Manipulation Modes Research Articles

Design and analysis of CRISPR-Cas experiments.

A large and ever-expanding set of CRISPR-Cas systems now enables the rapid and flexible manipulation of genomes in both targeted and large-scale experiments. Numerous software tools and analytical methods have been developed for the design and analysis of CRISPR-Cas experiments, including resources to design optimal guide RNAs for various modes of manipulation and to analyze the results of such experiments. A major recent focus has been the development of comprehensive tools for use on data from large-scale CRISPR-based genetic screens. As this field continues to progress, a clear ongoing challenge is not only to innovate, but to actively maintain and improve existing tools so that researchers across disciplines can rely on a stable set of excellent computational resources for CRISPR-Cas experiments.

Distinct modes of manipulation of rice auxin response factor OsARF17 by different plant RNA viruses for infection

Plant auxin response factor (ARF) transcription factors are an important class of key transcriptional modulators in auxin signaling. Despite the well-studied roles of ARF transcription factors in plant growth and development, it is largely unknown whether, and how, ARF transcription factors may be involved in plant resistance to pathogens. We show here that two fijiviruses (double-stranded RNA viruses) utilize their proteins to disturb the dimerization of OsARF17 and repress its transcriptional activation ability, while a tenuivirus (negative-sense single-stranded RNA virus) directly interferes with the DNA binding activity of OsARF17. These interactions impair OsARF17-mediated antiviral defense. OsARF17 also confers resistance to a cytorhabdovirus and was directly targeted by one of the viral proteins. Thus, OsARF17 is the common target of several very different viruses. This suggests that OsARF17 plays a crucial role in plant defense against different types of plant viruses, and that these viruses use independently evolved viral proteins to target this key component of auxin signaling and facilitate infection.

Design, Modeling, and Control of a New Manipulating Climbing Robot Through Infrastructures Using Adaptive Force Control Method

SUMMARYIn this paper, design, modeling, and control of a grip-based climbing robot are performed, which consists of a triangular chassis and three actuating legs. This robot can climb through any trusses, pipeline, and scaffolds structures and can perform any inspectional and operational tasks in the high height which decreases the falling danger of operation and increases the safety of the workers. The proposed robot can be substituted for the workers to decrease the risk of death danger and increase the safety of the operation. Since these kinds of infrastructures are truss shaped, the traditional wheel-based climbing robots are not able to travel through these structures. Therefore, in this paper, a grip-based climbing robot is designed to accomplish the climbing process through the trusses and infrastructures in order to perform inspecting and manipulating tasks. Hence, a proper mechanism for the mentioned robot is designed and its related kinematic and kinetic models are developed. Robot modeling is investigated for two different modes including climbing and manipulating phases. Considering the redundancy of the proposed robot and the parallel mechanism employed in it, the active joints are selected in a proper way and its path planning is performed to accomplish the required missions. Concerning the climbing mode, the required computed torque method (CTM) is calculated by the inverse dynamics of the robot. However, for the manipulation mode, after path planning, two controlling strategies are employed, including feedback linearization (FBL) and adaptive force control, and their results are compared as well. It is shown that the latter case is preferable since the external forces implemented on the end effector tool is not exactly predetermined and thus, the controller should adapt the robot with the exerted force pattern of the manipulator. The modeling correctness is investigated by performing some analytic and comparative simulation scenarios in the MATLAB and comparing the results with the MSC-ADAMS ones, for both climbing and manipulating phases. The efficiency of the designed controller is also proved by implementing an unknown force pattern on the manipulator to check its efficiency toward estimating the mentioned implemented forces and compensating the errors. It is shown that the designed robot can successfully climb through a truss and perform its operating task by the aid of the employed adaptive controller in an accurate way.

