Antares alignment gimbal positioner

DOE Office of Scientific and Technical Information (OSTI.GOV)

Day, R.D.; Viswanathan, V.K.; Saxman, A.C.

1981-01-01

Antares is a 24-beam 40-TW carbon-dioxide (CO/sub 2/) laser fusion system currently under construction at the Los Alamos National Laboratory. The Antares alignment gimbal positioner (AGP) is an optomechanical instrument that will be used for target alignment and alignment of the 24 laser beams, as well as beam quality assessments. The AGP will be capable of providing pointing, focusing, and wavefront optical path difference, as well as aberration information at both helium-neon (He-Ne) and CO/sub 2/ wavelengths. It is designed to allow the laser beams to be aligned to any position within a 1-cm cube to a tolerance of 10more » ..mu..m.« less

The deterministic optical alignment of the HERMES spectrograph

NASA Astrophysics Data System (ADS)

Gers, Luke; Staszak, Nicholas

2014-07-01

The High Efficiency and Resolution Multi Element Spectrograph (HERMES) is a four channel, VPH-grating spectrograph fed by two 400 fiber slit assemblies whose construction and commissioning has now been completed at the Anglo Australian Telescope (AAT). The size, weight, complexity, and scheduling constraints of the system necessitated that a fully integrated, deterministic, opto-mechanical alignment system be designed into the spectrograph before it was manufactured. This paper presents the principles about which the system was assembled and aligned, including the equipment and the metrology methods employed to complete the spectrograph integration.

Development of a group work assessment pedagogy using constructive alignment theory.

PubMed

Croy, Suzanne R

2018-02-01

The purpose of this paper is to explore group work assessment underpinned by constructive alignment theory to develop a new assessment pedagogy. A review was undertaken of an existing module 'Mental Health Nursing 1', with student nurses participating in the BSc (Hons) Nursing Programme. Constructive alignment theory requires teachers to adopt a deep approach to learning where module learning outcomes are aligned with the teaching environment and modes of assessment. As the module progressed, reviewing the Mental Health Nursing 1 module became an excellent opportunity to begin to understand how constructive alignment theory can inform a group work assessment pedagogy. Working using a constructively aligned assessment process became a valuable learning experience for the module leader whilst at the same time revealed a gap in the research around the impact of constructively aligned teaching and group work assessment. Copyright © 2017 Elsevier Ltd. All rights reserved.

25 CFR Appendix D to Subpart C - Cost To Construct

Code of Federal Regulations, 2012 CFR

2012-04-01

... the Adequate Standard Characteristics (see Table 1). For roadways, the recommended design of the..., Pavement Costs, and Incidental Costs. For bridges, costs are derived from costs in the National Bridge...) with inadequate drainage and alignment that generally follows existing ground 100 4 A designed and...

Precise Alignment and Permanent Mounting of Thin and Lightweight X-ray Segments

NASA Technical Reports Server (NTRS)

Biskach, Michael P.; Chan, Kai-Wing; Hong, Melinda N.; Mazzarella, James R.; McClelland, Ryan S.; Norman, Michael J.; Saha, Timo T.; Zhang, William W.

2012-01-01

To provide observations to support current research efforts in high energy astrophysics. future X-ray telescope designs must provide matching or better angular resolution while significantly increasing the total collecting area. In such a design the permanent mounting of thin and lightweight segments is critical to the overall performance of the complete X-ray optic assembly. The thin and lightweight segments used in the assemhly of the modules are desigued to maintain and/or exceed the resolution of existing X-ray telescopes while providing a substantial increase in collecting area. Such thin and delicate X-ray segments are easily distorted and yet must be aligned to the arcsecond level and retain accurate alignment for many years. The Next Generation X-ray Optic (NGXO) group at NASA Goddard Space Flight Center has designed, assembled. and implemented new hardware and procedures mth the short term goal of aligning three pairs of X-ray segments in a technology demonstration module while maintaining 10 arcsec alignment through environmental testing as part of the eventual design and construction of a full sized module capable of housing hundreds of X-ray segments. The recent attempts at multiple segment pair alignment and permanent mounting is described along with an overview of the procedure used. A look into what the next year mll bring for the alignment and permanent segment mounting effort illustrates some of the challenges left to overcome before an attempt to populate a full sized module can begin.

Coherent control of molecular alignment of homonuclear diatomic molecules by analytically designed laser pulses.

PubMed

Zou, Shiyang; Sanz, Cristina; Balint-Kurti, Gabriel G

2008-09-28

We present an analytic scheme for designing laser pulses to manipulate the field-free molecular alignment of a homonuclear diatomic molecule. The scheme is based on the use of a generalized pulse-area theorem and makes use of pulses constructed around two-photon resonant frequencies. In the proposed scheme, the populations and relative phases of the rovibrational states of the molecule are independently controlled utilizing changes in the laser intensity and in the carrier-envelope phase difference, respectively. This allows us to create the correct coherent superposition of rovibrational states needed to achieve optimal molecular alignment. The validity and efficiency of the scheme are demonstrated by explicit application to the H(2) molecule. The analytically designed laser pulses are tested by exact numerical solutions of the time-dependent Schrodinger equation including laser-molecule interactions to all orders of the field strength. The design of a sequence of pulses to further enhance molecular alignment is also discussed and tested. It is found that the rotating wave approximation used in the analytic design of the laser pulses leads to small errors in the prediction of the relative phase of the rotational states. It is further shown how these errors may be easily corrected.

A Method of Surrogate Model Construction which Leverages Lower-Fidelity Information using Space Mapping Techniques

DTIC Science & Technology

2014-03-27

fidelity. This pairing is accomplished through the use of a space mapping technique, which is a process where the design space of a lower fidelity model...is aligned a higher fidelity model. The intent of applying space mapping techniques to the field of surrogate construction is to leverage the

25 CFR Appendix D to Subpart C - Cost To Construct

Code of Federal Regulations, 2011 CFR

2011-04-01

... would meet the Adequate Standard Characteristics (see Table 1). For roadways, the recommended design of... Costs, Pavement Costs, and Incidental Costs. For bridges, costs are derived from costs in the National...) with inadequate drainage and alignment that generally follows existing ground 100 4 A designed and...

25 CFR Appendix D to Subpart C - Cost To Construct

Code of Federal Regulations, 2014 CFR

2014-04-01

... would meet the Adequate Standard Characteristics (see Table 1). For roadways, the recommended design of... Costs, Pavement Costs, and Incidental Costs. For bridges, costs are derived from costs in the National...) with inadequate drainage and alignment that generally follows existing ground 100 4 A designed and...

25 CFR Appendix D to Subpart C - Cost To Construct

Code of Federal Regulations, 2013 CFR

2013-04-01

... would meet the Adequate Standard Characteristics (see Table 1). For roadways, the recommended design of... Costs, Pavement Costs, and Incidental Costs. For bridges, costs are derived from costs in the National...) with inadequate drainage and alignment that generally follows existing ground 100 4 A designed and...

25 CFR Appendix D to Subpart C - Cost To Construct

Code of Federal Regulations, 2010 CFR

2010-04-01

... would meet the Adequate Standard Characteristics (see Table 1). For roadways, the recommended design of... Costs, Pavement Costs, and Incidental Costs. For bridges, costs are derived from costs in the National...) with inadequate drainage and alignment that generally follows existing ground 100 4 A designed and...

76 FR 5649 - Tongue River Railroad Company, Inc.-Construction and Operation-Western Alignment

Federal Register 2010, 2011, 2012, 2013, 2014

2011-02-01

... River Railroad Company, Inc.--Construction and Operation-- Western Alignment ACTION: Notice of the re... construction and operation was issued in October, 2007. The PA was prepared in consultation with the Section... the rail line construction and operation on Wolf Mountain Battlefield. The alignment approved by the...

An ultra stable optical bench for the magnetic survey satellite

NASA Technical Reports Server (NTRS)

Wingate, C. A., Jr.; Coughlin, T. B.; Sullivan, R. M.

1978-01-01

The Magsat optical bench has been designed and built to hold the alignment of five optical elements to deflections of 1-2 arcsec during orbital operation. The bench has been designed to withstand alignment changes during the launch and prestabilization phases of the mission. Severe weight constraints, in conjunction with the thermal and structural requirements, led to the choice of graphite-fiber-reinforced epoxy egg crate core and face sheets for the bench construction. Active temperature control was necessary to meet thermal deflection objectives, and novel kinematic mountings were required to prevent spacecraft bending from deflecting the bench.

Wet-spinning fabrication of shear-patterned alginate hydrogel microfibers and the guidance of cell alignment

PubMed Central

Yang, You; Sun, Jing; Liu, Xiaolu; Guo, Zhenzhen; He, Yunhu; Wei, Dan; Zhong, Meiling; Guo, Likun; Zhang, Xingdong

2017-01-01

Abstract Native tissue is naturally comprised of highly-ordered cell-matrix assemblies in a multi-hierarchical way, and the nano/submicron alignment of fibrous matrix is found to be significant in supporting cellular functionalization. In this study, a self-designed wet-spinning device appended with a rotary receiving pool was used to continuously produce shear-patterned hydrogel microfibers with aligned submicron topography. The process that the flow-induced shear force reshapes the surface of hydrogel fiber into aligned submicron topography was systematically analysed. Afterwards, the effect of fiber topography on cellular longitudinal spread and elongation was investigated by culturing rat neuron-like PC12 cells and human osteosarcoma MG63 cells with the spun hydrogel microfibers, respectively. The results suggested that the stronger shear flow force would lead to more distinct aligned submicron topography on fiber surface, which could induce cell orientation along with fiber axis and therefore form the cell-matrix dual-alignment. Finally, a multi-hierarchical tissue-like structure constructed by dual-oriented cell-matrix assemblies was fabricated based on this wet-spinning method. This work is believed to be a potentially novel biofabrication scheme for bottom-up constructing of engineered linear tissue, such as nerve bundle, cortical bone, muscle and hepatic cord. PMID:29026644

Racing into Physics.

ERIC Educational Resources Information Center

Cross, Tina R.

2002-01-01

Presents an activity in which race cars are designed and constructed out of edible materials. Students explore relationships between speed, distance, and time using both math and science. Includes a chart that shows alignment with the National Science Education Standards. (DDR)

Fuzzy adaptive strong tracking scaled unscented Kalman filter for initial alignment of large misalignment angles

NASA Astrophysics Data System (ADS)

Li, Jing; Song, Ningfang; Yang, Gongliu; Jiang, Rui

2016-07-01

In the initial alignment process of strapdown inertial navigation system (SINS), large misalignment angles always bring nonlinear problem, which can usually be processed using the scaled unscented Kalman filter (SUKF). In this paper, the problem of large misalignment angles in SINS alignment is further investigated, and the strong tracking scaled unscented Kalman filter (STSUKF) is proposed with fixed parameters to improve convergence speed, while these parameters are artificially constructed and uncertain in real application. To further improve the alignment stability and reduce the parameters selection, this paper proposes a fuzzy adaptive strategy combined with STSUKF (FUZZY-STSUKF). As a result, initial alignment scheme of large misalignment angles based on FUZZY-STSUKF is designed and verified by simulations and turntable experiment. The results show that the scheme improves the accuracy and convergence speed of SINS initial alignment compared with those based on SUKF and STSUKF.

A Self-Alignment Algorithm for SINS Based on Gravitational Apparent Motion and Sensor Data Denoising

PubMed Central

Liu, Yiting; Xu, Xiaosu; Liu, Xixiang; Yao, Yiqing; Wu, Liang; Sun, Jin

2015-01-01

Initial alignment is always a key topic and difficult to achieve in an inertial navigation system (INS). In this paper a novel self-initial alignment algorithm is proposed using gravitational apparent motion vectors at three different moments and vector-operation. Simulation and analysis showed that this method easily suffers from the random noise contained in accelerometer measurements which are used to construct apparent motion directly. Aiming to resolve this problem, an online sensor data denoising method based on a Kalman filter is proposed and a novel reconstruction method for apparent motion is designed to avoid the collinearity among vectors participating in the alignment solution. Simulation, turntable tests and vehicle tests indicate that the proposed alignment algorithm can fulfill initial alignment of strapdown INS (SINS) under both static and swinging conditions. The accuracy can either reach or approach the theoretical values determined by sensor precision under static or swinging conditions. PMID:25923932

Using constructive alignment theory to develop nursing skills curricula.

PubMed

Joseph, Sundari; Juwah, Charles

2012-01-01

Constructive alignment theory has been used to underpin the development of curricula in higher education for some time (Biggs and Tang, 2007), however, its use to inform and determine skills curricula in nursing is less well documented. This paper explores the use of constructive alignment theory within a study of undergraduate student nurses undertaking clinical skill acquisition in the final year of a BSc (Hons) Nursing course. Students were followed up as newly qualified nurses (NQN) (n = 58) to ascertain the impact of skill acquisition in this way. Comparisons were made with newly qualified nurses who did not participate in a constructively aligned curriculum. This mixed methods study reported skill identification within the immediate post-registration period and evaluated the constructively aligned curriculum as having positive benefits for NQNs in terms of confidence to practice. This was supported by preceptors' views. The study recommends two process models for nursing skills curriculum development and reports that constructive alignment is a useful theoretical framework for nurse educators. Copyright © 2011 Elsevier Ltd. All rights reserved.

Draft Environmental Impact Report/Environmental Impact Statement, Proposed Marathon Industrial/Commercial Business Center Tract 5167, Hayward, California.

DTIC Science & Technology

1985-10-01

briefly summarized below: • Construction of the Alameda Industrial Transportation Corridor . r The addition of a third eastbound lane on West Winton Ave...proposed Alameda County Industrial Transportation Corridor alignment, and on the north by the Bockman Canal. The site is designated and zoned for...area and extends from the proposed Alameda County Industrial Transportation Corridor alignment to the San Francisco Bay. This area is planned for park

Desktop aligner for fabrication of multilayer microfluidic devices.

PubMed

Li, Xiang; Yu, Zeta Tak For; Geraldo, Dalton; Weng, Shinuo; Alve, Nitesh; Dun, Wu; Kini, Akshay; Patel, Karan; Shu, Roberto; Zhang, Feng; Li, Gang; Jin, Qinghui; Fu, Jianping

2015-07-01

Multilayer assembly is a commonly used technique to construct multilayer polydimethylsiloxane (PDMS)-based microfluidic devices with complex 3D architecture and connectivity for large-scale microfluidic integration. Accurate alignment of structure features on different PDMS layers before their permanent bonding is critical in determining the yield and quality of assembled multilayer microfluidic devices. Herein, we report a custom-built desktop aligner capable of both local and global alignments of PDMS layers covering a broad size range. Two digital microscopes were incorporated into the aligner design to allow accurate global alignment of PDMS structures up to 4 in. in diameter. Both local and global alignment accuracies of the desktop aligner were determined to be about 20 μm cm(-1). To demonstrate its utility for fabrication of integrated multilayer PDMS microfluidic devices, we applied the desktop aligner to achieve accurate alignment of different functional PDMS layers in multilayer microfluidics including an organs-on-chips device as well as a microfluidic device integrated with vertical passages connecting channels located in different PDMS layers. Owing to its convenient operation, high accuracy, low cost, light weight, and portability, the desktop aligner is useful for microfluidic researchers to achieve rapid and accurate alignment for generating multilayer PDMS microfluidic devices.

Desktop aligner for fabrication of multilayer microfluidic devices

PubMed Central

Li, Xiang; Yu, Zeta Tak For; Geraldo, Dalton; Weng, Shinuo; Alve, Nitesh; Dun, Wu; Kini, Akshay; Patel, Karan; Shu, Roberto; Zhang, Feng; Li, Gang; Jin, Qinghui; Fu, Jianping

2015-01-01

Multilayer assembly is a commonly used technique to construct multilayer polydimethylsiloxane (PDMS)-based microfluidic devices with complex 3D architecture and connectivity for large-scale microfluidic integration. Accurate alignment of structure features on different PDMS layers before their permanent bonding is critical in determining the yield and quality of assembled multilayer microfluidic devices. Herein, we report a custom-built desktop aligner capable of both local and global alignments of PDMS layers covering a broad size range. Two digital microscopes were incorporated into the aligner design to allow accurate global alignment of PDMS structures up to 4 in. in diameter. Both local and global alignment accuracies of the desktop aligner were determined to be about 20 μm cm−1. To demonstrate its utility for fabrication of integrated multilayer PDMS microfluidic devices, we applied the desktop aligner to achieve accurate alignment of different functional PDMS layers in multilayer microfluidics including an organs-on-chips device as well as a microfluidic device integrated with vertical passages connecting channels located in different PDMS layers. Owing to its convenient operation, high accuracy, low cost, light weight, and portability, the desktop aligner is useful for microfluidic researchers to achieve rapid and accurate alignment for generating multilayer PDMS microfluidic devices. PMID:26233409

Image stack alignment in full-field X-ray absorption spectroscopy using SIFT_PyOCL.

PubMed

Paleo, Pierre; Pouyet, Emeline; Kieffer, Jérôme

2014-03-01

Full-field X-ray absorption spectroscopy experiments allow the acquisition of millions of spectra within minutes. However, the construction of the hyperspectral image requires an image alignment procedure with sub-pixel precision. While the image correlation algorithm has originally been used for image re-alignment using translations, the Scale Invariant Feature Transform (SIFT) algorithm (which is by design robust versus rotation, illumination change, translation and scaling) presents an additional advantage: the alignment can be limited to a region of interest of any arbitrary shape. In this context, a Python module, named SIFT_PyOCL, has been developed. It implements a parallel version of the SIFT algorithm in OpenCL, providing high-speed image registration and alignment both on processors and graphics cards. The performance of the algorithm allows online processing of large datasets.

T-gate aligned nanotube radio frequency transistors and circuits with superior performance.

PubMed

Che, Yuchi; Lin, Yung-Chen; Kim, Pyojae; Zhou, Chongwu

2013-05-28

In this paper, we applied self-aligned T-gate design to aligned carbon nanotube array transistors and achieved an extrinsic current-gain cutoff frequency (ft) of 25 GHz, which is the best on-chip performance for nanotube radio frequency (RF) transistors reported to date. Meanwhile, an intrinsic current-gain cutoff frequency up to 102 GHz is obtained, comparable to the best value reported for nanotube RF transistors. Armed with the excellent extrinsic RF performance, we performed both single-tone and two-tone measurements for aligned nanotube transistors at a frequency up to 8 GHz. Furthermore, we utilized T-gate aligned nanotube transistors to construct mixing and frequency doubling analog circuits operated in gigahertz frequency regime. Our results confirm the great potential of nanotube-based circuit applications and indicate that nanotube transistors are promising building blocks in high-frequency electronics.

76 FR 19187 - City of Davenport, Iowa-Construction and Operation Exemption-in Scott County, Iowa

Federal Register 2010, 2011, 2012, 2013, 2014

2011-04-06

... the Eastern Iowa Industrial Center, an industrial park, with rail access. The City will hire an... design and in the rail alignment, OEA, the FHWA, the Iowa Department of Transportation, and the City...

Constructing Aligned Assessments Using Automated Test Construction

ERIC Educational Resources Information Center

Porter, Andrew; Polikoff, Morgan S.; Barghaus, Katherine M.; Yang, Rui

2013-01-01

We describe an innovative automated test construction algorithm for building aligned achievement tests. By incorporating the algorithm into the test construction process, along with other test construction procedures for building reliable and unbiased assessments, the result is much more valid tests than result from current test construction…

The Status of the Cms Experiment

NASA Astrophysics Data System (ADS)

Green, Dan

The CMS experiment was completely assembled in the fall of 2008 after a decade of design, construction and installation. During the last two years, cosmic ray data were taken on a regular basis. These data have enabled CMS to align the detector components, both spatially and temporally. Initial use of muons has also established the relative alignment of the CMS tracking and muon systems. In addition, the CMS calorimetry has been crosschecked with test beam data, thus providing an initial energy calibration of CMS calorimetry to about 5%. The CMS magnet has been powered and field mapped. The trigger and data acquisition systems have been installed and run at full speed. The tiered data analysis system has been exercised at full design bandwidth for Tier0, Tier1 and Tier2 sites. Monte Carlo simulation of the CMS detector has been constructed at a detailed geometric level and has been tuned to test beam and other production data to provide a realistic model of the CMS detector prior to first collisions.

Seamless, axially aligned, fiber tubes, meshes, microbundles and gradient biomaterial constructs

PubMed Central

Elia, Roberto; Firpo, Matthew A.; Kaplan, David L.; Peattie, Robert A.

2012-01-01

A new electrospinning apparatus was developed to generate nanofibrous materials with improved organizational control. The system functions by oscillating the deposition signal (ODS) of multiple collectors, allowing significantly improved nanofiber control by manipulating the electric field which drives the electrospinning process. Other electrospinning techniques designed to impart deposited fiber organizational control, such as rotating mandrels or parallel collector systems, do not generate seamless constructs with high quality alignment in sizes large enough for medical devices. In contrast, the ODS collection system produces deposited fiber networks with highly pure alignment in a variety of forms and sizes, including flat (8 × 8 cm2), tubular (1.3 cm diameter), or rope-like microbundle (45 μm diameter) samples. Additionally, the mechanism of our technique allows for scale-up beyond these dimensions. The ODS collection system produced 81.6 % of fibers aligned within 5° of the axial direction, nearly a four-fold improvement over the rotating mandrel technique. The meshes produced from the 9 % (w/v) fibroin/PEO blend demonstrated significant mechanical anisotropy due to the fiber alignment. In 37 °C PBS, aligned samples produced an ultimate tensile strength of 16.47 ± 1.18 MPa, a Young's modulus of 37.33 MPa, and a yield strength of 7.79 ± 1.13 MPa. The material was 300 % stiffer when extended in the direction of fiber alignment and required 20 times the amount of force to be deformed, compared to aligned meshes extended perpendicular to the fiber direction. The ODS technique could be applied to any electrospinnable polymer to overcome the more limited uniformity and induced mechanical strain of rotating mandrel techniques, and greatly surpasses the limited length of standard parallel collector techniques. PMID:22890517

Generalized design of a zero-geometric-loss, astigmatism-free, modified four-objective multipass matrix system.

PubMed

Guo, Yin; Sun, LiQun; Yang, Zheng; Liu, Zilong

2016-02-20

During this study we constructed a generalized parametric modified four-objective multipass matrix system (MMS). We used an optical system comprising four asymmetrical spherical mirrors to improve the alignment process. The use of a paraxial equation for the design of the front transfer optics yielded the initial condition for modeling our MMS. We performed a ray tracing simulation to calculate the significant aberration of the system (astigmatism). Based on the calculated meridional and sagittal focus positions, the complementary focusing mirror was easily designed to provide an output beam free of astigmatism. We have presented an example of a 108-transit multipass system (5×7 matrix arrangement) with a relatively larger numerical aperture source (xenon light source). The whole system exhibits zero theoretical geometrical loss when simulated with Zemax software. The MMS construction strategy described in this study provides an anastigmatic output beam and the generalized approach to design a controllable matrix spot pattern on the field mirrors. Asymmetrical reflective mirrors aid in aligning the whole system with high efficiency. With the generalized design strategy in terms of optics configuration and asymmetrical fabrication method in this paper, other kinds of multipass matrix system coupled with different sources and detector systems also can be achieved.

Optical Bench Interferometer - From LISA Pathfinder to NGO/eLISA

NASA Astrophysics Data System (ADS)

Taylor, A.; d'Arcio, L.; Bogenstahl, J.; Danzmann, K.; Diekmann, C.; Fitzsimons, E. D.; Gerberding, O.; Heinzel, G.; Hennig, J.-S.; Hogenhuis, H.; Killow, C. J.; Lieser, M.; Lucarelli, S.; Nikolov, S.; Perreur-Lloyd, M.; Pijnenburg, J.; Robertson, D. I.; Sohmer, A.; Tröbs, M.; Ward, H.; Weise, D.

2013-01-01

We present a short summary of some optical bench construction and alignment developments that build on experience gained during the LISA Pathfinder optical bench assembly. These include evolved fibre injectors, a new beam vector measurement system, and thermally stable mounting hardware. The beam vector measurement techniques allow the alignment of beams to targets with absolute accuracy of a few microns and 20 microradians. We also describe a newly designed ultra-low-return beam dump that is expected to be a crucial element in the control of ghost beams on the optical benches.

Design of an automated cart and mount for a hyperspectral imaging system to be used in produce fields

NASA Astrophysics Data System (ADS)

Lefcourt, Alan M.; Kistler, Ross; Gadsden, S. Andrew

2016-05-01

The goal of this project was to construct a cart and a mounting system that would allow a hyperspectral laser-induced fluorescence imaging system (HLIFIS) to be used to detect fecal material in produce fields. Fecal contaminated produce is a recognized food safety risk. Previous research demonstrated the HLIFIS could detect fecal contamination in a laboratory setting. A cart was designed and built, and then tested to demonstrate that the cart was capable of moving at constant speeds or at precise intervals. A mounting system was designed and built to facilitate the critical alignment of the camera's imaging and the laser's illumination fields, and to allow the HLIFIS to be used in both field and laboratory settings without changing alignments. A hardened mount for the Powell lens that is used to produce the appropriate illumination profile was also designed, built, and tested.

Curriculum Alignment: Exploring Student Perception of Learning Achievement Measures

ERIC Educational Resources Information Center

Kuhn, Kerri-Ann L.; Rundle-Thiele, Sharyn R.

2009-01-01

The importance of constructively aligned curriculum is well understood in higher education. Based on the principles of constructive alignment, this research considers whether student perception of learning achievement measures can be used to gain insights into how course activities and pedagogy are assisting or hindering students in accomplishing…

Curriculum Alignment Projects: Toward Developing a Need to Know

NASA Astrophysics Data System (ADS)

Pinkerton, K. David

2001-02-01

This study investigated means of designing a high school chemistry curriculum. A Curriculum Alignment Project (CAP) was used to coordinate one semester (18 weeks) of activities. CAPs are long-term, multiple-approach design and construction projects that provide students a concrete task to accomplish, rather than an abstract theme to appreciate. Topics were selected for their potential contribution to students' success on the CAP, not because the topics were coming up next in a textbook. One particular CAP, Bicarbonate Squeeze Play, is described in detail. After one cycle of CAPs, student motivation began to change from extrinsic to intrinsic; achievement on objective measures was holding steady; students' abilities to craft and carry out long-term plans for complex projects were improving; and the teacher was learning how to design curriculum that fostered students' need to know.

Optical design and system characterization of an imaging microscope at 121.6 nm

NASA Astrophysics Data System (ADS)

Gao, Weichuan; Finan, Emily; Kim, Geon-Hee; Kim, Youngsik; Milster, Thomas D.

2018-03-01

We present the optical design and system characterization of an imaging microscope prototype at 121.6 nm. System engineering processes are demonstrated through the construction of a Schwarzschild microscope objective, including tolerance analysis, fabrication, alignment, and testing. Further improvements on the as-built system with a correction phase plate are proposed and analyzed. Finally, the microscope assembly and the imaging properties of the prototype are demonstrated.

Overhead drilling: Comparing three bases for aligning a drilling jig to vertical

PubMed Central

Rempel, David; Star, Demetra; Barr, Alan; Janowitz, Ira

2010-01-01

Problem Drilling overhead into concrete or metal ceilings is a strenuous task done by construction workers to hang ductwork, piping, and electrical equipment. The task is associated with upper body pain and musculoskeletal disorders. Previously, we described a field usability evaluation of a foot lever and inverted drill press intervention devices that were compared to the usual method for overhead drilling. Both interventions were rated as inferior to the usual method based on poor setup time and mobility. Method Three new interventions, which differed on the design used for aligning the drilling column to vertical, were compared to the usual method for overhead drilling by commercial construction workers (n=16). Results The usual method was associated with the highest levels of regional body fatigue and the poorest usability ratings when compared to the three interventions. Conclusion Overall, the ‘Collar Base’ intervention design received the best usability ratings. Impact on Industry Intervention designs developed for overhead drilling may reduce shoulder fatigue and prevent subsequent musculoskeletal disorders. These designs may also be useful for other overhead work such as lifting and supporting materials (e.g., piping, ducts) that are installed near the ceiling. Workplace health and safety interventions may require multiple rounds of field-testing prior to achieving acceptable usability ratings by the end users. PMID:20630276

Design and Construction of a Multi-wavelength, Micromirror Total Internal Reflectance Fluorescence Microscope

PubMed Central

Larson, Joshua; Kirk, Matt; Drier, Eric A.; O’Brien, William; MacKay, James F.; Friedman, Larry; Hoskins, Aaron

2015-01-01

Colocalization Single Molecule Spectroscopy (CoSMoS) has proven to be a useful method for studying the composition, kinetics, and mechanisms of complex cellular machines. Key to the technique is the ability to simultaneously monitor multiple proteins and/or nucleic acids as they interact with one another. Here we describe a protocol for constructing a CoSMoS micromirror Total Internal Reflection Fluorescence Microscope (mmTIRFM). Design and construction of a scientific microscope often requires a number of custom components and a significant time commitment. In our protocol, we have streamlined this process by implementation of a commercially available microscopy platform designed to accommodate the optical components necessary for a mmTIRFM. The mmTIRF system eliminates the need for machining custom parts by the end-user and facilitates optical alignment. Depending on the experience-level of the microscope builder, these time-savings and the following protocol can enable mmTIRF construction to be completed within two months. PMID:25188633

Design and construction of a multiwavelength, micromirror total internal reflectance fluorescence microscope.

PubMed

Larson, Joshua; Kirk, Matt; Drier, Eric A; O'Brien, William; MacKay, James F; Friedman, Larry J; Hoskins, Aaron A

2014-10-01

Colocalization single-molecule spectroscopy (CoSMoS) has proven to be a useful method for studying the composition, kinetics and mechanisms of complex cellular machines. Key to the technique is the ability to simultaneously monitor multiple proteins and/or nucleic acids as they interact with one another. Here we describe a protocol for constructing a CoSMoS micromirror total internal reflection fluorescence microscope (mmTIRFM). Design and construction of a scientific microscope often requires a number of custom components and a substantial time commitment. In our protocol, we have streamlined this process by implementation of a commercially available microscopy platform designed to accommodate the optical components necessary for an mmTIRFM. The mmTIRF system eliminates the need for machining custom parts by the end user and facilitates optical alignment. Depending on the experience level of the microscope builder, these time savings and the following protocol can enable mmTIRF construction to be completed within 2 months.

Total Quality Management Practices and Their Effects on Organizational Performance

ERIC Educational Resources Information Center

Hung, Richard Yu-Yuan; Lien, Bella Ya-Hui

2004-01-01

This paper reports a study designed to examine the key concepts of Total Quality Management (TQM) implementation and their effects on organizational performance. Process Alignment and People Involvement are two key concepts for successful implementation of TQM. The purpose of this paper is to discuss how these two constructs affect organizational…

Constructing Domain-Specific Knowledge in Kindergarten: Relations among Knowledge, Intelligence, and Strategic Performance

ERIC Educational Resources Information Center

Alexander, Joyce M.; Johnson, Kathy E.; Leibham, Mary E.; DeBauge, Christiane

2005-01-01

Thirty kindergarten children from two classrooms participated in a 3-week curricular unit on dinosaurs designed to teach taxonomic relations and distinguishing features aligned with 15 dinosaur species. Both domain-specific learning and strategic performance on a Twenty Questions game were assessed twice throughout the curriculum, as well as…

Doubting Learning Outcomes in Higher Education Contexts: From Performativity towards Emergence and Negotiation

ERIC Educational Resources Information Center

Addison, Nicholas

2014-01-01

Learning Outcomes models, particularly constructive alignment, are the default 'theoretical' tool underpinning HE curriculum design in the UK despite continuing doubts as to their efficacy. With reference to the literature, this article summarises the history of the Learning Outcomes movement and charts the perceived benefits and deficits of…

Creativity-Based Assessment and Neural Understandings: A Discussion and Case Study Analysis

ERIC Educational Resources Information Center

Penaluna, Andrew; Coates, Jackie; Penaluna, Kathryn

2010-01-01

Purpose: Enabling entrepreneurial creativity is a key aim of UK Government; however, there is a dearth of constructively aligned models of teaching and assessment. This paper aims to introduce design-based pedagogies and to highlight cognitive approaches that develop innovative mindsets; it seeks to indicate their propensity for adoption in…

COACH: profile-profile alignment of protein families using hidden Markov models.

PubMed

Edgar, Robert C; Sjölander, Kimmen

2004-05-22

Alignments of two multiple-sequence alignments, or statistical models of such alignments (profiles), have important applications in computational biology. The increased amount of information in a profile versus a single sequence can lead to more accurate alignments and more sensitive homolog detection in database searches. Several profile-profile alignment methods have been proposed and have been shown to improve sensitivity and alignment quality compared with sequence-sequence methods (such as BLAST) and profile-sequence methods (e.g. PSI-BLAST). Here we present a new approach to profile-profile alignment we call Comparison of Alignments by Constructing Hidden Markov Models (HMMs) (COACH). COACH aligns two multiple sequence alignments by constructing a profile HMM from one alignment and aligning the other to that HMM. We compare the alignment accuracy of COACH with two recently published methods: Yona and Levitt's prof_sim and Sadreyev and Grishin's COMPASS. On two sets of reference alignments selected from the FSSP database, we find that COACH is able, on average, to produce alignments giving the best coverage or the fewest errors, depending on the chosen parameter settings. COACH is freely available from www.drive5.com/lobster

Constructing an Inquiry Orientation from a Learning Theory Perspective: Democratizing Access through Task Design

ERIC Educational Resources Information Center

Buell, Catherine A.; Greenstein, Steven; Wilstein, Zahava

2017-01-01

It is widely accepted in the mathematics education community that pedagogies oriented toward inquiry are aligned with a constructivist theory of learning, and that these pedagogies effectively support students' learning of mathematics. In order to promote such an orientation, we first separate the idea of inquiry from its conception as a…

Design and Construction of VUES: The Vilnius University Echelle Spectrograph

NASA Astrophysics Data System (ADS)

Jurgenson, Colby; Fischer, Debra; McCracken, Tyler; Sawyer, David; Giguere, Matt; Szymkowiak, Andrew; Santoro, Fernando; Muller, Gary

2016-03-01

In February 2014, the Yale Exoplanet Laboratory was commissioned to design, build, and deliver a high resolution (R=60,000) spectrograph for the 1.65m telescope at the Molėtai Astronomical Observatory. The observatory is operated by the Institute of Theoretical Physics and Astronomy at Vilnius University. The Vilnius University Echelle Spectrograph (VUES) is a white-pupil design that is fed via an octagonal fiber from the telescope and has an operational bandpass from 400nm to 880nm. VUES incorporates a novel modular optomechanical design that allows for quick assembly and alignment on commercial optical tables. This approach allowed the spectrograph to be assembled and commissioned at Yale using lab optical tables and then reassembled at the observatory on a different optical table with excellent repeatability. The assembly and alignment process for the spectrograph was reduced to a few days, allowing the spectrograph to be completely disassembled for shipment to Lithuania, and then installed at the observatory during a 10-day period in June of 2015.

An ontology-based semantic configuration approach to constructing Data as a Service for enterprises

NASA Astrophysics Data System (ADS)

Cai, Hongming; Xie, Cheng; Jiang, Lihong; Fang, Lu; Huang, Chenxi

2016-03-01

To align business strategies with IT systems, enterprises should rapidly implement new applications based on existing information with complex associations to adapt to the continually changing external business environment. Thus, Data as a Service (DaaS) has become an enabling technology for enterprise through information integration and the configuration of existing distributed enterprise systems and heterogonous data sources. However, business modelling, system configuration and model alignment face challenges at the design and execution stages. To provide a comprehensive solution to facilitate data-centric application design in a highly complex and large-scale situation, a configurable ontology-based service integrated platform (COSIP) is proposed to support business modelling, system configuration and execution management. First, a meta-resource model is constructed and used to describe and encapsulate information resources by way of multi-view business modelling. Then, based on ontologies, three semantic configuration patterns, namely composite resource configuration, business scene configuration and runtime environment configuration, are designed to systematically connect business goals with executable applications. Finally, a software architecture based on model-view-controller (MVC) is provided and used to assemble components for software implementation. The result of the case study demonstrates that the proposed approach provides a flexible method of implementing data-centric applications.

Biodegradable scaffolds designed to mimic fascia-like properties for the treatment of pelvic organ prolapse and stress urinary incontinence.

PubMed

Roman, Sabiniano; Mangir, Naside; Bissoli, Julio; Chapple, Christopher R; MacNeil, Sheila

2016-05-01

There is an urgent clinical need for better synthetic materials to be used in surgical support of the pelvic floor. The aim of the current study was to construct biodegradable synthetic scaffolds that mimic the three-dimensional architecture of human fascia, which can integrate better into host tissues both mechanically and biologically. Therefore, four different polylactic acid (PLA) scaffolds with various degrees of fibre alignment were electrospun by modifying the electrospinning parameters. Physical and mechanical properties were assessed using a BOSE electroforce tensiometer. The attachment, viability and extracellular matrix production of adipose-derived stem cells cultured on the polylactic acid scaffolds were evaluated. The bulk density of the scaffolds decreased as the proportion of aligned fibres increased. Scaffolds became stronger and stiffer with increasing amounts of aligned fibres as measured along the axis parallel to the fibre alignment. In addition, more total collagen was produced on scaffolds with aligned fibres and was organised in the direction of the aligned fibres. In conclusion, the electrospinning technique can be easily modified to develop biodegradable scaffolds with a spectrum of mechanical properties allowing extracellular matrix organisation towards human-like fascia. © The Author(s) 2016.

The Application of the Weighted k-Partite Graph Problem to the Multiple Alignment for Metabolic Pathways.

