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author:("Dutta, airbag")
1.  Binpairs: Utilization of Illumina Paired-End Information for Improving Efficiency of Taxonomic Binning of Metagenomic Sequences 
PLoS ONE  2014;9(12):e114814.
Motivation
Paired-end sequencing protocols, offered by next generation sequencing (NGS) platforms like Illumia, generate a pair of reads for every DNA fragment in a sample. Although this protocol has been utilized for several metagenomics studies, most taxonomic binning approaches classify each of the reads (forming a pair), independently. The present work explores some simple but effective strategies of utilizing pairing-information of Illumina short reads for improving the accuracy of taxonomic binning of metagenomic datasets. The strategies proposed can be used in conjunction with all genres of existing binning methods.
Results
Validation results suggest that employment of these “Binpairs” strategies can provide significant improvements in the binning outcome. The quality of the taxonomic assignments thus obtained are often comparable to those that can only be achieved with relatively longer reads obtained using other NGS platforms (such as Roche).
Availability
An implementation of the proposed strategies of utilizing pairing information is freely available for academic users at https://metagenomics.atc.tcs.com/binning/binpairs.
doi:10.1371/journal.pone.0114814
PMCID: PMC4281075  PMID: 25551450
2.  Facilitating myoelectric-control with transcranial direct current stimulation: a preliminary study in healthy humans 
Background
Functional Electrical Stimulation (FES) can electrically activate paretic muscles to assist movement for post-stroke neurorehabilitation. Here, sensory-motor integration may be facilitated by triggering FES with residual electromyographic (EMG) activity. However, muscle activity following stroke often suffers from delays in initiation and termination which may be alleviated with an adjuvant treatment at the central nervous system (CNS) level with transcranial direct current stimulation (tDCS) thereby facilitating re-learning and retaining of normative muscle activation patterns.
Methods
This study on 12 healthy volunteers was conducted to investigate the effects of anodal tDCS of the primary motor cortex (M1) and cerebellum on latencies during isometric contraction of tibialis anterior (TA) muscle for myoelectric visual pursuit with quick initiation/termination of muscle activation i.e. 'ballistic EMG control’ as well as modulation of EMG for 'proportional EMG control’.
Results
The normalized delay in initiation and termination of muscle activity during post-intervention 'ballistic EMG control’ trials showed a significant main effect of the anodal tDCS target: cerebellar, M1, sham (F(2) = 2.33, p < 0.1), and interaction effect between tDCS target and step-response type: initiation/termination of muscle activation (F(2) = 62.75, p < 0.001), but no significant effect for the step-response type (F(1) = 0.03, p = 0.87). The post-intervention population marginal means during 'ballistic EMG control’ showed two important findings at 95% confidence interval (critical values from Scheffe’s S procedure): 1. Offline cerebellar anodal tDCS increased the delay in initiation of TA contraction while M1 anodal tDCS decreased the same when compared to sham tDCS, 2. Offline M1 anodal tDCS increased the delay in termination of TA contraction when compared to cerebellar anodal tDCS or sham tDCS. Moreover, online cerebellar anodal tDCS decreased the learning rate during 'proportional EMG control’ when compared to M1 anodal and sham tDCS.
Conclusions
The preliminary results from healthy subjects showed specific, and at least partially antagonistic effects, of M1 and cerebellar anodal tDCS on motor performance during myoelectric control. These results are encouraging, but further studies are necessary to better define how tDCS over particular regions of the cerebellum may facilitate learning of myoelectric control for brain machine interfaces.
doi:10.1186/1743-0003-11-13
PMCID: PMC3931480  PMID: 24507410
Functional electrical stimulation; Myoelectric control; Transcranial direct current stimulation; Stroke; Brain machine interfaces
3.  Post-stroke balance rehabilitation under multi-level electrotherapy: a conceptual review 
Stroke is caused when an artery carrying blood from heart to an area in the brain bursts or a clot obstructs the blood flow thereby preventing delivery of oxygen and nutrients. About half of the stroke survivors are left with some degree of disability. Innovative methodologies for restorative neurorehabilitation are urgently required to reduce long-term disability. The ability of the nervous system to respond to intrinsic or extrinsic stimuli by reorganizing its structure, function, and connections is called neuroplasticity. Neuroplasticity is involved in post-stroke functional disturbances, but also in rehabilitation. It has been shown that active cortical participation in a closed-loop brain machine interface (BMI) can induce neuroplasticity in cortical networks where the brain acts as a controller, e.g., during a visuomotor task. Here, the motor task can be assisted with neuromuscular electrical stimulation (NMES) where the BMI will act as a real-time decoder. However, the cortical control and induction of neuroplasticity in a closed-loop BMI is also dependent on the state of brain, e.g., visuospatial attention during visuomotor task performance. In fact, spatial neglect is a hidden disability that is a common complication of stroke and is associated with prolonged hospital stays, accidents, falls, safety problems, and chronic functional disability. This hypothesis and theory article presents a multi-level electrotherapy paradigm toward motor rehabilitation in virtual reality that postulates that while the brain acts as a controller in a closed-loop BMI to drive NMES, the state of brain can be can be altered toward improvement of visuomotor task performance with non-invasive brain stimulation (NIBS). This leads to a multi-level electrotherapy paradigm where a virtual reality-based adaptive response technology is proposed for post-stroke balance rehabilitation. In this article, we present a conceptual review of the related experimental findings.
