Parallel FFT on ATM‐based networks of workstations

We consider parallel computing on a network of workstations using a connection-oriented protocol (e.g., Asynchronous Transfer Mode) for data communication. In a connection-oriented protocol, a virtual circuit of guaranteed bandwidth is established for each pair of communicating workstations. Since all virtual circuits do not have the same guaranteed bandwidth, a parallel application must deal with the unequal bandwidths between workstations. Since most works in the design of parallel algorithms assume equal bandwidths on all the communication links, they often do not perform well when executed on networks of workstations using connection-oriented protocols. In this paper, we first evaluate the performance degradation caused by unequal bandwidths on the execution of conventional parallel algorithms such as the fast Fourier transform and bitonic sort. We then present a strategy based on dynamic redistribution of data points to reduce the bottlenecks caused by unequal bandwidths. We also extend this strategy to deal with processor heterogeneity. Using analysis and simulation we show that there is a considerable reduction in the runtime if the proposed redistribution strategy is adopted. The basic idea presented in this paper can also be used to improve the runtimes of other parallel applications in connection-oriented environments. This revised version was published online in July 2006 with corrections to the Cover Date.     

Load balancing on temporally heterogeneous cluster of workstations for parallel simulated annealing

Simulated annealing (SA) is a general-purpose optimization technique widely used in various combinatorial optimization problems. However, the main drawback of this technique is a long computation time required to obtain a good quality of solution. Clusters have emerged as a feasible and popular platform for parallel computing in many applications. Computing nodes on many of the clusters available today are temporally heterogeneous. In this study, multiple Markov chain (MMC) parallel simulated annealing (PSA) algorithms have been implemented on a temporally heterogeneous cluster of workstations to solve the graph partitioning problem and their performance has been analyzed in detail. Temporal heterogeneity of a cluster of workstations is harnessed by employing static and dynamic load balancing techniques to further improve efficiency and scalability of the MMC PSA algorithms.     

Candidate chains, unfaithful spell-out, and outwards-looking phonologically-conditioned allomorphy

The question of whether phonologically-conditioned suppletive allomorphy can ever be outwardly sensitive has been a key point of contention in debates between parallel and serial theories of morpho-phonology. Purely serial theories bar outwardssensitivity altogether, while parallel theories permit it across the board. A few examples have been reported, demonstrating the need for some degree of parallelism, but are sufficiently limited to suggest that some degree of serialism is also required. This paper advances a proposal regarding when allomorphs compete serially and when they compete in parallel. Specifically, it proposes that there is a connection between outwards-sensitivity and feature mismatches in morphological spell-out, and suggests a revision to the theory of Optimal Interleaving (OI: Wolf in Optimal interleaving: serial phonology-morphology interaction in a constraint-based model, 2008) which captures this connection. A proposal is also made regarding how to model outwards-sensitive root allomorphy under OI’s assumptions.     

Single-trial classification of parallel pre-attentive and serial attentive processes using functional magnetic resonance imaging

Theories of perception have proposed a basic distinction between parallel pre-attentive and serial attentive modes of processing. However, chronometric measures are often ambiguous in separating parallel and serial processes. We have used the activity of attention-related regions of the human brain, measured with functional magnetic resonance imaging, to separate parallel from serial processes at the single-trial level in a visual quantification task. In this task, some have suggested the deployment of two qualitatively different processes, a fast parallel 'subitizing' for sets of one, two or three objects and a slow serial counting for larger sets. Our results indicate that attention-related regions of the posterior parietal and frontal cortices show a sudden increase in activity only from numerosity four onwards, confirming the parallel-serial dichotomy of subitizing and counting. Moreover, using the presence or absence of attentional shifts, as inferred from the activation of posterior parietal regions, we successfully predict whether, on a given trial, subjects deployed a serial exploration of the display or a parallel apprehension. Beyond the subitizing/counting debate, this approach may prove useful to probe the attentional demands of other cognitive tasks.     

