Miracle-dz/UniFAR-FTUs huggingface dataset:
How Do We Repair Vein Graft Stenoses?

Lower extremity vein grafts are associated with excellent primary and assisted primary long-term patency rates. ' However, secondary patency rates are poor regardless of the method used to remove thrombus and restore patency of the graft.2 Graft surveillance of lower extremity vein bypasses has been shown to be worthwhile for identifying a focal stenosis and repairing the lesion before graft thrombosis occurs.3 We have documented that lesions causing failing vein grafts can be repaired based on duplex ultrasonography alone without confirmatory arteriography performed in the radiology suite in about two thirds of cases.4 The ideal technique to repair a focal stenosis in a failing vein graft remains controversial. Various methods include (1) balloon angioplasty, (2) patch angioplasty, (3) replacement of the stenotic segment with an interposition vein graft, or (4) placement of a new "jump" graft around the stenotic segment. A "short" stenosis, (< 2 cm long) may be amenable to treatment with one of the first three options, while a "long" stenosis (> 2 cm long) is best treated with an interposition or jump graft. As a general rule, prosthetic patches or grafts are avoided whenever adequate vein is available to minimize development of intimal hyperplasia. Results of balloon angioplasty of focal stenoses in failing vein grafts have been mixed. Although some authors have reported good
Design of Ca2+‐independent Staphylococcus aureus sortase A mutants

The catalytic activity of Staphylococcus aureus sortase A (SaSrtA) is dependent on Ca2+, because binding of Ca2+ to Glu residues distal to the active site stabilizes the substrate binding site. To obtain Ca2+‐independent SaSrtA, we substituted two Glu residues in the Ca2+‐binding pocket (Glu105 and Glu108). Although single mutations decreased SaSrtA activity, mutations of both Glu105 and Glu108 resulted in Ca2+‐independent activity. Kinetic analysis suggested that the double mutations affect the substrate binding site, without affecting substrate specificity. This approach will allow us to develop SaSrtA variants suitable for various applications, including in vivo site‐specific protein modification and labeling. Biotechnol. Bioeng. 2012; 109: 2955–2961. © 2012 Wiley Periodicals, Inc.
Predictive models for the accumulation of a fluorescent marker protein in tobacco leaves according to the promoter/5′UTR combination

The promoter and 5′‐untranslated region (5′UTR) play a key role in determining the efficiency of recombinant protein expression in plants. Comparative experiments are used to identify suitable elements but these are usually tested in transgenic plants or in transformed protoplasts/suspension cells, so their relevance in whole‐plant transient expression systems is unclear given the greater heterogeneity in expression levels among different leaves. Furthermore, little is known about the impact of promoter/5′UTR interactions on protein accumulation. We therefore established a predictive model using a design of experiments (DoE) approach to compare the strong double‐enhanced Cauliflower mosaic virus 35S promoter (CaMV 35SS) and the weaker Agrobacterium tumefaciens Ti‐plasmid nos promoter in whole tobacco plants transiently expressing the fluorescent marker protein DsRed. The promoters were combined with one of three 5′UTRs (one of which was tested with and without an additional protein targeting motif) and the accumulation of DsRed was measured following different post‐agroinfiltration incubation periods in all leaves and at different leaf positions. The model predictions were quantitative, allowing the rapid identification of promoter/5′UTR combinations stimulating the highest and quickest accumulation of the marker protein in all leaves. The model also suggested that increasing the incubation time from 5 to 8 days would reduce batch‐to‐batch variability in protein yields. We used the model to identify promoter/5′UTR pairs that resulted in the least spatiotemporal variation in expression levels. These ideal pairs are suitable for the simultaneous, balanced production of several proteins in whole plants by transient expression. Biotechnol. Bioeng. 2013; 110: 471–482. © 2012 Wiley Periodicals, Inc.
Mobility assistance system for an electric wheelchair using annotated maps