Virtual reality and augmented reality at the service of increasing interactivity in MOOCs

The Massive Open Online Course (MOOC) presents an approach of learning to permit an online and a distant learning for internet users. These systems are confronted with several problems among which the most important: the lack of participants’ interactivity in the platform and the dropout of the participants. Those challenges need to be resolved to ensure better engagement and to encourage the participants to complete the training, by improving their understanding-level. The present paper focuses on the proposition of a solution that helps to solve the lack of the participants’ interaction with the platform and to decrease the dropout rate. To do so, a module of virtual manipulations’ creation (virtual simulations and practical activities) is proposed. This last is based on Augmented Reality (AR) or Virtual Reality (VR), with a multitude of manipulation methods depending on the instructor choice. Two manipulation modes are proposed: the online mode, where all the manipulations and the interactions are done online and streamingly, and the offline mode, where the users can download the manipulations to preform them locally. Finally, to test the effectiveness of our proposition, two MOOCs, with the same thematic, have been proposed. The first one was a traditional MOOC while the second one was a MOOC that proposes to the participants some virtual simulations and practical activities.

Programmable Ultralight Magnets via Orientational Arrangement of Ferromagnetic Nanoparticles within Aerogel Hosts

The actuation and levitation of air-suspended objects by a magnetic field, due to its noncontact and holonomic manipulation modes, are important technological capabilities for device applications. However, owing to a higher density of conventional ferromagnets or nanoparticle-containing polymers and strong magnetic fields required for actuation, fabricating lightweight materials with a sensitive magnetic response for weight critical applications is challenging. Here, we report ultralight aerogel-based magnets (aero-magnets) comprising assembled ferromagnetic nanomaterials with highly magnetic anisotropy where the magnetic domains can be programmed by external predesigned fields. To demonstrate the breadth of manufacturing methods for this breed of aero-magnet composites, both silica/nanocellulose aerogel hosts and ferromagnetic nanorod/nanoplatelet guests have been explored. Single and double domains with out-of-plane magnetization are programmed into the aero-magnets and characterized by magnetic force microscopy. The levitation and actuation of the aero-magnets are realized while exposed to a small external magnetic field of 11 mT and introduced to a switching circuit. Furthermore, the elastic moduli of the aero-magnets are estimated by dynamic magnetic responses of the ferromagnetic nanoparticles tightly tethered in the aerogel hosts under rapid cyclic fields. These programmable aero-magnets could serve as monolithic magnetic actuator units in the fields of tiny robots and aerospace components.

Chemical Synthesis at Surfaces with Atomic Precision: Taming Complexity and Perfection.

Scanning probe microscopy (SPM) is a powerful tool to study the structure and dynamics of molecules at surfaces and interfaces as well as to precisely manipulate atoms and molecules by applying an external force, by inelastic electron tunneling, or by means of an electric field. The rapid development of these SPM manipulation modes made it possible to achieve fine-control over fundamental processes in the physics of interfaces as well as chemical reactivity, such as adsorption, diffusion, bond formation, and bond dissociation with precision at the single atom/molecule level. Their controlled use for the fabrication of atomic-scale structures and synthesis of new, perhaps uncommon, molecules with programmed properties are reviewed. Opportunities and challenges towards the development of complex chemical systems are discussed, by analyzing potential future impacts in nanoscience and nanotechnology.

Magnetoresponsive Surfaces for Manipulation of Nonmagnetic Liquids: Design and Applications

AbstractMagnetic actuation provides a remote, nondestructive, and real‐time way for controllable liquid manipulation, which has promising technological applications for areas ranging from digital microfluidics, biochemical assays, and microreactors, to liquid collection. However, conventional magnetic liquid manipulation usually relies on incorporating magnetic particles into a liquid to empower its motion in response to an external magnetic field, resulting in considerable limitations of magnetic actuation in various applications. Recently, a range of magnetoresponsive surfaces (MRSs) with elaborately designed surface structures and/or compositions have enabled on‐demand liquid manipulation using magnetic fields, even when the liquids do not contain any magnetic particles. Here, the state‐of‐the‐art of MRSs capable of manipulation of nonmagnetic liquids is reviewed. Their preparation, different manipulation modes, including directed propulsion, spreading, and rebound, and the underlying working mechanisms are discussed. Based on the working principles, MRSs are classified into three categories, including surfaces with magnetic bendable microstructures, surfaces with switchable topographies, and surfaces infused with ferrofluids. Their applications in microfluidics, microreactors, liquid distributors and pumps, fog collection, and anti‐icing are presented. Finally, key challenges and the future prospects of MRSs are provided.