Imaging workstations for computer-aided primatology: promises and pitfalls

In this paper, the application of biomedical imaging workstations to primatology will be explained and evaluated. The technological basis, computer hardware and software aspects, and the various uses of several types of workstations will all be discussed. The types of workstations include: (1) Simple - these display-only workstations, which function as electronic light boxes, have applications as terminals to picture archiving and communication (PAC) systems. (2) Diagnostic reporting - image-processing workstations that include the ability to perform straightforward manipulations of gray scale and raw data values will be considered for operations such as histogram equalization (whether adaptive or global), gradient edge finders, contour generation, and region of interest, as well as other related functions. (3) Manipulation systems - three-dimensional modeling and computer graphics with application to radiation therapy treatment planning, and surgical planning and evaluation will be considered. A technology of prime importance in the function of these workstations lies in communications and networking. The hierarchical organization of an electronic computer network and workstation environment with the interrelationship of simple, diagnostic reporting, and manipulation workstations to a coaxial or fiber optic network will be analyzed.     

The use of surface electromyographic techniques in assessing musculoskeletal disorders in production operations

The use of surface electromyographic (SEMG) techniques in evaluating production line workstations is illustrated through the use of two case studies. Evaluation procedures are introduced. The results illustrate how SEMG can be used to document the strain upon muscles of the neck and shoulders and how workstations may be altered to comply with government regulations.     

Improvement of signal-to-noise ratio in electroantennogram responses using multiple insect antennae

Using an array of insect antennae connected in series or in parallel, electroantennogram (EAG) responses and noise levels were investigated in an attempt to improve signal-to-noise (S/N) ratio and sensitivity. Both the EAG response amplitude and noise level increased when the antennae of male Helicoverpa zea (Lepidoptera: Noctuidae) were connected in series. Due to lower relative increase in noise level than EAG amplitude as the number of antennae increased, the S/N ratio was also significantly improved by the serial connection. As a result the sensitivity of EAG was improved by the serial connection, which showed ca. ten-fold improvement in the threshold detection levels compared with a single antenna when four antennae were connected in series. In contrast to the serial connection, there were no differences in EAG amplitudes and overall noise levels when different numbers of antennae were connected in parallel. When only large-amplitude noise was taken into account, however, the S/N ratio was somewhat improved by the parallel connection. The frequency of overall noise remained at the same level both in the serial and in the parallel connection. However, the frequency of the large-amplitude noise increased in serial connection but decreased in parallel connection. The present study clearly indicates that both the sensitivity and S/N ratio of the EAG biosensor could be significantly improved by using the multiple antennal connections.     

All-atom computer simulations of amyloid fibrils disaggregation

Amyloidlike fibrils are found in many fatal diseases, including Alzheimer's disease, type II diabetes mellitus, transmissible spongiform encephalopathies, and prion diseases. These diseases are linked to proteins that have partially unfolded, misfolded, and aggregated into amyloidlike fibrils. The kinetics of amyloidlike fibrils aggregation is still hotly debated and remains an important open question. We have utilized the GNNQQNY crystal structure and high-temperature molecular dynamics simulation in explicit solvent to study the disaggregation mechanism of the GNNQQNY fibrils and to infer its likely aggregation pathways. A hexamer model and a 12-mer model both with two parallel β-sheets separated by a dry side-chain interface were adopted in our computational analysis. A cumulative time of 1 μs was simulated for the hexamer model at five different temperatures (298 K, 348 K, 398 K, 448 K, and 498 K), and a cumulative time of 2.1 μs was simulated for the 12-mer model at four temperatures (298 K, 398 K, 448 K, and 498 K). Our disaggregation landscape and kinetics analyses indicate that tetramers probably act as the transition state in both the hexamer and the 12-mer simulations. In addition, the 12-mer simulations show that the initial aggregation nucleus is with eight peptides. Furthermore, the landscape is rather flat from 8-mers to 12-mers, indicating the absence of major barriers once the initial aggregation nucleus forms. Thus, the likely aggregation pathway is from monomers to the initial nucleus of 8-mers with tetramers as the transition state. Transition state structure analysis shows that the two dominant transition state conformations are tetramers in the 3-1 and 2-2 arrangements. The predominant nucleus conformations are in peptide arrangements maximizing dry side-chain contacts. Landscape and kinetics analyses also indicate that the parallel β-sheets form earlier than the dry side-chain contacts during aggregation. These results provide further insights in understanding the early fibrils aggregation.     

Bio-diesel production directly from the microalgae biomass of Nannochloropsis by microwave and ultrasound radiation

This work offers an optimized method for the direct conversion of harvested Nannochloropsis algae into bio-diesel using two novel techniques. The first is a unique bio-technology-based environmental system utilizing flue gas from coal burning power stations for microalgae cultivation. This method reduces considerably the cost of algae production. The second technique is the direct transesterification (a one-stage method) of the Nannochloropsis biomass to bio-diesel production using microwave and ultrasound radiation with the aid of a SrO catalyst. These two techniques were tested and compared to identify the most effective bio-diesel production method. Based on our results, it is concluded that the microwave oven method appears to be the most simple and efficient method for the one-stage direct transesterification of the as-harvested Nannochloropsis algae.     