PubMed

Chen, Wenbin; Hendrix, William; Samatova, Nagiza F

2017-12-01

The problem of aligning multiple metabolic pathways is one of very challenging problems in computational biology. A metabolic pathway consists of three types of entities: reactions, compounds, and enzymes. Based on similarities between enzymes, Tohsato et al. gave an algorithm for aligning multiple metabolic pathways. However, the algorithm given by Tohsato et al. neglects the similarities among reactions, compounds, enzymes, and pathway topology. How to design algorithms for the alignment problem of multiple metabolic pathways based on the similarity of reactions, compounds, and enzymes? It is a difficult computational problem. In this article, we propose an algorithm for the problem of aligning multiple metabolic pathways based on the similarities among reactions, compounds, enzymes, and pathway topology. First, we compute a weight between each pair of like entities in different input pathways based on the entities' similarity score and topological structure using Ay et al.'s methods. We then construct a weighted k-partite graph for the reactions, compounds, and enzymes. We extract a mapping between these entities by solving the maximum-weighted k-partite matching problem by applying a novel heuristic algorithm. By analyzing the alignment results of multiple pathways in different organisms, we show that the alignments found by our algorithm correctly identify common subnetworks among multiple pathways.

Review of Lean Construction Conference Proceedings and Relationship to the Toyota Production System Framework

ERIC Educational Resources Information Center

Jacobs, Gideon Francois

2010-01-01

The objective of this study was to align the International Group of Lean Construction (IGLC) conference proceedings against the Toyota Production System (TPS) to determine how well research themes in construction studies align with the TPS framework. Factories around the world that have implemented the TPS framework have experienced impressive…

Rotational Alignment Altered by Source Position Correlations

NASA Technical Reports Server (NTRS)

Jacobs, Chris S.; Heflin, M. B.; Lanyi, G. E.; Sovers, O. J.; Steppe, J. A.

2010-01-01

In the construction of modern Celestial Reference Frames (CRFs) the overall rotational alignment is only weakly constrained by the data. Therefore, common practice has been to apply a 3-dimensional No-Net-Rotation (NNR) constraint in order to align an under-construction frame to the ICRF. We present evidence that correlations amongst source position parameters must be accounted for in order to properly align a CRF at the 5-10 (mu)as level of uncertainty found in current work. Failure to do so creates errors at the 10-40 (mu)as level.

Fast-SG: an alignment-free algorithm for hybrid assembly.

PubMed

Di Genova, Alex; Ruz, Gonzalo A; Sagot, Marie-France; Maass, Alejandro

2018-05-01

Long-read sequencing technologies are the ultimate solution for genome repeats, allowing near reference-level reconstructions of large genomes. However, long-read de novo assembly pipelines are computationally intense and require a considerable amount of coverage, thereby hindering their broad application to the assembly of large genomes. Alternatively, hybrid assembly methods that combine short- and long-read sequencing technologies can reduce the time and cost required to produce de novo assemblies of large genomes. Here, we propose a new method, called Fast-SG, that uses a new ultrafast alignment-free algorithm specifically designed for constructing a scaffolding graph using light-weight data structures. Fast-SG can construct the graph from either short or long reads. This allows the reuse of efficient algorithms designed for short-read data and permits the definition of novel modular hybrid assembly pipelines. Using comprehensive standard datasets and benchmarks, we show how Fast-SG outperforms the state-of-the-art short-read aligners when building the scaffoldinggraph and can be used to extract linking information from either raw or error-corrected long reads. We also show how a hybrid assembly approach using Fast-SG with shallow long-read coverage (5X) and moderate computational resources can produce long-range and accurate reconstructions of the genomes of Arabidopsis thaliana (Ler-0) and human (NA12878). Fast-SG opens a door to achieve accurate hybrid long-range reconstructions of large genomes with low effort, high portability, and low cost.

VCFtoTree: a user-friendly tool to construct locus-specific alignments and phylogenies from thousands of anthropologically relevant genome sequences.

PubMed

Xu, Duo; Jaber, Yousef; Pavlidis, Pavlos; Gokcumen, Omer

2017-09-26

Constructing alignments and phylogenies for a given locus from large genome sequencing studies with relevant outgroups allow novel evolutionary and anthropological insights. However, no user-friendly tool has been developed to integrate thousands of recently available and anthropologically relevant genome sequences to construct complete sequence alignments and phylogenies. Here, we provide VCFtoTree, a user friendly tool with a graphical user interface that directly accesses online databases to download, parse and analyze genome variation data for regions of interest. Our pipeline combines popular sequence datasets and tree building algorithms with custom data parsing to generate accurate alignments and phylogenies using all the individuals from the 1000 Genomes Project, Neanderthal and Denisovan genomes, as well as reference genomes of Chimpanzee and Rhesus Macaque. It can also be applied to other phased human genomes, as well as genomes from other species. The output of our pipeline includes an alignment in FASTA format and a tree file in newick format. VCFtoTree fulfills the increasing demand for constructing alignments and phylogenies for a given loci from thousands of available genomes. Our software provides a user friendly interface for a wider audience without prerequisite knowledge in programming. VCFtoTree can be accessed from https://github.com/duoduoo/VCFtoTree_3.0.0 .

Design of an Image Fusion Phantom for a Small Animal microPET/CT Scanner Prototype

NASA Astrophysics Data System (ADS)

Nava-García, Dante; Alva-Sánchez, Héctor; Murrieta-Rodríguez, Tirso; Martínez-Dávalos, Arnulfo; Rodríguez-Villafuerte, Mercedes

2010-12-01

Two separate microtomography systems recently developed at Instituto de Física, UNAM, produce anatomical (microCT) and physiological images (microPET) of small animals. In this work, the development and initial tests of an image fusion method based on fiducial markers for image registration between the two modalities are presented. A modular Helix/Line-Sources phantom was designed and constructed; this phantom contains fiducial markers that can be visualized in both imaging systems. The registration was carried out by solving the rigid body alignment problem of Procrustes to obtain rotation and translation matrices required to align the two sets of images. The microCT/microPET image fusion of the Helix/Line-Sources phantom shows excellent visual coincidence between different structures, showing a calculated target-registration-error of 0.32 mm.

Teaching Practices in ipad-Classrooms: Alignment of Didactical Designs, Mobile Devices and Creativity

ERIC Educational Resources Information Center

Jahnke, Isa

2013-01-01

Creativity is socially constructed and is not an objective fact at all. How do teachers perceive students' creativity and how can they foster students' creative learning? From two case studies, one in higher education and a second on iPad-classrooms in schools, the paper reflects on didactical concepts for creativity using mobile devices.…

A molecular-field-based similarity study of non-nucleoside HIV-1 reverse transcriptase inhibitors

NASA Astrophysics Data System (ADS)

Mestres, Jordi; Rohrer, Douglas C.; Maggiora, Gerald M.

1999-01-01

This article describes a molecular-field-based similarity method for aligning molecules by matching their steric and electrostatic fields and an application of the method to the alignment of three structurally diverse non-nucleoside HIV-1 reverse transcriptase inhibitors. A brief description of the method, as implemented in the program MIMIC, is presented, including a discussion of pairwise and multi-molecule similarity-based matching. The application provides an example that illustrates how relative binding orientations of molecules can be determined in the absence of detailed structural information on their target protein. In the particular system studied here, availability of the X-ray crystal structures of the respective ligand-protein complexes provides a means for constructing an 'experimental model' of the relative binding orientations of the three inhibitors. The experimental model is derived by using MIMIC to align the steric fields of the three protein P66 subunit main chains, producing an overlay with a 1.41 Å average rms distance between the corresponding Cα's in the three chains. The inter-chain residue similarities for the backbone structures show that the main-chain conformations are conserved in the region of the inhibitor-binding site, with the major deviations located primarily in the 'finger' and RNase H regions. The resulting inhibitor structure overlay provides an experimental-based model that can be used to evaluate the quality of the direct a priori inhibitor alignment obtained using MIMIC. It is found that the 'best' pairwise alignments do not always correspond to the experimental model alignments. Therefore, simply combining the best pairwise alignments will not necessarily produce the optimal multi-molecule alignment. However, the best simultaneous three-molecule alignment was found to reproduce the experimental inhibitor alignment model. A pairwise consistency index has been derived which gauges the quality of combining the pairwise alignments and aids in efficiently forming the optimal multi-molecule alignment analysis. Two post-alignment procedures are described that provide information on feature-based and field-based pharmacophoric patterns. The former corresponds to traditional pharmacophore models and is derived from the contribution of individual atoms to the total similarity. The latter is based on molecular regions rather than atoms and is constructed by computing the percent contribution to the similarity of individual points in a regular lattice surrounding the molecules, which when contoured and colored visually depict regions of highly conserved similarity. A discussion of how the information provided by each of the procedures is useful in drug design is also presented.

Mechanical alignment of particles for use in fabricating superconducting and permanent magnetic materials

DOEpatents

Nellis, William J.; Maple, M. Brian

1992-01-01

A method for mechanically aligning oriented superconducting or permanently magnetic materials for further processing into constructs. This pretreatment optimizes the final crystallographic orientation and, thus, properties in these constructs. Such materials as superconducting fibers, needles and platelets are utilized.

Maglev guideway design issues

DOE Office of Scientific and Technical Information (OSTI.GOV)

Plotkin, D.; Kim, S.

1997-05-01

This paper reports results from guideway analyses conducted as part of the National Maglev Initiative (NMI), a government-industry effort from 1989 to 1994, formed to encourage the development of US maglev technology and to assess its potential application within the US transportation system. Covered here are some key guideway design issues that were common to the designs assessed for the NMI, and to maglev guideways in general. They represent aspects that will need additional attention in future efforts to produce structurally sound and economical maglev guideways. These recommendations come from the analyses conducted by a team from the US Armymore » Construction Engineering Research Laboratories, the Civil Engineering Department of the University of Illinois, and Alfred Benesch and Company. The recommendations focus on design philosophy and the development of general design criteria, guideway maintenance and the provision for future alignment adjustment in both the guideway and the magnets, foundation design, and the long-term performance of guideway materials and reinforcement. Generally, one of the main challenges to guideway designers is to produce a structure that will be easily maintainable to the narrow tolerances and precise alignment required for practical high-speed maglev operation.« less

Finding the optical axis of a distant object using an optical alignment system based on a holographic marker

NASA Astrophysics Data System (ADS)

Zhuk, D. I.; Denisyuk, I. Yu.; Gutner, I. E.

2015-07-01

A way to construct a holographic indicator of the position of the central axis of a distant object based on recording a transmission hologram in a layer of photosensitive material and forming a remote real image before a light source is considered. A light source with a holographically formed marker designed for visual guidance to the object axis; it can be used to simplify aircraft landing on a glide path, preliminary visual alignment of large coaxial details of various machines, etc. Specific features of the scheme of recording a holographic marker and the reconstruction of its image are considered. The possibility of forming a remote holographic image marker, which can be aligned with a simultaneously operating reference laser system for determining the direction to an object and its optical axis, has been demonstrated experimentally.

Focusing on learning through constructive alignment with task-oriented portfolio assessment

NASA Astrophysics Data System (ADS)

Cain, A.; Grundy, J.; Woodward, C. J.

2018-07-01

Approaches to learning have been shown to have a significant impact on student success in technical units. This paper reports on an action research study that applied the principles of constructive alignment to improve student learning outcomes in programming units. The proposed model uses frequent formative feedback to engage students with unit material, and encourage them to adopt deep approaches to learning. Our results provide a set of guiding principles and a structured teaching approach that focuses students on meeting unit learning objectives, the goal of constructive alignment. The results are demonstrated via descriptions of the resulting teaching and learning environment, student results, and staff and student reflections.

Multiple network alignment via multiMAGNA+.

PubMed

Vijayan, Vipin; Milenkovic, Tijana

2017-08-21

Network alignment (NA) aims to find a node mapping that identifies topologically or functionally similar network regions between molecular networks of different species. Analogous to genomic sequence alignment, NA can be used to transfer biological knowledge from well- to poorly-studied species between aligned network regions. Pairwise NA (PNA) finds similar regions between two networks while multiple NA (MNA) can align more than two networks. We focus on MNA. Existing MNA methods aim to maximize total similarity over all aligned nodes (node conservation). Then, they evaluate alignment quality by measuring the amount of conserved edges, but only after the alignment is constructed. Directly optimizing edge conservation during alignment construction in addition to node conservation may result in superior alignments. Thus, we present a novel MNA method called multiMAGNA++ that can achieve this. Indeed, multiMAGNA++ outperforms or is on par with existing MNA methods, while often completing faster than existing methods. That is, multiMAGNA++ scales well to larger network data and can be parallelized effectively. During method evaluation, we also introduce new MNA quality measures to allow for more fair MNA method comparison compared to the existing alignment quality measures. MultiMAGNA++ code is available on the method's web page at http://nd.edu/~cone/multiMAGNA++/.

Microfluidic-enhanced 3D bioprinting of aligned myoblast-laden hydrogels leads to functionally organized myofibers in vitro and in vivo.

PubMed

Costantini, Marco; Testa, Stefano; Mozetic, Pamela; Barbetta, Andrea; Fuoco, Claudia; Fornetti, Ersilia; Tamiro, Francesco; Bernardini, Sergio; Jaroszewicz, Jakub; Święszkowski, Wojciech; Trombetta, Marcella; Castagnoli, Luisa; Seliktar, Dror; Garstecki, Piotr; Cesareni, Gianni; Cannata, Stefano; Rainer, Alberto; Gargioli, Cesare

2017-07-01

We present a new strategy for the fabrication of artificial skeletal muscle tissue with functional morphologies based on an innovative 3D bioprinting approach. The methodology is based on a microfluidic printing head coupled to a co-axial needle extruder for high-resolution 3D bioprinting of hydrogel fibers laden with muscle precursor cells (C2C12). To promote myogenic differentiation, we formulated a tailored bioink with a photocurable semi-synthetic biopolymer (PEG-Fibrinogen) encapsulating cells into 3D constructs composed of aligned hydrogel fibers. After 3-5 days of culture, the encapsulated myoblasts started migrating and fusing, forming multinucleated myotubes within the 3D bioprinted fibers. The obtained myotubes showed high degree of alignment along the direction of hydrogel fiber deposition, further revealing maturation, sarcomerogenesis, and functionality. Following subcutaneous implantation in the back of immunocompromised mice, bioprinted constructs generated organized artificial muscle tissue in vivo. Finally, we demonstrate that our microfluidic printing head allows to design three dimensional multi-cellular assemblies with an exquisite compartmentalization of the encapsulated cells. Our results demonstrate an enhanced myogenic differentiation with the formation of parallel aligned long-range myotubes. The approach that we report here represents a robust and valid candidate for the fabrication of macroscopic artificial muscle to scale up skeletal muscle tissue engineering for human clinical application. Copyright © 2017 The Author(s). Published by Elsevier Ltd.. All rights reserved.

Magnet-assisted device-level alignment for the fabrication of membrane-sandwiched polydimethylsiloxane microfluidic devices

NASA Astrophysics Data System (ADS)

Lu, J.-C.; Liao, W.-H.; Tung, Y.-C.

2012-07-01

Polydimethylsiloxane (PDMS) microfluidic device is one of the most essential techniques that advance microfluidics research in recent decades. PDMS is broadly exploited to construct microfluidic devices due to its unique and advantageous material properties. To realize more functionalities, PDMS microfluidic devices with multi-layer architectures, especially those with sandwiched membranes, have been developed for various applications. However, existing alignment methods for device fabrication are mainly based on manual observations, which are time consuming, inaccurate and inconsistent. This paper develops a magnet-assisted alignment method to enhance device-level alignment accuracy and precision without complicated fabrication processes. In the developed alignment method, magnets are embedded into PDMS layers at the corners of the device. The paired magnets are arranged in symmetric positions at each PDMS layer, and the magnetic attraction force automatically pulls the PDMS layers into the aligned position during assembly. This paper also applies the method to construct a practical microfluidic device, a tunable chaotic micromixer. The results demonstrate the successful operation of the device without failure, which suggests the accurate alignment and reliable bonding achieved by the method. Consequently, the fabrication method developed in this paper is promising to be exploited to construct various membrane-sandwiched PDMS microfluidic devices with more integrated functionalities to advance microfluidics research.

Prefocused objective-pinhole unit for beam expanding and spatial filtering.

PubMed

Antes, G P

1973-03-01

A beam-expanding and spatial-filtering device, the prefocused objective-pinhole unit (POP unit), is presented. The design is primarily aimed at greater simplicity in handling and construction than the commercially available lens-pinhole spatial filters (LPSF), for once the pinhole is fixed in the correct position with respect to the objective, the alignment of the whole unit can be made an easy matter.

Fine-tuning structural RNA alignments in the twilight zone.

PubMed

Bremges, Andreas; Schirmer, Stefanie; Giegerich, Robert

2010-04-30

A widely used method to find conserved secondary structure in RNA is to first construct a multiple sequence alignment, and then fold the alignment, optimizing a score based on thermodynamics and covariance. This method works best around 75% sequence similarity. However, in a "twilight zone" below 55% similarity, the sequence alignment tends to obscure the covariance signal used in the second phase. Therefore, while the overall shape of the consensus structure may still be found, the degree of conservation cannot be estimated reliably. Based on a combination of available methods, we present a method named planACstar for improving structure conservation in structural alignments in the twilight zone. After constructing a consensus structure by alignment folding, planACstar abandons the original sequence alignment, refolds the sequences individually, but consistent with the consensus, aligns the structures, irrespective of sequence, by a pure structure alignment method, and derives an improved sequence alignment from the alignment of structures, to be re-submitted to alignment folding, etc.. This circle may be iterated as long as structural conservation improves, but normally, one step suffices. Employing the tools ClustalW, RNAalifold, and RNAforester, we find that for sequences with 30-55% sequence identity, structural conservation can be improved by 10% on average, with a large variation, measured in terms of RNAalifold's own criterion, the structure conservation index.

Use artificial neural network to align biological ontologies.

PubMed

Huang, Jingshan; Dang, Jiangbo; Huhns, Michael N; Zheng, W Jim

2008-09-16

Being formal, declarative knowledge representation models, ontologies help to address the problem of imprecise terminologies in biological and biomedical research. However, ontologies constructed under the auspices of the Open Biomedical Ontologies (OBO) group have exhibited a great deal of variety, because different parties can design ontologies according to their own conceptual views of the world. It is therefore becoming critical to align ontologies from different parties. During automated/semi-automated alignment across biological ontologies, different semantic aspects, i.e., concept name, concept properties, and concept relationships, contribute in different degrees to alignment results. Therefore, a vector of weights must be assigned to these semantic aspects. It is not trivial to determine what those weights should be, and current methodologies depend a lot on human heuristics. In this paper, we take an artificial neural network approach to learn and adjust these weights, and thereby support a new ontology alignment algorithm, customized for biological ontologies, with the purpose of avoiding some disadvantages in both rule-based and learning-based aligning algorithms. This approach has been evaluated by aligning two real-world biological ontologies, whose features include huge file size, very few instances, concept names in numerical strings, and others. The promising experiment results verify our proposed hypothesis, i.e., three weights for semantic aspects learned from a subset of concepts are representative of all concepts in the same ontology. Therefore, our method represents a large leap forward towards automating biological ontology alignment.

Automated insertion of sequences into a ribosomal RNA alignment: An application of computational linguistics in molecular biology

DOE Office of Scientific and Technical Information (OSTI.GOV)

Taylor, R.C.

This thesis involved the construction of (1) a grammar that incorporates knowledge on base invariancy and secondary structure in a molecule and (2) a parser engine that uses the grammar to position bases into the structural subunits of the molecule. These concepts were combined with a novel pinning technique to form a tool that semi-automates insertion of a new species into the alignment for the 16S rRNA molecule (a component of the ribosome) maintained by Dr. Carl Woese's group at the University of Illinois at Urbana. The tool was tested on species extracted from the alignment and on a groupmore » of entirely new species. The results were very encouraging, and the tool should be substantial aid to the curators of the 16S alignment. The construction of the grammar was itself automated, allowing application of the tool to alignments for other molecules. The logic programming language Prolog was used to construct all programs involved. The computational linguistics approach used here was found to be a useful way to attach the problem of insertion into an alignment.« less

Automated insertion of sequences into a ribosomal RNA alignment: An application of computational linguistics in molecular biology

DOE Office of Scientific and Technical Information (OSTI.GOV)

Taylor, Ronald C.

This thesis involved the construction of (1) a grammar that incorporates knowledge on base invariancy and secondary structure in a molecule and (2) a parser engine that uses the grammar to position bases into the structural subunits of the molecule. These concepts were combined with a novel pinning technique to form a tool that semi-automates insertion of a new species into the alignment for the 16S rRNA molecule (a component of the ribosome) maintained by Dr. Carl Woese`s group at the University of Illinois at Urbana. The tool was tested on species extracted from the alignment and on a groupmore » of entirely new species. The results were very encouraging, and the tool should be substantial aid to the curators of the 16S alignment. The construction of the grammar was itself automated, allowing application of the tool to alignments for other molecules. The logic programming language Prolog was used to construct all programs involved. The computational linguistics approach used here was found to be a useful way to attach the problem of insertion into an alignment.« less

Constructive alignment of a research-informed teaching activity within an undergraduate diagnostic radiography curriculum: A reflection.

PubMed

Higgins, R; Hogg, P; Robinson, L

2017-09-01

To evaluate the learning experience of a level 5 (year 2) student cohort within a research-informed teaching (RiT) activity and to map findings against learning outcomes and level descriptors using constructive alignment. An online questionnaire was used to explore the level 5 student experience of a Research-informed Teaching (RiT) activity. Responses were retrospectively mapped against Framework for Higher Education Qualifications (FHEQ) level descriptors for level 5 using constructive alignment. Thirty one out of 46 level 5 students completed the questionnaire (67% response rate). Analysis of the questionnaire supported the integration of this RiT activity within the curriculum in terms of learning and research skill development by students. However, it was identified that this activity could be revised further to better align with level 5 descriptors and incorporate additional higher level cognitive processes. Learning outcomes for this RiT activity were constructively aligned with FHEQ level 5 descriptors. Recommendations are provided on how these could be further refined to ensure students undertake a more critical approach to the application of theory into practice. Discussion also considers how this process could be used to develop a similar RiT activity at level 6 (year 3). Copyright © 2016 The College of Radiographers. Published by Elsevier Ltd. All rights reserved.

Constructive Alignment in Economics Teaching: A Reflection on Effective Implementation

ERIC Educational Resources Information Center

McCann, Michael

2017-01-01

The typical approach to student-centred learning in Economics has focused on innovation within the classroom, with little thought given to how this complements teaching and learning and, crucially, assessment. This paper reflects on the implementation of constructive alignment in a final year managerial economics course. It demonstrates how it is…

Chinese Business Students' Changes in Beliefs and Strategy Use in a Constructively Aligned PBL Course

ERIC Educational Resources Information Center

Zhao, Ke; Zhang, Jie; Du, Xiangyun

2017-01-01

This study adopted a longitudinal retrospective case study approach to investigate Chinese business students' transitional learning experience in a problem-based learning (PBL) course with innovative assessment practices. The study focused on students' beliefs and strategy use in a constructively aligned PBL course for business communication.…

Challenges of Adopting Constructive Alignment in Action Learning Education

ERIC Educational Resources Information Center

Remneland Wikhamn, Björn

2017-01-01

This paper will critically examine how the two influential pedagogical approaches of action-based learning and constructive alignment relate to each other, and how they may differ in focus and basic assumptions. From the outset, they are based on similar underpinnings, with the student and the learning outcomes in the center. Drawing from…

The Columbia University Sub-micron Charged Particle Beam

PubMed Central

Randers-Pehrson, Gerhard; Johnson, Gary W.; Marino, Stephen A.; Xu, Yanping; Dymnikov, Alexander D.; Brenner, David J.

2009-01-01

A lens system consisting of two electrostatic quadrupole triplets has been designed and constructed at the Radiological Research Accelerator Facility (RARAF) of Columbia University. The lens system has been used to focus 6-MeV 4He ions to a beam spot in air with a diameter of 0.8 µm. The quadrupole electrodes can withstand voltages high enough to focus 4He ions up to 10 MeV and protons up to 5 MeV. The quadrupole triplet design is novel in that alignment is made through precise construction and the relative strengths of the quadrupoles are accomplished by the lengths of the elements, so that the magnitudes of the voltages required for focusing are nearly identical. The insulating sections between electrodes have had ion implantation to improve the voltage stability of the lens. The lens design employs Russian symmetry for the quadrupole elements. PMID:20161365

Monitoring fibrous scaffold guidance of three-dimensional collagen organisation using minimally-invasive second harmonic generation.

PubMed

Delaine-Smith, Robin M; Green, Nicola H; Matcher, Stephen J; MacNeil, Sheila; Reilly, Gwendolen C

2014-01-01

The biological and mechanical function of connective tissues is largely determined by controlled cellular alignment and therefore it seems appropriate that tissue-engineered constructs should be architecturally similar to the in vivo tissue targeted for repair or replacement. Collagen organisation dictates the tensile properties of most tissues and so monitoring the deposition of cell-secreted collagen as the construct develops is essential for understanding tissue formation. In this study, electrospun fibres with a random or high degree of orientation, mimicking two types of tissue architecture found in the body, were used to culture human fibroblasts for controlling cell alignment. The minimally-invasive technique of second harmonic generation was used with the aim of monitoring and profiling the deposition and organisation of collagen at different construct depths over time while construct mechanical properties were also determined over the culture period. It was seen that scaffold fibre organisation affected cell migration and orientation up to 21 days which in turn had an effect on collagen organisation. Collagen in random fibrous constructs was deposited in alternating configurations at different depths however a high degree of organisation was observed throughout aligned fibrous constructs orientated in the scaffold fibre direction. Three-dimensional second harmonic generation images showed that deposited collagen was more uniformly distributed in random constructs but aligned constructs were more organised and had higher intensities. The tensile properties of all constructs increased with increasing collagen deposition and were ultimately dictated by collagen organisation. This study highlights the importance of scaffold architecture for controlling the development of well-organised tissue engineered constructs and the usefulness of second harmonic generation imaging for monitoring collagen maturation in a minimally invasive manner.

Protein alignment algorithms with an efficient backtracking routine on multiple GPUs.

PubMed

Blazewicz, Jacek; Frohmberg, Wojciech; Kierzynka, Michal; Pesch, Erwin; Wojciechowski, Pawel

2011-05-20

Pairwise sequence alignment methods are widely used in biological research. The increasing number of sequences is perceived as one of the upcoming challenges for sequence alignment methods in the nearest future. To overcome this challenge several GPU (Graphics Processing Unit) computing approaches have been proposed lately. These solutions show a great potential of a GPU platform but in most cases address the problem of sequence database scanning and computing only the alignment score whereas the alignment itself is omitted. Thus, the need arose to implement the global and semiglobal Needleman-Wunsch, and Smith-Waterman algorithms with a backtracking procedure which is needed to construct the alignment. In this paper we present the solution that performs the alignment of every given sequence pair, which is a required step for progressive multiple sequence alignment methods, as well as for DNA recognition at the DNA assembly stage. Performed tests show that the implementation, with performance up to 6.3 GCUPS on a single GPU for affine gap penalties, is very efficient in comparison to other CPU and GPU-based solutions. Moreover, multiple GPUs support with load balancing makes the application very scalable. The article shows that the backtracking procedure of the sequence alignment algorithms may be designed to fit in with the GPU architecture. Therefore, our algorithm, apart from scores, is able to compute pairwise alignments. This opens a wide range of new possibilities, allowing other methods from the area of molecular biology to take advantage of the new computational architecture. Performed tests show that the efficiency of the implementation is excellent. Moreover, the speed of our GPU-based algorithms can be almost linearly increased when using more than one graphics card.

Phased-array laser radar: Concept and application

NASA Technical Reports Server (NTRS)

Kadrmas, K. A.

1973-01-01

The design and construction of a coaxial transmitter-receiver combination was investigated. Major emphasis was placed on simple permanent optical alignment, transmitter-receiver field of view matching, use of a pulsed gas laser as a transmitter maximum optical efficiency, complete digital control of data acquisition, and optical mount pointing and tracking. Also a means of expanding the coaxial transmitter-receiver concept to allow phased-array lidar, par-lidar was described.

Assembly Modulated by Particle Position and Shape: A New Concept in Self-Assembly.

PubMed

Tavacoli, Joe W; Heuvingh, Julien; Du Roure, Olivia

2017-11-10

In this communication we outline how the bespoke arrangements and design of micron-sized superparamagnetic shapes provide levers to modulate their assembly under homogeneous magnetic fields. We label this new approach, 'assembly modulated by particle position and shape' (APPS). Specifically, using rectangular lattices of superparamagnetic micron-sized cuboids, we construct distinct microstructures by adjusting lattice pitch and angle of array with respect to a magnetic field. Broadly, we find two modes of assembly: (1) immediate 2D jamming of the cuboids as they rotate to align with the applied field (rotation-induced jamming) and (2) aggregation via translation after their full alignment (dipole-dipole assembly). The boundary between these two assembly pathways is independent on field strength being solely a function of the cuboid's dimensions, lattice pitch, and array angle with respect to field-a relationship which we capture, along with other features of the assembly process, in a 'phase diagram'. In doing so, we set out initial design rules to build custom made assemblies. Moreover, these assemblies can be made flexible thanks to the hinged contacts of their particle building blocks. This flexibility, combined with the superparamagnetic nature of the architectures, renders our assembly method particularly appropriate for the construction of complex actuators at a scale hitherto not possible.

Conceptual design of the cryostat for the new high luminosity (HL-LHC) triplet magnets

NASA Astrophysics Data System (ADS)

Ramos, D.; Parma, V.; Moretti, M.; Eymin, C.; Todesco, E.; Van Weelderen, R.; Prin, H.; Berkowitz Zamora, D.

2017-12-01

The High Luminosity LHC (HL-LHC) is a project to upgrade the LHC collider after 2020-2025 to increase the integrated luminosity by about one order of magnitude and extend the physics production until 2035. An upgrade of the focusing triplets insertion system for the ATLAS and CMS experiments is foreseen using superconducting magnets operating in a pressurised superfluid helium bath at 1.9 K. This will require the design and construction of four continuous cryostats, each about sixty meters in length and one meter in diameter, for the final beam focusing quadrupoles, corrector magnets and beam separation dipoles. The design is constrained by the dimensions of the existing tunnel and accessibility restrictions imposing the integration of cryogenic piping inside the cryostat, thus resulting in a very compact integration. As the alignment and position stability of the magnets is crucial for the luminosity performance of the machine, the magnet support system must be carefully designed in order to cope with parasitic forces and thermo-mechanical load cycles. In this paper, we present the conceptual design of the cryostat and discuss the approach to address the stringent and often conflicting requirements of alignment, integration and thermal aspects.

Fine-tuning structural RNA alignments in the twilight zone

PubMed Central

2010-01-01

Background A widely used method to find conserved secondary structure in RNA is to first construct a multiple sequence alignment, and then fold the alignment, optimizing a score based on thermodynamics and covariance. This method works best around 75% sequence similarity. However, in a "twilight zone" below 55% similarity, the sequence alignment tends to obscure the covariance signal used in the second phase. Therefore, while the overall shape of the consensus structure may still be found, the degree of conservation cannot be estimated reliably. Results Based on a combination of available methods, we present a method named planACstar for improving structure conservation in structural alignments in the twilight zone. After constructing a consensus structure by alignment folding, planACstar abandons the original sequence alignment, refolds the sequences individually, but consistent with the consensus, aligns the structures, irrespective of sequence, by a pure structure alignment method, and derives an improved sequence alignment from the alignment of structures, to be re-submitted to alignment folding, etc.. This circle may be iterated as long as structural conservation improves, but normally, one step suffices. Conclusions Employing the tools ClustalW, RNAalifold, and RNAforester, we find that for sequences with 30-55% sequence identity, structural conservation can be improved by 10% on average, with a large variation, measured in terms of RNAalifold's own criterion, the structure conservation index. PMID:20433706

Engineering poly(hydroxy butyrate-co-hydroxy valerate) based vascular scaffolds to mimic native artery.

PubMed

Deepthi, S; Nivedhitha Sundaram, M; Vijayan, Ponni; Nair, Shantikumar V; Jayakumar, R

2018-04-01

Electrospun tri-layered fibrous scaffold incorporating VEGF and Platelet Factor Concentrate (PFC) in multiple layers having different layer architectures was designed to mimic native artery. The scaffold consisted of longitudinally aligned poly(hydroxy butyrate-co-hydroxy valerate) (PHBV) and poly(vinyl alcohol) (PVA) nanofibers (inner layer), radially aligned PHBV-elastin nanofibers (middle layer) to provide the bi-directional alignment and combination of longitudinally aligned PHBV-elastin and random PHBV/PVA multiscale fibers (peripheral layer). Tubular constructs of diameter <6 mm were developed. The developed electrospun fibers were characterised by Scanning Electron Microscope (SEM), Fourier Transform Infrared Spectroscopy and Tensile tests. Further the burst strength, compliance and stiffness index of tri-layered tubular scaffold was evaluated. SEM images of fibrous layers showed the typical longitudinal and radial alignment of fibers in the tubular construct. SEM images showed that the prepared PHBV nanofibers were in the range of 500-800 nm and PHBV microfibers were of 1-2 μm in diameter in the tri-layered electrospun membrane. PVA nanofibers were of size 200-250 nm. The tensile strength, percentage compliance and stiffness index of tri-layered membrane was in accordance with that of native small blood vessels. The developed tri-layered membrane was blood compatible, with hemolysis degree 0.85 ± 0.21% and did not activate platelets. Controlled release of VEGF and PFC was observed from the scaffold. The biocompatibility of the tri-layered scaffold was evaluated using HUVECs, SMCs and MSCs and SMCs infiltration from the outer layer was also evaluated. Specific protein expression for the HUVECs and SMCs was evaluated by flow cytometry and immunocytochemistry. HUVECs and SMCs exhibited good elongation and alignment along the direction of fibers and was found to maintain its CD31, VE-Cadherin and αSMA expression respectively. The results highlight the importance of bi-directional fiber alignment on the tri-layered electrospun scaffold as a suitable architectural prototype for vascular scaffolds to mimic the native arteries. Copyright © 2017 Elsevier B.V. All rights reserved.

Gene Composer: database software for protein construct design, codon engineering, and gene synthesis

PubMed Central

Lorimer, Don; Raymond, Amy; Walchli, John; Mixon, Mark; Barrow, Adrienne; Wallace, Ellen; Grice, Rena; Burgin, Alex; Stewart, Lance

2009-01-01

Background To improve efficiency in high throughput protein structure determination, we have developed a database software package, Gene Composer, which facilitates the information-rich design of protein constructs and their codon engineered synthetic gene sequences. With its modular workflow design and numerous graphical user interfaces, Gene Composer enables researchers to perform all common bio-informatics steps used in modern structure guided protein engineering and synthetic gene engineering. Results An interactive Alignment Viewer allows the researcher to simultaneously visualize sequence conservation in the context of known protein secondary structure, ligand contacts, water contacts, crystal contacts, B-factors, solvent accessible area, residue property type and several other useful property views. The Construct Design Module enables the facile design of novel protein constructs with altered N- and C-termini, internal insertions or deletions, point mutations, and desired affinity tags. The modifications can be combined and permuted into multiple protein constructs, and then virtually cloned in silico into defined expression vectors. The Gene Design Module uses a protein-to-gene algorithm that automates the back-translation of a protein amino acid sequence into a codon engineered nucleic acid gene sequence according to a selected codon usage table with minimal codon usage threshold, defined G:C% content, and desired sequence features achieved through synonymous codon selection that is optimized for the intended expression system. The gene-to-oligo algorithm of the Gene Design Module plans out all of the required overlapping oligonucleotides and mutagenic primers needed to synthesize the desired gene constructs by PCR, and for physically cloning them into selected vectors by the most popular subcloning strategies. Conclusion We present a complete description of Gene Composer functionality, and an efficient PCR-based synthetic gene assembly procedure with mis-match specific endonuclease error correction in combination with PIPE cloning. In a sister manuscript we present data on how Gene Composer designed genes and protein constructs can result in improved protein production for structural studies. PMID:19383142

Gene composer: database software for protein construct design, codon engineering, and gene synthesis.

PubMed

Lorimer, Don; Raymond, Amy; Walchli, John; Mixon, Mark; Barrow, Adrienne; Wallace, Ellen; Grice, Rena; Burgin, Alex; Stewart, Lance

2009-04-21

To improve efficiency in high throughput protein structure determination, we have developed a database software package, Gene Composer, which facilitates the information-rich design of protein constructs and their codon engineered synthetic gene sequences. With its modular workflow design and numerous graphical user interfaces, Gene Composer enables researchers to perform all common bio-informatics steps used in modern structure guided protein engineering and synthetic gene engineering. An interactive Alignment Viewer allows the researcher to simultaneously visualize sequence conservation in the context of known protein secondary structure, ligand contacts, water contacts, crystal contacts, B-factors, solvent accessible area, residue property type and several other useful property views. The Construct Design Module enables the facile design of novel protein constructs with altered N- and C-termini, internal insertions or deletions, point mutations, and desired affinity tags. The modifications can be combined and permuted into multiple protein constructs, and then virtually cloned in silico into defined expression vectors. The Gene Design Module uses a protein-to-gene algorithm that automates the back-translation of a protein amino acid sequence into a codon engineered nucleic acid gene sequence according to a selected codon usage table with minimal codon usage threshold, defined G:C% content, and desired sequence features achieved through synonymous codon selection that is optimized for the intended expression system. The gene-to-oligo algorithm of the Gene Design Module plans out all of the required overlapping oligonucleotides and mutagenic primers needed to synthesize the desired gene constructs by PCR, and for physically cloning them into selected vectors by the most popular subcloning strategies. We present a complete description of Gene Composer functionality, and an efficient PCR-based synthetic gene assembly procedure with mis-match specific endonuclease error correction in combination with PIPE cloning. In a sister manuscript we present data on how Gene Composer designed genes and protein constructs can result in improved protein production for structural studies.