doi:10.3389/fnins.2014.00403
PMCID: PMC4266025  PMID: 25565937
virtual reality; eye tracking; neuromuscular electrical stimulation; stroke; neurorehabilitation; non-invasive brain stimulation
4.  Understanding the sequential activation of Type III and Type VI Secretion Systems in Salmonella typhimurium using Boolean modeling 
Gut Pathogens  2013;5:28.
Background
Three pathogenicity islands, viz. SPI-1 (Salmonella pathogenicity island 1), SPI-2 (Salmonella pathogenicity island 2) and T6SS (Type VI Secretion System), present in the genome of Salmonella typhimurium have been implicated in the virulence of the pathogen. While the regulation of SPI-1 and SPI-2 (both encoding components of the Type III Secretion System - T3SS) are well understood, T6SS regulation is comparatively less studied. Interestingly, inter-connections among the regulatory elements of these three virulence determinants have also been suggested to be essential for successful infection. However, till date, an integrated view of gene regulation involving the regulators of these three secretion systems and their cross-talk is not available.
Results
In the current study, relevant regulatory information available from literature have been integrated into a single Boolean network, which portrays the dynamics of T3SS (SPI-1 and SPI-2) and T6SS mediated virulence. Some additional regulatory interactions involving a two-component system response regulator YfhA have also been predicted and included in the Boolean network. These predictions are aimed at deciphering the effects of osmolarity on T6SS regulation, an aspect that has been suggested in earlier studies, but the mechanism of which was hitherto unknown. Simulation of the regulatory network was able to recreate in silico the experimentally observed sequential activation of SPI-1, SPI-2 and T6SS.
Conclusions
The present study integrates relevant gene regulatory data (from literature and our prediction) into a single network, representing the cross-communication between T3SS (SPI-1 and SPI-2) and T6SS. This holistic view of regulatory interactions is expected to improve the current understanding of pathogenesis of S. typhimurium.
doi:10.1186/1757-4749-5-28
PMCID: PMC3849742  PMID: 24079299
Salmonella typhimurium; Salmonella pathogenicity island 1 (SPI-1); SPI-2; Type VI Secretion System (T6SS); Boolean modeling; Cross-talk network
5.  A Low-Cost Point-of-Care Testing System for Psychomotor Symptoms of Depression Affecting Standing Balance: A Preliminary Study in India 
The World Health Organization estimated that major depression is the fourth most significant cause of disability worldwide for people aged 65 and older, where depressed older adults reported decreased independence, poor health, poor quality of life, functional decline, disability, and increased chronic medical problems. Therefore, the objectives of this study were (1) to develop a low-cost point-of-care testing system for psychomotor symptoms of depression and (2) to evaluate the system in community dwelling elderly in India. The preliminary results from the cross-sectional study showed a significant negative linear correlation between balance and depression. Here, monitoring quantitative electroencephalography along with the center of pressure for cued response time during functional reach tasks may provide insights into the psychomotor symptoms of depression where average slope of the Theta-Alpha power ratio versus average slope of baseline-normalized response time may be a candidate biomarker, which remains to be evaluated in our future clinical studies. Once validated, the biomarker can be used for monitoring the outcome of a comprehensive therapy program in conjunction with pharmacological interventions. Furthermore, the frequency of falls can be monitored with a mobile phone-based application where the propensity of falls during the periods of psychomotor symptoms of depression can be investigated further.
doi:10.1155/2013/640861
PMCID: PMC3800576  PMID: 24205436
6.  Feasibility of Functional Electrical Stimulation-Assisted Neurorehabilitation following Stroke in India: A Case Series 
Functional Electrical Stimulation (FES) facilitates ambulatory function after paralysis by electrically activating the muscles of the lower extremities. The Odstock Dropped Foot Stimulator (ODFS, Odstock, UK) called ODFS Pace, was used for heel-switch triggered FES-assisted walking. The ODFS is recommended as an intervention for neurologically impaired gait in the Royal College of Physicians (UK) Clinical Guidelines on Stroke. Based on the guidelines by the National Institute of Clinical Excellence (NICE, UK), we started first clinical study in India on ODFS Pace as an orthotic intervention for daily use. In this preliminary study, we also investigated improvement in volitional walking following 6 sessions (3 times per week, for 2 weeks) of 30 minutes of FES-assisted treadmill walking on 7 chronic (>6 months after stroke) stroke survivors. We found that short-duration, moderately intensive FES-assisted gait therapy improved volitional gait in 3 out of 7 stroke survivors suffering from foot drop. Even in absence of improvement in volitional walking, there were no adverse effects and the subjects found heel-switch triggered FES-assisted walking mostly “easy” (6 out of 7). Therefore FES is promising as an orthotic intervention for daily use; however, tailoring the intensity and/or frequency based on patient's ability may make it viable as a therapeutic intervention.
