Specialized Array Research Articles

Complete Genome Sequence of Subcluster 5.2 Synechococcus sp. Strain CB0101, Isolated from the Chesapeake Bay.

Synechococcus sp. strain CB0101 is a model strain for cyanobacteria living in the estuarine environment. It is also a representative member of marine Synechococcus subcluster 5.2. The draft genome sequence of CB0101 was reported in 2014 with 454 sequencing. Here, we report the complete genome sequence of CB0101, obtained with PacBio sequencing. CB0101 contains a specialized array of genes which are involved in sensing, responding to, and persisting in the presence of environmental stress.

Tissue-specific study across the stem reveals the chemistry and transcriptome dynamics of birch bark.

Tree bark is a highly specialized array of tissues that plays important roles in plant protection and development. Bark tissues develop from two lateral meristems; the phellogen (cork cambium) produces the outermost stem-environment barrier called the periderm, while the vascular cambium contributes with phloem tissues. Although bark is diverse in terms of tissues, functions and species, it remains understudied at higher resolution. We dissected the stem of silver birch (Betula pendula) into eight major tissue types, and characterized these by a combined transcriptomics and metabolomics approach. We further analyzed the varying bark types within the Betulaceae family. The two meristems had a distinct contribution to the stem transcriptomic landscape. Furthermore, inter- and intraspecies analyses illustrated the unique molecular profile of the phellem. We identified multiple tissue-specific metabolic pathways, such as the mevalonate/betulin biosynthesis pathway, that displayed differential evolution within the Betulaceae. A detailed analysis of suberin and betulin biosynthesis pathways identified a set of underlying regulators and highlighted the important role of local, small-scale gene duplication events in the evolution of metabolic pathways. This work reveals the transcriptome and metabolic diversity among bark tissues and provides insights to its development and evolution, as well as its biotechnological applications.

Population, diversity, and restaurants: trends in the geography of cuisine variety in the Netherlands

Over the past two decades, research in regional science has paid considerable attention to the benefits of urban density and proximity, even though there has been tremendous progress within the same period in technologies that ease the friction of distance (e.g. mobile communication, high-speed internet). Many scholars argue that in spite of falling transportation costs for tradable goods and the proliferation of information and communication technology cities will always have a vital edge in facilitating face-to-face communication. We argue that even if this is the case, there still remains a host of benefits that have come to rely less on urban density and this will have implications for the future of cities. In the current study we focus on one particular type of benefit associated with urban size and density – namely, the availability of a specialized array of urban amenities. More precisely, we use regional data on the distribution of restaurants in the Netherlands, and differentiate them according to their cuisine type. We explore how the presence of cuisine variety relates to population density and diversity, and whether these relationships vary across different city sizes. We find that the explanatory power of population density and diversity diminishes over time, especially in smaller cities. We argue that these trends support the hypothesis that a reduction of spatial information frictions reduces the need for urban density, as benefits associated with larger cities – such as cuisine variety – can be increasingly found in smaller cities.

Coupling multielectrode array recordings with silver labeling of recording sites to study cervical spinal network connectivity.

Midcervical spinal interneurons form a complex and diffuse network and may be involved in modulating phrenic motor output. The intent of the current work was to enable a better understanding of midcervical "network-level" connectivity by pairing the neurophysiological multielectrode array (MEA) data with histological verification of the recording locations. We first developed a method to deliver 100-nA currents to electroplate silver onto and subsequently deposit silver from electrode tips after obtaining midcervical (C3-C5) recordings using an MEA in anesthetized and ventilated adult rats. Spinal tissue was then fixed, harvested, and histologically processed to "develop" the deposited silver. Histological studies verified that the silver deposition method discretely labeled (50-μm resolution) spinal recording locations between laminae IV and X in cervical segments C3-C5. Using correlative techniques, we next tested the hypothesis that midcervical neuronal discharge patterns are temporally linked. Cross-correlation histograms produced few positive peaks (5.3%) in the range of 0-0.4 ms, but 21.4% of neuronal pairs had correlogram peaks with a lag of ≥0.6 ms. These results are consistent with synchronous discharge involving mono- and polysynaptic connections among midcervical neurons. We conclude that there is a high degree of synaptic connectivity in the midcervical spinal cord and that the silver-labeling method can reliably mark metal electrode recording sites and "map" interneuron populations, thereby providing a low-cost and effective tool for use in MEA experiments. We suggest that this method will be useful for further exploration of midcervical network connectivity.NEW & NOTEWORTHY We describe a method that reliably identifies the locations of multielectrode array (MEA) recording sites while preserving the surrounding tissue for immunohistochemistry. To our knowledge, this is the first cost-effective method to identify the anatomic locations of neuronal ensembles recorded with a MEA during acute preparations without the requirement of specialized array electrodes. In addition, evaluation of activity recorded from silver-labeled sites revealed a previously unappreciated degree of connectivity between midcervical interneurons.

