Linear Index Coding and Representable Discrete Polymatroids

Discrete polymatroids are the multi-set analogue of matroids. In this paper, we explore the connections between linear index coding and representable discrete polymatroids. The index coding problem involves a sender which generates a set of messages X = {x(1), x(2), ... x(k)} and a set of receivers R which demand messages. A receiver R is an element of R is specified by the tuple (x, H) where x. X is the message demanded by R and H subset of X \textbackslash {x} is the side information possessed by R. It is first shown that a linear solution to an index coding problem exists if and only if there exists a representable discrete polymatroid satisfying certain conditions which are determined by the index coding problem considered. El Rouayheb et. al. showed that the problem of finding a multi-linear representation for a matroid can be reduced to finding a perfect linear index coding solution for an index coding problem obtained from that matroid. Multi-linear representation of a matroid can be viewed as a special case of representation of an appropriate discrete polymatroid. We generalize the result of El Rouayheb et. al. by showing that the problem of finding a representation for a discrete polymatroid can be reduced to finding a perfect linear index coding solution for an index coding problem obtained from that discrete polymatroid.

CTFS-ForestGEO: a worldwide network monitoring forests in an era of global change

Global change is impacting forests worldwide, threatening biodiversity and ecosystem services including climate regulation. Understanding how forests respond is critical to forest conservation and climate protection. This review describes an international network of 59 long-term forest dynamics research sites (CTFS-ForestGEO) useful for characterizing forest responses to global change. Within very large plots (median size 25ha), all stems 1cm diameter are identified to species, mapped, and regularly recensused according to standardized protocols. CTFS-ForestGEO spans 25 degrees S-61 degrees N latitude, is generally representative of the range of bioclimatic, edaphic, and topographic conditions experienced by forests worldwide, and is the only forest monitoring network that applies a standardized protocol to each of the world's major forest biomes. Supplementary standardized measurements at subsets of the sites provide additional information on plants, animals, and ecosystem and environmental variables. CTFS-ForestGEO sites are experiencing multifaceted anthropogenic global change pressures including warming (average 0.61 degrees C), changes in precipitation (up to +/- 30% change), atmospheric deposition of nitrogen and sulfur compounds (up to 3.8g Nm(-2)yr(-1) and 3.1g Sm(-2)yr(-1)), and forest fragmentation in the surrounding landscape (up to 88% reduced tree cover within 5km). The broad suite of measurements made at CTFS-ForestGEO sites makes it possible to investigate the complex ways in which global change is impacting forest dynamics. Ongoing research across the CTFS-ForestGEO network is yielding insights into how and why the forests are changing, and continued monitoring will provide vital contributions to understanding worldwide forest diversity and dynamics in an era of global change.

Emergency Handling in MICS based Body Area Network

Body Area Network, a new wireless networking paradigm, promises to revolutionize the healthcare applications. A number of tiny sensor nodes are strategically placed in and around the human body to obtain physiological information. The sensor nodes are connected to a coordinator or a data collector to form a Body Area Network. The tiny devices may sense physiological parameters of emergency in nature (e.g. abnormality in heart bit rate, increase of glucose level above the threshold etc.) that needs immediate attention of a physician. Due to ultra low power requirement of wireless body area network, most of the time, the coordinator and devices are expected to be in the dormant mode, categorically when network is not operational. This leads to an open question, how to handle and meet the QoS requirement of emergency data when network is not operational? Emergency handling becomes more challenging at the MAC layer, if the channel access related information is unknown to the device with emergency message. The aforementioned scenarios are very likely scenarios in a MICS (Medical Implant Communication Service, 402-405 MHz) based healthcare systems. This paper proposes a mechanism for timely and reliable transfer of emergency data in a MICS based Body Area Network. We validate our protocol design with simulation in a C++ framework. Our simulation results show that more than 99 p ercentage of the time emergency messages are reached at the coordinator with a delay of 400ms.

Sparse coding based VLAD for efficient image retrieval

Representing images and videos in the form of compact codes has emerged as an important research interest in the vision community, in the context of web scale image/video search. Recently proposed Vector of Locally Aggregated Descriptors (VLAD), has been shown to outperform the existing retrieval techniques, while giving a desired compact representation. VLAD aggregates the local features of an image in the feature space. In this paper, we propose to represent the local features extracted from an image, as sparse codes over an over-complete dictionary, which is obtained by K-SVD based dictionary training algorithm. The proposed VLAD aggregates the residuals in the space of these sparse codes, to obtain a compact representation for the image. Experiments are performed over the `Holidays' database using SIFT features. The performance of the proposed method is compared with the original VLAD. The 4% increment in the mean average precision (mAP) indicates the better retrieval performance of the proposed sparse coding based VLAD.

