Video on the Internet: An introduction to the digital encoding, compression, and transmission of moving image data

In this paper, we seek to provide an introduction to the fast-moving field of digital video on the Internet, from the viewpoint of the biological microscopist who might wish to store or access videos, for instance in image databases such as the BioImage Database (http://www.bioimage.org). We describe and evaluate the principal methods used for encoding and compressing moving image data for digital storage and transmission over the Internet, which involve compromises between compression efficiency and retention of image fidelity, and describe the existing alternate software technologies for downloading or streaming compressed digitized videos using a Web browser. We report the results of experiments on video microscopy recordings and three-dimensional confocal animations of biological specimens to evaluate the compression efficiencies of the principal video compression-decompression algorithms (codecs) and to document the artefacts associated with each of them. Because MPEG-1 gives very high compression while yet retaining reasonable image quality, these studies lead us to recommend that video databases should store both a high-resolution original version of each video, ideally either uncompressed or losslessly compressed, and a separate edited and highly compressed MPEG-1 preview version that can be rapidly downloaded for interactive viewing by the database user.     

The PSO family: deduction, stochastic analysis and comparison

The PSO algorithm can be physically interpreted as a stochastic damped mass-spring system: the so-called PSO continuous model. Furthermore, PSO corresponds to a particular discretization of the PSO continuous model. In this paper, we introduce a delayed version of the PSO continuous model, where the center of attraction might be delayed with respect to the particle trajectories. Based on this mechanical analogy, we derive a family of PSO versions. For each member of this family, we deduce the first and second order stability regions and the corresponding spectral radius. As expected, the PSO-family algorithms approach the PSO continuous model (damped-mass-spring system) as the size of the time step goes to zero. All the family members are linearly isomorphic when they are derived using the same delay parameter. If the delay parameter is different, the algorithms have corresponding stability regions of any order, but they differ in their respective force terms. All the PSO versions perform fairly well in a very broad area of the parameter space (inertia weight and local and global accelerations) that is close to the border of the second order stability regions and also to the median lines of the first order stability regions where no temporal correlation between trajectories exists. In addition, these regions are fairly similar for different benchmark functions. When the number of parameters of the cost function increases, these regions move towards higher inertia weight values (w=1) and lower total mean accelerations where the temporal covariance between trajectories is positive. Finally, the comparison between different PSO versions results in the conclusion that the centered version (CC-PSO) and PSO have the best convergence rates. Conversely, the centered-progressive version (CP-PSO) has the greatest exploratory capabilities. These features have to do with the way these algorithms update the velocities and positions of particles in the swarm. Knowledge of their respective dynamics can be used to propose a family of simple and stable algorithms, including hybrid versions.     

3DMolNavi: A web-based retrieval and navigation tool for flexible molecular shape comparison

Background

As Next-Generation Sequencing data becomes available, existing hardware environments do not provide sufficient storage space and computational power to store and process the data due to their enormous size. This is and will be a frequent problem that is encountered everyday by researchers who are working on genetic data. There are some options available for compressing and storing such data, such as general-purpose compression software, PBAT/PLINK binary format, etc. However, these currently available methods either do not offer sufficient compression rates, or require a great amount of CPU time for decompression and loading every time the data is accessed.

Results

Here, we propose a novel and simple algorithm for storing such sequencing data. We show that, the compression factor of the algorithm ranges from 16 to several hundreds, which potentially allows SNP data of hundreds of Gigabytes to be stored in hundreds of Megabytes. We provide a C++ implementation of the algorithm, which supports direct loading and parallel loading of the compressed format without requiring extra time for decompression. By applying the algorithm to simulated and real datasets, we show that the algorithm gives greater compression rate than the commonly used compression methods, and the data-loading process takes less time. Also, The C++ library provides direct-data-retrieving functions, which allows the compressed information to be easily accessed by other C++ programs.

Conclusions

The SpeedGene algorithm enables the storage and the analysis of next generation sequencing data in current hardware environment, making system upgrades unnecessary.     

