Predicting Off-target Effects in CRISPR-Cas9 System using Graph Convolutional Network

CRISPR-Cas9 is a powerful genome editing technology that has been widely applied in target gene repair and gene expression regulation. One of the main challenges for the CRISPR-Cas9 system is the occurrence of unexpected cleavage at some sites (off-targets) and predicting them is necessary due to its relevance in gene editing research. Very few deep learning models have been developed so far that predict the off-target propensity of single guide RNA (sgRNA) at specific DNA fragments by using artificial feature extract operations and machine learning techniques. Unfortunately, they implement a convoluted process that is difficult to understand and implement by researchers. This thesis focuses on developing a novel graph-based approach to predict off-target efficacy of sgRNA in CRISPR-Cas9 system that is easy to understand and replicate by researchers. This is achieved by creating a graph with sequences as nodes and by performing link prediction using Graph Convolutional Network (GCN) to predict the presence of links between sgRNA and off-target inducing target DNA sequences. Features for the sequences are extracted from within the sequences

Controlling the size distribution of nanoparticles through the use of physical boundaries during laser ablation in liquids

A simple, yet effective method of controlling the size and size distributions of nanoparticles produced as a result of laser ablation of target material is presented. The method employs the presence of physical boundaries on either sides of the ablation site. In order to demonstrate the potential of the method, experiments have been conducted with copper and titanium as the target materials that are placed in two different liquid media (water and isopropyl alcohol). The ablation of the target material immersed in the liquid medium has been carried out using an Nd:YAG laser. Significant differences in the size and size distributions are observed in the cases of nanoparticles produced with and without confining boundaries. It is seen that for any given liquid medium and the target material, the mean size of the nanoparticles obtained with the boundary-fitted target surface is consistently higher than that achieved in the case of open (flat) targets. The observed trend has been attributed to the plausible role(s) of the confining boundaries in prolonging the thermalisation time of the plasma plume. In order to ascertain that the observed differences in sizes of the nanoparticles produced with and without the presence of the physical barriers are predominantly because of the prolonged thermalisation of the plasma plume and not due to the possible formation of oxide layer, select experiments with gold as the target material in water have also been performed. The experiments also show that, irrespective of the liquid medium, the increase in the mean size of the copper-based nanoparticles due to the presence of physical boundaries is relatively higher than that observed in the case of titanium target material under similar experimental conditions.Comment: 24 pages, 9 figures, a part of this work has been published in Photonics Prague 2017, (Proc. SPIE 10603, Photonics, Devices, and Systems VII, 1060304) titled "A novel method for fabrication of size-controlled metallic nanoparticles

Rapid and even spreading of complex fluids over a large area in porous substrates

Rapid and even spreading of complex fluids over a large area on substrates like paper is required for chemical and biological sensing applications. Non-Newtonian flow behavior and the presence of multi-phase components pose a significant challenge to uniform flow in porous media. Specifically in the case of blood, for biosensing applications, fast spread on a large area is required to avoid coagulation and non-uniform component spread. In this work, we have developed a filter paper-based device to resolve this spreading challenge. We sandwich the filter paper between a matrix of nanofibrous membrane backed by polyethylene terephthalate (PET) sheets, forming a multi-scale porous network: one within the filter paper and the other between the PET sheet and the filter paper. By doing so, we decrease the overall resistance to flow while maintaining the same capillary suction pressure to obtain a quick, uniform spread of dyed liquids, milk solutions, and whole blood. The device design and concepts used here can be used in paper microfluidic applications and to develop devices for dried blood spot analysis, which utilize this fast flow while maintaining even spreading over a large area

Design and Implementation of Solar Charge Controller for Photovoltaic Systems

The paper presents a design of solar charge controller for PV energy system. A voltage regulator circuit, an Over-charging Protection circuit and an Over-discharging Protection circuit design are proposed in this paper. The voltage regulator circuit modulates the voltage variation at the output of solar panel and fed it to the Charging Controller circuit. The Over-charging controller circuit prevents overcharging of battery and helps to increase lifespan of battery. The Over-discharging circuit protects the battery by restricting flow of current from battery to PV panel. The entire model is implemented in hardware and results are observed and analyzed to examine the capability of the Solar Charge Controlle