Analysis of the hierarchical structure of the B. subtilis transcriptional regulatory network

The transcriptional regulation of gene expression is orchestrated by complex networks of interacting genes. Increasing evidence indicates that these `transcriptional regulatory networks' (TRNs) in bacteria have an inherently hierarchical architecture, although the design principles and the specific advantages offered by this type of organization have not yet been fully elucidated. In this study, we focussed on the hierarchical structure of the TRN of the gram-positive bacterium Bacillus subtilis and performed a comparative analysis with the TRN of the gram-negative bacterium Escherichia coli. Using a graph-theoretic approach, we organized the transcription factors (TFs) and sigma-factors in the TRNs of B. subtilis and E. coli into three hierarchical levels (Top, Middle and Bottom) and studied several structural and functional properties across them. In addition to many similarities, we found also specific differences, explaining the majority of them with variations in the distribution of s-factors across the hierarchical levels in the two organisms. We then investigated the control of target metabolic genes by transcriptional regulators to characterize the differential regulation of three distinct metabolic subsystems (catabolism, anabolism and central energy metabolism). These results suggest that the hierarchical architecture that we observed in B. subtilis represents an effective organization of its TRN to achieve flexibility in response to a wide range of diverse stimuli.

A Gaussian network model study suggests that structural fluctuations are higher for inactive states than active states of protein kinases

We performed Gaussian network model based normal mode analysis of 3-dimensional structures of multiple active and inactive forms of protein kinases. In 14 different kinases, a more number of residues (1095) show higher structural fluctuations in inactive states than those in active states (525), suggesting that, in general, mobility of inactive states is higher than active states. This statistically significant difference is consistent with higher crystallographic B-factors and conformational energies for inactive than active states, suggesting lower stability of inactive forms. Only a small number of inactive conformations with the DFG motif in the ``in'' state were found to have fluctuation magnitudes comparable to the active conformation. Therefore our study reports for the first time, intrinsic higher structural fluctuation for almost all inactive conformations compared to the active forms. Regions with higher fluctuations in the inactive states are often localized to the aC-helix, aG-helix and activation loop which are involved in the regulation and/or in structural transitions between active and inactive states. Further analysis of 476 kinase structures involved in interactions with another domain/protein showed that many of the regions with higher inactive-state fluctuation correspond to contact interfaces. We also performed extensive GNM analysis of (i) insulin receptor kinase bound to another protein and (ii) holo and apo forms of active and inactive conformations followed by multi-factor analysis of variance. We conclude that binding of small molecules or other domains/proteins reduce the extent of fluctuation irrespective of active or inactive forms. Finally, we show that the perceived fluctuations serve as a useful input to predict the functional state of a kinase.

Gamma oscillations in the midbrain spatial attention network: linking circuits to function

Gamma-band (25-140 Hz) oscillations are ubiquitous in mammalian forebrain structures involved in sensory processing, attention, learning and memory. The optic tectum (01) is the central structure in a midbrain network that participates critically in controlling spatial attention. In this review, we summarize recent advances in characterizing a neural circuit in this midbrain network that generates large amplitude, space-specific, gamma oscillations in the avian OT, both in vivo and in vitro. We describe key physiological and pharmacological mechanisms that produce and regulate the structure of these oscillations. The extensive similarities between midbrain gamma oscillations in birds and those in the neocortex and hippocampus of mammals, offer important insights into the functional significance of a midbrain gamma oscillatory code.

Secure Compute-and-Forward in a Bidirectional Relay

We consider the basic bidirectional relaying problem, in which two users in a wireless network wish to exchange messages through an intermediate relay node. In the compute-and-forward strategy, the relay computes a function of the two messages using the naturally occurring sum of symbols simultaneously transmitted by user nodes in a Gaussian multiple-access channel (MAC), and the computed function value is forwarded to the user nodes in an ensuing broadcast phase. In this paper, we study the problem under an additional security constraint, which requires that each user's message be kept secure from the relay. We consider two types of security constraints: 1) perfect secrecy, in which the MAC channel output seen by the relay is independent of each user's message and 2) strong secrecy, which is a form of asymptotic independence. We propose a coding scheme based on nested lattices, the main feature of which is that given a pair of nested lattices that satisfy certain goodness properties, we can explicitly specify probability distributions for randomization at the encoders to achieve the desired security criteria. In particular, our coding scheme guarantees perfect or strong secrecy even in the absence of channel noise. The noise in the channel only affects reliability of computation at the relay, and for Gaussian noise, we derive achievable rates for reliable and secure computation. We also present an application of our methods to the multihop line network in which a source needs to transmit messages to a destination through a series of intermediate relays.

