Directional Path Research Articles

Human Genome Replication Proceeds through Four Chromatin States

Advances in genomic studies have led to significant progress in understanding the epigenetically controlled interplay between chromatin structure and nuclear functions. Epigenetic modifications were shown to play a key role in transcription regulation and genome activity during development and differentiation or in response to the environment. Paradoxically, the molecular mechanisms that regulate the initiation and the maintenance of the spatio-temporal replication program in higher eukaryotes, and in particular their links to epigenetic modifications, still remain elusive. By integrative analysis of the genome-wide distributions of thirteen epigenetic marks in the human cell line K562, at the 100 kb resolution of corresponding mean replication timing (MRT) data, we identify four major groups of chromatin marks with shared features. These states have different MRT, namely from early to late replicating, replication proceeds though a transcriptionally active euchromatin state (C1), a repressive type of chromatin (C2) associated with polycomb complexes, a silent state (C3) not enriched in any available marks, and a gene poor HP1-associated heterochromatin state (C4). When mapping these chromatin states inside the megabase-sized U-domains (U-shaped MRT profile) covering about 50% of the human genome, we reveal that the associated replication fork polarity gradient corresponds to a directional path across the four chromatin states, from C1 at U-domains borders followed by C2, C3 and C4 at centers. Analysis of the other genome half is consistent with early and late replication loci occurring in separate compartments, the former correspond to gene-rich, high-GC domains of intermingled chromatin states C1 and C2, whereas the latter correspond to gene-poor, low-GC domains of alternating chromatin states C3 and C4 or long C4 domains. This new segmentation sheds a new light on the epigenetic regulation of the spatio-temporal replication program in human and provides a framework for further studies in different cell types, in both health and disease.

A WSN-Based Localization Scheme Considering the Reliability of RSSI Measurements

In this paper, we propose a localization scheme considering the reliability of RSSI (Received Signal Strength Indication) measurements in the WSN (Wireless Sensor Network) environment. This scheme attempts to reduce location errors due to indoor obstacles or environmental factors, when location calculations are based on RSSI. The standard deviation is used to evaluate the reliability of RSSI measurements from the reference node. Also, the directional path loss exponent is calculated through learning with respect to the reference node. The experimental results show that the proposed localization scheme improves the performance significantly in terms of location accuracy, compared to the existing RSSI-based approaches.

Measuring Efficiency in Price Space with an Application to Japanese Securities Firms

The authors exploit the duality between the directional output price distance function and the maximal revenue function to estimate the price efficiency of Japanese securities firms during 2000 to 2007, a period in which securities firms faced greater competitive pressures. The directional output price distance function gives the maximum feasible addition to output prices, given inputs and a revenue target. Output supply functions are theoretically derived from the directional output price distance function. The model estimates indicate that brokerage services are overproduced relative to underwriting services. In addition, they find that if securities firms were to become more efficient they could increase the prices charged for brokerage services and for underwriting securities, although the amount prices could be increased depends on the directional path used to inflate actual prices to the output price frontier.

Proportion-Based and Tendency-Based Bus Trajectory Prediction Models

At the terminal station, the path headway bias of a trip is linearly correlated to the travel time of the path when it is beyond a critical range, which marks the tendency between successive trips. A tendency-based model for trajectory prediction was proposed in which the path headway bias was assumed to be proportionally amplified at downstream stops with an increase in path travel time, when buses fall into the amplifying tendency, or remain the same, when buses fall into the maintaining tendency. The boundary of the tendency was calibrated by the relative performance between the proportion-based model and the history-based model. The calibrated tendency-based model succeeds in avoiding the amplification of nondirectional path headway bias in the proportion-based model by keeping buses in the maintaining tendency and promoting the amplification of directional path headway bias by allowing buses to fall into the amplifying tendency.