Stoichiometric differences in DNA molecules containing the atpA gene suggest mechanisms for the generation of mitochondrial genome diversity in maize

Four genomic arrangements of the maize mitochondrial atpA gene (encoding the α subunit of the F₁ ATPase), have been characterized. Most N (fertile) and S (male-sterile) cytoplasms contain two atpA arrangements of equal abundance. Prolonged exposure of blots of maize mitochondrial DNA probed with atpA-specific sequences show that cytoplasms previously reported to lack one of the atpA arrangements do contain the second arrangement but at low levels. Similarly, restriction fragments containing the atpA gene previously thought unique to male-sterile S and T cytoplasms are present in low abundance in fertile cytoplasms. These observations suggest that fertile and male-sterile cytoplasms of maize may be more closely related than previously thought, and suggest possible mechanisms to explain the observed mitochondrial genome diversity.     

A macroscopic ansatz to deduce the Hill relation

In this study, we derive the hyperbolic force-velocity relation of concentric muscular contraction, first formulated empirically by A.V. Hill in 1938, from three essential model assumptions: (1) the structural assembly of three well-known elements - i.e. active, parallel damping, and serial - fulfilling a force equilibrium, (2) the parallel damping coefficient explicitly depending on muscle force output and three parameters, and (3) the kinematic gearing ratio between active and serial element being assigned to a parameter. The energy source within the muscle represented by the force of the active element is an additional fifth parameter. As a result we find the Hill “constants” A and B as functions of our five model parameters. Using A and B values from literature on experimental data, we predict heat power release of our model. By calculating enthalpy rate and mechanical efficiency, we compare the model heat power to predictions from another Hill-type model, to Hill's original findings, and to findings from modern muscle heat measurements. We reconsider why the biggest share of heat rate during isometric contractions (maintenance heat) and the velocity-dependent heat rate during concentric contractions in addition to maintenance heat rate (shortening heat rate) may be traced back to the same mechanism represented by the kinematic gearing ratio. Namely, we suggest that the serial element transfers attachment-detachment fluctuations of actin-myosin crossbridges within one sarcomere to others in the same sarcomere and to those in parallel and in series. Numerically, in case of negligible passive muscular damping, we find the ratio between A and isometric force (relative A) to depend exclusively on the kinematic gearing ratio, whereas the maintenance heat rate scales with the square of relative A. Moreover, this mechanical coupling internal to the muscle fibres may also be behind the macroscopic force dependency of the overall parallel damping coefficient.     

Harnessing networked workstations as a powerful parallel computer: a general paradigm illustrated using three programs for genetic linkage analysis

It is widely accepted that parallel computers, which have theability to execute different parts of a program simultaneously,will offer dramatic speed–up for many time–consumingbiological computations. The paper describes how the use ofthe machine–independent parallel programming language,Linda, allows parallel programs to run on an institution^'s networkof workstations. In this way, an institution can harness existinghardware, which is often either idle or vastly underutilized,as a powerful ‘parallel machine’ with supercomputingcapability. The paper illustrates this very general paradigmby describing the use of Linda to parallelize three widely usedprograms for genetic linkage analysis, a mathematical techniqueused in gene mapping. The paper then discusses a number of technical,administrative and social issues that arise when creating sucha computational resource.     

Role of proline …︁ proline interactions in the packing of collagenlike poly(tripeptide) triple helices