A simple translation in cortical log-coordinates may account for the pattern of saccadic localization errors

During saccadic eye movements, the visual world shifts rapidly across the retina. Perceptual continuity is thought to be maintained by active neural mechanisms that compensate for this displacement, bringing the presaccadic scene into a postsaccadic reference frame. Because of this active mechanism, objects appearing briefly around the time of the saccade are perceived at erroneous locations, a phenomenon called perisaccadic mislocalization. The position and direction of localization errors can inform us about the different reference frames involved. It has been found, for example, that errors are not simply made in the direction of the saccade but directed toward the saccade target, indicating that the compensatory mechanism involves spatial compression rather than translation. A recent study confirmed that localization errors also occur in the direction orthogonal to saccade direction, but only for eccentricities far from the fovea, beyond the saccade target. This spatially specific pattern of distortion cannot be explained by a simple compression of space around the saccade target. Here I show that a change of reference frames (i.e., translation) in cortical (logarithmic) coordinates, taking into account the cortical magnification factor, can accurately predict these spatial patterns of mislocalization. The flashed object projects onto the cortex in presaccadic (fovea-centered) coordinates but is perceived in postsaccadic (target-centered) coordinates.     

Similar movements are associated with drastically different muscle contraction velocities

We investigated how kinematic redundancy interacts with the neurophysiological control mechanisms required for smooth and accurate, rapid limb movements. Biomechanically speaking, tendon excursions are over-determined because the rotation of few joints determines the lengths and velocities of many muscles. But how different are the muscle velocity profiles induced by various, equally valid hand trajectories? We used an 18-muscle sagittal-plane arm model to calculate 100,000 feasible shoulder, elbow, and wrist joint rotations that produced valid basketball free throws with different hand trajectories, but identical initial and final hand positions and velocities. We found large differences in the eccentric and concentric muscle velocity profiles across many trajectories; even among similar trajectories. These differences have important consequences to their neural control because each trajectory will require unique, time-sensitive reflex modulation strategies. As Sherrington mentioned a century ago, failure to appropriately silence the stretch reflex of any one eccentrically contracting muscle will disrupt movement. Thus, trajectories that produce faster or more variable eccentric contractions will require more precise timing of reflex modulation across motoneuron pools; resulting in higher sensitivity to time delays, muscle mechanics, excitation/contraction dynamics, noise, errors and perturbations. By combining fundamental concepts of biomechanics and neuroscience, we propose that kinematic and muscle redundancy are, in fact, severely limited by the need to regulate reflex mechanisms in a task-specific and time-critical way. This in turn has important consequences to the learning and execution of accurate, smooth and repeatable movements—and to the rehabilitation of everyday limb movements in developmental and neurological conditions, and stroke.     

ZTR: a new format for DNA sequence trace data

MOTIVATION: To produce an open and extensible file format for DNA trace data which produces compact files suitable for large-scale storage and efficient use of internet bandwidth. RESULTS: We have created an extensible format named ZTR. For a set of data taken from an ABI-3700 the ZTR format produces trace files which require 61.6% of the disk space used by gzipped SCFv3, and which can be written and read at greater speed. The compression algorithms used for the trace amplitudes are used within the National Center for Biotechnology Information (NCBI) trace archive. lmb.cam.ac.uk/pub/staden/io_lib/test_data.     

Improving transmission efficiency of large sequence alignment/map (SAM) files

Research in bioinformatics primarily involves collection and analysis of a large volume of genomic data. Naturally, it demands efficient storage and transfer of this huge amount of data. In recent years, some research has been done to find efficient compression algorithms to reduce the size of various sequencing data. One way to improve the transmission time of large files is to apply a maximum lossless compression on them. In this paper, we present SAMZIP, a specialized encoding scheme, for sequence alignment data in SAM (Sequence Alignment/Map) format, which improves the compression ratio of existing compression tools available. In order to achieve this, we exploit the prior knowledge of the file format and specifications. Our experimental results show that our encoding scheme improves compression ratio, thereby reducing overall transmission time significantly.     