An electric wheelchair is very useful for physically challenged or elderly people. A electric wheelchair can be equipped with a computer and sensors such as cameras and LIDARs to make it a robotic wheelchair. This opens the possibility to reduce the burden and increase the comfort of the users with use of robotics technology. In this paper, we begin with a dynamic shared control and propose to use a map with annotations to increase the user’s comfort while keeping safety. We provide a system with localization, which can relate the current position of the wheelchair to the annotations. Both quantitative evaluation and subjective survey demonstrate the effectiveness of the proposed method. Graphical Abstract
Autonomous design of functional structures

We present an algorithm that enables a humanoid robot to reason about its environment and use the available objects to build bridges, stairs and lever-fulcrum systems. Facing a challenge that is otherwise intractable, such as climbing a height or moving a heavy object, the proposed planner reasons about the physical limitations of the robot to design functional structures. Inducing constraints on the space of possible designs within a classical planning framework, the algorithm outputs feasible structures that can be used towards accomplishing goals. We present results in dynamic simulation with Golem Hubo, walking on a bridge to cross a hazardous area, and in real-world with Golem Krang, overturning 100 kg loads and pushing 240 kg obstacles. Graphical Abstract
Building object models through interactive perception and foveated vision

Autonomous robots that operate in unstructured environments must be able to seamlessly expand their knowledge base. To detect and manipulate previously unknown objects, a robot should be able to acquire new object knowledge even when no prior information about the objects or the environment is available. Additional information that is needed to identify new objects can come through motion cues induced by interactive manipulation. In the proposed system, changes in the scene are caused by a teacher manipulating the object to be learned. We propose to improve visual object learning and recognition by exploiting the advantages of foveated vision. The proposed approach first creates object hypotheses in peripheral stereo cameras. By directing its attention towards the identified object area in the foveal views, the robot can conduct a more thorough investigation of a smaller area of the scene, which is seen in higher resolution. We compare two methods for validating the hypotheses in the foveal views and experimentally show the advantages of foveated vision compared to stereo vision with a fixed field of view. Graphical Abstract
A decoupled sliding mode control for a continuum arm

The paper treats the control problem of a class of robots constituted by a chain of continuum segments. The technological model basis is a central, long and thin, highly flexible and elastic backbone. The segment control system is a decoupled one. The main parameters of the arm control are determined by the curvature and curvature gradient. The dynamic model is inferred. The primary benefit of the proposed method is that the dynamic equations are represented by a set of ODE’s in time instead of PDE’s in time and space, and the new curvature gradient lumped parameter model is used. A sliding mode control system is used in order to achieve the desired shape of the arm. The stability of the closed-loop control system is proven. Numerical simulations and an experimental platform are also provided to verify the effectiveness of the presented approach.
Reinforcement learning-based shared control for walking-aid robot and its experimental verification

A walking-aid robot is an assistive device for enabling safe, stable and efficient locomotion in elderly or disabled individuals. In this paper, we propose a reinforcement learning-based shared control (RLSC) algorithm for intelligent walking-aid robot to address existing control problems in cooperative walking-aid robot system. Firstly, the intelligent walking-aid robot and the human walking intention estimation algorithm are introduced. Due to the limited physical and cognitive capabilities of elderly and disabled people, robot control input assistance is provided to maintain tactile comfort and a sense of stability. Then, considering the robot’s ability to autonomously adapt to different user operation habits and motor abilities, the RLSC algorithm is proposed. By dynamically adjusting user control weight according to different user control efficiencies and walking environments, the robot can improve the user’s degree of comfort when using the device and automatically adapting to user’s behaviour. Finally, the effectiveness of our algorithm is verified by experiments in a specified environment. Graphical Abstract
Calcium and Phosphorus in Health and Disease

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Map segmentation for simultaneous localization and mapping in ruins

