Immunogen design for HIV-1 and influenza

Vaccines provide the most cost effective defense against pathogens. Although vaccines have been designed for a number of viral diseases, a vaccine against HIV-1 still remains elusive. In contrast while there are excellent influenza vaccines, these need to be changed every few years because of antigenic drift and shift The recent discovery of a large number of broadly neutralizing antibodies (bNAbs) and structural characterization of the conserved epitopes targeted by them presents an opportunity for structure based HIV-1 and influenza A vaccine design. We discuss strategies to design immunogens either targeting a particular antigenic region or focusing on native structure stabilization. This article is part of a Special Issue entitled: Recent advances in molecular engineering of antibody. (C) 2014 Elsevier B.V. All rights reserved.

Rapid divergence of ecotypes of an invasive plant

Invasive species demonstrate rapid evolution within a very short period of time allowing one to understand the underlying mechanism(s). Lantana camara, a highly invasive plant of the tropics and subtropics, has expanded its range and successfully established itself almost throughout India. In order to uncover the processes governing the invasion dynamics, 218 individuals from various locations across India were characterized with six microsatellites. By integrating genetic data with niche modelling, we examined the effect of drift and environmental selection on genetic divergence. We found multiple genetic clusters that were non-randomly distributed across space. Spatial autocorrelation revealed a strong fine-scale structure, i.e. isolation by distance. In addition, we obtained evidence of inhibitory effects of selection on gene flow, i.e. isolation by environmental distance. Perhaps, local adaptation in response to selection is offsetting gene flow and causing the populations to diverge. Niche models suggested that temperature and precipitation play a major role in the observed spatial distribution of this plant. Based on a non-random distribution of clusters, unequal gene flow among them and different bioclimatic niche requirements, we concluded that the emergence of ecotypes represented by two genetic clusters is underway. They may be locally adapted to specific climatic conditions, and perhaps at the very early stages of ecological divergence.

Graphene based multifunctional flame sensor

Recently, graphene has attracted much attention due to its unique electrical and thermal properties along with its high surface area, and hence presents an ideal sensing material. We report a novel configuration of a graphene based flame sensor by exploiting the response of few layer graphene to a flame along two different directions, where flame detection results from a difference in heat transfer mechanisms. A complete sensor module was developed with a signal conditioning circuit that compensates for any drift in the baseline of the sensor, along with a flame detection algorithm implemented in a microcontroller to detect the flame. A pre-defined threshold for either of the sensors is tunable, which can be varied based on the nature of the flame, hence presenting a system that can be used for detection of any kind of flame. This finding also presents a scalable method that opens avenues to modify complicated sensing schemes.

Simulation studies on Performance parameters of a TPC Polarimeter

X-ray polarimeters based on Time Projection Chamber (TPC) geometry are currently being studied and developed to make sensitive measurement of polarization in 2-10keV energy range. TPC soft X-ray polarimeters exploit the fact that emission direction of the photoelectron ejected via photoelectric effect in a gas proportional counter carries the information of the polarization of the incident X-ray photon. Operating parameters such as pressure, drift field and drift-gap affect the performance of a TPC polarimeter. Simulations presented here showcase the effect of these operating parameters on the modulation factor of the TPC polarimeter. Models of Garfield are used to study photoelectron interaction in gas and drift of electron cloud towards Gas Electron Multiplier (GEM). The emission direction is reconstructed from the image and modulation factor is computed. Our study has shown that Ne/DME (50/50) at lower pressure and drift field can be used for a TPC polarimeter with modulation factor of 50-65%.

A common stochastic accumulator with effector-dependent noise can explain eye-hand coordination

The computational architecture that enables the flexible coupling between otherwise independent eye and hand effector systems is not understood. By using a drift diffusion framework, in which variability of the reaction time (RT) distribution scales with mean RT, we tested the ability of a common stochastic accumulator to explain eye-hand coordination. Using a combination of behavior, computational modeling and electromyography, we show how a single stochastic accumulator to threshold, followed by noisy effector-dependent delays, explains eye-hand RT distributions and their correlation, while an alternate independent, interactive eye and hand accumulator model does not. Interestingly, the common accumulator model did not explain the RT distributions of the same subjects when they made eye and hand movements in isolation. Taken together, these data suggest that a dedicated circuit underlies coordinated eye-hand planning.