Guiding probabilistic search of the protein conformational space with structural profiles

The roughness of the protein energy surface poses a significant challenge to search algorithms that seek to obtain a structural characterization of the native state. Recent research seeks to bias search toward near-native conformations through one-dimensional structural profiles of the protein native state. Here we investigate the effectiveness of such profiles in a structure prediction setting for proteins of various sizes and folds. We pursue two directions. We first investigate the contribution of structural profiles in comparison to or in conjunction with physics-based energy functions in providing an effective energy bias. We conduct this investigation in the context of Metropolis Monte Carlo with fragment-based assembly. Second, we explore the effectiveness of structural profiles in providing projection coordinates through which to organize the conformational space. We do so in the context of a robotics-inspired search framework proposed in our lab that employs projections of the conformational space to guide search. Our findings indicate that structural profiles are most effective in obtaining physically realistic near-native conformations when employed in conjunction with physics-based energy functions. Our findings also show that these profiles are very effective when employed instead as projection coordinates to guide probabilistic search toward undersampled regions of the conformational space.     

RNACompress: Grammar-based compression and informational complexity measurement of RNA secondary structure

Background  

With the rapid emergence of RNA databases and newly identified non-coding RNAs, an efficient compression algorithm for RNA sequence and structural information is needed for the storage and analysis of such data. Although several algorithms for compressing DNA sequences have been proposed, none of them are suitable for the compression of RNA sequences with their secondary structures simultaneously. This kind of compression not only facilitates the maintenance of RNA data, but also supplies a novel way to measure the informational complexity of RNA structural data, raising the possibility of studying the relationship between the functional activities of RNA structures and their complexities, as well as various structural properties of RNA based on compression.     

Trajectory analysis of NMR structure calculations

Summary NMR as well as X-ray crystallography are used to determine the three-dimensional structures of macromolecules at atomic resolution. Structure calculation generates coordinates that are compatible with NMR data from randomly generated initial structures. We analyzed the trajectory taken by structures during NMR structure calculation in conformational space, assuming that the distance between two structures in conformational space is the root-mean-square deviation between the two structures. The coordinates of a structure in conformational space were obtained by applying the metric multidimensional scaling method. As an example, we used a 22-residue peptide, -Conotoxin GIIIA, and a simulated annealing protocol of XPLOR. We found that the three-dimensional solution of the multidimensional scaling analysis is sufficient to describe the overall configuration of the trajectories in conformational space. By comparing the trajectories of the entire calculation with those of the converged calculation, random sampling of conformational space is readily discernible. Trajectory analysis can also be used for optimization of protocols of NMR structure calculation, by examining individual trajectories.Abbreviations MD molecular dynamics - MDS multidimensional scaling - rmsd root-mean-square deviation - armsd angular rmsd - R multiple correlation coefficient - YASAP yet another simulated annealing protocol - PCA principal component analysis     

A Sensorimotor Model for Computing Intended Reach Trajectories

The presumed role of the primate sensorimotor system is to transform reach targets from retinotopic to joint coordinates for producing motor output. However, the interpretation of neurophysiological data within this framework is ambiguous, and has led to the view that the underlying neural computation may lack a well-defined structure. Here, I consider a model of sensorimotor computation in which temporal as well as spatial transformations generate representations of desired limb trajectories, in visual coordinates. This computation is suggested by behavioral experiments, and its modular implementation makes predictions that are consistent with those observed in monkey posterior parietal cortex (PPC). In particular, the model provides a simple explanation for why PPC encodes reach targets in reference frames intermediate between the eye and hand, and further explains why these reference frames shift during movement. Representations in PPC are thus consistent with the orderly processing of information, provided we adopt the view that sensorimotor computation manipulates desired movement trajectories, and not desired movement endpoints.     