The Gamma Matrix to Summarize Dense and Sparse Data Sets for Big Data Analytics

Data summarization is an essential mechanism to accelerate analytic algorithms on large data sets. On the other hand, array DBMSs enable scalable computation with large matrices. With that motivation in mind, we propose a parallel array operator, based on a specific form of matrix multiplication, that computes a comprehensive data summarization matrix. By deriving equivalent equations based on the summarization matrix, statistical methods are adapted to work in two phases: (1) Parallel summarization of the data set in one pass; (2) Iteration exploiting the summarization matrix in many intermediate computations. We prove our summarization matrix captures essential statistical properties of the data set and it allows iterative algorithms to work faster in main memory, by decreasing the number of times the data set is scanned, and by reducing the number of CPU operations. Specifically, we show our summarization matrix benefits statistical models, including PCA, linear regression, and variable selection. From a systems perspective, we carefully study the efficient computation of the summarization matrix on the SciDB parallel array DBMS and how to exploit it in the R language statistical system. To achieve best performance, we introduce two specialized array operators for dense and sparse data sets, respectively. We present an experimental evaluation comparing SciDB, R, a columnar DBMS (a fast SQL engine), and Spark (a popular Hadoop system). Our experiments show R working together with SciDB eliminates main memory and performance limitations from R. More importantly, our R+SciDB prototype is significantly faster and more scalable than Spark and the columnar DBMS.

Diversification and specialization of touch receptors in skin.

Our skin is the furthest outpost of the nervous system and a primary sensor for harmful and innocuous external stimuli. As a multifunctional sensory organ, the skin manifests a diverse and highly specialized array of mechanosensitive neurons with complex terminals, or end organs, which are able to discriminate different sensory stimuli and encode this information for appropriate central processing. Historically, the basis for this diversity of sensory specializations has been poorly understood. In addition, the relationship between cutaneous mechanosensory afferents and resident skin cells, including keratinocytes, Merkel cells, and Schwann cells, during the development and function of tactile receptors has been poorly defined. In this article, we will discuss conserved tactile end organs in the epidermis and hair follicles, with a focus on recent advances in our understanding that have emerged from studies of mouse hairy skin.

Differential Adeno-Associated Virus Serotype-Specific Interaction Patterns with Synthetic Heparins and Other Glycans

All currently identified primary receptors of adeno-associated virus (AAV) are glycans. Depending on the AAV serotype, these carbohydrates range from heparan sulfate proteoglycans (HSPG), through glycans with terminal α2-3 or α2-6 sialic acids, to terminal galactose moieties. Receptor identification has largely relied on binding to natural compounds, defined glycan-presenting cell lines, or enzyme-mediated glycan modifications. Here, we describe a comparative binding analysis of highly purified, fluorescent-dye-labeled AAV vectors of various serotypes on arrays displaying over 600 different glycans and on a specialized array with natural and synthetic heparins. Few glycans bind AAV specifically in a serotype-dependent manner. Differential glycan binding was detected for the described sialic acid-binding AAV serotypes 1, 6, 5, and 4. The natural heparin binding serotypes AAV2, -3, -6, and -13 displayed differential binding to selected synthetic heparins. AAV7, -8, -rh.10, and -12 did not bind to any of the glycans present on the arrays. For discrimination of AAV serotypes 1 to 6 and 13, minimal binding moieties are identified. This is the first study to differentiate the natural mixed heparin binding AAV serotypes 2, 3, 6, and 13 by differential binding to specific synthetic heparins. Also, sialic acid binding AAVs display differential glycan binding specificities. The findings are relevant for further dissection of AAV host cell interaction. Moreover, the definition of single AAV-discriminating glycan binders opens the possibility for glycan microarray-based discrimination of AAV serotypes in gene therapy.