Constructively Aligning the Curriculum of a "New Generation" Bachelor of Environments Degree from a Social Realism Perspective

ERIC Educational Resources Information Center

Onsman, Andrys

2015-01-01

This paper describes the process of constructively aligning a generalist undergraduate degree using a sociological structure of professional education. Drawing largely on the work of educational sociologists like Young, Winch and Muller, the process aimed to introduce the notion of recontextualization as the curriculum driver for the constructive…

Facilitating Constructive Alignment in Power Systems Engineering Education Using Free and Open-Source Software

ERIC Educational Resources Information Center

Vanfretti, L.; Milano, F.

2012-01-01

This paper describes how the use of free and open-source software (FOSS) can facilitate the application of constructive alignment theory in power systems engineering education by enabling the deep learning approach in power system analysis courses. With this aim, this paper describes the authors' approach in using the Power System Analysis Toolbox…

AlexSys: a knowledge-based expert system for multiple sequence alignment construction and analysis

PubMed Central

Aniba, Mohamed Radhouene; Poch, Olivier; Marchler-Bauer, Aron; Thompson, Julie Dawn

2010-01-01

Multiple sequence alignment (MSA) is a cornerstone of modern molecular biology and represents a unique means of investigating the patterns of conservation and diversity in complex biological systems. Many different algorithms have been developed to construct MSAs, but previous studies have shown that no single aligner consistently outperforms the rest. This has led to the development of a number of ‘meta-methods’ that systematically run several aligners and merge the output into one single solution. Although these methods generally produce more accurate alignments, they are inefficient because all the aligners need to be run first and the choice of the best solution is made a posteriori. Here, we describe the development of a new expert system, AlexSys, for the multiple alignment of protein sequences. AlexSys incorporates an intelligent inference engine to automatically select an appropriate aligner a priori, depending only on the nature of the input sequences. The inference engine was trained on a large set of reference multiple alignments, using a novel machine learning approach. Applying AlexSys to a test set of 178 alignments, we show that the expert system represents a good compromise between alignment quality and running time, making it suitable for high throughput projects. AlexSys is freely available from http://alnitak.u-strasbg.fr/∼aniba/alexsys. PMID:20530533

Designing of plant artificial chromosome (PAC) by using the Chlorella smallest chromosome as a model system.

PubMed

Noutoshi, Y; Arai, R; Fujie, M; Yamada, T

1997-01-01

As a model for plant-type chromosomes, we have been characterizing molecular organization of the Chlorella vulgaris C-169 chromosome I. To identify chromosome structural elements including the centromeric region and replication origins, we constructed a chromosome I specific cosmid library and aligned each cosmid clones to generate contigs. So far, more than 80% of the entire chromosome I has been covered. A complete clonal physical reconstitution of chromosome I provides information on the structure and genomic organization of plant genome. We propose our strategy to construct an artificial chromosome by assembling the functional chromosome structural elements identified on Chrorella chromosome I.

SATCHMO-JS: a webserver for simultaneous protein multiple sequence alignment and phylogenetic tree construction.

PubMed

Hagopian, Raffi; Davidson, John R; Datta, Ruchira S; Samad, Bushra; Jarvis, Glen R; Sjölander, Kimmen

2010-07-01

We present the jump-start simultaneous alignment and tree construction using hidden Markov models (SATCHMO-JS) web server for simultaneous estimation of protein multiple sequence alignments (MSAs) and phylogenetic trees. The server takes as input a set of sequences in FASTA format, and outputs a phylogenetic tree and MSA; these can be viewed online or downloaded from the website. SATCHMO-JS is an extension of the SATCHMO algorithm, and employs a divide-and-conquer strategy to jump-start SATCHMO at a higher point in the phylogenetic tree, reducing the computational complexity of the progressive all-versus-all HMM-HMM scoring and alignment. Results on a benchmark dataset of 983 structurally aligned pairs from the PREFAB benchmark dataset show that SATCHMO-JS provides a statistically significant improvement in alignment accuracy over MUSCLE, Multiple Alignment using Fast Fourier Transform (MAFFT), ClustalW and the original SATCHMO algorithm. The SATCHMO-JS webserver is available at http://phylogenomics.berkeley.edu/satchmo-js. The datasets used in these experiments are available for download at http://phylogenomics.berkeley.edu/satchmo-js/supplementary/.

Combining cell sheet technology and electrospun scaffolding for engineered tubular, aligned, and contractile blood vessels.

PubMed

Rayatpisheh, Shahrzad; Heath, Daniel E; Shakouri, Amir; Rujitanaroj, Pim-On; Chew, Sing Yian; Chan-Park, Mary B

2014-03-01

Herein we combine cell sheet technology and electrospun scaffolding to rapidly generate circumferentially aligned tubular constructs of human aortic smooth muscles cells with contractile gene expression for use as tissue engineered blood vessel media. Smooth muscle cells cultured on micropatterned and N-isopropylacrylamide-grafted (pNIPAm) polydimethylsiloxane (PDMS), a small portion of which was covered by aligned electrospun scaffolding, resulted in a single sheet of unidirectionally aligned cells. Upon cooling to room temperature, the scaffold, its adherent cells, and the remaining cell sheet detached and were collected on a mandrel to generating tubular constructs with circumferentially aligned smooth muscle cells which possess contractile gene expression and a single layer of electrospun scaffold as an analogue to a small diameter blood vessel's internal elastic lamina (IEL). This method improves cell sheet handling, results in rapid circumferential alignment of smooth muscle cells which immediately express contractile genes, and introduction of an analogue to small diameter blood vessel IEL. Copyright © 2013 Elsevier Ltd. All rights reserved.

Structure and method for controlling band offset and alignment at a crystalline oxide-on-semiconductor interface

DOEpatents

McKee, Rodney A.; Walker, Frederick J.

2003-11-25

A crystalline oxide-on-semiconductor structure and a process for constructing the structure involves a substrate of silicon, germanium or a silicon-germanium alloy and an epitaxial thin film overlying the surface of the substrate wherein the thin film consists of a first epitaxial stratum of single atomic plane layers of an alkaline earth oxide designated generally as (AO).sub.n and a second stratum of single unit cell layers of an oxide material designated as (A'BO.sub.3).sub.m so that the multilayer film arranged upon the substrate surface is designated (AO).sub.n (A'BO.sub.3).sub.m wherein n is an integer repeat of single atomic plane layers of the alkaline earth oxide AO and m is an integer repeat of single unit cell layers of the A'BO.sub.3 oxide material. Within the multilayer film, the values of n and m have been selected to provide the structure with a desired electrical structure at the substrate/thin film interface that can be optimized to control band offset and alignment.

Design of an Fiber-Coupled Laser Heterodyne Interferometer for the FLARE

NASA Astrophysics Data System (ADS)

Frank, Samuel; Yoo, Jongsoo; Ji, Hantao; Jara-Almonte, Jon

2016-10-01

The FLARE (Facility for Laboratory Reconnection Experiments), which is currently under construction at PPPL, requires a complete set of laboratory plasma diagnostics. The Langmuir probes that will be used in the device to gather local density data require a reliable interferometer system to serve as baseline for density measurement calibration. A fully fiber-coupled infrared laser heterodyne interferometer has been designed in order to serve as the primary line-integrated electron density diagnostic. Thanks to advances in the communications industry many fiber optic devices and phase detection methods have advanced significantly becoming increasingly reliable and inexpensive. Fully fiber coupling a plasma interferometer greatly simplifies alignment procedures needed since the only free space laser path needing alignment is through the plasma itself. Fiber-coupling also provides significant resistance to vibrational noise, a common problem in plasma interferometry systems. This device also uses a greatly simplified phase detection scheme in which chips, originally developed for the communications industry, capable of directly detecting the phase shift of a signal with high time resolution. The design and initial performance of the system will be discussed.

Electro-optic characteristics of 4-domain vertical alignment nematic liquid crystal display with interdigital electrode

NASA Astrophysics Data System (ADS)

Hong, S. H.; Jeong, Y. H.; Kim, H. Y.; Cho, H. M.; Lee, W. G.; Lee, S. H.

2000-06-01

We have fabricated a vertically aligned 4-domain nematic liquid crystal display cell with thin film transistor. Unlike the conventional method constructing 4-domain, i.e., protrusion and surrounding electrode which needs additional processes, in this study the pixel design forming 4-domain with interdigital electrodes is suggested. In the device, one pixel is divided into two parts. One part has a horizontal electric field in the vertical direction and the other part has a horizontal one in the horizontal direction. Such fields in the horizontal and vertical direction drive the liquid crystal director to tilt down in four directions. In this article, the electro-optic characteristics of cells with 2 and 4 domain have been studied. The device with 4 domain shows faster response time than normal twisted-nematic and in-plane switching cells, wide viewing angle with optical compensation film, and more stable color characteristics than 2-domain vertical alignment cell with similar structure.

Design of a versatile clinical aberrometer

NASA Astrophysics Data System (ADS)

Sheehan, Matthew; Goncharov, Alexander; Dainty, Chris

2005-09-01

We have designed an ocular aberrometer based on the Hartmann-Shack (HS) type wavefront sensor for use in optometry clinics. The optical system has enhanced versatility compared with commercial aberrometers, yet it is compact and user-friendly. The system has the capability to sense both on-axis and off-axis aberrations in the eye within an unobstructed 20 degree field. This capability is essential to collect population data for off-axis aberrations. This data will be useful in designing future adaptive optics (AO) systems to improve image quality of eccentric retinal areas, in particular, for multi-conjugate AO systems. The ability of the examiner to control the accommodation demand is a unique feature of the design that commercial instruments are capable of only after modification. The pupil alignment channel is re-combined with the sensing channel in a parallel path and imaged on a single CCD. This makes the instrument more compact, less expensive, and it helps to synchronize the pupil center with the HS spot coordinate system. Another advantage of the optical design is telecentric re-imaging of the HS spots, increasing the robustness to small longitudinal alignment errors. The optical system has been optimized with a ray-tracing program and its prototype is being constructed. Design considerations together with a description of the optical components are presented. Difficulties and future work are outlined.

Rod-Shaped Neural Units for Aligned 3D Neural Network Connection.

PubMed

Kato-Negishi, Midori; Onoe, Hiroaki; Ito, Akane; Takeuchi, Shoji

2017-08-01

This paper proposes neural tissue units with aligned nerve fibers (called rod-shaped neural units) that connect neural networks with aligned neurons. To make the proposed units, 3D fiber-shaped neural tissues covered with a calcium alginate hydrogel layer are prepared with a microfluidic system and are cut in an accurate and reproducible manner. These units have aligned nerve fibers inside the hydrogel layer and connectable points on both ends. By connecting the units with a poly(dimethylsiloxane) guide, 3D neural tissues can be constructed and maintained for more than two weeks of culture. In addition, neural networks can be formed between the different neural units via synaptic connections. Experimental results indicate that the proposed rod-shaped neural units are effective tools for the construction of spatially complex connections with aligned nerve fibers in vitro. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Designing a Bioengine for Detection and Analysis of Base String on an Affected Sequence in High-Concentration Regions

PubMed Central

Mandal, Bijoy Kumar; Kim, Tai-hoon

2013-01-01

We design an Algorithm for bioengine. As a program are enable optimal alignments searching between two sequences, the host sequence (normal plant) as well as query sequence (virus). Searching for homologues has become a routine operation of biological sequences in 4 × 4 combination with different subsequence (word size). This program takes the advantage of the high degree of homology between such sequences to construct an alignment of the matching regions. There is a main aim which is to detect the overlapping reading frames. This program also enables to find out the highly infected colones selection highest matching region with minimum gap or mismatch zones and unique virus colones matches. This is a small, portable, interactive, front-end program intended to be used to find out the regions of matching between host sequence and query subsequences. All the operations are carried out in fraction of seconds, depending on the required task and on the sequence length. PMID:24000321

Integrated manufacture of a freeform off-axis multi-reflective imaging system without optical alignment.

PubMed

Li, Zexiao; Liu, Xianlei; Fang, Fengzhou; Zhang, Xiaodong; Zeng, Zhen; Zhu, Linlin; Yan, Ning

2018-03-19

Multi-reflective imaging systems find wide applications in optical imaging and space detection. However, it is faced with difficulties in adjusting the freeform mirrors with high accuracy to guarantee the optical function. Motivated by this, an alignment-free manufacture approach is proposed to machine the optical system. The direct optical performance-guided manufacture route is established without measuring the form error of freeform optics. An analytical model is established to investigate the effects of machine errors to serve the error identification and compensation in machining. Based on the integrated manufactured system, an ingenious self-designed testing configuration is constructed to evaluate the optical performance by directly measuring the wavefront aberration. Experiments are carried out to manufacture a three-mirror anastigmat, surface topographical details and optical performance shows agreement to the designed expectation. The final system works as an off-axis infrared imaging system. Results validate the feasibility of the proposed method to achieve excellent optical application.

Scanning retarding field analyzer for plasma profile measurements in the boundary of the Alcator C-Mod tokamak

DOE Office of Scientific and Technical Information (OSTI.GOV)

Brunner, D.; LaBombard, B.; Ochoukov, R.

2013-03-15

A new Retarding Field Analyzer (RFA) head has been created for the outer-midplane scanning probe system on the Alcator C-Mod tokamak. The new probe head contains back-to-back retarding field analyzers aligned with the local magnetic field. One faces 'upstream' into the field-aligned plasma flow and the other faces 'downstream' away from the flow. The RFA was created primarily to benchmark ion temperature measurements of an ion sensitive probe; it may also be used to interrogate electrons. However, its construction is robust enough to be used to measure ion and electron temperatures up to the last-closed flux surface in C-Mod. Amore » RFA probe of identical design has been attached to the side of a limiter to explore direct changes to the boundary plasma due to lower hybrid heating and current drive. Design of the high heat flux (>100 MW/m{sup 2}) handling probe and initial results are presented.« less

Optical alignment procedure utilizing neural networks combined with Shack-Hartmann wavefront sensor

NASA Astrophysics Data System (ADS)

Adil, Fatime Zehra; Konukseven, Erhan İlhan; Balkan, Tuna; Adil, Ömer Faruk

2017-05-01

In the design of pilot helmets with night vision capability, to not limit or block the sight of the pilot, a transparent visor is used. The reflected image from the coated part of the visor must coincide with the physical human sight image seen through the nonreflecting regions of the visor. This makes the alignment of the visor halves critical. In essence, this is an alignment problem of two optical parts that are assembled together during the manufacturing process. Shack-Hartmann wavefront sensor is commonly used for the determination of the misalignments through wavefront measurements, which are quantified in terms of the Zernike polynomials. Although the Zernike polynomials provide very useful feedback about the misalignments, the corrective actions are basically ad hoc. This stems from the fact that there exists no easy inverse relation between the misalignment measurements and the physical causes of the misalignments. This study aims to construct this inverse relation by making use of the expressive power of the neural networks in such complex relations. For this purpose, a neural network is designed and trained in MATLAB® regarding which types of misalignments result in which wavefront measurements, quantitatively given by Zernike polynomials. This way, manual and iterative alignment processes relying on trial and error will be replaced by the trained guesses of a neural network, so the alignment process is reduced to applying the counter actions based on the misalignment causes. Such a training requires data containing misalignment and measurement sets in fine detail, which is hard to obtain manually on a physical setup. For that reason, the optical setup is completely modeled in Zemax® software, and Zernike polynomials are generated for misalignments applied in small steps. The performance of the neural network is experimented and found promising in the actual physical setup.

Theoferometer for High Accuracy Optical Alignment and Metrology

NASA Technical Reports Server (NTRS)

Toland, Ronald; Leviton, Doug; Koterba, Seth

2004-01-01

The accurate measurement of the orientation of optical parts and systems is a pressing problem for upcoming space missions, such as stellar interferometers, requiring the knowledge and maintenance of positions to the sub-arcsecond level. Theodolites, the devices commonly used to make these measurements, cannot provide the needed level of accuracy. This paper describes the design, construction, and testing of an interferometer system to fill the widening gap between future requirements and current capabilities. A Twyman-Green interferometer mounted on a 2 degree of freedom rotation stage is able to obtain sub-arcsecond, gravity-referenced tilt measurements of a sample alignment cube. Dubbed a 'theoferometer,' this device offers greater ease-of-use, accuracy, and repeatability than conventional methods, making it a suitable 21st-century replacement for the theodolite.

An optical storage cavity-based, Compton-backscatter x-ray source using the MKV free electron laser

NASA Astrophysics Data System (ADS)

Hadmack, Michael R.

A compact, high-brightness x-ray source is presently under development at the University of Hawai`i Free Electron Laser Laboratory. This source utilizes Compton backscattering of an infrared laser from a relativistic electron beam to produce a narrow beam of monochromatic x-rays. The scattering efficiency is greatly increased by tightly focusing the two beams at an interaction point within a near-concentric optical storage cavity, designed with high finesse to coherently stack the incident laser pulses and greatly enhance the number of photons available for scattering with the electron beam. This dissertation describes the effort and progress to integrate and characterize the most important and challenging aspects of the design of this system. A low-power, near-concentric, visible-light storage cavity has been constructed as a tool for the exploration of the performance, alignment procedures, and diagnostics required for the operation of a high power infrared storage cavity. The use of off-axis reflective focussing elements is essential to the design of the optical storage cavity, but requires exquisite alignment to minimize astigmatism and other optical aberrations. Experiments using a stabilized HeNe laser have revealed important performance characteristics, and allowed the development of critical alignment and calibration procedures, which can be directly applied to the high power infrared storage cavity. Integration of the optical and electron beams is similarly challenging. A scanning-wire beam profiler has been constructed and tested, which allows for high resolution measurement of the size and position of the laser and electron beams at the interaction point. This apparatus has demonstrated that the electron and laser beams can be co-aligned with a precision of less than 10 microm, as required to maximize the x-ray production rate. Equally important is the stabilization of the phase of the GHz repetition rate electron pulses arriving at the interaction point and driving the FEL. A feed-forward amplitude and phase compensation system has been built and demonstrated to substantially improve the uniformity of the electron bunch phase, thus enhancing both the laser performance and the beam stability required for efficient x-ray production. Results of all of these efforts are presented, together with a summary of future work.

Laser Transmitter Aims At Laser Beacon

NASA Technical Reports Server (NTRS)

Hemmati, Hamid; Lesh, James R.

1993-01-01

Transmitter part of developmental optical communication system. Compact, lightweight, partially-self-aiming laser transmitter built to verify some capabilities of developmental free-space optical communication system. Design capable of providing 0.5 Mbps data return over range equal to Moon-Earth distance. Breadboard of transmitting terminal constructed and tested in laboratory. Prototype transmitter includes receiving circuitry that keeps it aimed at beacon, once brought into initial alignment within about 1.7 degrees of line of sight to beacon.

Pupil Alignment Considerations for Large, Deployable Space Telescopes

NASA Technical Reports Server (NTRS)

Bos, Brent J.; Ohl, Raymond G.; Kubalak, Daivd A.

2011-01-01

For many optical systems the properties and alignment of the internal apertures and pupils are not critical or controlled with high precision during optical system design, fabrication or assembly. In wide angle imaging systems, for instance, the entrance pupil position and orientation is typically unconstrained and varies over the system s field of view in order to optimize image quality. Aperture tolerances usually do not receive the same amount of scrutiny as optical surface aberrations or throughput characteristics because performance degradation is typically graceful with misalignment, generally only causing a slight reduction in system sensitivity due to vignetting. But for a large deployable space-based observatory like the James Webb Space Telescope (JWST), we have found that pupil alignment is a key parameter. For in addition to vignetting, JWST pupil errors cause uncertainty in the wavefront sensing process that is used to construct the observatory on-orbit. Furthermore they also open stray light paths that degrade the science return from some of the telescope s instrument channels. In response to these consequences, we have developed several pupil measurement techniques for the cryogenic vacuum test where JWST science instrument pupil alignment is verified. These approaches use pupil alignment references within the JWST science instruments; pupil imaging lenses in three science instrument channels; and unique pupil characterization features in the optical test equipment. This will allow us to verify and crosscheck the lateral pupil alignment of the JWST science instruments to approximately 1-2% of their pupil diameters.

Design and development of a new SRF cavity cryomodule for the ATLAS intensity upgrade

NASA Astrophysics Data System (ADS)

Kedzie, Mark; Conway, Zachary; Fuerst, Joel; Gerbick, Scott; Kelly, Michael; Morgan, James; Ostroumov, Peter; O'Toole, Michael; Shepard, Kenneth

2012-06-01

The ATLAS heavy ion linac at Argonne National Laboratory is undergoing an intensity upgrade that includes the development and implementation of a new cryomodule containing four superconducting solenoids and seven quarter-wave drift-tube-loaded superconducting rf cavities. The rf cavities extend the state of the art for this class of structure and feature ASME code stamped stainless steel liquid helium containment vessels. The cryomodule design is a further evolution of techniques recently implemented in a previous upgrade [1]. We provide a status report on the construction effort and describe the vacuum vessel, thermal shield, cold mass support and alignment, and other subsystems including couplers and tuners. Cavity mechanical design is also reviewed.

Mechanics of oriented electrospun nanofibrous scaffolds for annulus fibrosus tissue engineering.

PubMed

Nerurkar, Nandan L; Elliott, Dawn M; Mauck, Robert L

2007-08-01

Engineering a functional replacement for the annulus fibrosus (AF) of the intervertebral disc is contingent upon recapitulation of AF structure, composition, and mechanical properties. In this study, we propose a new paradigm for AF tissue engineering that focuses on the reconstitution of anatomic fiber architecture and uses constitutive modeling to evaluate construct function. A modified electrospinning technique was utilized to generate aligned nanofibrous polymer scaffolds for engineering the basic functional unit of the AF, a single lamella. Scaffolds were tested in uniaxial tension at multiple fiber orientations, demonstrating a nonlinear dependence of modulus on fiber angle that mimicked the nonlinearity and anisotropy of native AF. A homogenization model previously applied to native AF successfully described scaffold mechanical response, and parametric studies demonstrated that nonfibrillar matrix, along with fiber connectivity, are key contributors to tensile mechanics for engineered AF. We demonstrated that AF cells orient themselves along the aligned scaffolds and deposit matrix that contributes to construct mechanics under loading conditions relevant to the in vivo environment. The homogenization model was applied to cell-seeded constructs and provided quantitative measures for the evolution of matrix and interfibrillar interactions. Finally, the model demonstrated that at fiber angles of the AF (28 degrees -44 degrees ), engineered material behaved much like native tissue, suggesting that engineered constructs replicate the physiologic behavior of the single AF lamella. Constitutive modeling provides a powerful tool for analysis of engineered AF neo-tissue and native AF tissue alike, highlighting key mechanical design criteria for functional AF tissue engineering.

Establishing Alignment in Aphasia Couples Therapy in a Woman with Wernicke's Aphasia: A Case Study

ERIC Educational Resources Information Center

Boles, Larry

2015-01-01

Alignment refers to the interactive use of similar words to accomplish a linguistic and cognitive "common ground" in conversations. Alignment is thought to be unconscious, relying on priming mechanisms. This occurs uniquely in conversational contexts and has been shown in choices of words, grammatical constructions, and even indirect…

Development of a Mirror Pointing Mechanism for an Atmospheric Gas Measurement Instrument

NASA Technical Reports Server (NTRS)

Graham, Michael; Belous, Adel; Brown, Jeffrey; Podolske, James

1998-01-01

Development of the Open Path Tunable Infrared Monitor of the Atmosphere (OPTIMA) instrument involved designing a pair of motion systems that could maintain a precise alignment and spatial distance between two mirrors installed on the NASA DC-8 research laboratory aircraft. This is the first airborne optical instrument that allows direct measurement of the gases in the freestream airflow on the exterior of the aircraft. One mirror is mounted within a specially constructed open port cavity in the cabin of the aircraft and the second is mounted 6 meters away on top of the inboard port side (number 2) engine pylon. Three co-aligned laser beams are reflected between the two mirrors 64 times in a Herriott pattern. The resulting sample path length of 384 meters is used to perform a spectral absorption analysis of the airflow between the mirrors. To compensate for normal wing movement and engine oscillations both mirrors were designed as continuously driven mechanisms to maintain alignment within allowable limits. The motion systems of the two mirror assemblies provide five degrees of freedom and are designed to maintain a pointing accuracy within seven arc-sec with a response frequency in 6xcess of 10 Hz. The pylon motion system incorporates controlled pitch and yaw movement. The fuselage motion system compensates for pitch variation as well as linear translation for focal length and vertical aiming of the laser beam via a controlled beam guidance mechanism.

Construction and quality assurance of large area resistive strip Micromegas for the upgrade of the ATLAS Muon Spectrometer at LHC/CERN

NASA Astrophysics Data System (ADS)

Lösel, P.

2017-06-01

Large area Micromegas detectors will be employed for the first time in high-energy physics experiments. To cope with increasing background rates, associated with the steadily increasing luminosity of LHC to 10 times design luminosity, the present detector technology in the current innermost stations of the muon endcap system of the ATLAS experiment (the Small Wheel), will be replaced in 2019/2020 by resistive strip Micromegas and small strip TGC detectors. Both technologies will provide tracking and trigger information. In the "New Small Wheel" the Micromegas will be arranged in eight detection layers built of trapezoidally shaped quadruplets of four different sizes covering in total about 1200 m2 of detection plane. In order to achieve 15 % transverse momentum resolution for 1 TeV muons, a challenging mechanical precision is required in the construction of each active plane, with an alignment of the readout strips at the level of 30 μm RMS along the precision coordinate and 80 μm RMS perpendicular to the plane. Each individual Micromegas plane must achieve a spatial resolution better than 100 μm at background rates up to 15 kHz/cm2 while being operated in an inhomogeneous magnetic field (B <= 0.3 T). The required mechanical precision for the production of the components and their assembly, on such large area detectors, is a key point and must be controlled during construction and integration. Particularly the alignment of the readout strips within a quadruplet appears to be demanding. The readout strips are etched on PCB boards using photolithographic processes. Depending on the type of the module, 3 or 5 PCB boards need to be joined and precisely aligned to form a full readout plane. The precision in the alignment is reached either by use of precision mechanical holes or by optical masks, both referenced to the strip patterns. Assembly procedures have been developed to build the single panels with the required mechanical precision and to assemble them in a module including the four metallic micro-meshes. Methods to confirm the precision of components and assembly are based on precise optical devices and X-ray or cosmic muon investigations. We will report on the construction procedures for the Micromegas quadruplets, on the quality control procedures and results, and on the assembly and calibration methods.

Beliefs about language development: construct validity evidence.

PubMed

Donahue, Mavis L; Fu, Qiong; Smith, Everett V

2012-01-01

Understanding language development is incomplete without recognizing children's sociocultural environments, including adult beliefs about language development. Yet there is a need for data supporting valid inferences to assess these beliefs. The current study investigated the psychometric properties of data from a survey (MODeL) designed to explore beliefs in the popular culture, and their alignment with more formal theories. Support for the content, substantive, structural, generalizability, and external aspects of construct validity of the data were investigated. Subscales representing Behaviorist, Cognitive, Nativist, and Sociolinguistic models were identified as dimensions of beliefs. More than half of the items showed a high degree of consensus, suggesting culturally-transmitted beliefs. Behaviorist ideas were most popular. Bilingualism and ethnicity were related to Cognitive and Sociolinguistic beliefs. Identifying these beliefs may clarify the nature of child-directed speech, and enable the design of language intervention programs that are congruent with family and cultural expectations.

Channeled Scaffolds for Engineering Myocardium with Mechanical Stimulation

PubMed Central

Zhang, Ting; Wan, Leo Q.; Xiong, Zhuo; Marsano, Anna; Maidhof, Robert; Park, Miri; Yan, Yongnian; Vunjak-Novakovic, Gordana

2011-01-01

The characteristics of the matrix (composition, structure, mechanical properties) and external culture environment (pulsatile perfusion, physical stimulation) are critically important for engineering functional myocardial tissue. We report the development of chitosan-collagen scaffolds with micro-pores and an array of parallel channels (~200 μm in diameter) that were specifically designed for cardiac tissue engineering with mechanical stimulation. The scaffolds were designed to have the structural and mechanical properties similar to those of the native human heart matrix. Scaffolds were seeded with neonatal rat heart cells and subjected to dynamic tensile stretch using a custom-designed bioreactor. The channels enhanced oxygen transport and facilitated the establishment of cell connections within the construct. The myocardial patches (14 mm in diameter, 1–2 mm thick) consisted of metabolically active cells and started to contract synchronously after 3 days of culture. Mechanical stimulation with high tensile stresses promoted cell alignment, elongation, and the expression of connexin-43 (Cx-43). This study confirms the importance of scaffold design and mechanical stimulation for the formation of contractile cardiac constructs. PMID:22081518

Channelled scaffolds for engineering myocardium with mechanical stimulation.

PubMed

Zhang, Ting; Wan, Leo Q; Xiong, Zhuo; Marsano, Anna; Maidhof, Robert; Park, Miri; Yan, Yongnian; Vunjak-Novakovic, Gordana

2012-10-01

The characteristics of the matrix (composition, structure, mechanical properties) and external culture environment (pulsatile perfusion, physical stimulation) of the heart are important characteristics in the engineering of functional myocardial tissue. This study reports on the development of chitosan-collagen scaffolds with micropores and an array of parallel channels (~ 200 µm in diameter) that were specifically designed for cardiac tissue engineering using mechanical stimulation. The scaffolds were designed to have similar structural and mechanical properties of those of native heart matrix. Scaffolds were seeded with neonatal rat heart cells and subjected to dynamic tensile stretch using a custom designed bioreactor. The channels enhanced oxygen transport and facilitated the establishment of cell connections within the construct. The myocardial patches (14 mm in diameter, 1-2 mm thick) consisted of metabolically active cells that began to contract synchronously after 3 days of culture. Mechanical stimulation with high tensile stress promoted cell alignment, elongation, and expression of connexin-43 (Cx-43). This study confirms the importance of scaffold design and mechanical stimulation for the formation of contractile cardiac constructs. Copyright © 2011 John Wiley & Sons, Ltd.

Signal Design for Improved Ranging Among Multiple Transceivers

NASA Technical Reports Server (NTRS)

Young, Lawrence; Tien, Jeffrey; Srinivasan, Jeffrey

2004-01-01

"Ultra-BOC" (where "BOC" signifies "binary offset carrier") is the name of an improved generic design of microwave signals to be used by a group of spacecraft flying in formation to measure ranges and bearings among themselves and to exchange telemetry needed for these measurements. Ultra-BOC could also be applied on Earth for diverse purposes -- for example, measuring relative positions of vehicles on highways for traffic-control purposes and determining the relative alignments of machines operating in mines and of construction machines and structures at construction sites. Ultra-BOC provides for rapid and robust acquisition of signals, even when signal-to-noise ratios are low. The design further provides that each spacecraft or other platform constantly strives to acquire and track the signals from the other platforms while simultaneously transmitting signals that provide full range, bearing, and telemetry service to the other platforms. In Ultra-BOC, unlike in other signal designs that have been considered for the same purposes, it is not necessary to maneuver the spacecraft or other platforms to obtain the data needed for resolving integer-carrier-cycle phase ambiguities.

Automated fiber pigtailing machine

DOEpatents

Strand, Oliver T.; Lowry, Mark E.

1999-01-01

The Automated Fiber Pigtailing Machine (AFPM) aligns and attaches optical fibers to optoelectonic (OE) devices such as laser diodes, photodiodes, and waveguide devices without operator intervention. The so-called pigtailing process is completed with sub-micron accuracies in less than 3 minutes. The AFPM operates unattended for one hour, is modular in design and is compatible with a mass production manufacturing environment. This machine can be used to build components which are used in military aircraft navigation systems, computer systems, communications systems and in the construction of diagnostics and experimental systems.

In silico design, construction and cloning of Trastuzumab humanized monoclonal antibody: A possible biosimilar for Herceptin

PubMed Central

Akbarzadeh-Sharbaf, Soudabeh; Yakhchali, Bagher; Minuchehr, Zarrin; Shokrgozar, Mohammad Ali; Zeinali, Sirous

2012-01-01

Background: There is a novel hypothesis in that antibodies may have specificity for two distinct antigens that have been named “dual specificity”. This hypothesis was evaluated for some defined therapeutic monoclonal antibodies (mAbs) such as Trastuzumab, Pertuzumab, Bevacizumab, and Cetuximab. In silico design and construction of expression vectors for trastuzumab monoclonal antibody also in this work were performed. Materials and Methods: First, in bioinformatics studies the 3D structures of concerned mAbs were obtained from the Protein Data Bank (PDB). Three-dimensional structural alignments were performed with SIM and MUSTANG softwares. AutoDock4.2 software also was used for the docking analysis. Second, the suitable genes for trastuzumab heavy and light chains were designed, synthesized, and cloned in the prokaryotic vector. These fragments individually were PCR amplified and cloned into pcDNA™ 3.3-TOPO® and pOptiVEC™ TOPO® shuttle vectors, using standard methods. Results: First, many bioinformatics tools and softwares were applied but we did not meet any new dual specificity in the selected antibodies. In the following step, the suitable expression cascade for the heavy and light chains of Trastuzumab therapeutic mAb were designed and constructed. Gene cloning was successfully performed and created constructs were confirmed using gene mapping and sequencing. Conclusions: This study was based on a recently developed technology for mAb expression in mammalian cells. The obtained constructs could be successfully used for biosimilar recombinant mAb production in CHO DG44 dihydrofolate reductase (DHFR) gene deficient cell line in the suspension culture medium. PMID:23210080

WEB-server for search of a periodicity in amino acid and nucleotide sequences

NASA Astrophysics Data System (ADS)

E Frenkel, F.; Skryabin, K. G.; Korotkov, E. V.

2017-12-01

A new web server (http://victoria.biengi.ac.ru/splinter/login.php) was designed and developed to search for periodicity in nucleotide and amino acid sequences. The web server operation is based upon a new mathematical method of searching for multiple alignments, which is founded on the position weight matrices optimization, as well as on implementation of the two-dimensional dynamic programming. This approach allows the construction of multiple alignments of the indistinctly similar amino acid and nucleotide sequences that accumulated more than 1.5 substitutions per a single amino acid or a nucleotide without performing the sequences paired comparisons. The article examines the principles of the web server operation and two examples of studying amino acid and nucleotide sequences, as well as information that could be obtained using the web server.

Twin-Mirrored-Galvanometer Laser-Light-Sheet Generator

NASA Technical Reports Server (NTRS)

Rhodes, David B.; Franke, John M.; Jones, Stephen B.; Leighty, Bradley D.

1991-01-01

Multiple, rotating laser-light sheets generated to illuminate flows in wind tunnels. Designed and developed to provide flexibility and adaptability to wide range of applications. Design includes capability to control size and location of laser-light sheet in real time, to generate horizontal or vertical sheets, to sweep sheet repeatedly through volume, to generate multiple sheets with controllable separation, and to rotate single or multiple laser-light sheets. Includes electronic equipment and laser mounted on adjustable-height platform. Twin-mirrored galvanometer unit supported by tripod to reduce vibration. Other possible applications include use in construction industry to align beams of building. Artistic or display applications also possible.

RNA-SeQC: RNA-seq metrics for quality control and process optimization.

PubMed

DeLuca, David S; Levin, Joshua Z; Sivachenko, Andrey; Fennell, Timothy; Nazaire, Marc-Danie; Williams, Chris; Reich, Michael; Winckler, Wendy; Getz, Gad

2012-06-01

RNA-seq, the application of next-generation sequencing to RNA, provides transcriptome-wide characterization of cellular activity. Assessment of sequencing performance and library quality is critical to the interpretation of RNA-seq data, yet few tools exist to address this issue. We introduce RNA-SeQC, a program which provides key measures of data quality. These metrics include yield, alignment and duplication rates; GC bias, rRNA content, regions of alignment (exon, intron and intragenic), continuity of coverage, 3'/5' bias and count of detectable transcripts, among others. The software provides multi-sample evaluation of library construction protocols, input materials and other experimental parameters. The modularity of the software enables pipeline integration and the routine monitoring of key measures of data quality such as the number of alignable reads, duplication rates and rRNA contamination. RNA-SeQC allows investigators to make informed decisions about sample inclusion in downstream analysis. In summary, RNA-SeQC provides quality control measures critical to experiment design, process optimization and downstream computational analysis. See www.genepattern.org to run online, or www.broadinstitute.org/rna-seqc/ for a command line tool.

Construction, alignment, and implementation of an acousto-optical deflector-based system for patterned uncaging with ultraviolet light.

PubMed

Civillico, Eugene F; Shoham, Shy; O'Connor, Daniel H; Sarkisov, Dmitry V; Wang, Samuel S-H

2012-08-01

The method of patterned photoactivation is a natural fit for the study of neuronal dendritic integration. Photoactivatable molecules that influence a wide range of extracellular and intracellular neurophysiological functions are available. The choice of photosensitive molecules depends on the research question and will influence the design of the experimental apparatus. An acousto-optical deflector (AOD)-based system can be used for rapid ultraviolet (UV) photolysis in arbitrary spatial and temporal patterns. Photolysis-activated "caged" diffusible molecules or newer light-sensitive membrane proteins can be used in this system. This protocol describes the addition of a UV beam for uncaging to a homebuilt two-photon microscope. The goal is to get UV light from the light source (laser) to the approximate center of the objective's back aperture, passing through a pair of perpendicularly oriented AODs along the way. The protocol also describes the fine alignment of the UV beam and the implementation of AOD-based beam steering. Performing the final alignment with the beam passing through the AODs will ensure that the system is optimized for the idiosyncrasies of the crystals.