Human exposure levels of PAEs in an e-waste recycling area: Get insight into impacts of spatial variation and manipulation mode

Phthalic acid esters (PAEs) are one important category of additives in plastics, which are ubiquitous products of e-waste recycling areas, where PAEs are released to the environment intensively and higher exposure level is expected for the employees. This study investigated human exposure levels of PAEs in an e-waste recycling area (Ziya Circular Economy Park (ZCEP) in Tianjin, China) with intending to explore the impacts of residence spatial variation and dismantling manipulation mode. We collected 157 urine samples from three sites around ZCEP with different distances from the core dismantling site and urinary phthalate metabolites (mPAEs) concentrations were measured and were compared among these three sites. The exposure levels of PAEs exhibited spatial variation according to the distance from the core dismantling site, and urinary median ∑mPAEs concentrations (389 ng/mL) of the employees in ZCEP were significantly higher than those of residents in Ziya town (285 ng/mL) and the downtown of Jinghai district (207 ng/mL) (p < 0.05). Moreover, PAEs exposure levels were significantly affected by the manipulation modes in the e-waste recycling area and the urinary median ∑mPAEs concentrations in the employees of family workshops (401 ng/mL) were significantly higher than those in plants with centralized management (298 ng/mL). There were obvious differences on the urinary median mPAEs concentrations between subgroups based on age, BMI, and sex; however, no significant statistical associations were found between PAEs exposure levels and these socio-demographic indices (p > 0.05). Besides, there was no correlation between exposure levels of different PAEs and their physicochemical parameters like the logKow (p > 0.05).

A Teleoperation Interface for Loco-Manipulation Control of Mobile Collaborative Robotic Assistant

This letter presents a novel teleoperation interface that enables remote loco-manipulation control of a MObile Collaborative robotic Assistant (MOCA). MOCA is a new research platform developed at the Istituto Italiano di Tecnologia (IIT), which is composed of a lightweight manipulator arm, a Pisa/IIT SoftHand, and a mobile platform driven by four omni-directional wheels. A whole-body impedance controller is consequently developed to ensure accurate tracking of the impedance and position trajectories at MOCA end-effector by considering the causal interactions in such a dynamic system. The proposed teleoperation interface provides the user with two control modes: locomotion and manipulation. The locomotion mode receives inputs from a personalized human center-of-pressure model, which enables real-time navigation of the MOCA mobile base in the environment. The manipulation mode receives inputs from a tele-impedance interface, which tracks human arm endpoint stiffness and trajectory profiles in real time and replicates them using the MOCA's whole-body impedance controller. To evaluate the performance of the proposed teleoperation interface in the execution of remote tasks with dynamic uncertainties, a sequence of challenging actions, i.e., navigation, door opening, and wall drilling, has been considered in the experimental setup.

Compressive Sensing on Diverse STEM Scans: Real-time Feedback, Low-dose and Dynamic Range

Scanning Transmission Electron Microscopy (STEM) has become the main stay for materials characterization on atomic level, with applications ranging from visualization of localized and extended defects to mapping order parameter fields. In the last several years, attention was attracted by potential of STEM to explore beam induced chemical processes and especially manipulating atomic motion, enabling atom-by-atom fabrication. These applications, as well as traditional imaging of beam sensitive materials, necessitate increasing dynamic range of STEM between imaging and manipulation modes, and increasing absolute scanning/imaging speeds, that can be achieved by combining sparse sensing methods with non-rectangular scanning trajectories. Here we developed a general method for real-time reconstruction of sparsely sampled images from high-speed, non-invasive and diverse scanning pathways. This approach is demonstrated on both the synthetic data where ground truth is known and the experimental STEM data. This work lays the foundation for future tasks such as optimal design of dose efficient scanning strategies and real-time adaptive inference and control of e-beam induced atomic fabrication.

