Sensory cues employed for the acquisition of familiarity-dependent recognition of a shoal of conspecifics by climbing perch (Anabas testudineus Bloch)

In this study we showed that a freshwater fish, the climbing perch (Anabas testudineus) is incapable of using chemical communication but employs visual cues to acquire familiarity and distinguish a familiar group of conspecifics from an unfamiliar one. Moreover, the isolation of olfactory signals from visual cues did not affect the recognition and preference for a familiar shoal in this species.

Simultaneous acquisition of three NMR spectra in a single experiment for rapid resonance assignments in metabolomics

NMR-based approach to metabolomics typically involves the collection of two-dimensional (2D) heteronuclear correlation spectra for identification and assignment of metabolites. In case of spectral overlap, a 3D spectrum becomes necessary, which is hampered by slow data acquisition for achieving sufficient resolution. We describe here a method to simultaneously acquire three spectra (one 3D and two 2D) in a single data set, which is based on a combination of different fast data acquisition techniques such as G-matrix Fourier transform (GFT) NMR spectroscopy, parallel data acquisition and non-uniform sampling. The following spectra are acquired simultaneously: (1) C-13 multiplicity edited GFT (3,2)D HSQC-TOCSY, (2) 2D H-1- H-1] TOCSY and (3) 2D C-13- H-1] HETCOR. The spectra are obtained at high resolution and provide high-dimensional spectral information for resolving ambiguities. While the GFT spectrum has been shown previously to provide good resolution, the editing of spin systems based on their CH multiplicities further resolves the ambiguities for resonance assignments. The experiment is demonstrated on a mixture of 21 metabolites commonly observed in metabolomics. The spectra were acquired at natural abundance of C-13. This is the first application of a combination of three fast NMR methods for small molecules and opens up new avenues for high-throughput approaches for NMR-based metabolomics.

Creating a specialist protein resource network: a meeting report for the protein bioinformatics and community resources retreat

During 11-12 August 2014, a Protein Bioinformatics and Community Resources Retreat was held at the Wellcome Trust Genome Campus in Hinxton, UK. This meeting brought together the principal investigators of several specialized protein resources (such as CAZy, TCDB and MEROPS) as well as those from protein databases from the large Bioinformatics centres (including UniProt and RefSeq). The retreat was divided into five sessions: (1) key challenges, (2) the databases represented, (3) best practices for maintenance and curation, (4) information flow to and from large data centers and (5) communication and funding. An important outcome of this meeting was the creation of a Specialist Protein Resource Network that we believe will improve coordination of the activities of its member resources. We invite further protein database resources to join the network and continue the dialogue.

SInCRe-structural interactome computational resource for Mycobacterium tuberculosis

We have developed an integrated database for Mycobacterium tuberculosis H37Rv (Mtb) that collates information on protein sequences, domain assignments, functional annotation and 3D structural information along with protein-protein and protein-small molecule interactions. SInCRe (Structural Interactome Computational Resource) is developed out of CamBan (Cambridge and Bangalore) collaboration. The motivation for development of this database is to provide an integrated platform to allow easily access and interpretation of data and results obtained by all the groups in CamBan in the field of Mtb informatics. In-house algorithms and databases developed independently by various academic groups in CamBan are used to generate Mtb-specific datasets and are integrated in this database to provide a structural dimension to studies on tuberculosis. The SInCRe database readily provides information on identification of functional domains, genome-scale modelling of structures of Mtb proteins and characterization of the small-molecule binding sites within Mtb. The resource also provides structure-based function annotation, information on small-molecule binders including FDA (Food and Drug Administration)-approved drugs, protein-protein interactions (PPIs) and natural compounds that bind to pathogen proteins potentially and result in weakening or elimination of host-pathogen protein-protein interactions. Together they provide prerequisites for identification of off-target binding.