Novel actuation design of a gait trainer with shadow leg approach.

PubMed

Meuleman, Jos; Meuleman, Jos; van Asseldonk, Edwin H F; van der Kooij, Herman

2013-06-01

Robotic gait training has developed since the end of the 20(th) century, yet there is much room for improvement in the design of the robots. With the conventional exoskeleton structures, donning of patients in a gait trainer usually is a cumbersome process due to the need of joint alignments and normal walking is often hindered due to obstructed arm swing. Our goal was to design a gait training robots that overcomes these limitations. We propose a novel design in which these drawbacks are reduced to a great amount. By using a parallel structure behind the patient (shadow leg) that is connected to the patient joints with rods, little alignment is needed, the area lateral to the hip is left free, and thus arm swing is not obstructed. The construction is lightweight, because the actuators are mounted on a fixed base and the transmission of power is executed with light weight rods. An end stop in the shadow leg prevents hyper extension of the patient's knee. The relationship between motor displacement and human joint rotations is nonlinear. In this paper we derive the nonlinear relationships between motors and patient joints and verify these. calculations with a measurement. The device has been built, now tests with subjects are required to assess if subjects can indeed walk normally in the robot.

Structure-activity relationships of cannabinoids: A joint CoMFA and pseudoreceptor modelling study

NASA Astrophysics Data System (ADS)

Schmetzer, Silke; Greenidge, Paulette; Kovar, Karl-Artur; Schulze-Alexandru, Meike; Folkers, Gerd

1997-05-01

A cannabinoid pseudoreceptor model for the CB1-receptor has been constructed for 31 cannabinoids using the molecular modelling software YAK. Additionally, two CoMFA studies were performed on these ligands, the first of which was conducted prior to the building of the pseudoreceptor. Its pharmacophore is identical with the initial superposition of ligands used for pseudoreceptor construction. In contrast, the ligand alignment for the second CoMFA study was taken directly from the final cannabinoid pseudoreceptor model. This altered alignment gives markedly improved cross-validated r2 values as compared to those obtained from the original alignment with{{r}}_{{{cross}}}^2 values of 0.79 and 0.63, respectively, for five components. However, the pharmacophore alignment has the better predictive ability. Both the CoMFA and pseudoreceptor methods predict the free energy of binding of test ligands well.

* Fabrication and Characterization of Biphasic Silk Fibroin Scaffolds for Tendon/Ligament-to-Bone Tissue Engineering.

PubMed

Font Tellado, Sònia; Bonani, Walter; Balmayor, Elizabeth R; Foehr, Peter; Motta, Antonella; Migliaresi, Claudio; van Griensven, Martijn

2017-08-01

Tissue engineering is an attractive strategy for tendon/ligament-to-bone interface repair. The structure and extracellular matrix composition of the interface are complex and allow for a gradual mechanical stress transfer between tendons/ligaments and bone. Thus, scaffolds mimicking the structural features of the native interface may be able to better support functional tissue regeneration. In this study, we fabricated biphasic silk fibroin scaffolds designed to mimic the gradient in collagen molecule alignment present at the interface. The scaffolds had two different pore alignments: anisotropic at the tendon/ligament side and isotropic at the bone side. Total porosity ranged from 50% to 80% and the majority of pores (80-90%) were <100-300 μm. Young's modulus varied from 689 to 1322 kPa depending on the type of construct. In addition, human adipose-derived mesenchymal stem cells were cultured on the scaffolds to evaluate the effect of pore morphology on cell proliferation and gene expression. Biphasic scaffolds supported cell attachment and influenced cytoskeleton organization depending on pore alignment. In addition, the gene expression of tendon/ligament, enthesis, and cartilage markers significantly changed depending on pore alignment in each region of the scaffolds. In conclusion, the biphasic scaffolds fabricated in this study show promising features for tendon/ligament-to-bone tissue engineering.

Construction, characterization, and environmental testing of a Laue lens prototype using Fe and Al crystals

NASA Astrophysics Data System (ADS)

Wade, C.; Barrière, N. M.; Tomsick, J. A.; Hanlon, L.; Boggs, S. E.; Lowell, A.; von Ballmoos, P.; Massahi, S.

2018-07-01

Laue lenses use Bragg diffraction to concentrate soft γ-rays onto a detector. This decoupling of the collecting area from the detector volume can generate a significant increase in sensitivity for applications in astrophysics and nuclear medicine. A demonstrator lens was constructed at the UC Berkeley's Space Sciences Laboratory in 2014 by gluing 48 Fe and Al diffracting crystals to an aluminium substrate. The goal was to demonstrate a fast and accurate assembly technique that is compatible with the large number of crystals required to fabricate a Laue lens telescope for astronomical observations. We present here the lens design, the assembly technique we used, and the results of measurements of the angular misalignments before and after curing of the glue and during environmental testing (thermal, vacuum, and vibration). We conclude that our alignment technique is fast enough to assemble a full lens made of several thousand crystals. The achieved alignment accuracy had an average of 32.7‧‧ and a standard deviation of 44.1‧‧. The accuracy could be improved by using an alternative glue or by having better control over the asymmetry angle resulting from the crystal cut.

Improving scanner wafer alignment performance by target optimization

NASA Astrophysics Data System (ADS)

Leray, Philippe; Jehoul, Christiane; Socha, Robert; Menchtchikov, Boris; Raghunathan, Sudhar; Kent, Eric; Schoonewelle, Hielke; Tinnemans, Patrick; Tuffy, Paul; Belen, Jun; Wise, Rich

2016-03-01

In the process nodes of 10nm and below, the patterning complexity along with the processing and materials required has resulted in a need to optimize alignment targets in order to achieve the required precision, accuracy and throughput performance. Recent industry publications on the metrology target optimization process have shown a move from the expensive and time consuming empirical methodologies, towards a faster computational approach. ASML's Design for Control (D4C) application, which is currently used to optimize YieldStar diffraction based overlay (DBO) metrology targets, has been extended to support the optimization of scanner wafer alignment targets. This allows the necessary process information and design methodology, used for DBO target designs, to be leveraged for the optimization of alignment targets. In this paper, we show how we applied this computational approach to wafer alignment target design. We verify the correlation between predictions and measurements for the key alignment performance metrics and finally show the potential alignment and overlay performance improvements that an optimized alignment target could achieve.

HAlign-II: efficient ultra-large multiple sequence alignment and phylogenetic tree reconstruction with distributed and parallel computing.

PubMed

Wan, Shixiang; Zou, Quan

2017-01-01

Multiple sequence alignment (MSA) plays a key role in biological sequence analyses, especially in phylogenetic tree construction. Extreme increase in next-generation sequencing results in shortage of efficient ultra-large biological sequence alignment approaches for coping with different sequence types. Distributed and parallel computing represents a crucial technique for accelerating ultra-large (e.g. files more than 1 GB) sequence analyses. Based on HAlign and Spark distributed computing system, we implement a highly cost-efficient and time-efficient HAlign-II tool to address ultra-large multiple biological sequence alignment and phylogenetic tree construction. The experiments in the DNA and protein large scale data sets, which are more than 1GB files, showed that HAlign II could save time and space. It outperformed the current software tools. HAlign-II can efficiently carry out MSA and construct phylogenetic trees with ultra-large numbers of biological sequences. HAlign-II shows extremely high memory efficiency and scales well with increases in computing resource. THAlign-II provides a user-friendly web server based on our distributed computing infrastructure. HAlign-II with open-source codes and datasets was established at http://lab.malab.cn/soft/halign.

Alignment of nematic liquid crystals by inhomogeneous surfaces

NASA Astrophysics Data System (ADS)

Ong, Hiap Liew; Hurd, Alan J.; Meyer, Robert B.

1985-01-01

Variable oblique alignment of nematic liquid crystals has been achieved on microscopically inhomogeneous surfaces. The surfaces consist of small patches favoring vertical (homeotropic) alignment surrounded by a matrix favoring a planar alignment. The construction of these surfaces employs randomly distributed microscopic metal islands formed by certain metals as vapor-deposited films. Larger scale periodic patterns were made as well to verify the techniques. The results are interpreted in terms of a continuum elasticity theory and azimuthal degeneracy is also discussed.

Iterative non-sequential protein structural alignment.

PubMed

Salem, Saeed; Zaki, Mohammed J; Bystroff, Christopher

2009-06-01

Structural similarity between proteins gives us insights into their evolutionary relationships when there is low sequence similarity. In this paper, we present a novel approach called SNAP for non-sequential pair-wise structural alignment. Starting from an initial alignment, our approach iterates over a two-step process consisting of a superposition step and an alignment step, until convergence. We propose a novel greedy algorithm to construct both sequential and non-sequential alignments. The quality of SNAP alignments were assessed by comparing against the manually curated reference alignments in the challenging SISY and RIPC datasets. Moreover, when applied to a dataset of 4410 protein pairs selected from the CATH database, SNAP produced longer alignments with lower rmsd than several state-of-the-art alignment methods. Classification of folds using SNAP alignments was both highly sensitive and highly selective. The SNAP software along with the datasets are available online at http://www.cs.rpi.edu/~zaki/software/SNAP.

High-speed multiple sequence alignment on a reconfigurable platform.

PubMed

Oliver, Tim; Schmidt, Bertil; Maskell, Douglas; Nathan, Darran; Clemens, Ralf

2006-01-01

Progressive alignment is a widely used approach to compute multiple sequence alignments (MSAs). However, aligning several hundred sequences by popular progressive alignment tools requires hours on sequential computers. Due to the rapid growth of sequence databases biologists have to compute MSAs in a far shorter time. In this paper we present a new approach to MSA on reconfigurable hardware platforms to gain high performance at low cost. We have constructed a linear systolic array to perform pairwise sequence distance computations using dynamic programming. This results in an implementation with significant runtime savings on a standard FPGA.

Accelerating large-scale protein structure alignments with graphics processing units

PubMed Central

2012-01-01

Background Large-scale protein structure alignment, an indispensable tool to structural bioinformatics, poses a tremendous challenge on computational resources. To ensure structure alignment accuracy and efficiency, efforts have been made to parallelize traditional alignment algorithms in grid environments. However, these solutions are costly and of limited accessibility. Others trade alignment quality for speedup by using high-level characteristics of structure fragments for structure comparisons. Findings We present ppsAlign, a parallel protein structure Alignment framework designed and optimized to exploit the parallelism of Graphics Processing Units (GPUs). As a general-purpose GPU platform, ppsAlign could take many concurrent methods, such as TM-align and Fr-TM-align, into the parallelized algorithm design. We evaluated ppsAlign on an NVIDIA Tesla C2050 GPU card, and compared it with existing software solutions running on an AMD dual-core CPU. We observed a 36-fold speedup over TM-align, a 65-fold speedup over Fr-TM-align, and a 40-fold speedup over MAMMOTH. Conclusions ppsAlign is a high-performance protein structure alignment tool designed to tackle the computational complexity issues from protein structural data. The solution presented in this paper allows large-scale structure comparisons to be performed using massive parallel computing power of GPU. PMID:22357132

Construction and characterization of the fringe field monochromator for a field emission gun

PubMed

Mook; Kruit

2000-04-01

Although some microscopes have shown stabilities sufficient to attain below 0.1 eV spectral resolution in high-resolution electron energy loss spectroscopy, the intrinsic energy width of the high brightness source (0.3-0.6 eV) has been limiting the resolution. To lower the energy width of the source to 50 meV without unnecessary loss of brightness, a monochromator has been designed consisting of a short (4 mm) fringe field Wien filter and a 150 nm energy selection slit (nanoslit) both to be incorporated in the gun area of the microscope. A prototype has been built and tested in an ultra-high-vacuum setup (10(-9) mbar). The monochromator, operating on a Schottky field emission gun, showed stable and reproducible operation. The nanoslits did not contaminate and the structure remained stable. By measuring the current through the slit structure a direct image of the beam in the monochromator could be attained and the monochromator could be aligned without the use of a microscope. Good dispersed imaging conditions were found indicating an ultimate resolution of 55 meV. A Mark II fringe field monochromator (FFM) was designed and constructed compatible with the cold tungsten field emitter of the VG scanning transmission microscope. The monochromator was incorporated in the gun area of the microscope at IBM T.J. Watson research center, New York. The monochromator was aligned on 100 kV and the energy distribution measured using the monochromator displayed a below 50 meV filtering capability. The retarding Wien filter spectrometer was used to show a 61 meV EELS system resolution. The FFM is shown to be a monochromator which can be aligned without the use of the electron microscope. This makes it directly applicable for scanning transmission microscopy and low-voltage scanning electron microscopy, where it can lower the resolution loss which is caused by chromatic blur of the spot.

Functional assembly of engineered myocardium by electrical stimulation of cardiac myocytes cultured on scaffolds.

PubMed

Radisic, Milica; Park, Hyoungshin; Shing, Helen; Consi, Thomas; Schoen, Frederick J; Langer, Robert; Freed, Lisa E; Vunjak-Novakovic, Gordana

2004-12-28

The major challenge of tissue engineering is directing the cells to establish the physiological structure and function of the tissue being replaced across different hierarchical scales. To engineer myocardium, biophysical regulation of the cells needs to recapitulate multiple signals present in the native heart. We hypothesized that excitation-contraction coupling, critical for the development and function of a normal heart, determines the development and function of engineered myocardium. To induce synchronous contractions of cultured cardiac constructs, we applied electrical signals designed to mimic those in the native heart. Over only 8 days in vitro, electrical field stimulation induced cell alignment and coupling, increased the amplitude of synchronous construct contractions by a factor of 7, and resulted in a remarkable level of ultrastructural organization. Development of conductive and contractile properties of cardiac constructs was concurrent, with strong dependence on the initiation and duration of electrical stimulation.

Automated design of degenerate codon libraries.

PubMed

Mena, Marco A; Daugherty, Patrick S

2005-12-01

Degenerate codon libraries are frequently used in protein engineering and evolution studies but are often limited to targeting a small number of positions to adequately limit the search space. To mitigate this, codon degeneracy can be limited using heuristics or previous knowledge of the targeted positions. To automate design of libraries given a set of amino acid sequences, an algorithm (LibDesign) was developed that generates a set of possible degenerate codon libraries, their resulting size, and their score relative to a user-defined scoring function. A gene library of a specified size can then be constructed that is representative of the given amino acid distribution or that includes specific sequences or combinations thereof. LibDesign provides a new tool for automated design of high-quality protein libraries that more effectively harness existing sequence-structure information derived from multiple sequence alignment or computational protein design data.

Cofactor specificity switch in Shikimate dehydrogenase by rational design and consensus engineering.

PubMed

García-Guevara, Fernando; Bravo, Iris; Martínez-Anaya, Claudia; Segovia, Lorenzo

2017-08-01

Consensus engineering has been used to design more stable variants using the most frequent amino acid at each site of a multiple sequence alignment; sometimes consensus engineering modifies function, but efforts have mainly been focused on studying stability. Here we constructed a consensus Rossmann domain for the Shikimate dehydrogenase enzyme; separately we decided to switch the cofactor specificity through rational design in the Escherichia coli Shikimate dehydrogenase enzyme and then analyzed the effect of consensus mutations on top of our design. We found that consensus mutations closest to the 2' adenine moiety increased the activity in our design. Consensus engineering has been shown to result in more stable proteins and our findings suggest it could also be used as a complementary tool for increasing or modifying enzyme activity during design. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

The Rail Alignment Environmental Impact Statement: An Update

DOE Office of Scientific and Technical Information (OSTI.GOV)

R. Sweeney

2005-01-20

On July 23,2002, the President of the United States signed into law a joint resolution of the United States Congress designating the Yucca Mountain site in Nye County, Nevada, for development as a geologic repository for the disposal of spent nuclear fuel and high-level radioactive waste. If the US. Nuclear Regulatory Commission authorizes construction of the repository and receipt and possession of spent nuclear fuel and high-level radioactive at Yucca Mountain, the U.S. Department of Energy (DOE) would be responsible for transporting these materials to the Yucca Mountain repository as part of its obligation under the Nuclear Waste Policy Act.more » Part of the site recommendation decision included the analysis of a nation-wide shipping campaign to the proposed repository site. The ''Final Environmental Impact Statement for a Geologic Repository for the Disposal of Spent Nuclear Fuel and High-Level Radioactive Waste at Yucca Mountain, Nye County, Nevada'' (February 2002) (Repository EIS) evaluated the potential impacts of the transportation of 70,000 Metric Tons of Heavy Metal spent nuclear fuel and high-level radioactive waste from 77 locations around the nation to the potential repository in Nevada over a 24 year shipping campaign. In the Repository EIS, DOE identified mostly rail as its preferred mode of transportation, both nationally and in the State of Nevada. In December 2003, based on public comments and the environmental analyses in the Repository EIS, DOE identified a preference for the Caliente rail corridor in Nevada. On April 8, 2004, DOE issued a Record of Decision (ROD) on the Mode of Transportation and Nevada Rail Corridor for the Disposal of Spent Nuclear Fuel and High-Level Radioactive Waste at Yucca Mountain, Nye County, Nevada. In this ROD, the DOE announced that it had decided to select the mostly rail scenario analyzed in the Repository EIS as the transportation mode both on a national basis and in the State of Nevada. Under the mostly rail scenario, the DOE would rely on a combination of rail, truck and possibly barge to transport to the repository site at Yucca Mountain up to 70,000 MTHM of spent nuclear fuel and high-level radioactive waste, with most of the spent nuclear fuel and high-level radioactive waste being transported by rail. This will ultimately require construction of a rail line in Nevada to the repository. In addition, the DOE has decided to select the Caliente rail corridor in which to examine potential alignments within which to construct that rail line. A corridor is a strip of land, approximately 400 meters (0.25 miles) wide, that encompasses one of several possible routes through which DOE could build a rail line. An alignment is the specific location of a rail line in a corridor, and would likely be 60 meters [200 feet] or less in width. Also on April 8, 2004, DOE issued a Notice of Intent to Prepare an Environmental Impact Statement for the Alignment, Construction, and Operation of a Rail Line to a Geologic Repository at Yucca Mountain, Nye County, NV. In the Notice of Intent, the Department announced its intent to prepare a Rail Alignment EIS to assist in selecting a possible alignment for construction of a rail line that would connect the repository at Yucca Mountain to an existing main rail line in Nevada. The Rail Alignment EIS also would consider the potential construction and operation of a rail-to-truck intermodal transfer facility, proposed to be located at the confluence of an existing mainline railroad and a highway, to support legal-weight truck transportation until the rail system is fully operational. This corridor is approximately 513 kilometers (319 miles) long and would cost an estimated $880 million (2001 dollars). Should DOE decide to build the Caliente corridor, it may be the longest rail line built in the United States since the Transcontinental Railroad was constructed in 1869. Some of the challenges in building this rail corridor are steep grades (the corridor crosses over 7 mountain ranges), isolated terrain, possible tunnels, and stakeholder acceptance.« less

Enhancement of the Microscopy Facilities at the NSLS X1A Beamline

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jacobson, Chris

1999-08-31

As originally proposed, the authors constructed a new Scanning Transmission X-ray Microscope, STXM IV. The design and construction was led by Chris Jacobsen, and involved graduate students Michael Feser, Mary Carlucci-Dayton and Tobias Beetz. This microscope has the following new features: It has a new and improved high resolution scanning stage that should make it possible to perform higher resolution imaging without distortions. Preliminary results indicate that the stage performs as designed. It has an enclosure that can be evacuated and backfilled with helium. This makes it possible to perform imaging in the neighborhood of the nitrogen and oxygen edgesmore » without interference from residual air. It has a motorized detector stage for easy interchange of detectors and alignment microscope. We expect to use this to align the new segmented detector which makes it possible to perform brightfield and dark field microscopy simultaneously, and to record images in differential phase contrast as well. The microscope is located upstream of cryoSTXM, the instrument we use to examine specimens in a frozen hydrated state. The design of STXM IV is such that it makes it quick and easy to switch between STXM IV and cryo-STXM operations and vice versa. IEEE488 based control electronics provides multiple channels of data collection. The microscope is run from a LINUX PC with all new software, developed in-house. The stages for the zone plate and the order sorting aperture (OSA) have kinematic mounts. This way different sets of zone plates (optimized for different wavelengths and working distances) can be exchanged without the need for complete realignment of the instrument. The enclosure can be used as a glove-box, making it possible to examine specimens which require anaerobic handling.« less

Micrometer scale guidance of mesenchymal stem cells to form structurally oriented large-scale tissue engineered cartilage.

PubMed

Chou, Chih-Ling; Rivera, Alexander L; Williams, Valencia; Welter, Jean F; Mansour, Joseph M; Drazba, Judith A; Sakai, Takao; Baskaran, Harihara

2017-09-15

Current clinical methods to treat articular cartilage lesions provide temporary relief of the symptoms but fail to permanently restore the damaged tissue. Tissue engineering, using mesenchymal stem cells (MSCs) combined with scaffolds and bioactive factors, is viewed as a promising method for repairing cartilage injuries. However, current tissue engineered constructs display inferior mechanical properties compared to native articular cartilage, which could be attributed to the lack of structural organization of the extracellular matrix (ECM) of these engineered constructs in comparison to the highly oriented structure of articular cartilage ECM. We previously showed that we can guide MSCs undergoing chondrogenesis to align using microscale guidance channels on the surface of a two-dimensional (2-D) collagen scaffold, which resulted in the deposition of aligned ECM within the channels and enhanced mechanical properties of the constructs. In this study, we developed a technique to roll 2-D collagen scaffolds containing MSCs within guidance channels in order to produce a large-scale, three-dimensional (3-D) tissue engineered cartilage constructs with enhanced mechanical properties compared to current constructs. After rolling the MSC-scaffold constructs into a 3-D cylindrical structure, the constructs were cultured for 21days under chondrogenic culture conditions. The microstructure architecture and mechanical properties of the constructs were evaluated using imaging and compressive testing. Histology and immunohistochemistry of the constructs showed extensive glycosaminoglycan (GAG) and collagen type II deposition. Second harmonic generation imaging and Picrosirius red staining indicated alignment of neo-collagen fibers within the guidance channels of the constructs. Mechanical testing indicated that constructs containing the guidance channels displayed enhanced compressive properties compared to control constructs without these channels. In conclusion, using a novel roll-up method, we have developed large scale MSC based tissue-engineered cartilage that shows microscale structural organization and enhanced compressive properties compared to current tissue engineered constructs. Tissue engineered cartilage constructs made with human mesenchymal stem cells (hMSCs), scaffolds and bioactive factors are a promising solution to treat cartilage defects. A major disadvantage of these constructs is their inferior mechanical properties compared to the native tissue, which is likely due to the lack of structural organization of the extracellular matrix of the engineered constructs. In this study, we developed three-dimensional (3-D) cartilage constructs from rectangular scaffold sheets containing hMSCs in micro-guidance channels and characterized their mechanical properties and metabolic requirements. The work led to a novel roll-up method to embed 2-D microscale structures in 3-D constructs. Further, micro-guidance channels incorporated within the 3-D cartilage constructs led to the production of aligned cell-produced matrix and enhanced mechanical function. Copyright © 2017 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Solar radiation control using nematic curvilinear aligned phase (NCAP) liquid crystal technology

NASA Astrophysics Data System (ADS)

vanKonynenburg, Peter; Marsland, Stephen; McCoy, James

1987-11-01

A new, advanced liquid crystal technology has made economical, large area, electrically-controlled windows a commercial reality. The new technology, Nematic Curvilinear Aligned Phase (NCAP), is based on a polymeric material containing small droplets of nematic liquid crystal which is coated and laminated between transparent electrodes and fabricated into large area field effect devices. NCAP windows feature variable solar transmission and reflection through a voltage-controlled scattering mechanism. Laminated window constructions provide the excellent transmission and visibility of glass in the powered condition. In the unpowered condition, the windows are highly translucent, and provide 1) blocked vision for privacy, security, and obscuration of information, and 2) glare control and solar shading. The stability is excellent during accelerated aging tests. Degradation mechanisms which can limit performance and lifetime are discussed. Maximum long term stability is achieved by product designs that incorporate the appropriate window materials to provide environmental protection.

Characterization of typical platelet injector flow configurations. [liquid propellant rocket engines

NASA Technical Reports Server (NTRS)

Hickox, C. E.

1975-01-01

A study to investigate the hydraulic atomization characteristics of several novel injector designs for use in liquid propellant rocket engines is presented. The injectors were manufactured from a series of thin stainless steel platelets through which orifices were very accurately formed by a photoetching process. These individual platelets were stacked together and the orifices aligned so as to produce flow passages of prescribed geometry. After alignment, the platelets were bonded into a single, 'platelet injector', unit by a diffusion bonding process. Because of the complex nature of the flow associated with platelet injectors, it was necessary to use experimental techniques, exclusively, throughout the study. Large scale models of the injectors were constructed from aluminum plates and the appropriate fluids were modeled using a glycerol-water solution. Stop-action photographs of test configurations, using spark-shadowgraph or stroboscopic back-lighting, are shown.

Beam alignment based on two-dimensional power spectral density of a near-field image.

PubMed

Wang, Shenzhen; Yuan, Qiang; Zeng, Fa; Zhang, Xin; Zhao, Junpu; Li, Kehong; Zhang, Xiaolu; Xue, Qiao; Yang, Ying; Dai, Wanjun; Zhou, Wei; Wang, Yuanchen; Zheng, Kuixing; Su, Jingqin; Hu, Dongxia; Zhu, Qihua

2017-10-30

Beam alignment is crucial to high-power laser facilities and is used to adjust the laser beams quickly and accurately to meet stringent requirements of pointing and centering. In this paper, a novel alignment method is presented, which employs data processing of the two-dimensional power spectral density (2D-PSD) for a near-field image and resolves the beam pointing error relative to the spatial filter pinhole directly. Combining this with a near-field fiducial mark, the operation of beam alignment is achieved. It is experimentally demonstrated that this scheme realizes a far-field alignment precision of approximately 3% of the pinhole size. This scheme adopts only one near-field camera to construct the alignment system, which provides a simple, efficient, and low-cost way to align lasers.

Some aspects of SR beamline alignment

NASA Astrophysics Data System (ADS)

Gaponov, Yu. A.; Cerenius, Y.; Nygaard, J.; Ursby, T.; Larsson, K.

2011-09-01

Based on the Synchrotron Radiation (SR) beamline optical element-by-element alignment with analysis of the alignment results an optimized beamline alignment algorithm has been designed and developed. The alignment procedures have been designed and developed for the MAX-lab I911-4 fixed energy beamline. It has been shown that the intermediate information received during the monochromator alignment stage can be used for the correction of both monochromator and mirror without the next stages of alignment of mirror, slits, sample holder, etc. Such an optimization of the beamline alignment procedures decreases the time necessary for the alignment and becomes useful and helpful in the case of any instability of the beamline optical elements, storage ring electron orbit or the wiggler insertion device, which could result in the instability of angular and positional parameters of the SR beam. A general purpose software package for manual, semi-automatic and automatic SR beamline alignment has been designed and developed using the developed algorithm. The TANGO control system is used as the middle-ware between the stand-alone beamline control applications BLTools, BPMonitor and the beamline equipment.

Automated fiber pigtailing machine

DOEpatents

Strand, O.T.; Lowry, M.E.

1999-01-05

The Automated Fiber Pigtailing Machine (AFPM) aligns and attaches optical fibers to optoelectronic (OE) devices such as laser diodes, photodiodes, and waveguide devices without operator intervention. The so-called pigtailing process is completed with sub-micron accuracies in less than 3 minutes. The AFPM operates unattended for one hour, is modular in design and is compatible with a mass production manufacturing environment. This machine can be used to build components which are used in military aircraft navigation systems, computer systems, communications systems and in the construction of diagnostics and experimental systems. 26 figs.

In-situ temperature-controllable shear flow device for neutron scattering measurement--an example of aligned bicellar mixtures.

PubMed

Xia, Yan; Li, Ming; Kučerka, Norbert; Li, Shutao; Nieh, Mu-Ping

2015-02-01

We have designed and constructed a temperature-controllable shear flow cell for in-situ study on flow alignable systems. The device has been tested in the neutron diffraction and has the potential to be applied in the small angle neutron scattering configuration to characterize the nanostructures of the materials under flow. The required sample amount is as small as 1 ml. The shear rate on the sample is controlled by the flow rate produced by an external pump and can potentially vary from 0.11 to 3.8 × 10(5) s(-1). Both unidirectional and oscillational flows are achievable by the setting of the pump. The instrument is validated by using a lipid bicellar mixture, which yields non-alignable nanodisc-like bicelles at low T and shear-alignable membranes at high T. Using the shear cell, the bicellar membranes can be aligned at 31 °C under the flow with a shear rate of 11.11 s(-1). Multiple high-order Bragg peaks are observed and the full width at half maximum of the "rocking curve" around the Bragg's condition is found to be 3.5°-4.1°. It is noteworthy that a portion of the membranes remains aligned even after the flow stops. Detailed and comprehensive intensity correction for the rocking curve has been derived based on the finite rectangular sample geometry and the absorption of the neutrons as a function of sample angle [See supplementary material at http://dx.doi.org/10.1063/1.4908165 for the detailed derivation of the absorption correction]. The device offers a new capability to study the conformational or orientational anisotropy of the solvated macromolecules or aggregates induced by the hydrodynamic interaction in a flow field.

Dynamic Mechanical and Nanofibrous Topological Combinatory Cues Designed for Periodontal Ligament Engineering.

PubMed

Kim, Joong-Hyun; Kang, Min Sil; Eltohamy, Mohamed; Kim, Tae-Hyun; Kim, Hae-Won

2016-01-01

Complete reconstruction of damaged periodontal pockets, particularly regeneration of periodontal ligament (PDL) has been a significant challenge in dentistry. Tissue engineering approach utilizing PDL stem cells and scaffolding matrices offers great opportunity to this, and applying physical and mechanical cues mimicking native tissue conditions are of special importance. Here we approach to regenerate periodontal tissues by engineering PDL cells supported on a nanofibrous scaffold under a mechanical-stressed condition. PDL stem cells isolated from rats were seeded on an electrospun polycaprolactone/gelatin directionally-oriented nanofiber membrane and dynamic mechanical stress was applied to the cell/nanofiber construct, providing nanotopological and mechanical combined cues. Cells recognized the nanofiber orientation, aligning in parallel, and the mechanical stress increased the cell alignment. Importantly, the cells cultured on the oriented nanofiber combined with the mechanical stress produced significantly stimulated PDL specific markers, including periostin and tenascin with simultaneous down-regulation of osteogenesis, demonstrating the roles of topological and mechanical cues in altering phenotypic change in PDL cells. Tissue compatibility of the tissue-engineered constructs was confirmed in rat subcutaneous sites. Furthermore, in vivo regeneration of PDL and alveolar bone tissues was examined under the rat premaxillary periodontal defect models. The cell/nanofiber constructs engineered under mechanical stress showed sound integration into tissue defects and the regenerated bone volume and area were significantly improved. This study provides an effective tissue engineering approach for periodontal regeneration-culturing PDL stem cells with combinatory cues of oriented nanotopology and dynamic mechanical stretch.

Dynamic Mechanical and Nanofibrous Topological Combinatory Cues Designed for Periodontal Ligament Engineering

PubMed Central

Kim, Joong-Hyun; Kang, Min Sil; Eltohamy, Mohamed; Kim, Tae-Hyun; Kim, Hae-Won

2016-01-01

Complete reconstruction of damaged periodontal pockets, particularly regeneration of periodontal ligament (PDL) has been a significant challenge in dentistry. Tissue engineering approach utilizing PDL stem cells and scaffolding matrices offers great opportunity to this, and applying physical and mechanical cues mimicking native tissue conditions are of special importance. Here we approach to regenerate periodontal tissues by engineering PDL cells supported on a nanofibrous scaffold under a mechanical-stressed condition. PDL stem cells isolated from rats were seeded on an electrospun polycaprolactone/gelatin directionally-oriented nanofiber membrane and dynamic mechanical stress was applied to the cell/nanofiber construct, providing nanotopological and mechanical combined cues. Cells recognized the nanofiber orientation, aligning in parallel, and the mechanical stress increased the cell alignment. Importantly, the cells cultured on the oriented nanofiber combined with the mechanical stress produced significantly stimulated PDL specific markers, including periostin and tenascin with simultaneous down-regulation of osteogenesis, demonstrating the roles of topological and mechanical cues in altering phenotypic change in PDL cells. Tissue compatibility of the tissue-engineered constructs was confirmed in rat subcutaneous sites. Furthermore, in vivo regeneration of PDL and alveolar bone tissues was examined under the rat premaxillary periodontal defect models. The cell/nanofiber constructs engineered under mechanical stress showed sound integration into tissue defects and the regenerated bone volume and area were significantly improved. This study provides an effective tissue engineering approach for periodontal regeneration—culturing PDL stem cells with combinatory cues of oriented nanotopology and dynamic mechanical stretch. PMID:26989897

Tough and flexible CNT-polymeric hybrid scaffolds for engineering cardiac constructs.

PubMed

Kharaziha, Mahshid; Shin, Su Ryon; Nikkhah, Mehdi; Topkaya, Seda Nur; Masoumi, Nafiseh; Annabi, Nasim; Dokmeci, Mehmet R; Khademhosseini, Ali

2014-08-01

In the past few years, a considerable amount of effort has been devoted toward the development of biomimetic scaffolds for cardiac tissue engineering. However, most of the previous scaffolds have been electrically insulating or lacked the structural and mechanical robustness to engineer cardiac tissue constructs with suitable electrophysiological functions. Here, we developed tough and flexible hybrid scaffolds with enhanced electrical properties composed of carbon nanotubes (CNTs) embedded aligned poly(glycerol sebacate):gelatin (PG) electrospun nanofibers. Incorporation of varying concentrations of CNTs from 0 to 1.5% within the PG nanofibrous scaffolds (CNT-PG scaffolds) notably enhanced fiber alignment and improved the electrical conductivity and toughness of the scaffolds while maintaining the viability, retention, alignment, and contractile activities of cardiomyocytes (CMs) seeded on the scaffolds. The resulting CNT-PG scaffolds resulted in stronger spontaneous and synchronous beating behavior (3.5-fold lower excitation threshold and 2.8-fold higher maximum capture rate) compared to those cultured on PG scaffold. Overall, our findings demonstrated that aligned CNT-PG scaffold exhibited superior mechanical properties with enhanced CM beating properties. It is envisioned that the proposed hybrid scaffolds can be useful for generating cardiac tissue constructs with improved organization and maturation. Copyright © 2014 Elsevier Ltd. All rights reserved.

Reimagining Game Design: Exploring the Design of Constructible Authentic Representations for Science Reasoning

NASA Astrophysics Data System (ADS)

Holbert, Nathan Ryan

Video games have recently become a popular space for educational design due to their interactive and engaging nature and the ubiquity of the gaming experience among youth. Though many researchers argue video games can provide opportunities for learning, educational game design has focused on the classroom rather than the informal settings where games are typically played. Educational games have been moderately successful at achieving learning gains on standardized items, but have failed to show improvements on related but distal problems. In this dissertation I develop and assess a new design principle, called constructible authentic representations for creating informal gaming experiences that players will actively draw on when reasoning in formal and real world contexts. These games provide players with opportunities to engage in meaningful construction with components that integrate relevant concepts to create in-game representations that visually and epistemologically align with related tools and representations utilized in the target domain. In the first phase of the dissertation, I observed children playing popular video games to better understand what in-game representations children attend to and how interactions with these representations contribute to intuitive ideas of encountered STEM content. Results from this study fed into the iterative design of two prototype video games, FormulaT Racing and Particles!, intending to give players useful knowledge resources for reasoning about kinematics and the particulate nature of matter respectively. Designed games encourage players to utilize and refine intuitive ideas about target content through the construction of domain relevant representations. To assess the effectiveness of these designs I conducted two studies of children ages 7-14 playing prototype games in informal settings. An analysis of pre- and post-game clinical interviews, domain specific tasks, and video and logging data of gameplay suggests players developed useful knowledge resources, likely gained and/or refined from experiences in-game, that are employed to solve non-game problems and tasks. Furthermore, players utilized in-game representations as objects-to-think-with when explaining real world phenomena and formal concepts. The results suggest that games designed to include constructible authentic representations can provide players with powerful and useful knowledge resources accessible when thinking and reasoning in a variety of contexts.

A study of the dynamic tire properties over a range of tire constructions

NASA Technical Reports Server (NTRS)

Nybakken, G. H.; Dodge, R. N.; Clark, S. K.

1973-01-01

The dynamic properties of four model aircraft tires of various construction were evaluated experimentally and compared with available theory. The experimental investigation consisted of measuring the cornering force and the self-aligning torque developed by the tires undergoing sinusoidal steering inputs while operating on a small scale, road-wheel tire testing apparatus. The force and moment data from the different tires are compared with both finite- and point-contact patch string theory predictions. In general, agreement between finite contact patch theory and experimental observation is good. A modified string theory is also presented in which coefficients for cornering force and self-aligning torque are determined separately. This theory improves the correspondence between the experimental and analytical data, particularly on tires with relatively high self-aligning torques.

Designing an oral health module for the Bachelor of Midwifery program at an Australian University.

