Department of Bioscience & Bioengineering

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IIT Jodhpur

The existence of rogue or freak waves in the ocean has been known for some time. They have been reported in the context of optical lattices and the financial market. We ask whether such waves are generic to late time behavior in nonlinear systems. In that vein, we examine the dynamics of an alignment of spherical elastic beads held within fixed, rigid walls at zero precompression when they are subjected to sufficiently rich initial conditions. Here we define such waves generically as unusually large energy fluctuations that sustain for short periods of time. Our simulations suggest that such unusually large fluctuations ("hot spots") and occasional series of such fluctuations through space and time ("rogue fluctuations") are likely to exist in the late time dynamics of the granular chain system at zero dissipation. We show that while hot spots are common in late time evolution, rogue fluctuations are seen in purely nonlinear systems (i.e., no precompression) at late enough times. We next show that the number of such fluctuations grows exponentially with increasing nonlinearity whereas rogue fluctuations decrease superexponentially with increasing precompression. Dissipation-free granular alignment systems may be possible to realize as integrated circuits and hence our observations may potentially be testable in the laboratory. © 2014 American Physical Society.

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Physical Review E - Statistical, Nonlinear, and Soft Matter Physics

Mechanical energy fluctuations in granular chains: The possibility of rogue fluctuations or waves

Cluster analysis is a technique that divides a given data set into a set of clusters in such a way that two objects from the same cluster are as similar as possible and the objects from different clusters are as dissimilar as possible. Arobust rough-fuzzy c-means clustering algorithm is applied here to identify clusters having similar objects. Each cluster of the robust rough-fuzzy clustering algorithm is represented by a set of three parameters, namely, cluster prototype, a possibilistic fuzzy lower approximation, and a probabilistic fuzzy boundary. The possibilistic lower approximation helps in discovering clusters of various shapes. The cluster prototype depends on the weighting average of the possibilistic lower approximation and probabilistic boundary. The reported algorithm is robust in the sense that it can find overlapping and vaguely defined clusters with arbitrary shapes in noisy environment. The effectiveness of the clustering algorithm, along with a comparison with other clustering algorithms, is demonstrated on synthetic as well as coding and non-coding RNA expression data sets using some cluster validity indices. © Springer India 2014.

Advances in Intelligent Systems and Computing

A new rough-fuzzy clustering algorithm and its applications

Somatosensory cortex of adult primates undergoes topographic reorganization following spinal cord or peripheral nerve injuries. Electrophysiological studies in monkeys show that after chronic lesions of dorsal columns of the spinal cord at cervical levels, there is an expansion of face representation into the deafferented hand region of area 3b of cortex. However, these techniques can sample only a limited portion of the brain. In order to help understand mechanisms of brain reorganization use of noninvasive tools in non-human primate experimental model is important. Use of blood oxygen level dependent-functional magnetic resonance imaging (BOLD-fMRI) to study brain reorganization in non-human primates has been extremely limited. Here, we show that in monkeys with long-term unilateral lesions of the dorsal columns at cervical levels, tactile stimulation of the chin showed BOLD activation in the deafferented hand region of contralesional area 3b in the post-central gyrus. In a monkey with a partial lesion of the dorsal columns, stimulations of both hand and chin activated the partially deafferented hand region. We also show that the somatotopic organization in the non-deafferented ipsilesional somatosensory cortex remained normal. © 2013 Springer-Verlag.

Brain Structure and Function

Large-scale reorganization of the somatosensory cortex of adult macaque monkeys revealed by fMRI

Adult mammalian brains undergo reorganization following deafferentations due to peripheral nerve, cortical or spinal cord injuries. The largest extent of cortical reorganization is seen in area 3b of the somatosensory cortex of monkeys with chronic transection of the dorsal roots or dorsal columns of the spinal cord. These injuries cause expansion of intact face inputs into the deafferented hand cortex, resulting in a change of representational boundaries by more than 7 mm. Here we show that large-scale reorganization in area 3b following spinal cord injuries is due to changes at the level of the brainstem nuclei and not due to cortical mechanisms. Selective inactivation of the reorganized cuneate nucleus of the brainstem eliminates observed face expansion in area 3b. Thus, the substrate for the observed expanded face representation in area 3b lies in the cuneate nucleus. © 2014 Macmillan Publishers Limited. All rights reserved.