DNABIT Compress - Genome compression algorithm

Data compression is concerned with how information is organized in data. Efficient storage means removal of redundancy from the data being stored in the DNA molecule. Data compression algorithms remove redundancy and are used to understand biologically important molecules. We present a compression algorithm, "DNABIT Compress" for DNA sequences based on a novel algorithm of assigning binary bits for smaller segments of DNA bases to compress both repetitive and non repetitive DNA sequence. Our proposed algorithm achieves the best compression ratio for DNA sequences for larger genome. Significantly better compression results show that "DNABIT Compress" algorithm is the best among the remaining compression algorithms. While achieving the best compression ratios for DNA sequences (Genomes),our new DNABIT Compress algorithm significantly improves the running time of all previous DNA compression programs. Assigning binary bits (Unique BIT CODE) for (Exact Repeats, Reverse Repeats) fragments of DNA sequence is also a unique concept introduced in this algorithm for the first time in DNA compression. This proposed new algorithm could achieve the best compression ratio as much as 1.58 bits/bases where the existing best methods could not achieve a ratio less than 1.72 bits/bases.     

A model to predict canine pelvic limb musculoskeletal geometry

We developed a model to predict the three-dimensional canine pelvic limb muscular geometry (i.e., all muscle moment arms during any instant in gait). Forty-one muscle origins and insertions, as well as external landmarks (to obtain anthropometric dimensions) were marked on both pelvic limbs of five dogs and digitized on biplanar radiographs. Reference frames in the pelvis, femur, and tibia established the three-dimensional coordinates of each origin, insertion, and landmark. A set of dimensionless 'scaled coordinates' was created by dividing the actual origin and insertion coordinates by selected anthropometric dimensions of each animal. Combining scaled coordinates from all ten limbs produced an averaged 'template' of scaled coordinates. To provide limited validation of the scaling procedure, we measured the anthropometric dimensions between externally palpable landmarks of two additional pelvic limbs. The anthropometric dimensions were multiplied by the averaged template coordinates to calculate two new sets of hindlimb muscle coordinates within the three bony reference frames. The two limbs then were dissected, muscle endpoints were marked, and biplanar radiographs of each of the limb segments were digitized. The actual coordinates so obtained were similar to those predicted by the template and anthropometric measures.     

Analysis of kinematic invariances of multijoint reaching movement

 There is a no unique relationship between the trajectory of the hand, represented in cartesian or extrinsic space, and its trajectory in joint angle or intrinsic space in the general condition of joint redundancy. The goal of this work is to analyze the relation between planning the trajectory of a multijoint movement in these two coordinate systems. We show that the cartesian trajectory can be planned based on the task parameters (target coordinates, etc.) prior to and independently of angular trajectories. Angular time profiles are calculated from the cartesian trajectory to serve as a basis for muscle control commands. A unified differential equation that allows planning trajectories in cartesian and angular spaces simultaneously is proposed. Due to joint redundancy, each cartesian trajectory corresponds to a family of angular trajectories which can account for the substantial variability of the latter. A set of strategies for multijoint motor control following from this model is considered; one of them coincides with the frog wiping reflex model and resolves the kinematic inverse problem without inversion. The model trajectories exhibit certain properties observed in human multijoint reaching movements such as movement equifinality, straight end-point paths, bell-shaped tangential velocity profiles, speed-sensitive and speed-insensitive movement strategies, peculiarities of the response to double-step targets, and variations of angular trajectory without variations of the limb end-point trajectory in cartesian space. In humans, those properties are almost independent of limb configuration, target location, movement duration, and load. In the model, these properties are invariant to an affine transform of cartesian space. This implies that these properties are not a special goal of the motor control system but emerge from movement kinematics that reflect limb geometry, dynamics, and elementary principles of motor control used in planning. All the results are given analytically and, in order to compare the model with experimental results, by computer simulations. Received: 6 April 1994/Accepted in revised form: 25 April 1995     

NGC: lossless and lossy compression of aligned high-throughput sequencing data

A major challenge of current high-throughput sequencing experiments is not only the generation of the sequencing data itself but also their processing, storage and transmission. The enormous size of these data motivates the development of data compression algorithms usable for the implementation of the various storage policies that are applied to the produced intermediate and final result files. In this article, we present NGC, a tool for the compression of mapped short read data stored in the wide-spread SAM format. NGC enables lossless and lossy compression and introduces the following two novel ideas: first, we present a way to reduce the number of required code words by exploiting common features of reads mapped to the same genomic positions; second, we present a highly configurable way for the quantization of per-base quality values, which takes their influence on downstream analyses into account. NGC, evaluated with several real-world data sets, saves 33–66% of disc space using lossless and up to 98% disc space using lossy compression. By applying two popular variant and genotype prediction tools to the decompressed data, we could show that the lossy compression modes preserve >99% of all called variants while outperforming comparable methods in some configurations.     