PubMed

Duff, Margaret; Dahlen, Hannah G; Burns, Elaine; Priddis, Holly; Schmied, Virginia; George, Ajesh

2017-03-01

Maternal oral health is important yet many pregnant women are unaware of its significance. Midwives are advised to promote oral health during pregnancy and are supported to do this in Australia through the Midwifery Initiated Oral Health training program. However, limited undergraduate education is being provided to midwifery students in this area. The objective of this paper is to describe how an innovative oral health education module for an undergraduate midwifery course in Australia was designed using a multidisciplinary approach. Midwives experienced in curriculum development and key investigators from the Midwifery Initiated Oral Health program designed the module using existing literature. Constructive alignment, blended learning and scaffolding were used in the design process. The draft module was then reviewed by midwifery academics and their feedback incorporated. The final module involves 4 h of teaching and learning and contains three components incorporated into first year course units. Each component is aligned with existing learning outcomes and incorporates blended learning approaches and tutorials/class activities as well as online quizzes and personal reflection. The module details key information (current evidence; basic anatomy/physiology; common oral conditions; and guidelines during pregnancy) that could better prepare students to promote oral health in clinical practice. This is the first time such an innovative, multidisciplinary approach has been undertaken embedding oral health in an undergraduate midwifery program in Australia. Copyright © 2017 Elsevier Ltd. All rights reserved.

Interwoven Aligned Conductive Nanofiber Yarn/Hydrogel Composite Scaffolds for Engineered 3D Cardiac Anisotropy.

PubMed

Wu, Yaobin; Wang, Ling; Guo, Baolin; Ma, Peter X

2017-06-27

Mimicking the anisotropic cardiac structure and guiding 3D cellular orientation play a critical role in designing scaffolds for cardiac tissue regeneration. Significant advances have been achieved to control cellular alignment and elongation, but it remains an ongoing challenge for engineering 3D cardiac anisotropy using these approaches. Here, we present a 3D hybrid scaffold based on aligned conductive nanofiber yarns network (NFYs-NET, composition: polycaprolactone, silk fibroin, and carbon nanotubes) within a hydrogel shell for mimicking the native cardiac tissue structure, and further demonstrate their great potential for engineering 3D cardiac anisotropy for cardiac tissue engineering. The NFYs-NET structures are shown to control cellular orientation and enhance cardiomyocytes (CMs) maturation. 3D hybrid scaffolds were then fabricated by encapsulating NFYs-NET layers within hydrogel shell, and these 3D scaffolds performed the ability to promote aligned and elongated CMs maturation on each layer and individually control cellular orientation on different layers in a 3D environment. Furthermore, endothelialized myocardium was constructed by using this hybrid strategy via the coculture of CMs on NFYs-NET layer and endothelial cells within hydrogel shell. Therefore, these 3D hybrid scaffolds, containing NFYs-NET layer inducing cellular orientation, maturation, and anisotropy and hydrogel shell providing a suitable 3D environment for endothelialization, has great potential in engineering 3D cardiac anisotropy.

Nanofabricated Racks of Aligned and Anchored DNA Substrates for Single-Molecule Imaging

PubMed Central

2009-01-01

Single-molecule studies of biological macromolecules can benefit from new experimental platforms that facilitate experimental design and data acquisition. Here we develop new strategies to construct curtains of DNA in which the molecules are aligned with respect to one another and maintained in an extended configuration by anchoring both ends of the DNA to the surface of a microfluidic sample chamber that is otherwise coated with an inert lipid bilayer. This “double-tethered” DNA substrate configuration is established through the use of nanofabricated rack patterns comprised of two distinct functional elements: linear barriers to lipid diffusion that align DNA molecules anchored by one end to the bilayer and antibody-coated pentagons that provide immobile anchor points for the opposite ends of the DNA. These devices enable the alignment and anchoring of thousands of individual DNA molecules, which can then be visualized using total internal reflection fluorescence microscopy under conditions that do not require continuous application of buffer flow to stretch the DNA. This unique strategy offers the potential for studying protein−DNA interactions on large DNA substrates without compromising measurements through application of hydrodynamic force. We provide a proof-of-principle demonstration that double-tethered DNA curtains made with nanofabricated rack patterns can be used in a one-dimensional diffusion assay that monitors the motion of quantum dot-tagged proteins along DNA. PMID:19736980

Nanofabricated racks of aligned and anchored DNA substrates for single-molecule imaging.

PubMed

Gorman, Jason; Fazio, Teresa; Wang, Feng; Wind, Shalom; Greene, Eric C

2010-01-19

Single-molecule studies of biological macromolecules can benefit from new experimental platforms that facilitate experimental design and data acquisition. Here we develop new strategies to construct curtains of DNA in which the molecules are aligned with respect to one another and maintained in an extended configuration by anchoring both ends of the DNA to the surface of a microfluidic sample chamber that is otherwise coated with an inert lipid bilayer. This "double-tethered" DNA substrate configuration is established through the use of nanofabricated rack patterns comprised of two distinct functional elements: linear barriers to lipid diffusion that align DNA molecules anchored by one end to the bilayer and antibody-coated pentagons that provide immobile anchor points for the opposite ends of the DNA. These devices enable the alignment and anchoring of thousands of individual DNA molecules, which can then be visualized using total internal reflection fluorescence microscopy under conditions that do not require continuous application of buffer flow to stretch the DNA. This unique strategy offers the potential for studying protein-DNA interactions on large DNA substrates without compromising measurements through application of hydrodynamic force. We provide a proof-of-principle demonstration that double-tethered DNA curtains made with nanofabricated rack patterns can be used in a one-dimensional diffusion assay that monitors the motion of quantum dot-tagged proteins along DNA.

Development of a Fourier-transform ion cyclotron resonance mass spectrometer-ion mobility spectrometer

NASA Astrophysics Data System (ADS)

Bluhm, Brian K.; Gillig, Kent J.; Russell, David H.

2000-11-01

In an effort to incorporate ion-molecule reaction chemistry with ion mobility measurements we designed and constructed a novel instrument that combines a Fourier-transform ion cyclotron resonance (ICR) mass spectrometer with an ion mobility drift cell and a time-of-flight mass spectrometer. Measured mobilities for Ar+ and CO+ in helium are in excellent agreement with accepted literature values demonstrating that there are no adverse effects from the magnetic field on ion mobility measurements. Drift cell pressure, extracted from the measured mobility of Ar+ in helium, indicate that a pressure of ˜0.25 Torr is achieved in the present configuration. There are significant technological challenges associated with combining ICR and ion mobility that occurred during construction of this instrument, such as differential pumping and aperture alignment are presented.

Aligned carbon nanotube-silicon sheets: a novel nano-architecture for flexible lithium ion battery electrodes.

PubMed

Fu, Kun; Yildiz, Ozkan; Bhanushali, Hardik; Wang, Yongxin; Stano, Kelly; Xue, Leigang; Zhang, Xiangwu; Bradford, Philip D

2013-09-25

Aligned carbon nanotube sheets provide an engineered scaffold for the deposition of a silicon active material for lithium ion battery anodes. The sheets are low-density, allowing uniform deposition of silicon thin films while the alignment allows unconstrained volumetric expansion of the silicon, facilitating stable cycling performance. The flat sheet morphology is desirable for battery construction. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

An optimal beam alignment method for large-scale distributed space surveillance radar system

NASA Astrophysics Data System (ADS)

Huang, Jian; Wang, Dongya; Xia, Shuangzhi

2018-06-01

Large-scale distributed space surveillance radar is a very important ground-based equipment to maintain a complete catalogue for Low Earth Orbit (LEO) space debris. However, due to the thousands of kilometers distance between each sites of the distributed radar system, how to optimally implement the Transmitting/Receiving (T/R) beams alignment in a great space using the narrow beam, which proposed a special and considerable technical challenge in the space surveillance area. According to the common coordinate transformation model and the radar beam space model, we presented a two dimensional projection algorithm for T/R beam using the direction angles, which could visually describe and assess the beam alignment performance. Subsequently, the optimal mathematical models for the orientation angle of the antenna array, the site location and the T/R beam coverage are constructed, and also the beam alignment parameters are precisely solved. At last, we conducted the optimal beam alignment experiments base on the site parameters of Air Force Space Surveillance System (AFSSS). The simulation results demonstrate the correctness and effectiveness of our novel method, which can significantly stimulate the construction for the LEO space debris surveillance equipment.

Reflecting on Graphs: Attributes of Graph Choice and Construction Practices in Biology

PubMed Central

Angra, Aakanksha; Gardner, Stephanie M.

2017-01-01

Undergraduate biology education reform aims to engage students in scientific practices such as experimental design, experimentation, and data analysis and communication. Graphs are ubiquitous in the biological sciences, and creating effective graphical representations involves quantitative and disciplinary concepts and skills. Past studies document student difficulties with graphing within the contexts of classroom or national assessments without evaluating student reasoning. Operating under the metarepresentational competence framework, we conducted think-aloud interviews to reveal differences in reasoning and graph quality between undergraduate biology students, graduate students, and professors in a pen-and-paper graphing task. All professors planned and thought about data before graph construction. When reflecting on their graphs, professors and graduate students focused on the function of graphs and experimental design, while most undergraduate students relied on intuition and data provided in the task. Most undergraduate students meticulously plotted all data with scaled axes, while professors and some graduate students transformed the data, aligned the graph with the research question, and reflected on statistics and sample size. Differences in reasoning and approaches taken in graph choice and construction corroborate and extend previous findings and provide rich targets for undergraduate and graduate instruction. PMID:28821538

42: DESIGNING A DASHBOARD FOR EVALUATION THE BUSINESS-IT ALIGNMENT STRATEGIES IN HOSPITALS ORGANIZATIONS

PubMed Central

piri, Zakieh; Raef, Behnaz; moftian, Nazila; dehghani, Mohamad; khara, Rouhallah

2017-01-01

Background and aims Business-IT Alignment Evaluation is One of the most important issues that managers should monitor and make decisions about it. Dashboard software combines data and graphical indicators to deliver at-a-glance summaries of information for users to view the state of their business and quickly respond. The aim of this study was to design a dashboard to assess the business-IT alignment strategies for hospitals organizations in Tehran University of Medical Sciences. Methods This is a functional-developmental study. Initially, we searched related databases (PubMed and ProQuest) to determine the key performance indicators of business-IT alignment for selecting the best model for dashboard designing. After selecting the Luftman model, the key indicators were extracted for designing the dashboard model. In the next stage, an electronic questionnaire was designed based on extracted indicators. This questionnaire sends to Hospital managers and IT administrators. Collected data were analyzed by Excel 2015 and displayed in dashboard page. Results The number of key performance indicators was 39. After recognition the technical requirements the dashboard was designed in Excel. The overall business-IT alignment rate in hospitals was 3.12. Amir-aalam hospital has the highest business-IT alignment rate (3.55) and vali-asr hospital has the lowest business-IT alignment rat (2.80). Conclusion Using dashboard software improves the alignment and reduces the time and energy compared with doing this process manually.

Anatomic tibial component design can increase tibial coverage and rotational alignment accuracy: a comparison of six contemporary designs.

PubMed

Dai, Yifei; Scuderi, Giles R; Bischoff, Jeffrey E; Bertin, Kim; Tarabichi, Samih; Rajgopal, Ashok

2014-12-01

The aim of this study was to comprehensively evaluate contemporary tibial component designs against global tibial anatomy. We hypothesized that anatomically designed tibial components offer increased morphological fit to the resected proximal tibia with increased alignment accuracy compared to symmetric and asymmetric designs. Using a multi-ethnic bone dataset, six contemporary tibial component designs were investigated, including anatomic, asymmetric, and symmetric design types. Investigations included (1) measurement of component conformity to the resected tibia using a comprehensive set of size and shape metrics; (2) assessment of component coverage on the resected tibia while ensuring clinically acceptable levels of rotation and overhang; and (3) evaluation of the incidence and severity of component downsizing due to adherence to rotational alignment and overhang requirements, and the associated compromise in tibial coverage. Differences in coverage were statistically compared across designs and ethnicities, as well as between placements with or without enforcement of proper rotational alignment. Compared to non-anatomic designs investigated, the anatomic design exhibited better conformity to resected tibial morphology in size and shape, higher tibial coverage (92% compared to 85-87%), more cortical support (posteromedial region), lower incidence of downsizing (3% compared to 39-60%), and less compromise of tibial coverage (0.5% compared to 4-6%) when enforcing proper rotational alignment. The anatomic design demonstrated meaningful increase in tibial coverage with accurate rotational alignment compared to symmetric and asymmetric designs, suggesting its potential for less intra-operative compromises and improved performance. III.

Development of a method of alignment between various SOLAR MAXIMUM MISSION experiments

NASA Technical Reports Server (NTRS)

1977-01-01

Results of an engineering study of the methods of alignment between various experiments for the solar maximum mission are described. The configuration studied consists of the instruments, mounts and instrument support platform located within the experiment module. Hardware design, fabrication methods and alignment techniques were studied with regard to optimizing the coalignment between the experiments and the fine sun sensor. The proposed hardware design was reviewed with regard to loads, stress, thermal distortion, alignment error budgets, fabrication techniques, alignment techniques and producibility. Methods of achieving comparable alignment accuracies on previous projects were also reviewed.

Second Language Writing Classification System Based on Word-Alignment Distribution

ERIC Educational Resources Information Center

Kotani, Katsunori; Yoshimi, Takehiko

2010-01-01

The present paper introduces an automatic classification system for assisting second language (L2) writing evaluation. This system, which classifies sentences written by L2 learners as either native speaker-like or learner-like sentences, is constructed by machine learning algorithms using word-alignment distributions as classification features…

Navigation and Alignment Aids Concept of Operations and Supplemental Design Information. Revision A

NASA Technical Reports Server (NTRS)

Kelly, Sean M.; Cryan, Scott P.

2016-01-01

The IDSS Navigation and Alignment Aids Concept of Operations and Supplemental Design Information document provides supplemental information to the IDSS IDD. The guide provides insight into the navigation and alignment aids design, and how those aids can be utilized by incoming vehicles for proximity operations and docking. The navigation aids are paramount to successful docking.

Predicting phenotype from genotype: Improving accuracy through more robust experimental and computational modeling

PubMed Central

Gallion, Jonathan; Koire, Amanda; Katsonis, Panagiotis; Schoenegge, Anne‐Marie; Bouvier, Michel

2017-01-01

Abstract Computational prediction yields efficient and scalable initial assessments of how variants of unknown significance may affect human health. However, when discrepancies between these predictions and direct experimental measurements of functional impact arise, inaccurate computational predictions are frequently assumed as the source. Here, we present a methodological analysis indicating that shortcomings in both computational and biological data can contribute to these disagreements. We demonstrate that incomplete assaying of multifunctional proteins can affect the strength of correlations between prediction and experiments; a variant's full impact on function is better quantified by considering multiple assays that probe an ensemble of protein functions. Additionally, many variants predictions are sensitive to protein alignment construction and can be customized to maximize relevance of predictions to a specific experimental question. We conclude that inconsistencies between computation and experiment can often be attributed to the fact that they do not test identical hypotheses. Aligning the design of the computational input with the design of the experimental output will require cooperation between computational and biological scientists, but will also lead to improved estimations of computational prediction accuracy and a better understanding of the genotype–phenotype relationship. PMID:28230923

Predicting phenotype from genotype: Improving accuracy through more robust experimental and computational modeling.

PubMed

Gallion, Jonathan; Koire, Amanda; Katsonis, Panagiotis; Schoenegge, Anne-Marie; Bouvier, Michel; Lichtarge, Olivier

2017-05-01

Computational prediction yields efficient and scalable initial assessments of how variants of unknown significance may affect human health. However, when discrepancies between these predictions and direct experimental measurements of functional impact arise, inaccurate computational predictions are frequently assumed as the source. Here, we present a methodological analysis indicating that shortcomings in both computational and biological data can contribute to these disagreements. We demonstrate that incomplete assaying of multifunctional proteins can affect the strength of correlations between prediction and experiments; a variant's full impact on function is better quantified by considering multiple assays that probe an ensemble of protein functions. Additionally, many variants predictions are sensitive to protein alignment construction and can be customized to maximize relevance of predictions to a specific experimental question. We conclude that inconsistencies between computation and experiment can often be attributed to the fact that they do not test identical hypotheses. Aligning the design of the computational input with the design of the experimental output will require cooperation between computational and biological scientists, but will also lead to improved estimations of computational prediction accuracy and a better understanding of the genotype-phenotype relationship. © 2017 The Authors. **Human Mutation published by Wiley Periodicals, Inc.

Simple chained guide trees give high-quality protein multiple sequence alignments

PubMed Central

Boyce, Kieran; Sievers, Fabian; Higgins, Desmond G.

2014-01-01

Guide trees are used to decide the order of sequence alignment in the progressive multiple sequence alignment heuristic. These guide trees are often the limiting factor in making large alignments, and considerable effort has been expended over the years in making these quickly or accurately. In this article we show that, at least for protein families with large numbers of sequences that can be benchmarked with known structures, simple chained guide trees give the most accurate alignments. These also happen to be the fastest and simplest guide trees to construct, computationally. Such guide trees have a striking effect on the accuracy of alignments produced by some of the most widely used alignment packages. There is a marked increase in accuracy and a marked decrease in computational time, once the number of sequences goes much above a few hundred. This is true, even if the order of sequences in the guide tree is random. PMID:25002495

Biomimetic approach to cardiac tissue engineering.

PubMed

Radisic, M; Park, H; Gerecht, S; Cannizzaro, C; Langer, R; Vunjak-Novakovic, G

2007-08-29

Here, we review an approach to tissue engineering of functional myocardium that is biomimetic in nature, as it involves the use of culture systems designed to recapitulate some aspects of the actual in vivo environment. To mimic the capillary network, subpopulations of neonatal rat heart cells were cultured on a highly porous elastomer scaffold with a parallel array of channels perfused with culture medium. To mimic oxygen supply by haemoglobin, the culture medium was supplemented with a perfluorocarbon (PFC) emulsion. Constructs cultivated in the presence of PFC contained higher amounts of DNA and cardiac markers and had significantly better contractile properties than control constructs cultured without PFC. To induce synchronous contractions of cultured constructs, electrical signals mimicking those in native heart were applied. Over only 8 days of cultivation, electrical stimulation induced cell alignment and coupling, markedly increased the amplitude of synchronous construct contractions and resulted in a remarkable level of ultrastructural organization. The biomimetic approach is discussed in the overall context of cardiac tissue engineering, and the possibility to engineer functional human cardiac grafts based on human stem cells.

Effect of alignment perturbations in a trans-tibial prosthesis user: A pilot study.

PubMed

Courtney, Anna; Orendurff, Michael S; Buis, Arjan

2016-04-01

A recurring complication in trans-tibial prosthetic limb users is "poor socket fit" with painful residuum-socket interfaces, a consequence of excess pressure. This is due to both poor socket fit and poor socket alignment; however, the interaction of these factors has not been quantified. Through evaluation of kinetic data this study aimed to articulate an interaction uniting socket design, alignment and interface pressures. The results will help to refine future studies and will hopefully help determine whether sockets can be designed, fitted and aligned to maximize mobility whilst minimizing injurious forces. Interface pressures were recorded throughout ambulation in one user with "optimal (reference) alignment" followed by 5 malalignments in a patellar tendon-bearing and a hydrocast socket. Marked differences in pressure distribution were discovered when equating the patellar tendon-bearing against the hydrocast socket and when comparing interface pressures from reference with offset alignment. Patellar tendon-bearing sockets were found to be more sensitive to alignment perturbations than hydrocast sockets. A complex interaction was found, with the most prominent finding demonstrating the requisite for attainment of optimal alignment: a translational alignment error of 10 mm can increase maximum peak pressures by 227% (mean 17.5%). Refinements for future trials are described and the necessity for future research into socket design, alignment and interface pressures has been estabilished.

BRIGHTEST SATELLITE GALAXY ALIGNMENT OF SLOAN DIGITAL SKY SURVEY GALAXY GROUPS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li Zhigang; Wang Yougang; Chen Xuelei

2013-05-01

We study the alignment signal between the distribution of the brightest satellite galaxies (BSGs) and the major axes of their host groups using the Sloan Digital Sky Survey group catalog constructed by Yang et al. After correcting for the effect of group ellipticity, a statistically significant ({approx}5{sigma}) major-axis alignment is detected and the alignment angle is found to be 43. Degree-Sign 0 {+-} 0. Degree-Sign 4. More massive and richer groups show a stronger BSG alignment. The BSG alignment around blue brightest central galaxies (BCGs) is slightly stronger than that around red BCGs. Red BSGs have a much stronger major-axismore » alignment than blue BSGs. Unlike BSGs, other satellites do not show very significant alignment with their group's major axis. We further explore BSG alignment using the semi-analytic model (SAM) constructed by Guo et al. In general, we found good agreement of the model with observations: BSGs in the SAM show a strong major-axis alignment that depends on group mass and richness in the same way as in observations and none of the other satellites exhibit prominent alignment. However, a discrepancy also exists in that the SAM shows a BSG color dependence opposite of that in observations, which is most probably induced by a missing large-scale environment ingredient in the SAM. The combination of two popular scenarios can explain the BSG alignment we detected. First, satellites merged into the group along the surrounding filaments, which are strongly aligned with the major axis of the group. Second, BSGs entered their host group more recently than other satellites, so they have preserved more information about their assembling history and major-axis alignment. In the SAM, we found positive evidence for the second scenario in the fact that BSGs merged into groups statistically more recently than other satellites. We also found that most of the BSGs (80%) were BCGs before they merged into groups and earlier merging BSGs tend to be closer to their BCGs than other BSGs. On the other hand, although the BSG color dependence in observations is the opposite of that in the SAM, it might also indicate that the first scenario is a good explanation.« less

fRMSDPred: Predicting Local RMSD Between Structural Fragments Using Sequence Information

DTIC Science & Technology

2007-04-04

machine learning approaches for estimating the RMSD value of a pair of protein fragments. These estimated fragment-level RMSD values can be used to construct the alignment, assess the quality of an alignment, and identify high-quality alignment segments. We present algorithms to solve this fragment-level RMSD prediction problem using a supervised learning framework based on support vector regression and classification that incorporates protein profiles, predicted secondary structure, effective information encoding schemes, and novel second-order pairwise exponential kernel

From Concrete to Abstract: A Story of Passion, Proof and Pedagogy

ERIC Educational Resources Information Center

Lawton, Fiona

2011-01-01

The author states her belief that mathematics is a human construct based on axiomatic systems, and that these constructs are both personal and social. She argues that to succeed in mathematics, learners' personal constructs need to be aligned with formal globally agreed mathematical conventions. Put more simply, she informs her students that…

Solving the shrinkage-induced PDMS alignment registration issue in multilayer soft lithography

NASA Astrophysics Data System (ADS)

Moraes, Christopher; Sun, Yu; Simmons, Craig A.

2009-06-01

Shrinkage of polydimethylsiloxane (PDMS) complicates alignment registration between layers during multilayer soft lithography fabrication. This often hinders the development of large-scale microfabricated arrayed devices. Here we report a rapid method to construct large-area, multilayered devices with stringent alignment requirements. This technique, which exploits a previously unrecognized aspect of sandwich mold fabrication, improves device yield, enables highly accurate alignment over large areas of multilayered devices and does not require strict regulation of fabrication conditions or extensive calibration processes. To demonstrate this technique, a microfabricated Braille display was developed and characterized. High device yield and accurate alignment within 15 µm were achieved over three layers for an array of 108 Braille units spread over a 6.5 cm2 area, demonstrating the fabrication of well-aligned devices with greater ease and efficiency than previously possible.

Tunable system for production of mirror and cusp configurations using chassis of permanent magnets

NASA Astrophysics Data System (ADS)

Hyde, Alexander; Bushmelov, Maxim; Batishchev, Oleg

2018-03-01

Compact arrays of permanent magnets have shown promise as replacements for electromagnets in applications requiring magnetic cusps and mirrors. An adjustable system capable of suspending and translating a pair of light, nonmagnetic chassis carrying such sources of magnetic field has been designed and constructed. Using this device to align two cylindrical chassis, strong solenoid-like domains of field, as well as classic biconic cusp and magnetic mirror topologies, are generated. Employing a pair of ring-shaped chassis instead, the superposition of their naturally-emitted cusps is demonstrated to produce sextupolar and octupolar magnetic fields.

Environmental Assessment for the Strategic Petroleum Reserve West Hackberry Facility Raw Water Intake Pipeline Replacement Cameron and Calcasieu Parishes, Louisiana

DOE Office of Scientific and Technical Information (OSTI.GOV)

N /A

The proposed action and three alternatives, including a No Build alternative, were evaluated along the existing RWIPL alignment to accommodate the placement of the proposed RWIPL. Construction feasibility, reasonableness and potential environmental impacts were considered during the evaluation of the four actions (and action alternatives) for the proposed RWIPL activities. Reasonable actions were identified as those actions which were considered to be supported by common sense and sound technical principles. Feasible actions were those actions which were considered to be capable of being accomplished, practicable and non-excessive in terms of cost. The evaluation process considered the following design specifications, whichmore » were determined to be important to the feasibility of the overall project. The proposed RWIPL replacement project must therefore: (1) Comply with the existing design basis and criteria, (2) Maintain continuity of operation of the facility during construction, (3)Provide the required service life, (4) Be cost effective, (5)Improve the operation and maintenance of the pipeline, and (6) Maintain minimal environmental impact while meeting the performance requirements. Sizing of the pipe, piping construction materials, construction method (e.g., open-cut trench, directional drilling, etc.) and the acquisition of new Right-of-Way (ROW) were additionally evaluated in the preliminary alternative identification, selection and screening process.« less

Alignment system for SGII-Up laser facility

NASA Astrophysics Data System (ADS)

Gao, Yanqi; Cui, Yong; Li, Hong; Gong, Lei; Lin, Qiang; Liu, Daizhong; Zhu, Baoqiang; Ma, Weixin; Zhu, Jian; Lin, Zunqi

2018-03-01

The SGII-Up laser facility in Shanghai is one of the most important high-power laser facilities in China. It is designed to obtain 24 kJ (3ω) of energy with a square pulse of 3 ns using eight laser beams (two bundles). To satisfy the requirements for the safety, efficiency, and quality, an alignment system is developed for this facility. This alignment system can perform automatic alignment of the preamplifier system, main amplifier system, and harmonic conversion system within 30 min before every shot during the routine operation of the facility. In this article, an overview of the alignment system is first presented. Then, its alignment characteristics are discussed, along with the alignment process. Finally, experimental results, including the alignment results and the facility performance, are reported. The results show that the far-field beam pointing alignment accuracy is better than 3 μrad, and the alignment error of the near-field beam centering is no larger than 1 mm. These satisfy the design requirements very well.

Development of a Cyclic Strain Bioreactor for Mechanical Enhancement and Assessment of Bioengineered Myocardial Constructs

PubMed Central

Salazar, Betsy H.; Cashion, Avery T.; Dennis, Robert G.; Birla, Ravi K.

2015-01-01

Purpose The purpose of this study was to develop enabling bioreactor technologies using a novel voice coil actuator system for investigating the effects of periodic strain on cardiac patches fabricated with rat cardiomyocytes. Methods The bioengineered muscle constructs used in this study were formed by culturing rat neonatal primary cardiac cells on a fibrin gel. The physical design of the bioreactor was initially conceived using Solidworks to test clearances and perform structural strain analysis. Once the software design phase was completed the bioreactor was assembled using a combination of commercially available, custom machined, and 3-D printed parts. We utilized the bioreactor to evaluate the effect of a 4-hour stretch protocol on the contractile properties of the tissue after which immunohistological assessment of the tissue was also performed. Results An increase in contractile force was observed after the strain protocol of 10% stretch at 1Hz, with no significant increase observed in the control group. Additionally, an increase in cardiac myofibril alignment, connexin 43 expression, and collagen type I distribution were noted. Conclusion In this study we demonstrated the effectiveness of a new bioreactor design to improve contractility of engineered cardiac muscle tissue. PMID:26577484

Development of a Cyclic Strain Bioreactor for Mechanical Enhancement and Assessment of Bioengineered Myocardial Constructs.

PubMed

Salazar, Betsy H; Cashion, Avery T; Dennis, Robert G; Birla, Ravi K

2015-12-01

The purpose of this study was to develop enabling bioreactor technologies using a novel voice coil actuator system for investigating the effects of periodic strain on cardiac patches fabricated with rat cardiomyocytes. The bioengineered muscle constructs used in this study were formed by culturing rat neonatal primary cardiac cells on a fibrin gel. The physical design of the bioreactor was initially conceived using Solidworks to test clearances and perform structural strain analysis. Once the software design phase was completed the bioreactor was assembled using a combination of commercially available, custom machined, and 3-D printed parts. We utilized the bioreactor to evaluate the effect of a 4-h stretch protocol on the contractile properties of the tissue after which immunohistological assessment of the tissue was also performed. An increase in contractile force was observed after the strain protocol of 10% stretch at 1 Hz, with no significant increase observed in the control group. Additionally, an increase in cardiac myofibril alignment, connexin 43 expression, and collagen type I distribution were noted. In this study we demonstrated the effectiveness of a new bioreactor design to improve contractility of engineered cardiac muscle tissue.

Two Simple and Efficient Algorithms to Compute the SP-Score Objective Function of a Multiple Sequence Alignment.

PubMed

Ranwez, Vincent

2016-01-01

Multiple sequence alignment (MSA) is a crucial step in many molecular analyses and many MSA tools have been developed. Most of them use a greedy approach to construct a first alignment that is then refined by optimizing the sum of pair score (SP-score). The SP-score estimation is thus a bottleneck for most MSA tools since it is repeatedly required and is time consuming. Given an alignment of n sequences and L sites, I introduce here optimized solutions reaching O(nL) time complexity for affine gap cost, instead of O(n2L), which are easy to implement.

English Medieval Churches, 'Festival Orientation' and William Wordsworth

NASA Astrophysics Data System (ADS)

Hoare, Peter G.; Ketel, Hans

2015-05-01

A church that is shown to be aligned with sunrise or sunset on the feast day of the saint to whom the building was dedicated is said to display 'festival orientation'. The earliest work to touch upon this practice in English dates from c. 1678. William Wordsworth gave impetus to the subject in two poems published in 1827; he also played a part in the design of St Mary's chapel (1823-4), Rydal, Cumbria in the English Lake District. The 14th-century St Catherine's chapel at Houghton St Giles, Norfolk, was constructed for the use of pilgrims on their way to nearby Walsingham. Careful measurement of the orientation and eastern horizon of these two buildings has shown that St Mary's is aligned with sunrise on the Marian festival of The Visitation (2 July), and St Catherine's is directed towards the rising Sun on the feast of St Catherine of Alexandria (25 November). It is only by taking into account the character of the horizon that meaningful tests for festival orientation may be carried out.

Photoresist thin-film effects on alignment process capability

NASA Astrophysics Data System (ADS)

Flores, Gary E.; Flack, Warren W.

1993-08-01

Two photoresists were selected for alignment characterization based on their dissimilar coating properties and observed differences on alignment capability. The materials are Dynachem OFPR-800 and Shipley System 8. Both photoresists were examined on two challenging alignment levels in a submicron CMOS process, a nitride level and a planarized second level metal. An Ultratech Stepper model 1500 which features a darkfield alignment system with a broadband green light for alignment signal detection was used for this project. Initially, statistically designed linear screening experiments were performed to examine six process factors for each photoresist: viscosity, spin acceleration, spin speed, spin time, softbake time, and softbake temperature. Using the results derived from the screening experiments, a more thorough examination of the statistically significant process factors was performed. A full quadratic experimental design was conducted to examine viscosity, spin speed, and spin time coating properties on alignment. This included a characterization of both intra and inter wafer alignment control and alignment process capability. Insight to the different alignment behavior is analyzed in terms of photoresist material properties and the physical nature of the alignment detection system.

Fluorescence guided lymph node biopsy in large animals using direct image projection device

NASA Astrophysics Data System (ADS)

Ringhausen, Elizabeth; Wang, Tylon; Pitts, Jonathan; Akers, Walter J.

2016-03-01

The use of fluorescence imaging for aiding oncologic surgery is a fast growing field in biomedical imaging, revolutionizing open and minimally invasive surgery practices. We have designed, constructed, and tested a system for fluorescence image acquisition and direct display on the surgical field for fluorescence guided surgery. The system uses a near-infrared sensitive CMOS camera for image acquisition, a near-infra LED light source for excitation, and DLP digital projector for projection of fluorescence image data onto the operating field in real time. Instrument control was implemented in Matlab for image capture, processing of acquired data and alignment of image parameters with the projected pattern. Accuracy of alignment was evaluated statistically to demonstrate sensitivity to small objects and alignment throughout the imaging field. After verification of accurate alignment, feasibility for clinical application was demonstrated in large animal models of sentinel lymph node biopsy. Indocyanine green was injected subcutaneously in Yorkshire pigs at various locations to model sentinel lymph node biopsy in gynecologic cancers, head and neck cancer, and melanoma. Fluorescence was detected by the camera system during operations and projected onto the imaging field, accurately identifying tissues containing the fluorescent tracer at up to 15 frames per second. Fluorescence information was projected as binary green regions after thresholding and denoising raw intensity data. Promising results with this initial clinical scale prototype provided encouraging results for the feasibility of optical projection of acquired luminescence during open oncologic surgeries.

Analyzing and synthesizing phylogenies using tree alignment graphs.

PubMed

Smith, Stephen A; Brown, Joseph W; Hinchliff, Cody E

2013-01-01

Phylogenetic trees are used to analyze and visualize evolution. However, trees can be imperfect datatypes when summarizing multiple trees. This is especially problematic when accommodating for biological phenomena such as horizontal gene transfer, incomplete lineage sorting, and hybridization, as well as topological conflict between datasets. Additionally, researchers may want to combine information from sets of trees that have partially overlapping taxon sets. To address the problem of analyzing sets of trees with conflicting relationships and partially overlapping taxon sets, we introduce methods for aligning, synthesizing and analyzing rooted phylogenetic trees within a graph, called a tree alignment graph (TAG). The TAG can be queried and analyzed to explore uncertainty and conflict. It can also be synthesized to construct trees, presenting an alternative to supertrees approaches. We demonstrate these methods with two empirical datasets. In order to explore uncertainty, we constructed a TAG of the bootstrap trees from the Angiosperm Tree of Life project. Analysis of the resulting graph demonstrates that areas of the dataset that are unresolved in majority-rule consensus tree analyses can be understood in more detail within the context of a graph structure, using measures incorporating node degree and adjacency support. As an exercise in synthesis (i.e., summarization of a TAG constructed from the alignment trees), we also construct a TAG consisting of the taxonomy and source trees from a recent comprehensive bird study. We synthesized this graph into a tree that can be reconstructed in a repeatable fashion and where the underlying source information can be updated. The methods presented here are tractable for large scale analyses and serve as a basis for an alternative to consensus tree and supertree methods. Furthermore, the exploration of these graphs can expose structures and patterns within the dataset that are otherwise difficult to observe.

Analyzing and Synthesizing Phylogenies Using Tree Alignment Graphs

PubMed Central

Smith, Stephen A.; Brown, Joseph W.; Hinchliff, Cody E.

2013-01-01

Phylogenetic trees are used to analyze and visualize evolution. However, trees can be imperfect datatypes when summarizing multiple trees. This is especially problematic when accommodating for biological phenomena such as horizontal gene transfer, incomplete lineage sorting, and hybridization, as well as topological conflict between datasets. Additionally, researchers may want to combine information from sets of trees that have partially overlapping taxon sets. To address the problem of analyzing sets of trees with conflicting relationships and partially overlapping taxon sets, we introduce methods for aligning, synthesizing and analyzing rooted phylogenetic trees within a graph, called a tree alignment graph (TAG). The TAG can be queried and analyzed to explore uncertainty and conflict. It can also be synthesized to construct trees, presenting an alternative to supertrees approaches. We demonstrate these methods with two empirical datasets. In order to explore uncertainty, we constructed a TAG of the bootstrap trees from the Angiosperm Tree of Life project. Analysis of the resulting graph demonstrates that areas of the dataset that are unresolved in majority-rule consensus tree analyses can be understood in more detail within the context of a graph structure, using measures incorporating node degree and adjacency support. As an exercise in synthesis (i.e., summarization of a TAG constructed from the alignment trees), we also construct a TAG consisting of the taxonomy and source trees from a recent comprehensive bird study. We synthesized this graph into a tree that can be reconstructed in a repeatable fashion and where the underlying source information can be updated. The methods presented here are tractable for large scale analyses and serve as a basis for an alternative to consensus tree and supertree methods. Furthermore, the exploration of these graphs can expose structures and patterns within the dataset that are otherwise difficult to observe. PMID:24086118

Indexing system for optical beam steering

NASA Technical Reports Server (NTRS)

Sullivan, Mark T.; Cannon, David M.; Debra, Daniel B.; Young, Jeffrey A.; Mansfield, Joseph A.; Carmichael, Roger E.; Lissol, Peter S.; Pryor, G. M.; Miklosy, Les G.; Lee, Jeffrey H.

1990-01-01

This paper describes the design and testing of an indexing system for optical-beam steering. The cryogenic beam-steering mechanism is a 360-degree rotation device capable of discrete, high-precision alignment positions. It uses low-precision components for its rough alignment and kinematic design to meet its stringent repeatability and stability requirements (of about 5 arcsec). The principal advantages of this design include a decoupling of the low-precision, large angular motion from the high-precision alignment, and a power-off alignment position that potentially extends the life or hold time of cryogenic systems. An alternate design, which takes advantage of these attributes while reducing overall motion, is also presented. Preliminary test results show the kinematic mount capable of sub-arc second repeatability.

Mechanical design of multiple zone plates precision alignment apparatus for hard X-ray focusing in twenty-nanometer scale

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shu, Deming; Liu, Jie; Gleber, Sophie C.

