AWAIS KHAN - Academia.edu (original) (raw)

Papers by AWAIS KHAN

Compendium of Plant Genomes, 2021

Genomic, genetic, and archaeobotanical findings have confirmed that alongside interspecific hybri... more Genomic, genetic, and archaeobotanical findings have confirmed that alongside interspecific hybridizations between Malus sieversii from Central Asia and wild species along the Silk Road, segmental duplications, point mutations, and clonal propagation have led to the fixation of traits in cultivated apples, unlike in annual crops. Moreover, there is minimal evidence for long-term intentional and targeted selection for fruit quality and horticultural traits; whereas, self-incompatibility, long juvenile phase, and clonal propagation have maintained genetic diversity in apples. Only modern (commercial) apple cultivars hint at the reduction of diversity and selection for commercially important traits. Furthermore, the wide phenotypic variations present in pre-breeding and advanced breeding material reveal that a great deal of genetic diversity is still maintained in the cultivated gene pool.

IEEE Access, 2021

This paper presents a compact, uni-planer wide band Multiple-Input-Multiple-Output (MIMO) antenna... more This paper presents a compact, uni-planer wide band Multiple-Input-Multiple-Output (MIMO) antenna. The designed antenna array has a compact size of (26mm x 31mm) covering a wide frequency band from 3.1GHz-11GHz. A partial ground plane shared by two radiating patches is used. A ground stub and a single column Electromagnetic Bandgap (EBG) structure in between the two radiating patches results in very low mutual coupling in the designed antenna. The proposed MIMO-antenna was evaluated through different performance metric indicators like channel capacity loss, far-field radiation pattern, S-parameters, envelope correlation coefficient, peak gain, diversity-gain and radiation efficiency. Our designed MIMO antenna has a very high isolation amongst the MIMO antennas (S 21 < −25dB), a high Diversity-Gain (DG > 9.995 dB), a very low Envelope Co-relation Coefficient of (ECC < 0.001) and low Channel-Capacity-Loss (CCL < 0.1bits/s/Hz). The said antenna has an average radiation efficiency of 85.5% and a peak gain of (5.67dB) within the ultra-wideband (UWB) spectrum. A 0.8mm thick FR-4 substrate is used to fabricate the MIMO-antenna and tested in an anechoic chamber. The measured results closely match with the simulated results. INDEX TERMS Channel capacity loss, electromagnetic band gap, envelope correlation coefficient, multiple input multiple output (MIMO), ultra wide band (UWB).

The Plant Cell, 2021

In cultivated tetraploid potato (Solanum tuberosum), reduction to diploidy (dihaploidy) allows fo... more In cultivated tetraploid potato (Solanum tuberosum), reduction to diploidy (dihaploidy) allows for hybridization to diploids and introgression breeding and may facilitate the production of inbreds. Pollination with haploid inducers (HIs) yields maternal dihaploids, as well as triploid and tetraploid hybrids. Dihaploids may result from parthenogenesis, entailing the development of embryos from unfertilized eggs, or genome elimination, entailing missegregation and the loss of paternal chromosomes. A sign of genome elimination is the occasional persistence of HI DNA in some dihaploids. We characterized the genomes of 919 putative dihaploids and 134 hybrids produced by pollinating tetraploid clones with three HIs: IVP35, IVP101, and PL-4. Whole-chromosome or segmental aneuploidy was observed in 76 dihaploids, with karyotypes ranging from 2n = 2x − 1 = 23 to 2n = 2x + 3 = 27. Of the additional chromosomes in 74 aneuploids, 66 were from the non-inducer parent and 8 from the inducer parent...

Scientific Reports, 2020

Development of apple (Malus domestica) cultivars resistant to fire blight, a devastating bacteria... more Development of apple (Malus domestica) cultivars resistant to fire blight, a devastating bacterial disease caused by Erwinia amylovora, is a priority for apple breeding programs. Towards this goal, the inactivation of members of the HIPM and DIPM gene families with a role in fire blight susceptibility (S genes) can help achieve sustainable tolerance. We have investigated the genomic diversity of HIPM and DIPM genes in Malus germplasm collections and used a candidate gene-based association mapping approach to identify SNPs (single nucleotide polymorphisms) with significant associations to fire blight susceptibility. A total of 87 unique SNP variants were identified in HIPM and DIPM genes across 93 Malus accessions. Thirty SNPs showed significant associations (p

