Extended Dynamic Mode Decomposition with Learned Koopman Eigenfunctions for Prediction and Control

This paper presents a novel learning framework to construct Koopman eigenfunctions for unknown, nonlinear dynamics using data gathered from experiments. The learning framework can extract spectral information from the full non-linear dynamics by learning the eigenvalues and eigenfunctions of the associated Koopman operator. We then exploit the learned Koopman eigenfunctions to learn a lifted linear state-space model. To the best of our knowledge, our method is the first to utilize Koopman eigenfunctions as lifting functions for EDMD-based methods. We demonstrate the performance of the framework in state prediction and closed loop trajectory tracking of a simulated cart pole system. Our method is able to significantly improve the controller performance while relying on linear control methods to do nonlinear control

Site-selection model for optimal transplantation of eelgrass Zostera marina in the northeastern US

A site-selection model for eelgrass Zostera marina L. ecosystem restoration was developed in the northeastern US to select optimal areas for transplanting eelgrass. The site-selection model synthesizes available historic and literature-based information, reference data, and simple field measurements to identify and prioritize locations for large-scale eelgrass transplantation. Model development was based on the physical and biological characteristics associated with the most successful transplant sites in a mitigation project for the New Hampshire Port Authority. The site-selection process is divided into 3 phases: (1) the first phase uses available environmental information to formulate a preliminary transplant suitability index (PTSI) for pre-screening and eliminating unsuitable sites; (2) the second phase involves field measurements of light availability and bioturbation as well as survival and growth of test transplants at priority sites identified by the PTSI; (3) a transplant suitability index (TSI) score is calculated for each site based on the PTSI and the results of field assessments. The TSI is a multiplicative index that eliminates sites which receive ratings of zero and gives high scores to those sites with the greatest potential for successful transplantation. We applied the TSI post hoc to the New Hampshire Port Project¹s eelgrass transplant sites, and subsequently the site-selection model was used in an eelgrass restoration project in New Bedford Harbor, Massachusetts. After 2 yr of transplanting, the New Bedford Harbor effort has resulted in success at 62% of the sites planted using the site-selection model

Analyzing Connections Between User Attributes, Images, and Text

This work explores the relationship between a person’s demographic/ psychological traits (e.g., gender, personality) and selfidentity images and captions. We use a dataset of images and captions provided by N = 1,350 individuals, and we automatically extract features from both the images and captions. We identify several visual and textual properties that show reliable relationships with individual differences between participants. The automated techniques presented here allow us to draw interesting conclusions from our data that would be difficult to identify manually, and these techniques are extensible to other large datasets. We believe that our work on the relationship between user characteristics and user data has relevance in online settings, where users upload billions of images each day (Meeker M, 2014. Internet trends 2014–Code conference. Retrieved May 28, 2014)

HIV-1 RNA genome dimerizes on the plasma membrane in the presence of Gag protein

Retroviruses package a dimeric genome comprising two copies of the viral RNA. Each RNA contains all of the genetic information for viral replication. Packaging a dimeric genome allows the recovery of genetic information from damaged RNA genomes during DNA synthesis and promotes frequent recombination to increase diversity in the viral population. Therefore, the strategy of packaging dimeric RNA affects viral replication and viral evolution. Although its biological importance is appreciated, very little is known about the genome dimerization process. HIV-1 RNA genomes dimerize before packaging into virions, and RNA interacts with the viral structural protein Gag in the cytoplasm. Thus, it is often hypothesized that RNAs dimerize in the cytoplasm and the RNA-Gag complex is transported to the plasma membrane for virus assembly. In this report, we tagged HIV-1 RNAs with fluorescent proteins, via interactions of RNA-binding proteins and motifs in the RNA genomes, and studied their behavior at the plasma membrane by using total internal reflection fluorescence microscopy. We showed that HIV-1 RNAs dimerize not in the cytoplasm but on the plasma membrane. Dynamic interactions occur among HIV-1 RNAs, and stabilization of the RNA dimer requires Gag protein. Dimerization often occurs at an early stage of the virus assembly process. Furthermore, the dimerization process is probably mediated by the interactions of two RNA-Gag complexes, rather than two RNAs. These findings advance the current understanding of HIV-1 assembly and reveal important insights into viral replication mechanisms

SEQADAPT: an adaptable system for the tracking, storage and analysis of high throughput sequencing experiments

<p>Abstract</p> <p>Background</p> <p>High throughput sequencing has become an increasingly important tool for biological research. However, the existing software systems for managing and processing these data have not provided the flexible infrastructure that research requires.</p> <p>Results</p> <p>Existing software solutions provide static and well-established algorithms in a restrictive package. However as high throughput sequencing is a rapidly evolving field, such static approaches lack the ability to readily adopt the latest advances and techniques which are often required by researchers. We have used a loosely coupled, service-oriented infrastructure to develop SeqAdapt. This system streamlines data management and allows for rapid integration of novel algorithms. Our approach also allows computational biologists to focus on developing and applying new methods instead of writing boilerplate infrastructure code.</p> <p>Conclusion</p> <p>The system is based around the Addama service architecture and is available at our website as a demonstration web application, an installable single download and as a collection of individual customizable services.</p