Marking and Measuring Single Microtubules by PRC1 and Kinesin-4

Error-free cell division depends on the assembly of the spindle midzone, a specialized array of overlapping microtubules that emerges between segregating chromosomes during anaphase. The molecular mechanisms by which a subset of dynamic microtubules from the metaphase spindle are selected and organized into a stable midzone array are poorly understood. Here, we show using in vitro reconstitution assays that PRC1 and kinesin-4, two microtubule-associated proteins required for midzone assembly, can tag microtubule plus ends. Remarkably, the size of these tags is proportional to filament length. We determine the crystal structure of the PRC1 homodimer and map the protein-protein interactions needed for tagging microtubule ends. Importantly, length-dependent microtubule plus-end-tagging by PRC1 is also observed in dividing cells. Our findings suggest how biochemically similar microtubules can be differentially marked, based on length, for selective regulation during the formation of specialized arrays, such as those required for cytokinesis.

Centrosome Polarization in T Cells: A Task for Formins

T-cell antigen receptor (TCR) engagement triggers the rapid reorientation of the centrosome, which is associated with the secretory machinery, toward the immunological synapse (IS) for polarized protein trafficking. Recent evidence indicates that upon TCR triggering the INF2 formin, together with the formins DIA1 and FMNL1, promotes the formation of a specialized array of stable detyrosinated MTs that breaks the symmetrical organization of the T-cell microtubule (MT) cytoskeleton. The detyrosinated MT array and TCR-induced tyrosine phosphorylation should coincide for centrosome polarization. We propose that the pushing forces produced by the detyrosinated MT array, which modify the position of the centrosome, in concert with Src kinase dependent TCR signaling, which provide the reference frame with respect to which the centrosome reorients, result in the repositioning of the centrosome to the IS.

Implosion characteristics of conical wirearray Z pinches on Qiangguang1 facility

Implosion and radiation characteristics of conical wire array in different regimes of implosion are investigated at the 1 MA Qiangguang-1 facility by X-ray self-emission diagnostics. Experimental results show that the shape of precursor plasma is also conical. The initial implosion takes place near the cathode by a stronger Lorenz force, forming a triangle-like structure that produces harder X ray. The current crossing the bubble in the front of the wire array near the anode persists in persist ablating, thereby leading to a zippered stagnation. The initial implosion of a bubble near the cathode is followed by the implosion zippering upwards as the zipper implosion speed is 2.59 107 cm/s. The results shows that the conical array has a broader X-ray power pulse than cylinderical wire array due to the zippered stagnation and zippered implosion of the array. The study of implosion characteristics of specialized axis symmetric wire array Z-pinch-like conical wire array can provide a valuable test bed for understanding the regime of implosion as well as theoretical model and magneto-hydrodynamic (MHD) codes, both of which primarily develop for the modeling of cylindrical wire array Z pinches.

Improved system for detection, localization, and classification of military impulse noise.

Impulse noise monitoring systems are needed for quantifying the magnitude and time of impulsive noise events to ensure compliance and to provide an archival record of noise emanating from military installations. Currently, there are several commercial systems; however, they report an overwhelming number of false events generated by windborne noise and distant non-military acoustic events. This can bias noise statistics to the point where a meaningful assessment of the acoustic sound levels from a site is not possible. APS, in collaboration with the University of Pittsburgh, have developed an improved noise monitoring system for mitigating windborne and other sources of non-military noise. This system includes a collection of remote sensors capable of detection, localization, and classification. Each sensor uses an acoustic array and real-time signal processing codes to estimate the noise source location. Mitigation of windborne events is accomplished using cross-channel correlation analysis, beamforming, and classification. A prototype of this system is installed at the Marine Corps Base Camp Lejeune where it has been automatically reporting and archiving detected impulse noise. In this paper, we will present the specialized array processing algorithms, system design, and its performance as determined by months of detection statistics accumulated in the field.

