132 research outputs found
Basal Jawed Vertebrate Phylogenomics Using Transcriptomic Data from Solexa Sequencing
No full textThe traditionally accepted relationships among basal jawed vertebrates have been challenged by some molecular phylogenetic analyses based on mitochondrial sequences. Those studies split extant gnathostomes into two monophyletic groups: tetrapods and piscine branch, including Chondrichthyes, Actinopterygii and sarcopterygian fishes. Lungfish and bichir are found in a basal position on the piscine branch. Based on transcriptomes of an armored bichir (Polypterus delhezi) and an African lungfish (Protopterus sp.) we generated, expressed sequences and whole genome sequences available from public databases, we obtained 111 genes to reconstruct the phylogenetic tree of basal jawed vertebrates and estimated their times of divergence. Our phylogenomic study supports the traditional relationship. We found that gnathostomes are divided into Chondrichthyes and the Osteichthyes, both with 100% support values (posterior probabilities and bootstrap values). Chimaeras were found to have a basal position among cartilaginous fishes with a 100% support value. Osteichthyes were divided into Actinopterygii and Sarcopterygii with 100% support value. Lungfish and tetrapods form a monophyletic group with 100% posterior probability. Bichir and two teleost species form a monophyletic group with 100% support value. The previous tree, based on mitochondrial data, was significantly rejected by an approximately unbiased test (AU test, p=0). The time of divergence between lungfish and tetrapods was estimated to be 391.8 Ma and the divergence of bichir from pufferfish and medaka was estimated to be 330.6 Ma. These estimates closely match the fossil record. In conclusion, our phylogenomic study successfully resolved the relationship of basal jawed vertebrates based on transtriptomes, EST and whole genome sequences.The traditionally accepted relationships among basal jawed vertebrates have been challenged by some molecular phylogenetic analyses based on mitochondrial sequences. Those studies split extant gnathostomes into two monophyletic groups: tetrapods and piscine branch, including Chondrichthyes, Actinopterygii and sarcopterygian fishes. Lungfish and bichir are found in a basal position on the piscine branch. Based on transcriptomes of an armored bichir (Polypterus delhezi) and an African lungfish (Protopterus sp.) we generated, expressed sequences and whole genome sequences available from public databases, we obtained 111 genes to reconstruct the phylogenetic tree of basal jawed vertebrates and estimated their times of divergence. Our phylogenomic study supports the traditional relationship. We found that gnathostomes are divided into Chondrichthyes and the Osteichthyes, both with 100% support values (posterior probabilities and bootstrap values). Chimaeras were found to have a basal position among cartilaginous fishes with a 100% support value. Osteichthyes were divided into Actinopterygii and Sarcopterygii with 100% support value. Lungfish and tetrapods form a monophyletic group with 100% posterior probability. Bichir and two teleost species form a monophyletic group with 100% support value. The previous tree, based on mitochondrial data, was significantly rejected by an approximately unbiased test (AU test, p=0). The time of divergence between lungfish and tetrapods was estimated to be 391.8 Ma and the divergence of bichir from pufferfish and medaka was estimated to be 330.6 Ma. These estimates closely match the fossil record. In conclusion, our phylogenomic study successfully resolved the relationship of basal jawed vertebrates based on transtriptomes, EST and whole genome sequences
Relationship between mercury concentration and size of long-jawed orb weaver spiders
No full textMethylmercury (MeHg) is an environmental contaminant that poses a serious threat to humans and wildlife. There are approximately 9 million water bodies in the United States alone that have all been contaminated with MeHg. Since there are so many water bodies, it is difficult to know the level of contamination for each, and whether or not they pose a threat to humans and/or wildlife. Ecologists use biosentinels, or a species that reflects the MeHg contamination of the aquatic ecosystem, in order to determine the level of contamination. In the present study, the author proposed the long-jawed orb weaver spider (Tetragnatha sp.) as a potential biosentinel for MeHg contamination of water bodies. The author collected spiders from 15 ponds in September and October of 2013, where she found a positive correlation between MeHg concentration and size of long-jawed orb weaver spiders. The author then found a positive relationship between MeHg concentration of the spiders and the overall MeHg contamination of the aquatic ecosystem, thus suggesting the long-jawed orb weaver spider is an effective biosentinel. This study proposes that long-jawed orb weaver spiders could be used as an efficient bioseninel to determine MeHg contamination in many of the 9 million water bodies across the United States
Ongoing Research in Jawed Fish Immunity: Structural and Functional Studies at the Protein and Cellular Levels
No full textThis eBook is a collection of articles from a Frontiers Research Topic. Frontiers Research Topics are very popular trademarks of the Frontiers Journals Series: they are collections of at least ten articles, all centered on a particular subject. With their unique mix of varied contributions from Original Research to Review Articles, Frontiers Research Topics unify the most influential researchers, the latest key findings and historical advances in a hot research area! Find out more on how to host your own Frontiers Research Topic or contribute to one as an author by contacting the Frontiers Editorial Office: frontiersin.org/about/contac