Constructing cranial ontogenetic trajectories: A comparison of growth,development, and chronological age proxies using a known‐age sample of Macaca mulatta

Recent morphometric research has generated opposing conclusions regarding the ontogenetic trajectories of catarrhine crania, possibly due to the ontogenetic proxies used to calculate them. Therefore, we used three surrogates: size, molar eruption, and chronological age to generate trajectories in a known‐age sample to produce ontogenetic trajectories and determine the similarities and differences between them. Forty‐three landmarks from an ontogenetic series of 160 Macaca mulatta crania, with associated ages at death, were used to produce ontogenetic trajectories of cranial shape change. These were computed by sex through multivariate regression of Procrustes aligned coordinates against three surrogates for ontogeny: natural log of centroid size (growth), molar eruption stage (development), and chronological age. These trajectories were compared by calculating the angles between them. Each trajectory was also used to produce simulated adults from juveniles, which were then compared with each other and actual adults. The different trajectories are nearly parallel as each of the surrogates track similar aspects of ontogenetic cranial shape change, but chronological age was the most divergent. Simulated adults produced using the developmental stage trajectories were most similar to actual adults. When simulated adults were produced from opposite sex trajectories, they resembled the sex from which the trajectory was produced, not the sex of the juvenile specimen. We discuss properties of the trajectories produced from each of the surrogates, the possible reasons for previously opposing conclusions, how these properties can inform future investigations, and how our investigation bears on analyses of heterochrony.     

Academic learning,a variational model

By assigning coordinates to the information space comprising all knowledge, rigorous mathematical interpretations can be placed on such terms as academic ability, memory and creativity such that these psychometric concepts can be incorporated into a framework of functional analysis which then permits the optimization of long-term academic learning processes through the location of the teaching trajectories in information space which will maximize the knowledge accumulated in a generalized educational system composed of a complex of subject-pupil-teacher interactions. The concepts of discrete and continuous information spaces are discussed in connection with subject-subject, subjectpupil and pupil-pupil interactions, and the advantages of using variational versus dynamic programming methods of optimizing alternative educational systems are evaluated.     

Step Detection in Single-Molecule Real Time Trajectories Embedded in Correlated Noise

Single-molecule real time trajectories are embedded in high noise. To extract kinetic or dynamic information of the molecules from these trajectories often requires idealization of the data in steps and dwells. One major premise behind the existing single-molecule data analysis algorithms is the Gaussian ‘white’ noise, which displays no correlation in time and whose amplitude is independent on data sampling frequency. This so-called ‘white’ noise is widely assumed but its validity has not been critically evaluated. We show that correlated noise exists in single-molecule real time trajectories collected from optical tweezers. The assumption of white noise during analysis of these data can lead to serious over- or underestimation of the number of steps depending on the algorithms employed. We present a statistical method that quantitatively evaluates the structure of the underlying noise, takes the noise structure into account, and identifies steps and dwells in a single-molecule trajectory. Unlike existing data analysis algorithms, this method uses Generalized Least Squares (GLS) to detect steps and dwells. Under the GLS framework, the optimal number of steps is chosen using model selection criteria such as Bayesian Information Criterion (BIC). Comparison with existing step detection algorithms showed that this GLS method can detect step locations with highest accuracy in the presence of correlated noise. Because this method is automated, and directly works with high bandwidth data without pre-filtering or assumption of Gaussian noise, it may be broadly useful for analysis of single-molecule real time trajectories.