doi:10.1155/2012/830873
PMCID: PMC3420748  PMID: 22953091
7.  Two-photon calcium imaging from motion-sensitive neurons in head-fixed Drosophila during optomotor walking behavior 
Nature methods  2010;7(7):535-540.
Drosophila melanogster is a model organism rich in genetic tools to manipulate and identify neural circuits involved in specific behaviors. Here we present a novel technique for two-photon calcium imaging in the central brain of head-fixed Drosophila walking on an air-supported ball. The ball’s motion is tracked at high resolution and can be treated as a proxy for the fly’s own movements. We used the genetically encoded calcium sensor, GCaMP3.0, to record from important elements of the motion-processing pathway, the horizontal-system (HS) lobula plate tangential cells (LPTCs) in the fly optic lobe. We presented motion stimuli to the tethered fly and found that calcium transients in HS-neurons correlated with robust optomotor behavior during walking. Our technique allows an entirely new set of questions to be addressed by monitoring behavior and physiology in identified neurons in a powerful genetic model organism with an extensive repertoire of walking behaviors.
doi:10.1038/nmeth.1468
PMCID: PMC2945246  PMID: 20526346
8.  Indian genetic disease database 
Nucleic Acids Research  2010;39(Database issue):D933-D938.
Indians, representing about one-sixth of the world population, consist of several thousands of endogamous groups with strong potential for excess of recessive diseases. However, no database is available on Indian population with comprehensive information on the diseases common in the country. To address this issue, we present Indian Genetic Disease Database (IGDD) release 1.0 (http://www.igdd.iicb.res.in)—an integrated and curated repository of growing number of mutation data on common genetic diseases afflicting the Indian populations. Currently the database covers 52 diseases with information on 5760 individuals carrying the mutant alleles of causal genes. Information on locus heterogeneity, type of mutation, clinical and biochemical data, geographical location and common mutations are furnished based on published literature. The database is currently designed to work best with Internet Explorer 8 (optimal resolution 1440 × 900) and it can be searched based on disease of interest, causal gene, type of mutation and geographical location of the patients or carriers. Provisions have been made for deposition of new data and logistics for regular updation of the database. The IGDD web portal, planned to be made freely available, contains user-friendly interfaces and is expected to be highly useful to the geneticists, clinicians, biologists and patient support groups of various genetic diseases.
doi:10.1093/nar/gkq1025
PMCID: PMC3013653  PMID: 21037256
9.  Distinct, ecotype-specific genome and proteome signatures in the marine cyanobacteria Prochlorococcus 
BMC Genomics  2010;11:103.
Background
The marine cyanobacterium Prochlorococcus marinus, having multiple ecotypes of distinct genotypic/phenotypic traits and being the first documented example of genome shrinkage in free-living organisms, offers an ideal system for studying niche-driven molecular micro-diversity in closely related microbes. The present study, through an extensive comparative analysis of various genomic/proteomic features of 6 high light (HL) and 6 low light (LL) adapted strains, makes an attempt to identify molecular determinants associated with their vertical niche partitioning.
Results
Pronounced strand-specific asymmetry in synonymous codon usage is observed exclusively in LL strains. Distinct dinucleotide abundance profiles are exhibited by 2 LL strains with larger genomes and G+C-content ≈ 50% (group LLa), 4 LL strains having reduced genomes and G+C-content ≈ 35-37% (group LLb), and 6 HL strains. Taking into account the emergence of LLa, LLb and HL strains (based on 16S rRNA phylogeny), a gradual increase in average aromaticity, pI values and beta- & coil-forming propensities and a decrease in mean hydrophobicity, instability indices and helix-forming propensities of core proteins are observed. Greater variations in orthologous gene repertoire are found between LLa and LLb strains, while higher number of positively selected genes exist between LL and HL strains.
Conclusion
Strains of different Prochlorococcus groups are characterized by distinct compositional, physicochemical and structural traits that are not mere remnants of a continuous genetic drift, but are potential outcomes of a grand scheme of niche-oriented stepwise diversification, that might have driven them chronologically towards greater stability/fidelity and invoked upon them a special ability to inhabit diverse oceanic environments.
doi:10.1186/1471-2164-11-103
PMCID: PMC2836286  PMID: 20146791

Results 1-9 (9)