Eye-hand coordination during a double-step task: evidence for a common stochastic accumulator

Many studies of reaching and pointing have shown significant spatial and temporal correlations between eye and hand movements. Nevertheless, it remains unclear whether these correlations are incidental, arising from common inputs (independent model); whether these correlations represent an interaction between otherwise independent eye and hand systems (interactive model); or whether these correlations arise from a single dedicated eye-hand system (common command model). Subjects were instructed to redirect gaze and pointing movements in a double-step task in an attempt to decouple eye-hand movements and causally distinguish between the three architectures. We used a drift-diffusion framework in the context of a race model, which has been previously used to explain redirect behavior for eye and hand movements separately, to predict the pattern of eye-hand decoupling. We found that the common command architecture could best explain the observed frequency of different eye and hand response patterns to the target step. A common stochastic accumulator for eye-hand coordination also predicts comparable variances, despite significant difference in the means of the eye and hand reaction time (RT) distributions, which we tested. Consistent with this prediction, we observed that the variances of the eye and hand RTs were similar, despite much larger hand RTs (similar to 90 ms). Moreover, changes in mean eye RTs, which also increased eye RT variance, produced a similar increase in mean and variance of the associated hand RT. Taken together, these data suggest that a dedicated circuit underlies coordinated eye-hand planning.

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.

Sandwiched assembly of ZnO nanowires between graphene layers for a self-powered and fast responsive ultraviolet photodetector

A heterostructure of graphene and zinc oxide (ZnO) nanowires (NWs) is fabricated by sandwiching an array of ZnO NWs between two graphene layers for an ultraviolet (UV) photodetector. This unique structure allows NWs to be in direct contact with the graphene layers, minimizing the effect of the substrate or metal electrodes. In this device, graphene layers act as highly conducting electrodes with a high mobility of the generated charge carriers. An excellent sensitivity is demonstrated towards UV illumination, with a reversible photoresponse even for a short period of UV illumination. Response and recovery times of a few milliseconds demonstrated a much faster photoresponse than most of the conventional ZnO nanostructure-based photodetectors. It is shown that the generation of a built-in electric field between the interface of graphene and ZnO NWs effectively contributes to the separation of photogenerated electron-hole pairs for photocurrent generation without applying any external bias. Upon application of external bias voltage, the electric field further increases the drift velocity of photogenerated electrons by reducing the charge recombination rates, and results in an enhancement of the photocurrent. Therefore, the graphene-based heterostructure (G/ZnO NW/G) opens avenues to constructing a novel heterostructure with a combination of two functionally dissimilar materials.

Sandwiched assembly of ZnO nanowires between graphene layers for a self-powered and fast responsive ultraviolet photodetector

A heterostructure of graphene and zinc oxide (ZnO) nanowires (NWs) is fabricated by sandwiching an array of ZnO NWs between two graphene layers for an ultraviolet (UV) photodetector. This unique structure allows NWs to be in direct contact with the graphene layers, minimizing the effect of the substrate or metal electrodes. In this device, graphene layers act as highly conducting electrodes with a high mobility of the generated charge carriers. An excellent sensitivity is demonstrated towards UV illumination, with a reversible photoresponse even for a short period of UV illumination. Response and recovery times of a few milliseconds demonstrated a much faster photoresponse than most of the conventional ZnO nanostructure-based photodetectors. It is shown that the generation of a built-in electric field between the interface of graphene and ZnO NWs effectively contributes to the separation of photogenerated electron-hole pairs for photocurrent generation without applying any external bias. Upon application of external bias voltage, the electric field further increases the drift velocity of photogenerated electrons by reducing the charge recombination rates, and results in an enhancement of the photocurrent. Therefore, the graphene-based heterostructure (G/ZnO NW/G) opens avenues to constructing a novel heterostructure with a combination of two functionally dissimilar materials.

Simulated long-term climate response to idealized solar geoengineering

Solar geoengineering has been proposed as a potential means to counteract anthropogenic climate change, yet it is unknown how such climate intervention might affect the Earth's climate on the millennial time scale. Here we use the HadCM3L model to conduct a 1000year sunshade geoengineering simulation in which solar irradiance is uniformly reduced by 4% to approximately offset global mean warming from an abrupt quadrupling of atmospheric CO2. During the 1000year period, modeled global climate, including temperature, hydrological cycle, and ocean circulation of the high-CO2 simulation departs substantially from that of the control preindustrial simulation, whereas the climate of the geoengineering simulation remains much closer to that of the preindustrial state with little drift. The results of our study do not support the hypothesis that nonlinearities in the climate system would cause substantial drift in the climate system if solar geoengineering was to be deployed on the timescale of a millennium.