Cryogenic Optical Performance of a Lightweighted Mirror Assembly for Future Space Astronomical Telescopes: Correlating Optical Test Results and Thermal Optical Model

A 43cm diameter stacked core mirror demonstrator was interferometrically tested at room temperature down to 250 degrees Kelvin for thermal deformation. The 2.5m radius of curvature spherical mirror assembly was constructed by low temperature fusing three abrasive waterjet core sections between two CNC pocket milled face sheets. The 93% lightweighted Corning ULE mirror assembly represents the current state of the art for future UV, optical, near IR space telescopes. During the multiple thermal test cycles, test results of interferometric test, thermal IR images of the front face were recorded in order to validate thermal optical model

Cryogenic Optical Performance of a Light-weight Mirror Assembly for Future Space Astronomical Telescopes: Optical Test Results and Thermal Optical Model

A 40 cm diameter mirror assembly was interferometrically tested at room temperature down to 250 degrees Kelvin for thermal deformation. The 2.5 m radius of curvature spherical mirror assembly was constructed by low temperature fusing three abrasive waterjet core sections between two face sheets. The 93% lightweighted Corning ULE mirror assembly represents the current state of the art for future UV, optical, near IR space telescopes. During the multiple thermal test cycles, test results of interferometric test, thermal IR images of the front face were recorded in order to validate thermal optical model

The International Consortium Investigating Neurocognition in Bipolar Disorder (ICONICâ BD)

Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/148257/1/bdi12748.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/148257/2/bdi12748_am.pd

Implementing Fault-tolerant Entangling Gates on the Five-qubit Code and the Color Code

We compare two different implementations of fault-tolerant entangling gates on logical qubits. In one instance, a twelve-qubit trapped-ion quantum computer is used to implement a non-transversal logical CNOT gate between two five qubit codes. The operation is evaluated with varying degrees of fault tolerance, which are provided by including quantum error correction circuit primitives known as flagging and pieceable fault tolerance. In the second instance, a twenty-qubit trapped-ion quantum computer is used to implement a transversal logical CNOT gate on two [[7,1,3]] color codes. The two codes were implemented on different but similar devices, and in both instances, all of the quantum error correction primitives, including the determination of corrections via decoding, are implemented during runtime using a classical compute environment that is tightly integrated with the quantum processor. For different combinations of the primitives, logical state fidelity measurements are made after applying the gate to different input states, providing bounds on the process fidelity. We find the highest fidelity operations with the color code, with the fault-tolerant SPAM operation achieving fidelities of 0.99939(15) and 0.99959(13) when preparing eigenstates of the logical X and Z operators, which is higher than the average physical qubit SPAM fidelities of 0.9968(2) and 0.9970(1) for the physical X and Z bases, respectively. When combined with a logical transversal CNOT gate, we find the color code to perform the sequence--state preparation, CNOT, measure out--with an average fidelity bounded by [0.9957,0.9963]. The logical fidelity bounds are higher than the analogous physical-level fidelity bounds, which we find to be [0.9850,0.9903], reflecting multiple physical noise sources such as SPAM errors for two qubits, several single-qubit gates, a two-qubit gate and some amount of memory error

Evaluation of surgical fixation methods for the implantation of melt electrowriting-reinforced hyaluronic acid hydrogel composites in porcine cartilage defects

The surgical repair of articular cartilage remains an ongoing challenge in orthopedics. Tissue engineering is a promising approach to treat cartilage defects; however, scaffolds must (i) possess the requisite material properties to support neocartilage formation, (ii) exhibit sufficient mechanical integrity for handling during implantation, and (iii) be reliably fixed within cartilage defects during surgery. In this study, we demonstrate the reinforcement of soft norbornene-modified hyaluronic acid (NorHA) hydrogels via the melt electrowriting (MEW) of polycaprolactone to fabricate composite scaffolds that support encapsulated porcine mesenchymal stromal cell (pMSC, three donors) chondrogenesis and cartilage formation and exhibit mechanical properties suitable for handling during implantation. Thereafter, acellular MEW-NorHA composites or MEW-NorHA composites with encapsulated pMSCs and precultured for 28 days were implanted in full-thickness cartilage defects in porcine knees using either bioresorbable pins or fibrin glue to assess surgical fixation methods. Fixation of composites with either biodegradable pins or fibrin glue ensured implant retention in most cases (80%); however, defects treated with pinned composites exhibited more subchondral bone remodeling and inferior cartilage repair, as evidenced by micro-computed tomography (micro-CT) and safranin O/fast green staining, respectively, when compared to defects treated with glued composites. Interestingly, no differences in repair tissue were observed between acellular and cellularized implants. Additional work is required to assess the full potential of these scaffolds for cartilage repair. However, these results suggest that future approaches for cartilage repair with MEW-reinforced hydrogels should be carefully evaluated with regard to their fixation approach for construct retention and surrounding cartilage tissue damage