The distribution of environmental features of the internal ruins which are formed by a randomly seismic disaster is unpredictable. Therefore, the existing methods of map segmentation, which need to preset parameters, cannot be directly used. Considering the lack of prior knowledge, a map segmentation method based on the spectral clustering is proposed in the framework of hierarchical simultaneous localization and mapping (SLAM) algorithm. The method solves the problem of incremental complexity of SLAM algorithm using the division of environment. In accordance with the similarity of observed environment, a weighted graph is established. The nodes in the graph are generated by measuring the expected information gain and position redundancy. Then, the graph is partitioned into subjective results of map segment based on the criterion of minimum normalized cut. On the basis of the inherent sparse of SLAM, the proposed algorithm not only reduces the cost of calculation, but also minimizes the loss of information in order to ensure the global consistency. Finally, the feasibility and effectiveness of the algorithm are verified by simulation and experiment. Graphical Abstract
Symmetry position/force hybrid control for cooperative object transportation using multiple humanoid robots

A symmetry position/force hybrid control framework for cooperative object transportation tasks with multiple humanoid robots is proposed in this paper. In a leader-follower type cooperation, follower robots plan their biped gaits based on the forces generated at their hands after a leader robot moves. Therefore, if the leader robot moves fast (rapidly pulls or pushes the carried object), some of the follower humanoid robots may lose their balance and fall down. The symmetry type cooperation discussed in this paper solves this problem because it enables all humanoid robots to move synchronously. The proposed framework is verified by dynamic simulations. Graphical Abstract
Prognostic efficacy of cardiac biomarkers for mortality in dialysis patients

Background: The high prevalence of cardiovascular mortality in the end‐stage renal disease population is well established. The aim of this current study was to document the relative prognostic significance of established cardiac biomarkers troponin T (TnT), troponin I (TnI), B‐type natriuretic peptide (BNP) and N‐terminal pro‐BNP (NT‐pro‐BNP) in this population.
Oxygen control of intracellular distribution of mitochondria in muscle fibers

Mitochondrial density in skeletal muscle fibers is governed by the demand for aerobic ATP production, but the heterogeneous distribution of these mitochondria appears to be governed by constraints associated with oxygen diffusion. We propose that each muscle fiber has an optimal mitochondrial distribution at which it attains a near maximal rate of ATP consumption (RATPase) while mitochondria are exposed to a minimal oxygen concentration, thus minimizing reactive oxygen species (ROS) production. We developed a coupled reaction–diffusion/cellular automata (CA) mathematical model of mitochondrial function and considered four fiber types in mouse extensor digitorum longus (EDL) and soleus (SOL) muscle. The developed mathematical model uses a reaction–diffusion analysis of metabolites including oxygen, ATP, ADP, phosphate, and phosphocreatine (PCr) involved in energy metabolism and mitochondrial function. A CA approach governing mitochondrial life cycles in response to the metabolic state of the fiber was superimposed and coupled to the reaction–diffusion approach. The model results show the sensitivity of important model outputs such as the RATPase, effectiveness factor (η) and average oxygen concentration available at each mitochondrion to local oxygen concentration in the fibers through variation in the CA model parameter θdet, which defines the sensitivity of mitochondrial death to the oxygen concentration. The predicted optimal mitochondrial distributions matched previous experimental findings. Deviations from this optimal distribution corresponding to higher CA model parameter values (a more uniform mitochondrial distribution) lead to lower aerobic rates. In contrast, distributions corresponding to lower CA model parameter values (a more asymmetric distribution) lead to an increased exposure of mitochondria to oxygen, usually without substantial increases in aerobic rates, which would presumably result in increased ROS production and thus increased risks of cytotoxicity. Biotechnol. Bioeng. 2013; 110:2513–2524. © 2013 Wiley Periodicals, Inc.
Development of a stable localized visual inspection system for underwater structures