Conformational energy computations were carried out on the packing of two identical collagenlike poly(tripeptide) triple helices in order to determine the energetics of favorable packing arrangements as a function of composition and chain length. The triple helices considered were [CH₃CO-(Gly-Pro-Pro)_nt-NHCH₃]₃ and [CH₃CO-(Gly-Pro-Ala)_nt-NHCH₃]₃, with n_t = 3, 4, and 5. The packing arrangements were characterized in terms of their intermolecular energies and orientation angles Ω₀ of the axes of the two triple helices. For short triple helices (n_t = 3 or 4), many low-energy orientations, with a wide range of values of Ω₀, can occur. When the triple helices are longer (n_t = 5), the only low-energy packing arrangements of two poly(Gly-Pro-Pro) triple helices are those with a nearly parallel orientation of the two helix axes, with Ω₀ ≈ ?10°. This result accounts for the observed parallel (rather than antiparallel) arrangement of collagen molecules in microfibril assembly and stands in contrast to the preferred antiparallel arrangement of a pair of α-helices. Since the preference for a parallel arrangement of these collagenlike triple helices is less pronounced in the case of poly(Gly-Pro-Ala), it appears that this preference is a consequence of the frequent presence of imino acids in position Y of the Gly-X-Y repeating triplet. In poly(Gly-Pro-Ala), most of the low-energy packing arrangements are parallel, but a few arrangements with low energies and high values of |Ω₀| occur. These packing arrangements have a high energy, however, when Pro is substituted for Ala, and thus they are not accessible for collagen with natural amino (imino) acid sequences. The computations reported here account for some of the characteristic features of collagen packing in terms of the local interaction energies of a pair of triple helices.     

Pelagic Sargassum community metabolism: Carbon and nitrogen

The production, nitrogen fixation, and release rates and fate of dissolved organic matter of a pelagic Sargassum community have been investigated at eight stations in the Gulf Stream and the Sargasso Sea. Net production and gross nitrogen fixation rates of Sargassum and epiphytes varied significantly between stations, 328 ± 114μg C (g dry wt)^?1h^?1 and 18 ± 7.4μg N g^?1h^?1, respectively. The net release rates of dissolved organic carbon (287 ± 150μg DOC g^?1h^?1) also showed the same variability between stations. On the other hand, the community carbon and nitrogen content, 268 ± 4.8 and 16.9 ± 2.4 mg g dry wt^?1, respectively, remained constant at all stations. The results of chemical measurements indicate that ≈ 0–50 % of the gross production was lost as a result of photosynthate release. From ¹⁴C-tracer experiments it was found that the planktonic and epiphytic heterotrophs mineralized 50–70 % of the photosynthate released by Sargassum and epiphytic algae. Based on the community gross production and fixation rates, carbon and nitrogen content, the amount of nitrogen required for the observed production rates, the Sargassum community appears to obtain a substantial part (40%) of its nitrogen from nitrogen fixation.     

Gene Differences between the Sex Ratio and Standard Gene Arrangements of the X Chromosome in DROSOPHILA PERSIMILIS

The sibling species Drosophila pseudoobscura and D. persimilis each carry two gene arrangements in the right arm of the X chromosome; Standard (ST) and Sex Ratio (SR). The SR sequence of D. persimilis and the ST sequence of D. pseudoobscura have the same banding pattern. These cytologically identical arrangements carry different alleles at the esterase-5 (Est-5) and phosphoglucomutase-1 ( Pgm-1) loci. All the alleles on the SR arrangement of D. persimilis are also present on the ST arrangement of that species, and the same allele was most common in all cases. However, the allele frequencies at the Pgm-1 locus are significantly different between the two arrangements. Within the ST arrangement of D. persimilis, the alleles at the Est-5 and Pgm-1 loci are in linkage equilibrium.     

Estimated copepod production rate and structure of mesozooplankton communities in the coastal Barents Sea during summer–autumn 2007

The southern Barents Sea is considered to be the most productive area in the Arctic Ocean; however, there are no assessments of daily production rates in the coastal waters. During the summer and autumn of 2007, we investigated the variation of mesozooplankton community structure relative to environmental conditions at 12 coastal stations. Copepods dominated the total zooplankton biomass and abundance during both periods. Diversity indices and the total biomass of zooplankton communities differed significantly between the two seasons. Cluster analyses revealed two distinct groups of stations which were associated with Ura Bay and the adjacent open sea, respectively. Daily production rates of the copepod species examined were calculated using three methods based on: (1) a temperature-dependent equation and (2) two multiple regressions that consider temperature, body weight, and chlorophyll a concentration. Significant seasonal differences for daily production rates were found using all three model equations (p?<?0.05): 358?±?188–1,775?±?791 versus 198?±?85–1,584?±?559?μg?dry?mass?m^?3?day^?1. Results of principal components analyses demonstrated that the abundance and biomass of herbivorous species were related to variation in chlorophyll a concentration while the abundance and biomass of other species (omnivorous copepods and Ctenophora) were related mainly with water temperature and salinity. Mesozooplankton biomass was higher during this study relative to previous studies. Computed copepod production rates were higher compared with other Arctic seas confirming a high productive potential of the coastal southern Barents Sea.     