La comunicación en disputa: el rol de educadores y científicos

&lt;p&gt;El artículo propone una reflexión sobre la integración de las TIC a la educación como un espacio de posibilidad de formación para la ciudadanía. Dicha integración en los espacios educativos se concibe como una oportunidad para promover una resignificación del papel de las instituciones con el fin de generar los cambios necesarios en el paradigma actual de la educación. Los principios fundantes del nuevo paradigma son señalados a través del análisis de los desafíos para los educadores y científicos, quienes deberían asumir, más efectivamente, una postura de productores de culturas y conocimientos con fuerte dimensión comunicativa. Entre los retos, se analiza la presencia de lo digital, todavía no universalizado y, lo más grave, concentrado en poderosas corporaciones, lo que desemboca en severas restricciones para la democracia en los medios y en las redes. Asimismo, se destacan los nuevos modos de manipulación en las redes digitales, que condicionan los accesos y usos por medio de algoritmos y prácticas comunicativas en línea. En ese sentido, se apuesta por una articulación entre educación y comunicación, con miras a una resignificación de la universidad, con el objetivo de comprometerse con la formación de ciudadanos para la emancipación social. Esta propuesta interpela a los educadores y científicos a ser intelectuales públicos con una postura comunicativa y política a través de la acción hacker, en el sentido de explorar las brechas de la estructura hegemónica para construir redes que tratan de diseminar la información y producción de conocimiento colaborativo, abierto y comprometido con la transformación social.&lt;/p&gt;

Dip-a-Dee-Doo-Dah: Bacteriophage-Mediated Rescoring of a Harmoniously Orchestrated RNA Metabolism.

RNA turnover and processing in bacteria are governed by the structurally divergent but functionally convergent RNA degradosome, and the mechanisms have been researched extensively in Gram-positive and Gram-negative bacteria. An emerging research field focuses on how bacterial viruses hijack all aspects of the bacterial metabolism, including the host machinery of RNA metabolism. This review addresses research on phage-based influence on RNA turnover, which can act either indirectly or via dedicated effector molecules that target degradosome assemblies. The structural divergence of host RNA turnover mechanisms likely explains the limited number of phage proteins directly targeting these specialized, host-specific complexes. The unique and nonconserved structure of DIP, a phage-encoded inhibitor of the Pseudomonas degradosome, illustrates this hypothesis. However, the natural occurrence of phage-encoded mechanisms regulating RNA turnover indicates a clear evolutionary benefit for this mode of host manipulation. Further exploration of the viral dark matter of unknown phage proteins may reveal more structurally novel interference strategies that, in turn, could be exploited for biotechnological applications.

A Tet/Q Hybrid System for Robust and Versatile Control of Transgene Expression in C. elegans

SummaryBinary gene regulatory tools such as the Tetracycline (Tet)-controlled transcription system have revolutionized genetic research in multiple organisms, but their applications to the worm remain very limited. Here we report that the canonical Tet system is largely inactive in the worm but can be adapted for the worm by introducing multiple modifications, a crucial one being the use of the transcription activation domain from the fungal Q binary system. The resultant Tet/Q hybrid system proves more robust and flexible than either of its precursors, enabling elaborate modes of transgene manipulation previously hard to achieve in the worm, including inducible intersectional regulation and, in combination with the Q system, independent control of distinct transgenes within the same cells. Furthermore, we demonstrated, as an example of its applications, that the hybrid system can tightly and efficiently control Cre expression. This study establishes Tet/Q as a premier binary system for worm genetic research.

Compressed Sensing of Scanning Transmission Electron Microscopy (STEM) With Nonrectangular Scans.

Scanning transmission electron microscopy (STEM) has become the main stay for materials characterization on atomic level, with applications ranging from visualization of localized and extended defects to mapping order parameter fields. In recent years, attention has focused on the potential of STEM to explore beam induced chemical processes and especially manipulating atomic motion, enabling atom-by-atom fabrication. These applications, as well as traditional imaging of beam sensitive materials, necessitate increasing the dynamic range of STEM in imaging and manipulation modes, and increasing the absolute scanning speed which can be achieved by combining sparse sensing methods with nonrectangular scanning trajectories. Here we have developed a general method for real-time reconstruction of sparsely sampled images from high-speed, noninvasive and diverse scanning pathways, including spiral scan and Lissajous scan. This approach is demonstrated on both the synthetic data and experimental STEM data on the beam sensitive material graphene. This work opens the door for comprehensive investigation and optimal design of dose efficient scanning strategies and real-time adaptive inference and control of e-beam induced atomic fabrication.