Outcomes of Integrated Agriscience Processes: A Synthesis of Research

As the trend to integrate science and agriculture education has reemerged, so has the research related to the integration of science into secondary agricultural education. The American Association of Agricultural Education responded to this trend by creating a special interest group called “Strengthening Academic Learning through Agricultural Education.” In 2005, Myers and Osborne developed the “Conceptual Model for Strengthening Academic Learning through Agricultural Education” to guide this group in identifying existing gaps in the literature and to help provide a directional path for future research. The purpose of this study was to use that conceptual model to review research, to make conclusions regarding the outcomes of efforts to integrate science and secondary agricultural education, and to identify gaps in the existing research. Recommendations and future questions for integrating science and agricultural education were posed by the authors.

Blast and Ballistic Trajectories in Combat Casualties: A Preliminary Analysis Using a Cartesian Positioning System With MDCT

The purpose of this study is to determine the agreement with which radiologists identify wound paths in vivo on MDCT and calculate missile trajectories on the basis of Cartesian coordinates using a Cartesian positioning system (CPS). Three radiologists retrospectively identified 25 trajectories on MDCT in 19 casualties who sustained penetrating trauma in Iraq. Trajectories were described qualitatively in terms of directional path descriptors and quantitatively as trajectory vectors. Directional descriptors, trajectory angles, and angles between trajectories were calculated based on Cartesian coordinates of entrance and terminus or exit recorded in x, y image and table space (z) using a Trajectory Calculator created using spreadsheet software. The consistency of qualitative descriptor determinations was assessed in terms of frequency of observer agreement and multirater kappa statistics. Consistency of trajectory vectors was evaluated in terms of distribution of magnitude of the angles between vectors and the differences between their paraaxial and parasagittal angles. In 68% of trajectories, the observers' visual assessment of qualitative descriptors was congruent. Calculated descriptors agreed across observers in 60% of the trajectories. Estimated kappa also showed good agreement (0.65-0.79, p < 0.001); 70% of calculated paraaxial and parasagittal angles were within 20° across observers, and 61.3% of angles between trajectory vectors were within 20° across observers. Results show agreement of visually assessed and calculated qualitative descriptors and trajectory angles among observers. The Trajectory Calculator describes trajectories qualitatively similar to radiologists' visual assessment, showing the potential feasibility of automated trajectory analysis.

Statistical Analysis of Multipath Clustering in an Indoor Office Environment

A parametric directional-based MIMO channel model is presented which takes multipath clustering into account. The directional propagation path parameters include azimuth of arrival (AoA), azimuth of departure (AoD), delay, and power. MIMO measurements are carried out in an indoor office environment using the virtual antenna array method with a vector network analyzer. Propagation paths are extracted using a joint 5D ESPRIT algorithm and are automatically clustered with the K-power-means algorithm. This work focuses on the statistical treatment of the propagation parameters within individual clusters (intracluster statistics) and the change in these parameters from one cluster to another (intercluster statistics). Motivated choices for the statistical distributions of the intracluster and intercluster parameters are made. To validate these choices, the parameters' goodness of fit to the proposed distributions is verified using a number of powerful statistical hypothesis tests. Additionally, parameter correlations are calculated and tested for their significance. Building on the concept of multipath clusters, this paper also provides a new notation of the MIMO channel matrix (named FActorization into a BLock-diagonal Expression or FABLE) which more visibly shows the clustered nature of propagation paths.

Goal PPs and Their Eventuality

I argue in this paper that Korean directional SVCs license telic accomplishment interpretation, which is derived by the interaction of V1, directional V2, and a goal PP. The goal PP functions as a secondary resultative predicate and contributes to bounded reading of the whole sentence, whether its head is -ey or -(u)lo. Discussing telic behavior of directional SVCs with an -(u)lo PP, I claim that their (a)telicity is not straightforwardly judged by the presence of the -(u)lo PP. The -(u)lo PP can denote either an unbounded directional path or a bounded goal path, which is determined by the combinatory work of [PP-V1-V2] usually with a semantic or pragmatic contribution of other lexical items. I also discuss aspectual properties and structural differences of directional SVCs, based on Ramchands (2009) first-phase event structure syntax.