Physical resource binding for a coarse-grain reconfigurable array using evolutionary algorithms

One of the challenges of designing for coarse-grain reconfigurable arrays is the need for mature tools. This is especially important because of the heterogeneity of the larger, more predefined (and hence more specialized) array elements. This work describes the use of a genetic algorithm (GA) to automate the physical binding phase of kernel design. We identify the generalizable features of an example platform and discuss suitable ways to harness the binding problem to a GA search engine.

Localization and speech perception by unilateral BAHA users

Objectives: Patients with unilateral hearing loss report difficulty hearing conversation on their impaired side, inability to localize sound, and diminished understanding of speech in background noise. The Bone-Anchored Cochlear Stimulator, or BAHA, has been shown to be useful for persons with unilateral complete sensorineural hearing loss in improving speech perception in noise using the Hearing-in-Noise Test (HINT). The purpose of the present study is to evaluate the effectiveness of BAHA in sound localization and speech tasks in noise for unilateral sensorineurally impaired listeners. Methods: Prospective study of 20 unilaterally hearing impaired subjects with sensorineural loss. All subjects were implanted with a BAHA on the poorer hearing side. All subjects underwent audiometric evaluation under headphones preoperatively to classify loss and degree. Soundfield measurements were conducted in a calibrated audiometric suite: HINT sentences and localization testing, with and without a CROS hearing aid or BAHA. Localization measurement was performed using a specialized array of 7 calibrated speakers at head level separated by 15 degrees. An error analysis matrix was generated to evaluate the confusions and degrees of separation of errors. Results: Results to date indicated that accuracy of identification of speaker localization was poorer than 50% for 100% of the sample in both unaided and aided conditions. Errors were severe, ie, more than 30 degrees of arc. In contrast, the improvement in speech perception, as obtained in the previous study, was observed. Conclusions: Use of the CROS or BAHA did not result in improved performance on the localization task for this sample.

Spar: a set of extensions to Java for scientific computation

AbstractWe present a set of language extensions that improve the expressiveness and performance of Java for scientific computation. The language extensions allow the manipulation of multi‐dimensional arrays to be expressed more naturally, and to be implemented more efficiently. Furthermore, data‐parallel programming is supported, allowing efficient parallelization of a large class of operations on arrays. We also provide language extensions to construct specialized array representations, such as symmetric, block, and sparse matrices. These extensions are: tuples, parameterized types, array subscript overloading, and the inline modifier. These extensions are not only useful in the construction of special array representations, but are also useful in their own right. Finally, we add complex numbers as a primitive type to the language. We evaluate our language extensions using performance results. We also compare relevant code fragments of our extended language with standard Java implementations and language extensions proposed by others. Copyright © 2003 John Wiley & Sons, Ltd.