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Directed Shape Morphing of Soft Kirigami Deployables
No full textThis study explores deployable structures inspired by nature’s morphogenesis, where biological systems inherently develop complex forms autonomously. Applying these principles, this research proposes a new approach where materials self-organize and morph from two-dimensional to three-dimensional shapes without traditional manufacturing constraints.Deployable structures offer significant advantages in compactness, simplifying storage and transportation, making them particularly valuable in fields like aerospace and biomedicine where tailored, precise forms are crucial. However, the transformation from planar to three-dimensional structures presents substantial challenges due to complex design interdependencies. To address this, the research develops kirigami based structures capable of deploying from a planar to a 3D shapes. Furthermore, these possess the ability of switching between stable states without continuous energy input, enhancing their functionality for various applications. Additionally, the study tackles the inverse design challenge through a novel integration of machine learning, optimizing design parameters for specific functional needs efficiently. This approach not only bridges the gap between static planar manufacturing and dynamic structural functionality but also creates a platform for a more intuitive, equipment-frugal way to tackle deployable systems, setting the stage for future innovations in the field
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Computational Methods in Slender Structures and Soft Robots
No full textSlender structures, existing in both natural environments (tendrils) and man-made systems (soft robots), often undergo geometrically nonlinear deformations and dramatic topological changes when subjected to simple boundary conditions or moderate external actuations, which pose extensive challenges to the traditional numerical and analytical methods. This dissertation focuses on the Discrete Differential Geometry (DDG)-based numerical frameworks for simulating the mechanical response in slender structures and soft robots, and makes four major contributions:First, we use a planar rod theory and incorporate Coulomb frictional contact, elastic/inelastic collision with ground, and inertial effects in a physically accurate manner, to simulate the dynamics of shape memory alloy (SMA)-powered soft robots. Our simulations show quantitative agreement when compared against with experiments, suggesting that our numerical approach represents a promising step toward the ultimate goal of a computational framework for soft robotic engineering. We then combine the same planar rod framework with a naive fluid-structure interaction model to perform the swimming of a seastar-inspired soft robot in water.Secondly, we numerically explore the propulsion of bacteria flagella in a low Reynolds fluid. We study the locomotion of a bacteria-inspired soft robot. Our numerical framework uses (i) Discrete Elastic Rods (DER) method to account for the elasticity of soft filament, (ii) Lighthill's Slender Body Theory (LSBT) for the long term hydrodynamic flow by helical flagellum, and (iii) Higdon's model for the hydrodynamics from spherical head. A data-driven approach is later employed to develop a control algorithm such that our flagella-inspired robot can follow a prescribed trajectory only by changing its rotation frequency. Then, to investigate the bundling behavior between two soft helical rods rotating side by side in a viscous fluid, we implement a coupled DER and Regularized Stokeslet Segment (RSS) framework. The contact between two rods is also considered in our numerical tool. A novel bundling behavior between two nearby helical rods is uncovered, whereby the filaments come across each other above a critical angular velocity.Our third contribution is to present a numerical method for both forward physics-based simulations and inverse form-finding problems in elastic gridshells. Our numerical framework on elastic gridshell first decomposes this special structure into multiple one dimensional rods and linkers, which can be performed by the well-established Discrete Elastic Rods (DER) algorithm. A stiffed spring between rods and linkages is later introduced to ensure the bending and twisting coupling at joint area. The inverse form finding problem -- compute the initial planar pattern from a given 3D configuration -- is directly solved by a contact-based procedure, without using any the conventional optimization-based algorithms. Several examples are used to show the effectiveness of the inverse design process.Finally, we compare Kirchhoff rod model, Sadowsky ribbon model, and FvK plate equations, to systematically characterize a group of slender structures, from narrow strip to wide plate. We consider a pre-buckled band under lateral end translation and quantity its supercritical pitchfork bifurcation. The one dimensional anisotropic rod can give a reasonable prediction when the strip is narrow, while fails to capture its width effect. A two dimensional plate approach, on the other hand, accurately anticipates the nonlinear deformations and the critical supercritical pitchfork points for both narrow and wide plates. We finally discuss in detail the issues of traditional one dimensional ribbon models at the inflection points, and then use an extensible ribbon model to bridge the gap between the Kirchhoff rod model and the classical Sadowsky ribbon model