The Role of Depression in Adolescent Smoking Trajectories

The public health significance of adolescent smoking and depression has been established, and the co-morbidity has been documented. However, the directionality of the relationship, mediating mechanisms, moderated effects, and the developmental heterogeneity between depression and smoking among adolescents are either unclear or have not been studied. Potential answers and future research needed to address four important questions are highlighted. One, what is the nature of the relationship between smoking and depression? Directionality has implications for distinct etiological and prevention intervention implications. Two, why is depression linked to smoking acquisition, and why does smoking contribute to the development of depression? Information regarding common and unique mechanisms by directional path will pinpoint intervention targets. Three, what modifies the impact of depression on smoking, and what modifies the impact of smoking on depression? This will provide critical information on who to target for an intervention. Four, how do we best capture co-morbidity between depression and smoking? When, how, and for whom is it established? We posit that co-morbidity should be considered within the longitudinal course of each co-occurring behavior. Identifying and characterizing conjoint developmental trajectories may optimize intervention type, timing, target, and content.

Multi‐block and path modelling procedures

AbstractThe author has developed a unified theory of path and multi‐block modelling of data. The data blocks are arranged in a directional path. Each data block can lead to one or more data blocks. It is assumed that there is given a collection of input data blocks. Each of them is supposed to describe one or more intermediate data blocks. The output data blocks are those that are at the ends of the paths and have no succeeding data blocks. The optimisation procedure finds weights for the input data blocks so that the size of the total loadings for the output data blocks are maximised. When the optimal weight vectors have been determined, the score and loading vectors for the data blocks in the path are determined. Appropriate adjustment of the data blocks is carried out at each step. Regression coefficients are computed for each data block that show how the data block is estimated by data blocks that lead to it. Methods of standard regression analysis are extended to this type of modelling. Three types of ‘strengths’ of relationship are computed for each set of two connected data blocks. First is the strength in the path, second the strength where only the data blocks leading to the last one are used and third if only the two are considered. Cross‐validation and other standard methods of linear regression are carried out in a similar manner. In industry, processes are organised in different ways. It can be useful to model the processes in the way they are carried out. By proper alignment of sub‐processes, overall model can be specified. There can be several useful path models during the process, where the data blocks in a path are the ones that are actual or important at given stages of the process. Data collection equipments are getting more and more advanced and cheap. Data analysis need to ‘catch up’ with the challenges that these new technology provides with. Copyright © 2008 John Wiley &amp; Sons, Ltd.

PREPROCESSING QUANTIFIED CONSTRAINT SATISFACTION PROBLEMS WITH VALUE REORDERING AND DIRECTIONAL ARC AND PATH CONSISTENCY

The Quantified Constraint Satisfaction Problem (QCSP) is an extension of the CSP that can be used to model combinatorial problems containing contingency or uncertainty. It allows for universally quantified variables that can model uncertain actions and events, such as the unknown weather for a future party, or an opponent's next move in a game. Although interest in QCSPs is increasing in recent years, the development of techniques for handling QCSPs is still at an early stage. For example, although it is well known that local consistencies are of primary importance in CSPs, only arc consistency has been extended to quantified problems. In this paper we contribute towards the development of solution methods for QCSPs in two ways. First, by extending directional arc and path consistency, two popular local consistencies in constraint satisfaction, to the quantified case and proposing an algorithm that achieves these consistencies. Second, by showing how value ordering heuristics can be utilized to speed up computation in QCSPs. We study the impact of preprocessing QCSPs with value reordering and directional quantified arc and path consistency by running experiments on randomly generated problems. Results show that our preprocessing methods can significantly speed up the QCSP solving process, especially on hard instances from the phase transition region.

