Simulating control of the ankle joint

Thesis (S.B.)--Massachusetts Institute of Technology, Dept. of Mechanical Engineering, 2012.Cataloged from PDF version of thesis.Includes bibliographical references (p. 33).Computing environments such as Matlab that are conventionally used to simulate dynamics of rigid body systems can be used to model interactions between the system and its environment. However, creating these simulations using Matlab or an equivalent is difficult and there is a need for a more convenient simulation environment for such problems. Two alternative programs, PyODE and OpenSim, were explored to evaluate their ability to fill this need. Models and simulations of the human ankle were created in PyODE. This program is useful for creating simple models where the programmer desires a high level of control over model parameters. Simulations of the ankle kicking a ball and taking a step were created to examine the effect of joint stiffness on these motions and help determine the usefulness of ODE as a simulation tool. Pre-existing models were analyzed in OpenSim. OpenSim is specifically designed for analyzing biomechanical systems. It allows for more complex models to be created but the user has more limited control over the model parameters.by Rebecca Vasquez.S.B

MANGANESE-REDUCING BACTERIAL COMMUNITIES FROM A HYPERSALINE ESTUARY IN SOUTH TEXAS UNDER CONDITIONS OF CHANGING SALINITY

Manganese reducing bacteria were quantified and enriched from sediments at two sites (ABC and LMT050) in the Laguna Madre of South Texas. Bacteria were tested for Mn(IV) reduction under different salinities. Denaturing gradient gel electrophoresis (DGGE) was used to profile bacterial communities from Mn(IV) saline enrichments. Results showed that the density of manganese reducing bacteria at ABC was 30X greater than LMT050. The ABC bacteria were able to reduce Mn(IV) at similar rates at different salinities; however, at LMT050, Mn(IV) reduction rates decreased at higher salinities. Three population genotypes were observed by DGGE. All were present and similarly abundant in LMT050 cultures at all salinities. In site ABC, one population was below detection at salt concentrations \u3c 60.0 ppt but observed at higher salt concentrations. We conclude that site ABC consists of a large manganese-reducing community that alters in structure when salinity changes, whereas site LMT050 contains a smaller but somewhat more adapted community

The Variable Vector Countermeasure Suit (V2Suit) for space habitation and exploration

The “Variable Vector Countermeasure Suit (V2Suit) for Space Habitation and Exploration” is a novel system concept that provides a platform for integrating sensors and actuators with daily astronaut intravehicular activities to improve health and performance, while reducing the mass and volume of the physiologic adaptation countermeasure systems, as well as the required exercise time during long-duration space exploration missions. The V2Suit system leverages wearable kinematic monitoring technology and uses inertial measurement units (IMUs) and control moment gyroscopes (CMGs) within miniaturized modules placed on body segments to provide a “viscous resistance” during movements against a specified direction of “down”—initially as a countermeasure to the sensorimotor adaptation performance decrements that manifest themselves while living and working in microgravity and during gravitational transitions during long-duration spaceflight, including post-flight recovery and rehabilitation. Several aspects of the V2Suit system concept were explored and simulated prior to developing a brassboard prototype for technology demonstration. This included a system architecture for identifying the key components and their interconnects, initial identification of key human-system integration challenges, development of a simulation architecture for CMG selection and parameter sizing, and the detailed mechanical design and fabrication of a module. The brassboard prototype demonstrates closed-loop control from “down” initialization through CMG actuation, and provides a research platform for human performance evaluations to mitigate sensorimotor adaptation, as well as a tool for determining the performance requirements when used as a musculoskeletal deconditioning countermeasure. This type of countermeasure system also has Earth benefits, particularly in gait or movement stabilization and rehabilitation.United States. National Aeronautics and Space Administration (Innovative Advanced Concepts Grant NNX11AR25G)United States. National Aeronautics and Space Administration (Innovative Advanced Concepts Grant NNX12AQ58G

Biochemical and functional characterization of glycosaminoglycans released from degranulating rat peritoneal mast cells: insights into the physiological role of endogenous heparin

We acknowledge the support of the Wellcome Trust for a grant to RL, CPP and NVR to support some of this work.The properties of commercially prepared heparin as an anticoagulant and antithrombotic agent in medicine are better understood than is the physiological role of heparin in its native form, where it is uniquely found in the secretory granules of mast cells. In the present study we have isolated and characterised the glycosaminoglycans (GAGs) released from degranulating rat peritoneal mast cells. Analysis of the GAGs by NMR spectroscopy showed the presence of both heparin and the galactosaminoglycan dermatan sulphate; heparinase digestion profiles and measurements of anticoagulant activity were consistent with this finding. The rat peritoneal mast cell GAGs significantly inhibited accumulation of leukocytes in the rat peritoneal cavity in response to IL-1β (p < 0.05, n = 6/group), and inhibited adhesion and diapedesis of leukocytes in the inflamed rat cremasteric microcirculation in response to LPS (p < 0.001, n = 4/group). FTIR spectra of human umbilical vein endothelial cells (HUVECs) were altered by treatment of the cells with heparin degrading enzymes, and restored by the addition of exogenous heparin. In conclusion, we have shown that rat peritoneal mast cells contain a mixture of GAGs that possess anticoagulant and anti-inflammatory properties.PostprintPeer reviewe