Assessment of groundwater quality status by using water quality index (WQI) and geographic information system (GIS) approaches: a case study of the Bokaro district, India

Abstract One hundred two groundwater samples were collected from the Bokaro district of Jharkhand state, India, during the pre-and post-monsoon seasons of the year 2014–2015. In the present study, groundwater samples were analysed for pH, TDS, TH, Ca2+, Mg2+, Na+, K+, Cl−, SO4 2−, HCO3 −, F− and NO3 − to evaluate the suitability of the groundwater for drinking purposes through geographic information system (GIS)-based water quality index (WQI) model. For quality assessment, values of analysed parameters of the groundwater samples were compared with the Bureau of Indian standards (BIS) and World Health Organization (WHO) water quality standards. The analytical results indicate slightly acidic to slightly alkaline nature of the groundwater in the study area. Concentrations of Ca2+, Mg2+, HCO3 −, F−, NO3 −, TDS and TH exceeded the desirable as well as permissible limits of drinking water quality standards recommended by the BIS (Indian Standard Drinking Water Specification, 2012) and WHO (Guidelines for drinking water quality: training pack, WHO, Geneva, 2004) in the study area during the pre- and post-monsoon seasons, respectively. However, Na+, K+, Cl− and SO4 2− concentrations were within the permissible limits during both seasons. The hydrochemical analysis of the studied groundwater samples documented with ternary and Durov diagram revealed that most of the groundwater samples belong to HCO3 − type of anions facies and no dominant type of cation facies. The GIS-based WQI maps for the study area indicate that the poor quality of water was found the maximum in the pre-monsoon season as compared to the post-monsoon season in the study area, respectively. The high values of WQI in the several groundwater samples of the Bokaro district indicate that water is not suitable for direct consumptions and it required sustainable treatment before its utilization for drinking uses

Insight into the design and fabrication of a leaf-mimicking micropump

A micropump is the heart of any microfluidic device that finds applications in several lab-on-chip devices. Passive micropumps are highly desirable for this purpose due to their ease of integration, low energy requirements and simplistic design and operation. The design of a plant leaf serves as a natural inspiration for developing an evaporation assisted passive micropump. The presence of branching channel like venation pattern ensures water distribution to the spongy mesophyll cells increasing the surface area for evaporation. However, due to its multiscale design and complexity of the venation pattern, emulating a leaf's design is challenging. Apart from the lack of understanding of design parameters that affect fluid flow, manufacturing limitations impede the development of such bio-inspired micropumps. Inspired by the multi-scale design of the leaf, in this work we propose a passive micropump mimicking the structure of a leaf. Employing evaporation and capillary pressure as the pumping mechanism, our leaf mimicking micropump consists of a microporous membrane integrated with a branched, fractal channel network resembling a leaf's venation pattern. Our proposed fabrication methodology is simple, scalable, inexpensive and uses readily available materials. We demonstrate a significant increase in the fluid flow rate due to the addition of this branched channel network. We support our experimental observations using an analytical model, wherein we discuss the design parameters that affect the pumping rate. Correspondingly, the performance of these micropumps can be optimized based on intrinsic and extrinsic factors as per the desired applications

Unicornuate uterus: case reports of heterogenous presentations challenging clinical diagnosis and management

Unicornuate uterus is an anomaly arising from defective lateral fusion of incompletely developed mullerian duct or paramesonephric duct with the contralateral duct. Pregnancy in non-communicating rudimentary horn can result in I and II trimester pregnancy losses along with maternal morbidity and mortality. Here we describe three such cases of unicornuate uterus with non-communicating rudimentary horn pregnancy, who presented to our hospital with pain in lower abdomen. Two of them with II trimester pregnancy landed in haemorrhagic shock owing to rupture of pregnant horn, though were revived by immediate intervention. Third patient who came with a definitive diagnosis of I trimester rudimentary horn pregnancy was managed electively by hemi-hysterectomy. Rupture of pregnant uterus can occur in II trimester when associated with uterine anomaly. Early sonographic diagnosis has a major offering in workup, management and prevention of mother from grave life threatening consequences