The robot-assisted system YunSRobot for soft endoscopy: a trial of remote manipulation on simulation models

Objective: To evaluate the feasibility and safety of the robot-assisted system YunSRobot for remote manipulation endoscopy. Methods: When the master of YunSRobot was installed in the gastroenterology office in Chinese PLA General Hospital, the robot slave and upper gastrointestinal simulation model (Takahashi Lm103, Japan) were installed at the same time in the State Key Laboratory of Robotics, Shenyang Institute of Automation. Three physicians were trained to operate the master robotics and performed gastroscopy on the simulation model based on network cloud. Each physician performed 3 procedures of oesophagogastroduodenoscopy (EGD) by YunSRobot using traditional manual endoscopy, on-site operating mode, and remote manipulation mode, respectively. The operating time, lumenal anatomic exposure, man-machine interaction and other parameters were recorded. Results: The number of standard pictures obtained by traditional manual endoscopy group, on-site operating group and remote manipulation group were 39.9±0.3, 39.8±0.4, 39.9±0.3, respectively. The images of all five lesions could be obtained by each operation. The operating time in the duodenum of remote group was longer than that of on-site group, with average time (78.2±16.0)s vs. (68.9±15.8)s (P=0.021) respectively. As to the operating time on other parts or total time, all three groups were comparable. Although there was a mean delay of (572.1±48.5) ms in remote operation group, the operation was still smooth. However, compared with on-site group, the percentage of clear view time in the duodenum was significantly shortened in remote group: [(77.8±8.2)% vs. (83.9±6.4)%, P=0.024]. Statistically significant difference was detected in percentage of clear view time neither in other sites, nor was in the total operating time between two groups. The operating time in each part of remote group was obviously longer than that of manual group as followings, pharyngeal (27.3±4.2) s vs. (9.2±1.3)s (P<0.001), esophageal (29.7±6.4)s vs. (19.3±1.6)s (P=0.004), stomach (56.7±17.0)s vs. (40.3±7.0)s (P=0.003), pylorus (20.2±5.5)s vs. (9.3±1.3)s (P<0.001), duodenum (78.2±16.0)s vs. (29.3±5.6)s (P<0.001). Thus the total operating time was also longer in remote group as (559.0±87.2)s vs. (253.1±16.6)s (P<0.001). The respective time in pharynx, esophagus, stomach, pylorus, duodenum, or the overall time was all longer in remote group than that in manual group. Conclusions: The soft endoscopy robot YunSRobot has satisfactory safety and stability. Remote upper gastrointestinal endoscopy can be completed based on common network and an endoscope simulation model with smooth operation. The inspection time by YunSRobot robot per part and the overall time are longer than those of manual operation on site, still, remote operating time meets the standard of upper gastrointestinal endoscopy.

Pan-senescence transcriptome analysis identified RRAD as a marker and negative regulator of cellular senescence

Cellular senescence, an irreversible proliferative arrest, functions in tissue remodeling during development and is implicated in multiple aging-associated diseases. While senescent cells often manifest an array of senescence-associated phenotypes, such as cell cycle arrest, altered heterochromatin architecture, reprogrammed metabolism and senescence-associated secretory phenotype (SASP), the identification of senescence cells has been hindered by lack of specific and universal biomarkers. To systematically identify universal biomarkers of cellular senescence, we integrated multiple transcriptome data sets of senescent cells obtained through different in vitro manipulation modes as well as age-related gene expression data of human tissues. Our analysis showed that RRAD (Ras-related associated with diabetes) expression is up-regulated in all the manipulation modes and increases with age in human skin and adipose tissues. The elevated RRAD expression was then confirmed in senescent human fibroblasts that were induced by Ras, H2O2, ionizing radiation, hydroxyurea, etoposide and replicative passage, respectively. Further functional study suggests that RRAD up-regulation acts as a negative feedback mechanism to counter cellular senescence by reducing the level of reactive oxygen species. Finally, we found both p53 and NF-κB bind to RRAD genomic regions and modulate RRAD transcription. This study established RRAD to be a biomarker as well as a novel negative regulator of cellular senescence.