Graphical Abstract To avert potential crisis from Japan’s aging infrastructure and declining birth rate, the Japanese Government is planning to introduce robotic technology for the inspection of social infrastructure (such as pipes, dams, and bridges). Recording underwater positions is a difficult task for human divers who undertake conventional dam inspections. This study presents the Anchor Diver 5.2 system for efficient and effectual dam inspection. Anchor Diver 5.2 is based on an extended-tether-maneuvered remotely operated vehicle (ROV) equipped with cameras. The ROV is lowered into water by a hoist system from a boat and implements a visual survey of the concrete underwater structure. To improve the visibility of the ROV in murky and cloudy water, a novel concept named Water Loupe is proposed. In addition, a simple boat-fixing method is proposed to provide a stable base on the water surface, and the underwater position of the ROV, which cannot be accessed by global positioning systems, is recorded using a feasible localization method. Finally, the developed system was evaluated in field experiments conducted in the Amagase Dam, Japan, and its merits and problems are discussed.
High‐throughput screening for transglutaminase activities using recombinant fluorescent proteins

Since detailed evaluation of specific transglutaminases (TGs) from various species requires identification of their substrate specificities, rapid substrate screening method by measurement of their relative activities is in great demand. Here, a novel evaluation method of TG activity was developed using two recombinant fluorescent proteins (FPs), that is, eYFP and DsRed, tagged with TG substrate peptides. By cross‐linking the two FPs based on the tagged target peptide sequences at their C‐terminus, the expression of co‐transformed TG allows quenching of the yellow fluorescence intensities. It was shown that the degree of in vivo fluorescent quenching by the TG activity agrees well with its in vitro reaction data, suggesting that this system can be used to identify relative substrate specificity of TGs for target peptide sequences. Using this method, the lysine substrates of TGs from Bacillus species (BTG) were evaluated, and the newly selected pentapeptide, KTKTN showed almost the same reactivity with the well‐known hexa‐lysine (K6) substrate for BTG reaction. Biotechnol. Bioeng. 2013;110: 2865–2873. © 2013 Wiley Periodicals, Inc.
Imaging Hepatocellular Carcinoma

Useful features in the imaging diagnosis of hepatocellular carcinoma include the identification of hypervascularity during the hepatic arterial phase, relative hypo-enhancement during the portal phase, and other features including a mosaic appearance, and portal venous enhancement of the pseudocapsule and internal septa. These characteristics correlate with gross pathology and histology, and can be assessed by the various imaging modalities. Magnetic resonance imaging is the optimal modality for detection and characterization of hepatocellular carcinoma and is the best modality for assessment of response after transarterial chemoembolization. Ultrasound contrast shows promise in increasing the utility of ultrasound for diagnosis and assessment of response. It is also invaluable in directing local ablative therapy. Multidetector technology is also improving the ability of CT to detect and characterize hepatocellular carcinoma. Overlap in imaging patterns with arterioportal shunts and dysplastic nodules still pose difficulties in diagnosis with all modalities, however.
Unfolding of a rectangular cloth from unarranged starting shapes by a Dual-Armed robot with a mechanism for managing recognition error and uncertainty

Graphical Abstract We propose a method for unfolding a rectangular cloth placed on a table in an arbitrary unarranged shape, using a dual arm robot. There are many situations where the manipulation of fabric products by dual arm robots is slow due to operation complexity. Also, observation of fabric products in unarranged shapes can be fraught with uncertainty, posing further difficulties for robotic manipulation. In this article, we address these problems for our specific task, implementing a ‘pinch and slide motion’ to address the former issue, and an operation selection mechanism implemented as a partially observable Markov decision process to address the latter. We used this approach to let a robot unfold a rectangular cloth, thereby experimentally verifying the effectiveness of our approach.
Alginate encapsulation parameters influence the differentiation of microencapsulated embryonic stem cell aggregates