Guanine tetraplex topology of human telomere DNA is governed by the number of (TTAGGG) repeats

Secondary structures of the G-rich strand of human telomere DNA fragments G₃(TTAG₃)_n, n = 1–16, have been studied by means of circular dichroism spectroscopy and PAGE, in solutions of physiological potassium cation concentrations. It has been found that folding of these fragments into tetraplexes as well as tetraplex thermostabilities and enthalpy values depend on the number of TTAG₃ repeats. The suggested topologies include, e.g. antiparallel and parallel bimolecular tetraplexes, an intramolecular antiparallel tetraplex, a tetraplex consisting of three parallel chains and one antiparallel chain, a poorly stable parallel intramolecular tetraplex, and both parallel and antiparallel tetramolecular tetraplexes. G₃(TTAG₃)₃ folds into a single, stable and very compact intramolecular antiparallel tetraplex. With an increasing repeat number, the fragment tetraplexes surprisingly are ever less thermostable and their migration and enthalpy decrease indicate increasing irregularities or domain splitting in their arrangements. Reduced stability and different topology of lengthy telomeric tails could contribute to the stepwise telomere shortening process.     

Attenuation of the entomopathogenic fungus Beauveria bassiana following serial in vitro transfers

Stability of pathogenicity in continuous in vitro cultivation is desirable for the purpose of large-scale production of a mycoinsecticide. Fungal biocontrol agents may lose virulence when maintain on artificial media, resulting in products of commercially inferior quality. In this research, two isolates (DEBI007 and DEBI008) of entomopathogenic fungus Beauveria bassiana were investigated for their stability following fifteen serial in vitro transfers assaying virulence to mealworm larvae, conidiation, and hyphal development on artificial culture as some fungal virulence determinants. Moreover, role of insect cuticle on fungal virulence restoration and protease 1 (Pr1) activity was considered as the most important factor. Although radial hyphal development and colony colour on in vitro culture was not affected following serial transfers, conidiation and Pr1 activity of both fungal isolates were reduced remarkably after fifteen transfers compared with control. Similarly, mean lethal concentration (LC₅₀) values were increased as the number of serial transfers on artificial diet increased, although these increases were not statistically significant in both isolates as the confidential limits of LC₅₀ values were overlapping. Our results revealed that attenuation of entomopathogenic fungi following serial in vitro transfers is a combination of interconnected factors. Other probable components such as pathogenicity determinants in this interaction should be explored in next researches.     

Orthogonal potency analysis of mesenchymal stromal cell function during ex vivo expansion

Adult bone marrow mesenchymal stromal cells (MSCs) have cross-functional, intrinsic potency that is of therapeutic interest. Their ability to regenerate bone, fat, and cartilage, modulate the immune system, and nurture the growth and function of other bone marrow hematopoietic stem/progenitor cells have all been evaluated by transplant applications of MSCs. These applications require the isolation and expansion scaled cell production. To investigate biophysical properties of MSCs that can be feasibly utilized as predictors of bioactivity during biomanufacturing, we used a low-density seeding model to drive MSCs into proliferative stress and exhibit the hallmark characteristics of in vitro aging. A low-density seeding method was used to generate MSCs from passages 1–7 to simulate serial expansion of these cells to maximize yield from a single donor. MSCs were subjected to three bioactivity assays in parallel to ascertain whether patterns in MSC age, size, and shape were associated with the outcomes of the potency assays. MSC age was found to be a predictor of adipogenesis, while cell and nuclear shape was strongly associated to hematopoietic-supportive potency. Together, these data evaluate morphological changes associated with cell potency and highlight new strategies for purification or alternatives to assessing MSC quality.     

Ivory Ornaments of the Aurignacian in Western Europe: Case studies from France and Germany

Here we present an overview of the personal ornaments of the Swabian Aurignacian and the Early Aurignacian sites of south-western France made from mammoth ivory. The production sequences for the serial manufacture of beads from these sites are quite similar. While the Swabian sites have yielded numerous different types of beads with a focus of the double-perforated bead, the nearly exclusive use of one bead-type, the perle en forme de panier, is striking at the sites of south-western France. Following the presentation of major inventories of ivory ornaments in the two regions concerned, we discuss potential factors underlying both the differences and the similarities we observe in these assemblages.