing GFP:TGBp3. TGBp3 moves between cells in Nicotiana benthamiana, but requires TGBp1 to move in N. tabacum leaves. In tobacco leaves GFP:TGBp3 accumulated in a pattern resembling the endoplasmic reticulum (ER). To determine if the ER network is important for GFP:TGBp3 and for PVX cell-to-cell movement, a single mutation inhibiting membrane binding of TGBp3 was introduced into GFP:TGBp3 and into PVX. This mutation disrupted movement of GFP:TGBp3 and PVX. Brefeldin A, which disrupts the ER network, also inhibited GFP:TGBp3 movement in both Nicotiana species. Two deletion mutations, that do not affect membrane binding, hindered GFP:TGBp3 and PVX cell-to-cell movement. Plasmids expressing GFP:TGBp2 and GFP:TGBp3 were bombarded to several other PVX hosts and neither protein moved between adjacent cells. In most hosts, TGBp2 or TGBp3 cannot move cell-to-cell.
Environmental and hormonal signals control diverse physiological processes in plants. The mechanisms by which plant cells perceive and transduce these signals are poorly understood. Understanding biochemical and molecular events involved in signal transduction pathways has become one of the most active areas of plant research. Research during the last 15 years has established that Ca2+ acts as a messenger in transducing external signals. The evidence in support of Ca2+ as a messenger is unequivocal and fulfills all the requirements of a messenger. The role of Ca2+ becomes even more important because it is the only messenger known so far in plants. Since our last review on the Ca2+ messenger system in 1987, there has been tremendous progress in elucidating various aspects of Ca(2+) -signaling pathways in plants. These include demonstration of signal-induced changes in cytosolic Ca2+, calmodulin and calmodulin-like proteins, identification of different Ca2+ channels, characterization of Ca(2+) -dependent protein kinases (CDPKs) both at the biochemical and molecular levels, evidence for the presence of calmodulin-dependent protein kinases, and increased evidence in support of the role of inositol phospholipids in the Ca(2+) -signaling system. Despite the progress in Ca2+ research in plants, it is still in its infancy and much more needs to be done to understand the precise mechanisms by which Ca2+ regulates a wide variety of physiological processes. The purpose of this review is to summarize some of these recent developments in Ca2+ research as it relates to signal transduction in plants.
BACKGROUND: The pattern and timing of the rise in complex multicellular life during Earth's history has not been established. Great disparity persists between the pattern suggested by the fossil record and that estimated by molecular clocks, especially for plants, animals, fungi, and the deepest branches of the eukaryote tree. Here, we used all available protein sequence data and molecular clock methods to place constraints on the increase in complexity through time. RESULTS: Our phylogenetic analyses revealed that (i) animals are more closely related to fungi than to plants, (ii) red algae are closer to plants than to animals or fungi, (iii) choanoflagellates are closer to animals than to fungi or plants, (iv) diplomonads, euglenozoans, and alveolates each are basal to plants+animals+fungi, and (v) diplomonads are basal to other eukaryotes (including alveolates and euglenozoans). Divergence times were estimated from global and local clock methods using 20-188 proteins per node, with data treated separately (multigene) and concatenated (supergene). Different time estimation methods yielded similar results (within 5%): vertebrate-arthropod (964 million years ago, Ma), Cnidaria-Bilateria (1,298 Ma), Porifera-Eumetozoa (1,351 Ma), Pyrenomycetes-Plectomycetes (551 Ma), Candida-Saccharomyces (723 Ma), Hemiascomycetes-filamentous Ascomycota (982 Ma), Basidiomycota-Ascomycota (968 Ma), Mucorales-Basidiomycota (947 Ma), Fungi-Animalia (1,513 Ma), mosses-vascular plants (707 Ma), Chlorophyta-Tracheophyta (968 Ma), Rhodophyta-Chlorophyta+Embryophyta (1,428 Ma), Plantae-Animalia (1,609 Ma), Alveolata-plants+animals+fungi (1,973 Ma), Euglenozoa-plants+animals+fungi (1,961 Ma), and Giardia-plants+animals+fungi (2,309 Ma). By extrapolation, mitochondria arose approximately 2300-1800 Ma and plastids arose 1600-1500 Ma. Estimates of the maximum number of cell types of common ancestors, combined with divergence times, showed an increase from two cell types at 2500 Ma to approximately 10 types at 1500 Ma and 50 cell types at approximately 1000 Ma. CONCLUSIONS: The results suggest that oxygen levels in the environment, and the ability of eukaryotes to extract energy from oxygen, as well as produce oxygen, were key factors in the rise of complex multicellular life. Mitochondria and organisms with more than 2-3 cell types appeared soon after the initial increase in oxygen levels at 2300 Ma. The addition of plastids at 1500 Ma, allowing eukaryotes to produce oxygen, preceded the major rise in complexity.