Variable Vector Countermeasure Suit (V2Suit) for Space Habitation and Exploration

The Variable Vector Countermeasure Suit (V2Suit) for Space Habitation and Exploration is a visionary system concept that will revolutionize space missions by providing a platform for integrating sensors and actuators with daily astronaut intravehicular activities to improve human health and performance. The V2Suit uses control moment gyroscopes (CMGs) within a miniaturized module placed on body segments to provide a viscous resistance during movements _ a countermeasure to the sensorimotor and musculoskeletal adaptation performance decrements that manifest themselves while living and working in microgravity and during gravitational transitions during long-duration spaceflight, including post-flight recovery and rehabilitation. Through an integrated design, system initialization, and control systems approach the V2Suit is capable of generating this viscous resistance along an arbitrarily specified direction of down. When movements are made, for example, parallel to that down direction a resistance is applied, and when the movement is perpendicular to that direction no resistance is applied. The V2Suit proposes to be a countermeasure to this spaceflight-related adaptation and de-conditioning and the unique sensorimotor characteristics associated with living and working in 0-G, which are critical for future long-duration space missions. This NIAC Phase II project leveraged the study results from Phase I and focused on detailing several aspects of the V2Suit concept, including a wearable CMG architecture, control steering laws, human-system integration evaluations, developing a brassboard prototype unit as a proof-of-concept, as well as evaluating the concept in the context of future space exploration missions. A human mission to Mars, such as that outlined in the Mars Design Reference Architecture 5.0, provides a framework for determining the concept of operations and requirements for the V2Suit system. Mars DRA 5.0 includes approximately 180 day 0-G transits to- and from- Mars, as well as a 500 day stay on the surface (~3/8-G) (Figure 3). Accordingly, there are four gravitational transitions associated with this mission: 1-G to 0-G (Earth launch), 0-G to 3/8-G (Mars landing), 3/8-G to 0-G (Mars launch), and 0-G to 1-G (Earth landing). This reference mission provided the basis for developing high-level operational requirements to guide the subsequent study and design of the key V2Suit components

IgG and IgM Autoantibody Differences in Discoid and Systemic Lupus Patients

Systemic lupus erythematosus (SLE) patients with discoid lupus erythematosus (DLE) were reported to have milder disease. To test this observation, we used sandwich arrays containing 98 autoantigens to compare autoantibody profiles of SLE subjects without DLE (DLE-SLE+) (N=9), SLE subjects with DLE (DLE+SLE+) (N=10), DLE subjects without SLE (DLE+SLE-) (N=11), and healthy controls (N=11). We validated differentially expressed autoantibodies using immunoassays in DLE-SLE+ (N=18), DLE+SLE+ (N=17), DLE+SLE- (N=23), and healthy subjects (N=22). Arrays showed 15 IgG autoantibodies (10 against nuclear antigens) and 4 IgM autoantibodies that were differentially expressed (q-value<0.05). DLE-SLE+ subjects had higher IgG autoantibodies against double-stranded DNA (dsDNA), single-stranded DNA (ssDNA), double-stranded RNA (dsRNA), histone H2A and H2B, and SS-A (52kDa) compared with all other groups including DLE+SLE+ subjects (P<0.05). Immunoassays measuring anti-dsDNA, -ssDNA, and -SS-A (52kDa) IgG autoantibodies showed similar trends (P<0.05). Healthy and DLE+SLE- subjects expressed higher IgM autoantibodies against alpha beta crystallin, lipopolysaccharide, heat-shock cognate 70, and desmoglein-3 compared with DLE+SLE+ and DLE-SLE+ subjects. IgG:IgM ratios of autoantibodies against nuclear antigens progressively rose from healthy to DLE-SLE+ subjects. In conclusion, lower IgG autoantibodies against nuclear antigens in DLE+SLE+ versus DLE-SLE+ subjects suggest that DLE indicates lower disease severity. Higher IgM autoantibodies against selected antigens in healthy and DLE+SLE- subjects may be nonpathogenic