Coupling geomorphology parameters with lithology for micro-level groundwater resource assessment: a case study from semi-arid hard rock terrain in Tamil Nadu, India

The standard procedure of groundwater resource estimation in India till date is based on the specific yield parameters of each rock type (lithology) derived through pumping test analysis. Using the change in groundwater level, specific yield, and area of influence, groundwater storage change could be estimated. However, terrain conditions in the form of geomorphological variations have an important bearing on the net groundwater recharge. In this study, an attempt was made to use both lithology and geomorphology as input variables to estimate the recharge from different sources in each lithology unit influenced by the geomorphic conditions (lith-geom), season wise separately. The study provided a methodological approach for an evaluation of groundwater in a semi-arid hard rock terrain in Tirunelveli, Tamil Nadu, India. While characterizing the gneissic rock, it was found that the geomorphologic variations in the gneissic rock due to weathering and deposition behaved differently with respect to aquifer recharge. The three different geomorphic units identified in gneissic rock (pediplain shallow weathered (PPS), pediplain moderate weathered (PPM), and buried pediplain moderate (BPM)) showed a significant variation in recharge conditions among themselves. It was found from the study that Peninsular gneiss gives a net recharge value of 0.13 m/year/unit area when considered as a single unit w.r.t. lithology, whereas the same area considered with lith-geom classes gives recharge values between 0.1 and 0.41 m/year presenting a different assessment. It is also found from this study that the stage of development (SOD) for each lith-geom unit in Peninsular gneiss varies from 168 to 230 %, whereas the SOD is 223 % for the lithology as a single unit.

Segregating Discourse Segments from Engineering Documents for Knowledge Acquisition

The broader goal of the research being described here is to automatically acquire diagnostic knowledge from documents in the domain of manual and mechanical assembly of aircraft structures. These documents are treated as a discourse used by experts to communicate with others. It therefore becomes possible to use discourse analysis to enable machine understanding of the text. The research challenge addressed in the paper is to identify documents or sections of documents that are potential sources of knowledge. In a subsequent step, domain knowledge will be extracted from these segments. The segmentation task requires partitioning the document into relevant segments and understanding the context of each segment. In discourse analysis, the division of a discourse into various segments is achieved through certain indicative clauses called cue phrases that indicate changes in the discourse context. However, in formal documents such language may not be used. Hence the use of a domain specific ontology and an assembly process model is proposed to segregate chunks of the text based on a local context. Elements of the ontology/model, and their related terms serve as indicators of current context for a segment and changes in context between segments. Local contexts are aggregated for increasingly larger segments to identify if the document (or portions of it) pertains to the topic of interest, namely, assembly. Knowledge acquired through such processes enables acquisition and reuse of knowledge during any part of the lifecycle of a product.

Performance evaluation of mobile agent based resource management protocol for MANETs

The nodes with dynamicity, and management without administrator are key features of mobile ad hoc networks (1VIANETs). Increasing resource requirements of nodes running different applications, scarcity of resources, and node mobility in MANETs are the important issues to be considered in allocation of resources. Moreover, management of limited resources for optimal allocation is a crucial task. In our proposed work we discuss a design of resource allocation protocol and its performance evaluation. The proposed protocol uses both static and mobile agents. The protocol does the distribution and parallelization of message propagation (mobile agent with information) in an efficient way to achieve scalability and speed up message delivery to the nodes in the sectors of the zones of a MANET. The protocol functionality has been simulated using Java Agent Development Environment (JADE) Framework for agent generation, migration and communication. A mobile agent migrates from central resource rich node with message and navigate autonomously in the zone of network until the boundary node. With the performance evaluation, it has been concluded that the proposed protocol consumes much less time to allocate the required resources to the nodes under requirement, utilize less network resources and increase the network scalability. (C) 2015 Elsevier B.V. All rights reserved.