Force and motion control of a tendon-driven hand exoskeleton actuated by shape memory alloys

Purpose Many people suffer from injuries related to their hand. This research aims to focus on the improvement of the previously developed smart glove by using position and force control algorithms. The new smart glove may be used for both physiotherapy and assistance. Design/methodology/approach The proposed robot uses shape memory alloy (SMA) actuators coupled to an under-actuated tendon-driven mechanism. The proposed device, which is presented as a wearable glove attached to an actuation module, is capable of exerting extremely high forces to grasp objects in various hand configurations. The device’s performance is studied in physiotherapy and object manipulation tasks. In the physiotherapy mode, hand motion frequency is controlled, whereas the grasping force is controlled in the object manipulation mode. To simulate the proposed system behavior, the kinematic and dynamic equations of the proposed system have been derived. Findings The achieved results verify that the system is suitable to be used as part of a rehabilitation device in which it can flex and extend fingers with accurate trajectories and grasp objects efficiently. Specifically, it will be shown that using six SMA wires with the diameter of 0.25 mm, the proposed robot can provide 45 N gripping force for the patients. Originality/value The proposed robot uses SMA actuators and an under-actuated tendon-driven mechanism. The resulted robotic system, which is presented as a wearable glove attached to an actuation module, is capable of exerting extremely high force levels to grasp objects in various hand configurations. It is shown that the motion and exerted force of the robot may be controlled effectively in practice.

Surface manipulation of a curved polycyclic aromatic hydrocarbon-based nano-vehicle molecule equipped with triptycene wheels

With a central curved chassis, a four-wheeled molecule-vehicle was deposited on a Au(111) surface and imaged at low temperature using a scanning tunneling microscope. The curved conformation of the chassis and the consequent moderate interactions of the four wheels with the surface were observed. The dI/dV constant current maps of the tunneling electronic resonances close to the Au(111) Fermi level were recorded to identify the potential energy entry port on the molecular skeleton to trigger and control the driving of the molecule. A lateral pushing mode of molecular manipulation and the consequent recording of the manipulation signals confirm how the wheels can step-by-step rotate while passing over the Au(111) surface native herringbone reconstructions. Switching a phenyl holding a wheel to the chassis was not observed for triggering a lateral molecular motion inelastically and without any mechanic push by the tip apex. This points out the necessity to encode the sequence of the required wheels action on the profile of the potential energy surface of the excited states to be able to drive a molecule-vehicle.

Variable-Friction Finger Surfaces to Enable Within-Hand Manipulation via Gripping and Sliding

The human hand is able to achieve an unparalleled diversity of manipulation actions. One contributor to this capability is the structure of the human finger pad, where soft internal tissue is surrounded by a layer of more rigid skin. This permits conforming of the finger pad around object contours for firm grasping, while also permitting low-friction sliding over object surfaces with a light touch. These varying modes of manipulation contribute to the common ability for in-hand-manipulation, where an object (such as a car key) may repositioned relative to the palm. In this letter, we present a simple mechanical analogy to the human finger pad, via a robotic finger with both high- and low-friction surfaces. The low-friction surface is suspended on elastic elements and recesses into a cavity when a sufficient normal force is applied (∼1.2 to 2.5 N depending on contact location), exposing the high-friction surface. We implement one “variable friction” finger and one “constant friction” finger on a 2-DOF gripper with a simple torque controller. With this setup, we demonstrate how within-hand rolling and sliding of an object may be achieved without the need for tactile sensing, high-dexterity, dynamic finger/object modeling, or complex control methods. The addition of an actuator to the finger design allows controlled switching between variable-friction and constant-friction modes, enabling precise object translation and reorientation within a grasp, via simple motion sequences. The rolling and sliding behaviors are characterized with experimentally verified geometric models.

A Modular Implant System for Multimodal Recording and Manipulation of the Primate Brain.

Neural circuitry can be investigated and manipulated using a variety of techniques, including electrical and optical recording and stimulation. At present, most neural interfaces are designed to accommodate a single mode of neural recording and/or manipulation, which limits the amount of data that can be extracted from a single population of neurons. To overcome these technical limitations, we developed a chronic, multi-scale, multi-modal chamber-based neural implant for use in non-human primates that accommodates electrophysiological recording and stimulation, optical manipulation, and wide-field imaging. We present key design features of the system and mechanical validation. We also present sample data from two non-human primate subjects to validate the efficacy of the design in vivo.