Convolutionally Coded Adaptive Space-Time MMSE Receiver for W-CDMA Systems in Multipath Channels

In this paper, we consider the use of convolutionally coded adaptive space-time minimum mean-square error (MMSE) receiver for wideband code division multiple access (W-CDMA) systems in multipath channels. In the adaptive space-time MMSE receiver, antenna array processing is combined with MMSE multiuser detection (MUD). Simulations are carried out to evaluate the performance in the directional multi path quasi-static Rayleigh fading channels. Simulation results show that substantial performance improvement may be obtained by using convolutional codes jointly with the adaptive space-time MMSE receiver. Only requirement to implement the receiver is a training sequence and a priori knowledge of the users’ timing for only the strongest path.

Relations between structural intensity and J-integral

The present study introduces the concept of structural intensity, which can be interpreted as power flux, into fracture mechanics. It is derived theoretically that the normal component of the structural intensity along crack edge equals J-integral. SI is the power flux or vector representation of the J-integral at the crack tip. Using the finite element method, the structural intensity can be easily calculated. The numerically calculated structural intensity is adopted to visualize the J-integral of a crack tip. Directional power flow path and magnitude at the crack tip is demonstrated schematically with the structural intensity, which facilitates convenient evaluation of the crack propagation status.

Comments on the article ?Applications of Directional Wavefield Decomposition, Phase Space, and Path Integral Methods to Seismic Wave Propagation and Inversion? [Pure Appl. Geophys. 159 (2002) 1637?1679

Comments on the article ?Applications of Directional Wavefield Decomposition, Phase Space, and Path Integral Methods to Seismic Wave Propagation and Inversion? [Pure Appl. Geophys. 159 (2002) 1637?1679

Reply to the Comments on the Article ?Applications of Directional Wavefield Decomposition, Phase Space, and Path Integral Methods to Seismic Wave Propagation and Inversion? [Pure Appl. Geophys. 159 (2002) pp. 1637?1679] by P. M. Jordan and M. F. Werby

Reply to the Comments on the Article ?Applications of Directional Wavefield Decomposition, Phase Space, and Path Integral Methods to Seismic Wave Propagation and Inversion? [Pure Appl. Geophys. 159 (2002) pp. 1637?1679] by P. M. Jordan and M. F. Werby

Passive Transport Disrupts Directional Path Integration by Rat Head Direction Cells

A subset of neurons in the rat limbic system encodes head direction (HD) by selectively discharging when the rat points its head in a preferred direction in the horizontal plane. The preferred firing direction is sensitive to the location of landmark cues, as well as idiothetic or self-motion cues (i.e., vestibular, motor efference copy, proprioception, and optic flow). Previous studies have shown that the preferred firing direction remains relatively stable (average shift +/- 18 degrees ) after the rat walks from a familiar environment into a novel one, suggesting that without familiar landmarks, the preferred firing direction can be maintained using idiothetic cues, a process called directional path integration. This study repeated this experiment and manipulated the idiothetic cues available to the rat as it moved between the familiar and novel environment. Motor efference copy/proprioceptive cues were disrupted by passively transporting the animal between the familiar and novel environment. Darkening the room as the animal moved to the novel environment eliminated optic flow cues. HD cell preferred firing directions shifted in the novel environment by an average of 30 degrees after locomotion from the familiar environment with the room lights off; by an average of 70 degrees after passive transport from the familiar environment with the room lights on; and by an average of 67 degrees after passive transport with the room lights off. These findings are consistent with the view that motor efference copy/proprioception cues are important for maintaining the preferred firing direction of HD cells under conditions requiring path integration.

A directional crack path criterion for crack growth in ductile materials subjected to shear and compressive loading under plane strain conditions

A directional crack growth criterion in a compressed elastic perfectly plastic material is considered. The conditions at the crack-tip are evaluated for a straight stationary crack with a small incipient kink. Remote load is a combined hydrostatic pressure and pure shear applied via a boundary layer. Crack surfaces in contact are assumed to develop homogenous Coulomb friction. The crack opening displacement of an extended kink is examined in a finite element analysis to judge the risk of opening mode failure. It has been found that the direction that maximizes the crack opening displacement of an extended kink tip coincides very well with a prediction of the crack growth direction obtained by using a criterion for continued crack growth direction discussed by the authors elsewhere [Int. J. Fract. 108 (2001) 351]. Moreover, the by the model predicted incipient crack growth directions are qualitatively comparable with reported crack paths obtained in ductile materials in a limited number of experiments performed under a combined load of in-plane shear and compression.