CheepSync: A Time Synchronization Service for Resource Constrained Bluetooth LE Advertisers

Clock synchronization is highly desirable in distributed systems, including many applications in the Internet of Things and Humans. It improves the efficiency, modularity, and scalability of the system, and optimizes use of event triggers. For IoTH, BLE - a subset of the recent Bluetooth v4.0 stack - provides a low-power and loosely coupled mechanism for sensor data collection with ubiquitous units (e.g., smartphones and tablets) carried by humans. This fundamental design paradigm of BLE is enabled by a range of broadcast advertising modes. While its operational benefits are numerous, the lack of a common time reference in the broadcast mode of BLE has been a fundamental limitation. This article presents and describes CheepSync, a time synchronization service for BLE advertisers, especially tailored for applications requiring high time precision on resource constrained BLE platforms. Designed on top of the existing Bluetooth v4.0 standard, the CheepSync framework utilizes low-level time-stamping and comprehensive error compensation mechanisms for overcoming uncertainties in message transmission, clock drift, and other system-specific constraints. CheepSync was implemented on custom designed nRF24Cheep beacon platforms (as broadcasters) and commercial off-the-shelf Android ported smartphones (as passive listeners). We demonstrate the efficacy of CheepSync by numerous empirical evaluations in a variety of experimental setups, and show that its average (single-hop) time synchronization accuracy is in the 10 mu s range.

Appraisal of groundwater resource in Holocene soil deposits by resistivity, hydrochemical and granulomerial studies in the Gulf of Mannar Coast from Southern India

This article is aimed to delineate groundwater sources in Holocene deposits area in the Gulf of Mannar Coast from Southern India. For this purpose 2-D electrical resistivity tomography (ERT), hydrochemical and granulomerical studies were carried out and integrated to identify hydrogeological structures and portable groundwater resource in shallow depths which in general appears in the coastal tracts. The 2-D ERT was used to determine the two-dimensional subsurface geological formations by multicore cable with Wenner array. Low resistivity of 1-5 Omega m for saline water appeared due to calcite at the depth of about 5 m below the ground level (bgl). Sea water intrusion was observed around the maximum resistivity as 5 Omega m at the 8 m depth, bgl in the calcite environs, but the calcareous sandstone layer shows around 15-64 Omega m at the 6 m depth, bgl. The hydrochemical variation of TDS, HCO3-, Cl-, Na+, K+, Ca2+, and Mg2+ concentrations was observed for the saline and sea water intrusion in the groundwater system. The granulometic analysis shows that the study area was under the sea between 5400 and 3000 year ago. The events of ice melting an unnatural ice-stone rain/hail among 5000-4000 years ago resulted in the inundation of sea over the area and deposits of late Holocene marine transgression formation up to Puthukottai quartzite region for a stretch of around 17 km.

Influence of recombination on acquisition and reversion of immune escape and compensatory mutations in HIV-1

Following transmission, HIV-1 adapts in the new host by acquiring mutations that allow it to escape from the host immune response at multiple epitopes. It also reverts mutations associated with epitopes targeted in the transmitting host but not in the new host. Moreover, escape mutations are often associated with additional compensatory mutations that partially recover fitness costs. It is unclear whether recombination expedites this process of multi-locus adaptation. To elucidate the role of recombination, we constructed a detailed population dynamics model that integrates viral dynamics, host immune response at multiple epitopes through cytotoxic T lymphocytes, and viral evolution driven by mutation, recombination, and selection. Using this model, we compute the expected waiting time until the emergence of the strain that has gained escape and compensatory mutations against the new host's immune response, and reverted these mutations at epitopes no longer targeted. We find that depending on the underlying fitness landscape, shaped by both costs and benefits of mutations, adaptation proceeds via distinct dominant pathways with different effects of recombination, in particular distinguishing escape and reversion. When adaptation at a single epitope is involved, recombination can substantially accelerate immune escape but minimally affects reversion. When multiple epitopes are involved, recombination can accelerate or inhibit adaptation depending on the fitness landscape. Specifically, recombination tends to delay adaptation when a purely uphill fitness landscape is accessible at each epitope, and accelerate it when a fitness valley is associated with each epitope. Our study points to the importance of recombination in shaping the adaptation of HIV-1 following its transmission to new hosts, a process central to T cell-based vaccine strategies. (C) 2015 The Authors. Published by Elsevier B.V. This is an open access article under the CC BY license.