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Design, Modeling and Control of Flexible Structures in Robotics Applications
No full textFlexible structures play a pivotal role in enabling novel forms of robotic locomotion, manipulation, and medical intervention. This dissertation investigates the design, modeling, and control of flexible structures across increasing geometric complexity—from rods, to rings, to shells—with an emphasis on their integration into robotic systems. First, we examine rod-like geometries inspired by bacterial flagella, where single and bi-flagellated robots leverage helical rod rotation to achieve propulsion in low Reynolds number environments. Second, we present pneumatic ring actuators that generate peristaltic motions for grasping and transporting irregular or soft objects, demonstrating robust manipulation without the need for complex control strategies. Finally, we extend the framework to pneumatic membrane shells for hemostasis applications, coupling soft structures with robotic arms to achieve precise deployment and pressure regulation on bleeding sites. Across all three case studies, we develop physics-based and data-driven models, integrate proprioceptive and external sensing for feedback, and design control strategies that link structural mechanics with task-specific robotic performance. Together, these contributions establish a unified perspective on how flexible structures—ranging from slender rods to curved shells—can be harnessed to expand the functionality, adaptability, and safety of next-generation robotic systems
Corporate social responsibility in Islam
No full textNotions of corporate social responsibility (CSR) have been suggested to be consistent with an Islamic view of society. Indeed, values and principles that have been central to Islam since the time of the holy Prophet Mohammed (Peace and Blessings be upon him) may serve as a foundation for notions of corporate social responsibility (CSR) similar to those in the West. Much contemporary discussion of CSR, however, has not recognized this. These discussions have largely been based on a Western orientation informed by Western religious values. Moreover, CSR has evolved literally in response to particular issues or problems that are specific to businesses in a Western context. This led to a lack of a comprehensive global context within which a wider perspective of CSR should be positioned. On the other hand, the notion of social responsibility and justice has been an integral part of Islamic society for nearly 14 centuries. However, the Islamic literature remains scattered, fragmented and lacks a coherent framework that would allow such a concept in Islam to be systematized. While Islamic philosophy is rich in precepts pertinent to CSR, these precepts have not yet been formally synthesized to present a systematic model with an explicit notion of CSR in Islam. Thus, there exists a gap in both the Western and Islamic literature. This was fruitfully exploited in this study to advance the understanding of the concept of CSR in a wider cultural and religious setting. This study explored this new territory and presented a conceptual framework of CSR in Islam based on Shariah (the Islamic legal and social system) derived from the holy Qur'an and Hadith. It provided both, a counterpart and a comparable base in the study of various issues relevant to CSR and international business from a much wider global perspective. It also provided significant insights into Islamic jurisprudence (Fiqh) regarding business practice. The consistency of the conceptual framework of CSR in Islam with contemporary business practices was explored using a survey of Islamic banks located in different parts of the world. The survey revealed that many current practices of Islamic banks mirror the expected behaviours or practices generated in the Islamic framework. In fact, it was possible to discern that the organizations surveyed implement the Islamic code of conduct rather extensively. Against this background, a consistency with the framework of CSR in Islam presented in this study was identified. Such consistency, however, was driven by legal requirements in adherence to Shariah rather than an explicit understanding or pursuit of CSR. The lack of a systematic framework with explicit notions of CSR from an Islamic perspective caused hindrance in implementing CSR practices in Islamic organizations. It follows that this study was a modest step towards filling this lacuna by presenting a systematic and coherent framework of CSR in Islam
Corporate Social Responsibility in Islam