Applications of Directional Wavefield Decomposition, Phase Space, and Path Integral Methods to Seismic Wave Propagation and Inversion

Recently, de Hoop and coworkers developed an asymptotic, seismic inversion formula for application in complex environments supporting multi-pathed and multi-mode wave propagation (DE HooP et al., 1999; DE HooP and BRANDSBERG-DAHL, 2000; STOLK and DE HooP, 2000). This inversion is based on the Born/Kirchhoff approximation, and employs the global, uniform asymptotic extension of the geometrical method of “tracing rays” to account for caustic phenomena. While this approach has successfully inverted the multicomponent, ocean-bottom data from the Valhall field in Norway, accounting for severe focusing effects (DE HooP and BRANDSBERG-DAHL, 2000), it is not able to account properly for wave phenomena neglected in the “high-frequency” limit (i.e., diffraction effects) and strong scattering effects. To proceed further and incorporate wave effects in a nonlinear inversion scheme, the theory of directional wavefield decomposition and the construction of the generalized Bremmer coupling series are combined with the application of modern phase space and path (functional) integral methods to, ultimately, suggest an inversion algorithm which can be interpreted as a method of “tracing waves.” This paper is intended to provide the seismic community with an introduction to these approaches to direct and inverse wave propagation and scattering, intertwining some of the most recent new results with the basic outline of the theory, and culminating in an outline of the extended, asymptotic, seismic inversion algorithm. Modeling at the level of the fixed-frequency (elliptic), scalar Helmholtz equation, exact and uniform asymptotic constructions of the well-known, and fundamentally important, square-root Helmholtz operator (symbol) provide the most important results.

The role of commutativity in constraint propagation algorithms

Constraing propagation algorithms form an important part of most of the constraint programming systems. We provide here a simple, yet very general framework that allows us to explain several constraint propagation algorithms in a systematic way. In this framework we proceed in two steps. First, we introduce a generic iteration algorithm on partial orderings and prove its correctness in an abstract setting. Then we instantiate this algorithm with specific partial orderings and functions to obtain specific constraint propagation algorithms. In particular, using the notions commutativity and semi-commutativity, we show that the AC-3, PC-2, DAC, and DPC algorithms for achieving (directional) arc consistency and (directional) path consistency are instances of a single generic algorithm. The work reported here extends and simplifies that of Apt [1999a].

Fluid-phase Endocytosis in the Amoebae of the Cellular Slime Mould Dictyostelium discoideum: Mathematical Modelling of Kinetics and pH Evolution

Fluid-phase endocytosis (pinocytosis) is a very active nutritive process in axenic strains of Dictyostelium discoideumamoebae. Fluorescein-labelled dextran was used as a dual fluid-phase and pH marker to characterize endocytosis pathway regarding the kinetics of fluid internalisation and vesicular pH. Continuous loading and pulse-chase experiments have been conducted. In the latter case, marker transit and efflux was monitored on cells loaded for short periods of time, washed then suspended in marker-free medium. To account simultaneously for fluid-phase endocytosis kinetics and pH evolution we have developed a mathematical model consisting of interconnected delay stages and compartments. A delay stage is defined as a directional path in which access to the following endocytic space occurs only after a characteristic transit time. In contrast to this behaviour, exit probability from a compartment is independent of the time spent in the compartment. The model describes correctly both the kinetics and pH changes in Dictyosteliumamoeba endocytic pathway. Useful estimates were obtained for kinetic constants, pH and fractional apparent volume of endocytic spaces. This modelling work provides a theoretical basis on which to design further experimental studies. It is of general applicability and could be useful to examine the characteristics of fluid-phase endocytosis in other eukaryotes.