Fulltext

Nature Communications

Large-scale reorganization of the somatosensory cortex following spinal cord injuries is due to brainstem plasticity

Increasing atmospheric carbon dioxide concentration (CO2) is an important component of global climate change that will have a significant impact on the productivity of crop plants. In recent years, growth and yield of agricultural crop plants have been shown to increase with elevated CO2 (EC) and have enticed considerable interest due to variation in the response of crop plants. In this study, comparative response of two mung bean cultivars (HUM-2 and HUM-6) was evaluated against EC at different growth stages under near-natural conditions for two consecutive years. The plants were grown in ambient as well as EC (700 ppm) in specially designed open-top chambers. Under elevated CO2, marked down-regulation of reactive oxygen species (ROS) levels, membrane disruption and activities of superoxide dismutase and catalase were noticed in both the cultivars, but the extent of reduction was more in HUM-6. As compared to ambient CO2, EC increased total chlorophyll, photosynthetic rate, growth and yield parameters. Cultivar-specific response was noticed as HUM-6 showed higher increase in yield attributes than HUM-2. Under CO2 treatment, soluble protein and reducing sugars decreased while total soluble sugars and starch showed an opposite trend. Principal component analysis showed that both the cultivars responded more or less similarly to EC in their respective groupings of physiological and growth parameters, but the magnitude of ROS and antioxidative enzymes was variable. The experimental findings depict that both the cultivars of mung bean showed contrasting response against EC and paved the way for selecting the suitable cultivar having higher productivity in a future high-CO2 environment. © 2014 Blackwell Verlag GmbH.

Journal of Agronomy and Crop Science

Cultivar specific response of CO2 fertilization on two tropical mung bean (vigna radiata l.) cultivars: ROS generation, antioxidant status, physiology, growth, yield and seed quality

Energy efficient voltage scheduling for multi-core processors is an important issue in the context of parallel and distributed computing. Dynamic voltage scaling (DVS) is used to reduce the energy consumption of cores. Nowadays processor vendors are providing software for DVS. We consider a system using a single multi-core processor with software controlled DVS having a finite set of discretely available core speeds. Our contribution to this work is solving a well-known energy efficient voltage scheduling problem on the considered system. The problem that we consider is to find a minimum energy voltage scheduling for a given computational load that has to be completed within a given deadline. First we show that the existing methods to solve this problem on other processor models fail to apply on our processor model. Then we formulate an Integer Program (IP) for the problem. Through a series of reductions we reduce the IP formulation of the problem into an Integer Linear Program (ILP) formulation and prove that the proposed IP for the problem can be solved in O(D(log(max(s(max), p) + 1) + qlog(Dp + 1)) + log(alpha ps(max)(3)D)(2q(4q + 3)log(max(Dp, C) + 2))(alpha 2q)) time where D is the given deadline, Cis the amount of computation that has to be completed within the deadline of D time units, p is the number of cores, q is the number of possible core speeds, s(max) is the maximum speed of cores, and cc and a are constants. (C) 2014 Elsevier Inc. All rights reserved.

APPLIED MATHEMATICAL MODELLING

Energy efficient voltage scheduling for multi-core processors with software controlled dynamic voltage scaling

In this study, we computationally investigate decision-making by individuals and the ensuing social structure of a primate species, chimpanzees, using Newton’s equations of classical mechanics, as opposed to agentbased analyses in which individual chimpanzees make independent decisions. Our model uses molecular dynamics simulation techniques to solve Newton’s equations and is able to approximate the movements of female and male chimpanzees, especially in relation to the available food resources, in a manner that is consistent with their observed behaviour in natural habitats. It is noteworthy that our Newtonian dynamicsbased model may allow us to make certain specific observations of their behaviour, some of which may be difficult to achieve through agentbased modelling exercises or even field studies. Chimpanzees tend to live in fission-fusion social groups, with varying number of individuals, in which both females and males tend to display intrasexual competition for valuable food resources while the males also compete for oestrus females. Most populations of the species are also restricted to a small range of habitats, a clear indication that they are especially vulnerable to the availability and distribution of food sources. With reasonable assumptions of chimpanzee behaviour, we have been able to analyse the clustering behaviour of individuals in relation to local food sources as also patterns of their migration across groups. Our simulated results are qualitatively consistent with field observations conducted on a particular semi-isolated population of chimpanzees in Bossou, Guinea, in western Africa. © 2014 by World Scientific Publishing Co. Pte. Ltd. All rights reserved.