Reliability Assessment of a Storm Water Drain Network

Most of the cities in India are undergoing rapid development in recent decades, and many rural localities are undergoing transformation to urban hotspots. These developments have associated land use/land cover (LULC) change that effects runoff response from catchments, which is often evident in the form of increase in runoff peaks, volume and velocity in drain network. Often most of the existing storm water drains are in dilapidated stage owing to improper maintenance or inadequate design. The drains are conventionally designed using procedures that are based on some anticipated future conditions. Further, values of parameters/variables associated with design of the network are traditionally considered to be deterministic. However, in reality, the parameters/variables have uncertainty due to natural and/or inherent randomness. There is a need to consider the uncertainties for designing a storm water drain network that can effectively convey the discharge. The present study evaluates performance of an existing storm water drain network in Bangalore, India, through reliability analysis by Advance First Order Second Moment (AFOSM) method. In the reliability analysis, parameters that are considered to be random variables are roughness coefficient, slope and conduit dimensions. Performance of the existing network is evaluated considering three failure modes. The first failure mode occurs when runoff exceeds capacity of the storm water drain network, while the second failure mode occurs when the actual flow velocity in the storm water drain network exceeds the maximum allowable velocity for erosion control, whereas the third failure mode occurs when the minimum flow velocity is less than the minimum allowable velocity for deposition control. In the analysis, runoff generated from subcatchments of the study area and flow velocity in storm water drains are estimated using Storm Water Management Model (SWMM). Results from the study are presented and discussed. The reliability values are low under the three failure modes, indicating a need to redesign several of the conduits to improve their reliability. This study finds use in devising plans for expansion of the Bangalore storm water drain system. (C) 2015 The Authors. Published by Elsevier B.V.

One-step synthesis of a cyclic 2,17-dioxo3,3](4,4 `)biphenylophane and first preparation of a microporous polymer network from a macrocyclic precursor by cyclotrimerization

One-step synthesis of a cyclic 2,17-dioxo3,3](4,4') biphenylophane (MC) was achieved in high yield; its structure was verified by single crystal X-ray analysis. As a first example, a microporous polymer network was formed from macrocycle MC via acid-catalysed cyclotrimerization yielding a BET surface area of ca. 570 m(2) g(-1).

Coding of relative size in monkey inferotemporal cortex

We seldom mistake a closer object as being larger, even though its retinal image is bigger. One underlying mechanism could be to calculate the size of the retinal image relative to that of another nearby object. Here we set out to investigate whether single neurons in the monkey inferotemporal cortex (IT) are sensitive to the relative size of parts in a display. Each neuron was tested on shapes containing two parts that could be conjoined or spatially separated. Each shape was presented in four versions created by combining the two parts at each of two possible sizes. In this design, neurons sensitive to the absolute size of parts would show the greatest response modulation when both parts are scaled up, whereas neurons encoding relative size would show similar responses. Our main findings are that 1) IT neurons responded similarly to all four versions of a shape, but tuning tended to be more consistent between versions with proportionately scaled parts; 2) in a subpopulation of cells, we observed interactions that resulted in similar responses to proportionately scaled parts; 3) these interactions developed together with sensitivity to absolute size for objects with conjoined parts but developed slightly later for objects with spatially separate parts. Taken together, our results demonstrate for the first time that there is a subpopulation of neurons in IT that encodes the relative size of parts in a display, forming a potential neural substrate for size constancy.

Spray: A Multi-Modal Localization System for Stationary Sensor Network Deployment

We present a localization system that targets rapid deployment of stationary wireless sensor networks (WSN). The system uses a particle filter to fuse measurements from multiple localization modalities, such as RF ranging, neighbor information or maps, to obtain position estimations with higher accuracy than that of the individual modalities. The system isolates different modalities into separate components which can be included or excluded independently to tailor the system to a specific scenario. We show that position estimations can be improved with our system by combining multiple modalities. We evaluate the performance of the system in both an indoor and outdoor environment using combinations of five different modalities. Using two anchor nodes as reference points and combining all five modalities, we obtain RMS (Root Mean Square) estimation errors of approximately 2.5m in both cases, while using the components individually results in errors within the range of 3.5 and 9 m.