Background: Apple is one of the most highly consumed fruits worldwide and is the largest fruit cr... more Background: Apple is one of the most highly consumed fruits worldwide and is the largest fruit crop produced in temperate regions. Fruit quality, safety and long-term storage are issues that are important to growers, distributors, and consumers. We present the first worldwide study on the apple fruit microbiome that examines questions regarding the composition and the assembly of microbial communities on and in apple fruit. Results: Results revealed that the composition and structure of the fungal and bacterial communities associated with ‘Royal Gala’ apple fruit at harvest maturity vary and are highly dependent on geographical location. The study also confirmed that the spatial variation in the fungal and bacterial composition of different fruit tissues exists at a global level. Fungal diversity varied significantly in fruit harvested in different geographical locations and suggest a potential link between location and the type and rate of postharvest diseases that develop in each ...

IEEE Sensors Journal, 2020

We present a common framework, for registering images to an atlas and for forming an unbiased atl... more We present a common framework, for registering images to an atlas and for forming an unbiased atlas, that tolerates the presence of pathologies such as tumors and traumatic brain injury lesions. This common framework is particularly useful when a sufficient number of protocol-matched scans from healthy subjects cannot be easily acquired for atlas formation and when the pathologies in a patient cause large appearance changes. Our framework combines a low-rank-plus-sparse image decomposition technique with an iterative, diffeomorphic, group-wise image registration method. At each iteration of image registration, the decomposition technique estimates a "healthy" version of each image as its low-rank component and estimates the pathologies in each image as its sparse component. The healthy version of each image is used for the next iteration of image registration. The low-rank and sparse estimates are refined as the image registrations iteratively improve. For unbiased atlas formation, at each iteration, the average of the low-rank images from the patients is used as the atlas image for the next iteration, until convergence. Since each iteration's atlas is comprised of low-rank components, it provides a population-consistent, pathology-free appearance. Evaluations of the proposed methodology are presented using synthetic data as well as simulated and clinical tumor MRI images from the brain tumor segmentation (BRATS) challenge from MICCAI 2012.

Background Although it is known that resistant rootstocks facilitate management of fire blight di... more Background Although it is known that resistant rootstocks facilitate management of fire blight disease, incited by Erwinia amylovora, the role of rootstock root traits in providing systemic defense against E. amylovora is unclear. In this study, the hypothesis that rootstocks of higher root vigor provide higher tolerance to fire blight infection in apples is tested. Several apple scion genotypes grafted onto a single rootstock genotype and non-grafted ‘M.7’ rootstocks of varying root vigor are used to assess phenotypic and molecular relationships between root traits of rootstocks and fire blight susceptibility of apple scion cultivars.Results It is observed that different root traits display significant (p < 0.05) negative correlations with fire blight susceptibility. In fact, root surface area partially dictates differential levels of fire blight susceptibility of ‘M.7’ rootstocks. Furthermore, contrasting changes in gene expression patterns of diverse molecular pathways accompa...

Apple scab, caused by Venturia inaequalis (Cke.) Wint., is a destructive fungal disease of major ... more Apple scab, caused by Venturia inaequalis (Cke.) Wint., is a destructive fungal disease of major apple cultivars worldwide, most of which are moderately to highly susceptible. Thus, development of scab resistant cultivars is one of the highest priorities of apple breeding programs. The principal source of resistance for breeding programs has been the scab resistance gene Rvi6 that originated from the Japanese crabapple Malus floribunda (Sieb.) sel. 821. Isolates of V. inaequalis able to overcome Rvi6 have been identified in Europe, but have not yet been reported on the American continents. We recently discovered scab infection on M. floribunda 821 trees in a research orchard at Geneva, New York, USA, where approximately 10% of the leaves bore profusely sporulating apple scab lesions, many of which had coalesced to cover entire leaves. Chlorosis and pinpoint pitting symptoms typical of failed infections by V. inaequalis on hosts bearing the Rvi6 and Rvi7 genes were also observed. We ...