An enhanced mechanical design of multiple zone plates precision alignment apparatus for hard x-ray focusing in a twenty-nanometer scale is provided. The precision alignment apparatus includes a zone plate alignment base frame; a plurality of zone plates; and a plurality of zone plate holders, each said zone plate holder for mounting and aligning a respective zone plate for hard x-ray focusing. At least one respective positioning stage drives and positions each respective zone plate holder. Each respective positioning stage is mounted on the zone plate alignment base frame. A respective linkage component connects each respective positioning stage and the respectivemore » zone plate holder. The zone plate alignment base frame, each zone plate holder and each linkage component is formed of a selected material for providing thermal expansion stability and positioning stability for the precision alignment apparatus.« less

Braided and Stacked Electrospun Nanofibrous Scaffolds for Tendon and Ligament Tissue Engineering.

PubMed

Rothrauff, Benjamin B; Lauro, Brian B; Yang, Guang; Debski, Richard E; Musahl, Volker; Tuan, Rocky S

2017-05-01

Tendon and ligament injuries are a persistent orthopedic challenge given their poor innate healing capacity. Nonwoven electrospun nanofibrous scaffolds composed of polyesters have been used to mimic the mechanics and topographical cues of native tendons and ligaments. However, nonwoven nanofibers have several limitations that prevent broader clinical application, including poor cell infiltration, as well as tensile and suture-retention strengths that are inferior to native tissues. In this study, multilayered scaffolds of aligned electrospun nanofibers of two designs-stacked or braided-were fabricated. Mechanical properties, including structural and mechanical properties and suture-retention strength, were determined using acellular scaffolds. Human bone marrow-derived mesenchymal stem cells (MSCs) were seeded on scaffolds for up to 28 days, and assays for tenogenic differentiation, histology, and biochemical composition were performed. Braided scaffolds exhibited improved tensile and suture-retention strengths, but reduced moduli. Both scaffold designs supported expression of tenogenic markers, although the effect was greater on braided scaffolds. Conversely, cell infiltration was superior in stacked constructs, resulting in enhanced cell number, total collagen content, and total sulfated glycosaminoglycan content. However, when normalized against cell number, both designs modulated extracellular matrix protein deposition to a similar degree. Taken together, this study demonstrates that multilayered scaffolds of aligned electrospun nanofibers supported tenogenic differentiation of seeded MSCs, but the macroarchitecture is an important consideration for applications of tendon and ligament tissue engineering.

In silico Analysis of 2085 Clones from a Normalized Rat Vestibular Periphery 3′ cDNA Library

PubMed Central

Roche, Joseph P.; Cioffi, Joseph A.; Kwitek, Anne E.; Erbe, Christy B.; Popper, Paul

2005-01-01

The inserts from 2400 cDNA clones isolated from a normalized Rattus norvegicus vestibular periphery cDNA library were sequenced and characterized. The Wackym-Soares vestibular 3′ cDNA library was constructed from the saccular and utricular maculae, the ampullae of all three semicircular canals and Scarpa's ganglia containing the somata of the primary afferent neurons, microdissected from 104 male and female rats. The inserts from 2400 randomly selected clones were sequenced from the 5′ end. Each sequence was analyzed using the BLAST algorithm compared to the Genbank nonredundant, rat genome, mouse genome and human genome databases to search for high homology alignments. Of the initial 2400 clones, 315 (13%) were found to be of poor quality and did not yield useful information, and therefore were eliminated from the analysis. Of the remaining 2085 sequences, 918 (44%) were found to represent 758 unique genes having useful annotations that were identified in databases within the public domain or in the published literature; these sequences were designated as known characterized sequences. 1141 sequences (55%) aligned with 1011 unique sequences had no useful annotations and were designated as known but uncharacterized sequences. Of the remaining 26 sequences (1%), 24 aligned with rat genomic sequences, but none matched previously described rat expressed sequence tags or mRNAs. No significant alignment to the rat or human genomic sequences could be found for the remaining 2 sequences. Of the 2085 sequences analyzed, 86% were singletons. The known, characterized sequences were analyzed with the FatiGO online data-mining tool (http://fatigo.bioinfo.cnio.es/) to identify level 5 biological process gene ontology (GO) terms for each alignment and to group alignments with similar or identical GO terms. Numerous genes were identified that have not been previously shown to be expressed in the vestibular system. Further characterization of the novel cDNA sequences may lead to the identification of genes with vestibular-specific functions. Continued analysis of the rat vestibular periphery transcriptome should provide new insights into vestibular function and generate new hypotheses. Physiological studies are necessary to further elucidate the roles of the identified genes and novel sequences in vestibular function. PMID:16103642

Finite element analysis of the Wolf Creek multispan curved girder bridge.

DOT National Transportation Integrated Search

2008-01-01

The use of curved girder bridges in highway construction has grown steadily during the last 40 years. Today, roughly 25% of newly constructed bridges have a curved alignment. Curved girder bridges have numerous complicating geometric features that di...

Alignment and use of the optical test for the 8.4-m off-axis primary mirrors of the Giant Magellan Telescope

NASA Astrophysics Data System (ADS)

West, S. C.; Burge, J. H.; Cuerden, B.; Davison, W.; Hagen, J.; Martin, H. M.; Tuell, M. T.; Zhao, C.; Zobrist, T.

2010-07-01

The Giant Magellan Telescope has a 25 meter f/0.7 near-parabolic primary mirror constructed from seven 8.4 meter diameter segments. Several aspects of the interferometric optical test used to guide polishing of the six off-axis segments go beyond the demonstrated state of the art in optical testing. The null corrector is created from two obliquelyilluminated spherical mirrors combined with a computer-generated hologram (the measurement hologram). The larger mirror is 3.75 m in diameter and is supported at the top of a test tower, 23.5 m above the GMT segment. Its size rules out a direct validation of the wavefront produced by the null corrector. We can, however, use a reference hologram placed at an intermediate focus between the two spherical mirrors to measure the wavefront produced by the measurement hologram and the first mirror. This reference hologram is aligned to match the wavefront and thereby becomes the alignment reference for the rest of the system. The position and orientation of the reference hologram, the 3.75 m mirror and the GMT segment are measured with a dedicated laser tracker, leading to an alignment accuracy of about 100 microns over the 24 m dimensions of the test. In addition to the interferometer that measures the GMT segment, a separate interferometer at the center of curvature of the 3.75 m sphere monitors its figure simultaneously with the GMT measurement, allowing active correction and compensation for residual errors. We describe the details of the design, alignment, and use of this unique off-axis optical test.

Constructively Aligning Technologies with Learning and Assessment in a Distance Education Master's Programme

ERIC Educational Resources Information Center

Rogerson-Revell, Pamela

2015-01-01

This paper reports on an action research study investigating the use of online learning activities or "e-tivities" to enhance the learning and assessment experience of students on a distance master's programme. The study suggests that to be successfully integrated in a programme, such activities need to be carefully aligned with learning…

Extending the enterprise evolution contextualisation model

NASA Astrophysics Data System (ADS)

de Vries, Marné; van der Merwe, Alta; Gerber, Aurona

2017-07-01

Enterprise engineering (EE) emerged as a new discipline to encourage comprehensive and consistent enterprise design. Since EE is multidisciplinary, various researchers study enterprises from different perspectives, which resulted in a plethora of applicable literature and terminology, but without shared meaning. Previous research specifically focused on the fragmentation of knowledge for designing and aligning the information and communication technology (ICT) subsystem of the enterprise in order to support the business organisation subsystem of the enterprise. As a solution for this fragmented landscape, a business-IT alignment model (BIAM) was developed inductively from existing business-IT alignment approaches. Since most of the existing alignment frameworks addressed the alignment between the ICT subsystem and the business organisation subsystem, BIAM also focused on the alignment between these two subsystems. Yet, the emerging EE discipline intends to address a broader scope of design, evident in the existing approaches that incorporate a broader scope of design/alignment/governance. A need was identified to address the knowledge fragmentation of the EE knowledge base by adapting BIAM to an enterprise evolution contextualisation model (EECM), to contextualise a broader set of approaches, as identified by Lapalme. The main contribution of this article is the incremental development and evaluation of EECM. We also present guiding indicators/prerequisites for applying EECM as a contextualisation tool.

Development of an embedded instrument for autofocus and polarization alignment of polarization maintaining fiber

NASA Astrophysics Data System (ADS)

Feng, Di; Fang, Qimeng; Huang, Huaibo; Zhao, Zhengqi; Song, Ningfang

2017-12-01

The development and implementation of a practical instrument based on an embedded technique for autofocus and polarization alignment of polarization maintaining fiber is presented. For focusing efficiency and stability, an image-based focusing algorithm fully considering the image definition evaluation and the focusing search strategy was used to accomplish autofocus. For improving the alignment accuracy, various image-based algorithms of alignment detection were developed with high calculation speed and strong robustness. The instrument can be operated as a standalone device with real-time processing and convenience operations. The hardware construction, software interface, and image-based algorithms of main modules are described. Additionally, several image simulation experiments were also carried out to analyze the accuracy of the above alignment detection algorithms. Both the simulation results and experiment results indicate that the instrument can achieve the accuracy of polarization alignment <±0.1 deg.

Optical Alignment of the JWST ISIM to the OTE Simulator (OSIM): Current Concept and Design Studies

NASA Technical Reports Server (NTRS)

Frey, Bradley J.; Davila, Pamela S.; Marsh, James M.; Ohl, Raymond G.; Sullivan, Joseph

2007-01-01

The James Webb Space Telescope's (JWST) Integrated Science Instrument Module (ISIM) is the scientific payload of the observatory and contai ns four science instruments. During alignment and test of the integrated ISIM (i.e. ISIM + science instruments) at NASA's Goddard Space Fli ght Center (GSFC), the Optical telescope element SIMulator (OSIM) wil l be used to optically stimulate the science instruments to verify their operation and performance. In this paper we present the design of two cryogenic alignment fixtures that will be used to determine and verify the proper alignment of OSIM to ISIM during testing at GSFC. The se fixtures, the Master Alignment Target Fixture (MATF) and the ISIM Alignment Target Fixture (IATF), will provide continuous, 6 degree of freedom feedback to OSIM during initial ambient alignment as well as during cryogenic vacuum testing.

Multiciliated cell basal bodies align in stereotypical patterns coordinated by the apical cytoskeleton

PubMed Central

Herawati, Elisa; Kanoh, Hatsuho

2016-01-01

Multiciliated cells (MCCs) promote fluid flow through coordinated ciliary beating, which requires properly organized basal bodies (BBs). Airway MCCs have large numbers of BBs, which are uniformly oriented and, as we show here, align linearly. The mechanism for BB alignment is unexplored. To study this mechanism, we developed a long-term and high-resolution live-imaging system and used it to observe green fluorescent protein–centrin2–labeled BBs in cultured mouse tracheal MCCs. During MCC differentiation, the BB array adopted four stereotypical patterns, from a clustering “floret” pattern to the linear “alignment.” This alignment process was correlated with BB orientations, revealed by double immunostaining for BBs and their asymmetrically associated basal feet (BF). The BB alignment was disrupted by disturbing apical microtubules with nocodazole and by a BF-depleting Odf2 mutation. We constructed a theoretical model, which indicated that the apical cytoskeleton, acting like a viscoelastic fluid, provides a self-organizing mechanism in tracheal MCCs to align BBs linearly for mucociliary transport. PMID:27573463

Carbon nanotube-incorporated collagen hydrogels improve cell alignment and the performance of cardiac constructs

PubMed Central

Sun, Hongyu; Zhou, Jing; Huang, Zhu; Qu, Linlin; Lin, Ning; Liang, Chengxiao; Dai, Ruiwu; Tang, Lijun; Tian, Fuzhou

2017-01-01

Carbon nanotubes (CNTs) provide an essential 2-D microenvironment for cardiomyocyte growth and function. However, it remains to be elucidated whether CNT nanostructures can promote cell–cell integrity and facilitate the formation of functional tissues in 3-D hydrogels. Here, single-walled CNTs were incorporated into collagen hydrogels to fabricate (CNT/Col) hydrogels, which improved mechanical and electrical properties. The incorporation of CNTs (up to 1 wt%) exhibited no toxicity to cardiomyocytes and enhanced cell adhesion and elongation. Through the use of immunohistochemical staining, transmission electron microscopy, and intracellular calcium-transient measurement, the incorporation of CNTs was found to improve cell alignment and assembly remarkably, which led to the formation of engineered cardiac tissues with stronger contraction potential. Importantly, cardiac tissues based on CNT/Col hydrogels were noted to have better functionality. Collectively, the incorporation of CNTs into the Col hydrogels improved cell alignment and the performance of cardiac constructs. Our study suggests that CNT/Col hydrogels offer a promising tissue scaffold for cardiac constructs, and might serve as injectable biomaterials to deliver cell or drug molecules for cardiac regeneration following myocardial infarction in the near future. PMID:28450785

Leveraging FPGAs for Accelerating Short Read Alignment.

PubMed

Arram, James; Kaplan, Thomas; Luk, Wayne; Jiang, Peiyong

2017-01-01

One of the key challenges facing genomics today is how to efficiently analyze the massive amounts of data produced by next-generation sequencing platforms. With general-purpose computing systems struggling to address this challenge, specialized processors such as the Field-Programmable Gate Array (FPGA) are receiving growing interest. The means by which to leverage this technology for accelerating genomic data analysis is however largely unexplored. In this paper, we present a runtime reconfigurable architecture for accelerating short read alignment using FPGAs. This architecture exploits the reconfigurability of FPGAs to allow the development of fast yet flexible alignment designs. We apply this architecture to develop an alignment design which supports exact and approximate alignment with up to two mismatches. Our design is based on the FM-index, with optimizations to improve the alignment performance. In particular, the n-step FM-index, index oversampling, a seed-and-compare stage, and bi-directional backtracking are included. Our design is implemented and evaluated on a 1U Maxeler MPC-X2000 dataflow node with eight Altera Stratix-V FPGAs. Measurements show that our design is 28 times faster than Bowtie2 running with 16 threads on dual Intel Xeon E5-2640 CPUs, and nine times faster than Soap3-dp running on an NVIDIA Tesla C2070 GPU.

PEG-nanotube liquid crystals as templates for construction of surfactant-free gold nanorods.

PubMed

Kameta, Naohiro; Shiroishi, Hidenobu

2018-05-03

Lyotropic liquid crystals, in which nanotubes coated with polyethylene glycol were aligned side-by-side in aqueous dispersions, acted as templates for the construction of surfactant-free gold nanorods with controllable diameters, functionalizable surfaces, and tunable optical properties.

In-situ temperature-controllable shear flow device for neutron scattering measurement—An example of aligned bicellar mixtures

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xia, Yan; Li, Ming; Kučerka, Norbert

We have designed and constructed a temperature-controllable shear flow cell for in-situ study on flow alignable systems. The device has been tested in the neutron diffraction and has the potential to be applied in the small angle neutron scattering configuration to characterize the nanostructures of the materials under flow. The required sample amount is as small as 1 ml. The shear rate on the sample is controlled by the flow rate produced by an external pump and can potentially vary from 0.11 to 3.8 × 10{sup 5} s{sup −1}. Both unidirectional and oscillational flows are achievable by the setting ofmore » the pump. The instrument is validated by using a lipid bicellar mixture, which yields non-alignable nanodisc-like bicelles at low T and shear-alignable membranes at high T. Using the shear cell, the bicellar membranes can be aligned at 31 °C under the flow with a shear rate of 11.11 s{sup −1}. Multiple high-order Bragg peaks are observed and the full width at half maximum of the “rocking curve” around the Bragg’s condition is found to be 3.5°–4.1°. It is noteworthy that a portion of the membranes remains aligned even after the flow stops. Detailed and comprehensive intensity correction for the rocking curve has been derived based on the finite rectangular sample geometry and the absorption of the neutrons as a function of sample angle [See supplementary material at http://dx.doi.org/10.1063/1.4908165 for the detailed derivation of the absorption correction]. The device offers a new capability to study the conformational or orientational anisotropy of the solvated macromolecules or aggregates induced by the hydrodynamic interaction in a flow field.« less

Development of a diode laser heterodyne spectrometer and observations of silicon monoxide in sunspots. Ph.D. Thesis

NASA Technical Reports Server (NTRS)

Glenar, D. A.

1981-01-01

A state of the art, tunable diode laser infrared heterodyne spectrometer was designed and constructed for ground based observations throughout the 8 to 12 micron atmospheric window. The instrument was optimized for use with presently available tunable diode lasers, and was designed as a flexible field system for use with large reflecting telescopes. The instrument was aligned and calibrated using laboratory and astronomical sources. Observations of SiO fundamental (v = 1-0) and hot band (v = 2-1) absorption features were made in sunspots near 8 microns using the spectrometer. The data permit an unambiguous determination of the temperature pressure relation in the upper layers of the umbral atmosphere, and support the sunspot model suggested by Stellmacher and Wiehr.

Statistical Significance of Optical Map Alignments

PubMed Central

Sarkar, Deepayan; Goldstein, Steve; Schwartz, David C.

2012-01-01

Abstract The Optical Mapping System constructs ordered restriction maps spanning entire genomes through the assembly and analysis of large datasets comprising individually analyzed genomic DNA molecules. Such restriction maps uniquely reveal mammalian genome structure and variation, but also raise computational and statistical questions beyond those that have been solved in the analysis of smaller, microbial genomes. We address the problem of how to filter maps that align poorly to a reference genome. We obtain map-specific thresholds that control errors and improve iterative assembly. We also show how an optimal self-alignment score provides an accurate approximation to the probability of alignment, which is useful in applications seeking to identify structural genomic abnormalities. PMID:22506568

Mechanical Design of NESSI: New Mexico Tech Extrasolar Spectroscopic Survey Instrument

NASA Technical Reports Server (NTRS)

Santoro, Fernando G.; Olivares, Andres M.; Salcido, Christopher D.; Jimenez, Stephen R.; Jurgenson, Colby A.; Hrynevych, Michael A.; Creech-Eakman, Michelle J.; Boston, Penny J.; Schmidt, Luke M.; Bloemhard, Heather;

National Ignition Facility Target Chamber

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wavrik, R W; Cox, J R; Fleming, P J

2000-10-05

On June 11, 1999 the Department of Energy dedicated the single largest piece of the National Ignition Facility (NIF) at Lawrence Livermore National Laboratory (LLNL) in Livermore, California. The ten (10) meter diameter aluminum target high vacuum chamber will serve as the working end of the largest laser in the world. The output of 192 laser beams will converge at the precise center of the chamber. The laser beams will enter the chamber in two by two arrays to illuminate 10 millimeter long gold cylinders called hohlraums enclosing 2 millimeter capsule containing deuterium, tritium and isotopes of hydrogen. The twomore » isotopes will fuse, thereby creating temperatures and pressures resembling those found only inside stars and in detonated nuclear weapons, but on a minute scale. The NIF Project will serve as an essential facility to insure safety and reliability of our nation's nuclear arsenal as well as demonstrating inertial fusion's contribution to creating electrical power. The paper will discuss the requirements that had to be addressed during the design, fabrication and testing of the target chamber. A team from Sandia National Laboratories (SNL) and LLNL with input from industry performed the configuration and basic design of the target chamber. The method of fabrication and construction of the aluminum target chamber was devised by Pitt-Des Moines, Inc. (PDM). PDM also participated in the design of the chamber in areas such as the Target Chamber Realignment and Adjustment System, which would allow realignment of the sphere laser beams in the event of earth settlement or movement from a seismic event. During the fabrication of the target chamber the sphericity tolerances had to be addressed for the individual plates. Procedures were developed for forming, edge preparation and welding of individual plates. Construction plans were developed to allow the field construction of the target chamber to occur parallel to other NIF construction activities. This was necessary to achieve the overall schedule. Plans had to be developed for the precise location and alignment of laser beam ports. Upon completion of the fabrication of the aluminum target chamber in a temporary structure the 130 ton sphere was moved from the temporary construction enclosure to its final location in the target building. Prior to the installation of a concrete shield and after completion of the welding of the chamber penetrations vacuum leak checking was performed to insure the vacuum integrity of target chamber. The entire spherical chamber external surface supports a 40 cm thick reinforced concrete shield after installation in the target building. The final task is a total survey of the laser ports and the contour machining of spacer plates so that laser devices attached to these ports meet the alignment criteria.« less

Evolutionary profiles from the QR factorization of multiple sequence alignments

PubMed Central

Sethi, Anurag; O'Donoghue, Patrick; Luthey-Schulten, Zaida

2005-01-01

We present an algorithm to generate complete evolutionary profiles that represent the topology of the molecular phylogenetic tree of the homologous group. The method, based on the multidimensional QR factorization of numerically encoded multiple sequence alignments, removes redundancy from the alignments and orders the protein sequences by increasing linear dependence, resulting in the identification of a minimal basis set of sequences that spans the evolutionary space of the homologous group of proteins. We observe a general trend that these smaller, more evolutionarily balanced profiles have comparable and, in many cases, better performance in database searches than conventional profiles containing hundreds of sequences, constructed in an iterative and computationally intensive procedure. For more diverse families or superfamilies, with sequence identity <30%, structural alignments, based purely on the geometry of the protein structures, provide better alignments than pure sequence-based methods. Merging the structure and sequence information allows the construction of accurate profiles for distantly related groups. These structure-based profiles outperformed other sequence-based methods for finding distant homologs and were used to identify a putative class II cysteinyl-tRNA synthetase (CysRS) in several archaea that eluded previous annotation studies. Phylogenetic analysis showed the putative class II CysRSs to be a monophyletic group and homology modeling revealed a constellation of active site residues similar to that in the known class I CysRS. PMID:15741270

Constructive Alignment and the Research Skills Development Framework: Using Theory to Practically Align Graduate Attributes, Learning Experiences, and Assessment Tasks in Undergraduate Midwifery

ERIC Educational Resources Information Center

Pretorius, Lynette; Bailey, Carolyn; Miles, Maureen

2013-01-01

Midwifery educators have to provide students with stimulating curricula that teach academic and vocational content, as well as transferable skills. The Research Skills Development (RSD) framework provides a conceptual model that allows educators to explicitly scaffold the development of their students' research skills. This paper aims to…

Abnormal arrangement of a collagen/apatite extracellular matrix orthogonal to osteoblast alignment is constructed by a nanoscale periodic surface structure.

PubMed

Matsugaki, Aira; Aramoto, Gento; Ninomiya, Takafumi; Sawada, Hiroshi; Hata, Satoshi; Nakano, Takayoshi

2015-01-01

Morphological and directional alteration of cells is essential for structurally appropriate construction of tissues and organs. In particular, osteoblast alignment is crucial for the realization of anisotropic bone tissue microstructure. In this article, the orientation of a collagen/apatite extracellular matrix (ECM) was established by controlling osteoblast alignment using a surface geometry with nanometer-sized periodicity induced by laser ablation. Laser irradiation induced self-organized periodic structures (laser-induced periodic surface structures; LIPSS) with a spatial period equal to the wavelength of the incident laser on the surface of biomedical alloys of Ti-6Al-4V and Co-Cr-Mo. Osteoblast orientation was successfully induced parallel to the grating structure. Notably, both the fibrous orientation of the secreted collagen matrix and the c-axis of the produced apatite crystals were orientated orthogonal to the cell direction. To the best of our knowledge, this is the first report demonstrating that bone tissue anisotropy is controllable, including the characteristic organization of a collagen/apatite composite orthogonal to the osteoblast orientation, by controlling the cell alignment using periodic surface geometry. Copyright © 2014 Elsevier Ltd. All rights reserved.

PCV: An Alignment Free Method for Finding Homologous Nucleotide Sequences and its Application in Phylogenetic Study.

PubMed

Kumar, Rajnish; Mishra, Bharat Kumar; Lahiri, Tapobrata; Kumar, Gautam; Kumar, Nilesh; Gupta, Rahul; Pal, Manoj Kumar

2017-06-01

Online retrieval of the homologous nucleotide sequences through existing alignment techniques is a common practice against the given database of sequences. The salient point of these techniques is their dependence on local alignment techniques and scoring matrices the reliability of which is limited by computational complexity and accuracy. Toward this direction, this work offers a novel way for numerical representation of genes which can further help in dividing the data space into smaller partitions helping formation of a search tree. In this context, this paper introduces a 36-dimensional Periodicity Count Value (PCV) which is representative of a particular nucleotide sequence and created through adaptation from the concept of stochastic model of Kolekar et al. (American Institute of Physics 1298:307-312, 2010. doi: 10.1063/1.3516320 ). The PCV construct uses information on physicochemical properties of nucleotides and their positional distribution pattern within a gene. It is observed that PCV representation of gene reduces computational cost in the calculation of distances between a pair of genes while being consistent with the existing methods. The validity of PCV-based method was further tested through their use in molecular phylogeny constructs in comparison with that using existing sequence alignment methods.

Highly sensitive piezo-resistive graphite nanoplatelet-carbon nanotube hybrids/polydimethylsilicone composites with improved conductive network construction.

PubMed

Zhao, Hang; Bai, Jinbo

2015-05-13

The constructions of internal conductive network are dependent on microstructures of conductive fillers, determining various electrical performances of composites. Here, we present the advanced graphite nanoplatelet-carbon nanotube hybrids/polydimethylsilicone (GCHs/PDMS) composites with high piezo-resistive performance. GCH particles were synthesized by the catalyst chemical vapor deposition approach. The synthesized GCHs can be well dispersed in the matrix through the mechanical blending process. Due to the exfoliated GNP and aligned CNTs coupling structure, the flexible composite shows an ultralow percolation threshold (0.64 vol %) and high piezo-resistive sensitivity (gauge factor ∼ 10(3) and pressure sensitivity ∼ 0.6 kPa(-1)). Slight motions of finger can be detected and distinguished accurately using the composite film as a typical wearable sensor. These results indicate that designing the internal conductive network could be a reasonable strategy to improve the piezo-resistive performance of composites.

Recent Developments in Ground-Borne Noise and Vibration Control

NASA Astrophysics Data System (ADS)

Nelson, J. T.

1996-05-01

Vibration control provisions available to the transit designer include (among others) precision straightened rail, ballast mats, floating slabs and very soft direct fixation fasteners, in addition to rail grinding, wheel truing, and continuous welded rail. Recently, the Los Angeles Metro has developed specifications for a soft resilient direct fixation fastener to fit the same base dimensions as the standard direct fixation fastener. In San Francisco, low resonance frequency (8 Hz) floating slabs have been constructed to mitigate predicted ground vibration impacts at nearby residential structures. In Atlanta, low resonance frequency loading slabs have been constructed to maintain a low vibration environment in a medical building planned to be built over the subway structure. In Portland and Pasadena, ballast mats have been recommended to control light rail transit ground vibration impacts on housing located at typically 35 feet from the alignment. Each of these provisions are briefly described in view of recent applications at U.S. transit systems.

CAMPways: constrained alignment framework for the comparative analysis of a pair of metabolic pathways.

PubMed

Abaka, Gamze; Bıyıkoğlu, Türker; Erten, Cesim

2013-07-01

Given a pair of metabolic pathways, an alignment of the pathways corresponds to a mapping between similar substructures of the pair. Successful alignments may provide useful applications in phylogenetic tree reconstruction, drug design and overall may enhance our understanding of cellular metabolism. We consider the problem of providing one-to-many alignments of reactions in a pair of metabolic pathways. We first provide a constrained alignment framework applicable to the problem. We show that the constrained alignment problem even in a primitive setting is computationally intractable, which justifies efforts for designing efficient heuristics. We present our Constrained Alignment of Metabolic Pathways (CAMPways) algorithm designed for this purpose. Through extensive experiments involving a large pathway database, we demonstrate that when compared with a state-of-the-art alternative, the CAMPways algorithm provides better alignment results on metabolic networks as far as measures based on same-pathway inclusion and biochemical significance are concerned. The execution speed of our algorithm constitutes yet another important improvement over alternative algorithms. Open source codes, executable binary, useful scripts, all the experimental data and the results are freely available as part of the Supplementary Material at http://code.google.com/p/campways/. Supplementary data are available at Bioinformatics online.

Turbine blade root design concept promises superior alignment

NASA Technical Reports Server (NTRS)

King, O. D.

1966-01-01

Blade-to-hub mounting concept assures excellent alignment integrity and results in elimination of some welding problems associated with designs. With this design, if rework is required, blade removal and replacement may be readily accomplished without damage to blade positioning media on the wheel hub.

HIP1 propagates in cyanobacterial DNA via nucleotide substitutions but promotes excision at similar frequencies in Escherichia coli and Synechococcus PCC 7942.

PubMed

Robinson, P J; Cranenburgh, R M; Head, I M; Robinson, N J

1997-04-01

The sequence 5'-GCGATCGC-3', designated HIP1, for highly iterated palindrome, was first identified at the borders of a gene-deletion event and subsequently shown to constitute up to 2.5% of the DNA in some cyanobacteria. It is now reported that HIP1 is polyphyletic, occurring in several distinct cyanobacterial lineages and not defining a clade. HIP1 does not introduce gaps into sequence alignments. It aligns with partial HIP1 sites in related sequences showing that it propagates by nucleotide substitutions rather than insertion. Constructs have been created to determine the frequencies at which deletion events occur between palindromes located within the selectable marker neo. Deletion between HIP1 sites was more frequent in Synechococcus PCC 7942 than deletion between control palindromes, 5'-CCGATCGG-3', designated PAL0. However, this is not due to a recombinase that recognises HIP1 and is peculiar to cyanobacteria because similar deletion frequencies were detected in Escherichia coli. Furthermore, the frequency of deletion of DNA flanked asymmetrically by one HIP1 site and one PAL0 site was less than the frequency of deletion of DNA flanked asymmetrically by identical copies of either palindrome. This is consistent with deletion by copy-choice.

Study of optical techniques for the Ames unitary wind tunnels. Part 1: Schlieren

NASA Technical Reports Server (NTRS)

Lee, George

1992-01-01

Alignment procedures and conceptual designs for the rapid alignment of the Ames Unitary Wind Tunnel schlieren systems were devised. The schlieren systems can be aligned by translating the light source, the mirrors, and the knife edge equal distances. One design for rapid alignment consists of a manual pin locking scheme. The other is a motorized electronic position scheme. A study of two optical concepts which can be used with the schlieren system was made. These are the 'point diffraction interferometers' and the 'focus schlieren'. Effects of vibrations were studied.

Construction and assembly of the wire planes for the MicroBooNE Time Projection Chamber

DOE PAGES

Acciarri, R.; Adams, C.; Asaadi, J.; ...

2017-03-09

As x-ray and electron tomography is pushed further into the nanoscale, the limitations of rotation stages become more apparent, leading to challenges in the alignment of the acquired projection images. Here we present an approach for rapid post-acquisition alignment of these projections to obtain high quality three-dimensional images. Our approach is based on a joint estimation of alignment errors, and the object, using an iterative refinement procedure. With simulated data where we know the alignment error of each projection image, our approach shows a residual alignment error that is a factor of a thousand smaller, and it reaches the samemore » error level in the reconstructed image in less than half the number of iterations. We then show its application to experimental data in x-ray and electron nanotomography.« less

Construction and assembly of the wire planes for the MicroBooNE Time Projection Chamber

DOE Office of Scientific and Technical Information (OSTI.GOV)

Acciarri, R.; Adams, C.; Asaadi, J.

As x-ray and electron tomography is pushed further into the nanoscale, the limitations of rotation stages become more apparent, leading to challenges in the alignment of the acquired projection images. Here we present an approach for rapid post-acquisition alignment of these projections to obtain high quality three-dimensional images. Our approach is based on a joint estimation of alignment errors, and the object, using an iterative refinement procedure. With simulated data where we know the alignment error of each projection image, our approach shows a residual alignment error that is a factor of a thousand smaller, and it reaches the samemore » error level in the reconstructed image in less than half the number of iterations. We then show its application to experimental data in x-ray and electron nanotomography.« less

Fabrication Process for Large Size Mold and Alignment Method for Nanoimprint System

NASA Astrophysics Data System (ADS)

Ishibashi, Kentaro; Kokubo, Mitsunori; Goto, Hiroshi; Mizuno, Jun; Shoji, Shuichi

Nanoimprint technology is considered one of the mass production methods of the display for cellular phone or notebook computer, with Anti-Reflection Structures (ARS) pattern and so on. In this case, the large size mold with nanometer order pattern is very important. Then, we describe the fabrication process for large size mold, and the alignment method for UV nanoimprint system. We developed the original mold fabrication process using nanoimprint method and etching techniques. In 66 × 45 mm2 area, 200nm period seamless patterns were formed using this process. And, we constructed original alignment system that consists of the CCD-camera system, X-Y-θ table, method of moiré fringe, and image processing system, because the accuracy of pattern connection depends on the alignment method. This alignment system accuracy was within 20nm.

Design of a self-aligned, wide temperature range (300 mK-300 K) atomic force microscope/magnetic force microscope with 10 nm magnetic force microscope resolution

DOE Office of Scientific and Technical Information (OSTI.GOV)

Karcı, Özgür; Department of Nanotechnology and Nanomedicine, Hacettepe University, Beytepe, 06800 Ankara; Dede, Münir

We describe the design of a wide temperature range (300 mK-300 K) atomic force microscope/magnetic force microscope with a self-aligned fibre-cantilever mechanism. An alignment chip with alignment groves and a special mechanical design are used to eliminate tedious and time consuming fibre-cantilever alignment procedure for the entire temperature range. A low noise, Michelson fibre interferometer was integrated into the system for measuring deflection of the cantilever. The spectral noise density of the system was measured to be ~12 fm/√Hz at 4.2 K at 3 mW incident optical power. Abrikosov vortices in BSCCO(2212) single crystal sample and a high density hardmore » disk sample were imaged at 10 nm resolution to demonstrate the performance of the system.« less

Optical alignment of the JWST ISIM to the OTE simulator (OSIM): current concept and design studies

NASA Astrophysics Data System (ADS)

Frey, Bradley J.; Davila, Pamela S.; Hagopian, John G.; Marsh, James M.; Ohl, Raymond G.; Wilson, Mark E.; Young, Philip J.

2007-09-01

The James Webb Space Telescope's (JWST) Integrated Science Instrument Module (ISIM) contains the observatory's four science instruments and their support subsystems. During alignment and test of the integrated ISIM at NASA's Goddard Space Flight Center (GSFC), the Optical telescope element SIMulator (OSIM) will be used to optically stimulate the science instruments to verify their operation and performance. In this paper we present the design of two cryogenic alignment fixtures that will be used to align the OSIM to the ISIM during testing at GSFC. These fixtures, the Master Alignment Target Fixture (MATF) and the ISIM Alignment Target Fixture (IATF), will provide continuous, six degree of freedom feedback to OSIM during initial ambient alignment as well as during cryogenic vacuum testing. These fixtures will allow us to position the OSIM and detect OSIM-ISIM absolute alignment to better than 180 microns in translation and 540 micro-radians in rotation. We will provide a brief overview of the OSIM system and we will also discuss the relevance of these fixtures in the context of the overall ISIM alignment and test plan.

Fibrin gels exhibit improved biological, structural, and mechanical properties compared with collagen gels in cell-based tendon tissue-engineered constructs.

PubMed

Breidenbach, Andrew P; Dyment, Nathaniel A; Lu, Yinhui; Rao, Marepalli; Shearn, Jason T; Rowe, David W; Kadler, Karl E; Butler, David L

2015-02-01

The prevalence of tendon and ligament injuries and inadequacies of current treatments is driving the need for alternative strategies such as tissue engineering. Fibrin and collagen biopolymers have been popular materials for creating tissue-engineered constructs (TECs), as they exhibit advantages of biocompatibility and flexibility in construct design. Unfortunately, a few studies have directly compared these materials for tendon and ligament applications. Therefore, this study aims at determining how collagen versus fibrin hydrogels affect the biological, structural, and mechanical properties of TECs during formation in vitro. Our findings show that tendon and ligament progenitor cells seeded in fibrin constructs exhibit improved tenogenic gene expression patterns compared with their collagen-based counterparts for approximately 14 days in culture. Fibrin-based constructs also exhibit improved cell-derived collagen alignment, increased linear modulus (2.2-fold greater) compared with collagen-based constructs. Cyclic tensile loading, which promotes the maturation of tendon constructs in a previous work, exhibits a material-dependent effect in this study. Fibrin constructs show trending reductions in mechanical, biological, and structural properties, whereas collagen constructs only show improved tenogenic expression in the presence of mechanical stimulation. These findings highlight that components of the mechanical stimulus (e.g., strain amplitude or time of initiation) need to be tailored to the material and cell type. Given the improvements in tenogenic expression, extracellular matrix organization, and material properties during static culture, in vitro findings presented here suggest that fibrin-based constructs may be a more suitable alternative to collagen-based constructs for tissue-engineered tendon/ligament repair.

Fibrin Gels Exhibit Improved Biological, Structural, and Mechanical Properties Compared with Collagen Gels in Cell-Based Tendon Tissue-Engineered Constructs

PubMed Central

Dyment, Nathaniel A.; Lu, Yinhui; Rao, Marepalli; Shearn, Jason T.; Rowe, David W.; Kadler, Karl E.; Butler, David L.