GBNV encoded movement protein (NSm) remodels ER network via C-terminal coiled coil domain

Plant viruses exploit the host machinery for targeting the viral genome-movement protein complex to plasmodesmata (PD). The mechanism by which the non-structural protein m (NSm) of Groundnut bud necrosis virus (GBNV) is targeted to PD was investigated using Agrobacterium mediated transient expression of NSm and its fusion proteins in Nicotiana benthamiana. GFP:NSm formed punctuate structures that colocalized with mCherry:plasmodesmata localized protein la (PDLP la) confirming that GBNV NSm localizes to PD. Unlike in other movement proteins, the C-terminal coiled coil domain of GBNV NSm was shown to be involved in the localization of NSm to PD, as deletion of this domain resulted in the cytoplasmic localization of NSm. Treatment with Brefeldin A demonstrated the role of ER in targeting GFP NSm to PD. Furthermore, mCherry:NSm co-localized with ER-GFP (endoplasmic reticulum targeting peptide (HDEL peptide fused with GFP). Co-expression of NSm with ER-GFP showed that the ER-network was transformed into vesicles indicating that NSm interacts with ER and remodels it. Mutations in the conserved hydrophobic region of NSm (residues 130-138) did not abolish the formation of vesicles. Additionally, the conserved prolines at positions 140 and 142 were found to be essential for targeting the vesicles to the cell membrane. Further, systematic deletion of amino acid residues from N- and C-terminus demonstrated that N-terminal 203 amino acids are dispensable for the vesicle formation. On the other hand, the C-terminal coiled coil domain when expressed alone could also form vesicles. These results suggest that GBNV NSm remodels the ER network by forming vesicles via its interaction through the C-terminal coiled coil domain. Interestingly, NSm interacts with NP in vitro and coexpression of these two proteins in planta resulted in the relocalization of NP to PD and this relocalization was abolished when the N-terminal unfolded region of NSm was deleted. Thus, the NSm interacts with NP via its N-terminal unfolded region and the NSm-NP complex could in turn interact with the ER membrane via the C-terminal coiled coil domain of NSm to form vesicles that are targeted to PD and there by assist the cell to cell movement of the viral genome complex. (C) 2015 Elsevier Inc. All rights reserved.

A quantitative imaging-based screen reveals the exocyst as a network hub connecting endocytosis and exocytosis

The coupling of endocytosis and exocytosis underlies fundamental biological processes ranging from fertilization to neuronal activity and cellular polarity. However, the mechanisms governing the spatial organization of endocytosis and exocytosis require clarification. Using a quantitative imaging-based screen in budding yeast, we identified 89 mutants displaying defects in the localization of either one or both pathways. High-resolution single-vesicle tracking revealed that the endocytic and exocytic mutants she4 Delta and bud6 Delta alter post-Golgi vesicle dynamics in opposite ways. The endocytic and exocytic pathways display strong interdependence during polarity establishment while being more independent during polarity maintenance. Systems analysis identified the exocyst complex as a key network hub, rich in genetic interactions with endocytic and exocytic components. Exocyst mutants displayed altered endocytic and post-Golgi vesicle dynamics and interspersed endocytic and exocytic domains compared with control cells. These data are consistent with an important role for the exocyst in coordinating endocytosis and exocytosis.

Action Recognition from Motion Capture Data using Meta-cognitive RBF Network Classifier

Action recognition plays an important role in various applications, including smart homes and personal assistive robotics. In this paper, we propose an algorithm for recognizing human actions using motion capture action data. Motion capture data provides accurate three dimensional positions of joints which constitute the human skeleton. We model the movement of the skeletal joints temporally in order to classify the action. The skeleton in each frame of an action sequence is represented as a 129 dimensional vector, of which each component is a 31) angle made by each joint with a fixed point on the skeleton. Finally, the video is represented as a histogram over a codebook obtained from all action sequences. Along with this, the temporal variance of the skeletal joints is used as additional feature. The actions are classified using Meta-Cognitive Radial Basis Function Network (McRBFN) and its Projection Based Learning (PBL) algorithm. We achieve over 97% recognition accuracy on the widely used Berkeley Multimodal Human Action Database (MHAD).