Proceedings of the Institution of Mechanical Engineers, Part I: Journal of Systems and Control Engineering, 2019

This article proposes a combination of linear and nonlinear sliding surfaces to design a new stru... more This article proposes a combination of linear and nonlinear sliding surfaces to design a new structure for terminal sliding mode control, capable of accepting a definite final time as an input data. The structures of both single-input-single-output and multi-input-multi-output systems are expressed. The controller operates in two modes: first, reaching the states to linear sliding surface, defining control parameters and rise time; second, switching to nonlinear sliding surface and defining a convergence time. Sum of rise time and convergence time, both of which as inputs, sets the final time. The control gains are adaptively tuned and parameter uncertainty in dynamics is considered in the design. The proposed method is implemented theoretically and experimentally on Scout robot in point-to-point motion and trajectory tracking. The results are compared to conventional terminal sliding mode control and finite-time state-dependent Riccati equation to assess the improvement.

The hexaploid sweetpotato (Ipomoea batatas (L.) Lam., 2n = 6x = 90) is an important staple food c... more The hexaploid sweetpotato (Ipomoea batatas (L.) Lam., 2n = 6x = 90) is an important staple food crop worldwide and has a vital role in alleviating famine in developing countries. Due to its high ploidy level, genetic studies in sweetpotato lag behind major diploid crops significantly. We built an ultra-dense multilocus integrated genetic map and characterized the inheritance system in a sweetpotato full-sib family using our newly implemented software, MAPpoly. The resulting genetic map revealed 96.5% collinearity between I. batatas and its diploid relative I. trifida. We computed the genotypic probabilities across the whole genome for all individuals in the mapping population and inferred their complete hexaploid haplotypes. We provide evidence that most of the meiotic configurations (73.3%) were resolved in bivalents, although a small portion of multivalent signatures (15.7%), among other inconclusive configurations (11.0%) were also observed. Except for low levels of preferential ...

Horticulture Research, 2019

Open Agriculture, 2017

The CGIAR Research Program (CRP) on Roots, Tubers and Bananas (RTB) includes vegetatively propaga... more The CGIAR Research Program (CRP) on Roots, Tubers and Bananas (RTB) includes vegetatively propagated staple crops linked by common breeding, seed, and postharvest issues, and by the frequency with which women are involved in their production and use. RTB crops are the backbone of food security across the humid tropics in sub-Saharan Africa (SSA) and in more localized areas of Asia and Latin America. Around 300 million poor people in developing countries currently depend on RTB value chains for food security, nutrition and income. Climate change poses challenges which could undo progress in poverty reduction and markedly increase food insecurity. This article examines planning and research for climate resilience across RTB crops, with a particular focus on the contrasting potato and sweet potato cases in SSA. A six-step framework for climatesmart breeding is proposed: (1) downscaling climate change models and crop modeling; (2) identifying and understanding key climate change respons...

Molecular plant, Jan 29, 2017

There is a rapidly rising trend in development and application of molecular marker assays for gen... more There is a rapidly rising trend in development and application of molecular marker assays for gene mapping and discovery in field crops and trees. Thus far more than 50 SNP arrays and 15 different types of genotyping-by-sequencing (GBS) platforms have been developed in more than 25 crop species and perennial trees. However, much less has been emphasized on developing ultra-high-throughput and cost-effective genotyping platforms for applied breeding programs. We discuss the scientific bottlenecks in existing SNP arrays and GBS technologies and the strategy to develop targeted platforms for crop molecular breeding. The concept of true breeding platforms implies to automated genotyping technologies, either array- or sequencing-based, targeting functional polymorphisms underpinning economic traits, providing desirable prediction accuracy for quantitative traits, and have universal application across genetic backgrounds in a crop. The development of such platforms face serious challenges...

The assembly of whole-chromosome pseudomolecules for plant genomes remains challenging due to pol... more The assembly of whole-chromosome pseudomolecules for plant genomes remains challenging due to polyploidy and high repeat content. We developed an approach for constructing complete pseudomolecules for polyploid species using genotyping-by-sequencing data from outcrossing mapping populations coupled with high coverage whole genome sequence data of a reference genome. Our approach combines de novo assembly with linkage mapping to arrange scaffolds into pseudomolecules. We show that the method is able to reconstruct simulated chromosomes for both diploid and tetraploid genomes. Comparisons to three existing genetic mapping tools show that our method outperforms the other methods in accuracy on both grouping and ordering, and is robust to the presence of substantial amounts of missing data and genotyping errors. We applied our method to three real datasets including a diploid Ipomoea trifida and two tetraploid potato mapping populations. The linkage maps show significant concordance wit...