2015-01-01

The prevalence of tendon and ligament injuries and inadequacies of current treatments is driving the need for alternative strategies such as tissue engineering. Fibrin and collagen biopolymers have been popular materials for creating tissue-engineered constructs (TECs), as they exhibit advantages of biocompatibility and flexibility in construct design. Unfortunately, a few studies have directly compared these materials for tendon and ligament applications. Therefore, this study aims at determining how collagen versus fibrin hydrogels affect the biological, structural, and mechanical properties of TECs during formation in vitro. Our findings show that tendon and ligament progenitor cells seeded in fibrin constructs exhibit improved tenogenic gene expression patterns compared with their collagen-based counterparts for approximately 14 days in culture. Fibrin-based constructs also exhibit improved cell-derived collagen alignment, increased linear modulus (2.2-fold greater) compared with collagen-based constructs. Cyclic tensile loading, which promotes the maturation of tendon constructs in a previous work, exhibits a material-dependent effect in this study. Fibrin constructs show trending reductions in mechanical, biological, and structural properties, whereas collagen constructs only show improved tenogenic expression in the presence of mechanical stimulation. These findings highlight that components of the mechanical stimulus (e.g., strain amplitude or time of initiation) need to be tailored to the material and cell type. Given the improvements in tenogenic expression, extracellular matrix organization, and material properties during static culture, in vitro findings presented here suggest that fibrin-based constructs may be a more suitable alternative to collagen-based constructs for tissue-engineered tendon/ligament repair. PMID:25266738

Embedded-Based Graphics Processing Unit Cluster Platform for Multiple Sequence Alignments

PubMed Central

Wei, Jyh-Da; Cheng, Hui-Jun; Lin, Chun-Yuan; Ye, Jin; Yeh, Kuan-Yu

2017-01-01

High-end graphics processing units (GPUs), such as NVIDIA Tesla/Fermi/Kepler series cards with thousands of cores per chip, are widely applied to high-performance computing fields in a decade. These desktop GPU cards should be installed in personal computers/servers with desktop CPUs, and the cost and power consumption of constructing a GPU cluster platform are very high. In recent years, NVIDIA releases an embedded board, called Jetson Tegra K1 (TK1), which contains 4 ARM Cortex-A15 CPUs and 192 Compute Unified Device Architecture cores (belong to Kepler GPUs). Jetson Tegra K1 has several advantages, such as the low cost, low power consumption, and high applicability, and it has been applied into several specific applications. In our previous work, a bioinformatics platform with a single TK1 (STK platform) was constructed, and this previous work is also used to prove that the Web and mobile services can be implemented in the STK platform with a good cost-performance ratio by comparing a STK platform with the desktop CPU and GPU. In this work, an embedded-based GPU cluster platform will be constructed with multiple TK1s (MTK platform). Complex system installation and setup are necessary procedures at first. Then, 2 job assignment modes are designed for the MTK platform to provide services for users. Finally, ClustalW v2.0.11 and ClustalWtk will be ported to the MTK platform. The experimental results showed that the speedup ratios achieved 5.5 and 4.8 times for ClustalW v2.0.11 and ClustalWtk, respectively, by comparing 6 TK1s with a single TK1. The MTK platform is proven to be useful for multiple sequence alignments. PMID:28835734

Embedded-Based Graphics Processing Unit Cluster Platform for Multiple Sequence Alignments.

PubMed

Wei, Jyh-Da; Cheng, Hui-Jun; Lin, Chun-Yuan; Ye, Jin; Yeh, Kuan-Yu

2017-01-01

High-end graphics processing units (GPUs), such as NVIDIA Tesla/Fermi/Kepler series cards with thousands of cores per chip, are widely applied to high-performance computing fields in a decade. These desktop GPU cards should be installed in personal computers/servers with desktop CPUs, and the cost and power consumption of constructing a GPU cluster platform are very high. In recent years, NVIDIA releases an embedded board, called Jetson Tegra K1 (TK1), which contains 4 ARM Cortex-A15 CPUs and 192 Compute Unified Device Architecture cores (belong to Kepler GPUs). Jetson Tegra K1 has several advantages, such as the low cost, low power consumption, and high applicability, and it has been applied into several specific applications. In our previous work, a bioinformatics platform with a single TK1 (STK platform) was constructed, and this previous work is also used to prove that the Web and mobile services can be implemented in the STK platform with a good cost-performance ratio by comparing a STK platform with the desktop CPU and GPU. In this work, an embedded-based GPU cluster platform will be constructed with multiple TK1s (MTK platform). Complex system installation and setup are necessary procedures at first. Then, 2 job assignment modes are designed for the MTK platform to provide services for users. Finally, ClustalW v2.0.11 and ClustalWtk will be ported to the MTK platform. The experimental results showed that the speedup ratios achieved 5.5 and 4.8 times for ClustalW v2.0.11 and ClustalWtk, respectively, by comparing 6 TK1s with a single TK1. The MTK platform is proven to be useful for multiple sequence alignments.

Design considerations for a compact infrared airborne imager to meet alignment and assembly requirements

NASA Astrophysics Data System (ADS)

Spencer, Harvey

2002-09-01

Helicopter mounted optical systems require compact packaging, good image performance (approaching the diffraction-limit), and must survive and operate in a rugged shock and thermal environment. The always-present requirement for low weight in an airborne sensor is paramount when considering the optical configuration. In addition, the usual list of optical requirements which must be satisfied within narrow tolerances, including field-of-view, vignetting, boresight, stray light rejection, and transmittance drive the optical design. It must be determined early in the engineering process which internal optical alignment adjustment provisions must be included, which may be included, and which will have to be omitted, since adding alignment features often conflicts with the requirement for optical component stability during operation and of course adds weight. When the system is to be modular and mates with another optical system, a telescope designed by different contractor in this case, additional alignment requirements between the two systems must be specified and agreed upon. Final delivered cost is certainly critical and "touch labor" assembly time must be determined and controlled. A clear plan for the alignment and assembly steps must be devised before the optical design can even begin to ensure that an arrangement of optical components amenable to adjustment is reached. The optical specification document should be written contemporaneously with the alignment plan to insure compatibility. The optics decisions that led to the success of this project are described and the final optical design is presented. A description of some unique pupil alignment adjustments, never performed by us in the infrared, is described.

SP-Designer: a user-friendly program for designing species-specific primer pairs from DNA sequence alignments.

PubMed

Villard, Pierre; Malausa, Thibaut

2013-07-01

SP-Designer is an open-source program providing a user-friendly tool for the design of specific PCR primer pairs from a DNA sequence alignment containing sequences from various taxa. SP-Designer selects PCR primer pairs for the amplification of DNA from a target species on the basis of several criteria: (i) primer specificity, as assessed by interspecific sequence polymorphism in the annealing regions, (ii) the biochemical characteristics of the primers and (iii) the intended PCR conditions. SP-Designer generates tables, detailing the primer pair and PCR characteristics, and a FASTA file locating the primer sequences in the original sequence alignment. SP-Designer is Windows-compatible and freely available from http://www2.sophia.inra.fr/urih/sophia_mart/sp_designer/info_sp_designer.php. © 2013 John Wiley & Sons Ltd.

Magnetic field design for selecting and aligning immunomagnetic labeled cells.

PubMed

Tibbe, Arjan G J; de Grooth, Bart G; Greve, Jan; Dolan, Gerald J; Rao, Chandra; Terstappen, Leon W M M

2002-03-01

Recently we introduced the CellTracks cell analysis system, in which samples are prepared based on a combination of immunomagnetic selection, separation, and alignment of cells along ferromagnetic lines. Here we describe the underlying magnetic principles and considerations made in the magnetic field design to achieve the best possible cell selection and alignment of magnetically labeled cells. Materials and Methods Computer simulations, in combination with experimental data, were used to optimize the design of the magnets and Ni lines to obtain the optimal magnetic configuration. A homogeneous cell distribution on the upper surface of the sample chamber was obtained with a magnet where the pole faces were tilted towards each other. The spatial distribution of magnetically aligned objects in between the Ni lines was dependent on the ratio of the diameter of the aligned object and the line spacing, which was tested with magnetically and fluorescently labeled 6 microm polystyrene beads. The best result was obtained when the line spacing was equal to or smaller than the diameter of the aligned object. The magnetic gradient of the designed permanent magnet extracts magnetically labeled cells from any cell suspension to a desired plane, providing a homogeneous cell distribution. In addition, it magnetizes ferro-magnetic Ni lines in this plane whose additional local gradient adds to the gradient of the permanent magnet. The resultant gradient aligns the magnetically labeled cells first brought to this plane. This combination makes it possible, in a single step, to extract and align cells on a surface from any cell suspension. Copyright 2002 Wiley-Liss, Inc.

A blended learning approach for teaching computer programming: design for large classes in Sub-Saharan Africa

NASA Astrophysics Data System (ADS)

Bayu Bati, Tesfaye; Gelderblom, Helene; van Biljon, Judy

2014-01-01

The challenge of teaching programming in higher education is complicated by problems associated with large class teaching, a prevalent situation in many developing countries. This paper reports on an investigation into the use of a blended learning approach to teaching and learning of programming in a class of more than 200 students. A course and learning environment was designed by integrating constructivist learning models of Constructive Alignment, Conversational Framework and the Three-Stage Learning Model. Design science research is used for the course redesign and development of the learning environment, and action research is integrated to undertake participatory evaluation of the intervention. The action research involved the Students' Approach to Learning survey, a comparative analysis of students' performance, and qualitative data analysis of data gathered from various sources. The paper makes a theoretical contribution in presenting a design of a blended learning solution for large class teaching of programming grounded in constructivist learning theory and use of free and open source technologies.

Characterization of a novel bioreactor system for 3D cellular mechanobiology studies.

PubMed

Cook, Colin A; Huri, Pinar Y; Ginn, Brian P; Gilbert-Honick, Jordana; Somers, Sarah M; Temple, Joshua P; Mao, Hai-Quan; Grayson, Warren L

2016-08-01

In vitro engineering systems can be powerful tools for studying tissue development in response to biophysical stimuli as well as for evaluating the functionality of engineered tissue grafts. It has been challenging, however, to develop systems that adequately integrate the application of biomimetic mechanical strain to engineered tissue with the ability to assess functional outcomes in real time. The aim of this study was to design a bioreactor system capable of real-time conditioning (dynamic, uniaxial strain, and electrical stimulation) of centimeter-long 3D tissue engineered constructs simultaneously with the capacity to monitor local strains. The system addresses key limitations of uniform sample loading and real-time imaging capabilities. Our system features an electrospun fibrin scaffold, which exhibits physiologically relevant stiffness and uniaxial alignment that facilitates cell adhesion, alignment, and proliferation. We have demonstrated the capacity for directly incorporating human adipose-derived stromal/stem cells into the fibers during the electrospinning process and subsequent culture of the cell-seeded constructs in the bioreactor. The bioreactor facilitates accurate pre-straining of the 3D constructs as well as the application of dynamic and static uniaxial strains while monitoring bulk construct tensions. The incorporation of fluorescent nanoparticles throughout the scaffolds enables in situ monitoring of local strain fields using fluorescent digital image correlation techniques, since the bioreactor is imaging compatible, and allows the assessment of local sample stiffness and stresses when coupled with force sensor measurements. In addition, the system is capable of measuring the electromechanical coupling of skeletal muscle explants by applying an electrical stimulus and simultaneously measuring the force of contraction. The packaging of these technologies, biomaterials, and analytical methods into a single bioreactor system has produced a powerful tool that will enable improved engineering of functional 3D ligaments, tendons, and skeletal muscles. Biotechnol. Bioeng. 2016;113: 1825-1837. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

The oryza map alignment project: the golden path to unlocking the genetic potential of wild rice species.

PubMed

Wing, Rod A; Ammiraju, Jetty S S; Luo, Meizhong; Kim, Hyeran; Yu, Yeisoo; Kudrna, Dave; Goicoechea, Jose L; Wang, Wenming; Nelson, Will; Rao, Kiran; Brar, Darshan; Mackill, Dave J; Han, Bin; Soderlund, Cari; Stein, Lincoln; SanMiguel, Phillip; Jackson, Scott

2005-09-01

The wild species of the genus Oryza offer enormous potential to make a significant impact on agricultural productivity of the cultivated rice species Oryza sativa and Oryza glaberrima. To unlock the genetic potential of wild rice we have initiated a project entitled the 'Oryza Map Alignment Project' (OMAP) with the ultimate goal of constructing and aligning BAC/STC based physical maps of 11 wild and one cultivated rice species to the International Rice Genome Sequencing Project's finished reference genome--O. sativa ssp. japonica c. v. Nipponbare. The 11 wild rice species comprise nine different genome types and include six diploid genomes (AA, BB, CC, EE, FF and GG) and four tetrapliod genomes (BBCC, CCDD, HHKK and HHJJ) with broad geographical distribution and ecological adaptation. In this paper we describe our strategy to construct robust physical maps of all 12 rice species with an emphasis on the AA diploid O. nivara--thought to be the progenitor of modern cultivated rice.

Computational design and engineering of polymeric orthodontic aligners.

PubMed

Barone, S; Paoli, A; Razionale, A V; Savignano, R

2016-10-05

Transparent and removable aligners represent an effective solution to correct various orthodontic malocclusions through minimally invasive procedures. An aligner-based treatment requires patients to sequentially wear dentition-mating shells obtained by thermoforming polymeric disks on reference dental models. An aligner is shaped introducing a geometrical mismatch with respect to the actual tooth positions to induce a loading system, which moves the target teeth toward the correct positions. The common practice is based on selecting the aligner features (material, thickness, and auxiliary elements) by only considering clinician's subjective assessments. In this article, a computational design and engineering methodology has been developed to reconstruct anatomical tissues, to model parametric aligner shapes, to simulate orthodontic movements, and to enhance the aligner design. The proposed approach integrates computer-aided technologies, from tomographic imaging to optical scanning, from parametric modeling to finite element analyses, within a 3-dimensional digital framework. The anatomical modeling provides anatomies, including teeth (roots and crowns), jaw bones, and periodontal ligaments, which are the references for the down streaming parametric aligner shaping. The biomechanical interactions between anatomical models and aligner geometries are virtually reproduced using a finite element analysis software. The methodology allows numerical simulations of patient-specific conditions and the comparative analyses of different aligner configurations. In this article, the digital framework has been used to study the influence of various auxiliary elements on the loading system delivered to a maxillary and a mandibular central incisor during an orthodontic tipping movement. Numerical simulations have shown a high dependency of the orthodontic tooth movement on the auxiliary element configuration, which should then be accurately selected to maximize the aligner's effectiveness. Copyright © 2016 John Wiley & Sons, Ltd.

Band alignment of atomic layer deposited MgO/Zn0.8Al0.2O heterointerface determined by charge corrected X-ray photoelectron spectroscopy

NASA Astrophysics Data System (ADS)

Yan, Baojun; Liu, Shulin; Yang, Yuzhen; Heng, Yuekun

2016-05-01

Pure magnesium (MgO) and zinc oxide doped with aluminum oxide (Zn0.8Al0.2O) were prepared via atomic layer deposition. We have studied the structure and band gap of bulk Zn0.8Al0.2O material by X-ray diffractometer (XRD) and Tauc method, and the band offsets and alignment of atomic layer deposited MgO/Zn0.8Al0.2O heterointerface were investigated systematically using X-ray photoelectron spectroscopy (XPS) in this study. Different methodologies, such as neutralizing electron gun, the use of C 1s peak recalibration and zero charging method, were applied to recover the actual position of the core levels in insulator materials which were easily influenced by differential charging phenomena. Schematic band alignment diagram, valence band offset (ΔEV) and conduction band offset (ΔEC) for the interface of the MgO/Zn0.8Al0.2O heterostructure have been constructed. An accurate value of ΔEV = 0.72 ± 0.11 eV was obtained from various combinations of core levels of heterojunction with varied MgO thickness. Given the experimental band gaps of 7.83 eV for MgO and 5.29 eV for Zn0.8Al0.2O, a type-II heterojunction with a ΔEC of 3.26 ± 0.11 eV was found. Band offsets and alignment studies of these heterojunctions are important for gaining deep consideration to the design of various optoelectronic devices based on such heterointerface.

Air-bridged Ohmic contact on vertically aligned si nanowire arrays: application to molecule sensors.

PubMed

Han, Hee; Kim, Jungkil; Shin, Ho Sun; Song, Jae Yong; Lee, Woo

2012-05-02

A simple, cost-effective, and highly reliable method for constructing an air-bridged electrical contact on large arrays of vertically aligned nanowires was developed. The present method may open up new opportunities for developing advanced nanowire-based devices for energy harvest and storage, power generation, and sensing applications. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Active and Passive Radiative Transfer Modeling with Preferentially-Aligned Particles

NASA Technical Reports Server (NTRS)

Adams, Ian Stuart

2017-01-01

The fluid dynamics of falling hydrometeors often results in preferential orientations that can affect both the intensity and polarization of electromagnetic radiation. In order to properly interpret remote sensing observations of ice and snow, such alignments should be considered when constructing databases of scattering particles; however, the inclusion of aligned particles increases the complexity of the scattering data. To demonstrate the use of scattering properties of preferentially-aligned particles, millimeter-wave brightness temperatures and radar observables, including reflectivity and linear depolarization ratio, are modeled using the Atmospheric Radiative Transfer Simulator (ARTS). The necessary scattering parameters for vector radiative transfer, particularly with respect to ARTS, are reviewed, and the exploitation of particle symmetries, as well as scattering reciprocity relationships, are detailed.

Chemical and Biological Defense: Designated Entity Needed to Identify, Align, and Manage DOD’s Infrastructure

DTIC Science & Technology

2015-06-01

Designated Leader, GAO-10-645 (Washington, D.C.: June 30, 2010). 35See GAO, Biological Defense: DOD Has Strengthened Coordination on Medical... on track to be designated a Leadership in Energy and Environmental Design facility. metabolic poisons, and pulmonary toxicants; nerve agent...CHEMICAL AND BIOLOGICAL DEFENSE Designated Entity Needed to Identify, Align, and Manage DOD’s Infrastructure

Music Performance Assessment: Exploring Three Approaches for Quality Rubric Construction

ERIC Educational Resources Information Center

DeLuca, Christopher; Bolden, Benjamin

2014-01-01

Assessing student performance is a central challenge for music educators. In alignment with previous research, this article asserts that rubrics provide a viable and useful structure for assessing music performance. To expand the potential of rubrics in music education, challenges to effective rubric construction are identified and addressed…

Automatic Construction of English/Chinese Parallel Corpora.

ERIC Educational Resources Information Center

Yang, Christopher C.; Li, Kar Wing

2003-01-01

Discussion of multilingual corpora and cross-lingual information retrieval focuses on research that constructed English/Chinese parallel corpus automatically from the World Wide Web. Presents an alignment method which is based on dynamic programming to identify one-to-one Chinese and English title pairs and discusses results of experiments…

Local-global alignment for finding 3D similarities in protein structures

DOEpatents

Zemla, Adam T [Brentwood, CA

2011-09-20

A method of finding 3D similarities in protein structures of a first molecule and a second molecule. The method comprises providing preselected information regarding the first molecule and the second molecule. Comparing the first molecule and the second molecule using Longest Continuous Segments (LCS) analysis. Comparing the first molecule and the second molecule using Global Distance Test (GDT) analysis. Comparing the first molecule and the second molecule using Local Global Alignment Scoring function (LGA_S) analysis. Verifying constructed alignment and repeating the steps to find the regions of 3D similarities in protein structures.

Downwind pre-aligned rotors for extreme-scale wind turbines

DOE PAGES

Loth, Eric; Steele, Adam; Qin, Chao; ...

2017-03-08

Downwind force angles are small for current turbines systems (1-5 MW) such that they may be readily accommodated by conventional upwind configurations. However, analysis indicates that extreme-scale systems (10-20 MW) will have larger angles that may benefit from downwind-aligned configurations. To examine potential rotor mass reduction, the pre-alignment concept was investigated a two-bladed configuration by keeping the structural and aerodynamic characteristics of each blade fixed (to avoids a complete blade re-design). Simulations for a 13.2 MW rated rotor at steady-state conditions show that this concept-level two-bladed design may yield 25% rotor mass savings while also reducing average blade stress overmore » all wind speeds. These results employed a pre-alignment on the basis of a wind speed of 1.25 times the rated wind speed. The downwind pre-aligned concept may also reduce damage equivalent loads on the blades by 60% for steady rated wind conditions. Even higher mass and damage equivalent load savings (relative to conventional upwind designs) may be possible for larger systems (15-20 MW) for which load-alignment angles become even larger. Furthermore, much more work is needed to determine whether this concept can be translated into a practical design that must meet a wide myriad of other criteria.« less

Downwind pre-aligned rotors for extreme-scale wind turbines

DOE Office of Scientific and Technical Information (OSTI.GOV)

Loth, Eric; Steele, Adam; Qin, Chao

Downwind force angles are small for current turbines systems (1-5 MW) such that they may be readily accommodated by conventional upwind configurations. However, analysis indicates that extreme-scale systems (10-20 MW) will have larger angles that may benefit from downwind-aligned configurations. To examine potential rotor mass reduction, the pre-alignment concept was investigated a two-bladed configuration by keeping the structural and aerodynamic characteristics of each blade fixed (to avoids a complete blade re-design). Simulations for a 13.2 MW rated rotor at steady-state conditions show that this concept-level two-bladed design may yield 25% rotor mass savings while also reducing average blade stress overmore » all wind speeds. These results employed a pre-alignment on the basis of a wind speed of 1.25 times the rated wind speed. The downwind pre-aligned concept may also reduce damage equivalent loads on the blades by 60% for steady rated wind conditions. Even higher mass and damage equivalent load savings (relative to conventional upwind designs) may be possible for larger systems (15-20 MW) for which load-alignment angles become even larger. Furthermore, much more work is needed to determine whether this concept can be translated into a practical design that must meet a wide myriad of other criteria.« less

Towards Evolving Electronic Circuits for Autonomous Space Applications

NASA Technical Reports Server (NTRS)

Lohn, Jason D.; Haith, Gary L.; Colombano, Silvano P.; Stassinopoulos, Dimitris

2000-01-01

The relatively new field of Evolvable Hardware studies how simulated evolution can reconfigure, adapt, and design hardware structures in an automated manner. Space applications, especially those requiring autonomy, are potential beneficiaries of evolvable hardware. For example, robotic drilling from a mobile platform requires high-bandwidth controller circuits that are difficult to design. In this paper, we present automated design techniques based on evolutionary search that could potentially be used in such applications. First, we present a method of automatically generating analog circuit designs using evolutionary search and a circuit construction language. Our system allows circuit size (number of devices), circuit topology, and device values to be evolved. Using a parallel genetic algorithm, we present experimental results for five design tasks. Second, we investigate the use of coevolution in automated circuit design. We examine fitness evaluation by comparing the effectiveness of four fitness schedules. The results indicate that solution quality is highest with static and co-evolving fitness schedules as compared to the other two dynamic schedules. We discuss these results and offer two possible explanations for the observed behavior: retention of useful information, and alignment of problem difficulty with circuit proficiency.

Dynamic Tensile Loading Improves the Functional Properties of Mesenchymal Stem Cell-Laden Nanofiber-Based Fibrocartilage

PubMed Central

Baker, Brendon M.; Shah, Roshan P.; Huang, Alice H.

2011-01-01

Fibrocartilaginous tissues such as the meniscus serve critical load-bearing roles, relying on arrays of collagen fibers to resist tensile loads experienced with normal activity. As these structures are frequently injured and possess limited healing capacity, there exists great demand for tissue-engineered replacements. Toward recreating the structural features of these anisotropic tissues in vitro, we employ scaffolds composed of co-aligned nanofibers that direct mesenchymal stem cell (MSC) orientation and the formation of organized extracellular matrix (ECM). Concomitant with ECM synthesis, the mechanical properties of constructs increase with free-swelling culture, but ultimately failed to achieve equivalence with meniscal fibrocartilage. As mechanical forces are essential to the development and maintenance of musculoskeletal tissues, this work examined the effect of cyclic tensile loading on MSC-laden nanofibrous constructs. We hypothesized that loading would modulate the transcriptional behavior of MSCs, spur the deposition of ECM, and lead to enhancements in construct mechanical properties compared to free-swelling controls. Fiber-aligned scaffolds were seeded with MSCs and dynamically loaded daily in tension or maintained as nonloaded controls for 4 weeks. With mechanical stimulation, fibrous gene expression increased, collagen deposition increased, and the tensile modulus increased by 16% relative to controls. These results show that dynamic tensile loading enhances the maturation of MSC-laden aligned nanofibrous constructs, suggesting that recapitulation of the structural and mechanical environment of load-bearing tissues results in increases in functional properties that can be exploited for tissue engineering applications. PMID:21247342

Dynamic tensile loading improves the functional properties of mesenchymal stem cell-laden nanofiber-based fibrocartilage.

PubMed

Baker, Brendon M; Shah, Roshan P; Huang, Alice H; Mauck, Robert L

2011-05-01

Fibrocartilaginous tissues such as the meniscus serve critical load-bearing roles, relying on arrays of collagen fibers to resist tensile loads experienced with normal activity. As these structures are frequently injured and possess limited healing capacity, there exists great demand for tissue-engineered replacements. Toward recreating the structural features of these anisotropic tissues in vitro, we employ scaffolds composed of co-aligned nanofibers that direct mesenchymal stem cell (MSC) orientation and the formation of organized extracellular matrix (ECM). Concomitant with ECM synthesis, the mechanical properties of constructs increase with free-swelling culture, but ultimately failed to achieve equivalence with meniscal fibrocartilage. As mechanical forces are essential to the development and maintenance of musculoskeletal tissues, this work examined the effect of cyclic tensile loading on MSC-laden nanofibrous constructs. We hypothesized that loading would modulate the transcriptional behavior of MSCs, spur the deposition of ECM, and lead to enhancements in construct mechanical properties compared to free-swelling controls. Fiber-aligned scaffolds were seeded with MSCs and dynamically loaded daily in tension or maintained as nonloaded controls for 4 weeks. With mechanical stimulation, fibrous gene expression increased, collagen deposition increased, and the tensile modulus increased by 16% relative to controls. These results show that dynamic tensile loading enhances the maturation of MSC-laden aligned nanofibrous constructs, suggesting that recapitulation of the structural and mechanical environment of load-bearing tissues results in increases in functional properties that can be exploited for tissue engineering applications.

What can the past of pay-for-performance tell us about the future of Value-Based Purchasing in Medicare?

PubMed

Ryan, Andrew M; Damberg, Cheryl L

2013-06-01

The Medicare program has implemented pay-for-performance (P4P), or Value-Based Purchasing, for inpatient care and for Medicare Advantage plans, and plans to implement a program for physicians in 2015. In this paper, we review evidence on the effectiveness of P4P and identify design criteria deemed to be best practice in P4P. We then assess the extent to which Medicare's existing and planned Value-Based Purchasing programs align with these best practices. Of the seven identified best practices in P4P program design, the Hospital Value-Based Purchasing program is strongly aligned with two of the best practices, moderately aligned with three, weakly aligned with one, and has unclear alignment with one best practice. The Physician Value-Based Purchasing Modifier is strongly aligned with two of the best practices, moderately aligned with one, weakly aligned with three, and has unclear alignment with one of the best practices. The Medicare Advantage Quality Bonus Program is strongly aligned with four of the best practices, moderately aligned with two, and weakly aligned with one of the best practices. We identify enduring gaps in P4P literature as it relates to Medicare's plans for Value-Based Purchasing and discuss important issues in the future of these implementations in Medicare. Copyright © 2013 Elsevier Inc. All rights reserved.

Building the BIKE: Development and Testing of the Biotechnology Instrument for Knowledge Elicitation (BIKE)

NASA Astrophysics Data System (ADS)

Witzig, Stephen B.; Rebello, Carina M.; Siegel, Marcelle A.; Freyermuth, Sharyn K.; Izci, Kemal; McClure, Bruce

2014-10-01

Identifying students' conceptual scientific understanding is difficult if the appropriate tools are not available for educators. Concept inventories have become a popular tool to assess student understanding; however, traditionally, they are multiple choice tests. International science education standard documents advocate that assessments should be reform based, contain diverse question types, and should align with instructional approaches. To date, no instrument of this type targeting student conceptions in biotechnology has been developed. We report here the development, testing, and validation of a 35-item Biotechnology Instrument for Knowledge Elicitation (BIKE) that includes a mix of question types. The BIKE was designed to elicit student thinking and a variety of conceptual understandings, as opposed to testing closed-ended responses. The design phase contained nine steps including a literature search for content, student interviews, a pilot test, as well as expert review. Data from 175 students over two semesters, including 16 student interviews and six expert reviewers (professors from six different institutions), were used to validate the instrument. Cronbach's alpha on the pre/posttest was 0.664 and 0.668, respectively, indicating the BIKE has internal consistency. Cohen's kappa for inter-rater reliability among the 6,525 total items was 0.684 indicating substantial agreement among scorers. Item analysis demonstrated that the items were challenging, there was discrimination among the individual items, and there was alignment with research-based design principles for construct validity. This study provides a reliable and valid conceptual understanding instrument in the understudied area of biotechnology.

NetCoffee: a fast and accurate global alignment approach to identify functionally conserved proteins in multiple networks.

PubMed

Hu, Jialu; Kehr, Birte; Reinert, Knut

2014-02-15

Owing to recent advancements in high-throughput technologies, protein-protein interaction networks of more and more species become available in public databases. The question of how to identify functionally conserved proteins across species attracts a lot of attention in computational biology. Network alignments provide a systematic way to solve this problem. However, most existing alignment tools encounter limitations in tackling this problem. Therefore, the demand for faster and more efficient alignment tools is growing. We present a fast and accurate algorithm, NetCoffee, which allows to find a global alignment of multiple protein-protein interaction networks. NetCoffee searches for a global alignment by maximizing a target function using simulated annealing on a set of weighted bipartite graphs that are constructed using a triplet approach similar to T-Coffee. To assess its performance, NetCoffee was applied to four real datasets. Our results suggest that NetCoffee remedies several limitations of previous algorithms, outperforms all existing alignment tools in terms of speed and nevertheless identifies biologically meaningful alignments. The source code and data are freely available for download under the GNU GPL v3 license at https://code.google.com/p/netcoffee/.

Surface tension-driven self-alignment.

PubMed

Mastrangeli, Massimo; Zhou, Quan; Sariola, Veikko; Lambert, Pierre

2017-01-04

Surface tension-driven self-alignment is a passive and highly-accurate positioning mechanism that can significantly simplify and enhance the construction of advanced microsystems. After years of research, demonstrations and developments, the surface engineering and manufacturing technology enabling capillary self-alignment has achieved a degree of maturity conducive to a successful transfer to industrial practice. In view of this transition, a broad and accessible review of the physics, material science and applications of capillary self-alignment is presented. Statics and dynamics of the self-aligning action of deformed liquid bridges are explained through simple models and experiments, and all fundamental aspects of surface patterning and conditioning, of choice, deposition and confinement of liquids, and of component feeding and interconnection to substrates are illustrated through relevant applications in micro- and nanotechnology. A final outline addresses remaining challenges and additional extensions envisioned to further spread the use and fully exploit the potential of the technique.

Aligning Game Activity with Educational Goals: Following a Constrained Design Approach to Instructional Computer Games

ERIC Educational Resources Information Center

Shelton, Brett E.; Scoresby, Jon

2011-01-01

We discuss the design, creation and implementation of an instructional game for use in a high school poetry class following a commitment to an educational game design principle of "alignment". We studied groups of instructional designers and an interactive fiction computer game they built. The game was implemented in a 9th grade English classroom…

Three-dimensional quantitative structure-activity relationship studies on UGT1A9-mediated 3-O-glucuronidation of natural flavonols using a pharmacophore-based comparative molecular field analysis model.

PubMed

Wu, Baojian; Morrow, John Kenneth; Singh, Rashim; Zhang, Shuxing; Hu, Ming

2011-02-01

Glucuronidation is often recognized as one of the rate-determining factors that limit the bioavailability of flavonols. Hence, design and synthesis of more bioavailable flavonols would benefit from the establishment of predictive models of glucuronidation using kinetic parameters [e.g., K(m), V(max), intrinsic clearance (CL(int)) = V(max)/K(m)] derived for flavonols. This article aims to construct position (3-OH)-specific comparative molecular field analysis (CoMFA) models to describe UDP-glucuronosyltransferase (UGT) 1A9-mediated glucuronidation of flavonols, which can be used to design poor UGT1A9 substrates. The kinetics of recombinant UGT1A9-mediated 3-O-glucuronidation of 30 flavonols was characterized, and kinetic parameters (K(m), V(max), CL(int)) were obtained. The observed K(m), V(max), and CL(int) values of 3-O-glucuronidation ranged from 0.04 to 0.68 μM, 0.04 to 12.95 nmol/mg/min, and 0.06 to 109.60 ml/mg/min, respectively. To model UGT1A9-mediated glucuronidation, 30 flavonols were split into the training (23 compounds) and test (7 compounds) sets. These flavonols were then aligned by mapping the flavonols to specific common feature pharmacophores, which were used to construct CoMFA models of V(max) and CL(int), respectively. The derived CoMFA models possessed good internal and external consistency and showed statistical significance and substantive predictive abilities (V(max) model: q(2) = 0.738, r(2) = 0.976, r(pred)(2) = 0.735; CL(int) model: q(2) = 0.561, r(2) = 0.938, r(pred)(2) = 0.630). The contour maps derived from CoMFA modeling clearly indicate structural characteristics associated with rapid or slow 3-O-glucuronidation. In conclusion, the approach of coupling CoMFA analysis with a pharmacophore-based structural alignment is viable for constructing a predictive model for regiospecific glucuronidation rates of flavonols by UGT1A9.

CombAlign: a code for generating a one-to-many sequence alignment from a set of pairwise structure-based sequence alignments.

PubMed

Zhou, Carol L Ecale

2015-01-01

In order to better define regions of similarity among related protein structures, it is useful to identify the residue-residue correspondences among proteins. Few codes exist for constructing a one-to-many multiple sequence alignment derived from a set of structure or sequence alignments, and a need was evident for creating such a tool for combining pairwise structure alignments that would allow for insertion of gaps in the reference structure. This report describes a new Python code, CombAlign, which takes as input a set of pairwise sequence alignments (which may be structure based) and generates a one-to-many, gapped, multiple structure- or sequence-based sequence alignment (MSSA). The use and utility of CombAlign was demonstrated by generating gapped MSSAs using sets of pairwise structure-based sequence alignments between structure models of the matrix protein (VP40) and pre-small/secreted glycoprotein (sGP) of Reston Ebolavirus and the corresponding proteins of several other filoviruses. The gapped MSSAs revealed structure-based residue-residue correspondences, which enabled identification of structurally similar versus differing regions in the Reston proteins compared to each of the other corresponding proteins. CombAlign is a new Python code that generates a one-to-many, gapped, multiple structure- or sequence-based sequence alignment (MSSA) given a set of pairwise sequence alignments (which may be structure based). CombAlign has utility in assisting the user in distinguishing structurally conserved versus divergent regions on a reference protein structure relative to other closely related proteins. CombAlign was developed in Python 2.6, and the source code is available for download from the GitHub code repository.

CAS-ATLID (co-alignment sensor of ATLID instrument) thermo-structural design and performance

NASA Astrophysics Data System (ADS)

Moreno, Javier; Serrano, Javier; González, David; Rodríguez, Gemma; Manjón, Andrés.; Vásquez, Eloi; Carretero, Carlos; Martínez, Berta

2017-11-01

This paper describes the main thermo-mechanical design features and performances of the Co-Alignment Sensor (CAS) developed by LIDAX and CRISA under ESA program with AIRBUS Defence and Space as industry prime.

Genome alignment with graph data structures: a comparison

PubMed Central

2014-01-01

Background Recent advances in rapid, low-cost sequencing have opened up the opportunity to study complete genome sequences. The computational approach of multiple genome alignment allows investigation of evolutionarily related genomes in an integrated fashion, providing a basis for downstream analyses such as rearrangement studies and phylogenetic inference. Graphs have proven to be a powerful tool for coping with the complexity of genome-scale sequence alignments. The potential of graphs to intuitively represent all aspects of genome alignments led to the development of graph-based approaches for genome alignment. These approaches construct a graph from a set of local alignments, and derive a genome alignment through identification and removal of graph substructures that indicate errors in the alignment. Results We compare the structures of commonly used graphs in terms of their abilities to represent alignment information. We describe how the graphs can be transformed into each other, and identify and classify graph substructures common to one or more graphs. Based on previous approaches, we compile a list of modifications that remove these substructures. Conclusion We show that crucial pieces of alignment information, associated with inversions and duplications, are not visible in the structure of all graphs. If we neglect vertex or edge labels, the graphs differ in their information content. Still, many ideas are shared among all graph-based approaches. Based on these findings, we outline a conceptual framework for graph-based genome alignment that can assist in the development of future genome alignment tools. PMID:24712884

Cardiac differentiation of cardiosphere-derived cells in scaffolds mimicking morphology of the cardiac extracellular matrix.

PubMed

Xu, Yanyi; Patnaik, Sourav; Guo, Xiaolei; Li, Zhenqing; Lo, Wilson; Butler, Ryan; Claude, Andrew; Liu, Zhenguo; Zhang, Ge; Liao, Jun; Anderson, Peter M; Guan, Jianjun

2014-08-01

Stem cell therapy has the potential to regenerate heart tissue after myocardial infarction (MI). The regeneration is dependent upon cardiac differentiation of the delivered stem cells. We hypothesized that timing of the stem cell delivery determines the extent of cardiac differentiation as cell differentiation is dependent on matrix properties such as biomechanics, structure and morphology, and these properties in cardiac extracellular matrix (ECM) continuously vary with time after MI. In order to elucidate the relationship between ECM properties and cardiac differentiation, we created an in vitro model based on ECM-mimicking fibers and a type of cardiac progenitor cell, cardiosphere-derived cells (CDCs). A simultaneous fiber electrospinning and cell electrospraying technique was utilized to fabricate constructs. By blending a highly soft hydrogel with a relatively stiff polyurethane and modulating fabrication parameters, tissue constructs with similar cell adhesion property but different global modulus, single fiber modulus, fiber density and fiber alignment were achieved. The CDCs remained alive within the constructs during a 1week culture period. CDC cardiac differentiation was dependent on the scaffold modulus, fiber volume fraction and fiber alignment. Two constructs with relatively low scaffold modulus, ∼50-60kPa, most significantly directed the CDC differentiation into mature cardiomyocytes as evidenced by gene expressions of cardiac troponin T (cTnT), calcium channel (CACNA1c) and cardiac myosin heavy chain (MYH6), and protein expressions of cardiac troponin I (cTnI) and connexin 43 (CX43). Of these two low-modulus constructs, the extent of differentiation was greater for lower fiber alignment and higher fiber volume fraction. These results suggest that cardiac ECM properties may have an effect on cardiac differentiation of delivered stem cells. Copyright © 2014 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Knowledge-based expert systems and a proof-of-concept case study for multiple sequence alignment construction and analysis.