A protocol for custom CRISPR Cas9 donor vector construction to truncate genes in mammalian cells using pcDNA3 backbone

Background Clustered regularly interspaced short palindromic repeat (CRISPR) RNA-guided adaptive immune systems are found in prokaryotes to defend cells from foreign DNA. CRISPR Cas9 systems have been modified and employed as genome editing tools in wide ranging organisms. Here, we provide a detailed protocol to truncate genes in mammalian cells using CRISPR Cas9 editing. We describe custom donor vector construction using Gibson assembly with the commonly utilized pcDNA3 vector as the backbone. Results We describe a step-by-step method to truncate genes of interest in mammalian cell lines using custom-made donor vectors. Our method employs 2 guide RNAs, mutant Cas9D10A nickase (Cas9 = CRISPR associated sequence 9), and a custom-made donor vector for homologous recombination to precisely truncate a gene of interest with a selectable neomycin resistance cassette (NPTII: Neomycin Phosphotransferase II). We provide a detailed protocol on how to design and construct a custom donor vector using Gibson assembly (and the commonly utilized pcDNA3 vector as the backbone) allowing researchers to obtain specific gene modifications of interest (gene truncation, gene deletion, epitope tagging or knock-in mutation). Selection of mutants in mammalian cell lines with G418 (Geneticin) combined with several screening methods: western blot analysis, polymerase chain reaction, and Sanger sequencing resulted in streamlined mutant isolation. Proof of principle experiments were done in several mammalian cell lines. Conclusions Here we describe a detailed protocol to employ CRISPR Cas9 genome editing to truncate genes of interest using the commonly employed expression vector pcDNA3 as the backbone for the donor vector. Providing a detailed protocol for custom donor vector design and construction will enable researchers to develop unique genome editing tools. To date, detailed protocols for CRISPR Cas9 custom donor vector construction are limited (Lee et al. in Sci Rep 5:8572, 2015; Ma et al. in Sci Rep 4:4489, 2014). Custom donor vectors are commercially available, but can be expensive. Our goal is to share this protocol to aid researchers in performing genetic investigations that require custom donor vectors for specialized applications (specific gene truncations, knock-in mutations, and epitope tagging applications)

Paraneoplastic thrombocytosis in ovarian cancer

&lt;p&gt;Background: The mechanisms of paraneoplastic thrombocytosis in ovarian cancer and the role that platelets play in abetting cancer growth are unclear.&lt;/p&gt; &lt;p&gt;Methods: We analyzed clinical data on 619 patients with epithelial ovarian cancer to test associations between platelet counts and disease outcome. Human samples and mouse models of epithelial ovarian cancer were used to explore the underlying mechanisms of paraneoplastic thrombocytosis. The effects of platelets on tumor growth and angiogenesis were ascertained.&lt;/p&gt; &lt;p&gt;Results: Thrombocytosis was significantly associated with advanced disease and shortened survival. Plasma levels of thrombopoietin and interleukin-6 were significantly elevated in patients who had thrombocytosis as compared with those who did not. In mouse models, increased hepatic thrombopoietin synthesis in response to tumor-derived interleukin-6 was an underlying mechanism of paraneoplastic thrombocytosis. Tumorderived interleukin-6 and hepatic thrombopoietin were also linked to thrombocytosis in patients. Silencing thrombopoietin and interleukin-6 abrogated thrombocytosis in tumor-bearing mice. Anti–interleukin-6 antibody treatment significantly reduced platelet counts in tumor-bearing mice and in patients with epithelial ovarian cancer. In addition, neutralizing interleukin-6 significantly enhanced the therapeutic efficacy of paclitaxel in mouse models of epithelial ovarian cancer. The use of an antiplatelet antibody to halve platelet counts in tumor-bearing mice significantly reduced tumor growth and angiogenesis.&lt;/p&gt; &lt;p&gt;Conclusions: These findings support the existence of a paracrine circuit wherein increased production of thrombopoietic cytokines in tumor and host tissue leads to paraneoplastic thrombocytosis, which fuels tumor growth. We speculate that countering paraneoplastic thrombocytosis either directly or indirectly by targeting these cytokines may have therapeutic potential. &lt;/p&gt

Genome Sequences of Mycobacteriophages Amgine, Amohnition, Bella96, Cain, DarthP, Hammy, Krueger, LastHope, Peanam, PhelpsODU, Phrank, SirPhilip, Slimphazie, and Unicorn

We report the genome sequences of 14 cluster K mycobacteriophages isolated using Mycobacterium smegmatis mc2155 as host. Four are closely related to subcluster K1 phages, and 10 are members of subcluster K6. The phage genomes span considerable sequence diversity, including multiple types of integrases and integration sites