Current Genomics, 2016

Drought stress caused by unpredictable precipitation poses a major threat to food production worl... more Drought stress caused by unpredictable precipitation poses a major threat to food production worldwide, and its impact is only expected to increase with the further onset of climate change. Understanding the effect of drought stress on crops and plants' response is critical for developing improved varieties with stable high yield to fill a growing food gap from an increasing population depending on decreasing land and water resources. When a plant encounters drought stress, it may use multiple response types, depending on environmental conditions, drought stress intensity and duration, and the physiological stage of the plant. Drought stress responses can be divided into four broad types: drought escape, drought avoidance, drought tolerance, and drought recovery, each characterized by interacting mechanisms, which may together be referred to as drought resistance mechanisms. The complex nature of drought resistance requires a multi-pronged approach to breed new varieties with stable and enhanced yield under drought stress conditions. High throughput genomics and phenomics allow marker-assisted selection (MAS) and genomic selection (GS), which offer rapid and targeted improvement of populations and identification of parents for rapid genetic gains and improved drought-resistant varieties. Using these approaches together with appropriate genetic diversity, databases, analytical tools, and well-characterized drought stress scenarios, weather and soil data, new varieties with improved drought resistance corresponding to grower preferences can be introduced into target regions rapidly.

2015 IEEE Vehicular Networking Conference (VNC), 2015

The European Telecommunications Standards Institute (ETSI) standard has defined the Basic Set of ... more The European Telecommunications Standards Institute (ETSI) standard has defined the Basic Set of Applications (BSA) which is composed of three main application classes road/traffic safety, traffic efficiency, and other value-added applications. Traffic safety applications strongly rely on the exchange of two types of safety messages that have been standardized by ETSI namely Cooperative Awareness Messages (CAMs) and Decentralized Environmental Notification Messages (DENMs). The ETSI's comprehensive and well documented standards present the structures and implementations guidelines of these safety messages yet there is lack of extensive work on the implementation and validation. Therefore, this paper presents a comprehensive architecture and implementation that has been developed to validate the potentials of CAM and DENM messaging capabilities. This paper evaluates the performance of CAM and DENM facilities through a custom IEEE 802.11p (ITS-G5) based prototype (IT2S) deployed in a field trial. The tests validates the CAM performance by tracking vehicles and various performance indicators such the packet error rate (PER), Received Signal strength (RSSI), connection distance between the OBUs and RSU, number of messages transmitted, GPS coordinates and successful packets received. Similarly, DENMs are validated by events such as traffic information, hazardous location and accidents. These tests motivate towards the unified solution for the implementation of a complete ITS.

Life Science Journal

The need of high definition video (HDV) is growing day by day. Keeping in need of HDV, the Joint ... more The need of high definition video (HDV) is growing day by day. Keeping in need of HDV, the Joint Collaborative Team on Video Coding (JCTVC) developed a new video coding project known as High Efficiency Video Coding (HEVC). The upcoming HEVC is designed to serve wide range of applications. However, it suffers from visually disturbing discontinuities known as blocking artifacts to achieve high compression ratio. HEVC employs in-loop filter to suppress these blocking artifacts. This paper describes the performance analysis of HEVC in-loop filter which comprises of deblocking and sample adaptive offset (SAO) filter. Various high definition video sequences of 1080p, 720p and 480p are used for evaluation. Simulation results show that in-loop filter can suppress blocking artifacts effectively without losing objective and subjective quality of video.

Objective: To compare polypropylene suture and skin staples for securing mesh in Lichtenstein ing... more Objective: To compare polypropylene suture and skin staples for securing mesh in Lichtenstein inguinal hernioplasty in terms of mean operating time and postoperative pain. Study Design: Randomized clinical trial. Place and Duration of Study: Surgical Ward, Combined Military Hospital, Kharian, from August 2011 to February 2012. Methodology: All individuals fulfilling inclusion criteria underwent elective Lichtenstein inguinal hernioplasty as admitted patients, under spinal anaesthesia and with aseptic measures. In group 1, during the operation, mesh fixation was done with 2/0 polypropylene suture and skin was closed with subcuticular 2/0 polypropylene suture whereas in group 2, the anchorage of mesh was done with skin staples and skin was closed with staples from the same stapler. Mean operative time and postoperative pain, assessed on a visual analog score, were compared between the groups. Results: The overall postoperative pain was lower (p = 0.026) when staples were used to ancho...