ARRAY SEISMOLOGY: METHODS AND APPLICATIONS

Since their development in the 1960s, seismic arrays have given a new impulse to seismology. Recordings from many uniform seismometers in a well‐defined, closely spaced configuration produce high‐quality and homogeneous data sets, which can be used to study the Earth's structure in great detail. Apart from an improvement of the signal‐to‐noise ratio due to the simple summation of the individual array recordings, seismological arrays can be used in many different ways to study the fine‐scale structure of the Earth's interior. They have helped to study such different structures as the interior of volcanos, continental crust and lithosphere, global variations of seismic velocities in the mantle, the core‐mantle boundary and the structure of the inner core. For this purpose many different, specialized array techniques have been developed and applied to an increasing number of high‐quality array data sets. Most array methods use the ability of seismic arrays to measure the vector velocity of an incident wave front, i.e., slowness and back azimuth. This information can be used to distinguish between different seismic phases, separate waves from different seismic events and improve the signal‐to‐noise ratio by stacking with respect to the varying slowness of different phases. The vector velocity information of scattered or reflected phases can be used to determine the region of the Earth from whence the seismic energy comes and with what structures it interacted. Therefore seismic arrays are perfectly suited to study the small‐scale structure and variations of the material properties of the Earth. In this review we will give an introduction to various array techniques which have been developed since the 1960s. For each of these array techniques we give the basic mathematical equations and show examples of applications. The advantages and disadvantages and the appropriate applications and restrictions of the techniques will also be discussed. The main methods discussed are the beam‐forming method, which forms the basis for several other methods, different slant stacking techniques, and frequency–wave number analysis. Finally, some methods used in exploration geophysics that have been adopted for global seismology are introduced. This is followed by a description of temporary and permanent arrays installed in the past, as well as existing arrays and seismic networks. We highlight their purposes and discuss briefly the advantages and disadvantages of different array configurations.

Combinatorial odor discrimination in the brain: Attractive and antagonist odor blends are represented in distinct combinations of uniquely identifiable glomeruli

The rules governing the central discrimination of odors are complex and poorly understood, but a growing body of evidence supports the hypothesis that olfactory glomeruli may represent functionally distinct coding modules in the brain. Testing this hypothesis requires that both the functional characteristics and the spatial position of the glomerulus under study be uniquely identifiable. To address these questions, we examined a specialized array of glomeruli (the macroglomerular complex; MGC) in the antennal lobe of male moths that receives input from olfactory receptor cells tuned specifically to female-released odorants that either promote upwind flight (conspecific sex pheromones) or inhibit it (interspecific antagonists). By using a three-dimensional reconstruction method based on high-resolution laser-scanning confocal microscopy, we generated precise spatial maps of the MGC glomeruli in two related noctuid species with similar pheromone chemistry, Heliothis virescens and Helicoverpa zea. To determine the breadth of tuning of individual MGC glomeruli in processing information about these social signals, we used intracellular recording and staining methods to examine the responses of projection (output) neurons that innervate MGC glomeruli and that each project an axon to higher integrative centers. In both species, a close correspondence was found between the odor specificity of the projection neurons and the glomerulus (or glomeruli) supplied by them. The binary blend of pheromone components for each species was represented by neural activity in only two distinct glomeruli in both H. virescens and H. zea. Odorants that antagonize upwind flight when they are added to the respective pheromonal blends evoked excitatory activity in output neurons restricted to a third glomerulus in the MGCs of both species. In summary, these results suggest that the selective activation of different combinations of functionally distinct MGC glomeruli is a general means for discriminating these specific attractant and antagonist chemical signals in the brain.

Combinatorial odor discrimination in the brain: Attractive and antagonist odor blends are represented in distinct combinations of uniquely identifiable glomeruli

The rules governing the central discrimination of odors are complex and poorly understood, but a growing body of evidence supports the hypothesis that olfactory glomeruli may represent functionally distinct coding modules in the brain. Testing this hypothesis requires that both the functional characteristics and the spatial position of the glomerulus under study be uniquely identifiable. To address these questions, we examined a specialized array of glomeruli (the macroglomerular complex; MGC) in the antennal lobe of male moths that receives input from olfactory receptor cells tuned specifically to female-released odorants that either promote upwind flight (conspecific sex pheromones) or inhibit it (interspecific antagonists). By using a three-dimensional reconstruction method based on high-resolution laser-scanning confocal microscopy, we generated precise spatial maps of the MGC glomeruli in two related noctuid species with similar pheromone chemistry, Heliothis virescens and Helicoverpa zea. To determine the breadth of tuning of individual MGC glomeruli in processing information about these social signals, we used intracellular recording and staining methods to examine the responses of projection (output) neurons that innervate MGC glomeruli and that each project an axon to higher integrative centers. In both species, a close correspondence was found between the odor specificity of the projection neurons and the glomerulus (or glomeruli) supplied by them. The binary blend of pheromone components for each species was represented by neural activity in only two distinct glomeruli in both H. virescensand H. zea. Odorants that antagonize upwind flight when they are added to the respective pheromonal blendsevoked excitatory activity in output neurons restricted to a third glomerulus in the MGCs of both species. In summary, these results suggest that the selective activation of different combinations of functionally distinct MGC glomeruli is a general means for discriminating these specific attractant and antagonist chemical signals in the brain. J. Comp. Neurol. 400:35–56, 1998. © 1998 Wiley-Liss, Inc.