PubMed

Aniba, Mohamed Radhouene; Siguenza, Sophie; Friedrich, Anne; Plewniak, Frédéric; Poch, Olivier; Marchler-Bauer, Aron; Thompson, Julie Dawn

2009-01-01

The traditional approach to bioinformatics analyses relies on independent task-specific services and applications, using different input and output formats, often idiosyncratic, and frequently not designed to inter-operate. In general, such analyses were performed by experts who manually verified the results obtained at each step in the process. Today, the amount of bioinformatics information continuously being produced means that handling the various applications used to study this information presents a major data management and analysis challenge to researchers. It is now impossible to manually analyse all this information and new approaches are needed that are capable of processing the large-scale heterogeneous data in order to extract the pertinent information. We review the recent use of integrated expert systems aimed at providing more efficient knowledge extraction for bioinformatics research. A general methodology for building knowledge-based expert systems is described, focusing on the unstructured information management architecture, UIMA, which provides facilities for both data and process management. A case study involving a multiple alignment expert system prototype called AlexSys is also presented.

Knowledge-based expert systems and a proof-of-concept case study for multiple sequence alignment construction and analysis

PubMed Central

Aniba, Mohamed Radhouene; Siguenza, Sophie; Friedrich, Anne; Plewniak, Frédéric; Poch, Olivier; Marchler-Bauer, Aron

2009-01-01

The traditional approach to bioinformatics analyses relies on independent task-specific services and applications, using different input and output formats, often idiosyncratic, and frequently not designed to inter-operate. In general, such analyses were performed by experts who manually verified the results obtained at each step in the process. Today, the amount of bioinformatics information continuously being produced means that handling the various applications used to study this information presents a major data management and analysis challenge to researchers. It is now impossible to manually analyse all this information and new approaches are needed that are capable of processing the large-scale heterogeneous data in order to extract the pertinent information. We review the recent use of integrated expert systems aimed at providing more efficient knowledge extraction for bioinformatics research. A general methodology for building knowledge-based expert systems is described, focusing on the unstructured information management architecture, UIMA, which provides facilities for both data and process management. A case study involving a multiple alignment expert system prototype called AlexSys is also presented. PMID:18971242

Effect of pillow height on the biomechanics of the head-neck complex: investigation of the cranio-cervical pressure and cervical spine alignment

PubMed Central

Yang, Hui; Zhou, Yan; Lin, Jin

2016-01-01

Background While appropriate pillow height is crucial to maintaining the quality of sleep and overall health, there are no universal, evidence-based guidelines for pillow design or selection. We aimed to evaluate the effect of pillow height on cranio-cervical pressure and cervical spine alignment. Methods Ten healthy subjects (five males) aged 26 ± 3.6 years were recruited. The average height, weight, and neck length were 167 ± 9.3 cm, 59.6 ± 11.9 kg, and 12.9 ± 1.2 cm respectively. The subjects lay on pillows of four different heights (H0, 110 mm; H1, 130 mm; H2, 150 mm; and H3, 170 mm). The cranio-cervical pressure distribution over the pillow was recorded; the peak and average pressures for each pillow height were compared by one-way ANOVA with repeated measures. Cervical spine alignment was studied using a finite element model constructed based on data from the Visible Human Project. The coordinate of the center of each cervical vertebra were predicted for each pillow height. Three spine alignment parameters (cervical angle, lordosis distance and kyphosis distance) were identified. Results The average cranial pressure at pillow height H3 was approximately 30% higher than that at H0, and significantly different from those at H1 and H2 (p < 0.05). The average cervical pressure at pillow height H0 was 65% lower than that at H3, and significantly different from those at H1 and H2 (p < 0.05). The peak cervical pressures at pillow heights H2 and H3 were significantly different from that at H0 (p < 0.05). With respect to cervical spine alignment, raising pillow height from H0 to H3 caused an increase of 66.4% and 25.1% in cervical angle and lordosis distance, respectively, and a reduction of 43.4% in kyphosis distance. Discussion Pillow height elevation significantly increased the average and peak pressures of the cranial and cervical regions, and increased the extension and lordosis of the cervical spine. The cranio-cervical pressures and cervical spine alignment were height-specific, and they were believed to reflect quality of sleep. Our results provide a quantitative and objective evaluation of the effect of pillow height on the biomechanics of the head-neck complex, and have application in pillow design and selection. PMID:27635354

Construction of an instant structured illumination microscope

PubMed Central

Curd, Alistair; Cleasby, Alexa; Makowska, Katarzyna; York, Andrew; Shroff, Hari; Peckham, Michelle

2015-01-01

A challenge in biological imaging is to capture high-resolution images at fast frame rates in live cells. The “instant structured illumination microscope” (iSIM) is a system designed for this purpose. Similarly to standard structured illumination microscopy (SIM), an iSIM provides a twofold improvement over widefield microscopy, in x, y and z, but also allows much faster image acquisition, with real-time display of super-resolution images. The assembly of an iSIM is reasonably complex, involving the combination and alignment of many optical components, including three micro-optics arrays (two lenslet arrays and an array of pinholes, all with a pitch of 222 μm) and a double-sided scanning mirror. In addition, a number of electronic components must be correctly controlled. Construction of the system is therefore not trivial, but is highly desirable, particularly for live-cell imaging. We report, and provide instructions for, the construction of an iSIM, including minor modifications to a previous design in both hardware and software. The final instrument allows us to rapidly acquire fluorescence images at rates faster than 100 fps, with approximately twofold improvement in resolution in both x–y and z; sub-diffractive biological features have an apparent size (full width at half maximum) of 145 nm (lateral) and 320 nm (axial), using a 1.49 NA objective and 488 nm excitation. PMID:26210400

Using concept mapping to design an indicator framework for addiction treatment centres.

PubMed

Nabitz, Udo; van Den Brink, Wim; Jansen, Paul

2005-06-01

The objective of this study is to determine an indicator framework for addiction treatment centres based on the demands of stakeholders and in alignment with the European Foundation for Quality Management (EFQM) Excellence Model. The setting is the Jellinek Centre based in Amsterdam, the Netherlands, which serves as a prototype for an addiction treatment centre. Concept mapping was used in the construction of the indicator framework. During the 1-day workshop, 16 stakeholders generated, prioritized and sorted 73 items concerning quality and performance. Multidimensional scaling and cluster analysis was applied in constructing a framework consisting of two dimensions and eight clusters. The horizontal axis of the indicator framework is named 'Organization' and has two poles, namely, 'Processes' and 'Results'. The vertical axis is named ' Task' and the poles are named 'Efficient treatment' and 'Prevention programs'. The eight clusters in the two-dimensional framework are arranged in the following, prioritized sequence: 'Efficient treatment network', 'Effective service', ' Target group', 'Quality of life', 'Efficient service', 'Knowledge transfer', 'Reducing addiction related problems', and 'Prevention programs'. The most important items in the framework are: 'patients are satisfied with their treatment', 'early interventions', and 'efficient treatment chain'. The indicator framework aligns with three clusters of the results criteria of the EFQM Excellence Model. It is based on the stakeholders' perspectives and is believed to be specific for addiction treatment centres. The study demonstrates that concept mapping is a suitable strategy for generating indicator frameworks.

Secondary science teachers' view toward and classroom translation of sustained professional development

NASA Astrophysics Data System (ADS)

Lewis, Elizabeth Blake

This study concerns the phenomenon of secondary science teacher learning and enacting instructional strategies learned at the Communication in Science Inquiry Project (CISIP) teacher professional development events, as well as teacher perception of, and relationship to, this year-long professional development program. The CISIP program teaches science teachers how to build scientific classroom discourse communities with their students. Some of the science teachers were previous participants in the professional development, and acted as mentor teachers. The research design employed an integrated conceptual framework of situated learning theory with an analytical lens of teachers' professional, institutional and affinity, identities. A multi-method approach was used to generate data. Throughout the 2007-2008 academic year, the teachers' fidelity to the professional development model was measured using a classroom observation instrument aligned with the professional development model. From these observation data a longitudinal model, using hierarchical linear modeling, was constructed. In addition, surveys and interview data were used to construct both whole group and case studies of two high school science teachers who taught biology at the same school. The results indicated that there was a significant difference between previous and new participants; specifically, the longer teachers had participated in the professional development, and adopted a mentorship role, the greater their fidelity of classroom instruction to the CISIP model. Additionally, the case study teacher who developed a CISIP model-aligned affinity identity implemented more of the instructional strategies than the teacher who maintained his school-based institutional identity.

Molecular crowding of collagen: a pathway to produce highly-organized collagenous structures.

PubMed

Saeidi, Nima; Karmelek, Kathryn P; Paten, Jeffrey A; Zareian, Ramin; DiMasi, Elaine; Ruberti, Jeffrey W

2012-10-01

Collagen in vertebrate animals is often arranged in alternating lamellae or in bundles of aligned fibrils which are designed to withstand in vivo mechanical loads. The formation of these organized structures is thought to result from a complex, large-area integration of individual cell motion and locally-controlled synthesis of fibrillar arrays via cell-surface fibripositors (direct matrix printing). The difficulty of reproducing such a process in vitro has prevented tissue engineers from constructing clinically useful load-bearing connective tissue directly from collagen. However, we and others have taken the view that long-range organizational information is potentially encoded into the structure of the collagen molecule itself, allowing the control of fibril organization to extend far from cell (or bounding) surfaces. We here demonstrate a simple, fast, cell-free method capable of producing highly-organized, anistropic collagen fibrillar lamellae de novo which persist over relatively long-distances (tens to hundreds of microns). Our approach to nanoscale organizational control takes advantage of the intrinsic physiochemical properties of collagen molecules by inducing collagen association through molecular crowding and geometric confinement. To mimic biological tissues which comprise planar, aligned collagen lamellae (e.g. cornea, lamellar bone or annulus fibrosus), type I collagen was confined to a thin, planar geometry, concentrated through molecular crowding and polymerized. The resulting fibrillar lamellae show a striking resemblance to native load-bearing lamellae in that the fibrils are small, generally aligned in the plane of the confining space and change direction en masse throughout the thickness of the construct. The process of organizational control is consistent with embryonic development where the bounded planar cell sheets produced by fibroblasts suggest a similar confinement/concentration strategy. Such a simple approach to nanoscale organizational control of structure not only makes de novo tissue engineering a possibility, but also suggests a clearer pathway to organization for fibroblasts than direct matrix printing. Copyright © 2012 Elsevier Ltd. All rights reserved.

Theoferometer for the Construction of Precision Optomechanical Assemblies

NASA Technical Reports Server (NTRS)

Korzun, Ashley M.

2006-01-01

The increasing difficulty of metrology requirements on projects involving optics and the alignment of instrumentation on spacecraft has reached a turning point. Requirements as low as 0.1 arcseconds for the static, rotational alignment of components within a coordinate system cannot be met with a theodolite, the alignment tool currently in use. A "theoferometer" is an interferometer mounted on a rotation stage with degrees of freedom in azimuth and elevation for metrology and alignment applications. The success of a prototype theoferometer in approaching these metrology requirements led to a redesign stressing mechanical, optical, and software changes to increase the sensitivity and portability of the unit. This paper covers the improvements made to the first prototype theoferometer, characteristic testing, and demonstration of the redesigned theoferometer s capabilities as a "theodolite replacement" and low-uncertainty metrology tool.

BEAUTY: an enhanced BLAST-based search tool that integrates multiple biological information resources into sequence similarity search results.

PubMed

Worley, K C; Wiese, B A; Smith, R F

1995-09-01

BEAUTY (BLAST enhanced alignment utility) is an enhanced version of the NCBI's BLAST data base search tool that facilitates identification of the functions of matched sequences. We have created new data bases of conserved regions and functional domains for protein sequences in NCBI's Entrez data base, and BEAUTY allows this information to be incorporated directly into BLAST search results. A Conserved Regions Data Base, containing the locations of conserved regions within Entrez protein sequences, was constructed by (1) clustering the entire data base into families, (2) aligning each family using our PIMA multiple sequence alignment program, and (3) scanning the multiple alignments to locate the conserved regions within each aligned sequence. A separate Annotated Domains Data Base was constructed by extracting the locations of all annotated domains and sites from sequences represented in the Entrez, PROSITE, BLOCKS, and PRINTS data bases. BEAUTY performs a BLAST search of those Entrez sequences with conserved regions and/or annotated domains. BEAUTY then uses the information from the Conserved Regions and Annotated Domains data bases to generate, for each matched sequence, a schematic display that allows one to directly compare the relative locations of (1) the conserved regions, (2) annotated domains and sites, and (3) the locally aligned regions matched in the BLAST search. In addition, BEAUTY search results include World-Wide Web hypertext links to a number of external data bases that provide a variety of additional types of information on the function of matched sequences. This convenient integration of protein families, conserved regions, annotated domains, alignment displays, and World-Wide Web resources greatly enhances the biological informativeness of sequence similarity searches. BEAUTY searches can be performed remotely on our system using the "BCM Search Launcher" World-Wide Web pages (URL is < http:/ /gc.bcm.tmc.edu:8088/ search-launcher/launcher.html > ).

A novel approach of ensuring layout regularity correct by construction in advanced technologies

NASA Astrophysics Data System (ADS)

Ahmed, Shafquat Jahan; Vaderiya, Yagnesh; Gupta, Radhika; Parthasarathy, Chittoor; Marin, Jean-Claude; Robert, Frederic

2017-03-01

In advanced technology nodes, layout regularity has become a mandatory prerequisite to create robust designs less sensitive to variations in manufacturing process in order to improve yield and minimizing electrical variability. In this paper we describe a method for designing regular full custom layouts based on design and process co-optimization. The method includes various design rule checks that can be used on-the-fly during leaf-cell layout development. We extract a Layout Regularity Index (LRI) from the layouts based on the jogs, alignments and pitches used in the design for any given metal layer. Regularity Index of a layout is the direct indicator of manufacturing yield and is used to compare the relative health of different layout blocks in terms of process friendliness. The method has been deployed for 28nm and 40nm technology nodes for Memory IP and is being extended to other IPs (IO, standard-cell). We have quantified the gain of layout regularity with the deployed method on printability and electrical characteristics by process-variation (PV) band simulation analysis and have achieved up-to 5nm reduction in PV band.

Design and realization of the optical and electron beam alignment system for the HUST-FEL oscillator

NASA Astrophysics Data System (ADS)

Fu, Q.; Tan, P.; Liu, K. F.; Qin, B.; Liu, X.

2018-06-01

A Free Electron Laser(FEL) oscillator with radiation wavelength at 30-100 μ m is under commissioning at Huazhong University of Science and Technology (HUST). This work presents the schematic design and realization procedures for the optical and beam alignment system in the HUST FEL facility. The optical cavity misalignment effects are analyzed with the code OPC + Genesis 1.3, and the tolerance of misalignment is proposed with the simulation result. Depending on undulator mechanical benchmarks, a laser indicating system has been built up as reference datum. The alignment of both optical axis and beam trajectory were achieved by this alignment system.

THE DARK ENERGY CAMERA

DOE Office of Scientific and Technical Information (OSTI.GOV)

Flaugher, B.; Diehl, H. T.; Alvarez, O.

2015-11-15

The Dark Energy Camera is a new imager with a 2.°2 diameter field of view mounted at the prime focus of the Victor M. Blanco 4 m telescope on Cerro Tololo near La Serena, Chile. The camera was designed and constructed by the Dark Energy Survey Collaboration and meets or exceeds the stringent requirements designed for the wide-field and supernova surveys for which the collaboration uses it. The camera consists of a five-element optical corrector, seven filters, a shutter with a 60 cm aperture, and a charge-coupled device (CCD) focal plane of 250 μm thick fully depleted CCDs cooled inside a vacuummore » Dewar. The 570 megapixel focal plane comprises 62 2k × 4k CCDs for imaging and 12 2k × 2k CCDs for guiding and focus. The CCDs have 15 μm × 15 μm pixels with a plate scale of 0.″263 pixel{sup −1}. A hexapod system provides state-of-the-art focus and alignment capability. The camera is read out in 20 s with 6–9 electron readout noise. This paper provides a technical description of the camera's engineering, construction, installation, and current status.« less

The Dark Energy Camera

DOE PAGES

Flaugher, B.

2015-04-11

The Dark Energy Camera is a new imager with a 2.2-degree diameter field of view mounted at the prime focus of the Victor M. Blanco 4-meter telescope on Cerro Tololo near La Serena, Chile. The camera was designed and constructed by the Dark Energy Survey Collaboration, and meets or exceeds the stringent requirements designed for the wide-field and supernova surveys for which the collaboration uses it. The camera consists of a five element optical corrector, seven filters, a shutter with a 60 cm aperture, and a CCD focal plane of 250-μm thick fully depleted CCDs cooled inside a vacuum Dewar.more » The 570 Mpixel focal plane comprises 62 2k x 4k CCDs for imaging and 12 2k x 2k CCDs for guiding and focus. The CCDs have 15μm x 15μm pixels with a plate scale of 0.263" per pixel. A hexapod system provides state-of-the-art focus and alignment capability. The camera is read out in 20 seconds with 6-9 electrons readout noise. This paper provides a technical description of the camera's engineering, construction, installation, and current status.« less

Force-controlled automatic microassembly of tissue engineering scaffolds

NASA Astrophysics Data System (ADS)

Zhao, Guoyong; Teo, Chee Leong; Hutmacher, Dietmar Werner; Burdet, Etienne

2010-03-01

This paper presents an automated system for 3D assembly of tissue engineering (TE) scaffolds made from biocompatible microscopic building blocks with relatively large fabrication error. It focuses on the pin-into-hole force control developed for this demanding microassembly task. A beam-like gripper with integrated force sensing at a 3 mN resolution with a 500 mN measuring range is designed, and is used to implement an admittance force-controlled insertion using commercial precision stages. Visual-based alignment followed by an insertion is complemented by a haptic exploration strategy using force and position information. The system demonstrates fully automated construction of TE scaffolds with 50 microparts whose dimension error is larger than 5%.

A novel bioreactor for the generation of highly aligned 3D skeletal muscle-like constructs through orientation of fibrin via application of static strain.

PubMed

Heher, Philipp; Maleiner, Babette; Prüller, Johanna; Teuschl, Andreas Herbert; Kollmitzer, Josef; Monforte, Xavier; Wolbank, Susanne; Redl, Heinz; Rünzler, Dominik; Fuchs, Christiane

2015-09-01

The generation of functional biomimetic skeletal muscle constructs is still one of the fundamental challenges in skeletal muscle tissue engineering. With the notion that structure strongly dictates functional capabilities, a myriad of cell types, scaffold materials and stimulation strategies have been combined. To further optimize muscle engineered constructs, we have developed a novel bioreactor system (MagneTissue) for rapid engineering of skeletal muscle-like constructs with the aim to resemble native muscle in terms of structure, gene expression profile and maturity. Myoblasts embedded in fibrin, a natural hydrogel that serves as extracellular matrix, are subjected to mechanical stimulation via magnetic force transmission. We identify static mechanical strain as a trigger for cellular alignment concomitant with the orientation of the scaffold into highly organized fibrin fibrils. This ultimately yields myotubes with a more mature phenotype in terms of sarcomeric patterning, diameter and length. On the molecular level, a faster progression of the myogenic gene expression program is evident as myogenic determination markers MyoD and Myogenin as well as the Ca(2+) dependent contractile structural marker TnnT1 are significantly upregulated when strain is applied. The major advantage of the MagneTissue bioreactor system is that the generated tension is not exclusively relying on the strain generated by the cells themselves in response to scaffold anchoring but its ability to subject the constructs to individually adjustable strain protocols. In future work, this will allow applying mechanical stimulation with different strain regimes in the maturation process of tissue engineered constructs and elucidating the role of mechanotransduction in myogenesis. Mechanical stimulation of tissue engineered skeletal muscle constructs is a promising approach to increase tissue functionality. We have developed a novel bioreactor-based 3D culture system, giving the user the possibility to apply different strain regimes like static, cyclic or ramp strain to myogenic precursor cells embedded in a fibrin scaffold. Application of static mechanical strain leads to alignment of fibrin fibrils along the axis of strain and concomitantly to highly aligned myotube formation. Additionally, the pattern of myogenic gene expression follows the temporal progression observed in vivo with a more thorough induction of the myogenic program when static strain is applied. Ultimately, the strain protocol used in this study results in a higher degree of muscle maturity demonstrated by enhanced sarcomeric patterning and increased myotube diameter and length. The introduced bioreactor system enables new possibilities in muscle tissue engineering as longer cultivation periods and different strain applications will yield tissue engineered muscle-like constructs with improved characteristics in regard to functionality and biomimicry. Copyright © 2015 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Aligning Biomolecular Networks Using Modular Graph Kernels

NASA Astrophysics Data System (ADS)

Towfic, Fadi; Greenlee, M. Heather West; Honavar, Vasant

Comparative analysis of biomolecular networks constructed using measurements from different conditions, tissues, and organisms offer a powerful approach to understanding the structure, function, dynamics, and evolution of complex biological systems. We explore a class of algorithms for aligning large biomolecular networks by breaking down such networks into subgraphs and computing the alignment of the networks based on the alignment of their subgraphs. The resulting subnetworks are compared using graph kernels as scoring functions. We provide implementations of the resulting algorithms as part of BiNA, an open source biomolecular network alignment toolkit. Our experiments using Drosophila melanogaster, Saccharomyces cerevisiae, Mus musculus and Homo sapiens protein-protein interaction networks extracted from the DIP repository of protein-protein interaction data demonstrate that the performance of the proposed algorithms (as measured by % GO term enrichment of subnetworks identified by the alignment) is competitive with some of the state-of-the-art algorithms for pair-wise alignment of large protein-protein interaction networks. Our results also show that the inter-species similarity scores computed based on graph kernels can be used to cluster the species into a species tree that is consistent with the known phylogenetic relationships among the species.

Quantification of Cardiomyocyte Alignment from Three-Dimensional (3D) Confocal Microscopy of Engineered Tissue.

PubMed

Kowalski, William J; Yuan, Fangping; Nakane, Takeichiro; Masumoto, Hidetoshi; Dwenger, Marc; Ye, Fei; Tinney, Joseph P; Keller, Bradley B

2017-08-01

Biological tissues have complex, three-dimensional (3D) organizations of cells and matrix factors that provide the architecture necessary to meet morphogenic and functional demands. Disordered cell alignment is associated with congenital heart disease, cardiomyopathy, and neurodegenerative diseases and repairing or replacing these tissues using engineered constructs may improve regenerative capacity. However, optimizing cell alignment within engineered tissues requires quantitative 3D data on cell orientations and both efficient and validated processing algorithms. We developed an automated method to measure local 3D orientations based on structure tensor analysis and incorporated an adaptive subregion size to account for multiple scales. Our method calculates the statistical concentration parameter, κ, to quantify alignment, as well as the traditional orientational order parameter. We validated our method using synthetic images and accurately measured principal axis and concentration. We then applied our method to confocal stacks of cleared, whole-mount engineered cardiac tissues generated from human-induced pluripotent stem cells or embryonic chick cardiac cells and quantified cardiomyocyte alignment. We found significant differences in alignment based on cellular composition and tissue geometry. These results from our synthetic images and confocal data demonstrate the efficiency and accuracy of our method to measure alignment in 3D tissues.

Braided and Stacked Electrospun Nanofibrous Scaffolds for Tendon and Ligament Tissue Engineering

PubMed Central

Rothrauff, Benjamin B.; Lauro, Brian B.; Yang, Guang; Debski, Richard E.; Musahl, Volker

2017-01-01

Tendon and ligament injuries are a persistent orthopedic challenge given their poor innate healing capacity. Nonwoven electrospun nanofibrous scaffolds composed of polyesters have been used to mimic the mechanics and topographical cues of native tendons and ligaments. However, nonwoven nanofibers have several limitations that prevent broader clinical application, including poor cell infiltration, as well as tensile and suture-retention strengths that are inferior to native tissues. In this study, multilayered scaffolds of aligned electrospun nanofibers of two designs–stacked or braided–were fabricated. Mechanical properties, including structural and mechanical properties and suture-retention strength, were determined using acellular scaffolds. Human bone marrow-derived mesenchymal stem cells (MSCs) were seeded on scaffolds for up to 28 days, and assays for tenogenic differentiation, histology, and biochemical composition were performed. Braided scaffolds exhibited improved tensile and suture-retention strengths, but reduced moduli. Both scaffold designs supported expression of tenogenic markers, although the effect was greater on braided scaffolds. Conversely, cell infiltration was superior in stacked constructs, resulting in enhanced cell number, total collagen content, and total sulfated glycosaminoglycan content. However, when normalized against cell number, both designs modulated extracellular matrix protein deposition to a similar degree. Taken together, this study demonstrates that multilayered scaffolds of aligned electrospun nanofibers supported tenogenic differentiation of seeded MSCs, but the macroarchitecture is an important consideration for applications of tendon and ligament tissue engineering. PMID:28071988

RNA-Seq Alignment to Individualized Genomes Improves Transcript Abundance Estimates in Multiparent Populations

PubMed Central

Munger, Steven C.; Raghupathy, Narayanan; Choi, Kwangbom; Simons, Allen K.; Gatti, Daniel M.; Hinerfeld, Douglas A.; Svenson, Karen L.; Keller, Mark P.; Attie, Alan D.; Hibbs, Matthew A.; Graber, Joel H.; Chesler, Elissa J.; Churchill, Gary A.

2014-01-01

Massively parallel RNA sequencing (RNA-seq) has yielded a wealth of new insights into transcriptional regulation. A first step in the analysis of RNA-seq data is the alignment of short sequence reads to a common reference genome or transcriptome. Genetic variants that distinguish individual genomes from the reference sequence can cause reads to be misaligned, resulting in biased estimates of transcript abundance. Fine-tuning of read alignment algorithms does not correct this problem. We have developed Seqnature software to construct individualized diploid genomes and transcriptomes for multiparent populations and have implemented a complete analysis pipeline that incorporates other existing software tools. We demonstrate in simulated and real data sets that alignment to individualized transcriptomes increases read mapping accuracy, improves estimation of transcript abundance, and enables the direct estimation of allele-specific expression. Moreover, when applied to expression QTL mapping we find that our individualized alignment strategy corrects false-positive linkage signals and unmasks hidden associations. We recommend the use of individualized diploid genomes over reference sequence alignment for all applications of high-throughput sequencing technology in genetically diverse populations. PMID:25236449

Room temperature infrared imaging sensors based on highly purified semiconducting carbon nanotubes.

PubMed

Liu, Yang; Wei, Nan; Zhao, Qingliang; Zhang, Dehui; Wang, Sheng; Peng, Lian-Mao

2015-04-21

High performance infrared (IR) imaging systems usually require expensive cooling systems, which are highly undesirable. Here we report the fabrication and performance characteristics of room temperature carbon nanotube (CNT) IR imaging sensors. The CNT IR imaging sensor is based on aligned semiconducting CNT films with 99% purity, and each pixel or device of the imaging sensor consists of aligned strips of CNT asymmetrically contacted by Sc and Pd. We found that the performance of the device is dependent on the CNT channel length. While short channel devices provide a large photocurrent and a rapid response of about 110 μs, long channel length devices exhibit a low dark current and a high signal-to-noise ratio which are critical for obtaining high detectivity. In total, 36 CNT IR imagers are constructed on a single chip, each consists of 3 × 3 pixel arrays. The demonstrated advantages of constructing a high performance IR system using purified semiconducting CNT aligned films include, among other things, fast response, excellent stability and uniformity, ideal linear photocurrent response, high imaging polarization sensitivity and low power consumption.

Engineering muscle cell alignment through 3D bioprinting.

PubMed

Mozetic, Pamela; Giannitelli, Sara Maria; Gori, Manuele; Trombetta, Marcella; Rainer, Alberto

2017-09-01

Processing of hydrogels represents a main challenge for the prospective application of additive manufacturing (AM) to soft tissue engineering. Furthermore, direct manufacturing of tissue precursors with a cell density similar to native tissues has the potential to overcome the extensive in vitro culture required for conventional cell-seeded scaffolds seeking to fabricate constructs with tailored structural and functional properties. In this work, we present a simple AM methodology that exploits the thermoresponsive behavior of a block copolymer (Pluronic ® ) as a means to obtain good shape retention at physiological conditions and to induce cellular alignment. Pluronic/alginate blends have been investigated as a model system for the processing of C2C12 murine myoblast cell line. Interestingly, C2C12 cell model demonstrated cell alignment along the deposition direction, potentially representing a new avenue to tailor the resulting cell histoarchitecture during AM process. Furthermore, the fabricated constructs exhibited high cell viability, as well as a significantly improved expression of myogenic genes vs. conventional 2D cultures. © 2017 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 105A: 2582-2588, 2017. © 2017 Wiley Periodicals, Inc.

Multi-channel dynamics in high harmonic generation of aligned CO2: ab initio analysis with time-dependent B-spline algebraic diagrammatic construction.

PubMed

Ruberti, M; Decleva, P; Averbukh, V

2018-03-28

Here we present a fully ab initio study of the high-order harmonic generation (HHG) spectrum of aligned CO 2 molecules. The calculations have been performed by using the molecular time-dependent (TD) B-spline algebraic diagrammatic construction (ADC) method. We quantitatively study how the sub-cycle laser-driven multi-channel dynamics, as reflected in the position of the dynamical minimum in the HHG spectrum, is affected by the full inclusion of both correlation-driven and laser-driven dipole interchannel couplings. We calculate channel-resolved spectral intensities as well as the phase differences between contributions of the different ionization-recombination channels to the total HHG spectrum. Our results show that electron correlation effectively controls the relative contributions of the different channels to the total HHG spectrum, leading to the opening of the new ones (1 2 Π u , 1 2 Σ), previously disregarded for the aligned molecular setup. We conclude that inclusion of many-electron effects into the theoretical interpretation of molecular HHG spectra is essential in order to correctly extract ultrafast electron dynamics using HHG spectroscopy.

A calibration rig for multi-component internal strain gauge balance using the new design-of-experiment (DOE) approach

NASA Astrophysics Data System (ADS)

Nouri, N. M.; Mostafapour, K.; Kamran, M.

2018-02-01

In a closed water-tunnel circuit, the multi-component strain gauge force and moment sensor (also known as balance) are generally used to measure hydrodynamic forces and moments acting on scaled models. These balances are periodically calibrated by static loading. Their performance and accuracy depend significantly on the rig and the method of calibration. In this research, a new calibration rig was designed and constructed to calibrate multi-component internal strain gauge balances. The calibration rig has six degrees of freedom and six different component-loading structures that can be applied separately and synchronously. The system was designed based on the applicability of formal experimental design techniques, using gravity for balance loading and balance positioning and alignment relative to gravity. To evaluate the calibration rig, a six-component internal balance developed by Iran University of Science and Technology was calibrated using response surface methodology. According to the results, calibration rig met all design criteria. This rig provides the means by which various methods of formal experimental design techniques can be implemented. The simplicity of the rig saves time and money in the design of experiments and in balance calibration while simultaneously increasing the accuracy of these activities.

P3: a practice focused learning environment

NASA Astrophysics Data System (ADS)

Irving, Paul W.; Obsniuk, Michael J.; Caballero, Marcos D.

2017-09-01

There has been an increased focus on the integration of practices into physics curricula, with a particular emphasis on integrating computation into the undergraduate curriculum of scientists and engineers. In this paper, we present a university-level, introductory physics course for science and engineering majors at Michigan State University called P3 (projects and practices in physics) that is centred around providing introductory physics students with the opportunity to appropriate various science and engineering practices. The P3 design integrates computation with analytical problem solving and is built upon a curriculum foundation of problem-based learning, the principles of constructive alignment and the theoretical framework of community of practice. The design includes an innovative approach to computational physics instruction, instructional scaffolds, and a unique approach to assessment that enables instructors to guide students in the development of the practices of a physicist. We present the very positive student related outcomes of the design gathered via attitudinal and conceptual inventories and research interviews of students’ reflecting on their experiences in the P3 classroom.

Design and manufacture of the integrated field unit for the NIRSpec spectrometer on JWST

NASA Astrophysics Data System (ADS)

Lobb, Daniel; Robertson, David; Closs, Martin; Barnes, Andy

2008-09-01

The NIRSpec imaging spectrometer, which forms part of the James Webb Space Telescope instrumentation, will include an integrated field unit (IFU). The IFU will be tasked specifically with efficient analysis of extended objects, including galaxies; it will accept a square image area at the spectrometer entrance field, dissect this area into 30 parallel sub-slits, and image the sub-slits end-to-end, forming a single virtual entrance slit. The IFU, uses all-mirror optics to operate over the spectral range 700nm to 5000nm. 95 mirrors and the main support structure are made in a common aluminium alloy, to achieve athermal performance down to an operating temperature of around 30K. Relatively complex mirror surface shapes are produced by diamond machining. The IFU has been designed and constructed by SSTL, with optics produced by CfAI; the unit is currently undergoing performance tests. This paper describes the IFU optical design and performance, and outlines the mirror manufacturing methods and alignment procedures.

A Mobile Robot for Locomotion Through a 3D Periodic Lattice Environment

NASA Technical Reports Server (NTRS)

Jenett, Benjamin; Cellucci, Daniel; Cheung, Kenneth

2017-01-01

This paper describes a novel class of robots specifically adapted to climb periodic lattices, which we call 'Relative Robots'. These robots use the regularity of the structure to simplify the path planning, align with minimal feedback, and reduce the number of degrees of freedom (DOF) required to locomote. They can perform vital inspection and repair tasks within the structure that larger truss construction robots could not perform without modifying the structure. We detail a specific type of relative robot designed to traverse a cuboctahedral (CubOct) cellular solids lattice, show how the symmetries of the lattice simplify the design, and test these design methodologies with a CubOct relative robot that traverses a 76.2 mm (3 in.) pitch lattice, MOJO (Multi-Objective JOurneying robot). We perform three locomotion tasks with MOJO: vertical climbing, horizontal climbing, and turning, and find that, due to changes in the orientation of the robot relative to the gravity vector, the success rate of vertical and horizontal climbing is significantly different.

Safety evaluation model of urban cross-river tunnel based on driving simulation.

PubMed

Ma, Yingqi; Lu, Linjun; Lu, Jian John

2017-09-01

Currently, Shanghai urban cross-river tunnels have three principal characteristics: increased traffic, a high accident rate and rapidly developing construction. Because of their complex geographic and hydrological characteristics, the alignment conditions in urban cross-river tunnels are more complicated than in highway tunnels, so a safety evaluation of urban cross-river tunnels is necessary to suggest follow-up construction and changes in operational management. A driving risk index (DRI) for urban cross-river tunnels was proposed in this study. An index system was also constructed, combining eight factors derived from the output of a driving simulator regarding three aspects of risk due to following, lateral accidents and driver workload. Analytic hierarchy process methods and expert marking and normalization processing were applied to construct a mathematical model for the DRI. The driving simulator was used to simulate 12 Shanghai urban cross-river tunnels and a relationship was obtained between the DRI for the tunnels and the corresponding accident rate (AR) via a regression analysis. The regression analysis results showed that the relationship between the DRI and the AR mapped to an exponential function with a high degree of fit. In the absence of detailed accident data, a safety evaluation model based on factors derived from a driving simulation can effectively assess the driving risk in urban cross-river tunnels constructed or in design.

Automated and Adaptable Quantification of Cellular Alignment from Microscopic Images for Tissue Engineering Applications

PubMed Central

Xu, Feng; Beyazoglu, Turker; Hefner, Evan; Gurkan, Umut Atakan

2011-01-01

Cellular alignment plays a critical role in functional, physical, and biological characteristics of many tissue types, such as muscle, tendon, nerve, and cornea. Current efforts toward regeneration of these tissues include replicating the cellular microenvironment by developing biomaterials that facilitate cellular alignment. To assess the functional effectiveness of the engineered microenvironments, one essential criterion is quantification of cellular alignment. Therefore, there is a need for rapid, accurate, and adaptable methodologies to quantify cellular alignment for tissue engineering applications. To address this need, we developed an automated method, binarization-based extraction of alignment score (BEAS), to determine cell orientation distribution in a wide variety of microscopic images. This method combines a sequenced application of median and band-pass filters, locally adaptive thresholding approaches and image processing techniques. Cellular alignment score is obtained by applying a robust scoring algorithm to the orientation distribution. We validated the BEAS method by comparing the results with the existing approaches reported in literature (i.e., manual, radial fast Fourier transform-radial sum, and gradient based approaches). Validation results indicated that the BEAS method resulted in statistically comparable alignment scores with the manual method (coefficient of determination R2=0.92). Therefore, the BEAS method introduced in this study could enable accurate, convenient, and adaptable evaluation of engineered tissue constructs and biomaterials in terms of cellular alignment and organization. PMID:21370940

Characterization of water-quality and bed-sediment conditions in Currituck Sound, North Carolina, prior to the Mid-Currituck Bridge construction, 2011–15

USGS Publications Warehouse

Wagner, Chad R.; Fitzgerald, Sharon; Antolino, Dominick J.

2015-12-24

The characterization of water-quality and bed-sediment chemistry in Currituck Sound along the proposed alignment of the Mid-Currituck Bridge summarized herein provides a baseline for determining the effect of bridge construction and bridge deck runoff on environmental conditions in Currituck Sound.

SUSTAINABLE ENERGY SYSTEMS DESIGN FOR A TRIBAL VILLAGE IN INDIA

EPA Science Inventory