No full textNotions of corporate social responsibility (CSR) have been suggested to be consistent with an Islamic view of society. Indeed, values and principles that have been central to Islam since the time of the holy Prophet Mohammed (Peace and Blessings be upon him) may serve as a foundation for notions of corporate social responsibility (CSR) similar to those in the West. Much contemporary discussion of CSR, however, has not recognized this. These discussions have largely been based on a Western orientation informed by Western religious values. Moreover, CSR has evolved literally in response to particular issues or problems that are specific to businesses in a Western context. This led to a lack of a comprehensive global context within which a wider perspective of CSR should be positioned. On the other hand, the notion of social responsibility and justice has been an integral part of Islamic society for nearly 14 centuries. However, the Islamic literature remains scattered, fragmented and lacks a coherent framework that would allow such a concept in Islam to be systematized. While Islamic philosophy is rich in precepts pertinent to CSR, these precepts have not yet been formally synthesized to present a systematic model with an explicit notion of CSR in Islam. Thus, there exists a gap in both the Western and Islamic literature. This was fruitfully exploited in this study to advance the understanding of the concept of CSR in a wider cultural and religious setting. This study explored this new territory and presented a conceptual framework of CSR in Islam based on Shariah (the Islamic legal and social system) derived from the holy Qur'an and Hadith. It provided both, a counterpart and a comparable base in the study of various issues relevant to CSR and international business from a much wider global perspective. It also provided significant insights into Islamic jurisprudence (Fiqh) regarding business practice. The consistency of the conceptual framework of CSR in Islam with contemporary business practices was explored using a survey of Islamic banks located in different parts of the world. The survey revealed that many current practices of Islamic banks mirror the expected behaviours or practices generated in the Islamic framework. In fact, it was possible to discern that the organizations surveyed implement the Islamic code of conduct rather extensively. Against this background, a consistency with the framework of CSR in Islam presented in this study was identified. Such consistency, however, was driven by legal requirements in adherence to Shariah rather than an explicit understanding or pursuit of CSR. The lack of a systematic framework with explicit notions of CSR from an Islamic perspective caused hindrance in implementing CSR practices in Islamic organizations. It follows that this study was a modest step towards filling this lacuna by presenting a systematic and coherent framework of CSR in Islam
Continuous security in DevOps environment: Integrating automated security checks at each stage of continuous deployment pipeline
No full textIn this digital transformation, when the world is witnessing record security breaches, and hackers are getting bolder and more sophisticated, the development of software quickly is not enough; however, an organization must secure the applications also. To get the secure application out of delivery team hands organization must make security not only a priority but also a standardized part of a daily operational procedure. It will be possible only when an organization integrates security checks and practices throughout the software development lifecycle to better defend their applications and protect their brand values. Therefore, this thesis has outlined a secure DevOps delivery workflow to achieve continuous security by infusing security controls, tools, compliance, and industry best practices, and automated security checks at each stage of the software development cycle, so that all the security testing is done seamlessly through a continuous delivery pipeline. Secure DevOps delivery workflow designed in this thesis will allow organizations to make security as standardized part of a daily operational procedure and results into resilient organization and culture of “everyone responsible for security,” “Scaling through automation,” and “Measurable outcomes.” Moreover, it will save team effort to put into building a better, faster, cheaper and more secure product with a focus on delivery of customers centric features instead of fighting with security-related bugs and compliances and fend off more attacks, leading to an overall more protected system. The secure seven-stage workflow gateway presented in this thesis are Requirements, Plan, Secure Develop, Build, Test, Deploy and Continuous Monitoring fully integrated with security checks at each stage. It is applicable and relevant to all DevOps enabled organization to improve productivity, organizational security learning, shift security to the left, and transform the application release cycle to produce more secure applications. At the end of this thesis, its outline, The Secure DevOps work value stream, to help DevOps team members to evaluate proposed seven-stage gateway workflow and provide everyone in the value stream with the fastest possible feedback about the security of what they are creating, enabling them to quickly detect and correct security problems as part of their work, which enables learning and prevents future errors. Security testing DevOps toolchain, set of security tools integrated within Continuous deployment pipeline to auto checks security at each stage of the workflow, to help the delivery team identify and fix flaws earlier in the delivery process before flaws exposed to the public without impeding agility and this shift security to the left. Secure DevOps workflow model by building security into every stage of the secure development life cycle, from the security requirements stages onwards, and this makes everyone responsible for security. Contributions of this thesis consist of: a secure seven-stage continuous security workflow infused with security controls, compliances and best practices; flow of work across continuous security value stream; Anatomy of continuous security assurance model; Toolchain to infuse automated security checks during CI/CD pipeline
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