Characterization of S-AKAP84, a Novel Developmentally Regulated A Kinase Anchor Protein of Male Germ Cells

In mammalian spermatozoa, most of the type II alpha isoform of cAMP-dependent protein kinase (PKAII alpha) is anchored at the cytoplasmic surface of a specialized array of mitochondria in the flagellar cytoskeleton. This places the catalytic subunits of PKAII alpha in proximity with potential target substrates in the cytoskeleton. The mechanism by which PKAII alpha is anchored at the outer surface of germ cell mitochondria has not been elucidated. We now report the cloning of a cDNA that encodes a novel, germ cell A kinase anchor protein (AKAP) designated S-AKAP84. S-AKAP84 comprises 593 amino acids and contains a centrally located domain that avidly binds regulatory subunits (RII alpha and RII beta) of PKAII alpha and PKAII beta. The 3.2-kilobase S-AKAP84 mRNA and the cognate S-AKAP84 RII binding protein are expressed principally in the male germ cell lineage. Expression of S-AKAP84 is tightly regulated during development. The protein accumulates as spermatids undergo nuclear condensation and tail elongation. The timing of S-AKAP84 expression is correlated with the de novo accumulation of RII alpha and RII beta subunits and the migration of mitochondria from the cytoplasm (round spermatids) to the cytoskeleton (midpiece in elongating spermatids). Residues 1-30 at the NH2 terminus of S-AKAP84 constitute a putative signal/anchor sequence that may target the protein to the outer mitochondrial membrane. Immunofluorescence analysis demonstrated that S-AKAP84 is co-localized with mitochondria in the flagellum.

Stabilization and post‐translational modification of microtubules during cellular morphogenesis

This review discusses the possible role of alpha-tubulin detyrosination, a reversible post-translational modification that occurs at the protein's C-terminus, in cellular morphogenesis. Higher eukaryotic cells possess a cyclic post-translational mechanism by which dynamic microtubules are differentiated from their more stable counterparts; a tubulin-specific carboxypeptidase detyrosinates tubulin protomers within microtubules, while the reverse reaction, tyrosination, is performed on the soluble protomer by a second tubulin-specific enzyme, tubulin tyrosine ligase. In general, the turnover of microtubules in undifferentiated, proliferating cells is so rapid that the microtubules accumulate very little detyrosinated tubulin; that is, they are enriched in tyrosinated tubulin. However, an early event common to at least three well-studied morphogenetic events--myogenesis, neuritogenesis, and directed cell motility--is the elaboration of a polarized array of stable microtubules that become enriched in detyrosinated tubulin. The formation of this specialized array of microtubules in specific locations in cells undergoing morphogenesis suggests that it plays an important role in generating cellular asymmetries.

New space domain processing technique for pulsed laser velocimetry

Current pulsed laser velocimetry data processing techniques offer high precision (1%) velocity estimates, but can require several hours of processing time on specialized array processors. Under some circumstances, a simple, fast, less accurate (~5%), data reduction technique, which also gives unambiguous velocity vector information is acceptable. In this work, we examine a direct space domain processing technique. The direct space domain processing technique was found to be far superior to any other techniques known, in achieving the objectives listed above. It employs a new data coding and reduction technique, where the particle time history information is used directly. Further, it has no 180 degrees directional ambiguity. A complex convection vortex flow was recorded and completely processed in under 2 min on an 80386 based PC, producing a 2-D map of the flow field containing over 300 velocity vectors.