Nature's Longest Threads: New Frontiers in the Mathematics and Physics of Information in Biology

Newtonian chimpanzees? A molecular dynamics approach to understanding decision-making by wild chimpanzees

Centrosome asymmetry has been implicated in stem cell fate maintenance in both flies and vertebrates [1, 2]. Drosophila neuroblasts, the neural precursors of the fly's central nervous system [3], contain molecularly and physically asymmetric centrosomes, established through differences in pericentriolar matrix (PCM) retention [4-7]. For instance, the daughter centriole maintains PCM and thus microtubule-organizing center (MTOC) activity through Polo-mediated phosphorylation of Centrobin (Cnb) [7, 8]. The mother centriole, however, quickly downregulates PCM and moves away from the apical cortex, randomly migrating through the cytoplasm until maturation sets in at prophase [4-6, 8]. How PCM downregulation is molecularly controlled is currently unknown, but it involves Pericentrin (PCNT)-like protein (PLP) to prevent premature Polo localization and thus MTOC activity [9]. Here, we report that the centriolar protein Bld10, the fly ortholog of Cep135, is required to establish centrosome asymmetry in Drosophila neuroblasts through shedding of Polo from the mother centrosome. bld10 mutants fail to downregulate Polo and PCM, generating two active, improperly positioned MTOCs. Failure to shed Polo and PCM causes spindle alignment and centrosome segregation defects, resulting in neuroblasts incorrectly retaining the older mother centrosome. Since Cep135 is implicated in primary microcephaly, we speculate that perturbed centrosome asymmetry could contribute to this rare neurodevelopmental disease. © 2014 Elsevier Ltd.

Current Biology

The centriolar protein Bld10/Cep135 is required to establish centrosome asymmetry in drosophila neuroblasts

Nearly a thousand mutations mapping to 60 different loci have been identified in cerebellar ataxias. However, almost 50% of the cases remain genetically uncharacterized and there is a difference in prevalence as well as in the phenotypic spectrum of ataxia among various geographical regions. This poses a challenge for setting up a genetic panel for screening ataxia. In our ataxic cohort of 1014 families, 61% are genetically uncharacterized (UC). We investigated the potential of whole exome sequencing in conjunction with homozygosity mapping (HM) to delineate the genetic defects in three uncharacterized families with recessive inheritance each manifesting some unusual phenotype: (i) infantile onset ataxia with hearing loss (IOAH), (ii) Juvenile onset cerebellar ataxia with seizures (JCS) and (iii) Friedreich ataxia-like (FA-like). We identified a novel missense mutation in c10orf2 in the family with IOAH, compound heterozygous mutations in CLN6 in the family with JCS and a homozygous frame-shift mutation in SACS in the FA-like patient. Phenotypes observed in our families were concordant with reported phenotypes of known mutations in the same genes thus obviating the need for functional validation. Our study revealed novel variations in three genes, c10orf2, CLN6, and SACS, that have so far not been reported in India. This study also demonstrates the utility of whole exome screening in clinics for early diagnosis. © 2013 John Wiley & Sons A/S.

Clinical Genetics

Novel mutations in typical and atypical genetic loci through exome sequencing in autosomal recessive cerebellar ataxia families

There is a need of smart attender calling system for efficient patient care especially for those who are unable to communicate with the health caregiver by natural means (vocal communication or through mobility; a common problem in intensive care unit (ICU)). Keeping the aforesaid perspective in mind, here we have developed a hand finger movement based attender calling system which is portable and wearable. The device is prepared by assembling a flex sensor on hand glove platform corresponding to its 'fore finger' position. Finger movement of the patient leads to flexion induced variation in output voltage. The circuit consists of a voltage comparator that compares the aforesaid output with respect to a preset voltage input obtained from a potentiometer (10 k). A comparative voltage ratio of magnitude above 1 enables the comparator to pass an electric signal to an APR9600 voice module located in remote place. This signal plays a prerecorded message from APR9600 module to alert the concerned persons about patient's need. The sensitivity of the setup can be adjusted by changing preset voltage of potentiometer as per the requirement of the patient. It is believed that the aforesaid system could be useful for ICU patient management and rehabilitation of vocally impaired person. © 2014 IEEE.