Pluripotent embryonic stem cells (ESCs) have tremendous potential as tools for regenerative medicine and drug discovery, yet the lack of processes to manufacture viable and homogenous cell populations of sufficient numbers limits the clinical translation of current and future cell therapies. Microencapsulation of ESCs within microbeads can shield cells from hydrodynamic shear forces found in bioreactor environments while allowing for sufficient diffusion of nutrients and oxygen through the encapsulation material. Despite initial studies examining alginate microbeads as a platform for stem cell expansion and directed differentiation, the impact of alginate encapsulation parameters on stem cell phenotype has not been thoroughly investigated. Therefore, the objective of this study was to systematically examine the effects of varying alginate compositions on microencapsulated ESC expansion and phenotype. Pre‐formed aggregates of murine ESCs were encapsulated in alginate microbeads composed of a high or low ratio of guluronic to mannuronic acid residues (High G and High M, respectively), with and without a poly‐L‐lysine (PLL) coating, thereby providing four distinct alginate bead compositions for analysis. Encapsulation in all alginate compositions was found to delay differentiation, with encapsulation within High G alginate yielding the least differentiated cell population. The addition of a PLL coating to the High G alginate prevented cell escape from beads for up to 14 days. Furthermore, encapsulation within High M alginate promoted differentiation toward a primitive endoderm phenotype. Taken together, the findings of this study suggest that distinct ESC expansion capacities and differentiation trajectories emerge depending on the alginate composition employed, indicating that encapsulation material physical properties can be used to control stem cell fate. Biotechnol. Bioeng. 2014;111: 618–631. © 2013 Wiley Periodicals, Inc.
Combinatorial engineering of mevalonate pathway for improved amorpha‐4,11‐diene production in budding yeast

Combinatorial genome integration of mevalonate pathway genes was performed with the aim of optimizing the metabolic flux for improved production of terpenoids in budding yeast. In the present study, we developed a novel δ‐integration platform to achieve multiple genome integrations through modulating the concentration of antibiotics. By exploiting carotenoid biosynthesis as screening module, we successfully created a library of yeast colonies appeared with various intensities of orange color. As proof‐of‐concept that carotenoid overproducers could serve to boost the titer of other terpenoids, we further tested engineered strains for the production of amorpha‐4,11‐diene, an important precursor for antimalarial drug. However, we experienced some limitations of the carotenoid‐based screening approach as it was only effective in detecting a small range of pathway activity improvement and further increasing mevalonate pathway activity led to a decreased orange color. By far, we were only able to obtain one mutant strain yielded more than 13‐fold amorpha‐4,11‐diene over parental strains, which was approximately 64 mg/L of caryophyllene equivalents. Further qPCR studies confirmed that erg10, erg13, thmg1 and erg12 involved in mevalonate pathway were overexpressed in this mutant strain. We envision the current δ‐integration platform would form the basis of a generalized technique for multiple gene integrations in yeast—a method that would be of significant interest to the metabolic engineering community. Biotechnol. Bioeng. 2014;111: 608–617. © 2013 Wiley Periodicals, Inc.
Computational fluid model incorporating liver metabolic activities in perfusion bioreactor

The importance of in vitro hepatotoxicity testing during early stages of drug development in the pharmaceutical industry demands effective bioreactor models with optimized conditions. While perfusion bioreactors have been proven to enhance mass transfer and liver specific functions over a long period of culture, the flow‐induced shear stress has less desirable effects on the hepatocytes liver‐specific functions. In this paper, a two‐dimensional human liver hepatocellular carcinoma (HepG2) cell culture flow model, under a specified flow rate of 0.03 mL/min, was investigated. Besides computing the distribution of shear stresses acting on the surface of the cell culture, our numerical model also investigated the cell culture metabolic functions such as the oxygen consumption, glucose consumption, glutamine consumption, and ammonia production to provide a fuller analysis of the interaction among the various metabolites within the cell culture. The computed albumin production of our 2D flow model was verified by the experimental HepG2 culture results obtained over 3 days of culture. The results showed good agreement between our experimental data and numerical predictions with corresponding cumulative albumin production of 2.9 × 10−5 and 3.0 × 10−5 mol/m3, respectively. The results are of importance in making rational design choices for development of future bioreactors with more complex geometries. Biotechnol. Biotechnol. Bioeng. 2014;111: 885–895. © 2013 Wiley Periodicals, Inc.